The most common adverse effects associated with bisphosphonates are renal toxicity, acute-phase reactions, gastrointestinal toxicity, osteonecrosis of the jaw, transitory fever and uveitis. We report a unique adverse case of vasculitis induced by clodronate.A 61-year-old Caucasian woman developed bilateral renal ischemia after kyphoplasty and clodronate treatment for lumbar vertebral fracture. Tests revealed a vasculitis due to clodronate treatment. The antithrombotic and immunosuppressive drugs allowed us to reduce the extent of the renal ischemia. In the following months the increased auto-antibodies returned to the healthy physiological range, but the chronic renal failure persisted.Drug-induced vasculitis is an inflammation of blood vessels caused by the use of various pharmaceutical agents. The spectrum of drug-induced vasculitis can range from cutaneous rashes to fatal multi-organ involvement. To the best of our knowledge this is the first documented case of drug-induced vasculitis caused by clodronate in the literature. Previously, it was verified that clodronate injection could increase the pro-apoptotic action on immune cells. Further studies are necessary to clarify the role of bisphosphonates on drug-inducing vasculitis. Clodronic acid, a first-generation bisphosphonate, has been successfully used in the treatment of high bone-turnover states, Paget’s disease and osteolytic bone metastases . It is aOur case documents a developing progressive necrosis of both kidneys after clodronic injection until now never described in the literature. Our clinical research allowed us to make a new pathogenetic hypothesis.A 61 year-old Caucasian woman , in good general health, suffered a lumbar spine trauma caused by a fall in her home. The clinical picture, X-ray and CT (computed tomography) scan showed a fracture of the L2 vertebral body. We performed a kyphoplasty with high density polymethylmethacrylate cement (PMMA) . The dual-energy X-ray absorptiometry (DEXA) exam confirmed the osteoporotic picture (T-score −4 DS). At that point we started an osteoporosis treatment. Considering the DEXA results and clinical signs of the patient, a bisphosphonate was administered . To treaIn the weeks following discharge, our patient began to complain of fever, arthritis, low back pain and acute abdominal pain and was hospitalized. A thorax-abdomen-pelvic CT scan showed a left kidney ischemia Figure A. At firAlthough we suspected a link between the extension of renal ischemia on the right kidney to the first thrombotic event, the antibodies’ positivity supported a diagnosis of immunological vasculitis, specifically systemic lupus erythematosus (SLE). We, therefore, started an immunosuppression therapy with cyclophosphamide  . The follow-up blood test to check anti-inflammatory and antibody parameters showed a progressive return to normality, which was achieved by the six month check-up.However, the good clinical response to immunosuppressive therapy, the absence of clinical signs of SLE and physiological range of antibodies allowed us to exclude the previous immunological hypotheses. We suspected, therefore, that the vasculitis may well have been caused by the clodronate.We suspended the immunosuppressive therapy and we planned periodic check-ups. After one year the CT showed a partial reduction of renal ischemia Figure C, even tIn this case, characterized by bilateral kidney necrosis, we made a diagnosis of vasculitis caused by clodronate. The primary diagnostic hypothesis was a renal thrombosis induced by cement embolism after kyphoplasty. In the literature, similar cases following vertebroplasty are reported as being due to cement overflow into paravertebral vessels, eventually reaching the renal artery ,14. In oFurther clinical exams showed the presence of antibodies, such as anti-ANCA, anti-ds DNA, anti-ANA and anti-MPO. Until this time, the patient had never undergone immunological tests. For this reason, we put forward the hypothesis of immunologic vasculitis caused by a silent form of systemic lupus erythematosus, activated by clodronate. This hypothesis is supported by an experimental study that verified the pro-apoptotic effect of clodronate, as well as its potential autoimmunity induction in SLE mononuclear circulating cells . In accoFurther clinical research did not show other SLE clinical signs. Given that drug-induced vasculitis (DIV) could mimic the symptoms of SLE and the spectrum of DIV can range from cutaneous rashes and petechiae or single organ involvement to fatal multi-organ failure with deaths commonly caused by massive pulmonary hemorrhage, we excluded SLE . At thisUntil now, no cases of DIV caused by clodronate have ever been reported. The offending drug and its metabolites may accumulate within neutrophils, bind to MPO and modify the latter’s configuration which may spread the autoimmune response to other autoantigens and turn them into immunogenic neutrophil proteins  . Some drThere is no standard approach to the treatment of DIV. The first step is the discontinuation of the medication. For patients with severe and active organ failure, intensive immunosuppressive therapy could improve organ function and prevent progression to severe, irreversible disease.In accordance with the literature, the diagnosis of DIV for our case is defined by the following: (a) the signs and symptoms of vasculitis were temporally related to using the offending drug, and regressed with its discontinuation; (b) blood levels of ANCA antibodies were positive; and (c) medical conditions that mimic vasculitis were excluded, especially malignancies .We report an adverse case of renal vasculitis induced by clodronate. Considering the ample use on a global scale of this drug for osteoporosis treatment, it is important to highlight the possibility of this adverse effect. Our experience could help in making a quick diagnosis and the timely start of the correct treatment in the future.Written informed consent was obtained from our patient for publication of this case report and accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.ADP and/or ATP: Adenosine-diphosphate and/or Adenosine-5′-triphosphate; ANA: Anti-nuclear autoantibodies; ANCA: Anti-neutrophil cytoplasmic antibody; anti-ds DNA: Anti-double-stranded DNA antibody; CT: Computed tomography; DEXA: Dual-energy x-ray absorptiometry; DIV: Drug-induced vasculitis; IU: International unit; MPO: Anti-myeloperoxidase antibodies; PMMA: Polymethylmethacrylate cement; SLE: Systemic lupus erythematosus.The authors declare that they have no competing interests.AN, AC, AP and BM cared for our patient during her hospital stay. AP and LM reviewed our patient’s diagnostic history, signs, laboratory data and investigations, and made the diagnosis. AN and GM wrote the manuscript and performed a literature search. All authors have read, edited and approved the final manuscript.


The association between fire-setting behavior and psychiatric or medical disorders remains poorly understood. Although a link between fire-setting behavior and various organic brain disorders has been established, associations between fire setting and focal brain lesions have not yet been reported. Here, we describe the case of a 24-year-old first time arsonist who suffered Todd’s paralysis prior to the onset of a bizarre and random fire-setting behavior.A case of a 24-year-old man with a sudden onset of a bizarre and random fire-setting behavior is reported. The man, who had been arrested on felony arson charges, complained of difficulties concentrating and of recent memory disturbances with leg weakness. A video-EEG recording demonstrated a close relationship between the focal motor impairment and a clear-cut epileptic ictal discharge involving the bilateral motor cortical areas. The SPECT result was statistically analyzed by comparing with standard SPECT images obtained from our institute . eZIS revealed hypoperfusion in cingulate cortex, basal ganglia and hyperperfusion in frontal cortex,. A neuropsychological test battery revealed lower than normal scores for executive function, attention, and memory, consistent with frontal lobe dysfunction.The fire-setting behavior and Todd’s paralysis, together with an unremarkable performance on tests measuring executive function fifteen months prior, suggested a causal relationship between this organic brain lesion and the fire-setting behavior. The case describes a rare and as yet unreported association between random, impulse-driven fire-setting behavior and damage to the brain and suggests a disconnection of frontal lobe structures as a possible pathogenic mechanism. The association between fire-setting behavior and psychiatric or medical disorders remains poorly understood. Thus far, studies on the characteristics of fire-setters have revealed associations with substance use disorders, personality disorders, mental retardation, schizophrenia-, mood-, and neurotic-spectrum disorders, and impulse-control disorders, including pyromania . Rare asA 24-year-old, right-handed Japanese man with a ninth-grade education was referred to us by the court for pre-trial evaluation. His sister, aunt and cousin have been suffering from epilepsy. He had no history of antisocial behavior. Fifteen months ago, he suffered from headache, nausea, vomiting, general malaise, abdominal discomfort, vertigo, and tinnitus during a shopping experience and could not maintain an upright stance or walk. He was transported to the hospital, and was diagnosed with vertigo and generalized anxiety disorder. Fourteen months ago he showed the same symptoms, as well as a loss of consciousness and numbness in the legs during a lunch break. Thirteen months ago, he stopped driving because he complained about headaches and vertigo, although he could move his legs. He could not remember this episode. Eight months ago a psychiatrist diagnosed epilepsy with an electroencephalogram (EEG) and started to administer clonazepam (1 mg). After this he spent most of his days fishing without a job.The suspect had been arrested on felony arson charges after starting at least five separate fires in residential neighborhoods in less than a month. The suspect, who had no prior arrests, indictments, or convictions, confessed to setting fires indiscriminately and seemingly without purpose to a bamboo broom, styrofoam, a towel, and a wooden board near a junior high school, a warehouse, a boat, and a shrine, respectively. When he set fire to some items he felt vertigo and could not maintain power in the legs.The pre-trial evaluation involved the assessment of (i) the examinee’s current mental state, (ii) the examinee’s criminal responsibility, primarily depending on the examinee’s mental state at the time of the offence, (iii) the examinee’s risk for criminal recidivism, and (iv) the suitability of a court order for mental health treatment to reduce criminal recidivism.Upon presentation, the examinee appeared to feel well but complained of difficulties concentrating and of a recent impairment in memory. He claimed to have had no intent to violate the law and appeared to have no explanation for his fire-setting behavior. He recalled waking up in the early morning hours and leaving his home to roam the residential neighborhood. He also recalled feeling somehow strange before setting fire to various items haphazardly. The examinee denied any sexual fantasies or arousal associated with the fire-setting behavior.The examinee was taking no regular medication but had a history of alcohol abuse since his adolescent years. Alcohol intoxication was therefore considered as a possible cause for the fire-setting behavior but was later dismissed as no evidence for recent alcohol consumption emerged.Initial multiaxial diagnostic assessment according to classifications provided by the