bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limited host availability disrupts the genetic correlation between virulence and transmission
Authors: Godinho Diogo P , Rodrigues Leonor R , Lefèvre Sophie , Delteil Laurane , Mira André F , Fragata Inês R , Magalhães Sara , Duncan Alison B 
Published: November 2023

Abstract
Virulence is expected to be linked to parasite fitness via transmission. However, it is not clear whether this relationship is genetically determined, nor if it differs when transmission occurs continuously during, or only at the end of, the infection period. Here, we used inbred lines of the macroparasitic spider mite Tetranychus urticae to disentangle genetic vs. nongenetic correlations among traits, while varying parasite density and opportunities for transmission. A positive genetic correlation between virulence and the number of transmitting stages produced was found under continuous transmission. However, if transmission occurred only at the end of the infection period, this genetic correlation disappeared. Instead, we observed a negative relationship between virulence and the number of transmitting stages, driven by density dependence. Thus, within-host density dependence caused by reduced opportunities for transmission may hamper selection for higher virulence, providing a novel explanation as to why limited host availability leads to lower virulence.
Placental evolution from a three-dimensional and multiscale structural perspective
Authors: Laundon Davis , Gostling Neil J , Sengers Bram G , Chavatte-Palmer Pascale , Lewis Rohan M 
Published: November 2023

Abstract
The placenta mediates physiological exchange between the mother and the fetus. In placental mammals, all placentas are descended from a single common ancestor and functions are conserved across species; however, the placenta exhibits radical structural diversity. The selective pressures behind this structural diversity are poorly understood. Traditionally, placental structures have largely been investigated by grouping them into qualitative categories. Assessing the placenta on this basis could be problematic when inferring the relative “efficiency” of a placental configuration to transfer nutrients from mother to fetus. We argue that only by considering placentas as three-dimensional (3D) biological structures, integrated across scales, can the evolutionary questions behind their enormous structural diversity be quantitatively determined. We review the current state of placental evolution from a structural perspective, detail where 3D imaging and computational modeling have been used to gain insight into placental function, and outline an experimental roadmap to answer evolutionary questions from a multiscale 3D structural perspective. Our approach aims to shed light on placental evolution, and can be transferred to evolutionary investigations in any organ system.
Eating patterns contribute to shaping the gut microbiota in the mucosal simulator of the human intestinal microbial ecosystem
Authors: Minnebo Yorick , De Paepe Kim , Raes Jeroen , Van de Wiele Tom 
Published: November 2023

Abstract
Eating patterns, i.e. meal frequency and circadian timing of meals, are often modified in weight loss and metabolic healing strategies. However, in-depth research into the effects on the gut microbiome remains scarce, particularly across various colon regions and niches. We identified eating patterns to contribute in shaping the in vitro gut biomass production, metabolism, and microbial community compositions by subjecting four faecal microbiomes to a pattern that is standardized for a dynamic gut model (feeding at 09, 17, and 01 h), a typical Western (breakfast, lunch, and dinner at 09, 13, and 19 h, respectively), and a time-restricted pattern (single meal at 09 h). While eating patterns moderately affected the microbiome (2.4% and 1.8% significant variation in proportional and quantitative microbial compositions, respectively), significant changes were noted in the time-restricted pattern, including increased Bacteroides, Butyricicoccus, Dialister, and Faecalibacterium abundances. Sampling every 4 h revealed no significant circadian fluctuations in biomass production, microbial community compositions, or functionality. Longer fasting times favoured the growth of slower-growing species, such as Akkermansia, Dialister, and Parasutterella over faster-growers, such as Pseudomonas and Stenotrophomonas. Our findings illustrate the importance of recording and considering eating patterns as a gut microbiome determinant in in vivo and in vitro dietary intervention studies.
Mutations in yeast Pcf11, a conserved protein essential for mRNA 3′ end processing and transcription termination, elicit the Environmental Stress Response
Authors: Graber Joel H , Hoskinson Derick , Liu Huiyun , Kaczmarek Michaels Katarzyna , Benson Peter S , Maki Nathaniel J , Wilson Christian L , McGrath Caleb , Puleo Franco , Pearson Erika , Kuehner Jason N , Moore Claire 
Published: November 2023

