Carbonic anhydrase IX (CAIX) protein has been correlated with progression and survival in patients with renal cell carcinoma (RCC). The prognostic value of CAIX in RCC however, remains inconclusive according to published works. This study aimed to analyze CAIX as a biological marker to predict RCC patient prognosis.A literature search of the PubMed and Web of Knowledge databases was performed to retrieve original studies from their inception to December of 2013. Fifteen studies, collectively including a total of 2611 patients with renal cell carcinoma, were carefully reviewed. Standard meta-analysis methods were applied to evaluate the prognostic impact of CAIX expression on patient prognosis. The hazard ratio (HR) and its 95% confidence interval (CI) were recorded for the relationship between CAIX expression and survival, and the data were analyzed using Review Manager 5.2 software and Stata software 11.0.P = 0.006), unfavorable progression-free survival  and worse overall survival . Furthermore, low CAIX expression was significantly associated with the presence of lymph node metastases (odds ratio (OR) = 0.31, 95% CI = 0.15–0.62, P = 0.0009) and distant metastases  and predicted a higher tumor grade .In patients with RCC, low CAIX expression was associated with poor disease-specific survival (HR = 1.89, 95% CI: 1.20–2.98, Low CAIX expression most likely indicates poor prognosis in RCC patients. Moreover, low CAIX expression was significantly associated with unfavorable clinicopathological factors. To strengthen our findings, further well-designed prospective studies should be conducted to investigate the role of CAIX expression in RCC. Renal cell carcinoma (RCC) is one of the most common solid cancers in humans, and its incidence is increasing annually worldwide Carbonic anhydrase IX, also named MN protein, was first identified in the human cervical carcinoma cell line HeLa in 1992 Recent large cohort studies with long-term follow up found that CAIX is not an independent prognostic marker for renal carcinoma In light of these conflicting results, it is of great value to investigate whether current evidence supports the use of CAIX as a prognostic marker in RCC. Therefore, this meta-analysis was conducted to elucidate the prognostic value of CAIX expression in RCC.A literature search of original articles concerning the prognostic role of CAIX in RCC was conducted on the Pubmed and Web of Knowledge databases. The search strategy included the following keywords: renal or kidney, cancer or carcinoma, “Carbonic anhydrase IX”, CAIX or CA9, and prognosis or survival. Original articles published until December, 2013 were included in the search. The following inclusion criteria were used for the analysis: study reported in English; diagnosis of renal cell carcinoma confirmed by histopathological methods; and CAIX level detected by immunohistochemistry (IHC) analysis of primary RCC tissue. There was no exclusion criterion for the number of patients in any single study. When multiple papers were reported by the same group based on a similar patient cohort, the report with the largest number of patients was included in this study.Data were extracted by two investigators (HZZ and GXL) independently. The extraction data included the basic information of the study , basic tumor characteristics (tumor stage and grade), cut-off value, and survival outcome . Any disagreement was discussed among the author group and a consensus was made.http://www.ohri.ca/programs/clinical_epidemiology/oxford.asp) (Table S1). Briefly, the quality of the studies assessment included three main categories as follows: (1) selection of cohort, (2) comparability of cohort, and (3) ascertainment of outcome. This scale consisted of eight-item instrument. A study is performed by awarding 1 star for high quality elements within the selection and outcome categories. In regards to comparability, it can be awarded a maximum of 2 stars. The total number of stars is then added up and a study with more stars is reflecting a better methodological quality. Any discrepancies were resolved by discussion among the author group.A quality assessment of each of the included studies was performed by two independent reviewers (HZZ and GXL) using the Newcastle-Ottawa Quality Assessment Scale for cohort studies  with 95% confidence intervals (CIs) were applied to describe the impact of CAIX expression on survival. When HRs and 95% CIs were provided within the included studies, these data were extracted directly for analysis. Otherwise, the Engauge Digitizer software (version 4.1) was applied to estimate the HRs and 95% CIs from the Kaplan-Meier survival curves, and the survival rate was extracted from the curves to reconstruct the HR and its standard error (SE) From the PubMed and Web of Knowledge electronic databases, 145 and 286 potentially relevant articles were identified, respectively. In total, 421 articles were obtained through our initial search. Using Endnote software, 110 duplicated papers were excluded. A screen of the titles and abstracts identified 50 papers eligible for the assessment of the prognostic value of CAIX status in patients with RCC. After carefully review of each of the 50 studies, certain studies were excluded for the following rationale: six studies evaluated CAIX status by enzyme-linked immunosorbent assay (ELISA) Table S2.The 15 studies analyzed were conducted in: USA (x6), Korea (x1), Spain (x1),UK (x1),Germany (x1),Brazil(x1), Japan (x1), Sweden (x1), Turkey (x1) and one study included cases from both the USA and France. Our meta-analysis included a total of 2,611 patients, with a median number of 112 patients per study (range: 42–730). Of the 15 studies, six were evaluated using multivariate analysis and nine (60%) were evaluated using univariate analysis. Disease specific survival (DSS) was reported in six studies, overall survival (OS) was evaluated in seven studies and progression-free survival (PFS) was reported in five studies. The clinical characteristics of the included studies and the quality assessment are shown in P = 0.006, 2 = 39.04; P<0.00001, I2 = 87%). In addition, a sensitivity analysis was performed. The omission of any one study did not significantly influence the results. On the premise of these stability results, there is no doubt that CAIX expression is a prognostic marker for DSS in patients with renal cell carcinoma. Moreover, subgroup analysis was performed by excluding the low quality studies , and the result showed that decreased CAIX expression was also associated with poorer DSS . The analysis had no heterogeneity , and the results were showed in .We aimed to determine whether CAIX expression levels were associated with the survival of patients with RCC. Six of the studies included were used to evaluate the association of low CAIX expression levels with DSS. The combined HR of the studies revealed that low CAIX expression levels were associated with poorer DSS in patients with RCC . Sensitivity analysis was conducted by sequential omission of any single study, the results showed low CAIX expression was correlated with unfavorable OS. Moreover, subgroup analysis was conducted by excluding the study with low quality , the low CAIX expression was also associated with poorer OS , and there was no significant heterogeneity . However, by excluded the study with low quality, there was no significant publication bias by statistical test  indicated no significant publication bias.Publication bias was assessed for DSS and OS, respectively. For DSS, the funnel plot of HR indicated some degree of publication bias , worse OS  and unfavorable PFS . These results indicate the potential of CAIX as a valuable biological marker to predict prognosis in patients with RCC. Interestingly, CAIX has been shown to be an effective biological marker for determining the best course of treatment for specific patients with RCC and is currently under further investigation P value did not reach the level of statistical significance (P = 0.06). Some reports have shown that low CAIX expression was associated with a more aggressive subtype in RCC Numerous studies have evaluated CAIX as a prognostic marker for RCC with conflicting results. Thus, this meta-analysis aimed to clarify the prognostic role of CAIX in RCC; the results suggest that low CAIX expression is associated with poor DSS , and only studies that measured CAIX expression levels with immunohistochemistry were included. Studies that measured CAIX expression levels using ELISA or real time-PCR were not included in our analysis. However, subgroup analysis was performed by excluding the studies with low quality scores, there was no significant heterogeneity for DSS and OS, respectively Click here for additional data file.Table S2Quality assessment of each study included.(DOCX)Click here for additional data file.Checklist S1PRISMA checklist for this meta-analysis.(DOC)Click here for additional data file.Data S1Raw data and the final data for survival outcome.(DOCX)Click here for additional data file.