Fourth Edition of the Diagnostic and Statistical Manual of Mental Disorders-Text Revision  revealed mild mental retardation. There was no evidence for delusions, hallucinations, manic episodes, or possible axis II disorders relevant to the fire-setting behavior. Axis III evaluation revealed a history of Todd’s paralysis, which raised the possibility of a delirious state as a possible cause for the observed fire-setting behavior . Axis IV++ (10.4 mg/l) were found. Serologic testing showed no evidence for infection with Treponemapallidum, Borreliaburgdorferi, hepatitis B or C viruses, or HIV 1/2.Laboratory results were normal or borderline pathologic. A diminished lymphocyte count (990/ml), a slightly elevated C-reactive protein (2.3 mg/l), and marginally diminished CaCerebral magnetic resonance imaging (MRI) revealed atrophy of the brain and dilated lateral ventricle Figure . An easyBilateral PP of the bilateral legs (motor deficits without sensory deficits) lasted approximately 5 minutes. He was confused during ictal events, and suffered from headache, and retrograde and anterograde amnesia after ictal events.Further examination showed that an electrocardiogram was normal. A video-EEG was performed. The tracing just before epilepsy was characterized by the presence of irregular slow waves Figure A. The trWe performed a number of neuropsychological tests with particular emphasis on the assessment of executive function and control . PerformMost likely, these cognitive impairments developed as a result of epilepsy. In particular, performance on the three WAIS-III subtests with low scores was normal in the pre-stroke condition: picture completion (score 8), block design (score 7), and digit symbol coding (score 8). The average premorbid intelligence quotient (IQ) score, obtained at the same time, was 63 . Treatment with carbamazepine was started and led to complete seizure control.Arson is frequently associated with psychiatric morbidity and with previous non-violent or violent offences . In contHowever, lesions in the hypoperfused regions within the frontal cortex and basal ganglia might result in a disconnection and deactivation of the frontal cortex. Consistent with this concept are more recent observations linking cognitive inflexibility with prefrontal depletion of serotonin . Moreovemensrea[Here we argue that, in our case, disconnection of the frontal lobe resulted in impairments of cognition, primarily executive functions involving planning and judgment, as well as partial loss of memory and impulse control functions. Together, this led to a bizarre type of impulse-driven, non-intentional fire-setting behavior. Consequently, the examinee’s capacity to form a specific intent at the time of the offence remained uncertain, implying lack of capacity to form mensrea, which, Based on our pre-trial evaluation, a diagnosis of personality change (disinhibited behavior) due to brain damage and dysfunction (DSM-IV-TR: 310.1) was made, combined with anosognosic features . The examinee was found not criminally responsible. However, the examinee was deemed at risk for criminal recidivism as no specific treatment for his condition existed. We recommended continuing prophylactic treatment with antiepileptic medication to help prevent further hypoxic-ischemic insults. The case was closed with a verdict of guilty by reason of legal sanity and the examinee was transferred to a prison. Neuropsychological reassessment may help estimate the examinee’s risk for future criminal recidivism.The fire-setting behavior and Todd’s paralysis, together with an unremarkable performance on tests measuring executive function fifteen months prior, suggested a causal relationship between this organic brain lesion and the fire-setting behavior. The case describes a rare and as yet unreported association between random, impulse-driven fire-setting behavior and damage to the brain and suggests a disconnection of frontal lobe structures as a possible pathogenic mechanism.DSM-IV-TR, The Fourth Edition of the Diagnostic and Statistical Manual of Mental Disorders, Text Revision; EEG, Electroencephalogram; eZIS, Z-score imaging system; MRI, Magnetic resonance imaging; WAIS-III, The Wechsler Adult Intelligence Scale-III; SPECT, Single-photon emission computed tomography.Authors have no competing interests to declare that are relevant to the content of this submission.MK and KM followed up the patient during the admission. YM and TN participated in EEG study. YI and YT examined SPECT study, HK, JT and HH examined psychological test examination, JA planed the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-244X/12/132/prepub


To examine if a multi-modal integrative intervention  impacts length of hospital stay (LOS) compared to historical controls in women undergoing surgery for known or suspected endometrial, ovarian, or cervical cancer.The multi-modal intervention combines various therapies into a cohesive program. Prior to surgery, participants receive explicit patient education, acupuncture and mind/body therapies to assist with physical and mental preparation for surgery. On the day of surgery, an epidural is placed prior to general anesthesia administration to manage post-operative pain. Patients undergo standard of care surgery. The evening after surgery, patients eat a high protein “surgical soft” dinner and nurses assist patients in walking down the hospital halls. Acupuncture is provided on post-operative days one and two for post-surgical pain relief, nausea control and for stimulation of bowel function. Patients’ electronic medical records are reviewed to obtain intra-operative and post-operative details including amount of medications administered, length of surgery, time of admission to post-anesthesia care unit, time of first ambulation out of the room, percent of diet eaten first 24 hours, nausea/pain level, discharge date/time/disposition, and patient satisfaction scores. The primary endpoint is the difference in patient LOS following surgery relative to a historical control. Secondary endpoints include FACT-G, State-Trait Anxiety Inventory, Patient Activated Measure before admission and roughly six months after discharge from the hospital.Forty-one women were enrolled to date. The preliminary analysis indicated an average LOS of 2.57 days as compared to 2.89 to 3.39 days for historical controls. Final analyses will be presented at the meeting.A bundled approach to care appears to reduce hospital LOS in women having surgery for endometrial, ovarian, or cervical cancer. Further research is needed to examine the efficacy of this approach in a controlled clinical trial.


Background. There is emerging evidence to support the use of granulocyte colony-stimulating factor (G-CSF) therapy in patients with acute ischemic stroke. Aims. To explore feasibility, safety, and preliminary efficacy of G-CSF therapy in patients with acute ischemic stroke. Patients and Method. In randomized study, 10 patients with acute ischemic stroke were recruited in 1 : 1 ratio to receive 10 μg/kg G-CSF treatment subcutaneously daily for five days with conventional care or conventional treatment alone. Efficacy outcome measures were assessed at baseline, one month, and after six months of treatment included Barthel Index (BI), National Institute of Health Stroke Scale, and modified Rankin Scale. Results. One patient in G-CSF therapy arm died due to raised intracranial pressure. No severe adverse effects were seen in rest of patients receiving G-CSF therapy arm or control arm. No statistically significant difference between intervention and control was observed in any of the scores though a trend of higher improvement of BI score is seen in the intervention group. Conclusion. Although this study did not have power to examine efficacy, it provides preliminary evidence of potential safety, feasibility, and tolerability of G-CSF therapy. Further studies need to be done on a large sample to confirm the results. Stroke is an important cause of mortality and morbidity worldwide . Despite+) cells and stimulates proliferation, maturation, and survival of the neutrophilic granulocyte lineage. It is widely employed to mobilize bone marrow stem cells in patients with leukaemia treated with bone marrow transplantation and chemotherapy-induced neutropenia for last two decades [Currently, few treatments exist for acute stroke, comprising mainly aspirin and thrombolytic drugs which have poor availability in the developing countries and very narrow time window for its intervention. A clear need exists to identify new drugs. Granulocyte colony stimulating-factor (G-CSF) is a cytokine that acts on hematopoietic stem CD344+ cells  decades , 6. ThesMeta-analysis from the animal studies suggested that G-CSF both reduces infarct size and enhances functional recovery, and its effect is presumably dose dependent .μg/kg G-CSF in patients with acute ischemic stroke and to assess the effect on circulating stem cell and blood cell counts.Three small clinical trials investigated the safety and feasibility and efficacy of stem cell mobilization by G-CSF in 7, 24, and 44 patients at different doses of G-CSF with acute ischemic stroke patients, respectively –10. In aAll patients with acute ischemic stroke attending the neurology services at All India Institute of Medical Sciences, New Delhi, between January 2008 and May 2008, were screened for eligibility of this study. Patients with stroke  were considered eligible if they fulfilled all of the following: age between 30 and 75 years, within seventh day from onset, computed tomography and/or magnetic resonance imaging scan of the brain showing no haematoma, and relevant lesions within the middle cerebral artery territory, Glasgow coma scale (GCS) score above eight (eye and motor score of more than six in patients with aphasia), Barthel index (BI) score of 55 or less, National Institute of health stroke Scale (NIHSS) score between 7 and 20, and inability to walk unaided or raise upper limb by 90 degree and clinically stable. A patient were defined as stable when they had normal respiration, was afebrile, had blood pressure less than mean arterial pressure of 125mmHg (but no hypotension defined as systolic BP <90 mmHg), and had fasting venous blood sugar level less than 200 mg% along with normal serum urea and electrolytes. Patients meeting the above criteria were excluded from the study if they had any one of the following: lacunar syndrome, intracranial pathologies , intubation, comorbidity likely to limit survival to less than three years, for example, malignant diseases, hepatic or renal failure, prestroke disability leading to dependence on others for activities of daily living, haematological dysfunction (a history of major bleeding requiring blood transfusion or of leukopenia thrombocytopenia), inaccessibility for followup, pregnancy or unwillingness to provide written informed consent (by self or next of kin). The study was approved by the Institute Ethics Committee of AIIMS.This was a 12-month duration, randomized, open-label, parallel-group study. Eligible consenting subjects were randomly assigned in a 1 : 1 ratio to G-CSF therapy for five days along with conventional management or conventional management alone. Patients were randomly allocated to one of the two groups, by use of a computer-generated simple randomization table. The randomized allocation of groups was performed by a blinded, independent coordinator not related to patient care in the study via telephonic call. Subsequent to random allocation to groups, intervention was not blinded.