bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Biologics and Small Molecule Agents on Postoperative Complications in Inflammatory Bowel Disease: A Systematic Review
Authors: Lee Kate E. , Sizemore J. Alexander , Kim Grace , Shen Bo , Sands Bruce E. 
Published: January 2024

BACKGROUND:
Patients with inflammatory bowel disease may require colectomy for severe disease unresponsive or refractory to pharmacological therapy. The question of the impact of biologic use on postoperative complications is a topic of active investigation.

OBJECTIVE:
A systematic literature review was performed to describe the current state of knowledge of the impact of perioperative biologic and tofacitinib use on postoperative complications in patients with inflammatory bowel disease.

DATA SOURCES:
PubMed and Cochrane databases were searched.

STUDY SELECTION:
Studies between January 2000 and January 2023, in any language, were searched, followed by a snowball search identifying further studies, in accordance with preferred reporting items for systematic reviews and meta-analyses guidelines. Articles regarding pediatric or endoscopic management were excluded.

INTERVENTIONS:
Preoperative or perioperative exposure to biologics in inflammatory bowel disease was included.

MAIN OUTCOME MEASURES:
Infectious and noninfectious complications, including anastomotic leaks, surgical site infections, urinary tract infections, pneumonia, sepsis, septic shock, postoperative length of stay, readmission, and reoperation, were the main outcomes measured.

RESULTS:
A total of 28 studies were included for analysis in this review, including 7 meta-analyses or systematic reviews, and 5 randomized studies. Snowball search identified 11 additional studies providing topical information. Overall, tumor necrosis factor inhibitors likely do not increase risk of postoperative adverse outcomes, while data on other biologics and small molecule agents are emerging.

LIMITATIONS:
This is a qualitative review including all study types. The varied nature of study types precludes quantitative comparison.

CONCLUSIONS:
Although steroids increase postoperative infectious and noninfectious complications, tumor necrosis factor inhibitors do not appear to increase postoperative infectious and non-infectious complications. There is a need for further perioperative data for other agents. See Video.
Obesity/cardiometabolic phenotype of heart failure with preserved ejection fraction: mechanisms to recent trials
Authors: Verma Raj , Dhingra Nitish K. , Connelly Kim A. 
Published: January 2024

Purpose of review
Heart failure with preserved ejection fraction (HFpEF) is a leading and growing cause of morbidity and mortality globally. Of the various phenotypes identified, the obesity (or cardiometabolic) phenotype appears to be most common. The purpose of this review is to provide the clinician with an abridged understanding of recent developments that have elucidated obesity/visceral adiposity as a central mechanism linking inflammation/immune dysregulation to the development of the HFpEF syndrome. Recent clinical trials examining the efficacy of pharmacological treatments that target obesity in HFpEF will also be discussed.

Recent findings
Recent data indicate that visceral adiposity and insulin resistance in HFpEF serve as key mechanisms driving inflammation and immune dysregulation, which play a critical role in the development of cardiac stiffness, diastolic dysfunction and fibrosis in HFpEF. In obesity, alterations in macrophage polarization, changes in innate and adaptive immune systems and altered myocardial energetics promote metabolic inflammation in HFpEF. Finally, emerging data suggest that inflammatory biomarkers, specifically, IL-6, may provide useful information about HFpEF severity and symptom burden in obesity.

Summary
The obesity phenotype of HFpEF is seen in upward of 80% with HFpEF. Obesity is not just a bystander, but plays an essential role in the pathobiology and clinical course of HFpEF. Targeting overweight/obesity in HFpEF with GLP-1 receptor agonists holds promise in these patients.
Strategies to Obtain and Deliver Blood Products Into Critically Injured Children
Authors: Sullivan Travis M. , Sippel Genevieve J. , Gestrich-Thompson Waverly V. , Burd Randall S. 
Published: January 2024

Objectives
Timely transfusion is associated with improved survival and a reduction in in-hospital morbidity. The benefits of early hemorrhagic shock recognition may be limited by barriers to accessing blood products and their timely administration. We examined how pediatric trauma programs obtain blood products, the types of rapid infusion models used, and the metrics tracked to improve transfusion process efficiency in their emergency department (ED).