Skin temperatures from eight healthy subjects were acquired while thermal sensation varied. To develop a thermal sensation estimation model, the mean skin temperature, temperature gradient, time differential of the temperatures, and average power of frequency band were calculated. A thermal sensation estimation model using temperatures of the fingertip and wrist showed the highest accuracy (mean root mean square error [RMSE]: 1.26 ± 0.31). An estimation model based on the three wrist skin temperatures showed a slightly better result to the model that used a single fingertip skin temperature (mean RMSE: 1.39 ± 0.18). When a personalized thermal sensation estimation model based on three wrist skin temperatures was used, the mean RMSE was 1.06 ± 0.29, and the correlation coefficient was 0.89. Thermal sensation estimation technology based on wrist skin temperatures, and combined with wearable devices may facilitate intelligent control of one’s thermal environment.Thermal comfort is an essential environmental factor related to quality of life and work effectiveness. We assessed the feasibility of wrist skin temperature monitoring for estimating subjective thermal sensation. We invented a wrist band that simultaneously monitors skin temperatures from the wrist ( Thermal comfort is expressed satisfaction with the surrounding thermal conditions, and it is a major condition among several comfort factors . Maintaietc. . Therefo* (SET*) should be considered [* indicates the equivalent air temperature of an environment at 50% relative humidity in which a subject, wearing clothing standardized for the activity concerned, has the same heat stress and thermoregulatory strain as in the actual environment [Thermal sensation is the sense of temperature between hot and cold, and it can be quantified using typical scales. For example, the numerical codes +3, +2, +1, 0, and −3 represent hot, warm, slightly warm, neutral, and cold, respectively, on the seven-point ASHRAE thermal sensation scale. Statistical analysis of the relationship between thermal sensation and thermal comfort showed that the comfort level was better than the onset of discomfort when thermal sensation votes (TSVs), based on nine-point analog scales, were between −1.5 and +2 . As thernsidered ,8. The Pironment . Howeverironment . As theret al. developed an estimation algorithm that can estimate individual thermal sensation from the finger skin temperature, and they used the algorithm to control the household air conditioner [r = 0.78 and 0.80, respectively) with the overall thermal sensation [To develop a model for personal thermal sensation estimation, many researchers have considered various physiological signals. Sugimoto proposed a wearable system that consisted of a tympanic temperature sensor, skin temperature sensors, and an electrocardiogram sensor with an accelerometer to evaluate individual thermal sensation . The meaditioner . In addiensation . AlthougRecently, a large number of wrist-type wearable devices that can monitor physiological signals have been released. Some wrist band devices such as the Basis Peak  and E4 wristband  provide wrist skin temperature monitoring. However, the feasibility of wrist skin temperature monitoring as a subjective thermal sensation estimation has not been sufficiently investigated. Although the analysis of data from a previous study indicated that the wrist would be the most responsive body location for evaluating thermal sensation, the estimation model based on wrist skin temperature was not provided and validated ,15. TherWe have invented a wrist band that can simultaneously monitor skin temperatures from three different parts of the wrist—the radial artery (RA) region, ulnar artery (UA) region, and upper wrist (UW)—as shown in The temperature sensing module was designed with a protruding shape to ensure stable contact with the skin. A film-type NTC thermistor  was used, and each temperature sensor was covered with an thin aluminum cover. As each subject’s wrist size is different, we designed the temperature sensing module so that it could be moved and suitably positioned on each subject’s wrist region. The temperature measurement circuit was composed of a Wheatstone Bridge electrical circuit with a differential amplifier and a 1-Hz low-pass filter as shown in After the sensing module and circuit were fabricated, each temperature sensor was calibrated for accurate temperature measurement. Sensor calibration was implemented using a stirred water bath, and we obtained the voltage output while heating the water from 19 °C to 41 °C. All sensors were attached to the copper plate floating on the water, and the surface temperature of the plate was measured using a wireless temperature sensing device . The relationship between the voltage output and temperature was curve fitted with a 4-order polynomial.2) participated in this study. Each subject wore trousers and a short-sleeve shirt (0.57 clo) [Eight healthy subjects  . To obseg) was also calculated. To comprehend the spectral characteristics, the BP was calculated. In a previous study, Nakayama et al. observed fluctuations in the peripheral skin temperature while one’s thermal sensation was between −2 and 2, and they surmised that the fluctuations resulted from the peripheral vessel’s vasomotion [As TSVs were surveyed every 2 min, skin temperature data were divided into 2-min segments. Then four parameters—the mean skin temperature (mSKT), time differential of the skin temperature (dSKT), temperature gradient between the measurement positions (gSKT), and average power of a specific frequency band (BP)—were calculated for each segment. The mSKT indicates the average skin temperature of a 2-min segment. As TSVs were surveyed every 2 min, the mean skin temperature was calculated based on 2-min segments. Also, dSKT was a useful predictor in various thermal sensation estimation models ,16, and somotion . TherefoTo estimate thermal sensation, multiple linear regression analysis was performed. Specifically, stepwise regression was conducted to determine a useful subset of predictors and prevent overfitting. In each analysis, the criteria for entering and removing variables were 0.05 and 0.10, respectively. An estimation model based on a single skin temperature from the finger or one of the three wrist regions was developed. In addition, a model that uses multiple skin temperatures from the finger and various wrist regions was established to determine the effect of multi-sensor fusion. Finally, we analyzed whether the personal estimation model would improve the accuracy of the thermal sensation estimation. After the model was developed, each estimation model was assessed using a validation dataset. The mean root mean square error (RMSE), mean bias, and Pearson’s correlation coefficient were calculated to compare the performance of each estimation model.During the experiment, 100,800 skin temperatures were acquired from each channel. Also, 840 TSVs were obtained—66 very hot (+4), 110 hot (+3), 159 warm (+2), 107 slightly warm (+1), 98 neutral (0), 86 slightly cool (−1), 52 cool (−2), 105 cold (−3), and 57 very cold (−4).r = 0.73). Among skin temperatures from the wrist region, the mean skin temperature from the RA region and UW had correlation coefficients of 0.67 and 0.66, respectively. The correlation coefficient between the skin temperature measured at the UA region and TSVs was 0.61. In addition to a single channel observation, we evaluated the relationship between the gSKT and thermal sensation  single fingertip skin temperature; (2) single wrist skin temperature; (3) skin temperatures measured around the wrist; and (4) skin temperatures measured around the finger and wrist. Also, as we used a 9-point thermal sensation scale, the maximum and minimum estimated thermal sensation were limited to +4 and −4, respectively. Each estimation model is shown in i.e., the fingertip and three wrist skin temperatures) showed the highest accuracy among the models. To evaluate and compare the performance of each estimation model, we calculated the mean RMSE, mean bias, and correlation coefficient. Specifically, the mean RMSE and bias were respectively calculated based on the validation data of each subject and then averaged. As shown in In addition, the estimation model based on three wrist skin temperatures showed a slightly better result to the model that used a single fingertip skin temperature. Among the models based on a single wrist skin temperature, the model with the RA or UW skin temperature provided a similar result. Thermal sensation estimation based on skin temperature from the UA region had the largest mean RMSE. After assessing the performance of six thermal sensation models, we established a personal thermal sensation estimation model, which was developed using individual data. As eight subjects participated in this study, each type of estimation model had eight different equations. Then each model was applied to the validation dataset of the corresponding subject. As shown in As various wrist-type wearable devices are available on the market, we evaluated the applicability of wrist skin temperature monitoring in thermal sensation estimation. Skin temperatures from three different parts of the wrist were monitored in sedentary people under various ambient temperatures, and the fingertip skin temperature was simultaneously measured. The highest accuracy was found using the estimation model based on the fingertip and three wrist skin temperatures. Also, the thermal sensation estimation model using the three wrist skin temperatures showed a slightly better performance to the model based on the fingertip skin temperature. When a personal estimation model was used, the accuracy of each model improved. In addition, the personal thermal sensation model based on the three wrist skin temperatures had a mean RMSE of 1.06 and a correlation coefficient of 0.89. Although a small group of subjects were included in the present study and the activity level was restricted to sedentary office work, we made an initial attempt to assess the feasibility of wrist skin temperatures for thermal sensation estimation and develop a specific estimation model based on wrist skin temperatures. Interest in thermal comfort is increasing with the desire to improve quality of life and energy conservation. Thus, wearable devices that can estimate thermal sensation may facilitate intelligent control of one’s thermal environment and provide personalized thermal comfort.


Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock. There aet al. [et al. [et al. [Although understudied, parchment has been the subject of prior ancient DNA (aDNA) research. For example, the Dead Sea scrolls have yielded mitochondrial DNA PCR fragments, which have been identified as ibex and goat ,10. Simiet al.  identifi [et al. ,13 also  [et al.  investig [et al. .However, PCR-based aDNA research has well-documented deficiencies, particularly with regard to controlling and estimating contamination ,15. A ceHere we present a molecular archaeological analysis of parchment using two historical samples from the Borthwick Institute for Archives at the University of York dated palaeographically to the seventeenth (PA1) and eighteenth (PA2) century, respectively. Both of these samples are identified as sheep and give high proportions of endogenous DNA with very low contamination from other species or co-specific individuals, suggesting parchment as an excellent source of historic DNA. Following a conventional agricultural history narrative, PA1 predates the livestock ‘improvements' driven by Bakewell and Ellman among others, while PA2 falls into the period when the new breeds of sheep were being developed and spread. The variation uncovered shows the potential of genetics in localizing the geographical origins of artefacts.2.(a)et al. [et al. [et al. [Parchment samples of circa 5 × 5 mm from PA1 (seventeenth century) and PA2 (eighteenth century), were obtained from the Borthwick Institute for Archives parchment discards, and incubated twice for 1 h in 50 mM ammonium bicarbonate buffer (pH 8.0) at 65°C following the method of van Doorn et al. . The fir [et al. ,27. Camp [et al.  have con(b)2 (approx. 0.05 g) pieces cut from both parchments, prepared using procedures previously described by our group [All DNA extractions were performed in a dedicated aDNA laboratory at Trinity College, Dublin, on the same parchment samples used for zooarchaeology by mass spectrometry (ZooMS). Given the pilot nature of this analysis, the maximum amount of starting material available was used for each extraction, with DNA retrieved from 2 × 2 cmur group ,30.(c)et al. [2O and 0.4 μl each of both the forward and reverse primers. Amplification reactions per library consisted of an initial denaturation step of 98°C for 30 s, then 12 cycles of 98°C for 10 s, 65°C for 30 s and 72°C for 30 s, followed by a final extension step of 72°C for 5 min. The final PCR products from each sample (two each) were then pooled and visualized on an Agilent 2100 Bioanalyzer using a DNA 1000 chip. Both samples were then combined in equimolar ratios and sequenced together on a single (SE 49 bp) lane of an Illumina HiSeq2000 at BGI.Illumina single read sequencing libraries were produced for each of the two parchment samples via PCR amplification of end-repaired-adapter-ligated DNA templates following . Sampleset al.  method o(d)http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter sequences were trimmed from the 3′ end of the reads using Cutadapt [Initial quality control of sequencing reads were performed using FastQC (Cutadapt . Cutadap(e)http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen) is a Perl wrapper script, which allows for the same sequencing library to be easily aligned to multiple reference genomes using Bowtie [FastQ Screen (g Bowtie . The per(f)The raw trimmed reads (30 bp minimum read length) were also aligned to the sheep reference genome (oviAri3) minus the mitochondrial genome  using BW(g)All sequencing reads were further aligned to the human genome (hg19) using BWA and SAMtools with identical parameters to the sheep (oviAri3) alignments above. Any reads that aligned to the human genome were then removed from subsequent analysis irrespective of mapping quality. SNPs were called using established protocols for aDNA NGS data ,24. Brie(h)The SNPs called from PA1 and PA2 were then doubled to create pseudo-diploid data and merged with data from the sheep HapMap   using PL(i)n = 23) to allow the placement of the parchment samples within this dataset. Multiple sequence alignments of both the modern and parchment mtDNA genomes were completed using the MUSCLE alignment algorithm [Full mitochondrial genomes were produced from alignments of the parchment reads to a modern mitochondrial reference genome (HM236176) with BWA. Redundant reads were then removed using SAMtools. Modern sheep mitochondrial reference genomes were downloaded from GenBank (lgorithm  implemenlgorithm . Neighbo3.(a)Identification of the source species of each parchment was completed using a combined proteomic/genomic approach. The results of both these analyses identified sheepskin as the likely origin ((b)n = 23; electronic supplementary material, table S1) including 17 domestic sheep and six other ovine samples. Both parchments were found to locate within the domestic sheep mitochondrial haplogroup B , which is predominant in both the modern and ancient sheep populations of Europe [In total, 25 314 reads aligned to the ovine mitochondrial genome after duplicate removal . To do this, haplotype informative polymorphic positions in both samples, outside the difficult to align 75–76 bp repeat motif located within the control region of the ovine mtDNA ,43, thatet al.  of a com(c)Both parchment samples were genotyped following established protocols for aDNA data ,24. A to4.Parchment is ubiquitous in the historical record and is an attractive source for aDNA analysis to elucidate the history of domestic species and address questions intrinsic to the material origins of documents. However, published reports of first generation parchment aDNA investigations indicate conflicting results, reporting both unique PCR amplification products from a single species ,13,44 anIn contrast to these results, our samples showed no signs of manufacture contamination in either proteomic or aDNA approaches. ZooMS identified sheepskin as the likely origin for both parchments and failed to retrieve any taxon-specific collagen masses for goat, pig or cow. FastQ Screen analysis of the raw DNA sequencing data identified the sheep genome as the most likely source for the majority of the sequences. This analysis also identified relatively few molecules that aligned uniquely to either the bovine, goat or human genome at zero mismatches; 1.0, 2.4 and 0.02% of all reads, respectively  . UndeterIn order to provide as pure a sheep dataset as possible, stringent filters were applied in a re-alignment of all reads to the sheep genome to remove putative human contaminants. For both parchment samples more than 45% of reads aligned to the ovine genome once clonally amplified products were removed . These nIf other parchments show similar levels of endogenous DNA content, DNA sequencing of historic domesticated animal genomes over a range of time periods could be accomplished, providing insights into the breeding history of domesticated animals; for example, into sheep breeding before, during and after the agricultural improvements of the eighteenth century that led to the emergence of regional breeds of sheep in Britain.de novo, or built on changes that were already in progress [Indeed, it is intriguing to note that the two items, both of them records held in the Borthwick Institute for Archives in York, seem to have different heat map distributions, which may represent different breeding strategies employed between these two time points ,46. The progress . As a pr5.The findings of this first NGS study of parchment have shown that parchment is a highly suitable substrate for large-scale aDNA analyses. We were able to retrieve 9 and 7% of the ovine genome from PA1 and PA2, respectively, at high quality  using just half a lane each of an Illumina HiSeq 2000. This result suggests that the production of whole historic domesticate genomes or targeted exon sequencing from parchment is a realistic possibility. We were able to provide a unique species assignment for both pieces using both proteomic and aDNA methods, and estimate an external contamination rate comparable to, and probably lower than from, other aDNA sources. Whole mitochondrial genomes produced from both samples allowed their placement within the most populous sheep haplogroup, and SNP data allowed an estimation of the modern day sheep breeds that most closely resemble the historic samples to be identified. Further sequencing of parchment samples from a variety of time periods and locations should allow for genetic maps from a variety of domestic species to be built, providing important insights into the past 1000 years of animal breeding history.


Prostatic mantle cell lymphoma (MCL) is a very rare entity with only 5 reported cases in the literature. We report a case of coexisting MCL and prostate adenocarcinoma (PCa) in an elderly male and review the morphologic features of classic and rare prostatic MCL subtypes. Careful morphologic evaluation and immunohistochemical findings of positive CD5, CD20, and cyclin D1 and negative CD23 and CD3 can guide us to the diagnosis of MCL. Given the fact that transurethral resection of prostate is done quite routinely, this paper draws attention to the manner in which long standing bladder outlet obstruction and postbiopsy prostate specimens with dense lymphoid infiltration can masquerade as lymphoma. It highlights the importance of exercising care while reviewing prostate specimens with evidence of chronic prostatitis so as not to miss this rare neoplasm. Mantle cell lymphoma (MCL) is a lymphoproliferative disorder accounting for about 3–10% of all non-Hodgkin lymphomas [We report incidental finding of MCL in a Gleason grade 6 (3 + 3) prostate adenocarcinoma (PCa). The patient had initially presented with the signs and symptoms of bladder outlet obstruction 10 years ago and underwent transurethral resection of prostate (TURP), and a histologic diagnosis of benign prostate hyperplasia (BPH) was made at that time. He presented this time with similar symptoms and markedly elevated prostate specific antigen (PSA) levels. A core biopsy was obtained to confirm PCa. Besides the obvious PCa, there was evidence of chronic prostatitis due to previous biopsy and recurrent bladder outlet obstruction. Careful morphologic examination of core tissue biopsy coupled with immunohistochemistry (IHC) led to the diagnosis of MCL, which was later confirmed by a bone marrow aspirate, biopsy, and flow cytometry. This case adds to the growing knowledge of presentation of this rare entity and highlights the importance of careful microscopic examination of lymphocytic infiltration and use of IHC to diagnose MCL, especially in the setting of chronic prostatitis.We present a case report of coexisting MCL and PCa in a 74-year-old male patient. The patient first presented in 2003 at the age of 63 years with increased frequency and nocturia. He underwent TURP and 26 grams of prostate curetting examined for histopathologic abnormality. The stained slides showed nodular proliferations of glandular and fibromuscular tissue admixed with chronic inflammatory infiltrate and a diagnosis of BPH was made at that time.