μg/kg subcutaneously administered daily for five days along with conventional treatment or conventional treatment alone. Intervention was given within two hours of randomization. We assessed safety of subcutaneous G-CSF infusion by recording the development of immediate or delayed reactions. Immediate reactions included allergic reactions . Leukocyte counts were measured on day one, three, five, and seven from blood samples. One week after the initiation of therapy, patients were discharged unless clinically warranted.All patients were evaluated according to a protocol that included demographic data, medical history, stroke risk factors, and neurological examination. To determine stroke severity, we used the BI  as an index of functional recovery and NIHSS score  as an index of neurological deficit. After all of the data had been recorded, patients were randomized to receive either subcutaneous human recombinant G-CSF  10 After discharge, all of the patients were followed up at one month; modified Rankin scale  as an index of functional recovery, along with BI and NIHSS, was recorded. Adverse events elicited included bone pain, headache, liver dysfunction, myocardial infarction, recurrence of stroke, and peripheral arterial thromboses. Subsequently, all of the patients were followed up at six and twelve months in the outpatient department, and neurological functions were assessed using all three scales. The 12-month scores from the BI, NIHSS, and mRS were used to assess treatment efficacy. Improvement was defined as the percentage change in mean group scores between baseline and 12 months. To evaluate tumor formation as a delayed complication, we performed a regular physical examination including visual inspection of skin and oral mucosa, a follow-up magnetic resonance imaging brain at one month and six-months, and whole body FDG-positron emission tomography at the end of 12 months.Analysis was done after completion of six-month followup. The primary analyses of efficacy and safety were performed on the intention to treat analysis. This included all patients who were randomized to receive treatment. Baseline characteristics and differences between G-CSF and control groups with different outcome measures were analyzed using Mann-Whitney U-tests. Data was analyzed using the SPSS statistical package, version 17.0 .Between January 2008 and May 2008, a total of 19 patients with acute ischemic stroke were screened for eligibility . Of thosAs per protocol numbers of patients completed trial were four in G-CSF arm and five in control arm. There were no losses to followup over the study period. Baseline characterises of individual patients is summarized in Improvement in BI, NIHSS, and mRS did not differ significantly between the G-CSF and control groups, Figures P < 0.005 and 0.01, resp.). Rise in mean leukocyte is represented in Rise in maximum leukocyte count at hospital stay from baseline and clinical outcome score in individual patients wise assessed at different time interval is given in G-CSF therapy was reasonably well tolerated. Of the five patients receiving G-CSF, one reported mild bone pain that lasted one day and subsided spontaneously. One patient in G-CSF arm had deep venous thrombosis in left lower limb that required hospitalisation and subsided with treatment. There were no aggravations of stroke symptoms during the course of therapy and hospital stay. There was no aggravation of limb weakness, speech impairment, or sensory impairment during the 12-month followup in either study group. No severe adverse effects were seen in any of patients receiving G-CSF therapy arm or control arm.This is the first preliminary randomized controlled study to explore safety and preliminary efficacy of G-CSF in patients with stroke from India. In accordance with previous studies, we found G-CSF therapy safe and well tolerated in five patients with acute stroke –10. We failed to find effectiveness of G-CSF in improving neurologic outcome in patients with acute ischemic stroke. With only five patients in each arm, the pilot study was not designed to have the power to detect outcome differences between the groups. Two points deserve some comments.Optimal dose of G-CSF: several studies have been completed at different doses of G-CSF. (μg/kg daily for five days appeared to be safe and reasonably well tolerated, and there was higher trend of improvement in Barthel index score in intervention group compared to control. Previous studies [μg/kg daily for five days protocol. To allow comparison of our results with the published studies and in future to facilitate meta-analyses, we have followed the same protocol. Several studies are ongoing with different doses of G-CSF in stroke and results of all studies will be helpful to determine the dose-response gradient of G-CSF. CD-34+ cells in peripheral blood increases significantly after G-CSF injection of 10 μg/kg for consecutive five days [3 [μg/kg daily for five days. In view of similar findings from other G-CSF trials [f G-CSF. . Our stu studies , 11 have days [3 . Our stuF trials –10 in stTiming of G-CSF injection: a therapeutics time window for intervention is a major promise of G-CSF therapy. Time of intervention used in clinical studies is summarised in + stem cells also effectively mobilized and appeared to be safe and well tolerated after G-CSF injection when treatment is delayed for month in ischemic stroke patients [patients . Wider tpatients  2010 (AXBased on the findings of the pilot study, Drug-Controller-General of India has approved our multicentric, phase I/II safety and efficacy, randomized controlled trial of G-CSF with 200 sample size of patients. Our planned clinical trial is to establish safety and explore efficacy of G-CSF therapy in acute stroke patients. The protocol is under consideration for funding in the Department of Biotechnology, Government of India.The study is with small number of sample size; however, other studies are ongoing and published in international journals with small number of sample sizes.μg/kg daily for five days appeared to be safe and well tolerated in five patients aged 35–75 years with acute ischemic stroke in accordance with other published G-CSF trials in stroke patients. However, in view of limited sample size, the results of the current study must be interpreted with caution. Further, large, adequately powered, multicenter randomized placebo-controlled, blinded trials are needed to test the efficacy of G-CSF in patients with acute ischemic stroke.In conclusion, G-CSF administered 10


Optic nerve hypoplasia (ONH) with/or without septo-optic dysplasia (SOD) is a known concomitant of congenital growth hormone deficiency (CGHD).Demographic and longitudinal data from KIGS, the Pfizer International Growth Database, were compared between 395 subjects with ONH/SOD and CGHD and 158 controls with CGHD without midline pathology.ONH/SOD subjects had higher birth length/weight, and mid-parental height SDS. At GH start, height, weight, and BMI SDS were higher in the ONH/SOD group. After 1 year of GH, both groups showed similar changes in height SDS, while weight and BMI SDS remained higher in the ONH/SOD group. The initial height responses of the two groups were similar to those predicted using the KIGS-derived prediction model for children with idiopathic GHD. At near-adult height, ONH/SOD and controls had similar height, weight, and BMI SDS.Compared to children with CGHD without midline defects, those with ONH/SOD presented with greater height, weight, and BMI SDS. These differences persisted at 1 year of GH therapy, but appeared to be overcome by long-term GH treatment. Mid-parental height SDS was also significantly greater in the ONH/SOD group  compared to the non-ONH/SOD CGHD group . Peak GH levels on stimulation testing were similar between the two groups. The ONH/SOD group had significantly more subjects with other hypothalamic-pituitary hormone deficiencies compared to the non-ONH/SOD CGHD group , with involvement of the thyroid and adrenal axes being the most common.Background characteristics were compared between the two groups Table . The birAt the start of GH therapy, both groups had similar chronological ages and bone ages. However, the ONH/SOD group had significantly greater height SDS , weight SDS , and BMI SDS  . The ONH/SOD group continued to have a significantly higher height SDS, weight SDS, and BMI SDS after one year of GH therapy . However, height SDS corrected for family height genetics was significantly greater in the comparator group after the first year of GH treatment Figure .NAH data were available for 59 subjects in the ONH/SOD group and 23 subjects in the non-ONH/SOD CGHD group  [At the time of GH initiation, the ONH/SOD group was significantly larger than the non-ONH/SOD CGHD group in all measures . The taller heights at diagnosis in the ONH/SOD group might relate to the associated ophthalmological manifestations of the condition leading to nystagmus and earlier referral. This group's greater genetic height potential might also be contributory. As for the higher weight and BMI, this may be associated with the intrinsic hypothalamic dysfunction seen in some patients with ONH/SOD causing hyperphagia.The two groups responded similarly to one year of GH therapy with a comparable increase in height and similar to that predicted using the KIGS-derived prediction model for first-year growth in GH-treated children with idiopathic GHD. As a result, the ONH/SOD group continued to have significantly greater height, along with weight and BMI, than did the non-ONH/SOD CGHD group. Although we recognize the small size of the subsets from both groups that attained NAH and the inherent uncertainty of being able to draw firm conclusions as a result, the available data suggest that the two groups have similar height, weight, and BMI at NAH. With height outcomes in both groups within 1 SD of the mean , this suggests that there is excellent adult height potential in children with congenital GH deficiency. Furthermore, these results suggest that long-term GH therapy can possibly prevent, minimize, and/or reverse the obesity that has been described in patients with ONH/SOD. Additional randomized prospective studies of GH therapy in patients with ONH/SOD are needed to investigate the effects of GH therapy specifically on obesity and body composition.In summary, children with ONH/SOD have different presenting characteristics, but similar and normal final height responses to GH therapy compared to children with non-ONH/SOD CGHD. Because ONH/SOD is a major risk factor for CGHD and these patients may not be as short as those with non-ONH/SOD CGHD, it is important for clinicians to have a high index of suspicion and begin screening these patients for CGHD as early as possible. GH therapy may have additional benefits in this patient population as well with regard to body composition thus making early diagnosis and treatment even more important.ONH: Optic nerve hypoplasia; SOD: septo-optic dysplasia; GH: growth hormone; NCGS: National Cooperative Growth Study; NAH: near-adult height; CGHD: congenital growth hormone deficiency; SDS: standard deviation scoreHK is a full-time employee of Pfizer Endocrine Care, KIGS/KIMS/ACROSTUDY, Sollentuna, Sweden. MG receives funding from Pfizer for institutional participation in KIGS ; for research subject participation in the multi-center clinical trial: "A Four-Year Open-Label Multi-Center Randomized Two-Arm Study of Genotropin in Idiopathic Short Stature Patients: Comparing an Individualized, Target-Driven Treatment Regimen to Standard Dosing of Genotropin," and for serving as a member of national and international KIGS advisory boards.AV participated in the design of the study and drafted the manuscript. HK participated in the design of the study and performed the statistical analyses. CF and MB participated in the study's design and coordination. MG conceived of the study, and participated in its design and coordination. All authors read and approved the final manuscript.


