bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chinese herbal medicine for varicocele in subfertile men A protocol for systematic review and meta-analysis
Authors: Tong Wenting , Zhao Zhimin , Tu Xuchong , He Shan , Wang Yongxing , Chen Ming , Zhang Hui 
Published: January 2023

AbstractBackgroundThe purpose of this protocol is to provide a updated systematic review and meta-analysis to prove the effectiveness and safety of Chinese herbal medicine in the treatment for the patients with varicocele.MethodThis protocol conforms to the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) and the recommendations of the Cochrane Collaboration Handbook. We selected qualified studies published as of May 1, 2022, and systematically searched 6 English database (Embase, Pubmed, Scopus, Web of Science, Cochrane Central of Controlled Trials (CENTRAL), andClinicaltrials.gov) and 5 Chinese database (China National Knowledge Infrastructure (CNKI), VIP Database for Chinese Technical Periodicals, Wanfandata, SinoMed, and Chinese Clinical Trial Registry). At the same time, relevant reviews and a list of references included in the study were retrieved, and Epistemonikos.org, ISI Web of Science and OpenGrey were manually searched to screen any other studies not included in the previous search. There will be no language restrictions. The inclusion criteria were clinical randomized controlled trial (RCT) involving the use of traditional Chinese medicine in the treatment of varicocele. The main results were fertility rate, adverse events, semen quality and scrotal pain score after 3 months, 6 months and 1 year follow-up. Bias analysis and evaluation will be performed based on risk of bias (ROB) assessment tool provided by the Cochrane Handbook. And use GRADEpro GDT to grade, evaluate and score the quality of the evidence. Heterogeneity will be judged by I2value. At the same time, report bias assessment, subgroup analysis and sensitivity analysis were carried out. According to the Cochrane Manual of Systematic Evaluation of Interventions (Higgins 2011), if the data showed sufficiently high quality and some degree of similarity, we included the data for the meta-analysis. For dichotomy data, we selected an effect scale relative risk (RR) represented by a 95% confidence interval (CI). The continuous data is expressed as mean difference (MD) or standardized mean difference (SMD).ResultThis study will provide high-quality evidence for the efficacy and safety of Chinese herbal medicine in the treatment of varicocele in subfertile men.ConclusionThis study will provide an effective and safe choice for Chinese herbal medicine to improve the fertility of patients with varicocele.EthicsThe data of this study are based on published studies and do not require additional ethical approval. We will publish our findings through peer-reviewed journals.PROSPERO database registration number: CRD42022331218
Magnitude of work-related musculoskeletal disorders and ergonomic risk practices among medical laboratory professionals in Northwest Ethiopia: A cross-sectional study
Authors: Alibsew Mekuriaw Temeche , Molla Habtamu , Shiferaw Melashu Balew , Misganaw Abay Sisay 
Published: January 2023

AbstractObjectiveThis study aimed to assess the magnitude of work-related musculoskeletal disorders (WMSDs) and ergonomic risk practices among medical laboratory professionals in North West Ethiopia.DesignFacility-based cross-sectional studyMethodsCross-sectional study design was employed among medical laboratory professionals (MLPs). The Nordic musculoskeletal questionnaire was adopted and used. In addition to questionnaires about socio-demographic characteristics and ergonomic risk practice, one-to-one interviews, and a direct observational checklist were used. Data was entered into Epi Data 3.1 and then exported and analyzed using SPSS version 25.0. Logistic regression analysis was used to estimate the 95% CI (AOR) at a cut-off value of p <0.05 for statistically significant tests.ResultsA total of 238 MLPs participated in the study. The magnitude of WMSDs was 116(48.7%). The most affected body parts were the lower back (20.6%) and wrists (16.4%). The magnitude of WMSDs among government-owned hospitals was the highest (56.4%). 67.6% MLPs never heard about ergonomics. The general mean score of workstations was 2.28. Ergonomic risk practices like repetitive movement and doing of high workload were significantly associated with WMSDs.ConclusionThe current findings revealed a high magnitude of WMSDs that strongly need applying preventive action before body symptoms developed. Improving and renovating workplace design and enhancing awareness of MLPs were the necessary measures to control ergonomic risk factors.
National Trends and Resource Utilization Associated with Penetrating Trauma Recidivism
Authors: Cho Nam Yong , Mabeza Russyan Mark , Bakhtiyar Syed Shahyan , Richardson Shannon , Ali Konmal , Tran Zachary , Benharash Peyman 
Published: January 2023

