bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypermutator emergence in experimental Escherichia coli populations is stress-type dependent
Authors: Callens Martijn , Rose Caroline J , Finnegan Michael , Gatchitch François , Simon Léna , Hamet Jeanne , Pradier Léa , Dubois Marie-Pierre , Bedhomme Stéphanie 
Published: May 2023

Abstract
Genotypes exhibiting an increased mutation rate, called hypermutators, can propagate in microbial populations because they can have an advantage due to the higher supply of beneficial mutations needed for adaptation. Although this is a frequently observed phenomenon in natural and laboratory populations, little is known about the influence of parameters such as the degree of maladaptation, stress intensity, and the genetic architecture for adaptation on the emergence of hypermutators. To address this knowledge gap, we measured the emergence of hypermutators over ~1,000 generations in experimental Escherichia coli populations exposed to different levels of osmotic or antibiotic stress. Our stress types were chosen based on the assumption that the genetic architecture for adaptation differs between them. Indeed, we show that the size of the genetic basis for adaptation is larger for osmotic stress compared to antibiotic stress. During our experiment, we observed an increased emergence of hypermutators in populations exposed to osmotic stress but not in those exposed to antibiotic stress, indicating that hypermutator emergence rates are stress type dependent. These results support our hypothesis that hypermutator emergence is linked to the size of the genetic basis for adaptation. In addition, we identified other parameters that covaried with stress type (stress level and IS transposition rates) that might have contributed to an increased hypermutator provision and selection. Our results provide a first comparison of hypermutator emergence rates under varying stress conditions and point towards complex interactions of multiple stress-related factors on the evolution of mutation rates.
Mitomycin C-induced effects on aerobic methanotrophs in a landfill cover soil; implications of a viral shunt?
Authors: Heffner Tanja , Kaupper Thomas , Heinrichs Mara , Lee Hyo Jung , Rüppel Nadine , Horn Marcus A , Ho Adrian 
Published: May 2023

Abstract
A viral shunt can occur when phages going through a lytic cycle, including lysogenic phages triggered by inducing agents (e.g. mitomycin C), results in host lysis and the release of cell constituents and virions. The impact of a viral shunt on the carbon, including methane cycle in soil systems is poorly understood. Here, we determined the effects of mitomycin C on the aerobic methanotrophs in a landfill cover soil. To an extent, our results support a mitomycin C-induced viral shunt, as indicated by the significantly higher viral-like particle (VLP) counts relative to bacteria, elevated nutrient concentrations (ammonium, succinate), and initially impaired microbial activities (methane uptake and microbial respiration) after mitomycin C addition. The trend in microbial activities at &lt;2 days largely corresponded to the expression of the pmoA and 16S rRNA genes. Thereafter (&gt;11 days), the active bacterial community composition significantly diverged in the mitomycin C-supplemented incubations, suggesting the differential impact of mitomycin C on the bacterial community. Collectively, we provide insight on the effects of mitomycin C, and potentially a viral shunt, on the bacteria in the soil environment.
Prevalence of pleuromutilin antibiotic resistance genes in different laying hen breeding stages in China
Authors: Feng Jing-Yi , Su Wen , Feng Yu-Xuan , Lin Cong , Xie Xian-Jun , Wu Jie , Lai Shan-Ming , Zhang An-Yun 
Published: May 2023

