Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and Characterization of Clinical Listeria monocytogenes in Beijing, China, 2014–2016

Listeria monocytogenes is an important foodborne pathogen with a significant impact on public health worldwide. A great number of outbreaks caused by L. monocytogenes has been reported, especially in the United States, and European countries. However, listeriosis has not yet been included in notifiable disease in China, and thus information on this infection has been scarce among the Chinese population. In this study, we described a 3-year surveillance of listeriosis in Beijing, China. Fifty-six L. monocytogenes strains isolated from 49 clinical infectious cases (27 pregnancy-associated infections and 22 non-pregnancy-associated infections) were analyzed by serotyping, pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and antimicrobial susceptibility testing between 2014 and 2016 in Beijing. The predominant serogroups were 1/2a,3a and 1/2b,3b,7 which accounted for 92% of the overall isolates. Four strains were serogroup 4b,4d,4e, isolated from patients with pregnancy-associated infections. Based on PFGE, these isolates were divided into 32 pulsotypes (PTs) and 3 clusters associated with serogroups. Ten PTs were represented by more than one isolate with PT09 containing the most number of isolates. MLST differentiated the isolates into 18 STs, without new ST designated. The three most common STs were ST8 (18.4%), ST5 (16.3%), and ST87 (12.2%), accounting for 46.9% of the isolates. STs prevalent in other parts of the world were also present in China such as ST1, ST2, ST5, ST8, and ST9 which caused maternal fetal infections or outbreaks. However, the STs and serogroup distribution of clinical L. monocytogenes in Beijing, China was different from those in other countries. Strains of ST1 and ST2 were isolated from patients with pregnancy-associated infection, whereas none of ST155 isolates caused pregnancy-associated cases. Surveillance of molecular characterization will provide important information for prevention of listeriosis. This study also enhances our understanding of genetic diversity of clinical L. monocytogenes in China.
Desiccation tolerance in Physcomitrella patens: Rate of dehydration and the involvement of endogenous abscisic acid (ABA).

The moss Physcomitrella patens, a model system for basal land plants, tolerates several abiotic stresses, including dehydration. We previously reported that Physcomitrella patens survives equilibrium dehydration to -13 MPa in a closed system at 91% RH. Tolerance of desiccation to water potentials below -100 MPa was only achieved by pretreatment with exogenous abscisic acid (ABA). We report here that gametophores, but not protonemata, can survive desiccation below -100 MPa after a gradual drying regime in an open system, without exogenous ABA. In contrast, faster equilibrium drying at 90% RH for 3-5 days did not induce desiccation tolerance in either tissue. Endogenous ABA accumulated in protonemata and gametophores under both drying regimes, so did not correlate directly with desiccation tolerance. Gametophores of a Ppabi3a/b/c triple knock out transgenic line also survived the gradual dehydration regime, despite impaired ABA signaling. Our results suggest that the initial drying rate, and not the amount of endogenous ABA, may be critical in the acquisition of desiccation tolerance. Results from this work will provide insight into ongoing studies to uncover the role of ABA in the dehydration response and the underlying mechanisms of desiccation tolerance in this bryophyte.
The Most Rapidly Declining Type I Supernova 2019bkc/ATLAS19dqr

We report observations of the hydrogen-deficient supernova (SN) 2019bkc/ATLAS19dqr. With B- and r-band decline between peak and 10 days post peak of mag and mag, respectively, SN 2019bkc is the most rapidly declining SN I discovered so far. While its closest matches are the rapidly declining SN 2005ek and SN 2010X, the light curves and spectra of SN 2019bkc show some unprecedented characteristics. SN 2019bkc appears “hostless,” with no identifiable host galaxy near its location, although it may be associated with the galaxy cluster MKW1 at z = 0.02. We evaluate a number of existing models of fast-evolving SNe, and we find that none of them can satisfactorily explain all aspects of SN 2019bkc observations.
Characteristics of client-identified helpful events in emotion-focused therapy for child abuse trauma

