bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Genomic Legacy of Aurochs hybridization in ancient and modern Iberian Cattle
Authors: Günther Torsten , Chisausky Jacob , Galindo-Pellicena M. Ángeles , Iriarte Eneko , Gardyn Oscar Cortes , Eusebi Paulina G. , García-González Rebeca , Urena Irene , Moreno Marta , Alday Alfonso , Rojo Manuel , Pérez Amalia , Rodríguez Cristina Tejedor , de Lagrán Iñigo García Martínez , Arsuaga Juan Luis , Carretero José-Miguel , Götherström Anders , Smith Colin , Valdiosera Cristina 
Published: July 2023

AbstractCattle have been a valuable economic resource and cultural icon since prehistory. From the initial expansion of domestic cattle into Europe during the Neolithic period, taurine cattle (Bos taurus) and their wild ancestor, the aurochs (B. primigenius), had overlapping ranges, leading to ample opportunities for mating (whether intended by farmers or not). We performed a bioarchaeological analysis of 24 Bos remains from Iberia dating from the Mesolithic to the Roman period. The archaeogenomic dataset allows us to investigate the extent of domestic-wild hybridization over time, providing insight into the species’ behavior and human hunting and management practices by aligning changes with cultural and genomic transitions in the archaeological record. Our results show frequent hybridization during the Neolithic and Chalcolithic, likely reflecting a mix of hunting and herding or relatively unmanaged herds, with mostly male aurochs and female domestic cattle involved in hybridization. This is supported by isotopic evidence consistent with ecological niche sharing, with only a few domestic cattle possibly being managed. The proportion of aurochs ancestry remains relatively constant from about 4000 years ago, probably due to herd management and selection against first generation hybrids, coinciding with other cultural transitions. The constant level of wild ancestry (∽20%) continues into modern western European breeds including the Spanish Lidia breed which is bred for its aggressiveness and fighting ability, but does not display elevated levels of aurochs ancestry. This study takes a genomic glance at the impact of human actions and wild introgression in the establishment of cattle as one of the most important domestic species today.
Human Cytomegalovirus in breast milk is associated with milk composition, the infant gut microbiome, and infant growth
Authors: Johnson Kelsey E. , Heisel Timothy , Fields David A. , Isganaitis Elvira , Jacobs Katherine M. , Knights Dan , Lock Eric F. , Rudolph Michael C. , Gale Cheryl A. , Schleiss Mark R. , Albert Frank W. , Demerath Ellen W. , Blekhman Ran 
Published: July 2023

AbstractHuman cytomegalovirus (CMV) is a highly prevalent herpesvirus that is often transmitted to the neonate via breast milk. Postnatal CMV transmission can have negative health consequences for preterm and immunocompromised infants, but any effects on healthy term infants are thought to be benign. Furthermore, the impact of CMV on the composition of the hundreds of bioactive factors in human milk has not been tested. Here, we utilize a cohort of exclusively breastfeeding full term mother-infant pairs to test for differences in the milk transcriptome and metabolome associated with CMV, and the impact of CMV in breast milk on the infant gut microbiome and infant growth. We find upregulation of the indoleamine 2,3-dioxygenase (IDO) tryptophan-to-kynurenine metabolic pathway in CMV+ milk samples, and that CMV+ milk is associated with decreasedBifidobacteriumin the infant gut. Our data indicate a complex relationship between milk CMV, milk kynurenine, and infant growth; with kynurenine positively correlated, and CMV viral load negatively correlated, with infant weight-for-length at 1 month of age. These results suggest CMV transmission, CMV-related changes in milk composition, or both may be modulators of full term infant development.
Identification of the active mechanism of aminoglycoside entry inV. choleraethrough characterization of sRNActrR,regulating carbohydrate utilization and transport
Authors: Pierlé Sebastian A. , Lang Manon , López-Igual Rocío , Krin Evelyne , Fourmy Dominique , Kennedy Sean P. , Val Marie-Eve , Baharoglu Zeynep , Mazel Didier 
Published: July 2023

