Miracle-dz/UniFAR-FTUs huggingface dataset:
Accumulation of Transposable Elements in Autosomes and Giant Sex Chromosomes of Omophoita (Chrysomelidae: Alticinae)

Coleoptera is the most diverse order among insects, and comparative molecular cytogenetic studies in this group are lacking. The species of Omophoita (Oedionychina) possess a karyotype of 2n = 22 = 10II+X+Y. They are interesting models for evolutionary cytogenetic studies due to giant sex chromosomes which are asynaptic during meiosis. Transposable elements (TEs) confer plasticity and mobility to genomes and are considered hotspots for DNA double-strand breaks and chromosomal rearrangements. The objective of the present study was to verify the role of TEs in the karyotype and in the size expansion of the giant sex chromosomes in Omophoita. Thus, different TEs were characterized in the Omophoita genome and localized in the chromosomes by fluorescence in situ hybridization (FISH). The DNA sequencing data revealed identity with TE families Tc1/Mariner and RTE/L1-56_XT. FISH showed signals of all TEs in the karyotypes and a high accumulation in the sex chromosomes of the 3 Omophoita species analyzed. These data suggest that the genome size expansion and the origin of the giant sex chromosomes of Omophoita are due to an intensive genomic invasion of TEs, as those characterized here as Tc1/Mariner-Ooc and RTE-Ooc. Differences in the chromosomal location of the TEs among the 3 species indicate that they have participated in the karyotype differentiation in Omophoita.
A practical approach to adjusting for population stratification in genome-wide association studies: principal components and propensity scores (PCAPS)

Abstract Genome-wide association studies (GWAS) are susceptible to bias due to population stratification (PS). The most widely used method to correct bias due to PS is principal components (PCs) analysis (PCA), but there is no objective method to guide which PCs to include as covariates. Often, the ten PCs with the highest eigenvalues are included to adjust for PS. This selection is arbitrary, and patterns of local linkage disequilibrium may affect PCA corrections. To address these limitations, we estimate genomic propensity scores based on all statistically significant PCs selected by the Tracy-Widom (TW) statistic. We compare a principal components and propensity scores (PCAPS) approach to PCA and EMMAX using simulated GWAS data under no, moderate, and severe PS. PCAPS reduced spurious genetic associations regardless of the degree of PS, resulting in odds ratio (OR) estimates closer to the true OR. We illustrate our PCAPS method using GWAS data from a study of testicular germ cell tumors. PCAPS provided a more conservative adjustment than PCA. Advantages of the PCAPS approach include reduction of bias compared to PCA, consistent selection of propensity scores to adjust for PS, the potential ability to handle outliers, and ease of implementation using existing software packages.
Functional Study of Carboxylesterase 1 Protein Isoforms

Carboxylesterase 1 (CES1) is a primary human hepatic hydrolase involved in hydrolytic biotransformation of numerous medications. Considerable interindividual variability in CES1 expression and activity has been consistently reported. Four isoforms of the CES1 protein are produced by alternative splicing (AS). In the current study, the activity and expression of each CES1 isoform are examined using transfected cell lines, and CES1 isoform composition and its impact on CES1 activity in human livers are determined. In transfected cells, isoforms 3 and 4 show mRNA and protein expressions comparable to isoforms 1 and 2, but have significantly impaired activity when hydrolyzing enalapril and clopidogrel. In individual human liver samples, isoforms 1 and 2 are the major forms, contributing 73–90% of the total CES1 protein expression. In addition, the protein expression ratios of isoforms 1 and 2 to isoforms 3 and 4 are positively associated with CES1 activity in the liver, suggesting that CES1 isoform composition is a factor contributing to the variability in hepatic CES1 function. Further investigations of the regulation of CES1 AS would improve the understanding of CES1 variability and help develop a strategy to optimize the pharmacotherapy of many CES1 substrate medications.
Predictors associated with an increased prevalence of postimplantation syndrome after thoracic endovascular aortic repair for type B aortic dissection†.