Abstract
Antimicrobial resistance is a rapidly evolving and extremely complex issue, particularly due to the use of various types of antimicrobials within human, animal, and environmental sectors. Pleuromutilin antibiotics are used to prevent and control respiratory diseases in the rearing stage of hen chicks, but the current status of pleuromutilin resistance in the laying hen breeding process is unclear. ATP-binding cassette transporters encoded by lsa(A), lsa(E), lsa(C), and vga(D) can be transferred by plasmids and transposons, thereby posing a potential dissemination risk. To investigate pleuromutilin resistance genes in the laying hen production chain in China, 95 samples from five environmental types were collected in four breeding stages to determine the abundances of the main resistance genes by qPCR, i.e. lsa(A), lsa(E), lsa(C), and vga(D). The abundance (5.16 log10GC/g) and detection rate (100%) of lsa(E) was highest in all of the samples, thereby suggesting high contamination with the lsa(E) gene across the large-scale laying hen breeding environment and feces. The lsa(A) (6.02 log10GC/g) and lsa(E) (6.18 log10GC/g) genes were most abundant in flies, and the abundance of vga(D) (4.50 log10GC/g) was highest in dust (P &lt; .05). In addition to feces, flies and dust were important sources of contamination with pleuromutilin resistance along the laying hen production chain. In summary, we determined the abundances of four pleuromutilin resistance genes in the laying hen production chain and provided direct evidence of pleuromutilin resistance transmission and environmental contamination. In particular, the chicken breeding stage needs further attention.
How do engineered Yarrowia lipolytica strains secrete free fatty acids: hints from comparative transcriptomics
Authors: Salvador López José Manuel , Vidal Lea , Adiutama Michelle Patricia , Van Nieuwerburgh Filip , Deforce Dieter , Nicaud Jean-Marc , Van Bogaert Inge Noëlle Adrienne 
Published: May 2023

Abstract
Yarrowia lipolytica has been considered one of the most promising platforms for the microbial production of fatty acids and derived products. The deletion of the faa1 gene coding for an acyl-CoA synthetase leads to the accumulation and secretion of free fatty acids (FFAs) into the extracellular space. The secretion of products is beneficial for the development of microbial cell factories to avoid intracellular inhibitory effects and reduce downstream processing costs. However, the mechanism behind the secretion of fatty acids is not well known. As a starting point, we compared the transcriptome of this mutant showing FFA secretion to a wildtype-like strain not showing this phenotype. The 12 most upregulated genes were evaluated for involvement in FFA secretion by the creation of deletion and overexpression mutants, among them MCH2, YMOH, three cell wall proteins CWP3, CWP4, and CWP11, M12B, and three proteins with unknown functions YUP1, YUP2, and YUP3. None of these proteins take a clear or isolated role in FFA export. As the transcriptomic data revealed an overrepresentation of cell wall-related proteins, some of them were further examined on a theoretical and experimental way. Surprisingly, overexpression of Ygpi led to the production of FFAs in the wildtype-like genetic background. Finally, some of the evaluated genes showed involvement in resistance to FFA toxicity.
Feasibility of the Implementation of LESS-CHRON in Clinical Practice: A Pilot Intervention Study in Older Patients With Multimorbidity
Authors: Mejías-Trueba Marta , Rodríguez-Pérez Aitana , Hernández-Quiles Carlos , Ollero-Baturone Manuel , Nieto-Martín María Dolores , Sánchez-Fidalgo Susana 
Published: May 2023

Abstract

Background and Objectives
Potentially inappropriate medication refers to the prescription of drugs whose risks outweigh the benefits. There are different pharmacotherapeutic optimization strategies to detect and avoid potentially inappropriate medications (PIMs), namely deprescription. The List of Evidence-Based Deprescribing for Chronic Patients (LESS-CHRON) criteria were designed as a tool to systematize the deprescribing process. LESS-CHRON has established itself as one of the most suitable to be applied in older (≥65 years) multimorbid patients. However, it has not been applied to these patients, to measure the impact on their treatment. For this reason, a pilot study was conducted to analyze the feasibility of implementing this tool in a care pathway.

Research Design and Methods
A pre–post quasi-experimental study was conducted. Older outpatients with multimorbidity from the Internal Medicine Unit of a benchmark Hospital were included. The main variable was feasibility in clinical practice, understood as the likelihood that the deprescribing intervention recommended by the pharmacist would be applied to the patient. Success rate, therapeutic, and anticholinergic burden, and other variables related to health care utilization were analyzed.

Results
A total of 95 deprescribing reports were prepared. Forty-three were evaluated by the physician who assessed the recommendations made by pharmacists. This translates into an implementation feasibility of 45.3%. The application of LESS-CHRON identified 92 PIMs. The acceptance rate was 76.7% and after 3 months 82.7% of the stopped drugs remained deprescribed. A reduction in anticholinergic burden and enhanced adherence was achieved. However, no improvement was found in clinical or health care utilization variables.

