The oropharynx subsite is characterized by complex anatomy not always accessible to physical exam, making radiologic imaging a potentially useful supplement for effective follow-up assessment. In this manuscript, the literature regarding the type of radiologic imaging modality and the frequency of obtaining imaging studies in the surveillance follow-up after treatment of oropharyngeal cancer is reviewed. While ultrasound and MRI have useful characteristics that deserve further study, PET/CT appears to have the best sensitivity and specificity for imaging surveillance follow-up of head and neck cancers including oropharyngeal cancer. A negative PET/CT is particularly useful as a predictor of prognosis and can guide the clinician as to when to stop obtaining additional imaging studies in the absence of clinical signs of recurrence. However, there is scant evidence that imaging surveillance can improve survival outcomes. Suggestions to guide future imaging surveillance research studies are provided.The increasing proportion of human papilloma virus-related oropharynx cancers has led to improved success in the treatment of this disease. However, the current low recurrence rate after treatment of oropharyngeal cancer highlights the continued need for, as well as the challenges of, designing an effective follow-up surveillance program. There are frequently multiple modalities used in the treatment of oropharyngeal cancer, resulting in short- and long-term tissue changes to the head and neck that challenge clinical distinction of recurrence  Treatment of oropharyngeal cancer includes the frequent use of organ-preservation chemoradiation protocols. Reports in the literature have shown high success with this approach, with advanced stage III/IV oropharyngeal cancers having >80% 2- and 5-year disease-free survival rates ,2. More et al. found that the majority of patients diagnosed with recurrent head and neck cancer had self-identified clinical symptoms or findings prior to routine surveillance office follow-up [The goal of a head and neck cancer surveillance program is to achieve earlier detection of recurrent cancer compared to patient self-identification through frequent, interval clinical assessment. To be beneficial, earlier detection should increase the likelihood of successful salvage therapy. However, there is limited data with regard to the benefits for any head and neck cancer surveillance program. The increased survival of patients with recurrent tumors diagnosed by routine surveillance reported in some studies have been criticized as being due, in part, to lead time bias  . Agrawalollow-up . In a suollow-up . There iet al. reported a 5-year overall recurrence rate of 18% following IMRT treatment of oropharyngeal cancer [et al. found that HPV-positive oropharyngeal cancer patients had up to twofold greater 5-year overall survival and less than half the recurrence rate of HPV-negative oropharyngeal cancer patients of the same stage [The proper assessment of any cancer surveillance program must consider 1) the recurrence rate, 2) the optimal method for surveillance, and 3) whether earlier detection of recurrence leads to increased rates of successful salvage treatment and improved survival. Currently, in North America, patients with oropharynx cancers, whether treated with chemoradiation or with primary surgery +/− adjuvant therapy, have a low recurrence rate compared to historic data . Recentlme stage . The lowA second consideration for a cancer surveillance program is the selection of the method for surveillance. Lacking any serum tumor marker or other diagnostic test for recurrence, most efforts have focused on radiologic imaging as the primary tool for head and neck cancer surveillance. It has been reported that radiologic imaging adds to the sensitivity of physical exam alone . Howevervs. 90.3%), specificity (93.3% vs. 20%), positive predictive value (96% vs. 70%), and negative predictive value (93% vs. 50%) for ultrasound compared to PET/CT [Ultrasound as a surveillance tool has the advantage of lower cost and the capability for use in conjunction with the routine clinical visit and exam. A previous report from our institution comparing ultrasound and PET/CT for staging and surveillance of head and neck and thyroid cancer found superior sensitivity . These authors concluded that PET/CT is a sensitive technique for the detection of recurrent head and neck cancer.Studies examining the role of PET in head and neck cancer surveillance have found notable benefits in the initial post-treatment period. Krabbe arcinoma . PET wasr period . In theiet al. examined the benefit of a single 12-month post-treatment PET/CT scan in 91 patients without clinical evidence of head and neck cancer recurrence [et al. also suggested that a PET/CT at 12 months may be useful, but that further studies are required to confirm this recommendation [Abgral currence . Fifty-tendation . These ainitial evaluation of chemoradiation treatment response, their analysis showed an overall pooled sensitivity of 94% for the detection of residual or recurrent disease at the primary site, with a sensitivity of 74% for residual or recurrent neck disease. The negative predictive values were 95% for the primary site and 96% for neck disease, whereas the positive predictive values were 75% for the primary site and 49% for the neck.A meta-analysis of 27 manuscripts on the utility of PET scans for the post-treatment follow-up of head and neck cancer was done by Isles and colleagues . While tet al. considered the negative predictive value of surveillance PET/CT in head and neck cancer [McDermott k cancer . That iset al. examined whether HPV status could augment the predictive utility of PET/CT interpretation in the post-treatment setting [versus 85% for the oropharynx cancer group overall. On multivariate analysis, HPV status and negative initial PET/CT were the only significant predictors of recurrence.In North America and some other areas of the world, HPV-related oropharynx cancers are increasingly prevalent, with a better associated prognosis and response to treatment ,9. Zhang setting . These a setting . The neget al. observed an improvement in the detection of locoregional recurrence in head and neck malignancies when F-18 FDG PET is combined with high-resolution contrast-enhanced CT [versus PET/high-resolution contrast-enhanced CT versus physical exam with in-office endoscopy. They found that PET/high-resolution contrast-enhanced CT had superior sensitivity and negative predictive value. They further reported that the findings of the positive PET/CT had an impact on treatment for 9 of the 103 patients in the study.It also appears that the technique of PET/CT is relevant in the utility of the imaging surveillance program. In many centers, the CT component of the combined PET study is with a non-contrast, low-definition technique whose intent is for anatomic correlation of the PET findings only. However, Rangaswamy anced CT . Their sA final consideration of a cancer surveillance program is whether the earlier detection of subclinical, asymptomatic recurrences leads to improved salvage outcomes. While the experience of most head and neck cancer physicians is that earlier detection of recurrence in oropharynx cancer does increase the opportunity for treatment cure, the evidence in the reported literature is less clear. The likelihood of salvage treatment success depends heavily on the site of recurrence, with local and/or regional recurrences more likely to be salvaged than distant recurrences.et al. studied the impact of PET/CT surveillance for detecting head and neck cancer recurrence at 12 and 24 months post-treatment [versus clinically detected recurrences. These authors concluded that PET/CT offers uncertain benefit to those with initial 3-month negative PET/CT, although it was acknowledged that larger prospective studies are needed to fully answer this question.Ho reatment . In a 10et al. suggested that PET/CT could be an effective surveillance tool for early detection of asymptomatic disease in patients treated for head and neck cancer; however, the outcomes of those patients with identified recurrences remained poor [Similarly, Dunsky ned poor . Their set al. recently carried out a systematic review of the evidence for use of PET/CT in the post-treatment surveillance follow-up setting for head and neck cancers [initial post-treatment evaluation. For these four studies, there was a pooled sensitivity of 75% to 100%, specificity of 92% to 95%, positive predictive value of 50% to 90%, and negative predictive value of 100%. These authors concluded that there is a lack of evidence supporting PET/CT for post-treatment surveillance of head and neck cancers beyond its use in the initial post-treatment evaluation. Standardization of methods of imaging surveillance and emphasis on the importance of conducting prospective multi-institutional studies was recommended.A difficulty in drawing conclusions from the published literature is the inconsistency in the design and analysis of imaging surveillance studies. Patel  cancers . These aThere are several methods for radiologic imaging which offer the promise of improved detection of cancer recurrence but have not yet found widespread application for oropharyngeal carcinoma -32. The Other strategies to improve cancer detection with radiologic imaging include the use of different contrast agents or probes to increase the imaging sensitivity for tumors -32. To dThe use of newer molecular probes other than 18F-fluorodeoxyglucose (18F-FDG) for PET imaging has also been reported . 18F-fluA summary of current and future imaging strategies for the detection of recurrent oropharynx carcinoma, with references, is shown in Table In summary, there is no high-level scientific evidence to guide us to the optimal strategy of radiologic imaging surveillance for patients treated for oropharynx cancer. However, based on mostly retrospective and single-institution case series reports as well as considering mainly studies that reported imaging surveillance results across all head and neck cancer tumor subsites, PET/CT appears the most sensitive and specific imaging modality for surveillance follow-up of treated oropharynx cancer. PET/CT scans obtained between 3 and 6 months after completion of treatment and at 12 months post-treatment have notable implications for prognosis. PET/CT has important clinical utility because of a generally high specificity and negative predictive value. If two consecutive negative PET/CT studies are obtained within an interval between 3 and 6 months, the likelihood of future recurrence is extremely low. HPV status may further enhance the predictive reliability of the PET/CT findings. However, additional studies are needed to quantify the clinical outcome benefits of an imaging surveillance program and to determine the most appropriate duration and frequency of obtaining imaging studies in this patient population.