OBJECTIVES The aim of this study was to identify patients who are at high risk of developing postimplantation syndrome (PIS) after thoracic endovascular aortic repair (TEVAR) for type B aortic dissection. METHODS This retrospective study included 646 patients who underwent TEVAR for type B aortic dissection between January 2010 and December 2015 at the Guangdong General Hospital. PIS was defined as fever (>38°C) and leucocytosis (>12 000 μl-1) without evidence of infection. The PIS rate was calculated, and a multivariable logistic regression model was used to investigate the factors related to PIS. RESULTS A total of 646 patients (58.8 ± 11.0 years, 87.9% men) were included in the analysis. PIS was diagnosed in 204 (31.6%) patients. Age <60 years [odds ratio (OR) 1.828, 95% confidence interval (CI) 1.277-2.619; P < 0.001), hypertension (OR 12.125, 95% CI 4.310-34.111; P < 0.001), >1 stent graft placed (OR 1.862, 95% CI 1.109-3.124; P = 0.011), arch vessel bypass (OR 2.107, 95% CI 1.397-3.176; P = 0.001) and Ankura stent graft placement (OR 1.951, 95% CI 1.298-2.933; P = 0.001) were positively associated with PIS, whereas statin use (OR 0.659, 95% CI 0.460-0.944; P = 0.023) was negatively associated with PIS in the multivariable logistic regression analysis based on a stepwise regression model. CONCLUSIONS Age <60 years, comorbid hypertension, >1 stent graft placed, arch vessel bypass and Ankura stent graft placement emerged as independent predictors of PIS. Stepwise increases in the prevalence of PIS were found to depend on the number of independent predictors.
Acute hemodynamic changes following high load and very low load lower body resistance exercise with and without the restriction of blood flow

Objective: To examine the acute changes in blood flow and blood pressure of very low load knee extensor exercise (15% one repetition maximum (1RM)) with and without different levels of applied pressure to determine how these effects might differ from high load exercise. We also sought to examine if this differed between men and women. Approach: A total of 90 participants (45 men, 45 women) were randomized into a very low load condition with no restriction 15/0, (n = 21), a very low load condition with 40% arterial occlusion pressure (15/40, n = 23), a very low load condition with 80% arterial occlusion pressure (15/80, n = 22), and a traditional high load condition (70/0, n = 24). Pre-post change in blood flow and blood pressure were compared across conditions. Evidence for or against the null hypothesis was quantified using Bayes factors (BF10). Main results: For blood flow, there was no evidence that the changes were different across conditions (BF10: 0.902). However, only the very low load free flow condition (15/0) had evidence to suggest a change (mean, (standard deviation)) from baseline (5.3 (9.1) ml · min−1; BF10: 3.687). Systolic pressure increased ~17 mmHg for the 15/0, 15/40, and 70/0 conditions, with no change in the 15/80 condition. There was no effect of sex for any variable. Significance: There was substantial variability in our blood flow measurements, making conclusions difficult for this variable. Of note, the blood pressure response was not augmented by blood flow restriction. The hemodynamic changes were also similar between sexes, indicating that men and women were not changing differently.
Reproducibility of dynamic cerebral autoregulation parameters: a multi-centre, multi-method study

Objective: Different methods to calculate dynamic cerebral autoregulation (dCA) parameters are available. However, most of these methods demonstrate poor reproducibility that limit their reliability for clinical use. Inter-centre differences in study protocols, modelling approaches and default parameter settings have all led to a lack of standardisation and comparability between studies. We evaluated reproducibility of dCA parameters by assessing systematic errors in surrogate data resulting from different modelling techniques. Approach: Fourteen centres analysed 22 datasets consisting of two repeated physiological blood pressure measurements with surrogate cerebral blood flow velocity signals, generated using Tiecks curves (autoregulation index, ARI 0–9) and added noise. For reproducibility, dCA methods were grouped in three broad categories: 1. Transfer function analysis (TFA)-like output; 2. ARI-like output; 3. Correlation coefficient-like output. For all methods, reproducibility was determined by one-way intraclass correlation coefficient analysis (ICC). Main results: For TFA-like methods the mean (SD; [range]) ICC gain was 0.71 (0.10; [0.49–0.86]) and 0.80 (0.17; [0.36–0.94]) for VLF and LF (p = 0.003) respectively. For phase, ICC values were 0.53 (0.21; [0.09–0.80]) for VLF, and 0.92 (0.13; [0.44–1.00]) for LF (p < 0.001). Finally, ICC for ARI-like methods was equal to 0.84 (0.19; [0.41–0.94]), and for correlation-like methods, ICC was 0.21 (0.21; [0.056–0.35]). Significance: When applied to realistic surrogate data, free from the additional exogenous influences of physiological variability on cerebral blood flow, most methods of dCA modelling showed ICC values considerably higher than what has been reported for physiological data. This finding suggests that the poor reproducibility reported by previous studies may be mainly due to the inherent physiological variability of cerebral blood flow regulatory mechanisms rather than related to (stationary) random noise and the signal analysis methods.
Citrus fruit intake and gastric cancer: The stomach cancer pooling (StoP) project consortium

