Takshan/R1 huggingface dataset:
A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes.

KEY MESSAGE: We report a linkage map for Apios americana and describe synteny with selected warm-season legumes. A translocation event in common bean and soybean is confirmed against Apios and Vigna species. Apios (Apios americana; "apios"), a tuberous perennial legume in the Phaseoleae tribe, was widely used as a food by Native Americans. Work in the last 40 years has led to several improved breeding lines. Aspects of the pollination biology (complex floral structure and tripping mechanism) have made controlled crosses difficult, and the previous reports indicated that the plant is likely primarily an outcrosser. We used a pseudo-testcross strategy to construct a genetic map specific to the maternal parent. The map was built using single-nucleotide polymorphism markers identified by comparing the expressed sequences of individuals in the mapping population against a de novo maternal reference transcriptome assembly. The apios map consists of 11 linkage groups and 1121 recombinationally distinct loci, covering ~ 938.6 cM. By sequencing the transcriptomes of all potential pollen parents, we were able to identify the probable pollen donors and to discover new aspects of the pollination biology in apios. No selfing was observed, but multiple pollen parents were seen within individual pods. Comparisons with genome sequences in other species in the Phaseoleae showed extended synteny for most apios linkage groups. This synteny supports the robustness of the map, and also sheds light on the history of the Phaseoleae, as apios is relatively early diverging in this tribe. We detected a translocation event that separates apios and two Vigna species from Phaseolus vulgaris and Glycine max. This apios mapping work provides a general protocol for sequencing-based construction of high-density linkage maps in outcrossing species with heterogeneous pollen parents.
Exacerbations and healthcare resource utilization among COPD patients in a Swedish registry-based nation-wide study.

BACKGROUND: Exacerbations of chronic obstructive pulmonary disease (COPD) are an important measure of disease severity in terms of impaired disease progression, increased recovery time, healthcare resource utilization, overall morbidity and mortality. We aimed to quantify exacerbation and healthcare resource utilization rates among COPD patients in Sweden with respect to baseline treatments, exacerbation history, and comorbidities. METHODS: Patients with a COPD or chronic bronchitis (CB) diagnosis in secondary care at age of ≥40 years on 1.7.2009 were identified and followed until 1.7.2010 or death. Severe exacerbations were defined as hospitalizations due to respiratory disease, and healthcare resource utilization was measured by all-cause hospitalizations and secondary care visits. Poisson regression was used adjusting for age, gender, time since COPD/CB diagnosis, and Charlson comorbidity index. RESULTS: In 88,548 patients (54% females, mean age 72 years), previous respiratory hospitalizations and current high use of COPD medication (double or triple therapy) predicted an 8.3-fold increase in severe exacerbation rates and 1.8-fold increase in healthcare resource utilization rates in the following year, compared to patients without combination treatment and/or history of severe exacerbations. CONCLUSIONS: COPD/CB patients with history of severe exacerbations and high use of COPD medication experienced a significantly increased rate of severe exacerbations and healthcare resource utilization during the one-year follow-up.
Development and validation of empirically derived frequency criteria for NSSI disorder using exploratory data mining.

Research suggesting nonsuicidal self-injury (NSSI) may belong in a distinct diagnostic category has led to the inclusion of NSSI disorder in the DSM-5 section for future study. There has been limited research, however, examining the validity of Criterion A (the frequency criterion). The current study aimed to examine the validity of the frequency criterion of NSSI disorder through the use of an exploratory data mining method, structural equation modeling trees, as a way to determine a NSSI frequency that optimally discriminates pathological NSSI from normative behavior among undergraduate students (n = 3,559), 428 who engaged in NSSI in the previous year. The model included psychopathology symptomology found to be comorbid with NSSI and cognitive-affective deficits commonly associated with NSSI. Results demonstrated a first split between individuals with 0 and 1 act of NSSI in the past year, as was expected. Among individuals with 1 or more previous acts, the optimal split was between those with 5 and 6 NSSI acts in the past year. Results from the current study suggest that individuals with 6 acts of NSSI in past year, compared with those with 5 acts or less, may represent a more severe group of self-injurers. These individuals reported higher levels of related psychopathology symptomology and cognitive-affective deficits, in addition to decreased quality of life. Findings have potential implications for the proposed frequency criteria of NSSI disorder and how pathological NSSI is characterized. ( PsycINFO Database Record
The relationship between non-suicidal self-injury and borderline personality disorder symptoms in a college sample.