HIV-1-infected elite controllers or suppressors (ES) maintain undetectable viral loads (< 50 copies/mL) without antiretroviral therapy. The mechanisms of suppression are incompletely understood. Modulation of HIV-1 replication by miRNAs has been reported, but the role of small RNAs in ES is unknown. Using samples from a well-characterized ES cohort, untreated viremic patients, and uninfected controls, we explored the PBMC miRNA profile and probed the relationships of miRNA expression, CD4+ T-cell counts, and viral load.miRNA profiles, obtained using multiple acquisition, data processing, and analysis methods, distinguished ES and uninfected controls from viremic HIV-1-infected patients. For several miRNAs, however, ES and viremic patients shared similar expression patterns. Differentially expressed miRNAs included those with reported roles in HIV-1 latency . Others, such as miR-31 and miR-31*, had no previously reported connection with HIV-1 infection but were found here to differ significantly with uncontrolled HIV-1 replication. Correlations of miRNA expression with CD4+ T-cell count and viral load were found, and we observed that ES with low CD4+ T-cell counts had miRNA profiles more closely related to viremic patients than controls. However, expression patterns indicate that miRNA variability cannot be explained solely by CD4+ T-cell variation.The intimate involvement of miRNAs in disease processes is underscored by connections of miRNA expression with the HIV disease clinical parameters of CD4 count and plasma viral load. However, miRNA profile changes are not explained completely by these variables. Significant declines of miRs-125b and -150, among others, in both ES and viremic patients indicate the persistence of host miRNA responses or ongoing effects of infection despite viral suppression by ES. We found no negative correlations with viral load in viremic patients, not even those that have been reported to silence HIV-1 in vitro, suggesting that the effects of these miRNAs are exerted in a focused, cell-type-specific manner. Finally, the observation that some ES with low CD4 counts were consistently related to viremic patients suggests that miRNAs may serve as biomarkers for risk of disease progression even in the presence of viral suppression. Untreated HIV-1 infection is characterized by viral replication and leads to suppression of the immune system and eventual death in most cases. A minority of individuals, known as elite controllers or elite suppressors (ES), are able in the absence of antiretroviral treatment to resist progression to HIV disease and to maintain peripheral blood viral loads below the limit of detection of current clinical assays (50 copies/mL). The mechanisms whereby this control is achieved remain incompletely understood despite substantial advances in recent years in the characterization of both host and viral factors associated with elite suppression . BecauseTo date, associations of host microRNA (miRNA) expression with HIV-1 elite suppression have not been described in the literature; however, there has been a strong focus on miRNA in cancer research and, increasingly, in investigations of infectious disease. miRNAs associated with medical conditions may serve as valuable biomarkers , especiain vivo expression and roles of miRNAs during lentiviral infection: in peripheral blood mononuclear cells (PBMC) , and six positive and eight negative controls (proprietary spike-in controls). Unlike traditional hybridization microarrays, NanoString does not associate targets with spatial coordinates; instead, the system generates copy numbers of target-specific molecular barcodes attached to detection probes, theoretically eliminating position-dependent effects. Raw data, which are proportional to copy number, were log-transformed and normalized by the quantile method after application of a manufacturer-supplied correction factor for 13 miRNAs. Data were filtered to exclude relatively invariant features (IQR = 0.5) and features below the detection threshold (defined by a cutoff corresponding to approximately one standard deviation above background levels) in at least half of the samples. Using R/Bioconductor and the filtered dataset, linear models for microarray data analysis , and 377 human miRNAs. Reverse transcription and pre-amplification were performed with the manufacturer's reagents (Applied Biosystems). Real time quantitative PCR was performed with an ABI 7900 real-time PCR machine , and data were collected with the manufacturer's SDS software. RQ Manager software (Applied Biosystems) was used to process the array data. Thresholds, set at 0.2, were checked individually and corrected as necessary. Data processing was done as described previously .Raw data and sets of quantile-normalized, filtered data from NanoString and TaqMan low-density arrays were deposited with the Gene Expression Omnibus  and areTaqMan miRNA assays (Applied Biosystems) were performed according to the manufacturer's protocol and as previously described  with eitData processing and analysis were conducted using tools from Microsoft Excel, GraphPad Prism , XLStat , BRB-ArrayTools  , the MulApproval for all studies was granted by the Johns Hopkins Institutional Review Board. All study participants provided informed consent in writing.The authors declare that they have no competing interests.KWW, JNB, and JEC conceived of and managed the study. JNB obtained samples. JEC provided resources. KWW and AKW performed the experiments. KWW analyzed the data and wrote the manuscript. JNB and JEC contributed to revision of the manuscript. All authors read drafts and approved the final manuscript.


Inadequate eating behavior and physical inactivity contribute to the current epidemic of childhood obesity. The aim of this study was to assess the association between eating behavior scores and childhood obesity in Chilean children.We recruited 126 obese, 44 overweight and 124 normal-weight Chilean children  according to the International Obesity Task Force (IOTF) criteria. Eating behavior scores were calculated using the Child Eating Behavior Questionnaire (CEBQ). Factorial analysis in the culturally-adapted questionnaire for Chilean population was used to confirm the original eight-factor structure of CEBQ. The Cronbach's alpha statistic  was used to assess internal consistency. Non-parametric methods were used to assess case-control associations.Eating behavior scores were strongly associated with childhood obesity in Chilean children. Childhood obesity was directly associated with high scores in the subscales "enjoyment of food" (P < 0.0001), "emotional overeating" (P < 0.001) and "food responsiveness" (P < 0.0001). Food-avoidant subscales "satiety responsiveness" and "slowness in eating" were inversely associated with childhood obesity (P < 0.001). There was a graded relation between the magnitude of these eating behavior scores across groups of normal-weight, overweight and obesity groups.Our study shows a strong and graded association between specific eating behavior scores and childhood obesity in Chile. Eating habits and inclinations to food are acquired in early childhood, representing behavior traits that may change over time according to personal experiences -3. In adA number of psychometric instruments have been used to assess eating behavior traits in children and adults for predicting risk of eating disorders and body weight-related problems. Some questionnaires are useful to complete food intake information and to assess feeding practices such as for example, eating in front of the TV or purchasing habits . Eating Chile, as well as other countries in Latin-America, has suffered a nutrition transition in the last 2 decades, with changes in life-styles towards an increased consumption of high-energy foods and sedentary habits. What makes Chile an interesting example in nutrition transition is that this process occurred at a much faster rate than other countries in the region, with a rapid decline in under-nutrition (from 16% in 1985 to <1% in 1995) and stunting (low-height-for-age), from 10% to 2% in the same period ,13. At tWe conducted a case-control study in the city of Santiago (Chile) with n = 126 obese and n = 124 normal-weight children , classified according to the IOTF criteria  during t2). Waist circumference was measured using a non-elastic tape just above the uppermost lateral border of iliac crest, at the end of a normal expiration. The pubertal stage  was documented in all children according to the classification of Tanner through self-assessment using pictures [Anthropometric measurements were carried out using standardized techniques by trained personnel ,19. Heigpictures -23. Nutrpictures .CEBQ is a 35-item questionnaire that evaluates eight subscales of eating behavior: Food Responsiveness , Enjoyment of Food , Emotional Over-Eating , Desire to Drink , Slowness in Eating , Satiety Responsiveness , Food Fussiness  and Emotional Under-Eating  . The firCEBQ was translated to Chilean-Spanish language through a direct and reverse translation procedure, and subsequently adapted for the Chilean culture through the assessment of responses from ten child-mother duos . Direct It has been reported that CEBQ shows adequate internal consistency, test-retest reliability, and stability over time . In our In the factorial analysis, seven factors with eigenvalues above 1.0 explaining 62% of total variance were identified using the principal component extraction method . The scree plot [See Additional File We have used radar charts to graphically represent the multidimensionality of childhood eating behavior measured through CEBQ scores [See Additional File http://www.stata.com.Summary statistics of CEBQ scores are shown as quartiles. Non-parametric statistical tests  were used to assess association between study variables. Additional association analyses between obesity and CEQB scores were carried out by creating 1:1 age-gender matched datasets for case-control comparisons. All statistical analyses were carried out with the STATA 11.0 package Table We have not found overall significant differences in "food-approach" CEBQ scores by gender . However, we found significantly higher scores for "food-avoidant" CEBQ subscales in girls compared to boys, as in SE (P < 0.001), SR (P = 0.04) and EUE (P = 0.03), without finding significant differences for FF (P = 0.99). As a consequence of this, the sum of the "food-approach" CEBQ scores were not significantly different when comparing boys and girls (P = 0.58) [See Additional File There was no significant association between age and "food-approach" CEBQ scores when girls and boys were evaluated separately, except for a inverse relation between age and scores of EOE in girls . We also found a direct association between age and EUE scores in girls . When taking the sum of "food-approach" or "food-avoidant" CEBQ scores by gender, a significant direct association was only found between age and the sum of "food-avoidant" CEBQ scores in girls .It has been described that eating behavior, measured through CEBQ in children, is a relatively stable trait over time, showing a good reproducibility and high internal consistency . A clearThe original 8-factor structure was not perfectly replicated in our study since an important degree of overlapping has been found between SE and SR . HoweverWe have been evaluating the best way to represent graphically the multidimensionality of childhood eating behavior. After evaluating different options of multivariate charts, we have arrived to the so-called multivariate radar charts. We have used this type of chart to report child eating behavior to Chilean families, who understand it very well and consider useful. This type of chart defines two polygons: the upper polygon representing positive attitudes to food intake, and the lower polygon for negative attitudes to food intake. Although the ratio of areas of the upper and lower polygons might be a considered as a gross index for general children eating behavior, this index is in fact not adequate because the shapes and areas of the polygons are modified by only changing the order of the subscales. On the contrary, the sum of either "food-approach" or "food-avoidant" scores are not affected by this distorting effect and their ratio is used in Figure There are few publications that have evaluated eating behavior in children through the CEBQ ,11,27. TOur data of Chilean children confirmed the strong association between specific eating behavior scores and childhood obesity found in previous studies. We found a direct association between obesity and "food-approach" subscales such as "enjoyment of food", "food responsiveness" and "emotional over-eating". On the other hand, scores of "food-avoidant" subscales "satiety responsiveness" and "slowness in eating") were inversely associated with body weight.BMI: body mass index; CEBQ: Child Eating