Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect on early renal function of various dynamic preservation strategies in a preclinical pig ischemia–reperfusion autotransplant model

The aims of this study were to determine the most optimal timing to start machine perfusion during kidney preservation to improve early graft function and to evaluate the impact of temperature and oxygen supply during machine perfusion in a porcine ischemia–reperfusion autotransplant model. The left kidney of an approximately 40‐kg female Belgian Landrace pig was exposed to 30 minutes of warm ischemia via vascular clamping and randomized to 1 of 6 study groups: (1) 22‐hour static cold storage (SCS) (n = 6), (2) 22‐hour hypothermic machine perfusion (HMP) (n = 6), (3) 22‐hour oxygenated HMP (n = 7), (4) 20‐hour HMP plus 2‐hour normothermic perfusion (NP) (n = 6), (5) 20‐hour SCS plus 2‐hour oxygenated HMP (n = 7), and (6) 20‐hour SCS plus 2‐hour NP (n = 6). Graft recovery measured by serum creatinine level was significantly faster for continuous HMP preservation strategies compared with SCS alone and for all end‐ischemic strategies. The active oxygenated 22‐hour HMP group demonstrated a significantly faster recovery from early graft function compared with the 22‐hour nonactive oxygenated HMP group. Active oxygenation was also found to be an important modulator of a faster increase in renal flow during HMP preservation. Continuous oxygenated HMP applied from the time of kidney procurement until transplant might be the best preservation strategy to improve early graft function.
Why Do Neonatologists in Scandinavian Countries and the Netherlands Make Life-and-death Decisions So Different?

A comparison of practice and of policies regarding neonatal end-of-life care between Scandinavian countries and the Netherlands reveals interesting differences, which are summarized in 3 topics. An examination of the policies regarding the care of extremely premature newborns reveals unexpected differences between Scandinavian countries and the Netherlands. Three topics related to decision-making at the beginning and at the end of life are identified and discussed.
Role of homologous recombination genes RAD51, RAD52, and RAD59 in the repair of lesions caused by γ‐radiation to cycling and G2/M‐arrested cells of Candida albicans

We have analysed the role of homologous recombination (HR) genes on the repair of double‐strand breaks induced by γ‐ionising radiation in Candida albicans. Depletion of either CaRad51 or CaRad52 caused a dramatic drop in the number of survivors compared with wild type, whereas depletion of CaRad59 caused a moderate decrease. Besides, compared with Saccharomyces cerevisiae, C. albicans relies more on HR proteins for repair of ionising radiation lesions. Pulse‐field electrokaryotypes of survivors identified genetic alterations mainly in the form of aneuploidy in HR mutants and chromosome length polymorphism and ectopic translocation in wild type. Increasing irradiation (4 to 80 krad) of both cycling and nocodazole‐treated (G2/M‐arrested) cells revealed a gradual loss of chromosomes, larger chromosomes being more affected than smaller ones. For cycling wild‐type cells, shattered chromosomes were progressively restored following incubation in yeast extract, peptone, dextrose medium, but not in phosphate‐buffered saline, and this accompanied by a moderate increase in colony‐forming units, suggesting that repair was followed by replication of survivors. Irradiated G2/M arrested cells from wild type but not from HR mutants partially restored the chromosome ladder following incubation (4–8 hr) in yeast peptone dextrose–nocodazole. However, HR mutants showed a chromosome shattering pattern similar to wild type, an indication that lesions other than double‐strand breaks, likely single‐strand break, are responsible for their drastically reduced survivability.
Visualising convolutional neural network decisions in automated sleep scoring