BACKGROUND: Non-suicidal self-injury (NSSI) is a major concern in both clinical and non-clinical populations. It has been approximated that 65-80% of individuals with borderline personality disorder (BPD) engage in some form of NSSI. Despite such high co-morbidity, much still remains unknown about the relationship between NSSI and BPD symptomatology. The goal of the current study was to identify individual BPD symptoms and higher order BPD factors that increase one's vulnerability of NSSI engagement among a college sample. It was hypothesized that the BPD factor of emotion dysregulation and the BPD symptoms of affect instability and intense anger/aggression would be associated with the presence and frequency of NSSI. METHOD: Seven hundred twenty four undergraduates (61.2% female) completed self-report measures of BPD symptomology and NSSI history. RESULTS: Regression analyses revealed that among the individual BPD symptoms, past suicidality, impulsivity, chronic emptiness, and identity disturbance were each significantly, positively associated with lifetime history of NSSI, whereas unstable relationships were negatively associated with lifetime history of NSSI. The BPD symptom associated with NSSI frequency was dissociation. Among the BPD factors, emotion dysregulation and disturbed relatedness were both associated with NSSI history, but only disturbed relatedness was associated with NSSI frequency. CONCLUSION: Findings show partial support for the importance of emotion dysregulation in the relationship between NSSI and BPD symptomatology, but also suggest that the relationship may be more complex and not solely based on emotion dysregulation.
Infections following arthroscopic rotator cuff repair: incidence, risk factors, and prophylaxis.

PURPOSE: The primary aim of the present study was to determine the incidence of infections following arthroscopic rotator cuff repair in a single department over a 10-year period. Secondary goals included the evaluation of potential risk factors for infections and to investigate the efficacy of perioperative antibiotic prophylaxis in the reduction of infectious complications. METHODS: A retrospective evaluation of 3294 all-arthroscopic rotator cuff repairs performed between 2004 and 2014 at a single institution was conducted to determine the rate of infection in all-arthroscopic rotator cuff repairs. Detailed data including demographics, co-morbidities, initial surgical procedure, time from index surgery to infection, clinical presentation, isolated pathogens, and subsequent treatment were recorded of patients with infections. Univariate logistic regression was performed, and a multivariate model was developed to identify variables that were predictive of infections following arthroscopic rotator cuff repair. RESULTS: The rate of infection was 8.5/1000 in whom rotator cuff repairs were performed (95 % CI 0.58-1.23 %) during the study period. The most commonly identified pathogen was Staphylococcus epidermidis (n = 11, 39.3 %), followed by Propionibacterium acnes (n = 8, 28.6 %) and Staphylococcus aureus (n = 2, 7.1 %). Patients presented at our institution with signs of infection an average of 28.9 ± 14.7 days after the index surgery. The leading symptom that was present in all patients was diffuse or localized shoulder pain, followed by local signs of infection in 19 (67.9 %), secretion in 14 (50 %), and fever in 9 (32.1 %) patients, respectively. Univariate and multivariate analyses identified the male gender, age over 60, and duration of surgery over 90 min as predictive factors for infection. Administration of perioperative antibiotic prophylaxis was an independent mitigating factor for postoperative infection and reduced the infection rate from 1.54 % (95 % CI 0.98-2.30 %) to 0.28 % (95 % CI 0.10-0.67 %). CONCLUSIONS: The overall incidence of infection was 8.5/1000 arthroscopic rotator cuff repairs over a 10-year period. Gender, age, and length of surgery were identified as predictive factors for infection. The administration of perioperative antibiotic prophylaxis significantly reduced the overall risk of infection and is therefore recommended in all-arthroscopic rotator cuff repairs. However, current prophylactic treatment strategies were not equally efficient for all types of pathogens. LEVEL OF EVIDENCE: Retrospective comparative study, Level III.
Do delays in data availability limit the implementation of near real-time vaccine safety surveillance using the Clinical Practice Research Datalink?

