Takshan/R1 huggingface dataset:
Prevalence of antibodies to a new histo-blood system: the FORS system.

BACKGROUND: In 1987, three unrelated English families were reported with a putative blood subgroup called Apae. Swedish researchers later found evidence leading to abolishment of the Apae subgroup and establishment instead of the FORS blood group system (System 31 - ISBT, 2012). It is important to know the prevalence of antibodies in order to make the best decisions in transfusion medicine. Cells expressing the Forssman saccharide, such as sheep erythrocytes, are needed to detect the anti-Forssman antibody. The aim of this study was to define the prevalence of human anti-Forssman antibody. MATERIALS AND METHODS: Plasma samples from 800 individuals were studied. Sheep erythrocytes or Forssman "kodecytes" were mixed with the plasma samples using the tube technique. Plasma from an Apae individual was used as a negative control and monoclonal anti-Forssman antibody (M1/22.25.8HL cell line supernatant) was used as the positive control. RESULTS: Of the 800 individuals tested, one was negative for the presence of anti-Forssman antibody. We compared the anti-Forssman antibody reaction pattern between genders and found that males have weaker reactions than females, both at room temperature (p=0.026) and at 37 °C (p=0.043). We also investigated the reaction pattern of anti-Forssman antibody in relation to ABO and Rh blood group types without finding any significant differences. DISCUSSION: Sheep erythrocytes are suitable for searching for human anti-Forssman antibody. The quantity of anti-Forssman antibodies in plasma is higher in females than in males. In the population (n=800) studied here, we found one individual lacking the anti-Forssman antibody. These results contribute to the data already published, confirming that FORS is a rare blood group.
Bowel ultrasound for predicting surgical management of necrotizing enterocolitis: a systematic review and meta-analysis.

BACKGROUND: Necrotizing enterocolitis (NEC) is a devastating inflammatory disease of the intestinal tract that represents a significant source of morbidity and mortality in preterm infants. Imaging of the abdomen is valuable for timely diagnosis and close monitoring of disease progression in NEC. Bowel ultrasound (US) is increasingly being recognized as an important imaging tool for evaluating NEC that provides additional detail than plain abdominal radiographs. OBJECTIVE: To identify bowel US findings associated with surgical management or death in infants with NEC. MATERIALS AND METHODS: We searched Embase, PubMed, and the Cumulative Index to Nursing and Allied Health Literature for studies investigating the association between bowel US findings and surgical management or death in NEC. Selected articles were evaluated for quality of study methodology using the Newcastle-Ottawa Scale, and aggregate statistics for odds ratio (OR) and 95% confidence interval were calculated. RESULTS: Of 521 articles reviewed, 11 articles comprising 748 infants were evaluated for quality. Nine of the studies were retrospective and from single-center experiences. Pooled analysis showed that focal fluid collections (OR 17.9, 3.1-103.3), complex ascites (OR 11.3, 4.2-30.0), absent peristalsis (OR 10.7, 1.7-69.0), pneumoperitoneum (OR 9.6, 1.7-56.3), bowel wall echogenicity (OR 8.6, 3.4-21.5), bowel wall thinning (OR 7.11.6-32.3), absent perfusion (OR 7.0, 2.1-23.8), bowel wall thickening (OR 3.9, 2.4-6.1) and dilated bowel (OR 3.5, 1.8-6.8) were associated with surgery or death in NEC. In contrast, portal venous gas (OR 3.0, 0.8-10.6), pneumatosis intestinalis (OR 2.1, 0.9-5.1), increased bowel perfusion (OR 2.6, 0.6-11.1) and simple ascites (OR 0.54, 0.1-2.5) were not associated with surgery or death. CONCLUSION: This meta-analysis identified several bowel US findings that are associated and not associated with surgery or death in NEC. Bowel US may be useful for early identification of high-risk infants with NEC who may benefit from more aggressive treatment, including surgery. Future studies are needed to determine whether the addition of bowel US in NEC evaluation would improve outcomes.
Pediatric Esophageal Foreign Body: Possible Role for Digital Tomosynthesis.

