bluuebunny/crossref_metadata_2025_split huggingface dataset:
A systems immunology approach to investigate cytokine responses to viruses and bacteria and their association with disease
Authors: Lin Lijing , Curtin John A. , Regis Eteri , Hirsman Aurica , Howard Rebecca , Tutino Mauro , Edwards Michael R. , Prosperi Mattia , Simpson Angela , Rattray Magnus , Custovic Adnan , Johnston Sebastian L. 
Published: August 2022

AbstractPatterns of human immune responses to viruses and bacteria and how this impacts risk of infections or onset/exacerbation of chronic respiratory diseases are poorly understood. In a population-based birth cohort, we measured peripheral blood mononuclear cell responses (28 cytokines) to respiratory viruses and bacteria, Toll-like receptor ligands and phytohemagglutinin, in 307 children. Cytokine responses were highly variable with > 1000-fold differences between children. Machine learning revealed clear distinction between virus-associated and bacteria-associated stimuli. Cytokines clustered into three functional groups (anti-viral, pro-inflammatory and T-cell derived). To investigate mechanisms potentially explaining such variable responses, we investigated cytokine Quantitative Trait Loci (cQTLs) of IL-6 responses to bacteria and identified nine (eight novel) loci. Our integrative approach describing stimuli, cytokines and children as variables revealed robust immunologically and microbiologically plausible clustering, providing a framework for a greater understanding of host-responses to infection, including novel genetic associations with respiratory disease.
Convolutional neural networks for the automatic segmentation of lumbar paraspinal muscles in people with low back pain
Authors: Wesselink E. O. , Elliott J. M. , Coppieters M. W. , Hancock M. J. , Cronin B. , Pool-Goudzwaard A. , Weber II K. A. 
Published: August 2022

AbstractThe size, shape, and composition of paraspinal muscles have been widely reported in disorders of the cervical and lumbar spine. Measures of size, shape, and composition have required time-consuming and rater-dependent manual segmentation techniques. Convolutional neural networks (CNNs) provide alternate timesaving, state-of-the-art performance measures, which could realise clinical translation. Here we trained a CNN for the automatic segmentation of lumbar paraspinal muscles and determined the impact of CNN architecture and training choices on segmentation performance. T2-weighted MRI axial images from 76 participants (46 female; age (SD): 45.6 (12.8) years) with low back pain were used to train CNN models to segment the multifidus, erector spinae, and psoas major muscles (left and right segmented separately). Using cross-validation, we compared 2D and 3D CNNs with and without data augmentation. Segmentation accuracy was compared between the models using the Sørensen-Dice index as the primary outcome measure. The effect of increasing network depth on segmentation accuracy was also investigated. Each model showed high segmentation accuracy (Sørensen-Dice index ≥ 0.885) and excellent reliability (ICC2,1 ≥ 0.941). Overall, across all muscles, 2D models performed better than 3D models (p = 0.012), and training without data augmentation outperformed training with data augmentation (p < 0.001). The 2D model trained without data augmentation demonstrated the highest average segmentation accuracy. Increasing network depth did not improve accuracy (p = 0.771). All trained CNN models demonstrated high accuracy and excellent reliability for segmenting lumbar paraspinal muscles. CNNs can be used to efficiently and accurately extract measures of paraspinal muscle health from MRI.
Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis
Authors: Silva Nuno M. , Kreutzer Susanne , Souleles Angelos , Triantaphyllou Sevasti , Kotsakis Kostas , Urem-Kotsou Dushka , Halstead Paul , Efstratiou Nikos , Kotsos Stavros , Karamitrou-Mentessidi Georgia , Adaktylou Fotini , Chondroyianni-Metoki Areti , Pappa Maria , Ziota Christina , Sampson Adamantios , Papathanasiou Anastasia , Vitelli Karen , Cullen Tracey , Kyparissi-Apostolika Nina , Lanz Andrea Zeeb , Peters Joris , Rio Jérémy , Wegmann Daniel , Burger Joachim , Currat Mathias , Papageorgopoulou Christina 
Published: August 2022