μg/L  and an enlarged prostate on digital rectal examination. An ultrasound revealed a prostate of 116 mL with no focal lesion and splenomegaly of 14.8 cm. A staging CT of the thorax, abdomen, and pelvis confirmed splenomegaly but showed no evidence of intrathoracic or intra-abdominal disease or involvement of LN. A CT head with contrast was normal. The patient also had systemic lupus erythematosus involving both the lungs and rib cage causing significant arthralgias, pleuritic chest pain, and fatigue. However, he had no weight loss, night sweats, or fevers and continued to remain active. His only treatment included Plaquenil and Finasteride. The patient was a retired heavy equipment mechanical operator, nonsmoker, and nondrinker. His family history revealed no history of autoimmune disorders, cancers, or lupus.He presented 10 years later in July 2013 with elevated PSA level of 17.16 9/L , consisting of 3.0 × 109/L  neutrophils, 0.6 × 109/L  lymphocytes, and 0.9 × 109/L  monocytes. The hemoglobin was 8 g/dL , hematocrit was 0.241 , and platelet count was 49 × 109/L . The serum lactate dehydrogenase was 169 U/L . Blood coagulation profile, serum electrolytes, and liver and renal function tests were within normal limits. The patient's Eastern Cooperative Oncology Group (ECOG) performance status was 0. Based on these parameters, the patient's mantle cell lymphoma international prognostic index score was calculated as 1 (low risk 0–3).The blood work showed white blood cell count of 4.2 × 10 alpha-methylacyl-CoA racemase (AMACR), p63, and CK 5/6 confirmed areas of PCa and delineated the normal prostate glands. Normal glands with intact basal layer showed dark brown nuclear stain and absent AMACR staining. The PCa areas showed cytoplasmic red finely granular staining pattern and absence of basal layer  involving left base of the gland  with a Gal layer .Incidentally, it was found that several cores from right base, right apex, and left base showed infiltrate of small lymphocytes in the stroma of the prostate. The cells were monomorphic with round nuclei, compact chromatin, inconspicuous nucleoli, and no evidence of cytological atypia or mitotic activity . ImmunohIn January 2014, a bone marrow aspirate from right posterior iliac crest showed mild lymphocytosis, increased marrow cellularity, 1 : 1 GE ratio, and 60% small lymphocytes with irregular nuclear borders. Blasts accounted for 2% of the population. Flow cytometry revealed 42% of the events with kappa light chain restriction, and 50% of these clonal B cells were CD19/CD5 positive. CD23 and CD10 were negative. The bone marrow biopsy showed neoplastic lymphoid infiltrate in 50% of the biopsy specimen with interstitial and paratrabecular distribution. IHC showed CD5, CD20, and cyclin D1 positivity. The bone marrow aspirate and biopsy report were diagnostic of MCL.Our patient had involvement of the bone marrow and prostate and no systemic symptoms of fever, night sweats, or 10% weight loss in 6 months preceding admission and was thus classified as Ann Arbor stage IVA MCL. He is receiving bendamustine-rituximab chemotherapy since January 2014.MCL lymphomas of the prostate are rare events with only five cases reported in the literature –6. MCL iHistopathology of a classic MCL shows expansion of the mantle zone surrounding the LN germinal centre by monomorphic lymphocytes arranged in patterns ranging from vaguely nodular, diffuse follicular, and mantle zone to diffuse. In the vast majority of cases, there are small to medium sized lymphocytes with irregular nuclear contours, mimicking centrocytes of a germinal centre. The nuclear chromatin is dispersed and the nucleolus is often inconspicuous.Morphologic variants include the aggressive blastoid and pleomorphic types. The “blastoid” variant shows medium to large cells that closely resemble lymphoblasts with dispersed chromatin and a high mitotic rate of 20–30/10 hpf. A case report of a patient with lung and prostate cancer who developed blastic variant MCL, while being treated with imatinib mesylate for chronic myeloid leukemia, is described in the literature . The “plOther variants include the “small cell” and “marginal zone-like” type. The “small cell” type has small round lymphocytes with clumped chromatin mimicking a small lymphocytic lymphoma. The “marginal zone-like” variant has prominent foci of cells with abundant pale cytoplasm resembling marginal zone or monocytoid B cells seen in marginal zone lymphoma .IHC shows intense surface IgM/IgD (lambda restriction more common than kappa). Cells are usually positive for CD5, CD19, CD20, and CD22 which is consistent with their small B lymphocyte origin. They often lack CD23, BCL6, and CD10. Almost all cases show BCL2 positivity and express cyclin D1 which is involved in G1 to S phase cell cycle progression through activation of cyclin-dependent kinases. IGH gene on chromosome 14 and the BCL1 locus on chromosome 11. This results in deregulated overexpression of CCND1 and, in some cases, increased half-life of cyclin D1. This results in loss of cell cycle suppressive effects of retinoblastoma protein RB1 and p27kip1, resulting in MCL development [The cytogenetic abnormality underlying MCL involves t   translocation between immunoglobulin heavy-chainelopment .Thus the diagnosis of MCL relies on combination of morphologic and immunohistochemical features. Lymphoid follicles may not be readily appreciated and can be misdiagnosed as chronic prostatitis. The patient underwent TURP 10 years prior to a final pathologic diagnosis of BPH. At the time of this presentation, he again had symptoms of bladder outlet obstruction and very high PSA levels which prompted the treating physician to do a diagnostic core prostate biopsy. Besides the obvious PCa, we discovered MCL on routine hematoxylin and eosin staining and confirmed it with IHC.It is known that chronic prostatitis occurring as complication of bladder outlet obstruction or after an old prostate biopsy is a common finding. Extensive chronic inflammation in such cases may mimic prostatic lymphoma . In doubGiven the fact that TURP is done quite routinely and MCL of prostate is such a rare entity, this report emphasizes the importance of carefully inspecting for evidence of chronic prostatitis. In the absence of systemic symptoms and normal peripheral blood counts, postbiopsy prostate specimens with dense lymphoid infiltration may masquerade as lymphoma. A high degree of suspicion coupled with morphologic and IHC analysis showing positive CD5, CD20, and cyclin D1 and negative CD23 and CD3 can guide us to the diagnosis of MCL.


The lack of available vaccines and consistent sporadic transmission of WNV justify the need for mosquito vector control and prediction of their geographic distribution. However, the distribution of WNV transmission is dependent on the mosquito vector and the ecological requirements, which vary from one place to another.Culex nigripalpus and Cx. quinquefasciatus, was extracted within 5 km buffer zones around seropositive records of sentinel chickens in order to delineate their predicting variables and model the habitat suitability of probable infective mosquito using MaxEnt software. Different correlations between density data of the extracted mosquito vectors and 27 climate, land use-land cover, and land surface terrain variables were analyzed using linear regression analysis. Accordingly, the correlated predicting variables were used in building up habitat suitability model for the occurrence records of both mosquito vectors using MaxEnt.Presence/density data of two WNV mosquito vectors, Cx. nigripalpus. Precipitation of driest months was shown to be the best predicting variable for the density of this vector (R2 = 41.70). Whereas, two variables were proven to predict the distribution of Cx. quinquefasciatus density. Vegetation showed the maximum predicting gain to the density of this mosquito vector (R2 = 15.74), where nestling birds, in particular exotics, are found. Moreover, Jackknife analysis in MaxEnt demonstrated that urbanization and vegetation data layers significantly contribute in predicting habitat suitability of Cx. nigripalpus and Cx. quinquefasciatus occurrence, respectively, which justifies the contribution of the former in urban and the latter in epizootic transmission cycles of WNV. In addition, habitat suitability risk maps were produced for both vectors in response to their predicting variables.The density of both WNV mosquito vectors showed variation in their ecological requirements. Eight predicting variables, out of 27, had significant influence on density of For the first time in the study area, a quantitative relationship between 27 predicting variables and two WNV mosquito vectors within their foraging habitats was highlighted at the local scale. Accordingly, the predicting variables were used to produce a practical distribution map of probable infective mosquito vectors. This substantially helps in determining where suitable habitats are found. This will potentially help in designing target surveillance and control programmes, saving money, time and man-power. However, the suitability risk maps should be updated when serological and entomological data updates are available. West Nile virus (WNV) disease was reported for the first time in the United States in New York City during 1999 . Since tCulex nigripalpus Theobald and Cx. quinquefasciatus Say were recorded as the main vectors of WNV in the state of Florida [Cx. quinquefasciatus alongside with Cx. pipiens complex, were incriminated in the urban transmission cycle of WNV in northeastern and central parts of the USA [Both  Florida . The for Florida –8, where Florida , 9. Howe the USA –12. The Surveillance and control programmes of mosquito vectors are the most effective tools for arbovirus disease prevention . HoweverCx. pipiens, Cx. quinquefasciatus, and Cx. nigripalpus. The feeding preference of these mosquitoes may show significant variation from one place to another, consequently the disease transmission cycle may vary. Although these models are useful, their findings did not adequately account for the interrelationships between climate and non-climate variables such as LULC and Digital Elevation Models (DEM) and the overall influence of these interrelationships on arbovirus transmission cycles [The previous models of WNV transmission dynamics are based solely on hydrological and meteorological data , 15–17. n cycles . In addiCulex nigripalpus and Cx. quinquefasciatus may share some ecological habitats, but their biological and ecological requirements in terms of blood meal source, water habitat quality, vegetation type, and human activities may show significant variation. Distribution models that include climate, LULC, and DEM