Chronic stress (CS) was reported to associate with many complex diseases and stress-related diseases show strong comorbidity; however, molecular analyses have not been performed to date to evaluate common stress-induced biological processes across these diseases. We utilized networks constructed by genes from seven genetic databases of stress-related diseases or systems to explore the common mechanisms. Genes were connected based on the interaction information of proteins they encode. A common sub-network constructed by 561 overlapping genes and 8863 overlapping edges among seven networks was identified and it provides a common gene module among seven stress-related diseases/systems. This module is significantly overlapped with network that constructed by genes from the CS gene database. 36 genes with high connectivity (hub genes) were identified from seven networks as potential key genes in those diseases/systems, 33 of hub genes were included in the common module. Genes in the common module were enriched in 190 interactive gene ontology (GO) functional clusters which provide potential disease mechanism. In conclusion, by analyzing gene networks we revealed a stress-affected common gene module among seven stress-related diseases/systems which provides insight into the process of stress induction of disease and suggests potential gene and pathway candidates for further research. Chronic stress (CS) influences multiple systems and affects the generation and development of numerous complex disorders1346810111417In recent years, genetic and expressional studies have identified a significant number of disease-related genes, and the information has been organized into specific data resources1920In this study, we used genes from seven stress-related disease/system databases and one CS database to construct networks based on the interaction information of proteins they encode. These networks were analyzed as follows: 1) identify nodes with high connectivity (hub genes) of these diseases/systems to obtain key genes in the interactive system; 2) reveal a common gene module among different stress-related diseases/systems to provide molecules potentially related to disease comorbidity; and 3) determine the relationship between CS and disease/system common module. Based on the results of the network analysis, a pathway enrichment analysis was performed to determine potential biological mechanisms through which CS induces disease.Genes from genetic and expressional databases of neurodegeneration disease, mental disorders and other stress related diseases or systems were obtained and utilized for network analyses. Genes from AlzgeneThe database STRING 9.1To examine whether a common gene module exists among different stress-related diseases/systems, nodes and edges were compared among the seven stress-related disease and system networks and a common sub-network was constructed using the overlapping nodes and edges. These interactive nodes in the sub-network constructed the common gene module. Three properties of the module were analyzed: 1) network topological parameters; 2) overlapping genes shared between the module and hub genes; and 3) overlapping genes shared between the module and the CS gene set and network. The statistical significance of the overlap between common module and the CS gene set and network was determined by the Fisher’s exact test.To identify common biological processes underlying stress-related diseases, a GO pathway cluster enrichment analysis was performed on nodes in the disease/system common module using the online analysis tool DAVIDThe seven stress-related disease/system gene sets included 4637 genes , 190 GO functional pathway clusters were enriched and categorized into three types: t see in , Biologis see in  and Molen see in . Table 3In this study we constructed seven stress-related disease/system gene networks based on the interaction information of gene-encoded proteins. The average degrees of the disease/system genes are significantly higher than the average degrees of the entire human interactome, suggesting that disease/system genes and their first neighbors are more highly connected in the human interactome than random genes, so they may play roles in a tighter and more complex manner. The result also supports the hypothesis that disease genes tend to have higher degrees34Although common genes were not identified among the stress-related diseases/systems compared in this study, a common sub-network was identified among the seven disease/systems. Genes in this sub-network were most enriched in GO pathways that related to chemical homeostasis .


The aim of our study was to understand whether ovarian steroid hormones, and their response to the metabolic hormones leptin and IGF-I leptin, could be involved in the control of mink reproductive aging via changes in basal release of ovarian progesterone and estradiol. For this purpose, we compared the release of progesterone and estradiol by ovarian fragments isolated from young (yearlings) and old (3-5 years of age) minks cultured with and without leptin and IGF-I . We observed that isolated ovaries of older animals produced less progesterone but not less estradiol than the ovaries of young animals. Leptin addition stimulated estradiol release by the ovarian tissue of young animals but inhibited it in older females. Leptin did not influence progesterone output by the ovaries of either young or older animals. IGF-I inhibited estradiol output in young but not old animals, whereas progesterone release was inhibited by IGF-I irrespective of the animal age. Our observations demonstrate the involvement of both leptin and IGF-I in the control of mink ovarian steroid hormones release. Furthermore, our findings suggest that reproductive aging in minks can be due to (a) reduction in basal progesterone release and (b) alterations in the response of estradiol but not of progesterone to leptin and IGF-I. Summary: Both leptin and IGF-I are involved in the control of mink ovarian steroid hormone release. Reproductive aging can be due to (a) reduction in basal progesterone release and (b) alterations in the response of estradiol but not of progesterone to leptin and IGF-I. The age-dependent reduction in animal and human fecundity (reproductive aging) can be due to the reduced release of ovarian steroid hormones in females – mainly estrogen, estradiol and the progestogen, progesterone. These hormones promote ovarian follicullogenesis, oogenesis, ovulation and gravidity . The ageSirotkin et al., 2005Sirotkin et al., 2005Mustela vison) is a good model for the study of the endocrine control of reproduction and aging because these animals have numerous reproductive problems and age-dependent changes in fecundity. The farm breeding of these fur animals is important from an economical viewpoint, but the hormonal control of mink reproduction is insufficiently studied  and up-regulation (progesterone) of ovarian steroids by IGF-I is possible. These observations are in line with previous publications  concerniThe functional inter-relationships between leptin and IGF-I are not to be excluded. At least, the influence of leptin on ovarian IGF-I receptor ewe; , the effTaken together, our observations demonstrate the involvement of both leptin and IGF-I in the control of mink ovarian steroid hormone release. Furthermore, the findings suggest that reproductive aging can be due to (a) reduction in basal progesterone release and (b) alterations in response of estradiol (but not of progesterone) to leptin and IGF-I. Further studies are needed to help elucidate the processes of reproductive aging in minks  and to contribute to the solution to reproductive problems in other animals and humans.The present study was performed on female American minks of standard variation kept individually in metal cages at the Liesek farm  in standard conditions and feed ration . All theImmediately after pelting, the collected ovaries were transported to the laboratory in sterile physiological solution (0.9% NaCl); two hours after collection, the ovaries were dissected into quarters, washed three times in sterile physiological solution and cultured 48 h in Dulbecco's modified Eagle's medium (DMEM)/F-12 1:1+10% calf fetal serum+1% antibiotic-antimycotic solution  in Falcon 24-well plates , 2 ml medium per well. In addition, the samples were treated with 0, 1, 10 or 100 ng/ml of leptin and IGF-I . These concentrations correspond the levels of hormones expected in the mink blood  and the Concentrations of progesterone and estradiol were determined by RIA in 25-100 µl samples of incubation medium previously validated for use as a cell culture medium. We assayed progesterone using our own RIA systems . The antP<0.05 were considered significant.The data shown are the means of values obtained in two separate experiments performed on separate days with separate groups of ovaries, each obtained from 10-15 animals. Each experimental group was represented by six culture wells. Assays of hormonal content in the incubation medium were performed in duplicate. After RIA, the values of blank control (medium cultured without cell or exogenous hormones) were subtracted from the value determined in cell-conditioned serum-supplemented medium to exclude any non-specific background . The rates of substance secretion were calculated per mg ovarian tissue/day. Significant differences between the experiments were evaluated using two-way ANOVA. When the effects of treatments were revealed, data from the experimental and control groups were compared with the Wilcoxon–Mann–Whitney multiple range test using the SigmaPlot/SigmaStat program, version 11.0 . Differences from control at


Fibroadenoma is the most common benign solid breast lesion type and a very common cause for histologic assessment. To justify a conservative therapy, a highly specific discrimination between fibroadenomas and other breast lesions is crucial. Phase-contrast imaging offers improved soft-tissue contrast and differentiability of fine structures combined with the potential of 3-dimensional imaging. In this study we assessed the potential of grating-based phase-contrast CT imaging for visualizing diagnostically relevant features of fibroadenomas.Grating-based phase-contrast CT was performed on six ex-vivo formalin-fixed breast specimens containing a fibroadenoma and three samples containing benign changes that resemble fibroadenomas using Talbot Lau interferometry and a polychromatic X-ray source. Phase-contrast and simultaneously acquired absorption-based 3D-datasets were manually matched with corresponding histological slices. The visibility of diagnostically valuable features was assessed in comparison with histology as the gold-standard.In all cases, matching of grating-based phase-contrast CT images and histology was successfully completed. Grating-based phase-contrast CT showed greatly improved differentiation of fine structures and provided accurate depiction of strands of fibrous tissue within the fibroadenomas as well as of the diagnostically valuable dilated, branched ductuli of the fibroadenomas. A clear demarcation of tumor boundaries in all cases was provided by phase- but not absorption-contrast CT.Pending successful translation of the technology to a clinical setting and considerable reduction of the required dose, the data presented here suggest that grating-based phase-contrast CT may be used as a supplementary non-invasive diagnostic tool in breast diagnostics. Phase-contrast CT may thus contribute to the reduction of false positive findings and reduce the recall and core biopsy rate in population-based screening. Phase-contrast CT may further be used to assist during histopathological workup, offering a 3D view of the tumor and helping to identify diagnostically valuable tissue sections within large tumors. Fibroadenoma is the most common breast tumor type in young women with a median age of 25 years at the time of diagnosis Despite recent improvements in clinical breast imaging, an accurate diagnosis of fibroadenoma based on imaging alone remains challenging. In particular, population-based breast cancer screening has led to mammographic detection of an increased percentage of nonpalpable fibroadenomas, raising the need for augmented histologic assessment X-ray phase-contrast imaging (PCI) has recently been shown to increase soft tissue contrast compared to conventional absorption-based X-ray contrast, and may therefore prove particularly suited for overcoming some of the limitations in current breast imaging. While conventional X-ray techniques