bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits
Authors: Prohaska Alexandre , Rey-Serra Pol , Petit Johann , Petit Aurélie , Perrotte Justine , Rothan Christophe , Denoyes Béatrice 
Published: May 2024

Abstract
Fruit quality traits are major breeding targets in cultivated strawberry (Fragaria × ananassa). Taking into account the requirements of both growers and consumers when selecting high quality cultivars is a real challenge. Here, we used a diversity panel enriched with unique European accessions and the 50K FanaSNP array to highlight the evolution of strawberry diversity over the past 160 years, investigate the molecular basis of 12 major fruit quality traits by Genome-Wide Association Studies (GWAS), and provide genetic markers for breeding. Results show that considerable improvements of key breeding targets including fruit weight, firmness, composition and appearance occurred simultaneously in European and American cultivars. Despite the high genetic diversity of our panel, we observed a drop in nucleotide diversity in certain chromosomal regions, revealing the impact of selection. GWAS identified 71 associations with 11 quality traits and, while validating known associations (firmness, sugar), highlighted the predominance of new QTL, demonstrating the value of using untapped genetic resources. Three of the six selective sweeps detected are related to glossiness or skin resistance, two little-studied traits important for fruit attractiveness and, potentially, postharvest shelf-life. Moreover, major QTL for firmness, glossiness, skin resistance and susceptibility to bruising are found within a low diversity region of chromosome 3D. Stringent search for candidate genes underlying QTL uncovered strong candidates for fruit color, firmness, sugar and acid composition, glossiness and skin resistance. Overall, our study provides a potential avenue for extending shelf-life without compromising flavor and color as well as the genetic markers needed to achieve this goal.
Antibiotic Resistance of Urinary Tract Infection Recurrences in a Large Integrated US Healthcare System
Authors: Ku Jennifer H , Tartof Sara Y , Contreras Richard , Ackerson Bradley K , Chen Lie H , Reyes Iris A C , Pellegrini Michele , Schmidt Johannes E , Bruxvoort Katia J 
Published: May 2024

Abstract

Background
Data on antibiotic resistance of uropathogens for urinary tract infection (UTI) recurrences are lacking.

Methods
In a retrospective cohort of adults at Kaiser Permanente Southern California with culture-confirmed index uncomplicated UTI (uUTI) between January 2016 and December 2020, we examined the number and characteristics of subsequent culture-confirmed UTIs through 2021.

Results
We identified 148 994 individuals with a culture-confirmed index uUTI (88% female, 44% Hispanic; mean age, 51 years [standard deviation, 19 years]), of whom 19% developed a subsequent culture-confirmed UTI after a median 300 days (interquartile range, 126–627 days). The proportion of UTI due to Escherichia coli was highest for index uUTI (79%) and decreased to 73% for sixth UTI (UTI 6) (P for trend &lt; .001), while the proportion due to Klebsiella spp increased from index UTI (7%) to UTI 6 (11%) (P for trend &lt; .001). Nonsusceptibility to ≥1 and ≥3 antibiotic classes was observed in 57% and 13% of index uUTIs, respectively, and was higher for subsequent UTIs (65% and 20%, respectively, for UTI 6). Most commonly observed antibiotic nonsusceptibility patterns included penicillins alone (12%), and penicillins and trimethoprim-sulfamethoxazole plus ≥1 additional antibiotic class (9%).

Conclusions
Antibiotic nonsusceptibility is common in UTIs and increases with subsequent UTIs. Continuous monitoring of UTI recurrences and susceptibility patterns is needed to guide treatment decisions.
Extended-Spectrum β-Lactamase Shigella sonnei Cluster Among Men Who Have Sex With Men in Chicago, Illinois, July–October 2022
Authors: Faherty Emily A G , Kling Kendall , Barbian Hannah J , Qi Chao , Altman Shana , Dhiman Vineet K , Teran Richard , Anderson Kendall , Yuce Deniz , Smith Shamika , Richardson Morgan , Vogelzang Kara , Ghinai Isaac , Ruestow Peter , Heimler Ira , Menon Adil , Francois Watkins Louise K , Logan Naeemah , Kim Do Young , Pacilli Massimo , Kerins Janna , Black Stephanie 
Published: May 2024