AbstractThe aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolithic and 319 modern sequences. To test for population continuity through time in Greece, we use an original structured population continuity test that simulates DNA from different periods by explicitly considering the spatial and temporal dynamics of populations. We explore specific scenarios of the mode and tempo of the European Neolithic expansion along the Danubian axis applying spatially explicit simulations coupled with Approximate Bayesian Computation. We observe a striking genetic homogeneity for the maternal line throughout the Neolithic in Greece whereas population continuity is rejected between the Neolithic and present-day Greeks. Along the Danubian expansion axis, our best-fitting scenario supports a substantial decrease in mobility and an increasing local hunter-gatherer contribution to the gene-pool of farmers following the initial rapid Neolithic expansion. Οur original simulation approach models key demographic parameters rather than inferring them from fragmentary data leading to a better understanding of this important process in European prehistory.
Dilemma breaking in quantum games by joint probabilities approach
Authors: Legón Alexis R. , Medina Ernesto 
Published: August 2022

AbstractClassical games get fundamentally modified in the quantum realm because of non-locality and entanglement, that bypass some of the crucial features of the classical problem that define a dilemma. We will analyze how the dilemma can be shunted and even completely eliminated by the players using quantum strategies from the viewpoint of joint probabilities. In this approach, the game information (entropy) needs to be incorporated into the game strategies. We also connect the potential of the formalism of quantum games with the transmission of quantum information in quantum noisy channels and recent considerations of the connection between thermalization mechanisms in statistical mechanics, the many body problem and cooperative games considered here in the quantum regime.
Association of compliance with COVID-19 public health measures with depression
Authors: Byun Ju An , Sim Tae Jun , Lim Tae Yoon , Jang Sung-In , Kim Seung Hoon 
Published: August 2022

AbstractAlthough previous studies have demonstrated increased depression related to COVID-19, the reasons for this are not well-understood. We investigated the association of compliance with COVID-19 public health measures with depression. Data from the 2020 Korea Community Health Survey were analyzed. The main independent variable was compliance with rules based on three performance variables (social distancing, wearing a mask in indoor facilities, and outdoors). Depression was assessed using Patient Health Questionnaire-9 scores. Of 195,243 participants, 5,101 participants had depression. Bad and moderate performance scores for compliance were associated with depression (Bad score, men: adjusted odds ratio [aOR] = 2.24, 95% confidence interval [CI] = 1.29–3.87; women: aOR = 2.42, 95% CI = 1.42–4.13; moderate score, men: aOR = 1.31, 95% CI = 1.02–1.68; women: aOR = 1.28, 95% CI = 1.07–1.53). In the subgroup analysis, among the quarantine rules, not wearing a mask indoors was the most prominently associated with depression. In participants with a high level of education, non-compliance with quarantine rules was significantly associated with depression. People who do not comply with public health measures are more likely to be depressed. The preparation and observance of scientific quarantine rules can help mental health in the ongoing COVID-19 pandemic and another infectious disease pandemic that may come.
Selective electrochemical reduction of CO2 on compositionally variant bimetallic Cu–Zn electrocatalysts derived from scrap brass alloys
Authors: Badawy Ibrahim M. , Ismail Ahmed Mohsen , Khedr Ghada E. , Taha Manar M. , Allam Nageh K. 
Published: August 2022