rely on the absorption of radiation due to differing tissue-specific attenuation coefficients, PCI is based on the phase shift, influenced by the refractive index decrement Different methods have been established for PCI of the breast As a first study, we assessed imaging features of ex-vivo grating-based PC-CT for accurate characterization of fibroadenomas using a conventional X-ray source. In correlation with histopathology, characteristic features of fibroadenomas visible in PC-CT are described and the incremental value of grating-based PC-CT compared to absorption-based CT is outlined.This prospective ex-vivo study was conducted in accordance with the Declaration of Helsinki and was approved by the institutional review board . All participants gave written informed consent before inclusion after adequate explanation of the study protocol. Indication to breast surgery followed recommendation of the interdisciplinary tumor conference by the University of Munich Breast Center. Inclusion criteria were a histologically proven benign breast lesion in preoperative core biopsy or a breast lesion with benign imaging features and completed preoperative conventional breast diagnostics .Preoperative diagnostics included clinical breast examination, ultrasonography , mammography  and sonographically-guided core needle biopsy.Demographic parameters of all patients are listed in Patient 1 presented with a palpable mass in the right breast and positive familial history of breast cancer. Clinical examination revealed an oval, mobile mass of 2.5 cm diameter in the upper right lateral quadrant. Ultrasonography  in a 4% neutral-buffered formaldehyde solution. In cases where the sample size exceeded the container diameter , a selected representative and orientable tissue section of 3 cm maximum diameter was excised for the analysis.The underlying principles of grating-based phase-contrast imaging in general and the adaption of the method to conventional X-ray sources can be found in Weitkamp et al. 2 pixel size) and a Talbot-Lau interferometer. The interferometer consists of three gratings with periods of 5.4 µm that are installed in equal distances from each other. The first one (G0) is made of attenuating gold structures and is placed behind the source to create an array of individually coherent but mutually incoherent sources. This allows for interference effects being induced by the second grating (G1) called phase grating. The resulting pattern can then be analyzed by slightly moving the third grating (G2) perpendicular to the beam to draw conclusions on beam attenuation and refraction caused by the examined samples. The images that are acquired in this process for each radiographic projection are usually denoted as phase steps. In analogy to conventional CT, 3-dimensional datasets can finally be reconstructed by recording many projections from different angular positions over 180° or 360° and applying a filtered backprojection algorithm. In case of phase-contrast, the filter kernel has to be replaced by the imaginary Hilbert filter The experimental imaging setup used for the measurements is located at the Department of Physics and Institute of Medical Engineering of the Technische Universität München. It combines a rotating Molybdenum anode X-ray tube (ENRAF Nonius), a photon-counting pixilated imaging detector . The distances between the gratings were as well adjusted to further increase the visibility of the interferometer – an important performance parameter of a grating-based PC-CT system and directly associated to the achievable contrast-to-noise ratios. In addition, the quantum efficiency of the detector was improved by changing the thickness of the incorporated silicon sensor from 450 µm to 1 mm to cut down on unnecessary dose exposure of the samples and increase photon statistics.The setup changes allowed to decrease the number of projections per tomography and the exposure time per phase step from 1200 projections and 5 s (case 2 and 3) down to 800 projections and 3 s (case 6–9) while at the same time reducing image noise by a factor of 2.The tube current was set to 70 mA and a tube voltage of either 35 kVp or 40 kVp was applied during data acquisition. The choice for each setup configuration was always a trade-off between higher visibility (35 kVp) and more flux (40 kVp). The setup specifications and scan parameters of all measurements are listed in The sample containers were mounted directly in front of the phase grating and all but the first one were surrounded by water during the CT scan. The water bath was introduced to avoid the occurrence of too strong signals at the edges of the plastic cylinders that can degrade image quality. It further facilitates to perform quantitative tissue characterization as recently demonstrated in After PC-CT data acquisition, the formaldehyde-fixed samples were cut into 5 mm slices according to histopathological workup guidelines. The slices were dehydrated in an ascending alcohol series before embedding in hot paraffin wax. After solidification, the paraffin blocks were cut into 5 µm sections using a standard microtome and sections were stained with hematoxylin and eosin using standard protocols.Absorption-contrast and PC-CT data were automatically co-registered and manually matched with corresponding histological slices.PC- and absorption based CT data were successfully matched with corresponding histological sections based on characteristic macroscopic features and distribution of fatty tissue.tumor1 revealed a round shape with sharp borders and a white, gelatinous surface. The tumor reached the borders of the sample but appeared to be enclosed by a fibrous capsule. Histological workup confirmed the tumor as a fibroadenoma of 2.2 cm diameter, surrounded by fibrous-cystic mastopathy. Macroscopic examination of the excised tumor 2 was shelled out from the breast such that no surrounding breast tissue was adhering. Macroscopically, the tumor had a smooth, capsular surface. The cut face was pink and smooth, partially lobulated with white-grey septa of connective tissue between the lobuli. Histopathologic analysis  and the necessity of data acquisition after formalin fixation. Furthermore, due to modifications of the experimental setup during the study, not all samples were analyzed with the same imaging parameters. In particular, different gratings that were constantly advanced in quality were used and the distances between the gratings were adjusted in order to achieve an increased visibility and consecutively a higher contrast-to-noise ratio. The increase in quantum efficiency led to reduction of unnecessary dose and an increase in photon statistics. These changes led to a significantly reduced number of projections, exposure time and noise while maintaining constant image quality.The results presented here exemplify on the basis of a frequent solid breast tumor that PCI offers totally new imaging criteria that might complement breast diagnostics. We show here that PC-CT has theoretically the potential to improve breast imaging. Challenges to be overcome before the clinical implementation of the technique will be dose-reduction, integration into existing imaging systems as well as extensive evaluation in a blinded setup. Assuming that the technology can be successfully transferred to a clinical setting, grating-based PC-CT might serve as a complementary method for in-vivo and ex-vivo breast imaging.


We present a case of mitral valve (MV) replacement that resulted in multiple complications, as diagnosed by transesophageal echocardiography (TEE), including left ventricular outflow tract obstruction, aortic dissection and left ventricular rupture. We also describe that identification of bleeding originating from the posterior aspect of the heart by the surgical team should trigger a complete TEE evaluation for adequate diagnosis. An 84-year-old woman underwent a MV replacement. Weaning from cardiopulmonary bypass (CPB) revealed a late-peaking gradient of 44 mmHg over the left ventricular outflow tract caused by obstruction from a bioprosthetic strut. After proper surgical correction, TEE evaluation showed a type A aortic dissection that was subsequently repaired. After separation from CPB, the surgical team identified a major bleed that originated from the posterior aspect of the heart. Although the initial suspicion was injury to the atrioventricular groove, a complete TEE evaluation confirmed a left ventricular free wall rupture by showing the dissecting jet using colour-flow Doppler. TEE is an essential component in cardiac surgery for assessment of surgical repair and potential complications. Posterior bleeding should trigger a complete TEE examination with assessment of nearby structures to rule out a life-threatening pathology. Left ventricular free wall rupture can be identified using colour-flow Doppler.Multiple complications may occur after MVR.TEE is an essential component in the evaluation of surgical repair and its potential associated complications, including LVOT obstruction, aortic dissection and LV rupture.Posterior bleeding, from the region of AV groove, should trigger a complete TEE examination with assessment of nearby structures such as the atria, coronary sinus and myocardium to rule out a life threatening pathology.The diagnosis of a LV rupture can be confirmed with 2-D imaging and colour-flow Doppler demonstrating a dissecting jet through the myocardium. The role of intraoperative transesophageal echocardiography (TEE) has increased tremendously over the years. Today, intraoperative TEE is a class 1 indication for mitral valve (MV) surgery in the evaluation of pathology, surgical repair and associated complications. The authors present a case report highlighting the value of TEE in the assessment of multiple complications following MV replacement surgery including, left ventricular outflow tract obstruction, aortic dissection and left ventricular rupture. Written consent about utilization of patient information and imaging was obtained from the patient during the preoperative evaluation.Video 1http://movie-usa.glencoesoftware.com/video/10.1530/ERP-15-0026/video-1.This video demonstrates pre-repair clips and is divided into three sections. The initial images present a mid-esophageal four-chamber view showing a dilated left atrium and absence of mitral leaflet coaptation. The next section demonstrates severe mitral insufficiency by colour-flow Doppler. The last section shows a hyperdynamic left ventricle with absence of pericardial haematoma. View Video 1 at Download Video 1An 84-year-old woman with a diagnosis of severe MV regurgitation was referred to our institution for a MV replacement. Her past medical history included diastolic heart failure, pulmonary hypertension and paroxysmal atrial fibrillation. After uneventful induction of general anaesthesia, transesophageal echocardiographic (TEE) examination demonstrated a small retracted posterior leaflet with absence of coaptation. Additional findings included a hyperdynamic left ventricle (LV) with preserved systolic function and no regional wall motion abnormalities . WrittenIntraoperative findings showed no valvular calcification and a 29 mm St Jude Medical Epic porcine bioprosthesis was implanted without resection of native leaflets and subvalvular apparatus. As the patient was weaned from cardiopulmonary bypass (CPB), left ventricular outflow tract (LVOT) obstruction was observed. One of the bioprosthetic struts was seen in the LVOT , in addition to anterior leaflet remnants A. ContinVideo 2http://movie-usa.glencoesoftware.com/video/10.1530/ERP-15-0026/video-2.This video demonstrates post-repair clips with the appearance of a newly compressed coronary sinus. The next clip shows a transgastric mid-papillary view with a haematoma in the inferoseptal region of the myocardium with adjacent clotted blood. The last two clips demonstrate the LV rupture with colour-flow Doppler. LV: left ventricle. View Video 2 at Download Video 2Considering the prolonged total CPB time of over 6 h, the risk of additional aortic clamping and the age of the patient, the mid-ventricular rupture was repaired off pump. After achieving a reasonable haemostasis, the patient was transferred to the intensive care unit with substantial inotropic support. However, she died in the same evening. Autopsy was not permitted.The above-mentioned case describes three different complications after MV replacement surgery. TEE plays a central role in the evaluation of surgical repair and potential associated complications.The decision to return on CPB