Methods
We developed and distributed a self-report survey to members of the Pediatric Trauma Society. The survey consisted of 6 initial questions, including the respondent's role and institution, whether a blood storage refrigerator was present in their ED, the rapid infuser model used to transfuse critically injured children in their ED, if their program tracked 4 transfusion process metrics, and if a video recording system was present in the trauma bay. Based on these responses, additional questions were prompted with an option for a free-text response.

Results
We received 137 responses from 77 institutions. Most pediatric trauma programs have a blood storage refrigerator in the ED (n = 46, 59.7%) and use a Belmont rapid infuser to transfuse critically injured children (n = 45, 58.4%). The American College of Surgeons Level 1 designated trauma programs, or state-based equivalents, and “pediatric” trauma programs were more likely to have video recording systems for performance improvement review compared with lower designated trauma programs and “combined pediatric and adult” trauma programs, respectively.

Conclusions
Strategies to improve the timely acquisition and infusion of blood products to critically injured children are underreported. This study examined the current practices that pediatric trauma programs use to transfuse critically injured children and may provide a resource for trauma programs to cite for transfusion-related quality improvement.
Evaluation of homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional tissue-based immunofluorescence assays
Authors: Arce-Gallego Sara , Morgado Pablo Cresta , Delgado-Serrano Luisa , Simonetti Sara , Gonzalez Macarena , Marmolejo David , Morales-Barrera Rafael , Mir Gisela , Semidey Maria Eugenia , Lozano Paula Romero , Cordoba-Terreros Sarai , Mast Richard , de Albert Matias , Planas Jacques , Cuadras Mercè , Maldonado Xavier , Suarez Cristina , Casanova-Salas Irene , Nonell Lara , Dienstmann Rodrigo , Nuciforo Paolo , Vivancos Ana , Llop-Guevara Alba , Carles Joan , Serra Violeta , Mateo Joaquin 
Published: January 2024

AbstractPurposeMetastatic prostate cancer (mPC) is enriched for homologous recombination repair (HRR) gene alterations; these biomarkers have prognostic and predictive value. Next-generation sequencing (NGS) allows for patient stratification based on these biomarkers, but widespread clinical implementation is still limited. Moreover, not all mutations in HRR genes result in functional HRR loss in the tumor. We investigated the correlation between genomic and functional loss of HRR, using NGS and an optimized RAD51 immunofluorescence (RAD51-IF) assay in mPC clinical biopsies.Experimental designObservational study including patients with stage IV prostate cancer. Biopsies from either primary tumor or metastatic biopsies underwent NGS (targeted sequencing and/or whole-exome sequencing), and RAD51-IF. Clinical data was extracted from electronic patient records.Results219 biopsies from 187 patients were acquired, including primary (151/219) and metastatic (68/219) tumor biopsies collected either in the metastatic hormone- sensitive (169/219) or castration-resistant (50/219) setting. NGS (181 biopsies from 157 patients) showed frequent genomic alterations inTP53(40%),AR(15%),PTEN(14%), MYC (10%),BRCA2(9%),ATM(8%) andBRCA1(2%). Tissue for RAD51 IF was available for 206 samples; of those, 140/206 (68%) were evaluable for RAD51- IF. Based on a previously defined threshold of 10% RAD51-positive cells, 21% samples had RAD51-low results compatible with HRR deficiency (HRD). Sample matched RAD51-IF and genomics data were obtained for 128 biopsies (117 patients): RAD51-IF had a high sensitivity (68%) and specificity (85%) to identify cases withBRCA1/2alterations. Additionally, the RAD51-IF assay was able to identify restoration of HRR function in selected cases withBRCA2reversion mutations or BRCA1 expression.ConclusionsRAD51-IF is feasible in routine clinical samples from mPC patients and associates strongly with clinically relevant HRR gene alterations.
BERTE: High-precision hierarchical classification of transposable elements by a transfer learning method with BERT pre-trained model and convolutional neural network
Authors: Chen Yiqi , Qi Yang , Wu Yingfu , Zhang Fuhao , Liao Xingyu , Shang Xuequn 
Published: January 2024

