bluuebunny/crossref_metadata_2025_split huggingface dataset:
Triplication of the interferon receptor locus contributes to hallmarks of Down syndrome in a mouse model
Authors: Waugh Katherine A. , Minter Ross , Baxter Jessica , Chi Congwu , Galbraith Matthew D. , Tuttle Kathryn D. , Eduthan Neetha P. , Kinning Kohl T. , Andrysik Zdenek , Araya Paula , Dougherty Hannah , Dunn Lauren N. , Ludwig Michael , Schade Kyndal A. , Tracy Dayna , Smith Keith P. , Granrath Ross E. , Busquet Nicolas , Khanal Santosh , Anderson Ryan D. , Cox Liza L. , Estrada Belinda Enriquez , Rachubinski Angela L. , Lyford Hannah R. , Britton Eleanor C. , Fantauzzo Katherine A. , Orlicky David J. , Matsuda Jennifer L. , Song Kunhua , Cox Timothy C. , Sullivan Kelly D. , Espinosa Joaquin M. 
Published: June 2023

AbstractDown syndrome (DS), the genetic condition caused by trisomy 21, is characterized by variable cognitive impairment, immune dysregulation, dysmorphogenesis and increased prevalence of diverse co-occurring conditions. The mechanisms by which trisomy 21 causes these effects remain largely unknown. We demonstrate that triplication of the interferon receptor (IFNR) gene cluster on chromosome 21 is necessary for multiple phenotypes in a mouse model of DS. Whole-blood transcriptome analysis demonstrated that IFNR overexpression associates with chronic interferon hyperactivity and inflammation in people with DS. To define the contribution of this locus to DS phenotypes, we used genome editing to correct its copy number in a mouse model of DS, which normalized antiviral responses, prevented heart malformations, ameliorated developmental delays, improved cognition and attenuated craniofacial anomalies. Triplication of the Ifnr locus modulates hallmarks of DS in mice, suggesting that trisomy 21 elicits an interferonopathy potentially amenable to therapeutic intervention.
Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine
Authors: Schlosser Pascal , Scherer Nora , Grundner-Culemann Franziska , Monteiro-Martins Sara , Haug Stefan , Steinbrenner Inga , Uluvar Burulça , Wuttke Matthias , Cheng Yurong , Ekici Arif B. , Gyimesi Gergely , Karoly Edward D. , Kotsis Fruzsina , Mielke Johanna , Gomez Maria F. , Yu Bing , Grams Morgan E. , Coresh Josef , Boerwinkle Eric , Köttgen Michael , Kronenberg Florian , Meiselbach Heike , Mohney Robert P. , Akilesh Shreeram ,   GCKD Investigators, Schmidts Miriam , Hediger Matthias A. , Schultheiss Ulla T. , Eckardt Kai-Uwe , Oefner Peter J. , Sekula Peggy , Li Yong , Köttgen Anna 
Published: June 2023

AbstractThe kidneys operate at the interface of plasma and urine by clearing molecular waste products while retaining valuable solutes. Genetic studies of paired plasma and urine metabolomes may identify underlying processes. We conducted genome-wide studies of 1,916 plasma and urine metabolites and detected 1,299 significant associations. Associations with 40% of implicated metabolites would have been missed by studying plasma alone. We detected urine-specific findings that provide information about metabolite reabsorption in the kidney, such as aquaporin (AQP)-7-mediated glycerol transport, and different metabolomic footprints of kidney-expressed proteins in plasma and urine that are consistent with their localization and function, including the transporters NaDC3 (SLC13A3) and ASBT (SLC10A2). Shared genetic determinants of 7,073 metabolite–disease combinations represent a resource to better understand metabolic diseases and revealed connections of dipeptidase 1 with circulating digestive enzymes and with hypertension. Extending genetic studies of the metabolome beyond plasma yields unique insights into processes at the interface of body compartments.
Machine learning polysomnographically-derived electroencephalography biomarkers predictive of epworth sleepiness scale
Authors: Araujo Matheus , Ghosn Samer , Wang Lu , Hariadi Nengah , Wells Samantha , Saab Carl Y. , Mehra Reena 
Published: June 2023