Diets rich in vegetables and fruit have been associated with reduced risk of gastric cancer, and there is suggestive evidence that citrus fruits have a protective role. Our study aimed at evaluating and quantifying the association between citrus fruit intake and gastric cancer risk. We conducted a one‐stage pooled analysis including 6,340 cases and 14,490 controls from 15 case–control studies from the stomach cancer pooling (StoP) project consortium. Odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) of gastric cancer across study‐specific tertiles of citrus fruit intake (grams/week) were estimated by generalized linear mixed effect models, with logistic link function and random intercept for each study. The models were adjusted for sex, age, and the main recognized risk factors for gastric cancer. Compared to the first third of the distribution, the adjusted pooled OR (95% CI) for the highest third was 0.80 (0.73–0.87). The favourable effect of citrus fruits increased progressively until three servings/week and leveled off thereafter. The magnitude of the association was similar between cancer sub‐sites and histotypes. The analysis by geographic area showed no association in studies from the Americas. Our data confirm an inverse association between citrus fruits and gastric cancer and provide precise estimates of the magnitude of the association. However, the null association found in studies from America and in some previous cohort studies prevent to draw definite conclusions on a protective effect of citrus fruit consumption.
Synthesis, Experimental and Density Functional Theory (DFT) Studies on Solubility of Camptothecin Derivatives

Two camptothecin derivatives, 10-cyclohexyl-7-methyl-20(S)-camptothecin and 7-methyl-10-morpholino-20(S)-camptothecin, were synthesized and their differences in solubility were investigated using four chosen solvent systems. Based on our results, 10-cyclohexyl-7-methyl-20(S)-camptothecin exhibited higher solubilities than 7-methyl-10-morpholino-20(S)-camptothecin in polar aprotic solvents. However, these two camptothecin derivatives did not exhibit apparent differences in solubility between 5% dimethyl sulfoxide (DMSO)/95% normal saline co-solvent system and 5% dimethylacetamide (DMAC)/95% normal saline co-solvent system. To rationalize their differences in solubility, we also tried to perform a DFT-B3LYP study to investigate their interaction with one water molecule.
IIT(BHU)@IECSIL-FIRE2018: Language Independent Automatic Framework for Entity Extraction in Indian Languages

The paper discusses about our work submitted to the track IECSIL [3] organized by ARNEKT in conjunction with Forum for Information Retrieval and Evaluation 2018. The track primarily focuses on developing language independent system for information extraction on Indian languages. We focused on the identification and categorization of entities in the text. We used word embedding for the feature representation. We proposed Bidirectional LSTM recurrent neural network model for entity extraction from the provided text for the five Indian languages such as Hindi, Kannada, Malayalam, Tamil and Telugu. The proposed technique is evaluated in terms of two metrics, accuracy and F1-score.
SECURE COLLABORATIVE PROCESSING ARCHITECTURE FOR MITB ATTACK DETECTION

In this paper, we take a distributed architecture called Semantic Room (SR) which is capable of correlating events coming from several organizations participating in the SR, developed in the context of the EU Project COMIFIN, and we add privacy capability to the SR. The SR architecture consists of Edge Gateways deployed at each financial institution and a set of private clouds that form the SR collaborative processing system (CSP). Edge Gateways perform data pre-processing and anonymize data items, as prescribed by the SR contract, using Shamir secret sharing scheme. Anonymous data are sent to the CPS that aggregates information through MapReduce-based computations. The anonymous data resulting from the collaborative computation are revealed to the financial institutions only if suspicious cyber threat activities are detected. In this paper we show how this SR can be leveraged for detecting Man-In-TheBrowser attacks.
Sedentary Behavior and Physical Activity Patterns in Older Adults After Hip Fracture: A Call to Action.