Current sleep medicine relies on the supervised analysis of polysomnographic recordings, which comprise amongst others electroencephalogram (EEG), electromyogram (EMG), and electrooculogram (EOG) signals. Convolutional neural networks (CNN) provide an interesting framework for automated sleep classification, however, the lack of interpretability of its results has hampered CNN's further use in medicine. In this study, we train a CNN using as input Continuous Wavelet transformed EEG, EOG and EMG recordings from a publicly available dataset. The network achieved a 10-fold cross-validation Cohen's Kappa score of $\kappa = 0.71 \pm 0.01$. Further, we provide insights on how this network classifies individual epochs of sleep using Guided Gradient-weighted Class Activation Maps (Guided Grad-CAM). The proposed approach is able to produce fine-grained activation maps on time-frequency domain for each signal providing a useful tool for identifying relevant features in CNNs.
Heritability and genotype‐environment interactions for growth curve parameters in meat‐type quail fed different threonine:lysine ratios from hatching to 21 d of age

&NA; The aim of the present study was to estimate heritabilities and evaluate the existence of genotype‐environment interactions for growth curve parameters in quail fed diets containing different threonine:lysine ratios. A total of 4,441 body weight information from two genetic quail groups (LF1 and LF2) fed diets containing 0.66%, 0.71%, 0.76%, 0.81%, and 0.86% threonine:lysine ratios from hatching to 21 d of age were evaluated. From 22 to 35 d of age, quail received a single diet. The Gompertz model was used to estimate growth curve parameters. Genetic analyses were performed using random regression models, by Legendre polynomials of the second kind, considering homogeneity of residual variances. The following characteristics were evaluated: asymptotic weight, asymptotic growth rate, and inflection point. Increases in threonine:lysine ratios promoted higher heritability estimates for these variables in the LF1 genetic group compared to LF2, which indicates that the additive genetic variation was modified due to the environmental variation influenced by the evaluated amino acid ratios, with differences between both genetic groups. Thus, it is recommended that quail be selected in the 0.86% ratio in genetic group LF1 and 0.66% in genetic group LF2, where greater heritabilities were observed. Dispersion of individual breeding values along the environmental gradient was observed for all evaluated characteristics, in both genetic groups, suggesting the existence of genotype‐environment interactions for these variables. The evaluated amino acid ratios should be considered in quail breeding programs, since breeding value predictions for a determined threonine:lysine ratio are not valid for other ratios.
Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome*

It has been reported that about 30% of the HLA-I ligands are produced by proteasomal splicing of two noncontiguous fragments of a parental protein. We report that the identification of many of those spliced peptides is ambiguous. With an alternative workflow, based on de novo sequencing and subsequent verification with multiple search tools, we estimate that the upper bound for the proportion of cis-spliced peptides is 2–6%. Nevertheless, the true contribution of spliced peptides to the ligandome may be much smaller. Graphical Abstract Highlights Reported proteasomal spliced HLA peptides do not fit the consensus binding motifs. Their MS/MS spectrum matches suggest that many of them are ambiguous. Our workflow is based on de novo sequencing, alignment, and multiple search tools. The upper bound proportion of cis-spliced peptides is 2–6% and likely much smaller. Spliced peptides are short protein fragments spliced together in the proteasome by peptide bond formation. True estimation of the contribution of proteasome-spliced peptides (PSPs) to the global human leukocyte antigen (HLA) ligandome is critical. A recent study suggested that PSPs contribute up to 30% of the HLA ligandome. We performed a thorough reanalysis of the reported results using multiple computational tools and various validation steps and concluded that only a fraction of the proposed PSPs passes the quality filters. To better estimate the actual number of PSPs, we present an alternative workflow. We performed de novo sequencing of the HLA-peptide spectra and discarded all de novo sequences found in the UniProt database. We checked whether the remaining de novo sequences could match spliced peptides from human proteins. The spliced sequences were appended to the UniProt fasta file, which was searched by two search tools at a false discovery rate (FDR) of 1%. We find that 2–6% of the HLA ligandome could be explained as spliced protein fragments. The majority of these potential PSPs have good peptide-spectrum match properties and are predicted to bind the respective HLA molecules. However, it remains to be shown how many of these potential PSPs actually originate from proteasomal splicing events.
Housing and Feeding Management Practices Followed by Adopted and Non-adopted Goat Farmers Under Adopted Villages of Assam, India