for a second MV replacement was based on TEE findings of a LVOT obstruction from the strut of the bioprosthetic valve and anterior leaflets remnants. This is a well described phenomenon in the literature Intraoperative aortic dissection is a rare but potentially fatal iatrogenic complication of open-heart surgeries. The incidence of intraoperative aortic dissection in cardiac surgical procedures was found to be 0.13–0.35% in several retrospective studies, with a mortality rate ranging from 20% to 33%. Dissections mostly originate from the aortic cannulation, the cross-clamp site or at the site of the partial-occlusion clamp Rupture of the LV is a rare but often fatal complication after MV replacement. Classification of LV rupture can be categorized into three types based on the anatomical location of the rupture and the mechanism involved. Type 1 is a tear in the AVG associated with extensive decalcification of the MV annulus, resection of posterior leaflet or improper lifting of the heart. Type 2 is a tear at the base of the papillary muscle associated with excessive resection of posterior papillary muscle. Type 3 is a tear located between type 1 and type 2 lesions most often related to trauma of the posterior ventricular wall from a large prosthetic valve and penetration of a valve strut in the posterior myocardium In our case, bleeding was identified in the mid-ventricular region of the posterior wall. TEE examination confirmed a mid-ventricular rupture near the ventricular septum extending to the LV inferobasal segment with flow entering the pericardial space in systole, as documented by continuous wave Doppler. An echo-lucent haematoma was also visualized adjacent to clotted blood in the posterior region. The most likely etiology of the bleeding was a type 3 LV rupture of the posterior wall by penetration of a valvular strut.et al. Although bleeding from the region of the AV groove may originate from an AVG dissociation or rupture of the LV free wall, it is important to differentiate both mechanisms from other etiologies such as injury to the CS or left atrium. Haematoma in the AVG from CS trauma has previously been identified as an echo-lucent space adjacent to the left atrial wall with an absence of flow The patient was deceased and therefore could not give consent.C L Brassard, C Viens and A Denault helped review the original data and write the manuscript. P Couture helped review the original data and write the manuscript and served as the archival author.


Paraglaciecola sp. S66, was isolated from marine samples of eelgrass (Zostera sp.) and sequenced. The draft genome contains a large number of enzyme-encoding genes with predicted function against several complex polysaccharides found in the cell walls of algae.A novel agarolytic gammaproteobacterium,  Although many CAZymes targeting polysaccharides of terrestrial origin have been described, knowledge of the catalytic machineries degrading the complex marine polysaccharides is still limited. Agars and carrageenans are structural cell-wall polysaccharides of red seaweeds and are routinely used in solid growth media in laboratories and as stabilizers in conventional food and cosmetic products. Enzymatic degradation of these polysaccharides has recently received attention due to the potential bioactive properties of agaro- and carrageenan-oligosaccharides  collected at the coast of Northwest Zealand, Denmark, and was identified based on the ability to visibly degrade the agar growth medium. Genomic DNA was extracted from a liquid culture grown at 20°C in marine broth and sequenced on an Illumina HiSeq platform producing 150-bp paired-end reads from a short insert library. Assembly was performed using Velvet and Velvet optimizer  against a local version of the dbCAN database (Paraglaciecola sp. S66 can degrade and utilize a range of complex carbohydrates, including the sulfated polysaccharides found in algal cell walls.A large number of CAZymes were identified in the genome of S66 based on an HMMsearch (database , 9. A todatabase . BesidesLSNE00000000. The version described in this paper is the first version, LSNE01000000.This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession number


The dynamics of epigenomic marks in their relevant chromatin states regulate distinct gene expression patterns, biological functions and phenotypic variations in biological processes. The availability of high-throughput epigenomic data generated by next-generation sequencing technologies allows a data-driven approach to evaluate the similarities and differences of diverse tissue and cell types in terms of epigenomic features. While ChromImpute has allowed for the imputation of large-scale epigenomic information to yield more robust data to capture meaningful relationships between biological samples, widely used methods such as hierarchical clustering and correlation analysis cannot adequately utilize epigenomic data to accurately reveal the distinction and grouping of different tissue and cell types.We utilize a three-step testing procedure–ANOVA, t test and overlap test to identify tissue/cell-type- associated enhancers and promoters and to calculate a newly defined Epigenomic Overlap Measure (EPOM). EPOM results in a clear correspondence map of biological samples from different tissue and cell types through comparison of epigenomic marks evaluated in their relevant chromatin states.Correspondence maps by EPOM show strong capability in distinguishing and grouping different tissue and cell types and reveal biologically meaningful similarities between Heart and Muscle, Blood & T-cell and HSC & B-cell, Brain and Neurosphere, etc. The gene ontology enrichment analysis both supports and explains the discoveries made by EPOM and suggests that the associated enhancers and promoters demonstrate distinguishable functions across tissue and cell types. Moreover, the tissue/cell-type-associated enhancers and promoters show enrichment in the disease-related SNPs that are also associated with the corresponding tissue or cell types. This agreement suggests the potential of identifying causal genetic variants relevant to cell-type-specific diseases from our identified associated enhancers and promoters.The proposed EPOM measure demonstrates superior capability in grouping and finding a clear correspondence map of biological samples from different tissue and cell types. The identified associated enhancers and promoters provide a comprehensive catalog to study distinct biological processes and disease variants in different tissue and cell types. Our results also find that the associated promoters exhibit more cell-type-specific functions than the associated enhancers do, suggesting that the non-associated promoters have more housekeeping functions than the non-associated enhancers.The online version of this article (doi:10.1186/s12864-015-2303-9) contains supplementary material, which is available to authorized users. While all human tissue and cell types largely preserve the biological information in the DNA sequence of the human genome, the epigenomic landscapes of different tissue and cell types vary considerably, resulting in distinct gene expression programs, biological functions and phenotypic variations. Epigenomic information, such as DNA methylation, covalent histone modifications and DNA accessibility in each tissue and cell type can be investigated using high-throughput sequencing technologies such as Bisulfite-seq, ChIP-seq and DNase-seq . The genPrevious research mostly relied on gene expression profiles to study the relationships of samples from different tissue and cell types , 6. The k-means clustering on chromatin modifications from both promoters and enhancers [Histone modifications at enhancers and promoters in the human genome were found to both reflect and explain global cell-type-specific gene expression , 9. KundThe recent large-scale imputation of epigenomic datasets provided a more consistent and robust resource for capturing sample relationships and dynamic epigenomic information across cell types . Ernst eDespite the fact that hierarchical clustering and correlation analysis have been shown useful in studying the relationships of biological samples across tissue and cell types, there are many limitations in their use. In the tree representation of hierarchical clustering, it is often difficult to identify the number of groups. In correlation analysis, both Pearson and Spearman correlation coefficients usually provide a noisy correlation matrix of samples, making the detection of sample groups another challenge. Therefore, in order to find a clear correspondence map and distinct grouping of samples based on epigenomic features, we need new methods. Here we propose a new measure–Epigenome Overlap Measure (EPOM)–to distinguish different tissue and cell groups by performing a three-step testing procedure on large-scale epigenomic datasets.We describe our method in the following three subsections. In the first subsection, we introduce how the chromatin states are defined; in the second subsection, we describe how we select the histone marks (HMs) based on their relationships with the chromatin states of interest; in the third subsection, we introduce our main three-step testing procedure. The outline of our method is illustrated in Fig. We study and evaluate the capacity of our method in mapping and grouping different tissue and cell types using histone marks at both enhancer and promoter regions.In our study, we use chromatin states of genome-wide 200 bp regions learned by a 25-state multivariate Hidden Markov Model (HMM) . The chrp-values, which represent the enrichment of ChIP-seq read counts based on a Poisson distribution. A stronger signal represents a more statistically significant enrichment of histone modification [H3 lysine 4 monomethylation H3K4me1) was observed to distribute in a cell-type-specific manner and associate with enhancer regions: predicted enhancers showed H3K4me1 enrichment , 11. It  was obsefication . The orik-th candidate enhancer (or promoter) in the i-th tissue/cell type as μi,k. Then the kth null hypothesis can be expressed as We use ANOVA to test whether a histone mark has the same group mean signals across the 16 tissue and cell types. We denote the group mean signal of the mark at the α1 to the resulting Bonferroni-corrected p-values and refer to region k as a candidate associated enhancer (or promoter) if the null hypothesis Hk0, is rejected.We apply a threshold i and j and the k-th candidate associated enhancer (or promoter), the null hypothesis is We use one-tailed t-test to perform pairwise comparison between the 16 tissue/cell types, so as to identify the associated enhancers (or promoters) of each tissue/cell type. Given two different tissue/cell types α2 to the resulting p-values and we consider the signal of tissue/cell type i to be significantly higher than that of tissue/cell type j on region k if the null hypothesis Hijk0, is rejected. For the i-th tissue/cell type, if Hijk0, is rejected for more than m times among all j≠i, we define region k as an associated enhancer (or promoter) of tissue/cell type i. We separately identify the H3K4me1-based and H3K27ac-based associated enhancers and promoters of each tissue/cell type. Then we combine the information of the two histone marks by taking the union of their associated enhancers (or promoters). That is, for each tissue/cell type we take the union of the two marks’ associated enhancers (or promoters) and use the union as the associated enhancers (or promoters) of that tissue/cell type.We apply a threshold We perform the overlap test, described in next subsection, on the discovered associated enhancers (promoters) to calculate EPOM scores between every pair of tissue/cell types.Given the signals of H3K4me1 and H3K27ac on 124 reference epigenomes divided into 16 tissue and cell types (we excluded the three tissue and cell types that only contain one sample) and the locations of candidate enhancers and candidate promoters, we used a three-step testing procedure  regions whose HM signals do not have significant variations across all biological conditions . Step 2 consists of pairwise two-sample t-tests, which aim to find associated regions for each biological condition, such that these regions’ HM signals in this condition are significantly higher than in at least m other conditions. Steps 1 and 2 are not redundant but complementary to each other. Step 1 can largely reduce the number of candidate associated regions to be tested in Step 2, so that Step 2 will find the associated regions