bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstruction of 2 Independent Facial Defects Using A Single Paramedian Forehead Flap
Authors: Gonzalez-Parrilla Leonardo , Thuman Jenna , Awad Mahmoud , Patel Krishna 
Published: November 2024

Background:
The paramedian forehead flap (PMFF) has been well established for use in reconstruction limited to a single nasal outer layer defect and has recently gained recognition as an acceptable alternative to traditional methods of lower eyelid reconstruction. The use of a single, pedicled PMFF for the reconstruction of more than one defect has yet to be described.

Methods:
A 59-year-old male patient was originally diagnosed with large squamous cell carcinoma resulting in radical resection and ipsilateral neck dissection. Postoperative final pathology was read as basal cell carcinoma; due to close margins, the patient required adjuvant radiation therapy. Immediate reconstruction at index surgery included radial forearm free flap; however, the patient subsequently developed left eye symptoms due to lid retraction and nasal symptoms with a left alar defect. The authors report the use of a single pedicled PMFF to reconstruct 2 distinct ipsilateral defects in a radiated patient—nasal ala and lower eyelid.

Results:
At 6 months post-secondary reconstruction, both recipient sites of the single PMFF appear viable and in adequate position without contraction. The patient has persistent but much improved symptoms related to his eye and nasal defects.

Conclusion:
A single PMFF can be safely and effectively used in the reconstruction of 2 distinct facial defects in the appropriate patient.
The protocol for BROWSE-P (breast reconstruction outcomes with Strattice™ or Artia™ – pre-pectoral): a cohort study to assess long-term outcomes of immediate pre-pectoral implant based breast reconstruction with Strattice™ or Artia™
Authors: Johri Goonj , Wilson Rebecca L. , Barrett Emma , Murphy John A. , Dave Rajiv , Harvey James R. 
Published: November 2024

Introduction:
Techniques in implant-based breast reconstruction (IBBR) have evolved over the last 15 years due to the introduction of mesh or acellular dermal matrices (ADMs). Traditionally, total submuscular coverage progressed to upper pole muscle cover with lower pole ADM and now total or anterior ADM cover in the pre-pectoral plane. Data is scarce to support the pre-pectoral technique but, it is suggested to result in less postoperative pain, more natural cosmesis and avoidance of animation deformity. The BROWSE study concluded that subpectoral with Strattice™ IBBR resulted in better cosmesis and lower rates of capsular contracture when compared to the total submuscular technique. The BROWSE-P study aims to assess the safety profile of Artia™ a porcine derived ADM and review the long-term outcomes of pre-pectoral IBBR with Strattice™ and Artia™.

Methods and analysis:
BROWSE-P is a single center cohort study. Consecutive patients who have undergone immediate pre-pectoral IBBR with Strattice™ or Artia™ from January 2017 to December 2022 will be included. Demographic, operative, oncology, complication, and further surgery data with be collected to assess the rate of revision surgery and safety profile of Artia™. Those who have their implant reconstruction in situ will be invited for clinical assessment to assess for capsular contracture. Participants will also be asked to complete a BREAST-Q post-reconstruction module, to assess patient satisfaction and quality of life, and have medical photographs taken for an assessment of aesthetic outcome by a blinded panel using the 10-point Visser scale. We aim to collect data on 500 reconstructions and complete clinical assessment, patient reported outcomes and aesthetic assessment for 250 patients.
Predicting the need for additional intervention in prostate abscess treatment: Insights from a multicenter study and proposal of a Prostate Abscess Complexity Score
Authors: Pallares-Mendez Rigoberto , Armillas-Canseco Francisco , Martinez Diego Enrique , Bove Alfredo M. , Cervantes-Miranda Daniel E. , Brassetti Aldo , Hernandez-Aranda Katherine L. , Badillo-Gonzalez Miriam K. , Molgado-Garza Victor M. , Garcia-Saucedo Jesus , Castillejos-Molina Ricardo A. , Becerra-Cardenas Jaime , Simone Giuseppe , Gutierrez-Gonzalez Adrian 
Published: November 2024

Purpose:
To evaluate prostate abscess outcomes and identify predictors for additional intervention. Additionally, assess a complexity score for clinical decision-making.