Abstract
Drug-resistant shigellosis is increasing, particularly among men who have sex with men (MSM). During July–October 2022, an extended-spectrum β-lactamase–producing Shigella sonnei cluster of 9 patients was identified in Chicago, of whom 8 were MSM and 6 were festival attendees. The cluster also included 4 domestic travelers to Chicago. Sexual health care for MSM should include shigellosis diagnosis and prevention.
Distinct Gut Microbiota Signatures Associated With Progression of Atherosclerosis in People Living With Human Immunodeficiency Virus
Authors: Masiá Mar , García José A , García-Abellán Javier , Padilla Sergio , Fernández-González Marta , Agulló Vanesa , Gosalbes Maria José , Ruíz-Pérez Sonia , Mascarell Paula , Botella Angela , Gutiérrez Félix 
Published: May 2024

AbstractBackgroundThe relationship of microbiota composition dynamics and the progression of subclinical atherosclerosis in people with human immunodeficiency virus (PWH) remains unknown.MethodsA 96-week, prospective, longitudinal study was performed in virologically suppressed PWH. Carotid intima-media thickness (cIMT) measurements and stool samples were obtained at baseline and at 48- and 96-week visits. cIMT progression was defined as an increase of &gt;10% and/or detection of new carotid plaque. To profile the gut microbiome, amplification and sequencing of 16S ribosomal RNA (V3–V4 variable regions) were carried out, following the Illumina protocol. Sequencing was performed using the MiSeq platform.ResultsAt the baseline, 48-week, and 96-week visits, 191, 190, and 167 patients, respectively, had fecal samples available for microbiome analysis. Eighty-seven participants (43%) showed atherosclerosis progression, and 54 (26.7%) presented with new carotid plaque. No significant differences were observed in adjusted α-diversity indices between groups, defined by cIMT progression. β-Diversity, determined through principal coordinate analysis, showed that the groups exhibited distinct microbial profiles (P = .03; permutational multivariate analysis of variance). Longitudinal analysis with Analysis of Compositions of Microbiomes with Bias Correction 2, adjusted for traditional cardiovascular risk factors, status as men who have sex with men, and nadir CD4 count, revealed that cIMT progression was consistently associated with Agathobacter and Ruminococcus 2, while nonprogression was consistently associated with Prevotella 7.ConclusionsProgression of atherosclerosis in PWH might be associated with distinctive signatures in the gut microbiota.
Metabolic pathways and antimicrobial peptide resistance in bacteria
Authors: Elbediwi Mohammed , Rolff Jens 
Published: May 2024

Abstract
Antimicrobial resistance is a pressing concern that poses a significant threat to global public health, necessitating the exploration of alternative strategies to combat drug-resistant microbial infections. Recently, antimicrobial peptides (AMPs) have gained substantial attention as possible replacements for conventional antibiotics. Because of their pharmacodynamics and killing mechanisms, AMPs display a lower risk of bacterial resistance evolution compared with most conventional antibiotics. However, bacteria display different mechanisms to resist AMPs, and the role of metabolic pathways in the resistance mechanism is not fully understood. This review examines the intricate relationship between metabolic genes and AMP resistance, focusing on the impact of metabolic pathways on various aspects of resistance. Metabolic pathways related to guanosine pentaphosphate (pppGpp) and guanosine tetraphosphate (ppGpp) [collectively (p)ppGpp], the tricarboxylic acid (TCA) cycle, haem biosynthesis, purine and pyrimidine biosynthesis, and amino acid and lipid metabolism influence in different ways metabolic adjustments, biofilm formation and energy production that could be involved in AMP resistance. By targeting metabolic pathways and their associated genes, it could be possible to enhance the efficacy of existing antimicrobial therapies and overcome the challenges exhibited by phenotypic (recalcitrance) and genetic resistance toward AMPs. Further research in this area is needed to provide valuable insights into specific mechanisms, uncover novel therapeutic targets, and aid in the fight against antimicrobial resistance.
Distribution and expression of the aac(6′)-Im (aacA16) aminoglycoside resistance gene
Authors: Harmer Christopher J , Nelson Messiah J , Lebreton Francois , Lertsethtakarn Paphavee , McGann Patrick T , Hall Ruth M 
Published: May 2024

Abstract

Background
The aac(6′)-Im (aacA16) amikacin, netilmicin and tobramycin resistance gene cassette had been circulating globally undetected for many years in a sublineage of Acinetobacter baumannii global clone 2.