OBJECTIVES To characterize patterns of sedentary behavior and physical activity in older adults recovering from hip fracture and to determine characteristics associated with activity. METHODS Community-dwelling, Canadian adults (65 years+) who sustained hip fracture wore an accelerometer at the waist for seven days and provided information on quality of life, falls self-efficacy, cognitive functioning, and mobility. RESULTS There were 53 older adults (mean age [SD] 79.5 [7.8] years) enrolled in the study; 49 had valid data and demonstrated high levels of sedentary time (median [p10, p90] 591.3 [482.2, 707.2] minutes/day), low levels of light activity (186.6 [72.6, 293.7]), and MVPA (2 [0.1, 27.6]), as well as few daily steps (2467.7 [617.1, 6820.4]). Regression analyses showed that age, gender, gait speed, and time since fracture were associated with outcomes. CONCLUSIONS Older adults have long periods of sedentary time with minimal activity. Results are a call to action to encourage people to sit less and move more.
Autoimmunity and effector recognition in Arabidopsis thaliana can be uncoupled by mutations in the RRS1-R immune receptor.

Plant nucleotide-binding leucine-rich repeat (NLR) disease resistance proteins recognize specific pathogen effectors and activate a cellular defense program. In Arabidopsis thaliana (Arabidopsis), Resistance to Ralstonia solanacearum 1 (RRS1-R) and Resistance to Pseudomonas syringae 4 (RPS4) function together to recognize the unrelated bacterial effectors PopP2 and AvrRps4. In the plant cell nucleus, the RRS1-R/RPS4 complex binds to and signals the presence of AvrRps4 or PopP2. The exact mechanism underlying NLR signaling and immunity activation remains to be elucidated. Using genetic and biochemical approaches, we characterized the intragenic suppressors of sensitive to low humidity 1 (slh1), a temperature-sensitive autoimmune allele of RRS1-R. Our analyses identified five amino acid residues that contribute to RRS1-RSLH 1 autoactivity. We investigated the role of these residues in the RRS1-R allele by genetic complementation, and found that C15 in the Toll/interleukin-1 receptor (TIR) domain and L816 in the LRR domain were also important for effector recognition. Further characterization of the intragenic suppressive mutations located in the RRS1-R TIR domain revealed differing requirements for RRS1-R/RPS4-dependent autoimmunity and effector-triggered immunity. Our results provide novel information about the mechanisms which, in turn, hold an NLR protein complex inactive and allow adequate activation in the presence of pathogens.
When Learners Escape Models of Their Behavior

Modeling and measurement are stable in many domains, such as ballistics. So why are new models continually needed in other domains, such as macro-economic policy and spam filtering? Models always include unmeasured dimensions, but people (or any learners) can escape into those unmeasured dimensions. People don’t always try to escape, so we look for conditions where escape is likely, prompted by the insight that too much striving for measured goals hurts unmeasured goals. For example, science hiring’s quantity demands led to a drop in quality, eventually visible in the reproducibility crisis. We can also identify macro-level indicators such as increasing prices, new products, and divergent profits. Under the pressure of high protein prices, manufacturers of pet food (normally a commodity) substituted melamine for protein, gaming the way protein was measured. What can modelers do? First, modelers can try to change the conditions that caused escape pressure. Failing that, we can either speed up the evolution of our own models or slow down the evolution of others’ models. Techniques to speed up include better feedback, models that are simple or explainable or modular, and using multiple models (an ensemble). Techniques to slow down others include obscuring our own model so that it cannot be backward-engineered. In sum, domains that continually need new models typically have pressure for learners to escape the models. We should study conditions that make escape likely and better meta-modeling techniques to deal with it.
Detecting cervical precancer and reaching underscreened women by using HPV testing on self samples: updated meta-analyses