AbstractTransposable Elements (TEs) are abundant repeat sequences found in living organisms. They play a pivotal role in biological evolution and gene regulation and are intimately linked to human diseases. Existing TE classification tools can classify classes, orders, and superfamilies concurrently, but they often struggle to effectively extract sequence features. This limitation frequently results in subpar classification results, especially in hierarchical classification. To tackle this problem, we introduced BERTE, a tool for TE hierarchical classification. BERTE encoded TE sequences into distinctive features that consisted of both attentional and cumulativek-merfrequency information. By leveraging the multi-head self-attention mechanism of the pre-trained BERT model, BERTE transformed sequences into attentional features. Additionally, we calculated multiplek-merfrequency vectors and concatenate them to form cumulative features. Following feature extraction, a parallel Convolutional Neural Network (CNN) model was employed as an efficient sequence classifier, capitalizing on its capability for high-dimensional feature transformation. We evaluated BERTE’s performance on filtered datasets collected from 12 eukaryotic databases. Experimental results demonstrated that BERTE could improve the F1-score at different levels by up to 21% compared to current state-of-the-art methods. Furthermore, the results indicated that not only could BERT better characterize TE sequences in feature extraction, but also that CNN was more efficient than other popular deep learning classifiers. In general, BERTE classifies TE sequences with greater precision. BERTE is available athttps://github.com/yiqichen-2000/BERTE.
A taxonomy based on acoustic features of some Iranian cicadas and calling song description ofChloropsalta smaragdulaHaupt, 1920 (Hem: Cicadidae) from Isfahan, Iran
Authors: Mehdipour Maedeh , Riede Klaus , Sendi Jalal Jalali , Zamanian Hossein , Mohammadi-Mobarakeh Akbar 
Published: January 2024

AbstractThis paper compiles parameters of calling songs from 14 cicada species inhabiting Iran. In addition, calling song parameters ofChloropsalta smaragdulawere analyzed for the first time. A taxonomy based on song parameters was designed, including Iranian cicadasTibicen plebejus,Cicadatra lorestanica,Cicadivetta tibialis,Tettigetta golestani,Pagiphora annulata,Tibicina haematodes,Cicada orni, Pagiphora annulata,Chloropsalta smaragdula,Cicadatra hyalina,Psalmocharias querula,Cicadatra persica,Cicadatra alhageos,Cicadatra atraandCicadatra barbodiout of 44 species reported from Iran. In addition to common acoustic parameters, four new complex spectral features such as variance, kurtosis, spectral centroid and short time energy were used. These additional features were necessary to construct a comprehensive identification key based on acoustic parameters. Our acoustic identification system provides a highly accurate species recognition method, which could be of general relevance in cicada taxonomy.
Mitochondrial fission surveillance is coupled toCaenorhabditis elegansDNA and chromosome segregation integrity
Authors: Yang Xiaomeng , Meng Fanfan , Wei Ruichen , Liu Dianchen , Gong Xuan , Ruvkun Gary , Wei Wei 
Published: January 2024

AbstractMitochondrial fission and fusion are tightly regulated to specify mitochondrial abundance, localization, and arrangement during cell division as well as in the diverse differentiated cell types and physiological states. However, the regulatory pathways for such mitochondrial dynamics are less explored than the mitochondrial fission and fusion components. Here we report a large-scale screen for genes that regulate mitochondrial fission. Mitochondrial fission defects cause a characteristic asymmetric fluorescent pattern in embryos carrying mitochondrial stress reporter genes. Using this asymmetric activation, we performed RNAi screens that identified 3 kinase genes from a ∼500-kinase library and another 11 genes from 3,300 random genes that function in mitochondrial fission. Many of these identified genes play roles in chromosome segregation. We find that chromosome missegregation and genome instability lead to dysregulation of mitochondrial fission in a manner independent of Drp-1. ATL-1, theC. elegansATR orthologue, plays a protective role in alleviating the mitochondrial fission defect caused by chromosome missegregation. This establishes a screening paradigm for identifying mitochondrial fission regulators which reveals the role of ATR in surveilling mitochondrial fission to mitigate dysregulation caused by improper chromosome segregation.
Floria: Fast and accurate strain haplotyping in metagenomes
Authors: Shaw Jim , Gounot Jean-Sebastien , Chen Hanrong , Nagarajan Niranjan , Yu Yun William 
Published: January 2024