The present investigation was conducted to study the housing and feeding management practices followed by adopted and non-adopted goat farmers in three rural village’s viz. Nahira, Tepesia and Tetelia adopted by “All India Co-ordinated Research Project (AICRP) on Goat Improvement”, Goat Research Station, Assam Agricultural University, Byrnihut, Guwahati. A total of one hundred and five goat farmers adopted under the project and another one hundred and five non-adopted goat farmers from the adopted villages were selected randomly for collection of data. The total sample size was 210. It was observed that 91.43 and 78.10 per cent of adopted and non-adopted goat farmers respectively had separate goat sheds, 87.62 and 72.38 per cent, respectively had closed type of houses, 68.57 and 66.67 per cent, respectively used corrugated iron sheets as roof material, 28.57 and 80.95 per cent, respectively had earthen floor sheds. The common feeding practice of majority of adopted (54.29%) and non-adopted (84.76%) goat farmers were browsing and grazing while 45.71 and 15.24 per cent of adopted and non-adopted goat farmers respectively provided concentrates along with browsing and grazing. An average 85.71 and 56.19 per cent of adopted and non-adopted farmers respectively provided salt to their animals. To conclude management practices namely housing, feeding, health care, breeding and mortality of Assam hill goats were better in adopted goat farmers than in non-adopted goat farmers.
Real-world clinical evidence on rivaroxaban, dabigatran, and apixaban compared with vitamin K antagonists in patients with nonvalvular atrial fibrillation: a systematic literature review

ABSTRACT Introduction: Several comparative real-world effectiveness studies on direct oral anticoagulants (DOACs) have been conducted, but an overview of the available evidence remains to be developed, which could provide a better understanding of the value of DOACs relative to vitamin K antagonists (VKAs). Areas covered: A systematic literature review was conducted on the available real-world evidence (RWE) of three DOACs (rivaroxaban, dabigatran, and apixaban) compared with VKAs (e.g. warfarin), in patients with nonvalvular atrial fibrillation (NVAF). This systematic literature review included RWE published up to December 2016. Studies with > 50 patients reporting on incident and prevalent NVAF cases were included. The following databases were searched: Medline, Embase, and the Cochrane Library. Outcomes of interest included thromboembolic events, all-cause mortality, bleeding events, and non-persistence. Of the 562 RWE DOACs articles retrieved, 49 presented results for rivaroxaban versus VKAs, 79 for dabigatran versus VKAs, and 18 for apixaban versus VKAs. Substantial heterogeneity was found across patient population, outcome definition, and follow-up period. Major bleeding, ischemic stroke, and intracranial hemorrhage were the most frequent outcomes analyzed. Expert commentary: Overall, the RWE studies were aligned with the Phase 3 trials. However, conflicting results were reported for several outcomes of interest.
Assessment and Change: An Exploration of Documented Assessment Activities and Outcomes by Canadian Psychiatrists

Introduction: Fellows of the Royal College of Physicians and Surgeons of Canada are required to participate in assessment activities for all new 5-year cycles beginning on or after January 2014 to meet the maintenance of certification program requirements. This study examined the assessment activities which psychiatrists reported in their maintenance of certification e-portfolios to determine the types and frequency of activities reported; the resultant learning, planned learning, and/or changes to the practice they planned or implemented; and the interrelationship between the types of assessment activities, learning that was affirmed or planned, and changes planned or implemented. Methods: A total of 5000 entries from 2195 psychiatrists were examined. A thematic analysis drawing on the framework analysis was undertaken of the 2016 entries. Results: There were 3841 entries for analysis; 1159 entries did not meet the criteria for assessment. The most commonly reported activities were self-assessment programs, feedback on teaching, regular performance reviews, and chart reviews. Less frequent were direct observation, peer supervision, and reviews by provincial medical regulatory authorities. In response to the data, psychiatrists affirmed that their practices were appropriate, identified gaps they intended to address, planned future learning, and/or planned or implemented changes. The assessment activities were internally or externally initiated and resulted in no or small changes (accommodations and adjustments) or redirections. Discussion: Psychiatrists reported participating in a variety of assessment activities that resulted in variable impact on learning and change. The study underscores the need to ensure that assessments being undertaken are purposeful, relevant, and designed to enable identification of outcomes that impact practice.
Matching networks for personalised human activity recognition