PURPOSE: Near real-time vaccine safety surveillance (NRTVSS) using electronic health records has been used to detect timely vaccine safety signals. Trial implementation of NRTVSS using the Clinical Practice Research Datalink (CPRD) has shown that there is limited power to detect safety signals for rare events. Delays in recording outcomes and receiving data influence the power and timeliness to identify a signal. Our work aimed to compare how different sources of delays influence power and expected time to signal to implement NRTVSS using CPRD. METHODS: We studied seasonal influenza vaccine/Guillain-Barré syndrome and performed power and expected time to signal calculations for the 2013-2014/2014-2015 seasons. We used the Poisson-based maximised sequential probability ratio test, which compares observed-to-expected events. For each study season, we obtained an average Guillain-Barré syndrome/seizures age-sex-adjusted rate from the 5 previous seasons and then used this rate to calculate the expected number of events, assuming a 42-day risk-window. Calculations were performed for detecting rate ratios of 1.5 to 10. We compared power and timeliness considering combinations of the presence/absence of delays in recording outcomes and in receiving data. The R-package Sequential was used. RESULTS: In general, there was ≥80% power to detect increases in risk of ≥4 at the end of the season. Assuming absence of delays slightly improved power (a maximum increase of 4%) but did not noticeably reduce time to detect a signal. CONCLUSION: Removing delays in data availability is insufficient to significantly improve the performance of a NRTVSS system using CPRD. Expansion of CPRD data is required. KEY POINTS The Clinical Practice Research Datalink (CPRD) can be used to implement near real-time vaccine safety surveillance, but there is limited power to detect signals for rare outcomes. Delays in recording outcomes and in receiving data might limit power and timeliness of a system. We assessed the influence of these sources of delays to inform data providers of the steps required to improve a system using CPRD data. Removing delays in recording outcomes and receiving data is unlikely to significantly improve the performance of a system using CPRD data. Expansion of the data available is needed.
Further education improves cognitive reserve and triggers improvement in selective cognitive functions in older adults: The Tasmanian Healthy Brain Project.

INTRODUCTION: The strong link between early-life education and subsequent reduced risk of dementia suggests that education in later life could enhance cognitive function and may reduce age-related cognitive decline and protect against dementia. METHODS: Episodic memory, working memory, executive function, and language processing performances were assessed annually over 4 years in 359 healthy older adults who attended university for a minimum of 12 months (intervention) and were compared against 100 healthy adult controls. RESULTS: Multiple group latent growth curve modeling revealed a significant improvement in language processing capacity over time in the intervention group. No changes were detected for episodic memory, working memory, or executive function. DISCUSSION: These results suggest that complex mental stimulation resulting from late-life further education results in improved crystallized knowledge but no changes to fluid cognitive functions.
Comparison between Glioblastoma and Primary Central Nervous System Lymphoma Using MR Image-based Texture Analysis.

PURPOSE: To elucidate differences between glioblastoma (GBM) and primary central nervous system lymphoma (PCNSL) with magnetic resonance (MR) image-based texture features. METHODS: This was an Institutional Review Board (IRB)-approved retrospective study. Consecutive, pathologically proven, initially treated 44 patients with GBM and 16 patients with PCNSL were enrolled. We calculated a total of 67 image texture features on the largest contrast-enhancing lesion in each patient on post-contrast T1-weighted images. Texture analyses included first-order features (histogram) and second-order features calculated with gray level co-occurrence matrix, gray level run length matrix (GLRLM), gray level size zone matrix, and multiple gray level size zone matrix. All texture features were measured by two neuroradiologists independently and the intraclass correlation coefficients were calculated. Reproducible features with the intraclass correlation coefficients of greater than 0.7 were used for hierarchical clustering between the cases and the features along with unpaired t statistics-based comparisons under the control of false discovery rate (FDR) < 0.05. Principal component analysis (PCA) was performed to find the predominant features in evaluating the differences between GBM and PCNSL. RESULTS: Twenty-one out of the 67 features satisfied the acceptable intraclass correlation coefficient and the FDR constraints. PCA suggested first-order entropy, median, GLRLM-based run length non-uniformity, and run percentage as the distinguished features. Compared with PCNSL, run percentage and median were significantly lower, and entropy and run length non-uniformity were significantly higher in GBM. CONCLUSIONS: Among MR image-based textures, first-order entropy, median, GLRLM-based run length non-uniformity, and run percentage are considered to enhance differences between GBM and PCNSL.
Transarterial Ethanol Ablation Combined with Transarterial Chemoembolization for Hepatocellular Carcinoma with Portal Vein Tumor Thrombus.