Behavior Questionnaire; DZ: dizygotic; EI: energy intake; EF: enjoyment of food; EOE: emotional over-eating; EUE: emotional under-eating; FF: food fussiness; FR: food responsiveness; IOTF: International Obesity Task Force; MZ: monozygotic; SE: slowness in eating; SR: satiety responsiveness; TEE: total energy expenditure; TEDS: Twin Early Development Study.The authors declare that they have no competing interests.JLS designed, supervised and participated in the conduction of the research, JLS, JHU, MIH, AG, SS, P.A., PDV, GW, RC and AMO conducted the research, JLS, JHU and MIH analyzed the data and wrote the paper. JLS and M.I.H. had primary responsibility for the final content. All authors have read and approved the final manuscript.Scree-plot for the identification of CEBQ factors in Chilean children 6 - 12 years-old. Eight factors were identified with eigenvalue > 1.0 using factor analysis with the principal component extraction method. The scree plot shows that either the eight-factor or the seven-factor solutions are both acceptable given the slope of the chart.Click here for fileMultivariate radar chart representing the information of the Child Eating Behavior Questionnaire (CEBQ). In this graphic, scores for each subscale were projected in such a way that the upper part of the chart shows the four "food-approach" subscales related with positive inclinations to food intake while the lower part shows the four "food-avoidant" subscales.Click here for fileWeighed sum of "food approach" CEBQ subscales in Chilean children from 6 - 12 years. The "Food-approach" subscales: FR (Food Responsiveness), EF (Enjoyment of Food), EOE  and DD (Desire to Drink), scores were not significantly different when comparing boys and girls (P = 0.58).Click here for fileWeighed sum of "food avoidant" CEBQ subscales in Chilean children from 6 -12 years. The "Food-avoidant" subscales: SE (Slowness in Eating), SR (Satiety Responsiveness), FF (Food Fussiness) and EUE , a strong significant differences were found when comparing boys and girls in relation to the "food-avoidant" CEBQ scores (P = 0.006).Click here for file


In addition to increasing the number of bacterial and archaeal essential genes determined by genome-wide gene essentiality screens, DEG 10 also harbors essential noncoding RNAs, promoters, regulatory sequences and replication origins. These essential genomic elements are determined not only in vitro, but also in vivo, under diverse conditions including those for survival, pathogenesis and antibiotic resistance. We have developed customizable BLAST tools that allow users to perform species- and experiment-specific BLAST searches for a single gene, a list of genes, annotated or unannotated genomes. Therefore, DEG 10 includes essential genomic elements under different conditions in three domains of life, with customizable BLAST tools.The combination of high-density transposon-mediated mutagenesis and high-throughput sequencing has led to significant advancements in research on essential genes, resulting in a dramatic increase in the number of identified prokaryotic essential genes under diverse conditions and a revised essential-gene concept that includes all essential genomic elements, rather than focusing on protein-coding genes only. DEG 10, a new release of the Database of Essential Genes (available at  Delineating a set of essential genomic elements and proteins that make up a living organism helps to understand critical cellular processes that sustain life . IdentifBacillus subtilis (Escherichia coli (Reverse genetics (from gene disruption to phenotypic characterization) has been extensively used to experimentally determine essential genes. One standard method is to perform targeted mutagenesis in a particular gene of interest. Classical examples include essential gene determination in subtilis  and Eschhia coli , in whichia coli . Indeed,hia coli . Anotherhia coli  or microhia coli , which sin vitro and in vivo, rather than focusing only on rich media in cell culture.The combination of high-density transposon-mediated mutagenesis and high-throughput sequencing has resulted in significant advancements in the study of essential genes . This mehttp://www.nmpdr.org/FIG/eggs.cgi) and OGEE  , but also in vivo (intact mice)  , not onlct mice) , not onlct mice) , antibioct mice) , bile acct mice) ,25 and bct mice) .DEG 10 hosts archaeal essential genes determined from the first gene essentiality screen in an archaeal genome .DEG 10 hosts both essential and nonessential protein-coding genes.DEG 10 is integrated with customizable BLAST tools that allow users to perform species- and experiment-specific searches for a single gene, a list of genes, annotated or unannotated genomes.We constructed a database of essential genes (DEG) in 2004 , and DEGwww.essentialgene.org) reflects the progress of the research on essential genes by including essential genomic elements under different conditions in three domains of life, with customizable BLAST tools.Therefore, DEG 10  to identify a set of essential genes for the commensal B. thetaiotaomicron in vitro. Next, they examined the genes critical for fitness in vivo, i.e. in a mammalian gut ecosystem by colonizing bacterial mutants in germ-free mice. By comparing the input (before inoculation) and output (recovered bacteria), 280 genes showed underrepresentation, suggesting them to be critical for in vivo fitness. By changing the experimental conditions such as in the presence of human gut-associated bacteria, they identified five adjacent genes that conferred fitness disadvantages during monoassociation of germ-free mice, while showing no impact on bacterial growth in vitro, thus highlighting the importance of the in vivo context in determining gene essentiality  and two in vivo conditions (carriage and infection), and have identified over 1,800 genotype-phenotype genetic interactions and associated pathways , formed in 2007, is to generate mutant mouse lines with all genes deleted one by one . A recenenerated , DEG 10 on study .P-values. The output is unprocessed BLAST raw results.To perform BLAST search for a single gene. The major improvement for this option is that users now can perform species-specific BLAST search, in addition to having the option to change To perform BLAST search for a list of genes. Users can submit a list of protein or DNA sequences, and the BLAST output will be organized and processed to generate an XML file that is parsed by the Biopython module . The outTo perform BLAST search for annotated genome sequences. Because of the increasing pace of genome sequencing, in many cases users need to analyze whole-genome sequences. By using this option, users can submit a whole-genome sequence or scaffold, with annotation information, i.e. either in the GenBank format or by uploading Protein Table Files (PTT format).To perform BLAST search for unannotated genome sequences. If users need to analyze whole-genome sequences that have not been annotated, DEG is integrated with two gene-finding programs, Zcurve  and GlimWith the aforementioned new tools, users can perform BLAST searches for single genes, multiple genes, annotated genomes or unannotated genomes with filters to restrict the search to a subset of species or experiments with desirable P-values.Performing homologous searches with the BLAST program  against Arabidopsis thaliana . Funding for open access charge: In part by the National Natural Science Foundation of China ; Program for New Century Excellent Talents in University [No. NCET-12-0396].Startup fund from Conflict of interest statement. None declared.


This short communication focuses the on articular cartilage and the subchondral bone, both of which play important roles in the development of osteoarthritis (OA). There are indications that estrogen-deficiency, as the post-menopausal state, accelerate the development of OA.We investigated, which extracellular matrix (ECM) protein, proteases and different pro-inflammatory factors was up- or down-regulated in the knee joint tissue in response to estrogen-deficiency in rats induced by ovariectomy. These data support previous findings that several metalloproteinases (MMPs) and cysteine proteases are co-regulated with numerous collagens and proteoglycans that are important for cartilage integrity. Furthermore quite a few pro-inflammatory cytokines were regulated by estrogen deprivation.We found multiple genes where regulated in the joint by estrogen-deficiency, many of which correspond well with our current knowledge of the pathogenesis of OA. It supports that estrogen-deficiency (e.g. OVX) may accelerate joint deterioration. However, there are also data that draw attention the need for better understanding of the synergy between proteases and tissue turnover. Comparable studies have been done in other species [Post-menopausal women have a higher incident rate of osteoarthritis (OA) and osteoporosis (OP) than that of age-matched men ,2. There species . We inveSix month old female rats were either ovariectomized  or sham operated (n = 5). After recovery the rats were house under standard conditions for 8 weeks, and terminated. All animal experiments were approved by the local ethical authorities . The knees were isolated right after termination and the cartilage and subchondral compartment was detached from the tibia and flash frozen in liquid nitrogen  increased or decreased expression of individual genes when comparing the OVX and sham group, which gave a list of 2.959 and 579 genes, respectively. An objective search where made on database terms: Extracellular matrix protein, Protease/Proteinase, Cytokine, Growth factor, Bone and Cartilage. From these searched, literature based and subjectively guided sorting was done on structural proteins involved in cartilage and bone tissue remodeling and destruction, as well as cartilage and bone related factors. Each of the genes in question was reviewed by searches (term: "gene name" cartilage and/or bone) on Pubmed 2+ and regulate matrix mineralization [A total of nine relevant ECM proteins genes were found to be differentially expressed in the OVX group compared to the sham group Figure . Only onlization . There wlization . Throughlization . Type IVlization . Two cholization . Lamininlization .Eight ECM degrading proteases were up-regulated in the joints of the OVX rats Figure . MetalloSix proteases were down-regulated; MMP3 and the aggrecanases ADAMTS-like 4, ADAM15 and ADAMTS5, as well as bone morphogenic protein (BMP) 1 and tissue inhibitor metalloproteinase 3 (TIMP3) Figure . MMP3 caNext we searched for factors directly involved in bone and/or cartilage regulation. We found that five genes were significantly up-regulated and 11 were significantly down-regulated in the OVX animals Figure . SclerosWe were interested in investigating the effect of ovariectomy (i.e. estrogen deficiency) on the joint. Here we use a rodent model that in previous study has been shown to develop bone and cartilage changes, resembling pathological features of OA. We have made a guided search on ECM molecules, matrix proteases and cytokines/growth factors that have previously been directly implicated in bone and cartilage turnover. Although the search was made electronically, it is still somewhat subjective, because the database keywords may not be ubiquitous and fulfilling. Nevertheless we found several differentially express genes, which are known to play a role in development of joint degenerative disease such as OA.Animal studies have shown that by inhibiting osteoclast activity, the histo-pathological score (cf. Mankin) could be markedly reduced, suggesting that osteoclasts play a central role in OA and cartilage breakdown. Also bone formation cells, osteoblast, seem to play an important role in OA: osteoblasts isolated from subchondral bone of OA hips demonstrate an altered and more active phenotype. Furthermore, IGF-1  has been shown to be elevated in OA-subchondral explant cultures.In conclusion, we found that extracellular matrix proteins, proteases and paracrine factors known to be involved in joint degenerative diseases were either down- or up-regulated in response to estrogen-depletion. As a whole, the data support current knowledge; however there are some discrepancies, which stresses that more investigation is needed to fully understand the pathogenesis of post-menopausal OA.The authors declare that they have no competing interests.Conception and design: RHN, MAK, AB. Analysis and interpretation of the data: ACBJ. Drafting of the article: ACBJ. Critical revision of the article for important intellectual content, MAK, MA, NH, FS and ML. Final approval of the article: MAK. Provision of study materials or patients: N/A. Statistical expertise: AB. Obtaining of funding: MAK. Administrative, technical, or logistic support: N/A. Collection and assembly of data: ACBJ. All authors have approved this final version of the manuscript.