AbstractThe electrocatalytic reduction of carbon dioxide (CO2RR) into value-added fuels is a promising initiative to overcome the adverse effects of CO2 on climate change. Most electrocatalysts studied, however, overlook the harmful mining practices used to extract these catalysts in pursuit of achieving high-performance. Repurposing scrap metals to use as alternative electrocatalysts would thus hold high privilege even at the compromise of high performance. In this work, we demonstrated the repurposing of scrap brass alloys with different Zn content for the conversion of CO2 into carbon monoxide and formate. The scrap alloys were activated towards CO2RR via simple annealing in air and made more selective towards CO production through galvanic replacement with Ag. Upon galvanic replacement with Ag, the scrap brass-based electrocatalysts showed enhanced current density for CO production with better selectivity towards the formation of CO. The density functional theory (DFT) calculations were used to elucidate the potential mechanism and selectivity of the scrap brass catalysts towards CO2RR. The d-band center in the different brass samples with different Zn content was elucidated.
New insights into the raw milk microbiota diversity from animals with a different genetic predisposition for feed efficiency and resilience to mastitis
Authors: Tarrah Armin , Callegaro Simone , Pakroo Shadi , Finocchiaro Raffaella , Giacomini Alessio , Corich Viviana , Cassandro Martino 
Published: August 2022

AbstractThe main objective of this study was to assess the microbiota diversity in milk samples collected from Holstein cows with different estimated breeding values for predicted feed efficiency, milk coagulation, resilience to mastitis, and consequently, to study its effects on milk quality. One hundred and twenty milk samples were collected in two seasons (summer and winter) from different commercial dairy farms in the Nord-east of Italy. For each trait, 20 animals divided into two groups of the high (10 cows) and the low (10 cows) were selected to study the microbiota profile using 16S rRNA metabarcoding sequencing. The alpha and beta diversity analysis revealed significant differences between the high and the low groups for feed efficiency and resilience to mastitis, while no significant difference was detected for milk coagulation. Moreover, remarkable differences among the taxa were detected between the two seasons, where the winter was more diverse than summer when applied the Chao1 index. Lastly, the linear discriminant analysis (LDA) effect size (LEfSe) indicated Aerococcus, Corynebacterium, Facklamia, and Psychrobacter taxa with more abundance in the high group of feed efficiency, whereas, in resilience to mastitis, only two genera of Mycoplana and Rhodococcus were more abundant in the low group. In addition, LEfSe analysis between the seasons showed significant differences in the abundance of Bacteroides, Lactobacillus, Corynebacterium, Escherichia, Citrobacter, Pantoea, Pseudomonas, and Stenotrophomonas. These findings indicate that the different genetic predisposition for feed efficiency and resilience to mastitis could affect the raw milk microbiota and, consequently, its quality. Moreover, we found more abundance of mastitis-associated bacteria in the milk of dairy cows with a higher feed efficiency index.
Glycerol monolaurate inhibition of human B cell activation
Authors: Fosdick Micaela G. , Loftus Shannon , Phillips Isabella , Zacharias Zeb R. , Houtman Jon C. D. 
Published: August 2022

AbstractGlycerol monolaurate (GML) is a naturally occurring antimicrobial agent used commercially in numerous products and food items. GML is also used as a homeopathic agent and is being clinically tested to treat several human diseases. In addition to its anti-microbial function, GML suppresses immune cell proliferation and inhibits primary human T cell activation. GML suppresses T cell activation by altering membrane dynamics and disrupting the formation of protein clusters necessary for intracellular signaling. The ability of GML to disrupt cellular membranes suggests it may alter other cell types. To explore this possibility, we tested how GML affects human B cells. We found that GML inhibits BCR-induced cytokine production, phosphorylation of signaling proteins, and protein clustering, while also changing cellular membrane dynamics and dysregulating cytoskeleton rearrangement. Although similar, there are also differences between how B cells and T cells respond to GML. These differences suggest that unique intrinsic features of a cell may result in differential responses to GML treatment. Overall, this study expands our understanding of how GML impacts the adaptive immune response and contributes to a broader knowledge of immune modulating monoglycerides.
The earliest segmental sternum in a Permian synapsid and its implications for the evolution of mammalian locomotion and ventilation
Authors: Bendel Eva-Maria , Kammerer Christian F. , Luo Zhe-Xi , Smith Roger M. H. , Fröbisch Jörg 
Published: August 2022