ABSTRACTBACKGROUNDWhile recurrent penetrating trauma has been associated with long-term mortality and disability, national data on factors associated with reinjury remain limited. We examined temporal trends, patient characteristics, and resource utilization associated with repeat firearm-related or stab injury across the US.METHODSThe 2010-2019 Nationwide Readmissions Database was queried to identify all hospitalizations for penetrating trauma. Recidivism was defined as those returned for subsequent penetrating injury within 60 days. We quantified injury severity using the International Classification of Diseases Trauma Mortality Prediction model. Trends in recidivism, length of stay (LOS), hospitalization costs, and rate of non-home discharge were then analyzed. Multivariable regression models were developed to assess the association of recidivism with outcomes of interest.RESULTSOf an estimated 968,717 patients (28.4% Gunshot, 71.6% Stab), 2.1% experienced recidivism within 60 days of initial injury. From 2010 to 2019, trauma recidivism of gunshot wound increased in annual incidence while that of stab remained stable. Patients experiencing penetrating trauma recidivism were more commonly male, younger and insured by Medicaid. Patients with recidivism had shorter index LOS, lower median index hospitalization cost and higher rates of non-home discharge. After risk adjustment, penetrating trauma recidivism was associated with significantly higher hospitalization costs, shorter time before readmission, and increased odds of non-home discharge. In addition, comorbid conditions of hypothyroidism and psychoses were associated with greater likelihood of stab wound recidivism.CONCLUSIONThe trend in penetrating trauma recidivism has been on the rise for the past decade. National efforts to improve post-discharge prevention and social support services for patients with penetrating trauma are warranted and may reduce the burden of recidivism.
Robotics-driven manufacturing of cartilaginous microtissues for the bio-assembly of skeletal implants
Authors: Decoene Isaak , Nasello Gabriele , de Costa Rodrigo Furtado Madeiro , Hall Gabriella Nilsson , Pastore Angela , Van Hoven Inge , Viseu Samuel Ribeiro , Verfaillie Catherine , Geris Liesbet , Luyten Frank P. , Papantoniou Ioannis 
Published: January 2023

AbstractAutomated technologies are attractive for enhancing a robust manufacturing of tissue engineered products for clinical translation. In this work, we present an automation strategy using a robotics platform for media changes of cartilaginous microtissues cultured in static microwell platforms. We use an automated image analysis pipeline to extract microtissue displacements and morphological features, which serve as input for statistical factor analysis. To minimize microtissue displacement and suspension leading to uncontrolled fusion, we performed a mixed factorial DoE on liquid handling parameters for large and small microwell platforms.As a result, 144 images, with 51 471 spheroids could be processed automatically. The automated imaging workflow takes 2 minutes per image, and it can be implemented for on-line monitoring of microtissues, thus allowing informed decision making during manufacturing. We found that time in culture is the main factor for microtissue displacements, explaining 10 % of the displacements. Aspiration and dispension speed were not significant at manual speeds or beyond, with an effect size of 1 %. We defined optimal needle placement and depth for automated media changes and we suggest that robotic plate handling could improve the yield and homogeneity in size of microtissue cultures. After three weeks culture, increased expression of COL2A1 confirmed chondrogenic differentiation and RUNX2 shows no osteogenic specification. Histological analysis showed the secretion of cartilaginous extracellular matrix. Furthermore, microtissue-based implants were capable of forming mineralized tissues and bone after four weeks of ectopic implantation in nude mice.We demonstrate the development of an integrated bioprocess for culturing and manipulation of cartilaginous microtissues. We anticipate the progressive substitution of manual operations with automated solutions for manufacturing of microtissue-based living implants.
Assessing the burden of rare DNA methylation deviations in schizophrenia
Authors: Hansen Christine Søholm , McQuillin Andrew , St Claire David , Mill Jonathan , Hannon Eilis , Sharp Andrew J. , Janecka Magdalena 
Published: January 2023