AbstractExcessive daytime sleepiness (EDS) causes difficulty in concentrating and continuous fatigue during the day. In the clinical setting, the assessment and diagnosis of EDS rely mostly on subjective questionnaires and verbal reports, which compromises the reliability of clinical diagnosis and the ability to robustly discern candidacy for available therapies and track treatment response. In this study, we used a computational pipeline for the automated, rapid, high-throughput, and objective analysis of previously collected encephalography (EEG) data to identify surrogate biomarkers for EDS, thereby defining the quantitative EEG changes in individuals with high Epworth Sleepiness Scale (ESS) (n = 31), compared to a group of individuals with low ESS (n = 41) at the Cleveland Clinic. The epochs of EEG analyzed were extracted from a large overnight polysomnogram registry during the most proximate period of wakefulness. Signal processing of EEG showed significantly different EEG features in the low ESS group compared to high ESS, including enhanced power in the alpha and beta bands and attenuation in the delta and theta bands. Our machine learning (ML) algorithms trained on the binary classification of high vs. low ESS reached an accuracy of 80.2%, precision of 79.2%, recall of 73.8% and specificity of 85.3%. Moreover, we ruled out the effects of confounding clinical variables by evaluating the statistical contribution of these variables on our ML models. These results indicate that EEG data contain information in the form of rhythmic activity that could be leveraged for the quantitative assessment of EDS using ML.
Colossal figure of merit and compelling HER catalytic activity of holey graphyne
Authors: Sajjad Muhammad , Nair Surabhi Suresh , Samad Yarjan Abdul , Singh Nirpendra 
Published: June 2023

AbstractHerein, we have conducted a comprehensive study to uncover the thermal transport properties and hydrogen evolution reaction catalytic activity of recently synthesized holey graphyne. Our findings disclose that holey graphyne has a direct bandgap of 1.00 eV using the HSE06 exchange–correlation functional. The absence of imaginary phonon frequencies in the phonon dispersion ensures its dynamic stability. The formation energy of holey graphyne turns out to be − 8.46 eV/atom, comparable to graphene (− 9.22 eV/atom) and h-BN (− 8.80 eV/atom). At 300 K, the Seebeck coefficient is as high as 700 μV/K at a carrier concentration of 1 × 1010 cm-2. The predicted room temperature lattice thermal conductivity (κl) of 29.3 W/mK is substantially lower than graphene (3000 W/mK) and fourfold smaller than C3N (128 W/mK). At around 335 nm thickness, the room temperature κl suppresses by 25%. The calculated p-type figure of merit (ZT) reaches a maximum of 1.50 at 300 K, higher than that of holey graphene (ZT = 1.13), γ-graphyne (ZT = 0.48), and pristine graphene (ZT = 0.55 × 10–3). It further scales up to 3.36 at 600 K. Such colossal ZT values make holey graphyne an appealing p-type thermoelectric material. Besides that, holey graphyne is a potential HER catalyst with a low overpotential of 0.20 eV, which further reduces to 0.03 eV at 2% compressive strain.
The real bacterial filtration efficiency to evaluate the effective protection of facemasks used for the prevention of respiratory diseases
Authors: Benito Pedro J. , Gutiérrez Álvaro , Rojo-Tirado Miguel A. 
Published: June 2023

AbstractThe real protection offered by facemasks to control the transmission of respiratory viruses is still undetermined. Most of the manufacturing regulations, as well as scientific studies, have focused on studying the filtration capacity of the fabrics from which they are made, ignoring the air that escapes through the facial misalignments, and which depends on the respiratory frequencies and volumes. The objective of this work was to define a Real Bacterial Filtration Efficiency for each type of facemask, considering the bacterial filtration efficiency of the manufacturers and the air that passes through them. Nine different facemasks were tested on a mannequin with three gas analyzers (measuring inlet, outlet, and leak volumes) inside a polymethylmethacrylate box. In addition, the differential pressure was measured to determine the resistance offered by the facemasks during the inhalation and exhalation processes. Air was introduced with a manual syringe for 180 s simulating inhalations and exhalations at rest, light, moderate and vigorous activities (10, 60, 80 and 120 L/min, respectively). Statistical analysis showed that practically half of the air entering to the system is not filtered by the facemasks in all intensities (p < 0.001, ηp2 = 0.971). They also showed that the hygienic facemasks filter more than 70% of the air, and their filtration does not depend on the simulated intensity, while the rest of the facemasks show an evidently different response, influenced by the amount of air mobilized. Therefore, the Real Bacterial Filtration Efficiency can be calculated as a modulation of the Bacterial Filtration Efficiencies that depends on the type of facemask. The real filtration capacity of the facemasks has been overestimated during last years since the filtration of the fabrics is not the real filtration when the facemask is worn.
Dynamic computed tomography manifestations of simulated wooden foreign bodies in blood-saline mixtures with variable concentrations and retention times
Authors: Zhu Daoming , Li Xiaoling , Zhao Huiyan , Zhou Meng , Zhu Honghao , Qin Daming , Tan Biyong , Zhang Xianzhuo , Hu Xingrong 
Published: June 2023