Objectives
To identify sources for the aac(6′)-Im fragment found in A. baumannii.

Methods
MinION long-read sequencing and Unicycler hybrid assemblies were used to determine the genetic context of the aac(6′)-Im gene. Quantitative reverse transcriptase PCR was used to measure expression.

Results
Among &gt;60 000 non-Acinetobacter draft genomes in the MRSN collection, the aac(6′)-Im gene was detected in Pseudomonas putida and Enterobacter hormaechei isolates recovered from patients in Thailand between 2016 and 2019. Genomes of multiply resistant P. putida MRSN365855 and E. hormaechei MRSN791417 were completed. The class 1 integron containing the aac(6′)-Im cassette was in the chromosome in MRSN365855, and in an HI2 plasmid in MRSN791417. However, MRSN791417 was amikacin susceptible and the gene was not expressed due to loss of the Pc promoter of the integron. Further examples of aac(6′)-Im in plasmids from or the chromosome of various Gram-negative species were found in the GenBank nucleotide database. The aac(6′)-Im context in integrons in pMRSN791417-8 and a Klebsiella plasmid pAMR200031 shared similarities with the aac(6′)-Im region of AbGRI2-Im islands in A. baumannii. In other cases, the cassette array including the aac(6′)-Im cassette was different.

Conclusions
The aac(6′)-Im gene is widespread, being found so far in several different species and in several different gene cassette arrays. The lack of amikacin resistance in E. hormaechei highlights the importance of correlating resistance gene content and antibiotic resistance phenotype.
Influence of fumarate on interspecies electron transfer and the metabolic shift induced in Clostridium pasteurianum by Geobacter sulfurreducens
Authors: Pérez-Bernal María Fernanda , Berthomieu Roland , Quéméner Elie Desmond-Le , Bernet Nicolas , Trably Eric 
Published: May 2024

Abstract

Aims
In previous studies, it was demonstrated that co-culturing Clostridium pasteurianum and Geobacter sulfurreducens triggers a metabolic shift in the former during glycerol fermentation. This shift, attributed to interspecies electron transfer and the exchange of other molecules, enhances the production of 1,3-propanediol at the expense of the butanol pathway. The aim of this investigation is to examine the impact of fumarate, a soluble compound usually used as an electron acceptor for G. sulfurreducens, in the metabolic shift previously described in C. pasteurianum.

Methods and Results
Experiments were conducted by adding along with glycerol, acetate, and different quantities of fumarate in co-cultures of G. sulfurreducens and C. pasteurianum. A metabolic shift was exhibited in all the co-culture conditions. This shift was more pronounced at higher fumarate concentrations. Additionally, we observed G. sulfurreducens growing even in the absence of fumarate and utilizing small amounts of this compound as an electron donor rather than an electron acceptor in the co-cultures with high fumarate addition.

Conclusions
This study provided evidence that interspecies electron transfer continues to occur in the presence of a soluble electron acceptor, and the metabolic shift can be enhanced by promoting the growth of G. sulfurreducens.
To weight or not to weight? The effect of selection bias in 3 large electronic health record-linked biobanks and recommendations for practice
Authors: Salvatore Maxwell , Kundu Ritoban , Shi Xu , Friese Christopher R , Lee Seunggeun , Fritsche Lars G , Mondul Alison M , Hanauer David , Pearce Celeste Leigh , Mukherjee Bhramar 
Published: May 2024

Abstract

Objectives
To develop recommendations regarding the use of weights to reduce selection bias for commonly performed analyses using electronic health record (EHR)-linked biobank data.

Materials and methods
We mapped diagnosis (ICD code) data to standardized phecodes from 3 EHR-linked biobanks with varying recruitment strategies: All of Us (AOU; n = 244 071), Michigan Genomics Initiative (MGI; n = 81 243), and UK Biobank (UKB; n = 401 167). Using 2019 National Health Interview Survey data, we constructed selection weights for AOU and MGI to represent the US adult population more. We used weights previously developed for UKB to represent the UKB-eligible population. We conducted 4 common analyses comparing unweighted and weighted results.