Abstract
The Pcf11 protein is an essential subunit of the large complex that cleaves and polyadenylates eukaryotic mRNA precursor. It has also been functionally linked to gene-looping, termination of RNA Polymerase II (Pol II) transcripts, and mRNA export. We have examined a poorly characterized but conserved domain (amino acids 142–225) of the Saccharomyces cerevisiae Pcf11 and found that while it is not needed for mRNA 3′ end processing or termination downstream of the poly(A) sites of protein-coding genes, its presence improves the interaction with Pol II and the use of transcription terminators near gene promoters. Analysis of genome-wide Pol II occupancy in cells with Pcf11 missing this region, as well as Pcf11 mutated in the Pol II CTD Interacting Domain, indicates that systematic changes in mRNA expression are mediated primarily at the level of transcription. Global expression analysis also shows that a general stress response, involving both activation and suppression of specific gene sets known to be regulated in response to a wide variety of stresses, is induced in the two pcf11 mutants, even though cells are grown in optimal conditions. The mutants also cause an unbalanced expression of cell wall-related genes that does not activate the Cell Wall Integrity pathway but is associated with strong caffeine sensitivity. Based on these findings, we propose that Pcf11 can modulate the expression level of specific functional groups of genes in ways that do not involve its well-characterized role in mRNA 3′ end processing.
Euler characteristic curves and profiles: a stable shape invariant for big data problems
Authors: Dłotko Paweł , Gurnari Davide 
Published: November 2023

Abstract
Tools of topological data analysis provide stable summaries encapsulating the shape of the considered data. Persistent homology, the most standard and well-studied data summary, suffers a number of limitations; its computations are hard to distribute, and it is hard to generalize to multifiltrations and is computationally prohibitive for big datasets. In this article, we study the concept of Euler characteristics curves for 1-parameter filtrations and Euler characteristic profiles for multiparameter filtrations. While being a weaker invariant in one dimension, we show that Euler characteristic–based approaches do not possess some handicaps of persistent homology; we show efficient algorithms to compute them in a distributed way, their generalization to multifiltrations, and practical applicability for big data problems. In addition, we show that the Euler curves and profiles enjoy a certain type of stability, which makes them robust tools for data analysis. Lastly, to show their practical applicability, multiple use cases are considered.
‘It doesn’t happen any other way’: relationship-building and reflexivity for equity-focused intersectoral practice (EquIP)
Authors: Phipps Erica , Bumstead Lynda , Butt Tanya , Crighton Eric J , Desjardins Nadine , Hart Robert , Oickle Dianne , Sánchez-Pimienta Carlos E , Schlonies Renee , Schonauer Misty , Umbach Jill , Masuda Jeffrey R 
Published: November 2023

Abstract
Intersectoral processes that bring together public institutions, civil society organizations and affected community members are essential to tackling complex health equity challenges. While conventional wisdom points to the importance of human relationships in fostering collaboration, there is a lack of practical guidance on how to do intersectoral work in ways that support authentic relationship-building and mitigate power differentials among people with diverse experiences and roles. This article presents the results of RentSafe EquIP, a community-based participatory research initiative conducted in Owen Sound, Canada, in the midst of a housing crisis. The research explored the potential utility of equity-focused intersectoral practice (EquIP), a novel approach that invests in human relationships and knowledge co-creation among professionals and affected members of the community. The three-phase EquIP methodology centred the grounded expertise of community members with lived/living experience of housing inadequacy to catalyze reflexive thinking by people in professional roles about the institutional gaps and barriers that prevent effective intersectoral response to housing-related inequities. The research demonstrated that EquIP can support agency professionals and community members to (i) engage in (re)problematization to redefine the problem statement to better include upstream drivers of inequity, (ii) support reflexivity among those in professional roles to identify institutional practices, policies and norms that perpetuate stigma and impede effective intersectoral response and (iii) spark individual and collective agency and commitment towards a more equity-focused intersectoral system. We conclude that the EquIP methodology is a promising approach for communities seeking to address persistent health equity and social justice challenges.
High-quality assembly and methylome of a Tibetan wild tree peony genome (Paeonia ludlowii) reveal the evolution of giant genome architecture
Authors: Xiao Pei-Xuan , Li Yuanrong , Lu Jin , Zuo Hao , Pingcuo Gesang , Ying Hong , Zhao Fan , Xu Qiang , Zeng Xiuli , Jiao Wen-Biao 
Published: November 2023