AbstractDiagnosing wooden foreign bodies (WFBs) using computed tomography (CT) is often missed, leading to adverse outcomes. This study aims to reduce misdiagnoses by exploring the density variation of blood-saline mixtures in ex vivo models. Twenty Cunninghamia lanceolata sticks, selected as WFB models, were randomly assigned to five groups: a control group (saline) and four experimental groups immersed in blood-saline mixtures with varying concentrations. The samples were then placed in a constant-temperature water bath at 36.8 °C. CT scans were performed in the lowest and highest density areas, and the volume of the low-density areas was measured at the post-processing workstation. Finally, the effects of time and concentration on imaging were analyzed, and fitting curves were generated. The blood-saline mixture concentration and time significantly affected the CT number in the three areas. WFB images changed dynamically over time, with two typical imaging signs: the bull's-eye sign on the short axis images and the tram line sign on the long axis images. Fitting curves of the CT number in the lowest density areas with different concentrations can quantify imaging changes. The CT number of the lowest density areas increased with time, following a logarithmic function type, while the CT number of the highest density areas exhibited a fast-rising platform type. The volume of the low-density areas decreased over time. The time of damage caused by WFBs and the influence of varying blood and tissue fluid contents at the damaged site should be considered in the diagnosis. Imaging changes from multiple CT scans at different times can aid in diagnosis.
Direct biomolecule discrimination in mixed samples using nanogap-based single-molecule electrical measurement
Authors: Ryu Jiho , Komoto Yuki , Ohshiro Takahito , Taniguchi Masateru 
Published: June 2023

AbstractIn single-molecule measurements, metal nanogap electrodes directly measure the current of a single molecule. This technique has been actively investigated as a new detection method for a variety of samples. Machine learning has been applied to analyze signals derived from single molecules to improve the identification accuracy. However, conventional identification methods have drawbacks, such as the requirement of data to be measured for each target molecule and the electronic structure variation of the nanogap electrode. In this study, we report a technique for identifying molecules based on single-molecule measurement data measured only in mixed sample solutions. Compared with conventional methods that require training classifiers on measurement data from individual samples, our proposed method successfully predicts the mixing ratio from the measurement data in mixed solutions. This demonstrates the possibility of identifying single molecules using only data from mixed solutions, without prior training. This method is anticipated to be particularly useful for the analysis of biological samples in which chemical separation methods are not applicable, thereby increasing the potential for single-molecule measurements to be widely adopted as an analytical technique.
The propagation speed of optical speckle
Authors: Wan Zhenyu , Yessenov Murat , Padgett Miles J. 
Published: June 2023

AbstractThat the speed of light in vacuum is constant is a cornerstone of modern physics. However, recent experiments have shown that when the light field is confined in the transverse plane, the observed propagation speed of the light is reduced. This effect is a consequence of the transverse structure which reduces the component of wavevector of the light in the direction of propagation, thereby modifying both the phase and group velocity. Here, we consider the case of optical speckle, which has a random transverse distribution and is ubiquitous with scales ranging from the microscopic to the astronomical. We numerically investigate the plane-to-plane propagation speed of the optical speckle by using the method of angular spectrum analysis. For a general diffuser with Gaussian scattering over an angular range of 5°, we calculate the slowing of the propagation speed of the optical speckle to be on the order of 1% of the free-space speed, resulting in a significantly higher temporal delay compared to the Bessel and Laguerre–Gaussian beams considered previously. Our results have implications for studying optical speckle in both laboratory and astronomical settings.
Blooming of a microbial community in an Ediacaran extreme volcanic lake system
Authors: Chraiki Ibtissam , Chi Fru Ernest , Somogyi Andrea , Bouougri El Hafid , Bankole Olabode , Ghnahalla Mohamed , El Albani Abderrazak 
Published: June 2023