OBJECTIVES: Foreign body (FB) ingestion is a common reason for emergency department visits, affecting more than 80,000 children in the United States annually. Whereas most ingested FBs are coins or other radiopaque objects, some are radiolucent FBs such as food. Digital tomosynthesis (DTS) is a radiographic technique that produces cross-sectional images with in-plane resolution similar to that of traditional radiographs. Our pilot study evaluated the sensitivity and specificity of DTS to detect FB in comparison to esophagram and clinical impression. METHODS: This was a retrospective review on patients aged 0 to 18 years with suspected esophageal FB who received an esophagram with DTS at our institution between January 2014 and June 2016. Digital tomosynthesis images were analyzed by 3 readers for identification of FB impaction and compared with esophagram and discharge diagnosis. This study was approved by our local institutional review board. RESULTS: A total of 17 patients underwent an esophagography with DTS for suspected esophageal FB, of which 9 (53%) were suspected of having an FB on esophagram. Compared with esophagram, DTS had a sensitivity of 44%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 62%. Compared with clinical impression, DTS had a sensitivity of 33%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 38%. CONCLUSIONS: This pilot study showed that chest DTS has a very high positive predictive value, compared with esophagram and clinical impression, in detecting radiolucent esophageal FBs in children. Chest DTS is a promising modality for ruling in the presence of a radiolucent esophageal FB.
Assessment of genetic variation within a global collection of lentil (Lens culinaris Medik.) cultivars and landraces using SNP markers.

BACKGROUND: Lentil is a self-pollinated annual diploid (2n = 2× = 14) crop with a restricted history of genetic improvement through breeding, particularly when compared to cereal crops. This limited breeding has probably contributed to the narrow genetic base of local cultivars, and a corresponding potential to continue yield increases and stability. Therefore, knowledge of genetic variation and relationships between populations is important for understanding of available genetic variability and its potential for use in breeding programs. Single nucleotide polymorphism (SNP) markers provide a method for rapid automated genotyping and subsequent data analysis over large numbers of samples, allowing assessment of genetic relationships between genotypes. RESULTS: In order to investigate levels of genetic diversity within lentil germplasm, 505 cultivars and landraces were genotyped with 384 genome-wide distributed SNP markers, of which 266 (69.2%) obtained successful amplification and detected polymorphisms. Gene diversity and PIC values varied between 0.108-0.5 and 0.102-0.375, with averages of 0.419 and 0.328, respectively. On the basis of clarity and interest to lentil breeders, the genetic structure of the germplasm collection was analysed separately for cultivars and landraces. A neighbour-joining (NJ) dendrogram was constructed for commercial cultivars, in which lentil cultivars were sorted into three major groups (G-I, G-II and G-III). These results were further supported by principal coordinate analysis (PCoA) and STRUCTURE, from which three clear clusters were defined based on differences in geographical location. In the case of landraces, a weak correlation between geographical origin and genetic relationships was observed. The landraces from the Mediterranean region, predominantly Greece and Turkey, revealed very high levels of genetic diversity. CONCLUSIONS: Lentil cultivars revealed clear clustering based on geographical origin, but much more limited correlation between geographic origin and genetic diversity was observed for landraces. These results suggest that selection of divergent parental genotypes for breeding should be made actively on the basis of systematic assessment of genetic distance between genotypes, rather than passively based on geographical distance.
Dissecting the pathobiology of altered MRI signal in amyotrophic lateral sclerosis: A post mortem whole brain sampling strategy for the integration of ultra-high-field MRI and quantitative neuropathology.

BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a clinically and histopathologically heterogeneous neurodegenerative disorder, in which therapy is hindered by the rapid progression of disease and lack of biomarkers. Magnetic resonance imaging (MRI) has demonstrated its potential for detecting the pathological signature and tracking disease progression in ALS. However, the microstructural and molecular pathological substrate is poorly understood and generally defined histologically. One route to understanding and validating the pathophysiological correlates of MRI signal changes in ALS is to directly compare MRI to histology in post mortem human brains. RESULTS: The article delineates a universal whole brain sampling strategy of pathologically relevant grey matter (cortical and subcortical) and white matter tracts of interest suitable for histological evaluation and direct correlation with MRI. A standardised systematic sampling strategy that was compatible with co-registration of images across modalities was established for regions representing phosphorylated 43-kDa TAR DNA-binding protein (pTDP-43) patterns that were topographically recognisable with defined neuroanatomical landmarks. Moreover, tractography-guided sampling facilitated accurate delineation of white matter tracts of interest. A digital photography pipeline at various stages of sampling and histological processing was established to account for structural deformations that might impact alignment and registration of histological images to MRI volumes. Combined with quantitative digital histology image analysis, the proposed sampling strategy is suitable for routine implementation in a high-throughput manner for acquisition of large-scale histology datasets. Proof of concept was determined in the spinal cord of an ALS patient where multiple MRI modalities (T1, T2, FA and MD) demonstrated sensitivity to axonal degeneration and associated heightened inflammatory changes in the lateral corticospinal tract. Furthermore, qualitative comparison of R2* and susceptibility maps in the motor cortex of 2 ALS patients demonstrated varying degrees of hyperintense signal changes compared to a control. Upon histological evaluation of the same region, intensity of signal changes in both modalities appeared to correspond primarily to the degree of microglial activation. CONCLUSION: The proposed post mortem whole brain sampling methodology enables the accurate intraindividual study of pathological propagation and comparison with quantitative MRI data, to more fully understand the relationship of imaging signal changes with underlying pathophysiology in ALS.
A temporal examination of calcium signaling in cancer- from tumorigenesis, to immune evasion, and metastasis.

Background: Although the study of calcium (Ca2+) is classically associated with excitable cells such as myocytes or neurons, the ubiquity of this essential element in all cellular processes has led to interest in other cell types. The importance of Ca2+ to apoptosis, cell signaling, and immune activation is of special import in cancer. Main: Here we review the current understanding of Ca2+ in each of these processes vital to the initiation, spread, and drug resistance of malignancies. We describe the involvement of Ca2+, and Ca2+ related proteins in cell cycle checkpoints and Ca2+ dependent apoptosis and discuss their roles in cellular immortalization. The role of Ca2+ in inter-cellular communication is also discussed in relevance to tumor-stromal communication, angiogenesis, and tumor microinvasion. The role that Ca2+ plays in immune surveillance and evasion is also addressed. Finally, we discuss the possibility of targeting Ca2+ singling to address the most pressing topics of cancer treatment: metastatic disease and drug resistance. Conclusion: This review discusses the current understanding of Ca2+ in cancer. By addressing Ca2+ facilitated angiogenesis, immune evasion, metastasis, and drug resistance, we anticipate future avenues for development of Ca2+ as a nexus of therapy.
Association Between Schizophrenia-Related Polygenic Liability and the Occurrence and Level of Mood-Incongruent Psychotic Symptoms in Bipolar Disorder.

