bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complications Related to the Securement Device in Peripheral Intravenous Catheters
Authors: Ferraz-Torres Marta , Sancho-Sena Elena , Corcuera-Martinez María Inés , Martinez-Garcia Oscar , Suarez-Mier María Belén 
Published: November 2024

Studies have not demonstrated the effectiveness of the different types of dressings in reducing the rate of complications. The purpose of this study was to determine which type of dressing is most beneficial in reducing the rate of complications. A total of 281 patients requiring a peripheral intravenous catheter were randomized to receive partially reinforced dressings or fully reinforced dressings (dressings with integral catheter securement). Patients were followed throughout their entire catheter course, and complications included infection, occlusion, phlebitis, accidental dislodgement, extravasation, and medical adhesive-related skin injury. Catheter outcome data were compared to determine whether statistically significant differences existed between the 2 groups. The groups had equivalent demographic characteristics and catheter indications. The average securement time with partially reinforced dressings was 2.72 days, and that for fully reinforced dressings was 2.64 days. However, catheters secured with fully reinforced dressings were associated with fewer total complications, such as infectious phlebitis (P = .043) and accidental dislodgement (P = .03). The fully reinforced securement device significantly reduced the rate of complications related to accidental dislodgement of the device and cases of infectious phlebitis. The use of fully reinforced dressings could reduce catheter-associated complications and improve the quality of patient care.
Impact of Severe Obesity on Major Perioperative Complications for Prolapse Surgery
Authors: Kisby Cassandra K. , Vermunt Jane , Maciejko Laura A. , Abd El Aziz Mohamed A. , Perry William , Occhino John A. 
Published: November 2024

(Abstracted from Urogynecology 2024;30:658–664)
Discussions surrounding surgical approach and minimizing complications and perioperative risks are necessary for many surgeries. Obesity introduces additional variables and risks that need to be discussed in making decisions about pelvic reconstructive surgery, particularly because it is associated with comorbidities such as diabetes, cardiovascular disease, chronic kidney disease, and others.
Evaluation of Postoperative Outcomes Following Early and Late Palate Repair: A Preclinical Study
Authors: Aellos Fabiana , Verma Ishita , Ly Melody , Hoy Mackenzie , Quach Tom , Rosbander Isabel , Sandoval Alejandro , Wolvis Eppo , Turkkahraman Hakan , Helms Jill A. 
Published: November 2024

Objective:
To quantitatively assess the impact of early versus late surgical intervention on midfacial growth using a mouse model.

Methods:
A full-thickness mucoperiosteal flap surgery was performed on newborn (P17) mice and on neonatal (P30) mice. High-resolution micro–computed tomographic imaging coupled with histomorphometric analyses was used to assess craniomaxillofacial growth. Histology and immunohistochemical analyses were used to assess cellular and molecular responses postsurgery.

Results:
Early surgical intervention at P17 resulted in significant midfacial growth arrest, with pronounced maxillary hypoplasia. Histomorphometric analyses revealed significant (P < 0.05) growth disruptions in the mid-palatal suture complex, including premature removal of the cartilaginous growth plate and its replacement by bone. In the suture itself, cell proliferation was significantly reduced (P < 0.05) compared with controls. The same surgical intervention performed in mice at P30 did not lead to significant midfacial growth arrest.

Conclusions:
Early surgical intervention in a mouse model mirrors the adverse growth outcomes in children undergoing early cleft repair. Molecular and cellular observations accompanying this midfacial growth arrest may inform therapeutic strategies to mitigate midfacial growth disturbances in patients and highlight the need for refined surgical techniques to minimize adverse growth outcomes.
Current management of acute appendicitis in adults: What you need to know
Authors: Diaz Jose J. , Ceresoli Marco , Herron Thomas , Coccolini Federico 
Published: November 2024