Discussion and Implications
The implementation of the tool in a care pathway is feasible. The intervention has achieved great acceptance and deprescribing has been successful in a not insignificant percentage. Future studies with a larger sample size are necessary to obtain more robust results in clinical and health care utilization variables.
Siglec cis-ligands and their roles in the immune system
Authors: Tsubata Takeshi 
Published: May 2023

Abstract
Sialic acid-binding immunoglobulin-like lectins are a family of membrane molecules primarily expressed in immune cells. Most of them are inhibitory receptors containing immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic tail. On the cell surface, sialic acid-binding immunoglobulin-like lectins are mostly bound by sialylated glycans on membrane molecules expressed in the same cell (cis-ligands). Although ligands of sialic acid-binding immunoglobulin-like lectins are not efficiently identified by conventional methods such as immunoprecipitation, in situ labeling including proximity labeling is useful in identifying both cis-ligands and the sialylated ligands expressed by other cells (trans-ligands) of sialic acid-binding immunoglobulin-like lectins. Interaction of the inhibitory sialic acid-binding immunoglobulin-like lectins with cis-ligands including both those with and without signaling function modulates the inhibitory activity of sialic acid-binding immunoglobulin-like lectins by multiple different ways. This interaction also modulates signaling function of the cis-ligands. So far, little is known about the role of the interaction between sialic acid-binding immunoglobulin-like lectins and the cis-ligands. Nonetheless, recent studies showed that the inhibitory activity of CD22 (also known as Siglec-2) is regulated by endogenous ligands, most likely cis-ligands, differentially in resting B cells and those in which B-cell antigen receptor is ligated. This differential regulation plays a role in quality control of signaling-competent B cells and also partial restoration of B-cell antigen receptor signaling in immunodeficient B cells.
Multivariate Models of Animal Sex: Breaking Binaries Leads to a Better Understanding of Ecology and Evolution
Authors: McLaughlin J F , Brock Kinsey M , Gates Isabella , Pethkar Anisha , Piattoni Marcus , Rossi Alexis , Lipshutz Sara E 
Published: May 2023

Synopsis
“Sex” is often used to describe a suite of phenotypic and genotypic traits of an organism related to reproduction. However, these traits—gamete type, chromosomal inheritance, physiology, morphology, behavior, etc.—are not necessarily coupled, and the rhetorical collapse of variation into a single term elides much of the complexity inherent in sexual phenotypes. We argue that consideration of “sex” as a constructed category operating at multiple biological levels opens up new avenues for inquiry in our study of biological variation. We apply this framework to three case studies that illustrate the diversity of sex variation, from decoupling sexual phenotypes to the evolutionary and ecological consequences of intrasexual polymorphisms. We argue that instead of assuming binary sex in these systems, some may be better categorized as multivariate and nonbinary. Finally, we conduct a meta-analysis of terms used to describe diversity in sexual phenotypes in the scientific literature to highlight how a multivariate model of sex can clarify, rather than cloud, studies of sexual diversity within and across species. We argue that such an expanded framework of “sex” better equips us to understand evolutionary processes, and that as biologists, it is incumbent upon us to push back against misunderstandings of the biology of sexual phenotypes that enact harm on marginalized communities.
Avian Heterothermy: A Review of Patterns and Processes
Authors: McKechnie Andrew E , Freeman Marc T , Brigham R Mark 
Published: May 2023