Human Activity Recognition (HAR) has many important applications in health care which include management of chronic conditions and patient rehabilitation. An important consideration when training HAR models is whether to use training data from a general population (subject-independent), or personalised training data from the target user (subject-dependent). Previous evaluations have shown personalised training to be more accurate because of the ability of resulting models to better capture individual users' activity patterns. However, collecting sufficient training data from end users may not be feasible for real-world applications. In this paper, we introduce a novel approach to personalised HAR using a neural network architecture called a matching network. Matching networks perform nearest-neighbour classification by reusing the class label of the most similar instances in a provided support set. Evaluations show our approach to substantially out perform general subject-independent models by more than 5% macro-averaged F1 score.
Oxidative, inflammatory, genetic, and epigenetic biomarkers associated with chronic obstructive pulmonary disorder

A large body of evidence indicates that chronic obstructive pulmonary disorder (COPD) is accompanied by oxidative stress and inflammatory and genetic pathways. Epidemiological studies indicate that COPD is a major cause of mortality and morbidity in the world. Recent research development in COPD focuses on accelerated aging and various oxidative stress biomarkers. It involves the clinical manifestation of the disease process and may also contain biochemical, immunological, physiological, morphological, and genetic aspects that add to the progressiveness of the disease. Herein, we summarize findings that highlight the role of dimensions of COPD in the investigation of oxidative stress, inflammatory responses, genetic and epigenetic studies, and pharmacological and dietary antioxidant intervention.
The long-term efficacy of STN vs GPi deep brain stimulation for Parkinson disease

Objective: This meta-analysis assessed the long-term efficacy of deep brain stimulation (DBS) of the subthalamic nucleus (STN) and globus pallidus interna (GPi) for Parkinson disease (PD). Methods: PubMed, Cochrane Library, and Clinical Trials databases were searched. Outcomes were unified Parkinson disease rating scale section (UPDRS) III off-medication score, Parkinson's disease questionnaire: 39 activities of daily living (PDQ-39 ADL) score, and levodopa-equivalent dosage after DBS. Results: During the off-medication state, pooled weighted mean difference (WMD) of UPDRS III score was . 69 (95% confidence interval [CI] = −1.77 to 3.16, P = .58). In subgroup analysis, WMD of UPDRS III off-medication scores from baseline to 2 years and 3 years post-DBS were −. 61 (95% CI = −2.97 to 1.75, P = .61) and 2.59 (95% CI = −2.30 to 7.47, P = .30). Pooled WMD of changes in tremor, rigidity, and gait scores were 1.12 (95% CI = −0.05 to 2.28, P = .06), 1.22 (95% CI = −0.51 to 2.94, P = .17) and . 37 (95% CI = −0.13 to 0.87, P = .15), respectively. After DBS, pooled WMD of PDQ-39 ADL and LED were −3.36 (95% CI = −6.36 to −0.36, P = .03) and 194.89 (95% CI = 113.16 to 276.63, P < .001). Conclusions: STN-DBS and GPi-DBS improve motor function and activities of daily living for PD. Differences in the long-term efficacy for PD on motor symptoms were not observed.
Effects of spironolactone in heart failure with preserved ejection fraction