that not only have high signals in one biological condition but also have strong signal variations across conditions. In addition, Step 1 can largely reduce computational time in Step 2, so as to increase the computational efficiency of the EPOM method. Step 2 is necessary to identify associated regions that carry cell-type-specific characteristics, because it centers on each biological condition in its search for associated regions. The two steps together ensure that the identified associated regions have strong differentiating capability of biological conditions and thus serve as good candidates for the overlap test in Step 3.In this paper, we set the thresholds as A and B. We consider the union of the associated enhancers (or promoters) of all tissue/cell types after step 2 as the population and A and B as two samples drawn from the population. The null hypothesis is that A and B are two independent samples, while the alternative hypothesis is that A and B are dependent samples. The test statistic is the number of regions shared by A and B. Given n (the population size), |A| and |B| (the sizes of A and B), the larger the test statistics is, the higher the likelihood that the null hypothesis will be rejected. The p-value of the test statistic is calculated as: The overlap test, a procedure to check the significance of the overlap of two samples, has been demonstrated as a powerful procedure to map developmental stages from the same or different species based on transcriptomic data . Here weA and B as Then we define the EPOM score between samples A and B are dependent and the more epigenomic characteristics they share, and vice versa.The larger the EPOM score is, the more likely that k-means clustering and Pearson correlation that promoter regions are largely invariant across different tissue/cell types [From the chromatin states discovered by the 25-state HMM model , we idenll types . On the We summarize the EPOM scores of all pairwise comparisons based on the identified associated enhancers and associated promoters respectively. The two resulting matrices were plotted as heatmaps to illustrate the correspondence maps of epigenomes, as shown in Fig. 33m=13 instead of m=14, the discovered associated enhancers and associated promoters would become less cell-type-specific. The resulting EPOM scores are consequently less distinguishable and the correspondence maps  of the testing procedure we use a lower threshold m=14), the results from the two marks are generally the same; when using the lower threshold (m=13), the results from the two marks are still consistent, but with different scores for certain off-diagonal patterns  in Step 2, we used H3K4me1 and H3K27ac’s associated enhancers (or promoters) separately to perform the overlap test in Step 3. When using the higher threshold (Another case worth attention is how the EPOM scores change if we summarize the associated enhancers (or promoters) in Step 2 of the testing procedure by taking the intersection of associated enhancers (or promoters) identified for each mark  in up to 200 kb distance. Assignment of a gene to an associated enhancer was counted in both upstream and downstream directions, while assignment of a gene to an associated promoter was counted only in the promoter’s downstream direction. The numbers and proportions of the potential target genes assigned to the associated enhancers and promoters are summarized in Fig. Noticing that real enhancers and promoters can span across regions much longer than 200 bp, we merged the adjacent associated enhancers or promoters and re-identified the potential target genes of the merged associated enhancers or promoters – and found that the associated promoters have around 1.5−6 times cell-type-specific GO terms compared with the associated enhancers. This again implies that in terms of the 200 bp regions, the associated promoters are more cell-type-specific than associated enhancers.We performed gene ontology (GO)  enrichmeThe annotations of top enriched GO terms in each tissue and cell type  have identified millions of genetic variants associated with common traits and diseases. However, selecting informative single-nucleotide polymorphisms (SNPs) that have main effects on diverse diseases remains a great challenge . It was p-values) >0) and 85 are significantly enriched  >1) in associated enhancers of at least one tissue/cell type; 61 are enriched and 39 are significantly enriched in associated promoters of at least one tissue/cell type . EPOM compares different tissue and cell types based on the similarity of histone modification marks evaluated in their relevant chromatin states. The proposed measure is calculated via a three-step testing procedure including ANOVA, t test and overlap test. Compared to traditional correlation analysis, EPOM is able to create a much clearer mapping pattern across 16 tissue and cell types. By tuning the thresholds in the testing procedure, EPOM can perform either grouping or identity mapping of biological samples based on epigenomic features. The associated enhancers and associated promoters identified by EPOM are good indicators of tissue/cell epigenomic characteristics, and they are important genomic regions for downstream analysis such as regulatory network analysis, GO enrichment analysis and GWAS studies. Results under different settings  all demonstrate the effectiveness of our approach compared with correlation analysis in finding clear correspondence maps of biological samples. Moreover, the resulting EPOM scores reveal biologically meaningful patterns between similar tissue/cell types and confirm the belief that epigenomic landscapes are powerful resources for understanding cellular identity , 31. Thep-value threshold, and the marks that have large numbers of differential regions will be good candidates for EPOM. The rationale behind this selection approach is that EPOM prefers the marks carrying more cell-type-specific information on the genomic regions of interest. We implement this selection approach in Additional file The EPOM method can be easily extended to study the relationships between diverse tissue/cell types based on signals of any epigenetic marks in genomic regions of interest. Here we suggest an efficient approach to systematically select epigenetic marks for EPOM if no specific marks are of prior interest. The selection will be based on the number of regions where each mark has differential signals across biological conditions. The differential regions of each mark can be found by the Step 1 (ANOVA) in our testing procedure given a specified We identified the associated enhancers/promoters’ potential target genes in each tissue and cell type and used the top enriched GO terms in these genes to predict the biological functions of the associated enhancers and promoters. The results of GO enrichment analysis confirm the similarities of tissues and cell types found by EPOM and provide functional explanations for the underlying regulatory mechanisms leading to these patterns. The EPOM scores, together with the GO enrichment results, suggest that the associated enhancers and promoters have well captured the epigenomic characteristics of their corresponding tissue and cell types. An important future direction is to incorporate three-dimensional (3D) chromatin structures into the identification of the target genes of associated enhancers/promoters. The Hi-C technology makes it possible to decipher 3D chromatin structures and to thus reveal more accurate and complete interactions between genes and regulatory regions , 34. HowDespite the previous belief that chromatin states at promoters are largely invariant across diverse cell types , 37, ourMore functional analyses based on disease ontology further confirm that the discovered associated regions carry important disease-relevant characteristics of their corresponding tissue/cell types. The identified associated enhancers and promoters can be good resources for understanding the epigenomic mechanisms of different tissue and cell types. It is a great challenge now to interpret the biological mechanisms and effects of the large amounts of identified SNPs. A common approach was to simply study the overlap between the SNPs and regulatory elements such as histone modification marks, binding sites of transcription factors and promoter regions . Howeverhttp://egg2.wustl.edu/roadmap/web_portal/imputed.html#chr_imp. The data for SNP annotation is available at http://jjwanglab.org/gwasdb. The associated enhancer and promoter regions identified by EPOM are available at http://www.stat.ucla.edu/~jingyi.li/software-and-data.html or http://www.stat.ucla.edu/~jingyi.li/data/EpOM/associated_enhancers_and_promoters.tar.gz.zip.The epigenomic datasets supporting the results of this article are available at the web portal of the Roadmap Epigenomics Project. Both the data of the 25-state Imputation Based Chromatin State Model and the imputed signals of histone modification marks are available at


Since approximately 1.6 percent of men and women will be diagnosed with kidney and renal pelvis cancer during their lifetime, there is a growing interest in non-invasive kidney sparing therapy for renal cancer. As a consequence, several patient studies investigated the feasibility of high intensity focused ultrasound (HIFU) for the thermal ablation of renal masses. The majority of these studies used either a hand-held extracorporeal ultrasound transducer with ultrasound imaging for guidance or a laparoscopic approach. Drawbacks of these techniques are the lack of respiratory motion compensation, no means to observe the energy deposition in real time, the complexity of the probe positioning, and the risks of bleeding and tumor spillage. Alternatively, recent preclinical studies have demonstrated the feasibility of magnetic resonance guided high intensity focused ultrasound (MR-HIFU) interventions on the kidney with respect to motion compensated real-time thermometry and acoustic energy delivery. Here, we extend this prior work to investigate in an animal study if MR-HIFU can deliver a reliable confluent volumetric lesion in the renal cortex in a clinically relevant time-frame.An anesthetized Dalland land pig was placed on its right side on a clinical Sonalleve MR-HIFU therapy system, which is integrated with a 1.5T Achieva MRI  with minor modifications. Both acoustic energy delivery and MR-thermometry were respiratory gated  and active surface cooling was employed to prevent undesired near-field damage. A honeycomb pattern of seven ablation cells  was positioned in the cortex of the kidney as shown in figure All ablation cells reached peak temperatures > 80°C during the sonications, resulting in a lethal thermal dose over the entire delineated target area. DCE-MRI displayed a confluent non-perfused volume within the cortex and partly within the medulla with a volume of ±2 ml as shown in figure


Cerebral Cavernous malformations (CCM) occur in less than 1% of the general population, and one-third may have more than one lesion. Headaches alone may accompany CCM in up to 10% patients although micro-haemorrhage with accompanying headache is more common.A 67-year old male presented with a 15-year history of episodes of sudden onset left facial pain with dysesthesia in the fifth cranial nerve V1 distribution and left sided headache. The frequency of facial pain has increased with daily episodes of occurrence, exacerbated by movements. His headache impact score HIT-6 was 71. The patient’s family history is a sister died of a stroke, another from multiple sclerosis and a nephew died at 15-years-old of cerebral haemorrhage. On examination there were signs consistent with a brainstem lesion. Extensive scanning demonstrated no haemorrhage into any lesion and confirming multiple foci including a pontine lesion. Genetic testing confirmed a CCM2 mutation heterozygous deletion of two-nucleotides and 50% risk of inheritance of the c76_77del to family members.Pontine CCM can precipitate in migrainous-type headache and atypical facial nerve distribution symptoms due to disruption of the trigeminovascular system (TGVS). The Periaqueductal Grey area (PAG) is involved in modulating pain through both ascending and descending projections, the latters connections to the TGVS that inhibits nociceptive afferent information. CCM lesion is also disrupting the Nucleus Raphe Magnus (NRM), acting as a migraine generator.The diagnosis for the cause of this intractable facial pain and headache is the large pontine CCM lesion disinhibiting fibres of the TGVS.No conflict of interest.