AbstractAncient aquatic sediments are critical archives for studying early microbial life and the types of environments in which they thrived. The recently characterized Amane Tazgart microbialites in the Anti-Atlas, Morocco, are a rare and well-preserved non-marine deposit that evolved in an alkaline volcanic lake setting during the Ediacaran Period. A multiproxy geochemical toolbox reveals evidence pointing to spatio-temporal ecosystem organization and succession related to changing lake water chemistry. This is marked by secular transition from a cold/dry climate, hypersaline alkaline thermophilic and anoxic–oxic community, to a stable state warm/wet climate fully oxygenated fresh to brackish water ecosystem, predominated by oxygenic stromatolites. Extreme dissolved Arsenic concentrations suggest that these polyextremophiles required robust detoxification mechanisms to circumvent arsenic toxicity and phosphate deficiency. We propose that self-sustaining and versatile anoxic to oxic microbial ecosystems thrived in aquatic continental settings during the Ediacaran Period, when complex life co-evolved with a rise in atmospheric oxygen content.
The genetics of a “femaleness/maleness” score in cardiometabolic traits in the UK biobank
Authors: Vosberg Daniel E. , Pausova Zdenka , Paus Tomáš 
Published: June 2023

AbstractWe recently devised continuous “sex-scores” that sum up multiple quantitative traits, weighted by their respective sex-difference effect sizes, as an approach to estimating polyphenotypic “maleness/femaleness” within each binary sex. To identify the genetic architecture underlying these sex-scores, we conducted sex-specific genome-wide association studies (GWASs) in the UK Biobank cohort (females: n = 161,906; males: n = 141,980). As a control, we also conducted GWASs of sex-specific “sum-scores”, simply aggregating the same traits, without weighting by sex differences. Among GWAS-identified genes, while sum-score genes were enriched for genes differentially expressed in the liver in both sexes, sex-score genes were enriched for genes differentially expressed in the cervix and across brain tissues, particularly for females. We then considered single nucleotide polymorphisms with significantly different effects (sdSNPs) between the sexes for sex-scores and sum-scores, mapping to male-dominant and female-dominant genes. Here, we identified brain-related enrichment for sex-scores, especially for male-dominant genes; these findings were present but weaker for sum-scores. Genetic correlation analyses of sex-biased diseases indicated that both sex-scores and sum-scores were associated with cardiometabolic, immune, and psychiatric disorders.
The nut-and-bolt motion of a bacteriophage sliding along a bacterial flagellum: a complete hydrodynamics model
Authors: Karabasov Sergey A. , Zaitsev Mihail A. , Nerukh Dmitry A. 
Published: June 2023

AbstractThe ‘nut-and-bolt’ mechanism of a bacteriophage-bacteria flagellum translocation motion is modelled by numerically integrating the 3D Stokes equations using a Finite-Element Method (FEM). Following the works by Katsamba and Lauga (Phys Rev Fluids 4(1): 013101, 2019), two mechanical models of the flagellum-phage complex are considered. In the first model, the phage fiber wraps around the smooth flagellum surface separated by some distance. In the second model, the phage fiber is partly immersed in the flagellum volume via a helical groove imprinted in the flagellum and replicating the fiber shape. In both cases, the results of the Stokes solution for the translocation speed are compared with the Resistive Force Theory (RFT) solutions (obtained in Katsamba and Lauga Phys Rev Fluids 4(1): 013101, 2019) and the asymptotic theory in a limiting case. The previous RFT solutions of the same mechanical models of the flagellum-phage complex showed opposite trends for how the phage translocation speed depends on the phage tail length. The current work uses complete hydrodynamics solutions, which are free from the RFT assumptions to understand the divergence of the two mechanical models of the same biological system. A parametric investigation is performed by changing pertinent geometrical parameters of the flagellum-phage complex and computing the resulting phage translocation speed. The FEM solutions are compared with the RFT results using insights provided from the velocity field visualisation in the fluid domain.
Evaluation of the capability and reproducibility of RECIST 1.1. measurements by technologists in breast cancer follow-up: a pilot study
Authors: Gouel Pierrick , Callonnec Françoise , Levêque Émilie , Valet Céline , Blôt Axelle , Cuvelier Clémence , Saï Sonia , Saunier Lucie , Pepin Louis-Ferdinand , Hapdey Sébastien , Libraire Julie , Vera Pierre , Viard Benjamin 
Published: June 2023