Background Heart failure with preserved ejection fraction (HFpEF) is a common syndrome, accounting for more than one half of all heart failure patients, which is associated with high morbidity and mortality. But there is little evidence-based therapeutic strategies for the management of HFpEF. Previous studies reported the effects of spironolactone on HFpEF; however, the results were inconsistent. In this meta-analysis, we evaluated the effects of spironolactone on HFpEF. Methods Articles were searched on PubMed, EMBASE, and COCHRANE databases before May, 2017, and were supplemented by hand searches of reference lists of included studies and review articles. Eligible articles were restricted to randomized controlled trials (RCTs). The odds ratios (ORs) of the dichotomous data, mean difference (MD) of continuous data, and 95% confidence intervals (CIs) were calculated to assess the effects of spironolactone in patients with HFpEF. Results A total of 7 studies including 4147 participants were analyzed. There were significant improvements on the E/e′ index (MD −1.38; 95% CI, −2.03 to −0.73; P < .0001) and E/A velocity ratio (MD −0.05; 95% CI, −0.10 to −0.00; P = .03) under spironolactone treatment compared with placebo, while there was no effect on the deceleration time (MD 1.04; 95% CI, −8.27 to 10.35; P = .83). Subgroup analyses on the E/A velocity ratio showed that there was obvious benefit from spironolactone therapy in patients with follow-up periods >6 months but not in those with follow-up periods ⩽6 months. There was no reduction in all-cause mortality and hospitalization compared with placebo. And no improvement in 6-minute walk distance was seen compared with placebo. Conclusion This meta-analysis demonstrates that the use of spironolactone improves left ventricular diastolic function in patients with HFpEF, whereas it has no effect on all-cause mortality and hospitalization, and the 6-minute walk distance. Further larger size, multicenter, RCTs are required to confirm the effects of spironolactone on patients with HFpEF.
The role of social support in the association between childhood trauma and depression among HIV-infected and HIV-uninfected individuals

Childhood trauma (CT) – emotional, physical or sexual abuse, or emotional or physical neglect – has been associated with HIV infection and can lead to poor health outcomes and depression in adulthood. Though the impact of CT on depression may be decreased by social support, this may not be true of individuals living with HIV, due to the additive traumatic effects of both CT and acquisition of HIV. This study examined social support, depression, and CT among HIV-infected (n = 134) and HIV-uninfected (n = 306) men and women. Participants (N = 440) were assessed regarding sociodemographic characteristics, CT, depression, and social support. Participants were racially and ethnically diverse, 36 ± 9 years of age on average, and 44% had an income of less than USD$500 a month. Among HIV-uninfected individuals, social support explained the association between depression in persons with CT (b = 0.082, bCI [0.044, 0.130]). Among HIV-infected individuals, after accounting for sociodemographic characteristics, social support did not explain the association between depression and CT due to lower levels of social support among HIV-infected individuals [95% CI: −0.006, 0.265]. The quality of social support may differ among HIV-infected persons due to decreased social support and smaller social networks among those living with HIV. Depressive symptoms among those living with HIV appear to be less influenced by social support, likely due to the additive effects of HIV infection combined with CT.
Long non-coding RNA MEG3 suppresses survival, migration, and invasion of cervical cancer

Background Long non-coding RNAs nowadays emerge as important biomarkers or potential therapeutic targets discussed in human cancers. Among them, maternally expressed gene 3 (MEG3) is known to be decreased in a variety of malignancies, and this affects tumor cellular proliferation, migration, and invasion. Materials and methods Quantitative real-time PCR was performed to detect the expression of MEG3 in normal cervical epithelium, cervical intraepithelial neoplasia, and cervical squamous cell carcinoma tissues. Gain-of-function and loss-of-function studies were carried out to determine the effect of MEG3 on cell survival, migration, and invasion, which was evaluated by CCK-8 assay, wound healing assay, and transwell assays. mRNA and protein expression of Rac1 were finally determined by quantitative real-time PCR and immunoblotting, respectively. In addition, rescue experiments were performed by overexpression of Rac1. Results The expression of MEG3 was downregulated in cervical intraepithelial neoplasia and squamous cell carcinoma tissues. Forced expression of MEG3 led to reduced abilities of cell survival. Overexpression of MEG3 also inhibited cell migration and invasion in vitro. Cell proliferation marker and EMT markers were changed consistently with the phenotype. In addition, Rac1 was inhibited by MEG3 overexpression at both transcriptional and translational levels. Also, Rac1 could rescue the phenotype caused by long non-coding RNA MEG3. And, it negatively correlated with MEG3 expression in cervical cancer (CC) tissues and cell lines. Conclusion Our findings revealed that MEG3 could negatively regulate CC cell survival, migration, and invasion. It might serve as an important target for CC treatment.