The drive towards organic computing is gaining momentum. Interestingly, the building blocks for such architectures is based on molecular ensembles extending from nucleic acids to synthetic molecules. Advancement in this direction requires devising precise nanoscopic experiments and model calculations to decipher the mechanisms governing the integration of a large number of molecules over time at room-temperature. Here, we report on ultrahigh-resolution scanning tunnelling microscopic measurements to register the motion of molecules in the absence of external stimulus in liquid medium. We observe the collective behavior of individual molecules within a swarm which constantly iterate their position to attain an energetically favourable site. Our approach provides a consistent pathway to register molecular self-assembly in sequential steps from visualising thermodynamically driven repair of defects up until the formation of a stable two-dimensional configuration. These elemental findings on molecular surface dynamics, self-repair and intermolecular kinetic pathways rationalised by atom-scale simulations can be explored for developing new models in algorithmic self-assembly to realisation of evolvable hardware. The interaction of simple individual units within an ensemble that leads to advanced collective behavior without any chain of control is generally referred to as swarm intelligence 1341367Similar to the self-organised structures at the macroscale, unsupervised ordering also takes place at molecular length scales, driven by the process of self-assembly141541622232425262829The subject matter that remains to be fully clarified is that of the mechanisms leading to the formation of a self-assembled molecular architecture in real-time under innate conditions at room-temperature. This is of significant research interest as knowing the stepwise evolution of molecular systems and pattern formation can serve in modelling algorithms that can be explored in effectively predicting design of new materials formed through self-assembly. Additionally, such information can have broad implications in sectors where bottom-up self-assembly plays a crucial role such as biomolecular computationin situ probe microscope capable of capturing stunning real-space snaphots and time-elapsed images of fullerene molecular dynamics at the liquid-metal interface at room-temperature. We observe the local dynamic relocation of individual fullerene molecules and subtle differences in molecular motion as a function of their respective position within the swarm. Crucially, we were able to provide direct experimental evidence for defect formation and healing at a molecular scale. We further rely on atomic-scale molecular dynamics (MD) simulations to compute the intermolecular and metal-molecule interaction energies and quantify the differences in molecular motion as a function of their respective position within the matrix. There is a clear thermodynamic benefit for self-assembly into the observed automatically-healed and tightly-packed patterns. These preliminary design rules gleaned from precise nanoscopic measurements and theoretical calculations can be directly applied in designing new algorithms and refining if possible previously reported step-by-step equilibration rules framed for agent-based algorithms32In this article we report on the application of a high resolution 60) molecular layer were performed is shown in 60 molecules with an intermolecular distance (measured between the center of one fullerene cage to the other) of ~1 nm is shown in the zoomed-in three-dimensional in situ STM image (recorded 10 minutes after drop casting the C60 solution on the gold surface). Previously it has been shown that it is possible to trigger a cascading electrical response through a well-ordered molecular layer by applying an input voltage pulse at a specific location over a single molecule within the layer, opening up possibilities for programming molecular circuitsA schematic description of the liquid-cell within which the STM imaging measurements on a fullerene (Cin situ STM snapshot (recorded immediately after deposition on gold thin film supported on mica substrate) of C60 molecules in three dimensional format showing regions which are partially ordered and the majority of the molecules in a disordered phase as a result of competitive adsorption mechanisms. Zooming-in on a selected region shows well resolved single C60 molecular units within local domains  which follows the geometry of the selfish herd60 molecules assembling on Au(111) in bulk solvent medium). From the simulation cells  of 30 ns of room temperature dynamics. 60 coordination number is increased in steps. The RMSF values are computed from the centres of mass of each C60 molecule and the values are averaged over multiple molecules (binned according to C60 coordination number) and temporal structures. The simulation data indicates that the low-coordination species are more mobile than buried species, thereby substantiating the STM findings.To better understand and quantitatively map the location-specific differences in single molecule mobility, we performed molecular dynamics (MD) simulations taking into account the actual experimental conditions olecules  and the n energy . Time- ain situ STM image of a C60 molecular layer recorded immediately after liquid-phase deposition on gold thin film supported on halide substrate (see methods section for sample preparation) is shown in 60 molecules near holes as measured by RMSF fluctuations in computed C60 positions  and data can be recorded closer to video-rates by upgrading the electronics design (bandwidth of power amplifier and feedback control system) of the scanning probe microscope and achieving suitable signal-to-noise ratioCapturing minute structural fluctuations in the cooperative behaviour of molecules and registering features such as molecular error correction is experimentally challenging especially at the liquid-solid interface222939in-situ STM image of a molecular layer showing the arrangement of individual molecules within the matrix and areas adjacent to the molecules that remain empty. The computed free energy profile in 60 molecule to Au(111) plus an additional 1.0 eV that is obtained from intermolecular packing, as the C60 node is connected to six neighbouring nodes. This thermodynamic driver towards pristine SAMs is due purely to C60-C60 van der Waals packing interactions. The plot shows an average benefit of −0.2 ± 0.1 eV obtained for each additional contact made as the C60 goes from an isolated adsorbate (coordination number of zero) to a maximally coordinated (coordination number of six) node in the hexagonally-close packed monolayer. Note the free energy benefit becomes small in the middle of cluster-formation  were purchased from Alfa Aesar in powder form and dispersed in n-tetradecane solvent (Sigma Aldrich) at a concentration of 10−2 M using a low-power sonic bath procedure for ten minutes followed by centrifugation at 1500 rpm for 60 minutes. 10 μL of the as-prepared supernatant C60 solution was gently drop casted onto the gold thin film, placed within a Teflon-based liquid-cell for subsequent STM imaging at room-temperature. For the metal substrate 100 nm of Au (99.99%) was electron-beam evaporated  onto freshly cleaved mica  at a rate of 1 Å s−1. Such metal thin films on mica were found to contain nanoscale defects that impeded molecular self-assembly. For engineering defect-free and ultra flat gold thin films, we employ halide support platforms on which gold was evaporated using identical protocols as reported previouslyThe Cn-tetradecane liquid medium. The in situ STM measurements were performed in state-of-the-art noise free laboratories with excellent noise, vibration, temperature and humidity control. The bias voltage is applied to the sample and the metal tip is grounded through the high-sensitive preamplifier. The pre-amplifier employed in this study is capable of current detection as low as 1pA. Image processing was performed using Gwyddion 2.39. To avoid tip artifacts the STM metal probe was calibrated by measuring standard reference differential conductance spectra and imaging over blank Au(111) surface.The STM measurements were performed in constant-current mode at room-temperature using a Veeco Scanning Tunnelling Microscope, Nanoscope IIIa, Multimode (Scanner model: E- Scanner). A mechanically cut Pt/Ir wire  was used as the STM probe. For real-time tracking of molecular dynamics the STM probe was scanned at a speed of 1 ms/line with a tip drift rate of ~1 nm/min in 60 physisorption energies on Au(111) were calculated using two independent methods, van der Waals corrected DFT60 monolayer assembly was modelled using molecular dynamics simulations. Full details of the methods and models used are given in the supporting information.The CHow to cite this article: Nirmalraj, P. N. et al. Capturing the embryonic stages of self-assembly - design rules for molecular computation. Sci. Rep.5, 10116; doi: 10.1038/srep10116 (2015).