AbstractThe sternum is a stabilizing element in the axial skeleton of most tetrapods, closely linked with the function of the pectoral girdle of the appendicular skeleton. Modern mammals have a distinctive sternum characterized by multiple ossified segments, the origins of which are poorly understood. Although the evolution of the pectoral girdle has been extensively studied in early members of the mammalian total group (Synapsida), only limited data exist for the sternum. Ancestrally, synapsids exhibit a single sternal element and previously the earliest report of a segmental sternum in non-mammalian synapsids was in the Middle Triassic cynodontDiademodon tetragonus. Here, we describe the well-preserved sternum of a gorgonopsian, a group of sabre-toothed synapsids from the Permian. It represents an ossified, multipartite element resembling the mammalian condition. This discovery pulls back the origin of the distinctive “mammalian” sternum to the base of Theriodontia, significantly extending the temporal range of this morphology. Through a review of sternal morphology across Synapsida, we reconstruct the evolutionary history of this structure. Furthermore, we explore its role in the evolution of mammalian posture, gait, and ventilation through progressive regionalization of the postcranium as well as the posteriorization of musculature associated with mammalian breathing.
A pro-inflammatory and fibrous cap thinning transcriptome profile accompanies carotid plaque rupture leading to stroke
Authors: Bazan Hernan A. , Brooks Ashton J. , Vongbunyong Kenny , Tee Christin , Douglas Hunter F. , Klingenberg Natasha C. , Woods T. Cooper 
Published: August 2022

AbstractAtherosclerotic plaque rupture is the etiology of ischemic stroke and myocardial infarction. The molecular mechanisms responsible for rupture remain unclear, in part, due to the lack of data from plaques at the time of rupture. Ribosome-depleted total RNA was sequenced from carotid plaques obtained from patients undergoing carotid endarterectomy with high-grade stenosis and either (1) a carotid-related ischemic cerebrovascular event within the previous 5 days ('recently ruptured,' n = 6) or (2) an absence of a cerebrovascular event ('asymptomatic,' n = 5). Principal component analysis confirmed plaque rupture was responsible for the greatest percentage of the variability between samples (23.2%), and recently ruptured plaques were enriched for transcripts associated with inflammation and extracellular matrix degradation. Hierarchical clustering achieved differentiation of the asymptomatic from the recently ruptured plaques. This analysis also found co-expression of transcripts for immunoglobulins and B lymphocyte function, matrix metalloproteinases, and interferon response genes. Examination of the differentially expressed genes supported the importance of inflammation and inhibition of proliferation and migration coupled with an increase in apoptosis. Thus, the transcriptome of recently ruptured plaques is enriched with transcripts associated with inflammation and fibrous cap thinning and support further examination of the role of B lymphocytes and interferons in atherosclerotic plaque rupture.
Predicting outcome of patients with prolonged disorders of consciousness using machine learning models based on medical complexity
Authors: Liuzzi Piergiuseppe , Magliacano Alfonso , De Bellis Francesco , Mannini Andrea , Estraneo Anna 
Published: August 2022

AbstractPatients with severe acquired brain injury and prolonged disorders of consciousness (pDoC) are characterized by high clinical complexity and high risk to develop medical complications. The present multi-center longitudinal study aimed at investigating the impact of medical complications on the prediction of clinical outcome by means of machine learning models. Patients with pDoC were consecutively enrolled at admission in 23 intensive neurorehabilitation units (IRU) and followed-up at 6 months from onset via the Glasgow Outcome Scale—Extended (GOSE). Demographic and clinical data at study entry and medical complications developed within 3 months from admission were collected. Machine learning models were developed, targeting neurological outcomes at 6 months from brain injury using data collected at admission. Then, after concatenating predictions of such models to the medical complications collected within 3 months, a cascade model was developed. One hundred seventy six patients with pDoC (M: 123, median age 60.2 years) were included in the analysis. At admission, the best performing solution (k-Nearest Neighbors regression, KNN) resulted in a median validation error of 0.59 points [IQR 0.14] and a classification accuracy of dichotomized GOS-E of 88.6%. Coherently, at 3 months, the best model resulted in a median validation error of 0.49 points [IQR 0.11] and a classification accuracy of 92.6%. Interpreting the admission KNN showed how the negative effect of older age is strengthened when patients’ communication levels are high and ameliorated when no communication is present. The model trained at 3 months showed appropriate adaptation of the admission prediction according to the severity of the developed medical complexity in the first 3 months. In this work, we developed and cross-validated an interpretable decision support tool capable of distinguishing patients which will reach sufficient independence levels at 6 months (GOS-E > 4). Furthermore, we provide an updated prediction at 3 months, keeping in consideration the rehabilitative path and the risen medical complexity.
Altered gene expression profiles impair the nervous system development in individuals with 15q13.3 microdeletion
Authors: Körner Marek B. , Velluva Akhil , Bundalian Linnaeus , Radtke Maximilian , Lin Chen-Ching , Zacher Pia , Bartolomaeus Tobias , Kirstein Anna S. , Mrestani Achmed , Scholz Nicole , Platzer Konrad , Teichmann Anne-Christin , Hentschel Julia , Langenhan Tobias , Lemke Johannes R. , Garten Antje , Abou Jamra Rami , Le Duc Diana 
Published: August 2022