variables may give detailed information on variation of suitable habitats between both mosquito vectors and the virus transmission dynamics.To address the limitations of previous studies, we developed a habitat suitability model for probable infective WNV mosquito vectors within their flight range using data records on mosquito vector occurrence and WNV seropositive sentinel chickens. In addition, we addressed the interrelationships between climate, LULC and DEM variables and their overall influence on the habitat suitability of probable infective mosquito vectors using the Maximum Entropy (MaxEnt) tool. The current study was conducted in St. John’s County, Fl. A total of 43 mosquito species were previously reported inhabiting a great diversity of salt and fresh water habitats throughout the County , 21. Ele2 intermingled between the St. Johns River to the west and the Atlantic Ocean to the east.St. John’s County is located in northeastern Florida, USA, with a total area of 1588 kmSixty chickens (21-week old) were distributed over 12 locations in the county from the beginning of April through December every year during 2007–2013 to monitor arbovirus activity. Approximately 2.0 ml of blood was taken from each chicken’s wing vein once a week. Blood samples were kept in labeled vacutainers (Fisher Scientific®) and transported back to the laboratory at the AMCD Base Station in St. Augustine Beach where they were centrifuged at 4375 RPM for 15 minutes. Samples were then placed in a labeled and sealed plastic bag, shipped to the Florida State Department of Health (FDOH) Virus Laboratory in Tampa, Florida and tested for WNV. Samples were sent on the first operation day of the week and results reported by the end of the same week. Once a chicken seroconverted, it was removed, destroyed, and replaced with a new one at its respective location.A 5 km buffer zone around positive seroconversions was generated using a geoprocessing toolbox in ArcGIS ver. 10.0)  of adult host seeking mosquito vectors were monitored by AMCD using CDC light traps  baited with dry ice  at 68 permanent locations in the County. Traps were placed outdoors at the beginning of March through the last week of November during 2007–2013. Traps were suspended 1 m above ground surface by a shepherd’s hook and operated for 18–20 h using a 12 V battery. Mosquito collections were transported weekly from the field to the AMCD facility for further identification to species level using the taxonomic keys of Darsie & Ward .To predict the habitat suitability of WNV mosquito vectors, 19 bioclimatic variables (11 layers of temperature and 8 precipitation indices) and elevation layers were obtained from the WorldClim database ver.1.4   to 90° (high elevation). Aspect ratio indicates the orientation of the slope, eventually this ratio reflects the places of water accumulation and larval mosquito establishment , 30. AspBecause the distribution of mosquitoes is greatly affected by the human population as a source of blood meal , urban aThe surface water has been extensively used in previous studies as an indicator for mosquito distribution range . TherebyA total of 27 bioclimatic, LULC and DEM data layers Table  were cliThe MaxEnt software v. 3.3 –41 was uThe contribution of predicting variables in our model was evaluated using Jackknife analysis in MaxEnt. The predicted habitat probability was categorized into five classes using the natural area breaks in ArcGIS utilizing the training omission rate at 10 percentile training presence value produced from MaxEnt: very low (0–0.1), low (> 0.1–0.2), medium (> 0.2–0.4), high (> 0.4–0.6), and very high (> 0.6) using natural breaks in the symbology tools in ArcGIS.The presence records of both mosquito vectors were randomly partitioned for model evaluation into two subsamples: 75 % of the records were used for training and building up the model, and 25 % of the records were used for testing the model’s accuracy. The duplicate records of WNV mosquito vectors within ~1 km of the same cell size were excluded .Five replicate runs were assigned in running the model to generate the average, maximum, minimum and median of the distribution range of mosquito vectors. Two thresholds have been used to examine the performance accuracy of our model based on Phillips et al.  and PhilTo increase the potentiality of the habitat suitability model and maximize the sampling effort of extracted mosquito vectors, a separate ASCII file generated from the 5 km buffer zones was included and weighted to the corresponding mosquito vector density . AccordiCx. nigripalpus demonstrated a significant correlation with eight predicting variables . Three of these variables were temperature related variables namely temperature isothermality (Bio3), temperature seasonality (Bio4), and mean temperature of coldest quarter (Bio11). In addition, three precipitation related variables correlated with this mosquito vector density: the annual precipitation (Bio12) and precipitation of wettest (Bio13) and driest months (Bio14). Urbanization (r(5) = -38.61, AICc = 943.00, R2 = 29.52, P < 0.05) and hill shade (r(2) = -222.06, AICc = 945.12, R2 = 19.39, P < 0.01) showed significant association with the density of Cx. nigripalpus (Table r(9) = 24.09, AICc = 940.58, R2 = 41.70, P < 0.05) with density of Cx. nigripalpus  (r(2) = -28.63, AICc = 858.29, R2 = 7.37, P < 0.01) and vegetation (LAI) (r(3) = -0.93, AICc = 854.22, R2 = 15.74, P < 0.01). Both precipitation of driest month (Bio14) (R2 = 41.7) and LAI (R2 = 15.74) were demonstrated to be the key predictors for both Cx. nigripalpus and Cx. quinquefasciatus, respectively, in association with the other predicting factors . MaxEnt predicted an average of 99 km2 of very high suitable habitat (predicted risk probability > 0.60), which is 6.11 % of the total area of St. John’s County  was predicted at hill shade ranges 180–181, and temperature of the coldest quarter (Bio 11) < 21 °C with AUC training gain of 0.80  significantly improved the predictive power by up to 32.5 %. The highest training gain was shared with precipitation related variables and urbanization (29.6 and 25.5 %). In addition, hill shade shared reduced training gain (12.4 %) in predicting suitable habitats of this mosquito vector , representing 15.37 % of the total area of the County   use ~1 km resolution remote sensing data layers in terms of climate, ecological, and DEM variables, (ii) ranking the average contribution of predicting variables correlated to the density and presence of WNV mosquito vectors, and (iii) production of practical distribution risk map for the probable infective mosquito vectors confined to their flight range around seropositive records at local scale to prioritize the surveillance and control activities.Cx. nigripalpus was sporadically distributed in the central and southwestern areas. Unlikely, the habitat suitability produced for Cx. quinquefasciatus was largely confined to the western areas of the county  and driest (R2 = 40.70) months have a significant role in predicting Cx. nigripalpus density during the dry season , and water breeding habitats , 26. Botan blood , 15–17. an blood , 15–17. asciatus .Although no WNV human cases were recorded during the study period, the transmission potential still exists due to the availability of competent mosquito vectors, reservoir hosts, probably exotic birds, and suitable ecological habitats. In addition, the lack of data on vector survival rate, feeding preference, gonotrophic cycle period, and competence for the study area prevented us including this information in building up our model. Our spatial distribution model shed light on the information gap in vector capacity parameters, which are needed to deeply understand when, precisely, transmission onset occurs in St. John’s County.The distribution of these mosquito vectors, like other exophilic mosquitoes, are influenced by surrounding climate and ecological variables. In addition, this distribution gives deep insights on the virus circulation between the bridging and main mosquito vector, reservoir bird and human hosts. The findings of some previous models showed great potential in understanding the biology and ecology of WNV mosquito vectors in state of Florida , 16, 22,Unlike previous models, we tried to model the spatial distribution of probable infective mosquitoes using the mosquito presence records within their flight range around WNV seropositive records of sentinel chickens. Since arbovirus transmission is vector-density dependent, we evaluated the response of both vectors’ density to their predicting variables. The LRM provides reliable information on the influence of the predicting variables on mosquito vectors density. In this regard, the predicting variables were evaluated and selected using AICc values. Statistical LRM potentially resolves the significant discrepancy in predicting variables for both mosquito vectors. This discrepancy reflects variation in ecological requirements between both mosquito species. The potentiality of the current prediction model was proven by the high AUC values produced by MaxEnt, indicating that occurrence records were likely to be assigned a higher probability of presence than background sites.Cx. nigripalpus in regards to their density and presence records. Their contribution was demonstrated by LRM and MaxEnt tools in terms of R2 values and percent contribution, respectively. The contribution of precipitation in driest  and wettest  months reflects their significance in determining the habitat suitability for this mosquito vector during dry and wet seasons. The shared high predictive power by temperature related variables (32.5 %) confirmed the association between this mosquito vector, reservoir hosts, and human population, especially during the dry season. The significance of urbanization in predicting Cx. nigripalpus demonstrates the suitability of this habitat for mosquito vector density (R2 = 29.52) and presence probability (25.5 %).Unsurprisingly, temperature and precipitation related variables significantly increased the prediction gain of probable infective Accordingly, precipitation in the driest months, during the dry season in May – June, may play a major role in shifting breeding habitats of this mosquito and bring them in contact with WNV infected host birds . AlternaCx. nigripalpus and correlated variables within mosquito vector foraging habitats. The temperature of the coldest quarter (< 21 °C) contributed significantly in predicting the occurrence and spatial distribution of this mosquito vector.The contribution of temperature in predicting density and distribution of this mosquito vector was highlighted in a mathematical simulation model by Lord & Day , in whicLand topography and geomorphology were potentially used in predicting suitable water habitats of mosquitoes , 31, 47.Cx. nigripalpus using LRM and MaxEnt. Hill shade was used in previous studies as a predicting