Materials and methods:
This is a retrospective, multicenter study including 62 consecutively admitted prostate abscess patients. Primary treatment involved antibiotics or a combination with transrectal ultrasound-guided aspiration (TRUS-GA) or transurethral resection of the prostate with abscess deroofing. Outcomes were assessed by comparing resolution with primary treatment to additional intervention. Additional intervention involved escalation to TRUS-GA, repeat TRUS-GA, or transurethral resection of the prostate with abscess deroofing. The sample was further categorized by Prostate Abscess Complexity Score (PACS) into complex and noncomplex. Risk factors, clinical features, abscess characteristics, and reintervention predictors were analyzed using logistic regression and receiver operating characteristic analysis.

Results:
Sixty-two patients were included, 47 (75.8%) responded well to primary treatment, while 15 (24.2%) needed additional intervention. Risk factors for additional intervention included multifocal abscess (P = 0.005), septa (P = 0.023), bilateral involvement (P = 0.008), abscess diameter ≥3 cm (P = 0.040), and volume ≥20 cc (P ≤ 0.001). The PACS, considering abscess focality, septa, laterality, polarity, abscess diameter, and volume, showed 73% sensitivity and 74% specificity in predicting additional intervention (P = 0.001) with a threshold of ≥6 points to classify as complex. Among complex cases, 80% required additional intervention, compared to 34% in noncomplex cases (P = 0.002).

Conclusion:
This study highlights personalized treatment for prostate abscess. Identified risk factors (multifocal abscess, septa, bilateral involvement, large abscess diameter, and increased volume) provide insights into predicting the need for additional interventions. The proposed PACS offers a valuable tool for clinical decision-making when ≥6 points are encountered.
Impact of SARS-CoV-2 Infection on Antimicrobial Resistance Gene Profiles in the Upper Respiratory Tract: A Cross-Sectional Study
Authors: Tomar Siddharth Singh , Khairnar Krishna 
Published: November 2024

AbstractObjectivesTo investigate the impact of SARS-CoV-2 infection on the antimicrobial resistance (AMR) gene profiles in the upper respiratory tract (URT) and To evaluate variations in AMR gene diversity, abundance, and ESKAPE-associated AMR in URT. By comparing SARS-CoV-2-positive patients to healthy controls.Methods95 URT swab samples from SARS-CoV-2-positive (n=48) and RTPCR-negative control participants (n=47) collected from central India. Metagenomic DNA was extracted, and metagenomic sequencing was performed using the Illumina NextSeq550 platform. Sequencing data were analysed using the Chan Zuckerberg ID pipeline for Antimicrobial resistance (AMR) gene detection and taxonomic profiling. Chao1, Shannon and Simpson diversity indices, Bray-Curtis dissimilarity, and Bayesian regression, were used to identify significant differences in AMR gene abundance and microbial associations.ResultsThe Chao1 index (p=0.01651) of SARS-CoV-2 samples indicated significantly higher AMR gene richness than the controls. Resistance genes, such as mecA, blaOXA-48, and blaNDM-1, showed higher abundance in SARS-CoV-2 samples. These genes were found to be linked to high-priority pathogens likeKlebsiella pneumoniae, Escherichia coli,andStaphylococcus aureus. Bayesian regression demonstrated that SARS-CoV-2 infection is a significant factor in elevated AMR gene abundance (β = 1.549, HDI [1.409, 1.691]). Females showed higher AMR levels than males (β = 0.261, HDI [0.167, 0.350]), and the model outputs showed no significant age correlation. Sankey diagrams and heatmaps showed higher AMR gene diversity and abundance in the SARS-CoV-2 group.ConclusionsSARS-CoV-2 infection alters the URT’s AMR gene profile and increases the resistance genes’ abundance and diversity. The results indicate a requirement to enhance AMR surveillance of COVID-19 patients to adapt antimicrobial stewardship strategies and reduce the chances of secondary infections. It is, therefore, essential to carry out more extensive studies to analyze temporal variations and the effects of antibiotic overuse on AMR evolution.
An obligate symbiont ofHaematomyzus elephantiswith a strongly reduced genome resembles symbiotic bacteria in sucking lice
Authors: Říhová Jana Martin , Vodička Roman , Hypša Václav 
Published: November 2024