AbstractThe possible active entry of aminoglycosides in bacterial cells has been debated since the development of this antibiotic family. Here we report the identification of their active transport mechanism inVibriospecies. We combined genome-wide transcriptional analysis and fitness screens to identify alterations driven by treatment ofV. choleraewith sub-minimum inhibitory concentrations (sub-MIC) of the aminoglycoside tobramycin. RNA-seq data showed downregulation of the small non-coding RNAncRNA586during such treatment, while Tn-seq revealed that inactivation of this sRNA was associated with improved fitness in the presence of tobramycin. This sRNA is located near sugar transport genes and previous work on a homologous region inVibrio tasmaniensissuggested that this sRNA stabilizes gene transcripts for carbohydrate transport and utilization, as well as phage receptors. The role forncRNA586, hereafter namedctrR, in the transport of both carbohydrates and aminoglycosides, was further investigated. Flow cytometry on cells treated with a fluorescent aminoglycoside confirmed the role ofctrRand of carbohydrate transporters in differential aminoglycoside entry. Despite sequence diversity,ctrRshowed functional conservation across the Vibrionales. This system in directly modulated by carbon sources, suggesting regulation by carbon catabolite repression, a widely conserved mechanism in Gram-negative bacteria, priming future research on aminoglycoside uptake by sugar transporters in other bacterial species.
Exploring the molecular makeup of support cells in insect camera eyes
Authors: Rathore Shubham , Stahl Aaron , Benoit Joshua B. , Buschbeck Elke K. 
Published: July 2023

AbstractAnimals generally have either compound eyes, which have evolved repeatedly in different invertebrates, or camera eyes, which have evolved many times across the animal kingdom. Both eye types include two important kinds of cells: photoreceptor cells, which can be excited by light, and non-neuronal support cells (SupCs), which provide essential support to photoreceptors. Despite many examples of convergence in eye evolution, similarities in the gross developmental plan and molecular signatures have been discovered, even between phylogenetically distant and functionally different eye types. For this reason, a shared evolutionary origin has been considered for photoreceptors. In contrast, only a handful of studies, primarily on the compound eyes ofDrosophila melanogaster, have demonstrated molecular similarities in SupCs.D. melanogasterSupCs (Semper cells and primary pigment cells) are specialized eye glia that share several molecular similarities with certain vertebrate eye glia, including Müller glia. This led us to speculate whether there are conserved molecular signatures of SupCs, even in functionally different eyes such as the image-forming larval camera eyes of the sunburst diving beetleThermonectus marmoratus. To investigate this possibility, we used an in-depth comparative whole-tissue transcriptomics approach. Specifically, we dissected the larval principal camera eyes into SupC- and retina-containing regions and generated the respective transcriptomes. Our analysis revealed several conserved features of SupCs including enrichment of genes that are important for glial function (e.g. gap junction proteins such as innexin 3), glycogen production (glycogenin), and energy metabolism (glutamine synthetase 1 and 2). To evaluate the extent of conservation, we compared our transcriptomes with those of fly (Semper cells) and vertebrate (Müller glia) eye glia as well as respective retinas.T. marmoratusSupCs were found to have distinct genetic overlap with both fly and vertebrate eye glia. These results provide molecular evidence for the deep conservation of SupCs in addition to photoreceptor cells, raising essential questions about the evolutionary origin of eye-specific glia in animals.
Analysis ofDrosophilaand mouse mutants reveals that Peroxidasin is required for tissue mechanics and full viability
Authors: Peebles K. Elkie , LaFever Kimberly S. , Page-McCaw Patrick S. , Colon Selene , Wang Dan , Stricker Aubrie M. , Ferrell Nicholas , Bhave Gautam , Page-McCaw Andrea 
Published: July 2023