precursor for water suitable habitats of malaria vectors [In the present study, hill shade was used as a promising remote sensing data that reflects areas with surface water accumulation . Hill sh vectors .Cx. quinquefasciatus was evidently correlated with vegetation and mean temperature diurnal range. Vegetation is important for mosquitoes as a source of sugar meal, but also reflects nestling habitats for reservoir bird hosts, probably human hosts in rural areas. Feeding preference of this mosquito vector is reportedly varied [Density of y varied ; howevery varied –8. AccorAlthough some previous models showed potential in understanding the empirical correlations between WNV transmission and some ecological and climate variables in the state of Florida, these models encountered some limitations. These models predicted the spatial distribution risk of virus circulation based on sampling points rather than the flight range area of probable infective mosquito vectors at the local scale. Other models may not be applicable in other landscapes due to the heterogeneity in climate and environmental variables. The variation of landscape and climate variables greatly impact the biology and ecology of mosquito vectors in terms of feeding preference, habitat suitability, and the distribution of reservoir bird host(s), especially exotic birds.In this model, we demonstrated how GIS, remote sensing data, and habitat suitability modeling tools can be used efficiently to analyze and identify suitable habitats for infective WNV mosquito vectors and assess the distribution risk of this disease at a local scale. Our model is very novel in addressing limitations of previous similar models at the local scale. The risk maps produced will effectively help in determining where suitable habitats are found. This will potentially help in targeted surveillance and control programmes, which will save money, time and man-power, especially if the suitability risk maps are updated with serological and entomological data when available.The availability of consistent temporal data, in terms of mosquito and remote sensing, limit our current spatial model to delineate accurately, when WNV transmission can occur. Further temporal analysis is needed to couple the current spatial model with the updated data on mosquito distribution to give more detailed information on where and when the suitable habitats of WNV transmission may occur. In addition, information on vector capacity in regards to vector competence, survival rate, and gonotrophic cycle period, need to be considered in building up the spatial-temporal models. Eventually this will give deep insights on the competency of mosquito vector populations in transmitting WNV.AICc, Corrected Akaike information criterion (AICc); AMCD, Anastasia mosquito control district; ASCII, American standard code for information interchange; AUC, area under curve; Bioclim, bioclimate variables; Cx, culex; DEM, digital elevation model; FDOH, Florida Department of Health; hrs, hours; km, kilometer; LAI, leaf area index; LRM, linear regression model; LULC, land use - land cover; MaxEnt, maximum entropy; MODIS, Moderate Resolution Image Spectroradiometer (MODIS); NDVI, Normalized difference vegetation index (NDVI); ROC, receiver operating characteristics; WNV, West Nile Virus


The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers) was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E) component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7–40.7 Mb) and on chromosome 8 (20.3–21.9 Mb). Across experiments, the soil type/ growth medium showed more correlations with plant growth than the container dimensions. Although the correlations among studies and genetic co-location of root traits from a range of study systems points to their potential utility to represent responses in field studies, the best correlations were observed when the two setups had some similar properties. Due to the co-location of the identified genomic regions  with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought. This study also highlights the utility of characterizing a small set of 20 genotypes for root growth, drought response, and related genomic regions. Strategies to address the urgent need for improved rice productivity under drought stress, which affects 23 million hectares in Asia alone , will liGiven the general tendency of rice to grow roots mostly in shallow zones of the soil profile, deep root growth has long been considered an advantageous trait for improving the performance of rice under drought stress , 8, 9. SIn addition to the uncertainty about the link between certain physiological traits and grain yield, a high degree of environmental variation that is typical to rainfed rice environments , 14, 15 To take advantage of rice genetic diversity and the currently available genomic tools, another goal of this study was to link root traits with genomic regions. This study was conducted using the OryzaSNP panel , which iThe OryzaSNP panel, a set of 20 diverse rice genotypes that have been mapped for 160,000 SNP markers, was used for this study . Root exThe root phenotyping systems in this study included soil-filled cylinders of various sizes, soil-filled rhizotrons, cylinders in which root penetration of a non-woven fabric was assessed, hydroponics, a raised-bed line-source system, and field experiments ; Table 2Several types of root experiments in cylinders were conducted as part of this study. At the Barwale Foundation Maharajpet Farm, India (Ba10C), roots were evaluated in cylinders with three replications that were assembled from rolled 1-mm thick acrylic sheets with dimensions of 25 cm diam. x 120 cm height and sampled at 100 days after sowing. Cylinders of 19–20 cm diam. X 105–120 cm height were used in lysimeter studies conducted at IRRI, Philippines (IR08C), and ICRISAT, India (IC09C), and were previously reported ); experi2 plots in two replicates. A lowland field experiment was conducted under well-watered and drought conditions at the Barwale Foundation Maharajpet Farm, India (Ba10F) in 2010 with 0.8 m2 plots with two replications in which drought was imposed 45 days from the day of transplanting and irrigation was given once in 15 days to maintain 3–4 cycles of stress across the season. All field studies were conducted on research stations and no specific permission was required for these activities.In the field experiments at Tamil Nadu Agricultural University, India (TN10F and TN11F), rice lines were evaluated for drought response and root traits during the wet seasons of 2010 and 2011 under flooded and rainfed conditions in experimental fields of the University at Agricultural Research Station, Paramakudi, India , 23, 24.The experiments at Nagoya University (Na10F and Na11F) were conducted in a watertight soil bed with line source sprinkler system under a rain-out shelter. The watertight soil bed was constructed with a frame fitted with an impermeable plastic sheet that was then filled with soil, in order to prevent percolation or lateral seepage of water. Irrigation was applied as water mist from the nozzles of a PVC pipe installed at the center of the bed. The soil depth in the bed was 20 cm and the soil moisture gradient was created perpendicular to the water source (PVC pipe) ranging from -2.3 to -10.5 kPa , -10.5 to -39.2 kPa , and -39.2 to -285.6 kPa . Under such conditions, root traits other than deep root growth that contribute to plant growth may be identified for a specified range of drought intensity. Plants were transplanted 21 days after seeding in the bed and grown until heading. Root sampling was conducted using the round monolith method with diameter of 15 cm and height of 20 cm as described previously .control—shoot biomassstress)/shoot biomasscontrol x 100], % RDW reduction by drought [(RDWcontrol—RDW stress)/ RDWcontrol x 100], % MRL increase by drought [(MRLstress—MRL control)/ MRLcontrol x 100], %DR increase by drought [%DRstress—%DRcontrol], and % grain yield reduction by drought [(grain yieldcontrol—grain yieldstress)/grain yieldcontrol x 100]. The 20 OryzaSNP genotypes studied showed a range of flowering times, including some that were photoperiod sensitive and some that did not flower in certain seasons. Our strategy was to initiate the drought stress early enough to target reproductive stage in all studies in which grain yield was measured, but in some cases no flowering occurred and grain yield was therefore not determined due to photoperiod sensitivity (i.e. in genotypes Nipponbare and Rayada).The percentage of deep roots (%DR) was calculated from root dry weight data as the proportion of roots below the depth of 20 cm  or 30 cm  in relation to the root dry weight sampled from all depths, except in the NW experiment where the proportion of roots that had penetrated the non-woven fabric in relation to total root dry weight was used. Unifying measurements across all root experiments were maximum root depth (MRL), root dry weight (RDW), and % deep roots (%DR). Shoot dry biomass was determined around the time of root sampling and could be compared between drought stress and control treatments in experiments Ba10C, CS09C, CS10C, IC09C, IR08C, IR08FL, IR09dFL, Na10F, Na11F, and TN11F. Stress response indices were calculated as % shoot biomass reduction by drought [, maximum root depth (MRL), and % deep roots %DR; . Of thesCorrelation matrices  indicateAcross all experiments, the environment (E) component explained the majority of the variation (85–95%) for RDW, and MRL, %DR, and among traits was lowest for yield 60%; . The genAccording to the cluster analysis across all experiments, the genotypes  and enviA correlation analysis of aus, indica, and japonica introgression blocks (data from ) with MRChromosome maps of introgression blocks that were significantly correlated with root traits and grain yield under both drought stress and well-watered control treatment) revealed alignment of the greatest numbers of introgression blocks to two chromosome regions. One on chromosome 1 (39.7–40.7 Mb) in which root dry weight, percent deep roots, and grain yield aligned ; and theThe results of this study emphasize the high degree of sensitivity of rice to environmental effects, and the identified genomic hot spots reflect the possibility of strong functional relationships between root growth and yield. This highlights the advantages of studying multiple whole-plant traits rather than individual components .Of the three root traits analyzed, RDW appeared to be the most consistent according to: A) consistent trends in RDW response to drought stress in all study systems , B) the Across the range of field and container study systems in the current study, no consistent distinctions were observed among root traits. In a precursor to this study comparing the practicality of the protocols and genotypic performance in hydroponics, rhizotron, and non-woven fabric systems , it was Environmental