Abstract
Tree peony belongs to one of the Saxifragales families, Paeoniaceae. It is one of the most famous ornamental plants, and is also a promising woody oil plant. Although two Paeoniaceae genomes have been released, their assembly qualities are still to be improved. Additionally, more genomes from wild peonies are needed to accelerate genomic-assisted breeding. Here we assemble a high-quality and chromosome-scale 10.3-Gb genome of a wild Tibetan tree peony, Paeonia ludlowii, which features substantial sequence divergence, including around 75% specific sequences and gene-level differentials compared with other peony genomes. Our phylogenetic analyses suggest that Saxifragales and Vitales are sister taxa and, together with rosids, they are the sister taxon to asterids. The P. ludlowii genome is characterized by frequent chromosome reductions, centromere rearrangements, broadly distributed heterochromatin, and recent continuous bursts of transposable element (TE) movement in peony, although it lacks recent whole-genome duplication. These recent TE bursts appeared during the uplift and glacial period of the Qinghai–Tibet Plateau, perhaps contributing to adaptation to rapid climate changes. Further integrated analyses with methylome data revealed that genome expansion in peony might be dynamically affected by complex interactions among TE proliferation, TE removal, and DNA methylation silencing. Such interactions also impact numerous recently duplicated genes, particularly those related to oil biosynthesis and flower traits. This genome resource will not only provide the genomic basis for tree peony breeding but also shed light on the study of the evolution of huge genome structures as well as their protein-coding genes.
Incidental Dysplasia During Total Proctocolectomy With Ileoanal Pouch: Is It Associated With Worse Outcomes?
Authors: Maspero Marianna , Otero Ana , Lavryk Olga , Holubar Stefan D , Lipman Jeremy , Gorgun Emre , Liska David , Kessler Hermann , Valente Michael , Steele Scott R , Hull Tracy 
Published: November 2023

Abstract

Background
Patients with inflammatory bowel disease (IBD) are at increased risk of colorectal cancer. In cases of invisible or nonendoscopically resectable dysplasia found at colonoscopy, total proctocolectomy with ileal pouch anal anastomosis can be offered with good long-term outcomes; however, little is known regarding cancer-related outcomes when dysplasia is found incidentally after surgery on final pathology.

Methods
Using our prospectively collected pouch registry, we identified patients who had preoperative colonic dysplasia or dysplasia found only after colectomy. Patients with cancer preoperatively or after colectomy were excluded. Included patients were divided into 3 groups: PRE (+preoperative biopsy, negative final pathology), BOTH (+preoperative biopsy and final pathology), and POST (negative preoperative biopsy, +final pathology). Long-term outcomes in the 3 groups were assessed.

Results
In total, 517 patients were included: PRE = 125, BOTH = 254, POST = 137. After a median follow-up of 12 years (IQR 3-21), there were no differences in overall, disease-free, or pouch survival between groups. Cancer/dysplasia developed in 11 patients: 3 (2%) in the PRE, 5 (2%) in the BOTH, and 3 (2%) in the POST group. Only 1 cancer-related death occurred in the entire cohort (PRE group). Disease-free survival at 10 years was 98% for all groups (P = .97). Pouch survival at 10 years was 96% for PRE, 99% for BOTH, and 97% for POST (P = .24).

Conclusions
The incidental finding of dysplasia on final pathology after proctocolectomy was not associated with worsened outcomes compared with preoperatively diagnosed dysplasia.
Machine-learning-based prediction of survival and mitral regurgitation recurrence in patients undergoing mitral valve repair
Authors: Kang Yoonjin , Sohn Suk Ho , Choi Jae Woong , Hwang Ho Young , Kim Kyung Hwan 
Published: November 2023

Abstract

OBJECTIVES
This study was conducted to assess long-term clinical outcomes after mitral valve repair using machine-learning techniques.

METHODS
We retrospectively evaluated 436 consecutive patients (mean age: 54.7 ± 15.4; 235 males) who underwent mitral valve repair between January 2000 and December 2017. Actuarial survival and freedom from significant (≥ moderate) mitral regurgitation (MR) were clinical end points. To evaluate the independent risk factors, random survival forest (RSF), extreme gradient boost (XGBoost), support vector machine, Cox proportional hazards model and general linear models with elastic net regularization were used. Concordance indices (C-indices) of each model were estimated.