ABSTRACT
Acute appendicitis is one of the most common acute surgical diseases in the world today. Acute appendicitis can present with a well-recognized clinical presentation with abdominal pain which localize in the right lower quadrant. This presentation is more typical in men than in women of child baring age. Several clinical and laboratory calculations can be used to increase the likelihood of making a correct diagnosis. Various imaging modalities can be used to make the diagnosis which include ultrasound, computer tomography, and magnetic resonance imaging. Each study has well known sensitivity/specificity of positive predictive value of making the diagnosis of appendicitis. The management of acute appendicitis is based on the presentation of the patient and dividing it into uncomplicated and complicated disease. Each requires management with antibiotics and followed with timely appendectomy. Recent studies have demonstrated nonoperative management of uncomplicated appendicitis without no fecalith that can be managed with antibiotics alone. Complicated acute appendicitis should undergo timely surgical intervention. Patients presenting with a large appendiceal abscess or phlegmon should undergo percutaneous drainage and antibiotic management. There are certain patient populations that should be considered for surgical intervention. Pregnant patients as well as immunosuppressed patients should undergo timely surgical intervention to decrease the risk of complications. This review outlines the current principles of the diagnosis, imaging, and treatment of acute appendicitis based on the best available evidence of acute appendicitis in adults.
Quantifying Functional Conservation of Human and Mouse Regulatory Elements via FUNCODE
Authors: Fang Weixiang , Chen Chaoran , Zhang Boyang , Wang Yi , Zhao Ruzhang , Zhou Weiqiang , Ji Hongkai 
Published: November 2024

SummaryEvolutionary conservation is crucial for understanding genome functions and lays the foundation for using animal models in studying human diseases. However, conventional conservation scores based on DNA sequence evolution do not capture the dynamic biochemical activities of DNA elements, termed functional conservation. Quantifying functional conservation has been limited by the availability of functional genomic data matched across species. To address this, we developed FUNCODE, a framework for characterizing functional conservation throughin silicosample matching. Applying FUNCODE to 2,595 uniformly processed datasets from the Encyclopedia of DNA Elements (ENCODE), we generated genome-wide FUNCODE scores for human and mouse regulatory elements, identifying 3.3 million functionally conserved human-mouse element pairs. We demonstrate FUNCODE’s diverse applications, including annotating 78,501 novel regulatory elements, transferring 37,968 high-resolution human ENCODE Hi-C loops in immune lineages to mice, identifying conserved functional signals for disease modeling, and enhancing cross-species integration of single-cell omics data.
DNA-SaM, a robust system for large-scale data storage
Authors: Huang Xiaoluo , Wang Yu , Xu Jiaxin , Nie Ziang , Huang Jiaquan , Wu Yaxin , Qin Zhiwei , Dai Junbiao , Wang Yang 
Published: November 2024

AbstractDNA data storage offers a viable strategy to address the impending data explosion. Early attempts to harness DNA as a storage medium have encountered scalability limitations, largely due to the complexity of codec algorithms, the generation of biochemically harmful sequences and lack of a robust architecture. We present “DNA-SaM”, a novel system designed for DNA data storage, which achieves linear computational complexity and strict bio-constraint adherence, ensuring high coding efficiency and fidelity. It encoded data at speeds surpassing classic systems by over 2 orders of magnitude, with this superiority changes across various encoding algorithms. Importantly, DNA-SaM effectively eliminates any sequence that could be deleterious toin vitroandin vivobiochemical processes, including homopolymer runs, tandem repeat motifs, and potential promoter sequences,etc. It also involves an advanced DNA data storage architecture that incorporates a two-tiered indexing system and a novel “storage unit” distribution paradigm for large-scale data storage. It is further validated by practical data storage bothin vitroandin vivowith a 100% success rate. Our system is capable of storing data over 1039PB, which marks a critical advancement in the scalability of DNA-based data storage.
Natural variation of the streptococcal Group A carbohydrate biosynthesis genes impacts host-pathogen interaction
Authors: Tamminga Sara M. , Schipper Kim , Murner Nicholas , Davies Matthew , Berkhout Paul , Bessen Debra E. , Hendriks Astrid , Korotkova Natalia , Pannekoek Yvonne , van Sorge Nina M. 
Published: November 2024