AbstractBasement membranes are thin strong sheets of extracellular matrix. They provide mechanical and biochemical support to epithelia, muscles, nerves, and blood vessels, among other tissues. The mechanical properties of basement membranes are conferred in part by Collagen IV (Col4), an abundant protein of basement membrane that forms an extensive two-dimensional network through head-to-head and tail-to-tail interactions. After the Col4 network is assembled into a basement membrane, it is crosslinked by the matrix-resident enzyme Peroxidasin to form a large covalent polymer. Peroxidasin and Col4 crosslinking are highly conserved, indicating they are essential, but homozygous mutant mice have mild phenotypes. To explore the role of Peroxidasin, we analyzed mutants in Drosophila, including a newly generated catalytic null, and found that homozygotes were mostly lethal with 13% viable escapers. A Mendelian analysis of mouse mutants shows a similar pattern, with homozygotes displaying ∼50% lethality and ∼50% escapers. Despite the strong mutations, the homozygous escapers had low but detectable levels of Col4 crosslinking, indicating that inefficient alternative mechanisms exist and that are probably responsible for the viable escapers. Further, fly mutants have phenotypes consistent with a decrease in stiffness. Interestingly, we found that even after adult basement membranes are assembled and crosslinked, Peroxidasin is still required to maintain stiffness. These results suggest that Peroxidasin crosslinking may be more important than previously appreciated.
Chainsaw: protein domain segmentation with fully convolutional neural networks
Authors: Wells Jude , Hawkins-Hooker Alex , Bordin Nicola , Sillitoe Ian , Paige Brooks , Orengo Christine 
Published: July 2023

ABSTRACT0.1MotivationProtein domains are fundamental units of protein structure and play a pivotal role in understanding folding, function, evolution, and design. The advent of accurate structure prediction techniques has resulted in an influx of new structural data, making the partitioning of these structures into domains essential for inferring evolutionary relationships and functional classification.0.2ResultsThis manuscript presents Chainsaw, a supervised learning approach to domain parsing that achieves accuracy that surpasses current state-of-the-art methods. Chainsaw uses a fully convolutional neural network which is trained to predict the probability that each pair of residues is in the same domain. Domain predictions are then derived from these pairwise predictions using an algorithm that searches for the most likely assignment of residues to domains given the set of pairwise co-membership probabilities. Chainsaw matches CATH domain annotations in 78% of protein domains versus 72% for the next closest method. When predicting on AlphaFold models expert human evaluators were twice as likely to prefer Chainsaw’s predictions versus the next best method.0.3Availability and ImplementationCode implementation of Chainsaw is available atgithub.com/JudeWells/chainsaw.
Intraoperative lung ultrasound improves subcentimetric pulmonary nodule localization during VATS: Results of a retrospective analysis
Authors: Gambardella Claudio , Messina Gaetana , Pica Davide Gerardo , Bove Mary , Capasso Francesca , Mirra Rosa , Natale Giovanni , D'Alba Francesco Panini , Caputo Alessia , Leonardi Beatrice , Puca Maria Antonietta , Giorgiano Noemi Maria , Pirozzi Mario , Farese Stefano , Zotta Alessia , Miele Francesco , Vicidomini Giovanni , Docimo Ludovico , Fiorelli Alfonso , Ciardiello Fortunato , Fasano Morena 
Published: July 2023

AbstractBackgroundVideo‐assisted thoracoscopic surgery (VATS) resection of deep‐seated lung nodules smaller than 1 cm is extremely challenging. Several methods have been proposed to overcome this limitation but with not neglectable complications. Intraoperative lung ultrasound (ILU) is the latest minimally invasive proposed technique. The aim of the current study was to analyze the accuracy and efficacy of ILU associated with VATS to visualize solitary and deep‐seated pulmonary nodules smaller than 1 cm.MethodsPatients with subcentimetric solitary and deep‐seated pulmonary nodules were included in this retrospective study from November 2020 to December 2022. Patients who received VATS aided with ILU were considered as group A and patients who received conventional VATS as group B (control group). The rate of nodule identification and the time for localization with VATS alone and with VATS aided with ILU in each group were analyzed.ResultsA total of 43 patients received VATS aided with ILU (group A) and 31 patients received conventional VATS (group B). Mean operative time was lower in group A (p < 0.05). In group A all the nodules were correctly identified, while in group B in one case the localization failed. The time to identify the lesion was lower in group A (7.1 ± 2.2 vs. 13.8 ± 4.6; p < 0.05). During hospitalization three patients (6.5%; p < 0.05) in group B presented air leaks that were conservatively managed.ConclusionIntracavitary VATS‐US is a reliable, feasible, real‐time and effective method of localization of parenchymal lung nodules during selected wedge resection procedures.
Mind and skin: Exploring the links between inflammation, sleep disturbance and neurocognitive function in patients with atopic dermatitis
Authors: Cameron Shona , Donnelly Ali , Broderick Conor , Arichi Tomoki , Bartsch Ullrich , Dazzan Paola , Elberling Jesper , Godfrey Emma , Gringras Paul , Heathcote Lauren C. , Joseph Desaline , Wood Tobias C. , Pariante Carmine , Rubia Katya , Flohr Carsten 
Published: July 2023