Abstract This study investigated the characteristics of client-identified helpful events (n=29) in emotion-focused therapy for child abuse trauma (EFTT). Helpful events (HE) were identified on the Helpful Aspects of Therapy Questionnaire and in Post Therapy Interviews, located in video-taped therapy sessions, and compared to researcher-defined control events (CE) for each client. Results indicated a greater focus on childhood abuse (particularly during the imaginal confrontation procedure), higher levels of emotional arousal, and comparable alliance quality in HE compared to CE. HE contained deeper levels of experiencing compared to CE, but only for clients who achieved the greatest depth of experiencing. Client perspectives converged with theory and research on change processes in EFTT and have implications for practice and training.
Reduced Upper Limb Recovery in Subcortical Stroke Patients With Small Prior Radiographic Stroke

Background: Research imaging costs limit lesion-based analyses in already expensive large stroke rehabilitation trials. Despite the belief that lesion characteristics influence recovery and treatment response, prior studies have not sufficiently addressed whether lesion features are an important consideration in motor rehabilitation trial design. Objective: Using clinically-obtained neuroimaging, evaluate how lesion characteristics relate to upper extremity (UE) recovery and response to therapy in a large UE rehabilitation trial. Methods: We reviewed lesions from 297 participants with mild-moderate motor impairment in the Interdisciplinary Comprehensive Arm Rehabilitation Evaluation (ICARE) study and their association with motor recovery, measured by the UE Fugl-Meyer (UE-FM). Significant lesion features identified on correlational and bivariate analysis were further analyzed for associations with recovery and therapy response using longitudinal mixed models. Results: Prior radiographic stroke was associated with less recovery on UE-FM in participants with motor impairment from subsequent subcortical stroke (−5.8 points) and in the overall sample (−3.6 points), but not in participants with cortical or mixed lesions. Lesion volume was also associated with less recovery, particularly after subcortical stroke. Every decade increase in age was associated with 1 less point of recovery on UE-FM. Response to specific treatment regimens varied based on lesion characteristics. Subcortical stroke patients experienced slightly less recovery with higher doses of upper extremity task-oriented training. Participants with cortical or mixed lesions experienced more recovery with higher doses of usual and customary therapy. Other imaging features (leukoaraiosis, ischemic vs. hemorrhagic stroke) were not significant. Conclusions: ICARE clinical imaging revealed information useful for UE motor trial design: stratification of persons with and without prior radiographic stroke may be required in participants with subcortical stroke, the majority of motor rehabilitation trial participants. Most of the prior radiographic strokes were small and cortically-based, suggesting even minor prior brain injury remote to the acute stroke lesion may limit spontaneous and therapy-related recovery. Lesion location may be associated with response to different therapy regimens, but the effects are variable and of unclear significance.
The Transition from a Phytopathogenic Smut Ancestor to an Anamorphic Biocontrol Agent Deciphered by Comparative Whole-Genome Analysis[W][OPEN]

This work examines the relationship between the biocontrol agent Pseudozyma flocculosa and its fungal relatives, including the pathogen Ustilago maydis, finding subtle yet crucial genetic differences that may explain the nonpathogenic nature of P. flocculosa, including loss of a specific subset of candidate secreted effector proteins. Pseudozyma flocculosa is related to the model plant pathogen Ustilago maydis yet is not a phytopathogen but rather a biocontrol agent of powdery mildews; this relationship makes it unique for the study of the evolution of plant pathogenicity factors. The P. flocculosa genome of ∼23 Mb includes 6877 predicted protein coding genes. Genome features, including hallmarks of pathogenicity, are very similar in P. flocculosa and U. maydis, Sporisorium reilianum, and Ustilago hordei. Furthermore, P. flocculosa, a strict anamorph, revealed conserved and seemingly intact mating-type and meiosis loci typical of Ustilaginales. By contrast, we observed the loss of a specific subset of candidate secreted effector proteins reported to influence virulence in U. maydis as the singular divergence that could explain its nonpathogenic nature. These results suggest that P. flocculosa could have once been a virulent smut fungus that lost the specific effectors necessary for host compatibility. Interestingly, the biocontrol agent appears to have acquired genes encoding secreted proteins not found in the compared Ustilaginales, including necrosis-inducing-Phytophthora-protein- and Lysin-motif- containing proteins believed to have direct relevance to its lifestyle. The genome sequence should contribute to new insights into the subtle genetic differences that can lead to drastic changes in fungal pathogen lifestyles.
Epilepsy in Leigh Syndrome With Mitochondrial DNA Mutations