Physician-coded verbal autopsy (PCVA) is the most widely used method to determine causes of death (CODs) in countries where medical certification of death is uncommon. Computer-coded verbal autopsy (CCVA) methods have been proposed as a faster and cheaper alternative to PCVA, though they have not been widely compared to PCVA or to each other.We compared the performance of open-source random forest, open-source tariff method, InterVA-4, and the King-Lu method to PCVA on five datasets comprising over 24,000 verbal autopsies from low- and middle-income countries. Metrics to assess performance were positive predictive value and partial chance-corrected concordance at the individual level, and cause-specific mortality fraction accuracy and cause-specific mortality fraction error at the population level.The positive predictive value for the most probable COD predicted by the four CCVA methods averaged about 43% to 44% across the datasets. The average positive predictive value improved for the top three most probable CODs, with greater improvements for open-source random forest (69%) and open-source tariff method (68%) than for InterVA-4 (62%). The average partial chance-corrected concordance for the most probable COD predicted by the open-source random forest, open-source tariff method and InterVA-4 were 41%, 40% and 41%, respectively, with better results for the top three most probable CODs. Performance generally improved with larger datasets. At the population level, the King-Lu method had the highest average cause-specific mortality fraction accuracy across all five datasets (91%), followed by InterVA-4 (72% across three datasets), open-source random forest (71%) and open-source tariff method (54%).On an individual level, no single method was able to replicate the physician assignment of COD more than about half the time. At the population level, the King-Lu method was the best method to estimate cause-specific mortality fractions, though it does not assign individual CODs. Future testing should focus on combining different computer-coded verbal autopsy tools, paired with PCVA strengths. This includes using open-source tools applied to larger and varied datasets , so as to establish the performance for age- and sex-specific CODs. Verbal autopsy (VA) is used in areas with limited medical certification of death to obtain information on causes of death (CODs) -3. VA toPCVA has limitations in inter- and intra-observer differences in coding , but remHere, we compare the performance of four of the most promising CCVA methods - InterVA-4, King-Lu (KL), open source random forest (ORF) and open source tariff method (OTM) - across VA studies in several countries, covering more than 24,000 deaths, including community- and hospital-based deaths Table . We defiTable a priori probabilities based on expert consensus. InterVA-4 version 4.02 was used in this study, and the program with a full description of its logic can be freely obtained online [InterVA-4 assigns CODs using a Bayesian model with d online .The ORF is a data-driven, probabilistic method that builds upon a similar tool published by IHME . Random The OTM is a data-driven, probabilistic method that builds upon that published by IHME . The OTMThe KL method directly estimates cause-specific mortality fractions (CSMFs) without assigning individual CODs. Version 0.9-2.12 was used, for which a full description of the method and discussions of its performance have been published , and whiInterVA-4 uses pre-assigned Bayesian probabilities to assign the COD and thus does not require a training component. The remaining three methods required a training component, consisting of a subset of the original data with assigned CODs, from which the method learned the cause-specific symptom profiles. The trained algorithm was then used to predict CODs in the test dataset.Table The required format of input data varied by assignment method. Two slightly modified versions of each original dataset were created; one version to be used for the data-driven methods , and another for InterVA-4, which only uses specific indicators . InterVAPositive predictive value (PPV) and partial chance-corrected concordance (PCCC) were used to measure agreement for individual COD assignment. PPV is the proportion of assigned CODs that were the ‘true’ COD , and is a common metric in hospital-based VA comparison studies . PCCC istrue)), and subtracting this term from one [At the population level, accuracy was measured using CSMF absolute accuracy and error. CSMF error is the absolute difference between the estimated and reference CSMFs, summed across all causes. CSMF accuracy, as proposed by Murray et al., is determined by dividing the CSMF error by 2 for all CCVA methods for the most probable COD averaged 43% to 44% for all datasets, with the highest PPV being 58% for ORF, followed by 52% for OTM, both on the MDS data , followed by InterVA-4 (72% across three datasets), ORF (71%) and OTM 54%). Except for KL, the remaining CCVA methods traded best performance by dataset, with no clear trend , and not whether the underlying COD assigned by the physician was correct. Validation of PCVA is limited by the lack of a true reference standard in countries where verbal autopsy is performed -3,9. NonThe performance of each CCVA method at individual assignment improved when trained and tested on a larger number of cases, most likely due to a greater number of cases from which to learn the distinct relationships between specific symptom profiles and CODs. The differences in the field and coding methods across studies would tend to reduce the observed differences in PCVA and CCVA between the various comparisons . This might have contributed to the observed comparability of the results for the four CCVA methods. With larger studies and more standardized field and physician coding methods, any real, underlying differences between various CCVA methods may become apparent. Finally, we note that InterVA-4 has a threshold of probability for designating the most probable cause , whereas ORF and OTM select the most probable causes without applying any thresholds.On an individual level, no single method was able to replicate physician assignment of COD more than about half the time. At the population level, the King-Lu method was the best method to estimate CSMFs, though it does not assign individual CODs. However, good population-level agreement accuracy does not guarantee good individual agreement ,22. A keOur study is the largest cross-country comparison of current CCVA methods versus PCVA, covering about twice as many deaths as an earlier multi-country study , and incDifferent CCVA methods have various strengths and weaknesses depending on the study scenario and study objective. An ideal solution could involve a combination of automated methods to obtain robust individual- and population-level estimates. In the medium term, it appears unwise and certainly premature to recommend that automated systems replace physicians in coding VAs. CCVA methods could be used in parallel with physician coding to increase speed, efficiency and quality of coding. Future work may focus on the performance of a combination of various automated methods, and must extend to larger datasets and explore specifics for important age groups , by gender, and across various settings of home- and hospital-based deaths. Future studies need to also place specific emphasis on testing computer based methods on a random sample of deaths in countries, as this would be much more useful in determining the true underlying CSMF at the population level .CCVA: computer-coded verbal autopsy; COD: cause of death; CSMF: cause-specific mortality fraction; HCE: health care experience; ICD-10: International Classification of Diseases-10; IHME: Institute for Health Metrics and Evaluation; KL: King-Lu verbal autopsy method; MDS: Million Death Study; ORF: open-source random forest; OTM: open-source tariff method; PCCC: partial chance-corrected concordance; PCVA: physician-certified verbal autopsy; PPV: positive predictive value; VA: verbal autopsy.The authors declare that they have no competing interests.ND, LA and PM conducted the analysis. All authors contributed to data interpretation and critical revisions of the paper. All authors read and approved the final manuscript.Details of the open-source random forest and tariff methods. Explanation of the major logical steps of the open-source random forest and tariff methods.Click here for fileDescription of comparison metrics. Formulas and explanation of positive predictive value, partial chance-corrected concordance, CSMF error and CSMF accuracy.Click here for fileFull results of CCVA comparisons on several dataset splits. Results presented by CCVA method, dataset, dataset splits, and top and top-three cause of death predictions.Click here for file


Lesions of anogenital mammary-like glands are rare, and only 44 female cases have been reported. Herein, we describe a particularly rare case of phyllodes tumor of anogenital mammary-like glands in a 41-year-old male presenting anal bleeding. Papillectomy was performed. The excised tumor was circumscribed in shape, and after it was sliced into sections, it was noted that there were leaf-like slits on the surface of cut side. Under the microscope, the tumor was found to be biphasic, with a bland glandular epithelium and low-to-intermediate cellular stroma, which together created the leaf-like slits. Gynecomastoid hyperplasia was evident at the periphery. The epithelium showed immuno-activity for ER, PR, AR, and GCDFP-15. The stromal cells showed positive staining for CD34 and vimentin. The morphology and immunophenotype were similar to benign phyllodes tumors of breast. To the best of our knowledge, this case report represents the first case of phyllodes tumor of anogenital mammary-like glands with gynecomastoid hyperplasia at the periphery in a male patient. To make a diagnosis, we had to differentiate this lesion from hidradenoma papilliferum of skin appendage, phyllodes tumor of ectopic prostatic tissue, and other tumors of anogenital mammary-like glands analogous to the breast tumor . While gynecomastia of male breast is usually a result of hormone imbalance, our patient’s tumor did not seem to be related to peripheral hormone status in the anogenital mammary-like glands. Nevertheless, because hormone imbalance has been strongly related to male breast cancer, hormone levels may need to be followed in male patients who have this rare malady.http://www.diagnosticpathology.diagnomx.eu/vs/1509145815899177The virtual slide(s) for this article can be found here:  Ectopic breast tissue in the vulva was first identified by Hartung in 1872, and it has long been considered caudal remnants of the milk ridges, though mammary type tissue has been reported to be a normal constituent of the anogenital area (1991) . Herein,A 41-year-old Taiwanese male with a previous history of hypertension and major depressive disorder under control with medication came to the outpatient clinic of the Division of Gastroenterology complaining of recent anal bleeding. Physical examination and colon fiberoscopy revealed a subepithelial tumor at anal verge  and stained with hematoxylin-eosin. Immunohistochemistry stains were performed using Leica BOND-MAX. We performed immunostaining for: estrogen receptor (Clone 6F11); progesterone (Clone 16); androgen receptor (Clone AR27); gross cystic disease fluid protein 15 (Clone 23A3); vimentin (Clone SRL33); CD34 (Clone QBEnd/10); actin (Clone HHF35); smooth muscle actin(SMA) ; Ki-67(MIB-1) (Clone GM010); Cytokeratin 7(CK7) (CloneOV-TL 12/30); Prostatic Acid Phosphatase (PSAP) (Clone PASE/4LJ); prostate-specific antigen (PSA) (Clone 35H9); Pan-cytokeratin (Clone AE1/AE3).Grossly, the subepithelial tumor measured 2.4 cm at the greatest circumference. It was grey-white, mildly firm, well-circumscribed with a cleft-like appearance (Figure Microscopically, the circumscribed tumor was composed of the biphasic components of glandular epithelium and stromal component, together forming leaf-like slits Figure a. The glIn the immunohistochemical study, the luminal ductal epithelium showed positive for ER and PR and focal positive for AR and GCDFP-15 Figure a-d. The The patient remained in the hospital for three days and recovery was unremarkable. He was discharged on day 4. As of 20 months post-surgery, there was no local recurrence.Lesions of AGMLG present as a spectra of morphologic changes synonymous with those in the breast, including lactating adenoma, hidradenoma papilliferum, syringoadenoma papilliferum, fibroadenoma, phyllodes tumor, pseudoangiomatous stromal hyperplasia, extramammary Paget’s disease and other malignancies arising from AGMLG . Benign We performed differential diagnoses to exclude possible hidradenoma papilliferum of skin appendage, phyllodes tumor of ectopic prostatic tissue, and tumors of AGMLG which are analogous with the breast neoplasm. Hidradenoma papilliferum can also be found in the anal region -9. HowevBenign lesions in AGMLG outnumber malignant ones more than they do in the breast, possibly because the anus has more superficial locations . In all According to Sandra J. , there is always concurrent gynecomastia in fibroadenoma of breast in men . Both gyThe alterations in ratio of androgen to estrogen may be influenced by many factors . In middIn summary, herein we have introduced the first case of a male patient with a phyllodes tumor in anogenital mammary-like glands. Gynecomastoid hyperplasia of AGMLG was also identified, though no hormone imbalance or breast manifestations were found. We are unsure whether the phyllodes tumor of AGMLG lesion in our male patient was indeed a localized lesion or whether he would develop breast cancer in the future. Further study is needed to establish the clinical significance of this manifestation.Written informed consent was obtained from the patient for publication of this case report and accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.AGMLG: Anogenital mammary-like glands.The authors declare that they have no competing interests.HHT conceived the study, participated in its design, coordinated research efforts, and helped draft and edit the manuscript. SPH participated in the pathological analysis and drafted the manuscript. TMK and P-CC contributed to the collection of clinical data. All authors read and approved the final version of the manuscript.