Results
For AOU and MGI, estimated phecode prevalences decreased after weighting (weighted-unweighted median phecode prevalence ratio [MPR]: 0.82 and 0.61), while UKB estimates increased (MPR: 1.06). Weighting minimally impacted latent phenome dimensionality estimation. Comparing weighted versus unweighted phenome-wide association study for colorectal cancer, the strongest associations remained unaltered, with considerable overlap in significant hits. Weighting affected the estimated log-odds ratio for sex and colorectal cancer to align more closely with national registry-based estimates.

Discussion
Weighting had a limited impact on dimensionality estimation and large-scale hypothesis testing but impacted prevalence and association estimation. When interested in estimating effect size, specific signals from untargeted association analyses should be followed up by weighted analysis.

Conclusion
EHR-linked biobanks should report recruitment and selection mechanisms and provide selection weights with defined target populations. Researchers should consider their intended estimands, specify source and target populations, and weight EHR-linked biobank analyses accordingly.
Becoming Nature: Classifying Encounters in Interspecies Contact Zones
Authors: Grant Annetta , Canniford Robin , Shankar Avi 
Published: May 2024

Abstract
Nature affords transformations to consumers’ social, embodied, and temporal experiences. Yet, consumer research has yet to consider how wild species contribute to and are affected by experiential consumption in nature. With data from an ethnography of fly fishing, we theorize human–fish interactions as encounters in interspecies contact zones. Our findings explain how these encounters are established, engendering processes of interspecies becoming that transform both species. We discuss how these transformations are ordered by power relationships that classify roles for entities enrolled in consumption assemblages. Often, humans exert power over other living entities by classifying them as resources for consumption. Yet, we also discover more reciprocal expressions of power between humans and other species. With consumption as a major contributor to the decline of wild species populations, we discuss theoretical and practical implications of our work that are intended to stimulate further research.
Introducing two improved methods for approximating radiative cooling in hydrodynamical simulations of accretion discs
Authors: Young Alison K , Celeste Maggie , Booth Richard A , Rice Ken , Koval Adam , Carter Ethan , Stamatellos Dimitris 
Published: May 2024

ABSTRACT
The evolution of many astrophysical systems depends strongly on the balance between heating and cooling, in particular star formation in giant molecular clouds and the evolution of young protostellar systems. Protostellar discs are susceptible to the gravitational instability, which can play a key role in their evolution and in planet formation. The strength of the instability depends on the rate at which the system loses thermal energy. To study the evolution of these systems, we require radiative cooling approximations because full radiative transfer is generally too expensive to be coupled to hydrodynamical models. Here, we present two new approximate methods for computing radiative cooling that make use of the polytropic cooling approximation. This approach invokes the assumption that each parcel of gas is located within a spherical pseudo-cloud, which can then be used to approximate the optical depth. The first method combines the methods introduced by Stamatellos et al. and Lombardi et al. to overcome the limitations of each method at low and high optical depths, respectively. The second method, the ‘modified Lombardi’ method, is specifically tailored for self-gravitating discs. This modifies the scale height estimate from the method of Lombardi et al. using the analytical scale height for a self-gravitating disc. We show that the modified Lombardi method provides an excellent approximation for the column density in a fragmenting disc, a regime in which the existing methods fail to recover the clumps and spiral structures. We therefore recommend this improved radiative cooling method for more realistic simulations of self-gravitating discs.
Evolution of Chromosomal Inversions across an Avian Radiation
Authors: Knief Ulrich , Müller Ingo A , Stryjewski Katherine F , Metzler Dirk , Sorenson Michael D , Wolf Jochen B W 
Published: May 2024