AbstractAtopic dermatitis (AD) is a chronic, pruritic and inflammatory, dry skin condition with many known comorbidities. These include airway disease, food allergies, atopic eye disease and autoimmune conditions. Furthermore, there is often significant sleep disturbance as well as increased psychological distress and mental health problems. Severe AD therefore often has a significant impact on the quality of life of both patients and their families. In this review we discuss recent findings on the putative links between AD, its association with itch, sleep disturbance and neuropsychiatric morbidity, including the role of inflammation in these conditions. Itch was thought to predominantly drive sleep disruption in AD. We now understand changes in sleep influence immune cell distribution and the associated inflammatory cytokines, which suggests a bidirectional relationship between AD and sleep. We also increasingly recognize inflammation as a key driver in psychological symptoms and disorders. The link between cutaneous, systemic and possible brain inflammation could at least in part be driven by the sleep deprivation and itch‐driven neuronal proliferation seen in AD.
MPP2 interacts with SK2 to rescue the excitability of glutamatergic neurons in the BLA and facilitate the extinction of conditioned fear in mice
Authors: Peng Xiaohan , Chen Panpan , Zhang Yang , Wu Ke , Ji Ningning , Gao Jinghua , Wang Hui , Zhang Yong‐mei , Xu Tie , Hua Rong 
Published: July 2023

AbstractAimsThe basolateral amygdala (BLA) plays an integral role in anxiety disorders (such as post traumatic stress disorder) stem from dysregulated fear memory. The excitability of glutamatergic neurons in the BLA correlates with fear memory, and the afterhyperpolarization current (IAHP) mediated by small‐conductance calcium‐activated potassium channel subtype 2 (SK2) dominates the excitability of glutamatergicneurons. This study aimed to explore the effect of MPP2 interacts with SK2 in the excitability of glutamatergic neurons in the BLA and the extinction of conditioned fear in mice.MethodsFear memory was analyzed via freezing percentage. Western blotting and fluorescence quantitative PCR were used to determine the expression of protein and mRNA respectively. Electrophysiology was employed to measure the excitability of glutamatergic neurons and IAHP.ResultsFear conditioning decreased the levels of synaptic SK2 channels in the BLA, which were restored following fear extinction. Notably, reduced expression of synaptic SK2 channels in the BLA during fear conditioning was caused by the increased activity of protein kinase A (PKA), while increased levels of synaptic SK2 channels in the BLA during fear extinction were mediated by interactions with membrane‐palmitoylated protein 2 (MPP2).ConclusionsOur results revealed that MPP2 interacts with the SK2 channels and rescues the excitability of glutamatergic neurons by increasing the expression of synaptic SK2 channels in the BLA to promote the normalization of anxiety disorders and provide a new direction for the treatment.
Perceptions and knowledge of protein in dairy and plant‐based alternatives among stakeholders in the US marketplace
Authors: Schlepphorst Katherine I. , Clark Bridget E. , Pope Lizzy , Donahue Reilly , Belarmino Emily H. 
Published: July 2023

AbstractThis study explores beliefs about protein in dairy and plant‐based (PB) alternatives among stakeholders in the US marketplace and whether beliefs are associated with product preferences. Eight thousand and fifty‐two unique comments submitted to the US Food and Drug Administration (FDA) in response to a request for public input on the labelling of PB dairy alternatives (FDA‐2018‐N‐3522) were coded. Of these, 383 (4.8%) discussed protein and were analysed for protein‐specific themes. Themes were examined in relation to the submitter's product preference. Most comments that discussed protein focused on protein content and/or health outcomes believed to be associated with intake. Only one commenter who preferred dairy demonstrated an inaccurate understanding of protein content in dairy and PB alternatives, although nearly all failed to identify fortified soy beverage as an appropriate protein replacement; meanwhile, 14.2% who preferred PB alternatives demonstrated an inaccurate understanding regarding protein content in dairy and PB products. The results suggest knowledge gaps exist regarding protein in PB dairy alternatives, especially among those who prefer non‐dairy options.
Creep-Fatigue Life Property of P91 Welded Piping Subjected to Bending and Torsional Moments at High Temperature
Authors: Okuno Kazuma , Arai Masayuki , Ito Kiyohiro , Nishida Hidetaka 
Published: July 2023