AbstractAlong with case-control group differences in DNA methylation (DNAm) identified in epigenomewide association studies (EWAS), multiple rare DNAm outliers may exist in subsets of cases, underlying the etiological heterogeneity of some disorders. This creates an impetus for novel approaches focused on detecting rare/private outliers in the individual methylomes. Here, we present a novel, data-driven method - Outlier Methylation Analysis (OMA) – which through optimization detects genomic regions with strongly deviating DNAm levels, which we call outlier methylation regions (OMRs).Focusing on schizophrenia (SCZ) - a neuropsychiatric disorder with a heterogeneous etiology – we applied the OMA method in two independent, publicly available SCZ case-control samples with DNAm array information. We found SCZ cases had an increased burden of OMRs compared to controls (IRR=1.22, p=1.8×10-8), and case OMRs were enriched in regions relevant to cellular differentiation and development (i.e. polycomb repressed elements in the Gm12878 differentiated cell line, p=1.9×10-5, and poised promoters in the H1hesc stem cell line, p=5.4×10-4). Furthermore, SCZ cases were ~2.5-fold enriched (p=1.1×10-3) for OMRs overlapping genesets associated with developmental processes. The OMR burden was reduced in clozapine-treated, compared to untreated, SCZ cases (IRR=0.88, p=9.5×10-3), and also associated with increased chronological age (IRR=1.01, p= 2.7×10-16).Our findings demonstrate an elevated burden of OMRs in SCZ, implying methylomic dysregulation in SCZ which could correspond to the etiological heterogeneity among cases. These results remain to be causally examined and replicated in other cohorts and tissues. For this, and applications in other traits, we offer the OMA method to the scientific community.
Mapping multidimensional content representations to neural and behavioral expressions of episodic memory
Authors: Wang Yingying , Lee Hongmi , Kuhl Brice A. 
Published: January 2023

AbstractHuman neuroimaging studies have shown that the contents of episodic memories are represented in distributed patterns of neural activity. However, these studies have mostly been limited to decoding simple, unidimensional properties of stimuli. Semantic encoding models, in contrast, offer a means for characterizing the rich, multidimensional information that comprises episodic memories. Here, we extensively sampled four human fMRI subjects to build semantic encoding models and then applied these models to reconstruct content from natural scene images as they were viewed and recalled from memory. First, we found that multidimensional semantic information was successfully reconstructed from activity patterns across visual and lateral parietal cortices, both when viewing scenes and when recalling them from memory. Second, whereas visual cortical reconstructions were much more accurate when images were viewed versus recalled from memory, lateral parietal reconstructions were comparably accurate across visual perception and memory. Third, by applying natural language processing methods to verbal recall data, we showed that fMRI-based reconstructions reliably matched subjects’ verbal descriptions of their memories. In fact, reconstructions from ventral temporal cortex more closely matched subjects’ own verbal recall than other subjects’ verbal recall of the same images. Fourth, encoding models reliably transferred across subjects: memories were successfully reconstructed using encoding models trained on data from entirely independent subjects. Together, these findings provide evidence for successful reconstructions of multidimensional and idiosyncratic memory representations and highlight the differential sensitivity of visual cortical and lateral parietal regions to information derived from the external visual environment versus internally-generated memories.
Evolutionary transcriptomics reveals longevity mostly driven by polygenic and indirect selection in mammals
Authors: Liu Weiqiang , Zhu Pingfen , Li Meng , Li Zihao , Yu Yang , Liu Gaoming , Du Juan , Wang Xiao , Yang Jing , Tian Ran , Seim Inge , Kaya Alaattin , Li Mingzhou , Li Ming , Gladyshev Vadim N. , Zhou Xuming 
Published: January 2023