Importance: Bipolar disorder (BD) overlaps schizophrenia in its clinical presentation and genetic liability. Alternative approaches to patient stratification beyond current diagnostic categories are needed to understand the underlying disease processes and mechanisms. Objective: To investigate the association between common-variant liability for schizophrenia, indexed by polygenic risk scores (PRSs), and psychotic presentations of BD. Design, Setting, and Participants: This case-control study in the United Kingdom used multinomial logistic regression to estimate differential PRS associations across categories of cases and controls. Participants included in the final analyses were 4436 cases of BD from the Bipolar Disorder Research Network. These cases were compared with the genotypic data for 4976 cases of schizophrenia and 9012 controls from the Type 1 Diabetes Genetics Consortium study and the Generation Scotland study. Data were collected between January 1, 2000, and December 31, 2013. Data analysis was conducted from March 1, 2016, to February 28, 2017. Exposures: Standardized PRSs, calculated using alleles with an association threshold of P < .05 in the second Psychiatric Genomics Consortium genome-wide association study of schizophrenia, were adjusted for the first 10 population principal components and genotyping platforms. Main Outcomes and Measures: Multinomial logit models estimated PRS associations with BD stratified by Research Diagnostic Criteria subtypes of BD, by lifetime occurrence of psychosis, and by lifetime mood-incongruent psychotic features. Ordinal logistic regression examined PRS associations across levels of mood incongruence. Ratings were derived from the Schedules for Clinical Assessment in Neuropsychiatry interview and the Bipolar Affective Disorder Dimension Scale. Results: Of the 4436 cases of BD, 2966 (67%) were female patients, and the mean (SD) age at interview was 46 [12] years. Across clinical phenotypes, there was an exposure-response gradient, with the strongest PRS association for schizophrenia (risk ratio [RR] = 1.94; 95% CI, 1.86-2.01), followed by schizoaffective BD (RR = 1.37; 95% CI, 1.22-1.54), bipolar I disorder subtype (RR = 1.30; 95% CI, 1.24-1.36), and bipolar II disorder subtype (RR = 1.04; 95% CI, 0.97-1.11). Within BD cases, there was an effect gradient, indexed by the nature of psychosis. Prominent mood-incongruent psychotic features had the strongest association (RR = 1.46; 95% CI, 1.36-1.57), followed by mood-congruent psychosis (RR = 1.24; 95% CI, 1.17-1.33) and BD with no history of psychosis (RR = 1.09; 95% CI, 1.04-1.15). Conclusions and Relevance: For the first time to date, a study shows a polygenic-risk gradient across schizophrenia and BD, indexed by the occurrence and level of mood-incongruent psychotic symptoms.
"Possibly positive or certainly uncertain?": participants' responses to uncertain diagnostic results from exome sequencing.

PurposeClinical genome sequencing produces uncertain diagnostic results, raising concerns about how to communicate the method's inherent complexities in ways that reduce potential misunderstandings and harm. This study investigates clinicians' communications and patient/participant responses to uncertain diagnostic results arising from a clinical exome sequencing research study, contributing empirical data to the debate surrounding disclosure of uncertain genomic information. MethodsWe investigated the communication and impact of uncertain diagnostic results using ethnographic observations of result disclosures with 21 adults and 11 parents of child patients, followed by two semistructured interviews with these same participants. ResultsParticipants understood their uncertain results in ways that were congruent with clinical geneticists' communications. They followed recommendations for further consultation, although family testing to resolve uncertainty was not always done. Participants were prepared for learning an uncertain result and grasped the key concept that it should not be used to guide health-care or other decisions. They did not express regret for having learned the uncertain result; most regarded it as potentially valuable in the future. ConclusionThis study suggests that uncertain diagnostic results from genome sequencing can be relayed to patients in ways they can understand and consistent with providers' interpretations, without causing undue harm.
Myopia in young adults is inversely related to an objective marker of ocular sun exposure: the Western Australian Raine cohort study.

PURPOSE: To determine the association between ocular sun exposure measured by conjunctival ultraviolet (UV) autofluorescence and myopic refractive error in young adults. DESIGN: Cross-sectional study. METHODS: setting: Population-based cohort in Western Australia. study population: Total of 1344 mostly white subjects aged 19-22 years in the Western Australian Pregnancy Cohort (Raine) Eye Health Study. observation procedures: Cycloplegic autorefraction, conjunctival ultraviolet autofluorescence photography, participant questionnaire. main outcome measures: Prevalence of myopic refractive error (spherical equivalent less than -0.50 diopters) and area of conjunctival ultraviolet autofluorescence in mm(2). RESULTS: There was an inverse relationship between myopic refractive error and ocular sun exposure, with more than double the prevalence of myopia in the lowest quartile of conjunctival autofluorescence than the highest quartile (33.0% vs 15.6%). Median area of autofluorescence was significantly lower in myopic than in nonmyopic subjects (31.9 mm(2) vs 47.9 mm(2), P < .001). These differences remained significant after adjustment for age, sex, parental history of myopia, and subject level of education. The use of corrective lenses did not explain the lower conjunctival autofluorescence observed in myopic subjects. CONCLUSIONS: In this young adult population, myopic refractive error was inversely associated with objectively measured ocular sun exposure, even after adjustment for potential confounders. This further supports the inverse association between outdoor activity and myopia.
Immersive and interactive virtual reality to improve learning and retention of neuroanatomy in medical students: a randomized controlled study.