Abstract
In recent years, the role of thermal power plants has shifted from providing a baseload to providing supplemental supply to compensate for fluctuations in the output of renewable energy sources. Thus, the operation of these plants involves frequent startup and shutdown cycles, which lead to extensive damage caused by creep and fatigue interactions. In addition, the piping utilized in thermal plants is subjected to a combined stress state composed of bending and torsional moments. In this study, a high-temperature fatigue testing machine capable of generating such a bending-torsional loading was developed. Creep-fatigue tests were conducted on P91 steel piping with weldment. The results clarified that the creep-fatigue life was reduced by the superposition of the torsional and bending moments and that it was further reduced by a holding load. It was shown that the creep-fatigue life of piping with weldment can be estimated accurately using the equivalent bending moment, which is composed of the torsional and bending moments. It was also confirmed that crack occurred in the heat-affected zone (HAZ) of the welded part, which has been often observed in actual thermal power equipment. From the finite element analysis, it was identified that cracking was initiated in the HAZ due to the accumulation of creep strain and increase in the hydrostatic pressure component during a holding load.
Determination of Multi-Component Failure in Automotive System Using Deep Learning
Authors: O’Donnell John , Yoon Hwan-Sik 
Published: July 2023

Abstract
The connectivity of modern vehicles allows for the monitoring and analysis of a large amount of sensor data from vehicles during their normal operations. In recent years, there has been a growing interest in utilizing this data for the purposes of predictive maintenance. In this paper, a multi-label transfer learning approach is proposed using 14 different pretrained convolutional neural networks retrained with engine simulation data to predict the failure conditions of a selected set of engine components. The retrained classifier networks are designed such that concurrent failure modes of an exhaust gas recirculation, compressor, intercooler, and fuel injectors of a four-cylinder diesel engine can be identified. Time-series simulation data of various failure conditions, which include performance degradation, are generated to retrain the classifier networks to predict which components are failing at any given time. The test results of the retrained classifier networks show that the overall classification performance is good, with the normalized value of mean average precision varying from 0.6 to 0.65 for most of the retrained networks. To the best of the authors’ knowledge, this work represents the first attempt to characterize such time-series data utilizing a multi-label deep learning approach.
Lower geriatric nutritional risk index is associated with a higher risk of all-cause mortality in patients with chronic obstructive pulmonary disease: a cohort study from the National Health and Nutrition Examination Survey 2013–2018
Authors: Chai Xuemin , Chen Yajuan , Li Youlun , Chi Jing , Guo Shuliang 
Published: July 2023

ObjectMalnutrition negatively affects patients with chronic obstructive pulmonary disease (COPD). This study aimed to explore the potential association between malnutrition, as defined by the Geriatric Nutritional Risk Index (GNRI), and all-cause mortality in patients with COPD using the National Health and Nutrition Examination Survey (NHANES).MethodThe data of 579 adults with COPD during NHANES 2013–2018 were analysed. Each patient was assigned to one of the two groups according to GNRI values: normal nutritional status (GNRI>98) and malnutrition status (GNRI≤98). Survival curves and Cox regressions were applied to evaluate the association between nutritional status and mortality.ResultsOverall, the mean age was 63.4±0.5 years, and 53.9% of the patients were women. The prevalence of malnutrition was 6.6%, and the Kaplan-Meier curves for all-cause mortality according to nutritional status showed that malnutrition was associated with a higher incidence of all-cause mortality. The Cox regression analysis found that in the unadjusted model, the HR was 2.30 (95% CI 1.24 to 4.27, p=0.01). In the fully adjusted model, the adjusted HR was 2.47 (95% CI 1.36 to 4.5, p=0.003). Furthermore, subgroup analysis revealed that the risk of death due to malnutrition increased more than threefold in the low education and cancer subgroups.ConclusionA low GNRI was an independent risk factor for all-cause mortality in patients with COPD.