BACKGROUND: The prognosis for hepatocellular carcinoma (HCC) with portal vein tumor thrombosis (PVTT) is extremely poor. OBJECTIVES: This study aimed to evaluate the safety and effectiveness of transarterial ethanol ablation (TEA) for the treatment of HCC with PVTT. METHODS: Patients were treated with TEA for PVTT under cone-beam computed tomography and traditional transarterial chemoembolization (TACE) with epirubicin for intrahepatic lesions. RESULTS: Seventeen men were successfully treated with TACE plus TEA. The mean overall survival was 18.3 ± 9.0 months (95% CI: 13.7 - 3.0 months). The quality of life (QoL) score increased from 56.9 ± 15.7 before the procedure to 88.5 ± 11.7 at 4 weeks after the procedure. Lipiodol accumulation grades of 3, 2, 1, and 0 were obtained in 3 (17.6%), 8 (47.1%), 6 (35.3%), and 0 (0%) patients, respectively. CONCLUSIONS: TEA is a safe and effective method for treating patients with PVTT, offering advantages for QoL, response rate after TEA, and OS.
Why lipostatic set point systems are unlikely to evolve.

OBJECTIVES: Body fatness is widely assumed to be regulated by a lipostatic set-point system, which has evolved in response to trade-offs in the risks of mortality. Increasing fatness makes the risk of starvation lower but increases the risk of predation. Yet other models are available. The aim of this work is to evaluate using mathematical modeling whether set-point systems are more likely to evolve than the alternatives. METHODS: I modeled the trade-off in mortality risks using a simple mathematical model, which generates an optimum level of fatness that is presumed to be the driver for the evolution of a set-point. I then mimicked the likely errors in this optimum level, that derive from the variation in the component parameters of the mortality curves using Markov Chain Monte Carlo (MCMC) simulation by Bayesian inference Using Gibbs Sampling (BUGS). RESULTS: The error propagation generated by the simulations showed that even very small errors in the model parameters were magnified enormously in the location of the optimum fatness level. If the model parameters had coefficients of variation of just 1% then the coefficient of variation in the optimum level of fatness was between 20 and 90%. In that situation, a set-point centered at the mathematical optimum from the component curves would be at the correct level of fatness that minimizes mortality, and hence maximizes fitness, on less than 8% of occasions. CONCLUSIONS: Set-point regulation of body fatness is hence highly unlikely to evolve where there is any realistic level of variation in the parameters that define mortality risks. Using further MCMC modeling, I show that a dual-intervention point system is more likely to evolve. This mathematical simulation work has important implications for how we interpret molecular work concerning regulation of adiposity.
Investigation of genetic variation and lifestyle determinants in vitamin D levels in Arab individuals.

BACKGROUND: Differences in the concentrations of circulating 25-hydroxyvitamin D [25(OH)D] are associated with a wide range of health outcomes; however, most studies on genetic variants that impact 25(OH)D levels have been conducted in European populations. Here we aimed to identify common genetic variants that affect vitamin D concentrations in individuals of self-reported Arab ethnicity. METHODS: The study included 1151 Arab subjects living in Kuwait. Common variants of single-nucleotide polymorphisms and genes previously associated with vitamin D levels, such as GC, PDE3B, CYP2R1, and NADSYN1, were genotyped. Raw vitamin D level data were corrected for age, body mass index, and sex and then normalized. Regression tree analyses were performed to identify the impact of genetic variants on vitamin D levels. RESULTS: Compared with other gene variants, the GC gene variants exhibited the greatest impact on vitamin D levels in our study population, of which rs2298850 had the lowest p value (0.003). Individuals homozygous for the derived allele C had lower vitamin D levels. Analyses of the interaction between the number of years for which the subjects had lived in Kuwait and genetic variation in the GC gene showed that those with the CC genotype of rs2298850 who had lived in Kuwait for < 51 years had a mean 25(OH)D level of 10 ng/ml, whereas those who were homozygous for the ancestral allele had a mean 25(OH)D level of 17 ng/ml. Furthermore, subjects who had lived in Kuwait for > 51 years had higher vitamin D levels (mean 28 ng/ml) regardless of the genotype of their GC gene. CONCLUSIONS: The GC gene may play a major role in determining vitamin D levels in Arab populations.
Incisional Hernia Rates After Laparoscopic or Open Abdominal Surgery-A Systematic Review and Meta-Analysis.