conditions, methodologies, and the different characteristics of each experimental setup likely influenced the genotypic responses in each experiment relative to the other experiments. For example, the separate response of the TNAU root measurements in terms of absolute values  Tables aDespite the OryzaSNP set being comprised of highly diverse genotypes, the genotype (G) component explained the smallest percent of variation for yield and root traits. OryzaSNP genotypes Dular, Azucena, and Moroberekan were previously classified as deep-rooted under drought in the field at IRRI and in lysimeters , 26. In Since no general genotypic trends were apparent across the environments in this study, this highlights the importance of genetic variation within an environment, which was significant. The relative effects of G, E, and G x E are largely dependent on the chosen range of environments used, and drought stress can occur at a range of severities and growth stages within a given environment. The results from this study imply that rice responses to drought for yield and root growth would be best evaluated within the target environment and under the conditions similar to those in which they will be used. As such, the range of methods presented here could be used as a guide from which future rice root researchers could choose a method, based on the goals of the experiment, the target drought environment, and the resources available.The lower E effect on yield compared to the root traits may reflect that A) all grain yield data were collected from field experiments  and root data were collected from a larger range of study systems, and B) root growth shows a higher sensitivity than grain yield to environmental conditions. A greater stability of grain yield to environmental variation than root traits may explain some of the previously reported lack of effects of root QTLs on grain yield , 47. FurDespite the strong E effect, the two genomic hot spots where multiple traits aligned on Chromosomes 1 and 8 were observed from a range of study systems; these traits included grain yield from field studies, root growth from field studies, and root traits from container systems Figs  and 7. Tsd1 located at 38.4 Mbp. The region on chromosome 1 was also similar to a locus significantly associated with root angle in a tropical japonica panel grown in a glass bead-based “Rhizoscope” system [qDTY1.1 [The hot spot on chromosome 1 identified in this study falls within one of the six hot spots identified from a meta-analysis of 1,467 QTLs reported to be related to root traits in rice . This is” system , and was” system . In addiqDTY1.1  and otheqDTY1.1 . Taken tThe hot spot on Chromosome 8 identified in this study co-locates with a key region for drought response in rice, in which more than 30 QTLs for traits including grain yield, plant type, spikelet fertility, and drought response traits including osmotic adjustment, cell membrane stability, and leaf relative water content have been reported . In the Unlike the recently published rice root GWAS study , the curThe higher frequency of japonica introgression regions that were correlated with yield and root traits in this study may be due to 1) the effect of having an introgression block data set where introgressions were identified by SNP relative to only the japonica reference genome variety (Nipponbare), that reduced the number and location of putative introgression blocks compared to that of the aus or indica types, and 2) the deeper and coarser types of roots of japonica genotypes —the rootA better understanding of the physiological and genetic components behind rice performance under drought will help guide approaches to improving rice response to drought. In an evaluation of rice drought response for yield and root growth where data were obtained from 37 environments and from 20 diverse genotypes, the GxE effect was lower for root traits than for grain yield, and no single genotype was significant in terms of performance across all environments. This confirms the high degree of sensitivity of rice to its environmental conditions and suggests that genotypic drought screening will be most effective when conducted in the targeted environmental conditions with germplasm that has some adaptation to these environments. However, the identification of two genomic hot spots at which 20 environments/traits aligned points to the possibility for improvement of the stability of rice drought response to diverse environmental conditions. The co-location of root traits from a range of study systems indicates the potential utility of container root study systems to represent responses that can be relevant to yield in field studies. Since the identified genomic regions co-located with QTL and meta-QTL for a number of previously reported root traits and also for a major-effect QTL for yield under drought, these regions are good candidates for detailed characterization to contribute to understanding the improvement of rice response to drought.S1 TableData previously reported by Henry et al (2011) are included in this table.(DOCX)Click here for additional data file.S2 TableData previously reported by Henry et al (2011), Gowda et al (2012), and Shrestha et al (2013) are included in this table.(DOCX)Click here for additional data file.S3 TableData previously reported by Gowda et al (2012) and Shrestha et al (2013) are presented in this table.(DOCX)Click here for additional data file.S4 TableData previously reported by Henry et al (2011), Gowda et al (2012), and Shrestha et al (2013) are included in this table.(DOCX)Click here for additional data file.S5 Table* = p<0.05, ** = p<0.01, *** = p<0.001. Data previously reported by Henry et al (2011) were used to calculate some of the results shown in this table.(DOCX)Click here for additional data file.S6 Table* = p<0.05, ** = p<0.01, *** = p<0.001. Data previously reported by Henry et al (2011), Gowda et al (2012), and Shrestha et al (2013) were used to calculate some of the results shown in this table.(DOCX)Click here for additional data file.S7 Table* = p<0.05, ** = p<0.01, *** = p<0.001. Data previously reported by Gowda et al (2012), and Shrestha et al (2013) were used to calculate some of the results shown in this table.(DOCX)Click here for additional data file.S8 Table* = p<0.05, ** = p<0.01, *** = p<0.001. Data previously reported by Henry et al (2011), Gowda et al (2012), and Shrestha et al (2013) were used to calculate some of the results shown in this table.(DOCX)Click here for additional data file.S9 TableThe analysis could not be conducted for %DR because only two experiments measured both yield and %DR.(DOCX)Click here for additional data file.S10 TableSignificant correlations are indicated by *<0.05, **<0.01, and ***<0.001.(DOCX)Click here for additional data file.S11 Table(DOCX)Click here for additional data file.S1 Fig(DOCX)Click here for additional data file.


Colombia contributes a significant proportion of malaria cases in the Americas, which are predominantly rural. However, in the last 8 years ~ 10 % of the endemic municipalities have also reported urban and peri-urban malaria cases, a growing concern for health authorities. This study focused on the characterization of the officially reported urban malaria cases.Plasmodium species and the presence of malaria vectors.A descriptive retrospective study based on secondary information provided by the Colombian National Surveillance System-SIVIGILA for the 2008–2012 period was conducted. A total of 17 municipalities with consistent and persistent reports of urban and peri-urban malaria were selected for analysis, which included site of origin and of residence, age, gender and ethnicity of patients, health system affiliation, Plasmodium falciparum infections (52.1 %). Median annual parasite index (API) was 6.4 per 1000 inhabitants . Between 2011 and 2012 complicated cases (2.4 %) and malaria in pregnant women (1.4 %) were reported. Study areas reported the presence of at least seven Anopheles species considered malaria vectors. These analyses did not allow ascertaining the presumable origin of the recorded urban cases due to the lack of a consensus on a definition of urban, peri-urban and rural limits and the lack of proper verification of the geographical source of infection.A total of 18,113 malaria cases were reported from urban and peri-urban areas of 17 endemic municipalities. Almost 70 % of the reports originated in localities in the departments of Chocó and Nariño, located on the Pacific Coast where a predominantly Afro-Colombian population, of individuals of under 30 years of age, was the most affected (80.7 %), mainly with The study indicates the probable presence of endemic, unstable and low-intensity malaria transmission in Colombian urban and peri-urban areas of a group of municipalities located mainly on the Pacific coast region and a few others in the eastern region. There is a need to unequivocally confirm the urban or peri-urban origin of the malaria cases reported and the transmission conditions, as well as to develop and implement new strategies for urban and peri-urban malaria control and elimination. Plasmodium falciparum, ~20 % by Plasmodium vivax, and a more limited number of cases by the other parasite species, including Plasmodium malariae and Plasmodium ovale [Malaria remains an important global health problem that affects mainly poor communities in Africa, Asia and Latin America, with an estimated ~198 million clinical malaria cases and ~584,000 deaths reported worldwide in 2013 [um ovale ; meanwhium ovale –9.In Latin America, Brazil has shown a population movement tendency to urban and peri-urban areas of cities in the Amazon region due forest colonization, road construction and the establishment of agricultural and mining settlements during the last decades of the 20th century, with an enormous impact on malaria transmission , 11. BetP. vivax and P. falciparum in towns such as Quibdó, Buenaventura and Puerto Gaitán [Anopheline species. This rapid urbanization of population with poor socio-economic conditions, inadequate housing infrastructure and lack of public services, usually leads to improper sanitation, poor drainage of surface water and the consequent development of water bodies and vegetation-rich areas [A similar situation exists in other Latin American countries, such as Peru, Ecuador and Colombia , 16, 17.o Gaitán –24. In ach areas , 23. TheAnopheles mosquitoes, including important malaria vectors, such as Anopheles albimanus, Anopheles nuneztovari s.l. and Anopheles darlingi, which appear to have the ability to colonize a variety of breeding sites, adapting to changing environments including urban and peri-urban areas [Moreover, in Colombia multiple factors, such as armed conflict, the presence of paramilitary groups, and illegal agriculture and mining, among others, significantly contribute to the displacement of rural populations to peri-urban