BACKGROUND: Spatial 3-dimensional understanding of the brain is essential to learning neuroanatomy, and 3-dimensional learning techniques have been proposed as tools to enhance neuroanatomy training. The aim of this study was to examine the impact of immersive virtual-reality neuroanatomy training and compare it to traditional paper-based methods. METHODS: In this randomized controlled study, participants consisted of first- or second-year medical students from the University of Saskatchewan recruited via email and posters displayed throughout the medical school. Participants were randomly assigned to the virtual-reality group or the paper-based group and studied the spatial relations between neural structures for 12 minutes after performing a neuroanatomy baseline test, with both test and control questions. A postintervention test was administered immediately after the study period and 5-9 days later. Satisfaction measures were obtained. RESULTS: Of the 66 participants randomly assigned to the study groups, 64 were included in the final analysis, 31 in the virtual-reality group and 33 in the paper-based group. The 2 groups performed comparably on the baseline questions and showed significant performance improvement on the test questions following study. There were no significant differences between groups for the control questions, the postintervention test questions or the 7-day postintervention test questions. Satisfaction survey results indicated that neurophobia was decreased. INTERPRETATION: Results from this study provide evidence that training in neuroanatomy in an immersive and interactive virtual-reality environment may be an effective neuroanatomy learning tool that warrants further study. They also suggest that integration of virtual-reality into neuroanatomy training may improve knowledge retention, increase study motivation and decrease neurophobia.
Does physical activity reduce the risk of prostate cancer? A systematic review and meta-analysis.

CONTEXT: Numerous observational epidemiologic studies have evaluated the association between physical activity and prostate cancer (PCa); however, the existing results are inconsistent. OBJECTIVE: To determine the association between physical activity and risk of PCa. EVIDENCE ACQUISITION: A systematic search was performed using the Medline, Embase, and Web of Science databases through 15 May 2011 to identify all English-language articles that examined the effect of physical activity on the risk of PCa. This meta-analysis was conducted according to the guidelines for the meta-analysis of observational studies in epidemiology. EVIDENCE SYNTHESIS: This meta-analysis consisted of 88,294 cases from 19 eligible cohort studies and 24 eligible case-control studies. When data from both types of studies were combined, total physical activity (TPA) was significantly associated with a decreased risk of PCa (pooled relative risk [RR]: 0.90; 95% confidence interval [CI], 0.84-0.95). The pooled RR for occupational physical activity (OPA) and recreational physical activity (RPA) were 0.81 (95% CI, 0.73-0.91) and 0.95 (95% CI, 0.89-1.00), respectively. Notably, for TPA, we observed a significant PCa risk reduction for individuals between 20 and 45 yr of age (RR: 0.93; 95% CI, 0.89-0.97) and between 45 and 65 yr of age (RR: 0.91; 95% CI, 0.86-0.97) who performed activities but not for individuals <20 yr of age or >65 yr of age. CONCLUSIONS: There appears to be an inverse association between physical activity and PCa risk, albeit a small one. Given that increasing physical activity has numerous other health benefits, men should be encouraged to increase their physical activity in both occupational and recreational time to improve their overall health and potentially decrease their risk of PCa.
Building Diversified Multiple Trees for classification in high dimensional noisy biomedical data.

PURPOSE: It is common that a trained classification model is applied to the operating data that is deviated from the training data because of noise. This paper will test an ensemble method, Diversified Multiple Tree (DMT), on its capability for classifying instances in a new laboratory using the classifier built on the instances of another laboratory. METHODS: DMT is tested on three real world biomedical data sets from different laboratories in comparison with four benchmark ensemble methods, AdaBoost, Bagging, Random Forests, and Random Trees. Experiments have also been conducted on studying the limitation of DMT and its possible variations. RESULTS: Experimental results show that DMT is significantly more accurate than other benchmark ensemble classifiers on classifying new instances of a different laboratory from the laboratory where instances are used to build the classifier. CONCLUSIONS: This paper demonstrates that an ensemble classifier, DMT, is more robust in classifying noisy data than other widely used ensemble methods. DMT works on the data set that supports multiple simple trees.