AbstractShotgun metagenomics allows for direct analysis of microbial community genetics, but scalable computational methods for the recovery of bacterial strain genomes from microbiomes remains a key challenge. We introduce Floria, a novel method designed for rapid and accurate recovery of strain haplotypes from short and long-read metagenome sequencing data, based on minimum error correction (MEC) read clustering and a strain-preserving network flow model. Floria can function as a standalone haplotyping method, outputting alleles and reads that co-occur on the same strain, as well as an end-to-end read-to-assembly pipeline (Floria-PL) for strain-level assembly. Benchmarking evaluations on synthetic metagenomes showed that Floria is>3×faster and recovers 21% more strain content than base-level assembly methods (Strainberry), while being over an order of magnitude faster when only phasing is required. Applying Floria to a set of 109 deeply sequenced nanopore metagenomes took<20 minutes on average per sample, and identified several species that have consistent strain heterogeneity. Applying Floria’s short-read haplotyping to a longitudinal gut metagenomics dataset revealed a dynamic multi-strainAnaerostipes hadruscommunity with frequent strain loss and emergence events over 636 days. With Floria, accurate haplotyping of metagenomic datasets takes mere minutes on standard workstations, paving the way for extensive strain-level metagenomic analyses.AvailabilityFloria is available athttps://github.com/bluenote-1577/floria, and the Floria-PL pipeline is available athttps://github.com/jsgounot/Floria_analysis_workflow.
Clinical progression of Parkinson’s disease in the early 21st century: Insights from AMP-PD dataset
Authors: Lewis Mechelle M. , Cheng Xinyi Vivian , Du Guangwei , Zhang Lijun , Li Changcheng , De Jesus Sol , Tabbal Samer D. , Mailman Richard , Li Runze , Huang Xuemei 
Published: January 2024

AbstractBackgroundParkinson’s disease (PD) therapeutic strategies have evolved since the introduction of levodopa in the 1960s, but there is limited data on their impact on disease progression markers.ObjectiveDelineate the current landscape of PD progression at tertiary subspecialty care and research centers.MethodUsing Accelerating Medicine Partnership-PD (AMP-PD) data harmonized from seven biomarker discovery studies (2010-2020), we extracted: overall [Schwab and England (S&E), PD Questionnaire (PDQ-39)]; motor [Movement Disorders Society Unified PD Rating Scale (MDS-UPDRS)-II and -III and Hoehn & Yahr (HY)]; and non-motor [MDS-UPDRS-I, University of Pennsylvania Smell Identification Test (UPSIT), Montreal Cognitive Assessment (MoCA), and Epworth Sleepiness Scale (ESS)] scores. Age at diagnosis was set as 0 years, and data were tracked for 15 subsequent years.ResultsSubjects’ (3,001 PD cases: 2,838 white, 1,843 males) mean age at diagnosis was 60.2±10.3 years and disease duration was 9.9±6.0 years at the baseline evaluation. Participants largely reported independence (S&E,5y: 86.6±12.3;10y: 78.9±19.3;15y: 78.5±17.0) and good quality of life (PDQ-39,5y: 15.5±12.3;10y: 22.1±15.8;15y: 24.3±14.4). Motor scores displayed a linear progression, whereas non-motor scores plateaued ∼10-15 years. Younger onset age correlated with slower overall (S&E), motor (MDS-UPDRS-III), and non-motor (UPSIT/MoCA) progression, and females had better overall motor (MDS-UPDRS-II-III) and non-motor (UPSIT) scores than males.ConclusionsTwenty-first century PD patients remain largely independent in the first decade of disease. Female and young age of diagnosis were associated with better clinical outcomes. There are data gaps for non-whites and metrics that gauge non-motor progression for >10 years after diagnosis.
Orthology inference at scale with FastOMA
Authors: Majidian Sina , Nevers Yannis , Yazdizadeh Kharrazi Ali , Warwick Vesztrocy Alex , Pascarelli Stefano , Moi David , Glover Natasha , Altenhoff Adrian M , Dessimoz Christophe 
Published: January 2024

AbstractThe surge in genome data, with ongoing efforts aiming to sequence 1.5M eukaryotes in a decade, could revolutionise genomics, revealing the origins, evolution, and genetic innovations of biological processes. Yet, traditional genomics methods scale poorly with such large datasets. Addressing this, “FastOMA” provides linear scalability, enabling the processing of thousands of eukaryotic genomes within a day. FastOMA maintains the high accuracy and resolution of the well-established OMA approach in benchmarks. FastOMA is available athttps://github.com/DessimozLab/FastOMA/.
Inheritance of old mitochondria controls early CD8+T cell fate commitment and is regulated by autophagy
Authors: Borsa Mariana , Lechuga-Vieco Ana Victoria , Kayvanjoo Amir H. , Yazicioglu Yavuz , Compeer Ewoud B. , Richter Felix C. , Bui Hien , Dustin Michael L. , Katajisto Pekka , Simon Anna Katharina 
Published: January 2024