AbstractStreptococcus pyogenes(S. pyogenes) is a leading cause of infection-related mortality in humans globally. The characteristic cell wall-anchored Group A Carbohydrate (GAC) is expressed by allS. pyogenesstrains and consists of a polyrhamnose backbone with alternatingN-acetylglucosamine (GlcNAc) side chains, of which 25% are decorated with glycerol phosphate (GroP). The genes in thegacA-Lcluster are critical for GAC biosynthesis withgacI-Lbeing responsible for the characteristic GlcNAc-GroP decoration, which confers the agglutination in rapid test diagnostic assays and contributes toS. pyogenespathogenicity. Seminal research papers describedS. pyogenesisolates, so-called A-variant strains, that lost the characteristic GlcNAc side chain following serial animal passage. We performed genomic analysis of a single viable historic parent/A-variant strain pair to reveal a premature inactivating stop codon ingacI, explaining the described loss of the GlcNAc side chain. Subsequently, we analyzed the genetic variation of the 12gacA-Lgenes in a collection of 2,044S. pyogenesgenome sequences. Although allgacgenes (gacA-L) displayed genetic variation, we only identified 31 isolates (1.5%) with a premature stop codon in one of thegacgenes. Nearly 40% of these isolates contained a premature stop codon ingacH. To study the functional consequences of the different premature stop codons for GacH function, we plasmid-expressed threegacHvariants in aS. pyogenes gacH-deficient strain. Cell wall analysis confirmed GacH loss-of-function through the significant reduction of GroP. Complementary, we showed that strains expressinggacHloss-of-function variants were completely resistant to the human bactericidal enzyme group IIA-secreted phospholipase. Overall, our data provide a comprehensive overview of the genetic variation of thegacA-Lgene cluster in a global population ofS. pyogenesstrains and the functional consequences ofgacHvariation for immune recognition and clearance.Data summaryAllS. pyogenesgenome sequences used for this analysis are available within the publication by Davieset al. (2019), ‘Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics’ Nature Genetics, 51(6):1035-43
A model, mixed-species urinary catheter biofilm derived from spinal cord injury patients
Authors: Noorian Parisa , Hamann Kailey , Hoque M. Mozammel , Espinoza-Vergara Gustavo , To Joyce , Leo Dominic , Chari Priyadarshini , Weber Gerard , Marial Obaydullah , Pryor Julie , Duggin Iain G. , Lee Bonsan Bonne , Rice Scott A. , McDougald Diane 
Published: November 2024

AbstractComplex multispecies biofilms consistently colonise the interior of indwelling urinary catheters, causing persistent asymptomatic bacteriuria and frequent symptomatic episodes in long-term catheterized individuals. Simple single-species models often fail to capture the complexities of mixed-species interactions, leading to limited conclusions about microbial behaviour and treatment efficacy. Additionally, using lab-based organisms can obscure the genomic diversity found in real-world infections. The primary objective of this study was to establish a stable and reproduciblein vitrobiofilm model derived from the multi-species clinical flora associated with catheter-related infections, reflecting the dynamics ofin vivoinfections. Biofilm samples from clinical catheters of spinal cord injury (SCI) participants were used to establish polymicrobial macro-fluidic models within catheters. Metagenomic techniques using short-read Illumina and long-read Oxford Nanopore sequencing was used to assess the community composition, produce metagenome-assembled genomes (MAGs), analyse strain-level phylogeny diversity and single nucleotide polymorphisms (SNP) of isolates. Antibiotic resistance tests using our models highlighted the drastic differences between planktonic bacteria, single-species, and multispecies biofilms.In silicoanalysis of antibiotic resistance further revealed a high number of varied resistance genes present in these communities. The models developed and characterised in this study are expected to facilitate more effective strategies to prevent and treat catheter-associated infections.
Multi-Omics Single-Cell Analysis Reveals Key Regulators of HIV-1 Persistence and Aberrant Host Immune Responses in Early Infection
Authors: Lee Dayeon , Choi Sin Young , Shin So-I , An Hyunsu , Choi Byeong-Sun , Park Jihwan 
Published: November 2024