HIV-1 integrase (IN) is a key component of the pre-integration complex (PIC) and is involved in several steps of retrovirus replication. IN cannot perform these functions on its own and need to recruit host cell proteins to efficiently carry out the different processes. Retroviral INs are flexible proteins showing high inter-domain flexibility. This intrinsic flexibility accounts for IN ability to interact with multiple partners, which in turn chaperones PIC formation and its multiple functions. Biochemical and structural studies have long been hampered due to the PIC dynamics and intrinsic flexibility. We demonstrated that the low solubility and inter-domain flexibility can be circumvented by forming stable and specific complexes with DNA or protein co-factors and by post-translational modifications.Hundreds of milligrams of stable complexes are needed for in vitro functional and structural studies. For this, we develop new technologies for high molecular weight transient complexes production as well as for functional and structural analysis . Structures have been solved by Cryo-EM and X-ray crystallography.We reconstruct in vitro stable and soluble complexes around IN. We solved the cryo-EM structures of the IN/LEDGF/DNA  and IN/LEDGF/INI1/DNA  complexes. Structures together with functional assays gave important hints on the functional role of LEDGF and INI1. Other sub-complexes of the PIC have been characterized. One of them is the IN/transportin-SR2/VBP1 complex (structure in progress). Our results suggest that the function of INI1 (core protein of the swi/snf chromatin remodeling complex) in HIV-1 replication is to stabilize the PIC in the host cell, by maintaining integrase in a stable constrained conformation which prevents non-specific interactions and auto integration on the route to its integration site within nucleosomes, while LEDGF  organizes and stabilizes an active integrase tetramer suitable for specific vDNA integration.


Schizophrenia is a complex disorder with relatively stable prevalence rates estimated at about 0.5–1% , dividing them into human vs. animal studies.Rodriguez et al. investigated the effect of neuropsychological battery on global functioning and quality of life in 36 first psychotic episode of schizophrenia spectrum disorder (FES) patients. The results indicated that patients with FES were significantly impaired in both visuospatial and verbal functioning compared to healthy controls. The authors concluded that the deficit in verbal functioning was a better predictor of global functioning and quality of life than visuospatial functioning.Chen et al. investigated the nature of prospective memory using event-related brain potentials in 20 symptomatically remitted patients with schizophrenia and 20 healthy controls. The results indicated that patients with schizophrenia performed worse on the prospective memory task compared to the healthy controls. In particular, the prospective positivity amplitude was significantly attenuated in symptomatically remitted schizophrenia patients.Schott et al. investigated whether dysfunctional processing of novel information by the medial temporal lobe may be a possible neural mechanism that contributes to the pathophysiology of delusions. The authors used fMRI to examine 16 unmedicated patients with paranoid schizophrenia and 20 age-matched healthy controls. Participants completed a visual target detection task that consisted of novel and familiar stimuli, and a standard and a target picture. All of the participants when shown the novel images had activation in the hippocampus, but only healthy controls showed a positive relationship between novelty-related hippocampal activation and recognition memory performance 24 h later, indicating a role of the hippocampus in positive symptoms.Salem and Moustafa discussed the implications of these findings.Although previous research . Patients with schizophrenia had enhanced thalamic connectivity with bilateral precentral gyrus, dorsal medial frontal gyrus, middle occipital gyrus, and lingual gyrus. These patients also had reduced connectivity in bilateral superior frontal gyrus, anterior cingulate cortex, inferior parietal lobe, and cerebellum. The findings indicated that the thalamus is over-connected during resting state in schizophrenia.Schwab et al. investigated saccadic latency modulation in patients with schizophrenia and their first-degree relatives. Participants  performed two visual tasks: a color task and a Landolt ring orientation task. Saccadic latency was measured with a video-based oculography. Results indicated that saccadic latencies were not modulated by visual processing of different content for patients with schizophrenia, but saccadic latencies were modulated for relatives and health controls.Hori et al. investigated the relationship between serum BDNF levels and decision making. They compared patients with schizophrenia (86) to healthy controls (51) in terms of their decision making ability and serum BDNF levels. Scores on the Iowa Gambling Task were lower for patients with schizophrenia compared to the controls. There was a negative correlation between the mean net scores on the final two blocks and serum BDNF levels. The authors concluded that the poor performance of patients with schizophrenia on the Iowa Gambling Task may be related to impaired sensitivity to reward and punishment due to depressive symptoms and reduced serum BDNF levels.Frydecka et al. compared the level of working memory impairments across patients with schizophrenia (n = 23), psychotic bipolar disorder (n = 19), non-psychotic bipolar disorder (n = 24), and healthy controls (n = 18). The results indicated that on more demanding working memory measures the group with schizophrenia and psychotic bipolar disorder performed poorer than the non-psychotic bipolar disorder group and healthy controls. There was a positive correlation of working memory performance with antipsychotic treatment and a negative correlation with depressive symptoms in bipolar disorder and with negative symptoms in the schizophrenia subgroup.Zhuo et al. investigated changes in resting-state functional connectivity density (rsFCD) in schizophrenia (n = 95) and healthy controls (93). The results indicated that patients with schizophrenia had increased rsFCD in the bilateral striatum and hippocampus and decreased rsFCD in the bilateral sensorimotor cortices and right occipital cortex.Wotruba et al. investigated functional brain correlates in the anticipation and reception of rewards and examined their possible association with symptoms in unmedicated people at risk for psychosis (n = 21) and healthy controls (n = 24). The results indicated that the same brain areas were recruited during processing of reward information in both at risk individuals and healthy controls. In contrast, during the anticipating rewards stage the at risk individuals showed additional activation in the posterior cingulate cortex and the medio- and superior-frontal gyrus.Garbarini et al. investigated whether patients with schizophrenia have an altered sense of agency during the observation of others' movements. A circles-lines task was used, in which participants had to draw lines while observing an examiner's hand draw circles. Results indicated an interference effect of the examiner's hand drawing circles on their hand drawing lines.Moustafa et al. provided an overview of homocysteine metabolism in psychiatric disorders with a focus on cognitive correlates. Several biological mechanisms linking homocysteine to biological underpinnings of psychiatric disorders were discussed and future directions and perspectives were indicated.Below, we summarize animal studies we covered in our research topic.Falsafi et al. examined which GABAB-containing receptor complexes are involved in a multiple T maze task. Twenty trained and untrained mice were exposed to the multiple T maze task. The results indicated that training increased GABAB1/1A containing receptor complexes in the hippocampus.Oliveras et al. investigated whether the Roman high-avoidance inbred strain (RHA-I) display prepulse inhibition (PPI) compared to Roman low-avoidance rats (RLA-I) and genetically heterogenous (NIH-HS) rats. More specifically, they examined whether PPI deficits predict spatial working memory impairments. The results indicated that the RHA-I rats had PPI and spatial working memory deficits compared to the other two groups.Nakao et al. examined the role of beta-anchoring and -regulatory protein (BARP) in higher brain functions. BARP knockout (KO) mice were generated and a comprehensive behavioral test battery was undertaken. The results indicated that these rats showed greatly reduced locomotor activity.Gruter et al. investigated the cellular mechanisms that may underlie hippocampal dysfunction in psychosis. Male Wistar rats were treated with irreversible NMDAR-antagonist, MK801. After 4 weeks, the treatment led to the loss of hippocampal long-term potentation (LTP). Expression of the early gene (Arc) was enhanced in the hippocampus of controls by spatial learning. The authors concluded that in psychosis, deficits in hippocampus-dependent memory may be due to the loss of hippocampal LTP.Niu et al. investigated whether the prepulse inhibition (PPI) response can be disturbed by the blockage of olfactory input. The results indicated that the PPI of the startle response was impaired by the blockage of olfactory sensory input. Microinjection of lidocaine/MK801 into the olfactory bulb impaired the PPI. The authors concluded that the olfactory system plays a role in the PPI of the startle response in rats.Pinnock et al. investigated whether activate muscarinic and potentially nicotine receptors (nAChRs) expressed by pontine receptors are responsible for the nicotine enhancement of prepulse inhibition (PPI). The results indicated that nAChR antagonists had limited effects on PPI. However, PnC microinfusions of the non-α7nAChR preferring antagonist TMPH into the PnC significantly reduced PPI.DeAngeli et al. investigated whether a change in the concentration of kynurenic acid  would affect reward related behavior. The rats that were treated with L-kynurenine showed increased sign-tracking behavior. The authors concluded that exposure to KYNA may increase the salience of cues related to reward. They also examined the effect of exposure to KYNA on hippocampal long-term potentiation (LTP). After a burst of high-frequency stimulation the rats treated with L-kynurenine showed no LTP, whereas vehicle-treated rats showed robust LTP.Richter et al. translated a human