AbstractThe maximum lifespan varies more than 100-fold in mammals. This experiment of nature may uncover of the evolutionary forces and molecular features that define longevity. To understand the relationship between gene expression variation and maximum lifespan, we carried out a comparative transcriptomics analysis of liver, kidney, and brain tissues of 106 mammalian species. We found that expression is largely conserved and very limited genes exhibit common expression patterns with longevity in all the three organs analyzed. However, many pathways, e.g., “Insulin signaling pathway”, and “FoxO signaling pathway”, show accumulated correlations with maximum lifespan across mammals. Analyses of selection features further reveal that methionine restriction related genes whose expressions associated with longevity, are under strong selection in long-lived mammals, suggesting that a common approach could be utilized by natural selection and artificial intervention to control lifespan. These results suggest that natural lifespan regulation via gene expression is likely to be driven through polygenic model and indirect selection.
Multiplexed Methylated DNA Immunoprecipitation Sequencing (Mx-MeDIP-Seq) to Study DNA Methylation Using Low Amounts of DNA
Authors: Ridha Inam , Xu Chenxi , Chung Yunro , Park Jin G , LaBaer Joshua , Murugan Vel 
Published: January 2023

AbstractDNA methylation is an epigenetic mark that has a crucial role in regulating gene expression. Aberrant DNA methylation results in severe diseases in humans, such as cancer, autoimmune disease, atherosclerosis, and cardiovascular diseases. Whole-genome bisulfite sequencing and methylated DNA immunoprecipitation are available to study DNA methylation changes, but they are typically used on a few samples at a time. Here, we developed a novel method called Multiplexed Methylated DNA Immunoprecipitation Sequencing (Mx-MeDIP-Seq), that can be used to analyze many DNA samples in parallel, requiring only small amounts of input DNA. In this method, 10 different DNA samples were fragmented, purified, barcoded, and pooled prior to immunoprecipitation. In a head-to-head comparison, we observed 99% correlation between MeDIP-Seq performed individually or combined as Mx-MeDIP-Seq. Moreover, multiplexed MeDIP led to more than 95% normalized percent recovery and a 25-fold enrichment ratio by qPCR, like the enrichment of the conventional method. This technique was successfully performed with as little as 25 ng of DNA, equivalent to 3400 to 6200 cells. Up to 10 different samples were processed simultaneously in a single run. Overall, the Mx-MeDIP-Seq method is cost-effective with faster processing to analyze DNA methylome, making this technique more suitable for high-throughput DNA methylome analysis.
SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
Authors: Pan Shaojun , Zhao Xing-Ming , Coelho Luis Pedro 
Published: January 2023

AbstractMotivationMetagenomic binning methods to reconstruct metagenome-assembled genomes (MAGs) from environmental samples have been widely used in large-scale metagenomic studies. The recently proposed semi-supervised binning method, SemiBin, achieved state-of-the-art binning results in several environments. However, this required annotating contigs, a computationally costly and potentially biased process.ResultsWe propose SemiBin2, which uses self-supervised learning to learn feature embeddings from the contigs. In simulated and real datasets, we show that self-supervised learning achieves better results than the semi-supervised learning used in SemiBin1 and that SemiBin2 outperforms other state-of-the-art binners. Compared to SemiBin1, SemiBin2 can reconstruct 8.3%–21.5% more high-quality bins and requires only 25% of the running time and 11% of peak memory usage in real short-read sequencing samples. To extend SemiBin2 to long-read data, we also propose ensemble-based DBSCAN clustering algorithm, resulting in 13.1%–26.3% more high-quality genomes than the second best binner for long-read data.Availability and ImplementationSemiBin2 is available as open source software athttps://github.com/BigDataBiology/SemiBin/and the analysis scripts used in the study can be found athttps://github.com/BigDataBiology/SemiBin2_benchmark.
Cyclic di-AMP traps proton-coupled K+transporters of the KUP family in an inward-occluded conformation
Authors: Fuss Michael F. , Wieferig Jan-Philip , Corey Robin A. , Hellmich Yvonne , Tascón Igor , Sousa Joana S. , Stansfeld Phillip J. , Vonck Janet , Hänelt Inga 
Published: January 2023