AbstractThe evaluation of tumor follow-up according to RECIST 1.1 has become essential in clinical practice given its role in therapeutic decision making. At the same time, radiologists are facing an increase in activity while facing a shortage. Radiographic technologists could contribute to the follow-up of these measures, but no studies have evaluated their ability to perform them. Ninety breast cancer patients were performed three CT follow-ups between September 2017 and August 2021. 270 follow-up treatment CT scans were analyzed including 445 target lesions. The rate of agreement of classifications RECIST 1.1 between five technologists and radiologists yielded moderate (k value between 0.47 and 0.52) and substantial (k value = 0.62 and k = 0.67) agreement values. 112 CT were classified as progressive disease (PD) by the radiologists, and 414 new lesions were identified. The analysis showed a percentage of strict agreement of progressive disease classification between reader-technologists and radiologists ranging from substantial to almost perfect agreement (range 73–97%). Analysis of intra-observer agreement was strong at almost perfect (k > 0.78) for 3 technologists. These results are encouraging regarding the ability of selected technologists to perform measurements according to RECIST 1.1 criteria by CT scan with good identification of disease progression.
Association of trabecular meshwork height with steroid-induced ocular hypertension
Authors: Cho Won Jeong , Kim Yitak , Kim Jung Dong , Kim Eun Woo , Bae Hyoung Won , Kim Chan Yun , Choi Wungrak 
Published: June 2023

AbstractIt is important to identify at-risk patients prior to administering steroid injections to prevent avoidable irreversible blindness inducted by steroid-induced ocular hypertension (SIOH). We aimed to investigate the association of SIOH following intravitreal dexamethasone implantation (OZURDEX) using anterior segment optical coherence tomography (AS-OCT). We conducted a retrospective case control study to assess the association between trabecular meshwork and SIOH. A total of 102 eyes that underwent both AS-OCT and intravitreal dexamethasone implant injection were divided into the post-steroid ocular hypertension and normal intraocular pressure groups. Ocular parameters that can contribute to intraocular pressure were measured using AS-OCT. Univariable logistic regression analysis was used to calculate the odds ratio of the SIOH and significant variables were further analyzed using a multivariable model. Trabecular meshwork (TM) height was significantly shorter in the ocular hypertension group (716.13 ± 80.55 μm) than that in the normal intraocular pressure group (784.27 ± 82.33 μm) (p < 0.001). The receiver operating characteristic curve technique analysis showed that the optimal cut-off of ≥ 802.13 μm for TM height specificity was 96.2%, and TM height with < 646.75 μm had a sensitivity of 94.70%. The odds ratio of the association was 0.990 (p = 0.001). TM height was identified as a newly observed association with SIOH. TM height can be assessed using AS-OCT, with acceptable sensitivity and specificity. Caution must be exercised while injecting steroids in patients with short TM height (especially < 646.75 μm) as it may cause SIOH and irreversible blindness.
Crack mechanism and experimental verification on straightening of AZ31B magnesium alloy plate
Authors: Wang Rong-Jun , Zhou Qi , Du Xiao-Zhong , Li Yu-Shan , Zhang Peng-Chong , Li Guang-Feng , Huang Zhi-Quan , Ma Li-Dong , Jiang Lian-Yun 
Published: June 2023

AbstractWhen plates with edge cracks in the rolling process is straightened by cyclic tensile and compressive stress, the tip of edge crack always accompanied by stress concentration, which leads to crack propagation. In this paper, damage parameters are imported into the plate straightening model based on determining the GTN damage parameters of magnesium alloy materials by inverse finite element calibration method, the influence of different straightening process schemes and prefabricated V-shaped crack geometry on crack growth is analyzed through the way of the combination of simulation and straightening experiment. The results show that the peak values of equivalent stress and equivalent strain under each straightening roll appear at the crack tip. The value of longitudinal stress and equivalent stain decrease with the distance to crack tip becomes larger. The peak value of longitudinal stress appears when the crack circumferential angle is about 100°, and the crack tip is easy to form crack propagation; when the plate passes roll 2 and roll 4, the equivalent stress and strain concentration at the crack tip are most obvious; when the reduction reaches a certain degree, the void volume fraction (VVF) reaches the VVF of the material breaking; with the increase of the entrance reduction, the number of VVF at the crack tip which reaches the material fracture increases, and the length of crack propagation increases; the stress concentration at the tip of V-shaped crack with large length–width ratio is obvious, and the VVF is more likely to reach the VVF at the time of material fracture, crack initiates and propagates easily.