AbstractThe parvorder Rhynchophthirina with a single genusHaematomyzusis a small group of ectoparasites related to sucking and chewing lice. Previous screening based on the 16S rRNA gene indicated thatHaematomyzusharbour a symbiotic bacterium whose DNA exhibits a strong shift in nucleotide composition typical of obligate mutualistic symbionts in insects. Within Phthiraptera, the most dramatically reduced genomes are found in the symbionts associated with sucking lice, living exclusively on mammal blood, compared to the less modified symbionts inhabiting the chewing lice, which feed on skin derivates. In this study, we investigate the genome characteristics of the symbiont associated withHaematomyzus elephantis. We sequenced and assembled theHaematomyzus elephantismetagenome, extracted a genome draft of its symbiotic bacterium, and show that the symbiont has a significantly reduced genome, which is with 0.39 Mbp the smallest genome among the symbionts known from Phthiraptera. Multigenic phylogenetic analysis places the symbiont into one of three clusters composed of long-branched symbionts from other insects. More specifically, it clusters together with symbionts from several other sucking lice, and also withWigglesworthia glossinidia, an obligate symbiont of tsetse flies. Consistent with the dramatic reduction of its genome, theH. elephantissymbiont lost many metabolic capacities. However, it retained functional pathways for four B vitamins, a trait typical for symbionts in blood-feeding insects. Considering genomic, metabolic, and phylogenetic characteristics, the new symbiont closely resembles those known from several sucking lice rather than chewing lice.ImportanceRhynchophthirina is a unique small group of permanent ectoparasites that is closely related to both sucking and chewing lice. These two groups of lice differ in their morphology, ecology, and feeding strategies. As a consequence of their different dietary sources, such as mammals’ blood versus vertebrate skin derivatives, they also exhibit distinct patterns of symbiosis with obligate bacterial symbionts. While Rhynchophthirina shares certain traits with sucking and chewing lice, the nature of its obligate symbiotic bacterium and its metabolic role are not known. In this study, we assemble genome of symbiotic bacterium fromHaematomyzus elphantis(Rhynchophthirina), demonstrating its close similarity and phylogenetic proximity to several symbionts of sucking lice. The genome is highly reduced (representing the smallest genome among louse-associated symbionts) and exhibits a significant loss of metabolic pathways. However, similar to other louse symbionts, it retains essential pathways for the synthesis of several B vitamins.
Neutrophil Extracellular Trap gene expression signatures identify prognostic and targetable signaling axes for inhibiting metastasis of pancreatic tumours
Authors: McDonald Paul C. , Topham James T , Awrey Shannon , Tavakoli Hossein , Carroll Rebekah , Brown Wells S. , Gerbec Zachary J. , Kalloger Steve E. , Karasinska Joanna M. , Tang Patricia , Goodwin Rachel , Jones Steven J. M. , Laskin Janessa , Marra Marco A , Morin Gregg B. , Renouf Daniel J. , Schaeffer David F. , Dedhar Shoukat 
Published: November 2024