Dysembryoplastic neuroepithelial tumor (DNT) is a benign neoplasm with typical supratentorial location, but the possibility of these rare tumors can also be located in the posterior fossa must be taken into account. We report a 21-year-old woman that suffered gait instability, headache, and diplopia. On CT-scan, an intraparenchymatous cerebellar tumor was disclosed. It was isodense, showing light enhancement after contrast administration. On MRI (T1-weighted image) the tumor was isointense, showing inhomogeneous hyperintensity after-gadolinium administration. On T2-weighted MRI, the tumor was inhomogenously hyperintense. At surgery, a solid and hypervascularized tumor was completely removed. Two years after surgery, the patient is symptom-free. Pathological study showed coexistence of areas of pilocytic astrocytoma with areas in which small rounded oligodendrocyte-like cells (OLC), with strong synaptophysin expression were identified. These neurocytic areas showed an eosinophilic matrix forming microcysts, and cells with aspect of “floating neurons” were occasionally identified. A complex form variant of DNT was diagnosed. Our case suggests that in presence of a cerebellar tumor with features of pilocytic astrocytoma, the possibility of a complex form variant of DNT should be considered. Dysembryoplastic neuroepithelial tumor (DNT) is a rare and benign neoplasm with typical supratentorial location , 2. NeveOur patient was a 21-year-old woman, suffering two weeks of gait instability, headache, and diplopia. CT-scan showed an isodense intraparenchymatous cerebellar tumor with light enhancement after contrast administration . T1-weigAfter posterior fossa surgery, a solid and hypervascularized tumor, with necrotic areas, was completely removed. Two years after surgery, the patient is symptom-free and control MRI shows absence of recurrence or residual tumor Figures . Pathological study of the resected tumor showed a nonhomogenous tissue with areas of ischemic necrosis and a great number of hyalinized and glomeruloid vessels. In the hamartomatous-like vessels, endothelial cells showed frequent Ki-67-positivity.Areas of pilocytic astrocytoma, with Rosenthal fibers and eosinophilic granular bodies were occasionally identified. These areas showed strong gliofibrillary acidic protein (GFAP)-positivity. In other areas, cerebellar cortex with abnormal positioning of Purkinje cells was identified, but unquestionable images of cortical dysplasia were not seen. In other areas, small rounded oligodendrocyte-like cells (OLC), showing strong synaptophysin expression were identified. These cells were dispersed in an eosinophilic matrix forming microcysts. Occasionally, larger cells were observed in the alveolar matrix, some of them with aspect of “floating neurons” and showing strong synaptophysin expression . With thDNT is a glioneuronal tumor whose main characteristic is the presence of OLC arranged around bundled axons and capillaries. The neuronal characterization of the small rounded cells and the presence of neurons floating in a myxoid matrix are the features useful in differentiating DNT from oligodendroglioma, which is important because DNT has an excellent prognosis following surgical removal.Our present case shows a cerebellar tumor with areas of pilocytic astrocytoma, and areas with small synapthophysin-positive cells suggesting a neurocytic component. Although the presence of synaptophysin-positive cells of variable size suggests a diagnosis of ganglioneurocytoma, the identification of “floating neurons” allowed us to a diagnosis of DNT. At present, the coexistence of features of pilocytic astrocytoma and DNT has been accepted in the so-called “complex form” of DNT . It is obvious that our case adds to the rare descriptions of cerebellar DNT and supports the variability of the so-called glioneuronal tumors . Due to


Protein-coding regions in human genes harbor 85% of the mutations that are associated with disease-related traits. Compared with whole-genome sequencing of complex samples, exome sequencing serves as an alternative option because of its dramatically reduced cost. In fact, exome sequencing has been successfully applied to identify the cause of several Mendelian disorders, such as Miller and Schinzel-Giedio syndrome. However, there remain great challenges in handling the huge data generated by exome sequencing and in identifying potential disease-related genetic variations.http://122.228.158.106/exomeassistant), a convenient tool for submitting and annotating single nucleotide polymorphisms (SNPs) and insertion/deletion variations (InDels), was developed to rapidly detect candidate disease-related genetic variations from exome sequencing projects. Versatile filter criteria are provided by Exome-assistant to meet different users’ requirements. Exome-assistant consists of four modules: the single case module, the two cases module, the multiple cases module, and the reanalysis module. The two cases and multiple cases modules allow users to identify sample-specific and common variations. The multiple cases module also supports family-based studies and Mendelian filtering. The identified candidate disease-related genetic variations can be annotated according to their sample features.In this study, Exome-assistant (In summary, by exploring exome sequencing data, Exome-assistant can provide researchers with detailed biological insights into genetic variation events and permits the identification of potential genetic causes of human diseases and related traits. Genome-wide genotyping has been very successful in elucidating the genetic basis of phenotypic traits, such as diseases . One of Indeed, exome sequencing has been successfully applied to the identification of allelic variants in the context of rare monogenic diseases. For example, exome sequencing was applied to a small number of unrelated, affected individuals and successfully identified a causative gene for Freeman-Sheldon syndrome . Ng. et However, the large amount of data generated by exome sequencing has still posed a bioinformatics challenge in mining the potential biological implications. Subsequently, several tools have become available for the detection of genetic variants from sequenced reads, such as Genome Analysis Tool-kit (GATK) , SAMtoolIn this study, Exome-assistant was developed to provide the research community with a user-friendly and efficient tool for analyzing large amounts of genetic variants identified from exome sequencing studies. Exome-assistant provides researchers with detailed biological insights into genetic variation events and facilitates the identification of the potential genetic causes of human diseases and related traits from exome sequencing.Exome-assistant consists of four modules: single case, two cases, multiple cases and re-analysis. The single case module is responsible for functional annotation and variations filtering. Two cases and multiple cases modules, which are based on the single case module, aim to identify the shared and unique variations between or among samples. In the multiple cases module, family-based study and Mendelian filtering can also be performed by Exome-assistant. The re-analysis module is designed to run previous submitted jobs with different parameters, which avoids resubmitting the sample data.http://hgdownload.cse.ucsc.edu) and integrated into Exome-assistant. Also integrated are the HapMap data, which are a resource of genotype data from ~4 million common SNPs derived from four human populations . It is used to calculate minor allele frequency (MAF) of SNPs in different populations and estimate whether a significant difference exists between the samples (p < 0.05) using a chi-square test. To better understand if the variations, especially non-synonymous variations, lead to functional alterations to the corresponding genes, the SIFT algorithm [The basic principle of the single case analysis is to annotate the SNPs/InDels based on the information from public databases Figure , which ilgorithm  was also′/3′-UTR variations and splice site variations, based on gene model definitions.Exome-assistant first scans the reference genome and the CCDS database to perform site/region specific annotations, and classifies the variations into missense variations, nonsense variations, read-through variations and synonymous coding variations. In addition, the variations are also searched against dbSNP and those that are not present in dbSNP are assigned as novel SNPs/InDels. The novel variations, plus the known disease-associated variations, are then further classified as intergenic variations, intronic variations, 5To explore the potential genetic variations involved in disease and traits, it is essential to reduce large numbers of variations into small subsets. The single case module provides users many criteria to filter the raw variation data. The criteria for filtering SNPs include: 1) whether the variation is novel or known to be disease-related; 2) whether the allele frequency is distinct from that in HapMap; 3) SNP mutation type; 4) SNP classification; and 5) impact of the SNP on the protein product. Meanwhile, the InDel filtering criteria include: 1) whether the InDel is novel or known to be disease-related; 2) whether the InDel is located in the coding region; 3) the mutation type of the InDel; and 4) the impact of InDel on the protein product.Sample comparison, which aims to identify phenotype-associated variations, especially those associated with disease, is widely used in genetic studies, where the different annotated variations are scanned among or between samples. Exome-assistant includes two cases and multiple cases analysis. The primary motivation for developing the two cases module was to identify potential rare disease causal variations and genes, as well as to provide the ability to consider lower frequency gene disorders. In the multiple cases analyses, after filtering by single case module, the variations shared by disease samples are selected and those present in control samples (if they are submitted) are excluded from further analysis. In addition, the variations shared by disease samples, whose number can be custom-defined and must be minimum of two, are considered as potential disease-causing genetic variations. Moreover, family-based analysis can be performed, in which the candidate disease-related SNPs/InDels shared by family can be detected by setting the family trios. In addition, the Mendelian filtering parameters were added for users, which allows supporting the Mendilian filtering of SNPs/InDels in rare Mendelian disease families.Exome-assistant supplies users with simple, user-friendly interface for analyzing extensively their variations from exome sequencing studies. The