AbstractThe clearance of human immunodeficiency virus-1 (HIV-1) remains a significant public health challenge due to impaired cellular immune responses and HIV-1 maintenance during acute infection. However, the genetic and epigenetic changes influencing the immune response on host infected cells remain unclear. Here, this study analyzes HIV-1 infected CD4+ T cells from peripheral blood mononuclear cells from people living with HIV-1 (PLWH) during early infection (<6 months) using single-cell RNA and ATAC sequencing. It is observed that HIV-1 hinders the antiviral response, particularly by interfering with the interferon signalling pathway. Multimodal analysis identifies KLF2 as a key transcription factor in infected CD4+ T cells. Moreover, cells harbouring HIV-1 provirus are predominantly identified as Th17 cells, which exhibit elevated KLF2 activity. This suggests an increased susceptibility to HIV-1 infection and a constrained immune response due to the quiescent characteristics of these cells. The finding provides insights into the immune mechanisms and key regulators of HIV-1 maintenance in CD4+ T cells during the early stages of infection.
An institutional COVID-19 initiative: creation of a biobank and serological data analysis in pre- and post-vaccination cohorts
Authors: Fernandes-Siqueira Lorena O , Melo Raphael RRA , Wermelinger Luciana S , Almeida Fabio CL , Salmon Didier , Ferreira Gustavo C , Da Poian Andrea T 
Published: November 2024

ABSTRACTThe COVID-19 pandemic has left a legacy in the management of health emergencies, but sentinel surveillance was relatively underused, despite its significant role in decision-making during epidemics. Here we describe a sentinel SARS-CoV-2 antigens’ serosurveillance carried out on a cohort of 395 individuals at a Brazilian institution, from October 2020 to December 2022. A total of 1,507 serum samples were analyzed for IgG and IgA against SARS-CoV-2 Spike (S) or nucleocapsid (N) proteins, in the pre- and post-vaccination periods. The latter included two doses of CoronaVac (group 1, G1), or ChAdOx-1 or BNT162b2 (group 2, G2), followed by heterologous booster doses. In the pre-vaccination phase, 26.5% of participants showed IgG positivity for S and 13.7% for N. After the vaccines’ first dose, S IgG response was positive in 66.6% or 98% of G1 or G2 participants, respectively, while 100% of the participants showed S IgG positivity after the second dose, and S IgG and IgA after the booster. This initiative enabled the examination of viral transmission beyond hospital environments, which is rarely explored in existing literature, and established protocols for managing future emergencies. In addition, a serum bank and a comprehensive database were established, now available to the scientific community.
Dissecting the molecular basis of variability for flowering time inCamelina sativa
Authors: Zhang Liyong , Bollina Venkatesh , Gao Peng , Parkin Isobel A. P. 
Published: November 2024

AbstractCamelina sativais an important polyploid oilseed crop with multiple favorable agronomic traits. Capturing the leaf transcriptome of 48 accessions ofC. sativasuggests allelic variation for gene expression levels and notably sub-genome dominance, both of which could provide opportunities for crop improvement. Flowering time (FT) is a crucial factor affecting the overall yield of crops. However, our understanding of the molecular mechanisms underlying FT regulation inC. sativaare still limited, partly due to its complex allohexaploid genome. In this study, weighted gene co-expression network analysis (WGCNA), expression quantitative trait loci (eQTL) analysis and transcriptome-wide association study (TWAS) were employed to explore the FT diversity among 48C. sativaaccessions and dissect the underlying molecular basis. Our results revealed a FT-related co-expressed gene module highly enriched withSOC1s andSOC1-like genes, and identified 10 significant FT-associated single nucleotide polymorphisms (SNPs) defining three haplotype groups; thus providing a molecular basis for future genetic improvements inC. sativabreeding.
Comparative and population genomics analyses of the regulatory Transcription Factor (TF)-DNA interaction
Authors: Joshi Manas , Duchen Pablo , Kapopoulou Adamandia , Laurent Stefan 
Published: November 2024