AbstractTumour associated neutrophils (TANs) can promote metastasis through the interaction of Neutrophil Extracellular Traps (NETs) with tumour cells. Here, we examined the contribution of NETs in the progression of Pancreatic Ductal Adenocarcinoma (PDAC), which is characterized by high metastatic propensity. We carried out consensus clustering and pathway enrichment analysis of NET-related genes in an integrated cohort of 369 resectable and metastatic PDAC patient tumour samples, and compiled two gene expression signatures comprising of either, integrin-actin cytoskeleton, and Epithelial to Mesenchymal Transition (EMT) signaling, or cell death signaling, which identified patients with very poor to better overall survival, respectively. Tumour Infiltrating neutrophils and NETs associate with ITGB1, CCDC25 and ILK, within clinical and experimental PDAC tumours. Functionally, exposure of PDAC cells to NETs identified a cytoskeletal dynamic-associated CCDC25/ITGB1/ILK signaling complex which stimulates EMT and migration/ invasion. Furthermore, NETosis-driven experimental metastasis of PDAC cells is significantly inhibited byILKknock down. Our data identify novel NET-related gene expression signatures for PDAC patient stratification, and reveal targetable signaling axes to prevent and treat disease progression and metastasis.
Comparing neurocognitive mechanisms of mathematical ability and fluency in children: insights from an fNIRS study
Authors: Yeo Alethea Yen Ning , Wang Fengjuan , Jamaludin Azilawati 
Published: November 2024

ABSTRACTBackgroundEarly proficiency in mathematics is a strong predictor of later academic success and life achievement, considering the practical skills that mastering the subject enables students to equip. Yet, there exists a paucity of research into the neural mechanisms supporting mathematical abilities in young children. Recent research utilises resting state functional connectivity (RSFC), a measure of the coherence of brain activity among brain regions in the absence of tasks, to understand the functional roles of these regions.MethodsWe analysed the RSFC of 45 children to investigate the intrinsic cognitive processes underpinning arithmetic processing in three regions of interest (ROIs): middle frontal gyrus, inferior parietal lobule, and precuneus. Correlations between RSFC among these regions and mathematics or math fluency scores, derived from the Wechsler Individual Achievement Test (WIAT-III), were examined.ResultsRSFC between the right precuneus and both the ipsilateral middle frontal gyrus and inferior parietal region may be associated with arithmetic processing speed and accuracy, while cross-hemispheric RSFC between the right precuneus and the left inferior parietal lobule appears to be associated with problem-solving and numeracy skills. RSFC between the right precuneus and left inferior parietal lobule differed in children performing below the 10thpercentile in mathematics (out of 45 participants).ConclusionsThe results suggest that children of the same age may follow different neural development trajectories. More targeted and differentiated interventions are essential to offer additional and early support for students struggling with mathematics.
A language model assistant for biocatalysis
Authors: Nana Teukam Yves Gaetan , Grisoni Francesca , Manica Matteo 
Published: November 2024

AbstractLanguage model assistants have transformed how researchers interact with computational tools, offering unprecedented capabilities in understanding and generating complex scientific queries. We introduce a language model assistant for biocatalysis (LM-ABC), a computational tool designed to streamline workflows in enzyme engineering research. LM-ABC integrates a large language model with domain-specific modules to facilitate biocatalysis research through natural language inputs. Its architecture employs the Reasoning and Acting (ReACT) framework for dynamic tool selection and chaining, enabling functionalities like binding site extraction and molecular dynamics simulations. LM-ABC can interpret and process user queries in the form of natural language, and interface with existing computational resources to generate relevant results for enzyme engineering. Additionally, LM-ABC is available via both command-line and web-based interfaces, which lowers the barriers for its usage and integration in various disciplines. Provided as open-source software, the LM-ABC contributes to the application of language models in computational biology, potentially accelerating enzyme engineering research processes.
Replicating dynamic immune responses at single-cell resolution within a microfluidic human skin equivalent
Authors: Hindle Sarah A. , Brook Holly Bachas , Chrysanthou Alexandra , Chambers Emma S. , Caley Matthew P. , Connelly John T. 
Published: November 2024