Background: Leigh syndrome is a mitochondrial cytopathy that presents as a neurodegenerative disease with apparent manifestation in the central nervous system. The aim of the present study was to describe its dominant neurological clinical features and analyze data related to epilepsy in Leigh syndrome accompanied by a mitochondrial DNA mutation. Methods: Whole mitochondrial sequencing was performed on 125 patients clinically suspected of Leigh syndrome. Among them, 25 patients were identified to have mitochondrial DNA associated Leigh syndrome. Electroencephalography (EEG) findings, semiology, brain imaging findings, and biochemical results, were evaluated. We also compared brain magnetic resonance imaging findings and biochemical features in patients with Leigh syndrome based on the presence of epilepsy. Results: Clinical seizures were observed in 14 out of 25 enrolled patients (56%), with focal seizures being the most common type (6/14, 42.8%). All patients were found to have slow and disorganized background neural activity while eight exhibited epileptic discharges on EEG. Mutations at base pairs 10,191 and 8,993 were revealed in a relatively larger number of patients of Leigh syndrome with epilepsy. The presence of gastrointestinal symptoms was significantly more frequent in the epilepsy group (P = 0.042). Diffuse cerebral atrophy was significantly increased (P = 0.042) and cortex signal abnormalities were also increased (P = 0.033) in the epilepsy group. Conclusions: Patients with Leigh syndrome and mitochondrial DNA mutations had a high proportion of central nervous system comorbidities, though the prevalence of epilepsy in this population was not particularly high. Various types of seizure and EEG findings are common in those with Leigh syndrome. Future imaging studies involving more patients and proper mitochondrial DNA mutation analyses are needed to further evaluate the natural course of Leigh syndrome with epilepsy.
Recurrent inhibition is decreased in patients with amyotrophic lateral sclerosis

Recurrent inhibitory pathways are powerful modulators of motor neuron excitability. Renshaw cell activation can both inhibit homologous motor neurons and disinhibit antagonists. In spastic spinal-cord-injured patients, recurrent inhibition is consistently increased, and clinical reductions in spasticity are associated with reduced recurrent inhibition. In this study, we evaluated 12 spastic patients with amyotrophic lateral sclerosis (ALS) to see whether a similar mechanism was operating. In contrast to spinal-cord-injured patients, spastic patients with ALS showed strikingly reduced recurrent inhibition, as assessed by a conditioned H-reflex technique, which produces a response (H') whose amplitude is inversely correlated with activity in recurrent inhibitory pathways. The mean ratio of the maximum H' response to the maximum H-reflex response (H'/H ratio) was 0.55, significantly greater than the ratio seen in normal subjects. Amplitude of the H' correlated with amplitude of the Achilles tendon reflex. Thus, in patients with classical ALS, recurrent inhibition appears to be abnormally reduced compared with control subjects, suggesting a different physiology for spasticity in this setting than in spinal cord transection.
Distributed Construction of Light Networks

A t-spanner H of a weighted graph G = (V, E, w) is a subgraph that approximates all pairwise distances up to a factor of t. The lightness of H is defined as the ratio between the weight of H to that of the minimum spanning tree. An (α, β)-Shallow Light Tree (SLT) is a tree of lightness β, that approximates all distances from a designated root vertex up to a factor of α. A long line of works resulted in efficient algorithms that produce (nearly) optimal light spanners and SLTs. Some of the most notable algorithmic applications of light spanners and SLTs are in distributed settings. Surprisingly, so far there are no known efficient distributed algorithms for constructing these objects in general graphs. In this paper we devise efficient distributed algorithms in the CONGEST model for constructing light spanners and SLTs, with near optimal parameters. Specifically, for any k ≥ 1 and 0 < ∈ < 1, we show a (2k − 1) · (1 + ∈)-spanner with lightness O(k·n1/k) can be built in [EQUATION] rounds (where n = |V| and D is the hop-diameter of G). In addition, for any α > 1 we provide an [EQUATION] rounds. The running times of our algorithms cannot be substantially improved. We also consider spanners for the family of doubling graphs, and devise a [EQUATION] rounds algorithm in the CONGEST model that computes a (1 + ∈)-spanner with lightness (log n)/∈O(1). As a stepping stone, which is interesting in its own right, we first develop a distributed algorithm for constructing nets (for arbitrary weighted graphs), generalizing previous algorithms that worked only for unweighted graphs.
Respiratory Fluoroquinolones Monotherapy vs. β-Lactams With or Without Macrolides for Hospitalized Community-Acquired Pneumonia Patients: A Meta-Analysis