AbstractNatural selection heavily influences the evolutionary trajectories of species by impacting their genotype to phenotype transitions. On the molecular level, these genotype to phenotype transitions are shaped by the regulatory sequences (RSs). In this study, we employed a combination of population and comparative genomics to investigate how natural selection affects specific RS classes involved in the regulatory transcription factor (TF)-DNA interactions. These interactions consist of two motifs, namely: TF-binding domains (TF-BDs) and TF-binding sites (TF-BSs). Using publicly available annotation data, we constructed the species-specific lists of the TF-BD and TF-BS regions. We also constructed a non-synonymous equivalent class for the TF-BS regions for making comparative analyses across the coding and non-coding regions. On applying some of the commonly used summary statistics, we found a consistent signal of purifying selection acting on TF-BDs, consistent with their functional importance. Interestingly, we also observed that non-coding TF-BS regions showed similar levels of constraint to that of coding regions for populations with large Ne. Concerning positive selection, we showed that the regulatory motifs of large Nespecies are, overall, subject to an increased intensity of positive selection. We found an overall positive correlation between the intensity of purifying and positive selection and the species-specific Ne, which is expected under drift-selection equilibrium. Finally, we contrasted the signal of positive selection inH. sapiensandD. melanogaster(outcrossing species) withA. thaliana(selfing species) and noted that selfing plays a key role in influencing the action of positive selection.
DNA methylation is a key determinant of response to targeted and immune checkpoint therapies in metastatic renal cell carcinoma
Authors: Jeanneret Florian , Schoch Sarah , Ballester Pedro , Symeonides Stefan N , Laird Alexander , Axelson Håkan , Pflieger Delphine , Battail Christophe 
Published: November 2024

AbstractThe response to targeted therapies and immune checkpoint inhibitors for patients suffering from metastatic clear cell renal cell carcinoma (ccRCC) is heterogeneous and currently not predictable in clinic. In this work, a comprehensive integrated study of 700 ccRCCs profiled by DNA methylation and RNA sequencing showed that the hyper-methylated tumors exhibited a worse prognosis, a higher fraction of cycling tumor cells and a lower activity of homeobox transcription factors. To translate the use of DNA methylation information into a clinical setting, we developed a simple model accurately predicting the ccRCC methylation subtypes (AUC-ROCs of 0.91) from two gene expression ratios (IGF2BP3/PCCA, TNNT1/TMEM88). In addition, these methylation subtypes were significantly associated with the therapeutic outcome of patients to anti-PD-1, mTOR inhibitor or tyrosine kinase inhibitor therapies. Overall, our framework for predicting the ccRCC DNA methylation subtypes from targeted gene expression data is easy to translate in clinic and contributes to better personalization of ccRCC therapies.
Minimal integrating shuttle vectors forSaccharomyces cerevisiaedepleted of restriction sites outside the polylinker region
Authors: Scutteri Lorenzo , Barth Patrick , Rahi Sahand Jamal 
Published: November 2024

ABSTRACTMany plasmids harbor unnecessary elements that complicate or hinder cloning tasks such as inserting one gene into another for protein domain grafting. In particular, restriction sites may be present in the backbone outside the polylinker region (multiple cloning site; MCS) and thus unavailable for use, and the overall length of a plasmid correlates with poorer ligation efficiency. To address these concerns, there has been a growing interest in minimal plasmids. Here, we describe the design and validation of a collection of six minimal integrating shuttle vectors for genetic manipulation inSaccharomyces cerevisiae. We constructed the plasmids usingde novogene synthesis and consisting only of a yeast selection marker (HIS3, TRP1, LEU2, URA3, natMX6, orKanMX), a bacterial selection marker (Ampicillin resistance), an origin of replication (ORI), and the MCS flanked by M13 forward and reverse sequences. We use truncated variants of these elements where available and eliminated all other sequences typically found in plasmids. The MCS consists of ten unique restriction sites. To our knowledge, at sizes ranging from approximately 2.6 kb to 3.5 kb, these are the smallest shuttle vectors described for yeast. Further, we removed common restriction sites in the open reading frames (ORFs) and terminators, freeing up approximately 30 cut sites in each plasmid. We named our pLS series in accordance with the well-known pRS vectors, which are on average 63% larger: pLS403 (HIS3), pLS404 (TRP1), pLS405 (LEU2), pLS406 (URA3), pLS408 (natMX6), and pLS410 (KanMX). These minimal vector backbones open up new opportunities for efficient molecular biology and genetic manipulation inSaccharomyces cerevisiae.