BACKGROUND: Incisional hernias are one of the most common long-term complications associated with open abdominal surgery. The aim of this review and meta-analysis was to systematically assess laparoscopic versus open abdominal surgery as a general surgical strategy in all available indications in terms of incisional hernia occurrence. METHODS: A systematic literature search was performed to identify randomized controlled trials comparing incisional hernia rates after laparoscopic versus open abdominal surgery in all indications. Random effects meta-analyses were calculated and presented as risk differences (RD) with their corresponding 95 % confidence intervals (CI). RESULTS: 24 trials (3490 patients) were included. Incisional hernias were significantly reduced in the laparoscopic group (RD -0.06, 95 % CI [-0.09, -0.03], p = 0.0002, I (2) = 75). The advantage of the laparoscopic procedure persisted in the subgroup of total-laparoscopic interventions (RD -0.14, 95 % CI [-0.22, -0.06], p = 0.001, I (2) = 87 %), whereas laparoscopically assisted procedures did not show a significant reduction of incisional hernias compared to open surgery (RD -0.01, 95 % CI [-0.03, 0.01], p = 0.31, I (2) = 35 %). Wound infections were significantly reduced in the laparoscopic group (RD -0.06, 95 % CI [-0.09, -0.03], p < 0.0001, I (2) = 35 %); overall postoperative morbidity was comparable in both groups (RD -0.06, 95 % CI [-0.13, 0.00], p = 0.06; I (2) = 64 %). Open abdominal surgery showed a significantly longer hospital stay compared to laparoscopy (RD -1.92, 95 % CI [-2.67, -1.17], p < 0.00001, I (2) = 87 %). At short-term follow-up, quality of life was in favor of laparoscopy. CONCLUSIONS: Incisional hernias are less frequent using the total-laparoscopic approach instead of open abdominal surgery. Whenever possible, the less traumatic access should be chosen.
Genetic polymorphisms associated with psoriasis and development of psoriatic arthritis in patients with psoriasis.

BACKGROUND: Psoriasis (PsO) is a chronic inflammatory disease with predominantly cutaneous manifestations. Approximately one third of patients with PsO develop psoriatic arthritis (PsA), whereas the remaining proportion of patients has isolated cutaneous psoriasis (PsC). These two phenotypes share common immunology, but with different heredity that might in part be explained by genetic variables. METHODS: Using a candidate gene approach, we studied 53 single nucleotide polymorphisms (SNPs) in 37 genes that regulate inflammation. In total, we assessed 480 patients with PsO from DERMBIO, of whom 151 had PsC for 10 years or more (PsC10), 459 patients with PsA from DANBIO, and 795 healthy controls. Using logistic regression analysis, crude and adjusted for age and gender, we assessed associations between genetic variants and PsO, PsC10, and PsA, as well as associations between genetic variants and development of PsA in PsO. RESULTS: Eleven polymorphisms in 10 genes were nominally associated with PsO and/or PsC and/or PsA (P < 0.05). After correction for multiple testing with a false discovery rate of 5%, two SNPs remained significant: TNF (rs361525) was associated with PsO, PsC10, and PsA; and IL12B (rs6887695) was associated with PsO. CONCLUSION: Among a cohort of Danish patients with moderate-to-severe psoriasis, two SNPs in the IL12B and TNF genes were associated with susceptibility of psoriasis. None of the SNPs were specifically associated with isolated cutaneous psoriasis or psoriatic arthritis.