Background: The choice of empirical antibiotic treatment for patients with community-acquired pneumonia (CAP) who are admitted to non-intensive care unit (ICU) hospital wards is complicated by the limited availability of evidence. We systematically reviewed the efficacy and safety of strategies of empirical treatment with respiratory fluoroquinolone monotherapy and β-lactam with or without macrolide for non-ICU hospitalized CAP patients. Methods: We searched databases including PubMed, the Cochrane Library (Issue11, 2018), EMbase, China National Knowledge Internet (CNKI), WanFang Data, VIP, and China Biology Medicine disc (CBMdisc) to identify randomized controlled trials (RCTs) involving the comparison of respiratory fluoroquinolone monotherapy and β-lactam with or without macrolide for the non-ICU hospitalized patients with CAP up to November 2018. Two reviewers independently screened literature according to the inclusion and exclusion criteria, extracted data, and assessed the risk of bias of the included studies. A meta-analysis was performed with the outcomes. Results: A total of 22 studies involving 6,235 patients were included. The results of the meta-analysis showed a non-significant trend toward an advantage to the respiratory fluoroquinolone in overall mortality (RR 0.82, 95% CI 0.65–1.02). No significant difference was found between the two strategies in clinical success (the intention-to-treat population: RR 1.03, 95% CI 0.99–1.08; the clinically evaluable population: RR 1.03, 95% CI 0.999–1.055; the population in which it was unclear whether intention-to-treat or per-protocol analysis was used: RR 1.04, 95% CI 0.99–1.09), microbiological treatment success (RR 1.04, 95% CI 0.997–1.092), and length of stay (SMD −0.06, 95% CI −0.16 to 0.04). The advantage of respiratory fluoroquinolone was statistically significant on the drug-related adverse events (RR 0.87, 95% CI 0.77–0.97). Conclusions: Current evidence shows that fluoroquinolone monotherapy has similar efficacy and favorable safety compared with β-lactam with or without macrolide for non-ICU hospitalized CAP patients. Since the limitation of region, quantity and quality of included studies, more RCTs with large scale and high quality are needed to verify the above conclusion.
An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens

The adaptation of rhizobia from the free-living state in soil to the endosymbiotic state comprises several physiological changes in order to cope with the extremely low oxygen availability (microoxia) within nodules. To uncover cellular functions required for bacterial adaptation to microoxia directly at the protein level, we applied a systems biology approach on the key rhizobial model and soybean endosymbiont Bradyrhizobium diazoefficiens USDA 110 (formerly B. japonicum USDA 110). As a first step, the complete genome of B. diazoefficiens 110spc4, the model strain used in most prior functional genomics studies, was sequenced revealing a deletion of a ~202 kb fragment harboring 223 genes and several additional differences, compared to strain USDA 110. Importantly, the deletion strain showed no significantly different phenotype during symbiosis with several host plants, reinforcing the value of previous OMICS studies. We next performed shotgun proteomics and detected 2,900 and 2,826 proteins in oxically and microoxically grown cells, respectively, largely expanding our knowledge about the inventory of rhizobial proteins expressed in microoxia. A set of 62 proteins was significantly induced under microoxic conditions, including the two nitrogenase subunits NifDK, the nitrogenase reductase NifH, and several subunits of the high-affinity terminal cbb3 oxidase (FixNOQP) required for bacterial respiration inside nodules. Integration with the previously defined microoxia-induced transcriptome uncovered a set of 639 genes or proteins uniquely expressed in microoxia. Finally, besides providing proteogenomic evidence for novelties, we also identified proteins with a regulation similar to that of FixK2: transcript levels of these protein-coding genes were significantly induced, while the corresponding protein abundance remained unchanged or was down-regulated. This suggested that, apart from fixK2, additional B. diazoefficiens genes might be under microoxia-specific post-transcriptional control. This hypothesis was indeed confirmed for several targets (HemA, HemB, and ClpA) by immunoblot analysis.
A Common Substitution ( Asn 291 Ser ) in Lipoprotein Lipase Is Associated with Increased Risk of Ischemic Heart Disease