AbstractT cell immunity is impaired during ageing, particularly in memory responses needed for efficient vaccination. Autophagy and asymmetric cell division (ACD) are cell biological mechanisms key to memory formation, which undergo a decline upon ageing. However, despite the fundamental importance of these processes in cellular function, the link between ACD andin vivofate decisions has remained highly correlative in T cells and in the field of mammalian ACD overall. Here we provide robust causal evidence linking ACD toin vivoT cell fate decisions and our data are consistent with the concept that initiation of asymmetric T cell fates is regulated by autophagy. Analysing the proteome of first-daughter CD8+T cells following TCR-triggered activation, we reveal that mitochondrial proteins rely on autophagy for their asymmetric inheritance and that damaged mitochondria are polarized upon first division. These results led us to evaluate whether mitochondria were asymmetrically inherited and to functionally address their impact on T cell fate. For this we used a novel mouse model that allows sequential tagging of mitochondria in mother and daughter cells, enabling their isolation and subsequentin vivoanalysis of CD8+T cell progenies based on pre-mitotic cell cargo. Autophagy-deficient CD8+T cells showed impaired clearance and symmetric inheritance of old mitochondria, suggesting that degradation events promote asymmetry and are needed to generate T cells devoid of old organelles. Daughter cells inheriting old mitochondria are more glycolytic and upon adoptive transfer show reduced memory potential, whereas daughter cells that have not inherited old mitochondria from the mother cell are long-lived and expand upon cognate-antigen challenge. Proteomic and single-cell transcriptomic analysis of cells inheriting aged mitochondria suggest that their early fate divergence relies on one carbon metabolism as a consequence of poor mitochondrial quality and function. These findings increase our understanding of how T cell diversity is early-imprinted during division and will help foster the development of strategies to modulate T cell function.Abstract FigureThe MitoSnap model allows tracking of pre-mitotic and post-mitotic cell cargoes.Both segregation and degradation (autophagy) contribute to the asymmetric inheritance of old mitochondria.Old mitochondria impact cell metabolism and function.Cells devoid of old mitochondria exhibit better memory potentialin vivo.
Assessing the effects of acute temperature changes of sea water temperature due to climate change on Scottish farmed Atlantic salmon and investigating genetic mitigation
Authors: Tsairidou Smaragda , van den Berg Jarl , Tapping Stephen , Sobolewska Halina , Hamilton Alastair 
Published: January 2024

AbstractChanges in growth, survival, maturation and health in Atlantic salmon post-smolts were observed under moderate and more extreme heat-wave conditions for the west coast of Scotland. A Scottish Atlantic salmon breeding programme population of 518 salmon of age 13-14 months, was observed for 4 weeks in summer, in tanks with ambient water temperature or ∼ 4 degrees and ∼ 8 degrees above ambient temperature. Data were recorded for the fish before and after the challenge. All fish were genotyped using a custom SNP (single nucleotide polymorphism) array (8,978 SNP genotypes after quality control). Temperature-dependant genotype-by-environment interactions and the potential for selective breeding to improve resilience were investigated. Statistical analyses revealed significant differences between thermal environments for body weight, average daily weight gain, and survival, while higher temperature induced earlier maturation, and an increase of gill health scores. QPCR (quantitative polymerase chain reaction) analyses revealed the presence ofAeromonas hydrophila, a pathogen typically more prevalent in warmer climates. Using genomic relationships and animal mixed models, body weight and average daily weight gain provided moderate heritabilities, while between-tank genetic correlations were close to 1, indicating no significant re-ranking of genotypes between the different thermal environments. These findings suggest that even short-term exposure to heat stress may be sufficient to negatively impact survival and gill health, and induce earlier maturation. However, observations took place within a commercial farm where having replicates for each thermal environment was not possible, hence further experiments with larger populations, exposed to more prolonged heat stress are needed.