Synopsis
Many birds reduce rest-phase energy demands through heterothermy, physiological responses involving facultative, reversible reductions in metabolic rate and body temperature (Tb). Here, we review the phylogenetic distribution and ecological contexts of avian heterothermy. Heterothermy has been reported in 140 species representing 15 orders and 39 families. Recent work supports the view that deep heterothermy is most pronounced in phylogenetically older taxa whereas heterothermy in passerines and other recently diverged taxa is shallower and confined to minimum Tb &gt; 20°C. The reasons why deep heterothermy is absent in passerines remain unclear; we speculate an evolutionary trade-off may exist between the capacity to achieve low heterothermic Tb and the tolerance of hyperthermic Tb. Inter- and intraspecific variation in heterothermy is correlated with factors including foraging ecology (e.g., territoriality and defense of food resources among hummingbirds), food availability and foraging opportunities (e.g., lunar phase predicts torpor use in caprimulgids), and predation risk. Heterothermy also plays a major role before and during migration. Emerging questions include the magnitude of energy savings associated with heterothermy among free-ranging birds, the role phylogenetic variation in the capacity for heterothermy has played in evolutionary radiations into extreme habitats, and how the capacity for heterothermy affects avian vulnerability to rapid anthropogenic climate change.
Skeletal dosimetry in a microCT image-based rat model for external photon irradiation
Authors: Zhang Xiaomin , Xu Xu , Ning Jing , Yuan Yong , Li Dawei , Ji Yunlong 
Published: May 2023

AbstractHuman skeletal dosimetry has experienced great developments in radiation protection in recent years by using the heterogeneous skeletal model. While for the rats experimentally used in radiation medicine, the investigation on skeletal dosimetry were mainly based on the homogeneous skeletal model, leading to inaccurate assessments of dose to radiosensitive tissues of red bone marrow (RBM) and bone surface. The purpose of this study is to develop a rat model with heterogeneous skeletal system and to investigate the dose difference in bone tissues for external photon irradiation. The high resolution of microCT images of a rat weighing 335 g were segmented into bone cortical, bone trabecular, bone marrow as well as other organs to construct the rat model. The absorbed dose to bone cortical, bone trabecular and bone marrow were calculated respectively by using Monte Carlo simulation for 22 external monoenergetic photon beams between 10 keV and 10 MeV under four different irradiation geometries conditions (left lateral [LL], right lateral [RL], dorsal–ventral [DV], ventral–dorsal [VD]). The calculated absorbed dose data were expressed as dose conversion coefficients and presented in this article, and the effect of irradiation conditions, photon energies and bone tissues density on the skeletal dose was discussed. The results showed that the dose conversion coefficients varying the photon energy for bone cortical, bone trabecular and bone marrow exhibit different trends and have the same sensitivity to irradiation conditions. The dose difference in bone tissues indicated that bone cortical and bone trabecular have significant attenuation effect on the energy deposition in bone marrow and bone surface for photon energies below 0.2 MeV. The set of dose conversion coefficients in this work can be used to determine the absorbed dose to skeletal system for external photon irradiation and to supplement the rat skeletal dosimetry.
Seasonality and Climatic Factors Associated With Human Rhinovirus/Enterovirus Nasopharyngeal Sample Positivity on Oahu, Hawai’i, 2016-2019
Authors: Marcelo Raymundo Z , Lustik Michael B , Jones Milissa U 
Published: May 2023

ABSTRACT

Introduction
Globally, human rhinoviruses/enteroviruses (HRVs/ENTs), indistinguishable on many widely available molecular platforms, are among the leading causes of the common cold. Geographic and climatic factors impact the peak activity of these viruses. In temperate climates, the peak activity of HRV occurs during autumn and spring whereas that of ENT occurs during autumn and summer. Both viruses are thought to peak during the rainy season in tropical climates like Hawai’i; however, data remain limited. We describe HRV/ENT seasonality and evaluate the climatic factors associated with peak activity among respiratory viral samples processed on Oahu, Hawai’i.

Materials and Methods
We conducted a retrospective analysis of all respiratory specimens submitted to Tripler Army Medical Center for multiplex polymerase chain reaction testing between May 2016 and May 2019. Among HRV/ENT-positive samples, we recorded the month and year of positivity. Summative monthly positive detection was calculated with peak months above the mean. Associations between temperature, precipitation levels, relative humidity, and wind speed by week and the number of positive samples for HRV/ENT were evaluated using Poisson regression. This analysis was conducted via IRB exempt protocol number 19R18.