Abstract
Chromosomal inversions are structural mutations that can play a prominent role in adaptation and speciation. Inversions segregating across species boundaries (trans-species inversions) are often taken as evidence for ancient balancing selection or adaptive introgression, but can also be due to incomplete lineage sorting. Using whole-genome resequencing data from 18 populations of 11 recognized munia species in the genus Lonchura (N = 176 individuals), we identify four large para- and pericentric inversions ranging in size from 4 to 20 Mb. All four inversions cosegregate across multiple species and predate the numerous speciation events associated with the rapid radiation of this clade across the prehistoric Sahul (Australia, New Guinea) and Bismarck Archipelago. Using coalescent theory, we infer that trans-specificity is improbable for neutrally segregating variation despite substantial incomplete lineage sorting characterizing this young radiation. Instead, the maintenance of all three autosomal inversions (chr1, chr5, and chr6) is best explained by selection acting along ecogeographic clines not observed for the collinear parts of the genome. In addition, the sex chromosome inversion largely aligns with species boundaries and shows signatures of repeated positive selection for both alleles. This study provides evidence for trans-species inversion polymorphisms involved in both adaptation and speciation. It further highlights the importance of informing selection inference using a null model of neutral evolution derived from the collinear part of the genome.
Riboswitch and small RNAs modulate btuB translation initiation in Escherichia coli and trigger distinct mRNA regulatory mechanisms
Authors: Bastet Laurène , Korepanov Alexey P , Jagodnik Jonathan , Grondin Jonathan P , Lamontagne Anne-Marie , Guillier Maude , Lafontaine Daniel A 
Published: May 2024

Abstract
Small RNAs (sRNAs) and riboswitches represent distinct classes of RNA regulators that control gene expression upon sensing metabolic or environmental variations. While sRNAs and riboswitches regulate gene expression by affecting mRNA and protein levels, existing studies have been limited to the characterization of each regulatory system in isolation, suggesting that sRNAs and riboswitches target distinct mRNA populations. We report that the expression of btuB in Escherichia coli, which is regulated by an adenosylcobalamin (AdoCbl) riboswitch, is also controlled by the small RNAs OmrA and, to a lesser extent, OmrB. Strikingly, we find that the riboswitch and sRNAs reduce mRNA levels through distinct pathways. Our data show that while the riboswitch triggers Rho-dependent transcription termination, sRNAs rely on the degradosome to modulate mRNA levels. Importantly, OmrA pairs with the btuB mRNA through its central region, which is not conserved in OmrB, indicating that these two sRNAs may have specific targets in addition to their common regulon. In contrast to canonical sRNA regulation, we find that OmrA repression of btuB is lost using an mRNA binding-deficient Hfq variant. Together, our study demonstrates that riboswitch and sRNAs modulate btuB expression, providing an example of cis- and trans-acting RNA-based regulatory systems maintaining cellular homeostasis.
Evaluating the oral delivery of GalNAc-conjugated siRNAs in rodents and non-human primates
Authors: Yu Mikyung , Qin June , Liu Xiumin , Ramsden Diane , Williams Brian , Zlatev Ivan , Guenther Dale , Matsuda Shigeo , Tymon Roxanne , Darcy Justin , Wong Catrina , Tsung Jamie , Zawaneh Peter , Chong Saeho , Theile Christopher S , Taneja Nathan , Rogers Arlin , Liu Ju , Castellanos-Rizaldos Elena , Bond Sarah , So Kawai , Denoncourt Jason , Castoreno Adam , Manoharan Muthiah , Wu Jing-Tao , Fitzgerald Kevin , Maier Martin A , Jadhav Vasant , Nair Jayaprakash K 
Published: May 2024

Abstract
Oral delivery is the most widely used and convenient route of administration of medicine. However, oral administration of hydrophilic macromolecules is commonly limited by low intestinal permeability and pre-systemic degradation in the gastrointestinal (GI) tract. Overcoming some of these challenges allowed emergence of oral dosage forms of peptide-based drugs in clinical settings. Antisense oligonucleotides (ASOs) have also been investigated for oral administration but despite the recent progress, the bioavailability remains low. Given the advancement with highly potent and durable trivalent N-acetylgalactosamine (GalNAc)-conjugated small interfering RNAs (siRNAs) via subcutaneous (s.c.) injection, we explored their activities after oral administration. We report robust RNA interference (RNAi) activity of orally administrated GalNAc–siRNAs co-formulated with permeation enhancers (PEs) in rodents and non-human primates (NHPs). The relative bioavailability calculated from NHP liver exposure was &lt;2.0% despite minimal enzymatic degradation in the GI. To investigate the impact of oligonucleotide size on oral delivery, highly specific GalNAc-conjugated single-stranded oligonucleotides known as REVERSIRs with different lengths were employed and their activities for reversal of RNAi effect were monitored. Our data suggests that intestinal permeability is highly influenced by the size of oligonucleotides. Further improvements in the potency of siRNA and PE could make oral delivery of GalNAc–siRNAs as a practical solution.