RESULTS
The operative mortality was 0.9% (N = 4). Reoperation was required in 15 patients (3.5%). In terms of C-index, the overall performance of the XGBoost (C-index 0.806) and RSF models (C-index 0.814) was better than that of the Cox model (C-index 0.733) in overall survival. For the recurrent MR, the C-index for XGBoost was 0.718, which was the highest among the 5 models. Compared to the Cox model (C-index 0.545), the C-indices of the XGBoost (C-index 0.718) and RSF models (C-index 0.692) were higher.

CONCLUSIONS
Machine-learning techniques can be a useful tool for both prediction and interpretation in the survival and recurrent MR. From the machine-learning techniques examined here, the long-term clinical outcomes of mitral valve repair were excellent. The complexity of MV increased the risk of late mitral valve-related reoperation.
Brill–Noether Theory of Hilbert Schemes of Points on Surfaces
Authors: Bayer Arend , Chen Huachen , Jiang Qingyuan 
Published: November 2023

Abstract
We show that Brill–Noether loci in Hilbert scheme of points on a smooth connected surface $S$ are non-empty whenever their expected dimension is positive and that they are irreducible and have expected dimensions. More precisely, we consider the loci of pairs $(I, s)$, where $I$ is an ideal that locally at the point $s$ of $S$ needs a given number of generators. We give two proofs. The first uses Iarrobino’s description [9] of the Hilbert–Samuel stratification of local punctual Hilbert schemes, and the second is based on induction via birational relationships between different Brill–Noether loci given by nested Hilbert schemes.
The Costly Vicious Cycle of Infections and Malnutrition
Authors: Sinha Pranay , Guerrant Richard L 
Published: November 2023

Abstract
Malnutrition, which continues to affect hundreds of millions of people worldwide, is both a cause and consequence of a range of infectious diseases. In this perspective piece, we provide an overview of the bidirectional relationship between malnutrition and infectious diseases. In addition to enteric infections, we use tuberculosis as a case study of this relationship between malnutrition and infectious diseases, and to demonstrate the potential of nutritional interventions to mitigate mortality and morbidity from infectious diseases. We conclude with suggestions on advancing our understanding of the vicious cycle of microbes and malnutrition and finding ways to break it.
WGS of a cluster of MDR Shigella sonnei utilizing Oxford Nanopore R10.4.1 long-read sequencing
Authors: Ritchie Gordon , Chorlton Samuel D , Matic Nancy , Bilawka Jennifer , Gowland Leah , Leung Victor , Stefanovic Aleksandra , Romney Marc G , Lowe Christopher F 
Published: November 2023

Abstract

Objectives
To utilize long-read nanopore sequencing (R10.4.1 flowcells) for WGS of a cluster of MDR Shigella sonnei, specifically characterizing genetic predictors of antimicrobial resistance (AMR).

Methods
WGS was performed on S. sonnei isolates identified from stool and blood between September 2021 and October 2022. Bacterial DNA from clinical isolates was extracted on the MagNA Pure 24 and sequenced on the GridION utilizing R10.4.1 flowcells. Phenotypic antimicrobial susceptibility testing was interpreted based on CLSI breakpoints. Sequencing data were processed with BugSeq, and AMR was assessed with BugSplit and ResFinder.

Results
Fifty-six isolates were sequenced, including 53 related to the cluster of cases. All cluster isolates were identified as S. sonnei by sequencing, with global genotype 3.6.1.1.2 (CipR.MSM5), MLST 152 and PopPUNK cluster 3. Core genome MLST (cgMLST, examining 2513 loci) and reference-based MLST (refMLST, examining 4091 loci) both confirmed the clonality of the isolates. Cluster isolates were resistant to ampicillin (blaTEM-1), trimethoprim/sulfamethoxazole (dfA1, dfrA17; sul1, sul2), azithromycin (ermB, mphA) and ciprofloxacin (gyrA S83L, gyrA D87G, parC S80I). No genomic predictors of resistance to carbapenems were identified.