Abstract Objective To evaluate the diagnostic accuracy of high-risk human papillomavirus (hrHPV) assays on self samples and the efficacy of self sampling strategies to reach underscreened women. Design Updated meta-analysis. Data sources Medline (PubMed), Embase, and CENTRAL from 1 January 2013 to 15 April 2018 (accuracy review), and 1 January 2014 to 15 April 2018 (participation review). Review methods Accuracy review: hrHPV assay on a vaginal self sample and a clinician sample; and verification of the presence of cervical intraepithelial neoplasia grade 2 or worse (CIN2+) by colposcopy and biopsy in all enrolled women or in women with positive tests. Participation review: study population included women who were irregularly or never screened; women in the self sampling arm (intervention arm) were invited to collect a self sample for hrHPV testing; women in the control arm were invited or reminded to undergo a screening test on a clinician sample; participation in both arms was documented; and a population minimum of 400 women. Results 56 accuracy studies and 25 participation trials were included. hrHPV assays based on polymerase chain reaction were as sensitive on self samples as on clinician samples to detect CIN2+ or CIN3+ (pooled ratio 0.99, 95% confidence interval 0.97 to 1.02). However, hrHPV assays based on signal amplification were less sensitive on self samples (pooled ratio 0.85, 95% confidence interval 0.80 to 0.89). The specificity to exclude CIN2+ was 2% or 4% lower on self samples than on clinician samples, for hrHPV assays based on polymerase chain reaction or signal amplification, respectively. Mailing self sample kits to the woman’s home address generated higher response rates to have a sample taken by a clinician than invitation or reminder letters (pooled relative participation in intention-to-treat-analysis of 2.33, 95% confidence interval 1.86 to 2.91). Opt-in strategies where women had to request a self sampling kit were generally not more effective than invitation letters (relative participation of 1.22, 95% confidence interval 0.93 to 1.61). Direct offer of self sampling devices to women in communities that were underscreened generated high participation rates (>75%). Substantial interstudy heterogeneity was noted (I2>95%). Conclusions When used with hrHPV assays based on polymerase chain reaction, testing on self samples was similarly accurate as on clinician samples. Offering self sampling kits generally is more effective in reaching underscreened women than sending invitations. However, since response rates are highly variable among settings, pilots should be set up before regional or national roll out of self sampling strategies.
Clinical application and outcomes of sentinel node navigation surgery in patients with early gastric cancer

Sentinel node navigation surgery (SNNS) has been recognized as a minimally invasive tool for individualized lymphadenectomy in patients with early gastric cancer (EGC). The aim of this study was to compare clinicopathological factors, adverse events, and clinical outcomes between sentinel node mapping (SNM) and SN dissection (SND) groups and assess the clinical utility of SNNS in patients with EGC. The clinical data of 157 patients with EGC, diagnosed as clinical T1N0M0 with tumors ≤ 40 mm, undergoing SNNS between March 2004 and April 2016 were retrospectively reviewed. Twenty-seven patients were excluded from the analysis. In the remaining 130 patients, 59 and 71 patients underwent standard lymphadenectomy for SNM and SND, respectively. The sentinel node detection rate in the SNM and SND groups was 98.3% (58/59) and 100% (71/71), respectively. Two (3.5%), 15 (25.9%), and 41 (70.7%) patients having sentinel nodes underwent total gastrectomy, proximal gastrectomy (PG), and distal gastrectomy (DG), respectively, in the SNM group. One (1.4%), 5 (7.0%), 10 (14.1%), 39 (54.9%), and 16 (22.5%) patients underwent PG, DG, segmental gastrectomy, local resection, and endoscopic submucosal dissection, respectively, in the SND group. There was no significant difference in postoperative complications between the SNM and SND groups (P = 0.781). Survival did not differ between the both groups (P = 0.856). The present results suggest that personalized surgery with SND provides technical safety and curability related with a favorable survival outcome in patients with EGC.
Detection of West Nile virus lineage 2 in North‐Eastern Spain (Catalonia)

Abstract In September 2017, West Nile virus (WNV) lineage 2 was detected in Catalonia (Northern Spain) in northern goshawks by passive surveillance. The phylogenetic analyses showed that it was related to the Central/Southern European strains, evidencing WNV lineage 2 spread to Western Europe. WNV local transmission was later detected in bearded vultures housed at the Wildlife Recovery center where the goshawk was transferred to. Further studies, before the following period of high mosquito activity, indicated that WNV had circulated intensively in poultry and horses but only surrounding of the area where the virus was detected. In other areas of Catalonia, circulation of flaviviruses different to WNV was identified. Public Health investigations failed to detect WNV infection in humans.