stability-flexibility paradigm to mice. Mice were trained in a touchscreen-paradigm to discriminate visual cues. Results provided evidence for the Dual State Theory that assumes an antagonistic relation between cognitive flexibility and stability.Ding et al. investigated whether N-methyl-D-aspartate receptor (NMDR) and Ca2+permeable α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor (AMPAR) activation in the striatum is necessary for cognitive flexibility. The findings suggested that NMDR-mediated glutamate transmission in the nucleus accumbens contributes more to cognitive execution than the dorsal striatum.In short, in this topic, we attempted to cover different aspects of schizophrenia symptoms, using both human and animal studies. The articles covered here explained the complexity of behavioral and neural abnormalities in schizophrenia, and further suggest future work in this area.All authors listed, have made substantial, direct and intellectual contribution to the work, and approved it for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Endothelial cell (EC) apoptosis plays a vital role in the pathogenesis of atherosclerosis in patients with diabetes mellitus (DM), but the underlying mechanism remains unclear. Cellular repressor of E1A-stimulated genes (CREG) is a novel gene reported to be involved in maintaining the homeostasis of ECs. Therefore, in the present study, we investigated the role of CREG in high glucose/high palmitate-induced EC apoptosis and to decipher the upstream regulatory mechanism underlying the transcriptional regulation of CREG.The expression of CREG and the rate of apoptosis were assessed in lower-limb atherosclerotic lesions from patients with type 2 DM (T2DM). Primary human umbilical vein endothelial cells (HUVECs) were isolated and cultured in a high glucose/high palmitate medium , and the over-expression and knock-down of CREG were performed in HUVECs to determine the role of CREG in EC apoptosis. The upstream regulatory mechanism of CREG was identified using a promoter-binding transcription-factor profiling array, chromatin immunoprecipitation (ChIP) assay and a mutation analysis.Compared with normal arteries from non-diabetic patients, reduced CREG expression and increased apoptosis were found in the endothelium of atherosclerotic lesions from patients with T2DM. In vitro treatment of HUVECs with a high glucose/high palmitate medium also resulted in decreased CREG expression and increased apoptosis. Moreover, high glucose/high palmitate induced-HUVEC apoptosis was increased by the knock-down of CREG and rescued by the over-expression of CREG. We also demonstrated that GATA1 was able to bind to the promoter of the human CREG gene. A deletion mutation at -297/-292 in the CREG promoter disrupted GATA1 binding and reduced the activation of CREG transcription by approximately 83.3%. Finally, the overexpression of GATA1 abrogated the high glucose/high palmitate-induced apoptosis in HUVECs.The over-expression of CREG inhibits high glucose/high palmitate-induced apoptosis in HUVECs. CREG is transcriptionally upregulated by GATA1. Thus, CREG might be a potential therapeutic target for intervention of vascular complications related to diabetes. Macrovascular complications  are the major causes of mortality in patients with type 2 diabetes mellitus (T2DM), accounting for more than 50% of diabetes-related deaths. DiabetiCellular repressor of E1A-stimulated genes (CREG) is a novel glycoprotein that is highly expressed in blood vessels under physiological conditions. It has In the present study, we chose an in vitro model of genetically modified HUVECs and exposed them to high glucose/high palmitate concentrations to explore the specific role of CREG in diabetes-associated EC apoptosis. To elucidate the upstream transcriptional regulation of CREG expression, we generated luciferase constructs to determine the core promoter of the CREG gene. Then a promoter-binding transcription-factor profiling array assay, a chromatin immunoprecipitation (ChIP) assay and mutations of the binding site were performed to determine the upstream transcriptional factors involved. Finally, the role of key transcriptional factor GATA1 in regulating the expression of CREG and high glucose/high palmitate-induced ECs apoptosis were determined. Our results demonstrate that the over-expression of CREG inhibits in HUVECs and that CREG is transcriptionally upregulated by GATA1. Thus CREG might be a potential therapeutic target for management of vascular complications in patients with DM.The use of human blood vessels and umbilical cords was approved by the Ethics Committee of General Hospital of Shenyang Military Region, and written informed consent was obtained from all patients. All animal experiments conformed to the Principles of Laboratory Animal Care formulated by the National Society for Medical Research and the Guide for the Care and Use of Laboratory Animals  and were approved by the Ethics Committee on the Care and Use of Laboratory Animals of General Hospital of Shenyang Military Region.Human Endothelial Culture Medium was purchased from Thermo Scientific . The FITC-Annexin V/PI Apoptosis Detection Kit was obtained from BD Biosciences . The Promoter-Binding TF Profiling Plate Array I (FA-2001) was obtained from Signosis . Dual-Luciferase Reporter Assay System (E1960), PGL4.12 (E6671) and PGL4.73 (E6911) vectors were purchased from Promega . The ChIP assay kit was obtained from Millipore . Plasmid pcDNA3.1 (+), a terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end-labelling (TUNEL) kit and TRIzol Reagent were purchased from Invitrogen . Antibodies against CREG  and GATA1 (ab181544) were purchased from Abcam . Antibodies against cleaved caspase-3 and GAPDH were obtained from Cell Signalling Technology . The enhanced chemiluminescence (ECL) Western Blotting System was purchased from GE Life Sciences . D-glucose, free fatty acid (FFA)-free bovine serum albumin (BSA), palmitate and other chemicals, if not specified otherwise, were purchased from Sigma-Aldrich .Lower extremity arterial blood vessels were obtained from amputees with diabetic PVD (n = 4) or from individuals who had suffered a traffic accident without PVD and diabetes (n = 4) enrolled between April 2015 and December 2015. Subjects were considered eligible if: (1) they were age 18 years or older, (2) they were awaiting a transtibial or transfemoral amputation, and (3) the primary cause of amputation was complications of PVD and diabetes or motor vehicle crashes without PVD or diabetes. Subjects were excluded if: (1) they had inadequate cognitive or language function to consent or participate, and (2) there was significant history of extremity trauma or tumour. The use of human vessels was approved by the Ethics Committee of the General Hospital of Shenyang Military Region and informed consents were also obtained from all patients. A total of ten patients approached for donation, two of them were excluded and eight of them met the study criteria to be enrolled. The collected human diseased and control arteries were properly treated for further analysis of CREG expression and apoptosis via immunostaining and immunoblotting.2 atmosphere as described previously . TUNEL sWe further detected the expression of GATA1 and CREG at both the transcription and protein level. Real-time PCR analysis showed that GATA1 and CREG expression increased by approximately 2-fold in GATA1 over-expressing HUVECs relative to expression in the control group . ImmunobThese data demonstrate that the over-expression of GATA1 activates CREG expression, leading to the protection of HUVECs against high glucose/high palmitate-induced apoptosis.Currently, accumulating evidence suggests that atherogenesis is stimulated by high circulating concentrations of glucose and FFAs, specifically palmitate. In the present study, we demonstrate for the first time that hCREG is transcriptionally activated by GATA1 and that regulation by this transcription factor helps protect the vascular endothelium of diabetic subjects against apoptosis. In this study, we obtained several novel findings that strongly support the presence of a protective role of CREG and its upstream regulation. Firstly, the expression of CREG was obviously decreased and endothelial apoptosis was increased in the atherosclerotic vasculature of diabetic patients when compared with the findings in non-diabetic control vessels. Secondly, under high concentrations of glucose (25 mM D-glucose) and different concentrations of palmitate , which simulate the pathological stimuli of poorly controlled T2DM in vivo, apoptosis increased and CREG expression decreased in HUVECs in a concentration dependent manner in vitro. Thirdly, elevating the expression of CREG antagonized HUVEC apoptosis, whereas suppressing CREG expression further increased HUVEC apoptosis induced by high glucose/high palmitate concentrations. Finally, GATA1 directly binds to the hCREG promoter and activates CREG expression, leading to the protection of HUVECs from the apoptosis induced by high glucose/high palmitate stimulation.ECs play a major role in regulating blood vessel development, homeostasis and remodelling, and in cardiovascular pathologies by virtue of their location between the blood and the surrounding tissues, 26. An Previous studies have reported that CREG might attenuate atherosclerotic endothelial apoptosis via the VEGF/PI3K/Akt pathway, but thein in vivo settings using suitable T2DM animal models that have been genetically modified in relation to their CREG or GATA1 expression.The limitations of our study are as follows. First, in addition to GATA1, several other transcription factors may positively and negatively regulate the expression of hCREG. As shown in our results, there is a trans-acting DNA element that represses the expression of hCREG located from -867 bp to -509 bp from the TSS. Future studies are needed to precisely define the minimum sequence length for this repressor and to identify potential TFs that bind to the site. In addition, the protective role and the underlying mechanisms of CREG demonstrated in our study are mainly from in vitro data, and these findings need to be further validated In conclusion, a reduction in CREG expression causes endothelial apoptosis that is induced by diabetes-related stimuli in vitro, which can be rescued by the over-expression of CREG. The upregulation of CREG can be achieved by the activation of GATA1, which binds directly to the promoter of CREG. CREG might be a therapeutic target for the management of macrovascular complications in diabetic patients.