input of Exome-assistant is the SNPs/InDels calling results, which are generated by SNPs/InDels calling tools, such as SAMtools , SOAPsnpExome-assistant provides flexible and intuitive windows for convenient analysis and viewing of the results. In addition, all the results, including the input list, intermediate annotation results and the last results can be downloaded in a gzip-compressed format from the results webpage. A typical result of a single case analysis contains three parts for SNPs/InDels: the summary information of input variations, the distribution of variation annotation and the detailed annotation of each variation Figure .The summary information provides an overview of input variations, including the number of input variations, unavailable variations (erroneous variations records), effective variations, and the parameters set by user to filter the variations. The distributions of variations are shown in the form of a histogram and show the percentages of each category of variations before and after variation filtering. The categories consist of intergenic, UTR-3, intron, syn-code, nonsense, splice site, UTR-5, read through, missense for SNPs, and AA-insertion, Non-coding, Frame shift, an AA-deletion for InDels.The detailed annotations of each variation are shown in a table format. The annotations of SNPs include dbSNP rs ID, gene name, transcript ID, amino-acid changes, frequency of SNP, mutation type, SNP functions (e.g. missense), prediction of functional damage to the protein product, etc. The annotations for InDels include SN (session number), coordinates on the chromosome, mutated strand, InDel sequence, substitution class, dbSNP ID, support frequency, gene name, and region of occurrence. In addition, links to other related databases, such as the gene annotation database, are also provided.In two cases and multiple case analyses, apart from the above information for each sample, the summary information of comparison between samples describes the percentages of shared and unique variations between the samples. Meanwhile, the detailed annotations of shared and unique variations are shown in separate tables, which enable choosing variations for further study.We used Exome-assistant to identify and characterize disease-related genes in Familial amyotrophic lateral sclerosis (ALS), based on a six exome sequencing sample data . The results identified a novel Cys146X mutation of SOD1 that is highly correlated with ALS . To compAs results, Exome-assistant obtained 711/36, 623/37 and 837/36 candidate SNPs/InDels in three ALS samples B340, B350 and B360, respectively. 129/5 candidate SNPs/InDels were shared by three ALS samples, among which 29/2 SNPs/InDels were novel and contained the reported disease-related SOD1 Cys147X variation. Meanwhile, ANNOVAR obtained 419/46, 438/43, and 513/52 candidate SNPs/InDels in the three ALS samples, respectively, and 88/5 were shared by three ALS samples, in which the SOD1 gene variation was also contained in the 12/1 novel shared SNPs/InDels. VAAST obtained 687/36, 604/37 and 799/36 candidate SNPs/InDels in the three ALS samples, and 90/5 were shared by three samples. In the annotated 50/0 novel shared SNPs/InDels, the SOD1 gene variation was also identified. The results supported the efficiency of Exome-assistant compared with other widely-used tools.Recent technological advances in next-generation sequencing have greatly benefited studies on genetic variation. Exome sequencing offers a cost effective method for comprehensively screening variations in complex samples. The analysis of these variations and the selection of those contributing to the phenotype, especially disease-related phenotypes, from a large amount of variation data present both challenges and promises. In this study, Exome-assistant was developed as a public resource to permit the annotation and analysis of genetic variants identified from exome sequencing studies.The main purpose of Exome-assistant is to provide a deep insight into genetic variation events. Exome-assistant provides a flexible and easy-to-use framework for annotating the variation results from next-generation sequencing platforms. Exome-assistant enables users to leverage the throughput and accuracy of the analysis, while facilitating its translation into biologically and biomedical meaningful results. Currently, Exome-assistant only supports the human genome, additional genomes of interest will be added in the future. Exome-assistant is free for non-commercial use and will be updated regularly. We welcome feedback from the user community. In the future, annotations of structural variations will be incorporated into Exome-assistant, and we will try to develop an FTP module, which allows users with limited internet connections to submit their data. In addition, further reference databases and parameters will be added in the future version of Exome-assistant, which will enable the user to filter non-disease related SNPs/InDels sites as much as possible, thus making the identified sites much more reliable. In summary, we believe that Exome-assistant will provide the scientific community with an integrated tool to assist their research into potential genetic variations contributing to diseases, based on data generated from exome sequencing.Project name: Exome-assistanthttp://122.228.158.106/exomeassistantAvailability: Operating system: Exome-assistant is a web server hosted on an Apache 2.0 HTTP server under Linux operating system. The server of Exome-assistant is equipped with four Quad-Core AMD processors (2.2 GHz each) and 32 GB of RAM.Programming Language: The front-end is implemented in PHP language, while the back-end pipeline is implemented in Perl language.License: None requiredAny restrictions to use by non-academics: NoThe web application is implemented independently of operating system and has been successfully tested with Microsoft Internet Explorer 8.0 and Firefox 2/3 .SNPs: Single nucleotide polymorphisms; InDels: Insertions and deletions; KEGG: Kyoto Encyclopedia of Genes and Genomes; GO: Gene ontology; ALS: Amyotrophic lateral sclerosis.The authors declare that they have no competing interests.QL and EJS developed the Exome-assistant web server and analysis pipeline, and drafted the manuscript. QJM, XW and XFL participated in pipeline development. XYL participated in drafting the manuscript and made substantial contributions to the conception of the study. ZSS and JYW were involved in planning of experiments and headed the project. ZSS and JYW revised the final version of the manuscript. All authors read and approved the final manuscript.


Yeast deletion-mutant collections have been successfully used to infer the mode-of-action of drugs especially by profiling chemical-genetic and genetic-genetic interactions on a genome-wide scale. Although tens of thousands of those profiles are publicly available, a lack of an accurate method for mining such data has been a major bottleneck for more widespread use of these useful resources.For general usage of those public resources, we designed FitRankDB as a general repository of fitness profiles, and developed a new search algorithm, FitSearch, for identifying the profiles that have a high similarity score with statistical significance for a given fitness profile. We demonstrated that our new repository and algorithm are highly beneficial to researchers who attempting to make hypotheses based on unknown modes-of-action of bioactive compounds, regardless of the types of experiments that have been performed using yeast deletion-mutant collection in various types of different measurement platforms, especially non-chip-based platforms.http://fitsearch.kaist.ac.kr.We showed that our new database and algorithm are useful when attempting to construct a hypothesis regarding the unknown function of a bioactive compound through small-scale experiments with a yeast deletion collection in a platform independent manner. The FitRankDB and FitSearch enhance the ease of searching public yeast fitness profiles and obtaining insights into unknown mechanisms of action of drugs. FitSearch is freely available at  S. cerevisiae, thousands of chemical-genetic profiles have been generated so far and are publicly available .BMC Genomics Volume 14 Supplement 1, 2013: Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Genomics. The full contents of the supplement are available online at http://www.biomedcentral.com/bmcgenomics/supplements/14/S1.This article has been published as part of Summary of FitSeach results of Clotrimazole, Latrunculin B, Benomyl, Cisplatin, and 2,4-DAPG.Click here for file


Summary: Most current stable isotope-based methodologies are targeted and focus only on the well-described aspects of metabolic networks. Here, we present NTFD (non-targeted tracer fate detection), a software for the non-targeted analysis of all detectable compounds derived from a stable isotope-labeled tracer present in a GC/MS dataset. In contrast to traditional metabolic flux analysis approaches, NTFD does not depend on any a priori knowledge or library information. To obtain dynamic information on metabolic pathway activity, NTFD determines mass isotopomer distributions for all detected and labeled compounds. These data provide information on relative fluxes in a metabolic network. The graphical user interface allows users to import GC/MS data in netCDF format and export all information into a tab-separated format.Availability: NTFD is C++- and Qt4-based, and it is freely available under an open-source license. Pre-compiled packages for the installation on Debian- and Redhat-based Linux distributions, as well as Windows operating systems, along with example data, are provided for download at http://ntfd.mit.edu/.Contact:gregstep@mit.edu Indeed, such methodologies are often incapable of discovering new phenomena that have yet to be described in detail. Furthermore, quantification of metabolites can be of limited use when characterizing dynamic processes like metabolism. Metabolic fluxes provide the ultimate readout of in vivo enzyme activity . Thus, NTFD provides a straightforward framework for combining the systems-level capabilities of traditional metabolomics approaches with the kinetic information that can only be ascertained through the use of isotopic tracers.Here, we present a software, non-targeted tracer fate detection (NTFD), which detects all observable metabolites labeled by a stable isotope tracer within a GC/MS dataset , which can be further processed with spreadsheet or statistics applications.Funding: Supported by the Fonds National de la Recherche (FNR), Luxembourg (ATTRACT A10/03 & AFR 1328318) and the German Research Foundation (DFG)HI1400/1-1.Conflict of Interest: none declared.