Conclusions
WGS with R10.4.1 enabled rapid sequencing and identification of an MDR S. sonnei community cluster. Genetic predictors of AMR were concordant with phenotypic antimicrobial susceptibility testing.
Embedding deep neural network in enhanced Schapery theory for progressive failure analysis of fiber reinforced laminates
Authors: Lin Shiyao , Post Alex , Waas Anthony M 
Published: November 2023

Abstract
Computational progressive failure analysis of carbon fiber reinforced polymer composite is of vital importance in the verification and validation process of the structural integrity and damage tolerance of modern lightweight aeronautical structures. Enhanced Schapery theory (EST) has been developed and applied to predict the damage pattern and load-bearing capacity of various composite structures. In this paper, EST is enhanced by a deep neural network (DNN) model, which enables fast and accurate predictions of matrix cracking angles under arbitrary stress states of any composite laminate. The DNN model is trained by TensorFlow based on data generated by a damage initiation criterion, which originates from the Mohr–Coulomb failure theory. The EST-DNN model is applied to open-hole tension/compression problems. The results from the EST-DNN model are obtained with no loss in accuracy. The results presented combine the efficient and accurate predicting capabilities brought by machine learning tools and the robustness and user-friendliness of the EST finite element model.
A multi-information combined convolutional neural network velocity spectrum automatic picking method
Authors: Jiang Run , Sun Xiaodong , Li Zhenchun , Peng Dongdong , Zhao Liang 
Published: November 2023

Abstract
Seismic velocity is a critical parameter in seismic exploration, and its accuracy significantly affects the reliability of data processing and interpretation results. However, manual velocity picking methods are not only inefficient but also time consuming, making them increasingly inadequate for meeting the demands of practical production work. This paper introduces the multi-information combination convolutional neural network (MCCN) velocity auto-picking method. Building on the foundation of convolutional neural networks, we have designed the network structure of the MCCN method specifically tailored to the characteristics of stacked velocity picking tasks. Given that velocity spectrum energy clusters exhibit both morphological and trend features, we use a regression convolutional neural network to enhance the accuracy of velocity picking. Furthermore, as the velocity spectrum contains interference from multiple waves and other noise, we employ a coordinate attention mechanism to mitigate the influence of interfering information. Our approach involves the simultaneous incorporation of velocity spectrum and CMP information through a dual-combination network, thereby further enhancing velocity picking accuracy. Finally, we compare our method with fully connected convolutional neural networks and manual velocity picking methods, demonstrating the practicality and precision of our proposed approach.
Long-term aspirin use and cancer risk: a 20-year cohort study
Authors: Skriver Charlotte , Maltesen Thomas , Dehlendorff Christian , Skovlund Charlotte Wessel , Schmidt Morten , Sørensen Henrik Toft , Friis Søren 
Published: November 2023

Abstract

Background
Long-term use of aspirin has been shown to reduce colorectal cancer risk, but the association remains inconclusive for individual noncolorectal cancers. We examined the association between long-term aspirin use and cancer risk in Denmark.

Methods
Using nationwide registries, we followed individuals aged 40-70 years at baseline (January 1, 1997) for cancer diagnoses through 2018. We assessed low-dose (75-150 mg) aspirin use according to continuity, duration, and cumulative amount. In addition, we explored associations with consistent high-dose (500 mg) aspirin use. Using Cox regression, we estimated multivariable-adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) with aspirin use for overall and site-specific cancer.

Results
Among 1 909 531 individuals, 422 778 were diagnosed with cancer during mean follow-up of 18.2 years. Low-dose aspirin use did not reduce the hazard ratio for cancer overall irrespective of continuity and duration of use (continuous use: HR = 1.04, 95% CI = 1.03 to 1.06). However, long-term (≥5 or ≥10 years) use was associated with at least 10% reductions in hazard ratios for several cancer sites: colon, rectum, esophagus, stomach, liver, pancreas, small intestine, head and neck, brain tumors, meningioma, melanoma, thyroid, non-Hodgkin lymphoma, and leukemia. Substantially elevated hazard ratios were found for lung and bladder cancer. In secondary analyses, consistent high-dose aspirin use was associated with reduced hazard ratios for cancer overall (HR = 0.89, 95% CI = 0.85 to 0.93) and for several cancer sites.

Conclusion
Long-term low-dose aspirin use was associated with slight to moderately reduced risks for several cancers but not for cancer overall owing to increased risk for some common cancers. Similar or slightly stronger inverse associations were observed for consistent use of high-dose aspirin.