AbstractThe 15q13.3 microdeletion has pleiotropic effects ranging from apparently healthy to severely affected individuals. The underlying basis of the variable phenotype remains elusive. We analyzed gene expression using blood from three individuals with 15q13.3 microdeletion and brain cortex tissue from ten mice Df[h15q13]/+. We assessed differentially expressed genes (DEGs), protein–protein interaction (PPI) functional modules, and gene expression in brain developmental stages. The deleted genes’ haploinsufficiency was not transcriptionally compensated, suggesting a dosage effect may contribute to the pathomechanism. DEGs shared between tested individuals and a corresponding mouse model show a significant overlap including genes involved in monogenic neurodevelopmental disorders. Yet, network-wide dysregulatory effects suggest the phenotype is not caused by a single critical gene. A significant proportion of blood DEGs, silenced in adult brain, have maximum expression during the prenatal brain development. Based on DEGs and their PPI partners we identified altered functional modules related to developmental processes, including nervous system development. We show that the 15q13.3 microdeletion has a ubiquitous impact on the transcriptome pattern, especially dysregulation of genes involved in brain development. The high phenotypic variability seen in 15q13.3 microdeletion could stem from an increased vulnerability during brain development, instead of a specific pathomechanism.
Kinetics of neutralizing antibodies against SARS-CoV-2 infection according to sex, age, and disease severity
Authors: Kim Yoonjung , Bae Joon-Yong , Kwon Kitae , Chang Hyun-Ha , Lee Won Kee , Park Heedo , Kim Jeonghun , Choi Isaac , Park Man-Seong , Kim Shin-Woo 
Published: August 2022

AbstractKnowledge of the factors affecting the difference in kinetics and longevity of the neutralizing antibody (nAb) response to SARS-CoV-2 is necessary to properly prioritize vaccination. In the present study, from March to December 2020, of the 143 patients who recovered from COVID-19, 87 underwent study visits scheduled every 3 months. Patient demographics and blood samples were collected followed by a plaque reduction neutralization test to analyze nAb titers. A linear mixed model was used to compare the effects of sex, age, and disease severity over time. Results demonstrated a gradual reduction in nAb titers over time with a significant decrease from 6 to 9 months post-COVID-19 infection (p < 0.001). In time-to-sex, age, and disease severity comparisons, reduction in nAb titers over time was unaffected by sex (p = 0.167), age (p = 0.188), or disease severity (p = 0.081). Additionally, the nAb titer was 1.46 times significantly higher in those aged ≥ 50 years than in those aged < 50 years (p = 0.036) irrespective of time Moreover, the nAb titer was 2.41 times higher in the moderate or above than that in the below moderate disease severity group (p < 0.001). However, no significant differences were observed in terms of sex (p = 0.300). Given the reduction in nAbs over time, maintaining protective neutralizing antibodies regardless of sex, age, or disease severity is needed.