areas in several regions. One such region is the Colombian Pacific coast, which has been reporting increasing urban and peri-urban malaria transmission , 26. Thian areas , 27–29. an areas –24, 30 wDespite growing and improving statistics and surveillance, it looks like a proportion of reported cases are actually not real urban or peri-urban cases, but the result of an erroneous classification and registration of cases, greatly due to problems regarding the following: (1) “urban setting” and “urban malaria” definitions, (2) origin of malaria cases, (3) lack of identification of mosquito breeding sites, and (4) lack of confirmation of the vector´s transmission capacity in urban settings. These factors cause uncertainty about the true extent and importance of urban or peri-urban malaria transmission. Solving these issues would be critical to adjusting the strategies for malaria prevention and control in urban areas.In conclusion, it appears that in contrast to the overall malaria decreasing trend at national level, the number of cases in urban settings is increasing and the growth rate is greater in urban than in rural settings. In response to the Millennium Development goals, Colombia has included the goal towards reducing malaria urban transmission in two recent government strategic policies: The Ten-Year Plan for Public Health (2012–2021) and the Integrated Management Strategy for Promotion, Prevention and Control of Vector-Borne Diseases (EGI-ETV) . To contA descriptive study was carried out using information obtained from records compiled by SIVIGILA, from January 1, 2008 to December 31, 2012. Information was collected using standard notification forms in which the malaria clinic is assigned to the municipality defined as the geographical area bounded by the urban perimeter as defined by an administrative agreement  and inclPlasmodium infection confirmed either by thick blood smear (TBS) or rapid diagnostic test (RDT).Case definition was established according to the SIVIGILA protocol in which a malaria case is a patient having visited malaria endemic areas, in this case urban or peri-urban settings, in the 15 days prior to the current or recent febrile episode (>37.5 °C) with Localities included in the analysis were administrative units  corresponding to urban and peri-urban areas with consistent and persistent malaria cases reports to SIVIGILA. Most of these localities have been historically reported as sites with urban transmission foci and reported entomological evidence of the presence of malaria mosquito vectors according to information from the vector borne diseases (VBD) Prevention and Control Programme of the Colombian Ministry of Health (MOH). The study focused on a total of 13 municipalities of departments located along the Pacific coast as follows: eight municipalities located in department of Chocó ; four in Department of Nariño ; and one in department of Valle del Cauca (Buenaventura). Four municipalities scattered in several departments of the central and Eastern regions of the country were also included in the analysis, namely: Pueblo Rico in department of Risaralda , Puerto Inírida, in department of Guainía, Miraflores in department of Guaviare (Eastern region), and Puerto Nariño, in Amazonas department (Southern region)  and from previous publications , 28, 34.®. Univariate analysis were performed using the software Tableau statistical software version 6.0®. A univariate analysis was performed for all variables. Measures of central tendency and dispersion were calculated. The API was calculated and urban population values used for each municipality were obtained from the projections of the 2005 Colombian census [T test at a 0.05 significance level to assess statistically significant differences between P. falciparum and P. vivax cases.Epidemiological and entomological variables were processed using Microsoft Exceln census . In ordeP. falciparum, whereas 46.1 % (8356) were P. vivax infections, with an additional 1.6 % (293) of cases due to mixed falciparum/vivax infections and 0.02 % (three cases) considered non-indigenous P. malariae cases.In total, 18,113 malaria cases classified as urban or peri-urban by SIVIGILA were recorded from 2008 to 2012 with an annual average of 3623 cases, a maximum of 6133 in 2010 and a minimum of 1853 in 2008. These cases corresponded to extreme APIs of 10.8 in 2010 and 3.4 in 2008, and an average API of 6.4 cases per 1000 inhabitants for the study period. The peak for 2010 correlates with the national malaria outbreak reported that year [Plasmodium species showed that the API was higher in men (6.4 cases per 1000) than in women (4.8 cases per 1000) with P. vivax predominant (61.2 %) among men and P. falciparum among women (44.3 %)  4536 cases), Istmina (Chocó) (2702 cases), Tumaco (Nariño) (2441 cases), Tadó (Chocó) (1898 cases) and Nóvita (Chocó) (1357 cases), which contributed about 70 % of the total urban and peri-urban cases for the study period. However, the transmission behaviour of urban malaria in each one of these areas showed a variable trend. Novita (Chocó) presented the highest API in 2011 whereas Barbacoas (Nariño) and Buenaventura  displayed the lowest API during this period. Tumaco (Nariño) presented with a hypo-endemic and decreasing transmission tendency. Miraflores (Guaviare) recorded a dramatic and sustained decline in the urban and peri-urban transmission trend , whereas Miraflores and Novita exhibited the highest annual P. vivax malaria indexes (>47 cases per 1000 inhabitants)  Table . Afro-deA total of 174 of the 7242 cases (2.4 %) reported in 2011 and 2012, were classified as complicated malaria cases, most of which (146 or 83.9 %) originated in Chocó, whereas the departments of Valle del Cauca and Nariño reported 19 and 7 cases, respectively. Moreover, during this period a total of 100 cases occurred in pregnant women of whom 69 % were from Choco, 18 % from Nariño, and 10 % from Valle del Cauca.Anopheles species were: An. albimanus, An. darlingi, Anopheles neivai, Anopheles nuneztovari,Anopheles lepidotus, Anopheles pseudopunctipennis, and Anopheles punctimacula, which in general were widely distributed in peri-urban areas and most of them overlapped in the different study settings [Anopheles spp in the urban area of Quibdó [The analysis of entomological data available from the Colombian INS indicates that predominant settings , 27, 28,f Quibdó  , the distribution of the reported urban and peri-urban cases displayed an equivalent proportion of P. falciparum and P. vivax cases. This is explained by the fact that most reported cases were from Chocó and Nariño departments, where the population is mainly composed of African descendant communities with a high prevalence of Duffy negative individuals [P. vivax blood infections while allowing the normal invasion and development of P. falciparum [Although at national level the overall malaria transmission presented a higher proportion of ividuals . The laclciparum –40.P. falciparum infection was significantly greater and the most affected groups were those of extreme ages (<5 and >60 years of age) [Our results, based on the official SIVIGILA records and Colombian INS data, are in agreement with previous studies conducted in Colombia in which other approaches and data sets were used , 28, 41  of age) , whereasAn. nuneztovari and An. albimanus mosquito species with peri-domiciliary adult bite rates up to 7.1 were also found [P. falciparum), only 24.4 % of these were confirmed as indigenous urban malaria cases [P. falciparum and P. vivax, with the greatest risk of transmission in proximity to areas of vegetation and excavations left by miners. The occurrence of malaria in children, students and housewives suggests that malaria transmission takes place inside households and at school neighborhoods [Previous studies have found that the main breeding sites for malaria peri-urban vector were located in excavations left by the miners, as well as lakes and ponds dedicated to fish farming where immature so found . Even thia cases . Malariaborhoods . Other fborhoods .Plasmodium transmission [There is a contrast between the decreasing trend of rural malaria and the stable or increasing records on urban malaria. This might be explained by multiple conditions that could favor the introduction of malaria into peri-urban and urban areas. In Colombia population movements from endemic rural areas is mostly due to the ongoing armed conflict, but more recently also to the dissemination of illegal mining and proliferation of illicit crops; all of these generate fear and threaten safety in rural communities. Additionally, the lack of incentives for rural communities to remain in their regions as well as the apparent stimulus by the government for urban population with the hope for better jobs, encourage the migration from rural to urban and peri-urban areas. The migration of malaria infected individuals contributes to generate conditions for the introduction and maintenance of smission  in peri-smission .Interestingly, in this study records of complicated malaria cases as well as malaria in pregnant women were found. In a previous study carried out in some of the same localities, most febrile patients in endemic areas attended the diagnostics service within 5 days of the onset of malaria symptoms , 44 whicThis study aimed at a better characterization of the reported urban and peri-urban malaria transmission and could serve as a reference transmission baseline at national scale to be further used for monitoring activities to evaluate compliance with the goal established by the INS-ETV (Vector-borne diseases) of eliminating urban and peri-urban malaria in Colombia by 2021. Although urban areas display different exposure risks and offer better opportunities for prevention and timely control due to the existing infrastructure, technological capabilities and access to health services , 47, 48,Anopheles. Environmental factors including precipitation, relative humidity and temperature also affect mosquito breeding [Although malaria in urban residents has been conclusively shown, it remains critical to determine the extent of local transmission, including the definition of associated entomological factors such as presence of mosquito breeding places, abundance and behaviour of adult breeding  and mustDespite the limitations described, this study documents the probable presence of endemic, unstable and low-intensity urban and peri-urban malaria cases in a group of municipalities located mainly on the Pacific coast region and a few others in the Eastern region. This study explored some key epidemiological factors related to malaria transmission in the urban settings selected to set up the grounds for ongoing prospective studies aimed at unequivocally confirming the urban or peri-urban origin of the malaria cases and the transmission conditions to aid in achieving the goal of urban malaria elimination in Colombia by 2021.