Results
During our study period, there were 7,143 nasopharyngeal respiratory samples sent for multiplex polymerase chain reaction testing, with 1,572 positive for HRV/ENT (22%). Nineteen percent of respiratory samples positive for HRV/ENT were additionally positive for one or more respiratory pathogens. The majority of HRV/ENT-positive samples arose from children &lt; 5 years of age (n = 959, 61%). Peak months were February, March, May, August, November, and December. After controlling for lagged count and year, average wind speed was the only climatic factor significantly associated with HRV/ENT sample positivity.

Conclusions
The peak monthly activity of HRV/ENT was similar to temperate climates with the exception of peak activity in February. Unlike other tropical climates, lower wind speed was associated with increased weekly HRV/ENT positivity and should be further explored as a transmission factor. Our study contributes to understanding the annual variability of HRV/ENT activity in tropical environments, which can inform clinician expectations regarding respiratory viral symptomatology in this region.
Codon Optimization Improves the Prediction of Xylose Metabolism from Gene Content in Budding Yeasts
Authors: Nalabothu Rishitha L , Fisher Kaitlin J , LaBella Abigail Leavitt , Meyer Taylor A , Opulente Dana A , Wolters John F , Rokas Antonis , Hittinger Chris Todd 
Published: May 2023

Abstract
Xylose is the second most abundant monomeric sugar in plant biomass. Consequently, xylose catabolism is an ecologically important trait for saprotrophic organisms, as well as a fundamentally important trait for industries that hope to convert plant mass to renewable fuels and other bioproducts using microbial metabolism. Although common across fungi, xylose catabolism is rare within Saccharomycotina, the subphylum that contains most industrially relevant fermentative yeast species. The genomes of several yeasts unable to consume xylose have been previously reported to contain the full set of genes in the XYL pathway, suggesting the absence of a gene–trait correlation for xylose metabolism. Here, we measured growth on xylose and systematically identified XYL pathway orthologs across the genomes of 332 budding yeast species. Although the XYL pathway coevolved with xylose metabolism, we found that pathway presence only predicted xylose catabolism about half of the time, demonstrating that a complete XYL pathway is necessary, but not sufficient, for xylose catabolism. We also found that XYL1 copy number was positively correlated, after phylogenetic correction, with xylose utilization. We then quantified codon usage bias of XYL genes and found that XYL3 codon optimization was significantly higher, after phylogenetic correction, in species able to consume xylose. Finally, we showed that codon optimization of XYL2 was positively correlated, after phylogenetic correction, with growth rates in xylose medium. We conclude that gene content alone is a weak predictor of xylose metabolism and that using codon optimization enhances the prediction of xylose metabolism from yeast genome sequence data.
MAGUS: machine learning and graph theory assisted universal structure searcher
Authors: Wang Junjie , Gao Hao , Han Yu , Ding Chi , Pan Shuning , Wang Yong , Jia Qiuhan , Wang Hui-Tian , Xing Dingyu , Sun Jian 
Published: May 2023

ABSTRACT
Crystal structure predictions based on first-principles calculations have gained great success in materials science and solid state physics. However, the remaining challenges still limit their applications in systems with a large number of atoms, especially the complexity of conformational space and the cost of local optimizations for big systems. Here, we introduce a crystal structure prediction method, MAGUS, based on the evolutionary algorithm, which addresses the above challenges with machine learning and graph theory. Techniques used in the program are summarized in detail and benchmark tests are provided. With intensive tests, we demonstrate that on-the-fly machine-learning potentials can be used to significantly reduce the number of expensive first-principles calculations, and the crystal decomposition based on graph theory can efficiently decrease the required configurations in order to find the target structures. We also summarized the representative applications of this method on several research topics, including unexpected compounds in the interior of planets and their exotic states at high pressure and high temperature (superionic, plastic, partially diffusive state, etc.); new functional materials (superhard, high-energy-density, superconducting, photoelectric materials), etc. These successful applications demonstrated that MAGUS code can help to accelerate the discovery of interesting materials and phenomena, as well as the significant value of crystal structure predictions in general.