AbstractThe intricate immunological functions of human skin involve the interplay between multiple different cell types as well as dynamic trafficking of leukocytes in and out the tissue, both of which are extremely challenging to replicate in vitro. To enable in vitro investigation of human skin immunology, we developed a microfluidic human skin equivalent (HSE) that supports the delivery of circulating immune cells via a vascular microchannel embedded within the dermis of a full-thickness construct. We demonstrated that stimulation of keratinocyte inflammation with lipopolysaccharide and nigericin promoted rapid monocyte recruitment out of the vascular channel and into the epidermal layer within 24 hours, followed by a second wave of monocyte migration into the dermis over a period of six days. Single-cell transcriptomic analysis of the tissue-resident and recruited cell populations revealed dynamic and cell-specific patterns of gene expression that were characteristic of acute activation and resolution of an inflammatory immune response.Moreover, comparison of the gene signatures of the monocyte-derived cells to in vivo populations provided molecular level validation of the model and indicated a differentiation trajectory of the monocytes through to mature dermal macrophages. To extend the microfluidic platform to additional applications, we also modelled age-associated immune dysfunction by the inclusion of senescent fibroblasts, which promoted increased monocyte recruitment into the HSE, replicating previous in vivo human studies. Thus, the microfluidic HSE presented here replicates key aspects of dynamic inflammatory immune responses within the skin and represents a tractable experimental tool for interrogating mechanisms of human skin immunology.
PanTax: Strain-level taxonomic classification of metagenomic data using pangenome graphs
Authors: Zhang Wenhai , Liu Yuansheng , Xu Jialu , Chen Enlian , Schönhuth Alexander , Luo Xiao 
Published: November 2024

AbstractMicrobes are omnipresent, thriving in a range of habitats from oceans to soils and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting the health of their hosts. Consequently, understanding the strain diversity within microbial communities is crucial, as variations between strains can lead to distinct phenotypic expressions or diverse biological functions. However, current methods for taxonomic classification from metagenomic sequencing data have several limitations, including their reliance solely on species resolution, support for either short or long reads, or their confinement to a given single species. Most notably, the majority of existing taxonomic classifiers rely solely on a single linear representative genome as a reference, which fails to capture the strain diversity, thereby introducing single-reference biases.Here, we present PanTax, a pangenome graph-based taxonomic classification method that overcomes the shortcomings of single-reference genome-based approaches, because pangenome graphs possess the capability to depict the genetic variability present across multiple evolutionarily or environmentally related genomes. PanTax provides a comprehensive solution to taxonomic classification for strain resolution, compatibility with both short and long reads, and compatibility with single or multiple species. Extensive benchmarking results demonstrate that PanTax drastically outperforms state-of-the-art approaches, primarily evidenced by its significantly higher precision or recall (at both species and strain levels), while maintaining comparable or better performance in other aspects across various datasets. PanTax is a user-friendly open-source tool that is publicly accessible athttps://github.com/LuoGroup2023/PanTax.
“The Association of the IL-1RA (rs315952) Cytokine Gene Polymorphism and Susceptibility to Systemic Lupus Erythematosus: A Meta-analysis”
Authors: Carlos Jan Mikkos L. , Gabriel Mary Angelei T. , Gatbunton Lark Joshua 
Published: November 2024

AbstractThrough a general retrospective analysis of the IL-1RAmspa11,100 (rs315952) cytokine gene polymorphism’s genotypes and alleles, the T/T genotype, along with the individual T allele, shows significant associations with the risk of Systemic Lupus Erythematosus (SLE). Meanwhile, the C/C and C/T genotypes, as well as the individual C allele, exhibited no significant associations. These results imply that having a homozygous genotype for the T allele increases the likelihood of SLE occurrence, while having a single C allele may induce a protective effect against the disease. To obtain these results, the researchers employed the analysis of six selected case-control and cross-sectional studies on healthy individuals SLE patients diagnosed through PCR tests. Forest plot construction was done to assess potential overlapping confidence intervals among the qualified studies. To identify the degree of heterogeneity among the papers, the odds ratio and the total confidence intervals, with the confidence interval set at 95%, were acquired through fixed and random effects models. Genotype and allele analyses with I2 statistics higher than 40% led to the funnel plot construction for outlier detection. Currently, the underlying processes that led to these genes’ and alleles’ varying outcomes to SLE risk remain elusive. Meanwhile, the subjects’ IL-1RA haplotypes may undermine these findings, along with the need for environmental consideration and the potential alteration of the gene and its corresponding alleles due to epigenetics. However, these findings still remain a possible starting point or reference for future studies.