Lipoprotein lipase degrades triglycerides in plasma and as a byproduct produces HDL particles. Genetic variation in lipoprotein lipase may therefore affect cardiovascular risk. We tested 9,214 men and women from a general population sample and 948 patients with ischemic heart disease for the Asn291Ser substitution in lipoprotein lipase. The allele frequency in the general population was 0.024 and 0.026 for women and men, respectively. In comparison with noncarriers, female heterozygous probands had increased plasma triglycerides ( D 5 0.23 mmol/liter), while HDL cholesterol was reduced in both female and male carriers ( D 5 0.18 mmol/liter and D 5 0.11 mmol/liter, respectively). A similar phenotype was found in six homozygous carriers. On multiple logistic regression analysis, plasma triglycerides and HDL cholesterol were independent predictors of ischemic heart disease in both genders. On univariate analysis, odds ratios for ischemic heart disease in probands were 1.89 in women (95% CI: 1.19–3.01) and 0.90 in men (95% CI: 0.62–1.31), and on multivariate analysis were 1.98 in women (95% CI: 1.11–3.53) and 1.02 in men (95% CI: 0.65–1.60). This study demonstrates that a single common mutation in the lipoprotein lipase gene is associated with elevated plasma triglycerides and reduced HDL cholesterol levels, whereby carriers, in particular women, seem to be predisposed to ischemic heart disease. It cannot be excluded, however, that male carriers of this substitution may represent a subset of low-HDL individuals without raised triglycerides not predisposed to ischemic heart disease. ( J. Clin. Invest. 1997. 99:1606–1613.)
Testing for the presence of positive-outcome bias in peer review: a randomized controlled trial.

BACKGROUND If positive-outcome bias exists, it threatens the integrity of evidence-based medicine. METHODS We sought to determine whether positive-outcome bias is present during peer review by testing whether peer reviewers would (1) recommend publication of a "positive" version of a fabricated manuscript over an otherwise identical "no-difference" version, (2) identify more purposefully placed errors in the no-difference version, and (3) rate the "Methods" section in the positive version more highly than the identical "Methods" section in the no-difference version. Two versions of a well-designed randomized controlled trial that differed only in the direction of the finding of the principal study end point were submitted for peer review to 2 journals in 2008-2009. Of 238 reviewers for The Journal of Bone and Joint Surgery and Clinical Orthopaedics and Related Research randomly allocated to review either a positive or a no-difference version of the manuscript, 210 returned reviews. RESULTS Reviewers were more likely to recommend the positive version of the test manuscript for publication than the no-difference version (97.3% vs 80.0%, P < .001). Reviewers detected more errors in the no-difference version than in the positive version (0.85 vs 0.41, P < .001). Reviewers awarded higher methods scores to the positive manuscript than to the no-difference manuscript (8.24 vs 7.53, P = .005), although the "Methods" sections in the 2 versions were identical. CONCLUSIONS Positive-outcome bias was present during peer review. A fabricated manuscript with a positive outcome was more likely to be recommended for publication than was an otherwise identical no-difference manuscript.
Significance of PTEN Mutation in Cellular Process, Prognosis, and Drug Selection in Clear Cell Renal Cell Carcinoma

It is well established that the PTEN (Phosphatase and Tensin Homolog) mutant is a frequently mutated gene found in clear cell renal cell carcinoma (ccRCC), making it a potential biomarker for individualized treatment opinions. Here, in the present study, we designed a method to evaluate the significance of the PTEN mutation in the prognosis and drug selection of ccRCC, determine the potential changing pathways and genes associated with the mechanisms. The most recent TCGA data shows that the PTEN mutation is found in 5% of ccRCC patients. In total, 2,569 genes were identified as DEGs. GO and KEGG analysis suggested that DEGs were significantly enriched in categories associated with cell division and multiple metabolic progressions. The top 10 genes, ranked by degree, were identified as hub genes from the protein–protein interaction network (PPI). What is more, patients with the PTEN mutation were associated with a worsened prognosis of ccRCC. Data from the GDSC database indicated that the selective AKT inhibitor, GSK690693, is a selective inhibitor for ccRCC with the PTEN mutation. Our findings have indicated that multiple genes and pathways may play a crucial role in PTEN mutation ccRCC, offering candidate targets and strategies for PTEN mutation ccRCC individualized treatment.