AbstractCyclic di-AMP is the only known essential second messenger in bacteria and archaea, regulating different proteins indispensable for numerous physiological processes. In particular, it controls various potassium and osmolyte transporters involved in osmoregulation. InBacillus subtilis, the K+/H+symporter KimA of the KUP family is inactivated by c-di-AMP. KimA sustains survival at potassium limitation at low external pH by mediating K+ions uptake. However, at elevated intracellular K+concentrations, further K+accumulation would be toxic. In this study, we reveal the molecular basis of how c-di-AMP binding inhibits KimA. We report cryo-EM structures of KimA with bound c-di-AMP in detergent solution and reconstituted in amphipols. By combining structural data with functional assays and molecular dynamics simulations we reveal how c-di-AMP modulates transport. We show that an intracellular loop in the transmembrane domain interacts with c-di-AMP bound to the adjacent cytosolic domain. This reduces the mobility of transmembrane helices at the cytosolic side of the K+binding site and therefore traps KimA in an inward-occluded conformation.
Fast and Accurate Cell Tracking: a real-time cell segmentation and tracking algorithm to instantly export quantifiable cellular characteristics from large scale image data
Authors: Chou Ting-Chun , You Li , Beerens Cecile , Feller Kate J. , Chien Miao-Ping 
Published: January 2023

AbstractQuantitative characterizations of cellular dynamics and features of individual cells from a large heterogenous population is essential to identify rare, disease-driving cells, which often exhibit aberrant cellular behaviors like abnormal division, aggressive migration or irregular phylogenetic cell lineages. A recent development in the combination of high-throughput screening microscopy with single cell profiling provides an unprecedented opportunity to decipher the underlying mechanisms of disease-driving phenotypes observed under a microscope. However, accurately and instantly processing large amounts of image data like longitudinal time lapse movies remains a technical challenge when an immediate analysis output (in minutes) of quantitative characterizations is required after data acquisition. Here we present a Fast and Accurate real-time Cell Tracking (FACT) algorithm, which combines GPU-based, ground truth-assisted trainable Weka segmentation and real-time Gaussian mixture model-based cell linking. FACT also implements an automatic cell track correction function to improve the tracking accuracy. With FACT, we can segment ∼20,000 cells in 2 seconds (∼4.5-27.5 times faster than state-of-the-art), and can export quantifiable features from the cell tracking results minutes after data acquisition (independent of the number of acquired image frames) with average 90-95% tracking precision. Such performance is not feasible with state-of-the-art cell tracking algorithms. We applied FACT to real-time identify directionally migrating glioblastoma cells with 96% precision and to identify rare, irregular cell lineages in a population of ∼10,000 cells from a 24hr-time lapse movie with an average 91% F1 score, results from both were exported instantly, mere minutes after image acquisition.
Comparative genomics of smut fungi suggest the ability of meiosis and mating in asexual species of the genusPseudozyma(Ustilaginales)
Authors: Steins Lena , Guerreiro Marco Alexandre , Duhamel Marine , Liu Fei , Wang Qi-Ming , Boekhout Teun , Begerow Dominik 
Published: January 2023

AbstractBackgroundThe Ustilaginales comprise hundreds of plant-parasitic fungi with a characteristic life cycle that directly links sexual reproduction and parasitism: One of the two mating-type loci codes for a transcription factor that not only facilitates mating, but also initiates the infection process. However, several species within the Ustilaginales have no described parasitic stage and were historically assigned to the genusPseudozyma. Molecular studies have shown that the group is polyphyletic, with members being scattered in various lineages of the Ustilag-inales. Together with recent findings of conserved fungal effectors in these non-parasitic species, this raises the question if parasitism has been lost recently and in multiple independent events or if there are hitherto undescribed parasitic stages of these fungi.ResultsIn this study, we sequenced genomes of fivePseudozymaspecies together with parasitic species from the Ustilaginales to compare their genomic capability to perform two central functions in sexual reproduction: mating and meiosis. While the loss of sexual capability is assumed in certain lineages and asexual species are common in Asco- and Basidiomycota, we were able to successfully annotate functional mating and meiosis genes that are conserved throughout the whole group.ConclusionOur data suggest that at least the key functions of a sexual lifestyle are maintained in the analyzed genomes, challenging the current understanding of the so-called asexual species with respect to their evolution and ecological role.