bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural basis of human SNAPc recognizing proximal sequence element of snRNA promoter
Authors: Sun Jianfeng , Li Xue , Hou Xuben , Cao Sujian , Cao Wenjin , Zhang Ye , Song Jinyang , Wang Manfu , Wang Hao , Yan Xiaodong , Li Zengpeng , Roeder Robert G. , Wang Wei 
Published: November 2022

AbstractIn eukaryotes, small nuclear RNAs (snRNAs) function in many fundamental cellular events such as precursor messenger RNA splicing, gene expression regulation, and ribosomal RNA processing. The snRNA activating protein complex (SNAPc) exclusively recognizes the proximal sequence element (PSE) at snRNA promoters and recruits RNA polymerase II or III to initiate transcription. In view that homozygous gene-knockout of SNAPc core subunits causes mouse embryonic lethality, functions of SNAPc are almost housekeeping. But so far, the structural insight into how SNAPc assembles and regulates snRNA transcription initiation remains unclear. Here we present the cryo-electron microscopy structure of the essential part of human SNAPc in complex with human U6-1 PSE at an overall resolution of 3.49 Å. This structure reveals the three-dimensional features of three conserved subunits (N-terminal domain of SNAP190, SNAP50, and SNAP43) and explains how they are assembled into a stable mini-SNAPc in PSE-binding state with a “wrap-around” mode. We identify three important motifs of SNAP50 that are involved in both major groove and minor groove recognition of PSE, in coordination with the Myb domain of SNAP190. Our findings further elaborate human PSE sequence conservation and compatibility for SNAPc recognition, providing a clear framework of snRNA transcription initiation, especially the U6 system.
PD-L1 negatively regulates antifungal immunity by inhibiting neutrophil release from bone marrow
Authors: Yu Yao , Wang Rong-Rong , Miao Nai-Jun , Tang Jia-Jie , Zhang Yun-Wei , Lu Xiang-Ran , Yan Pei-Yi , Wang Jing , Jia Xin-Ming 
Published: November 2022

AbstractProgrammed death ligand 1 (PD-L1) has been shown to be inducibly expressed on neutrophils to suppress host immunity during polymicrobial sepsis, virus and parasite infections. However, the role of PD-L1 on neutrophil-mediated antifungal immunity remains wholly unknown. Here, we show that the expression of PD-L1 on murine and human neutrophils was upregulated upon the engagement of C-type lectin receptor Dectin-1 with its ligand β-glucans, exposed on fungal pathogen Candida albicans yeast. Moreover, β-glucan stimulation induced PD-L1 translocation into nucleus to regulate the production of chemokines CXCL1 and CXCL2, which control neutrophil mobilization. Importantly, C. albicans infection-induced expression of PD-L1 leads to neutrophil accumulation in bone marrow, through mediating their autocrine secretion of CXCL1/2. Furthermore, neutrophil-specific deficiency of PD-L1 impaired CXCL1/2 secretion, which promoted neutrophil migration from bone marrow into the peripheral circulation, thereby conferring host resistance to C. albicans infection. Finally, either PD-L1 blockade or pharmacological inhibition of PD-L1 expression significantly increased neutrophil release from bone marrow to enhance host antifungal immunity. Our data together indicate that activation of Dectin-1/PD-L1 cascade by β-glucans inhibits neutrophil release from bone marrow reserve, contributing to the negative regulation of antifungal innate immunity, which functions as a potent immunotherapeutic target against life-threatening fungi infections.
The Health Gym: synthetic health-related datasets for the development of reinforcement learning algorithms
Authors: Kuo Nicholas I-Hsien , Polizzotto Mark N. , Finfer Simon , Garcia Federico , Sönnerborg Anders , Zazzi Maurizio , Böhm Michael , Kaiser Rolf , Jorm Louisa , Barbieri Sebastiano 
Published: November 2022

AbstractIn recent years, the machine learning research community has benefited tremendously from the availability of openly accessible benchmark datasets. Clinical data are usually not openly available due to their confidential nature. This has hampered the development of reproducible and generalisable machine learning applications in health care. Here we introduce the Health Gym - a growing collection of highly realistic synthetic medical datasets that can be freely accessed to prototype, evaluate, and compare machine learning algorithms, with a specific focus on reinforcement learning. The three synthetic datasets described in this paper present patient cohorts with acute hypotension and sepsis in the intensive care unit, and people with human immunodeficiency virus (HIV) receiving antiretroviral therapy. The datasets were created using a novel generative adversarial network (GAN). The distributions of variables, and correlations between variables and trends in variables over time in the synthetic datasets mirror those in the real datasets. Furthermore, the risk of sensitive information disclosure associated with the public distribution of the synthetic datasets is estimated to be very low.
WES data from 286 diffuse gliomas under the 2021 WHO Classification of Tumors of the Central Nervous System
Authors: Zhao Zheng , Zhang Ke-Nan , Sun Zhiyan , Yang Changlin , Wang Qiangwei , Li Guanzhang , Wang Zhiliang , Zeng Fan , Chai Ruichao , Qian Zenghui , Wang Zheng , Liu Yanwei , Ma Wenping , Wu Fan , Jiang Tao 
Published: November 2022

AbstractDiffuse gliomas (DGs) are the most common and lethal primary neoplasms in the central nervous system. The latest 2021 World Health Organization (WHO) Classification of Tumors of the Central Nervous System (CNS) was published in 2021, immensely changing the approach to diagnosis and decision making. As a part of the Chinese Glioma Genome Atlas (CGGA) project, our aim was to provide genomic profiling of gliomas in a Chinese cohort. Two hundred eighty six gliomas with different grades were collected over the last decade. Using the Illumina HiSeq platform, over 75.8 million high-quality 150 bp paired-end reads were generated per sample, yielding a total of 43.4 billion reads. We also collected each patient’s clinical and pathological information and used it to annotate their genetic data. All patients were diagnosed and classified by neuro-pathologist under the 2021 WHO classification. This dataset provides an important reference for researchers and will significantly advance our understanding of gliomas.
Catalytic DxD motif caged in Asx-turn and Met–aromatic interaction attenuates the pathogenic glycosylation of SseK2/NleB2 effectors
Authors: Koh Eunhee , Kim Uijin , Cho Hyun-Soo 
Published: November 2022

AbstractPathogenic bacteria encode virulent glycosyltransferases that conjugate various glycans onto host crucial proteins, which allows adhesion to mammalian cells and modulates host cellular processes for pathogenesis. Escherichia coli NleB1, Citrobacter rodentium NleB, and Salmonella enterica SseK1/3 type III effectors fatally glycosyltransfer N-acetyl glucosamine (GlcNAc) from UDP-GlcNAc to arginine residues of death domain-containing proteins that regulate host inflammation, intra-bacterial proteins, and themselves, whose post-translational modification disrupts host immune functions and prolongs bacterial viability inside host cells. However, unlike the similar NleB1/SseK1/SseK3, E. coli NleB2 and S. enterica SseK2 show deficient GlcNAcylation and neither intra-bacterial glycosylation nor auto-glycosylation. Here, as the major factor in SseK2/NleB2 deficiency, we focused on the catalytic Asp-x-Asp (DxD) motif conserved throughout all O-/N-glycosyltransferases to coordinate Mn2+. All DxD motifs in apo-glycosyltransferases form Type-I-turns for binding Mn2+, similar to the ligand-bound DxD motif, whereas TcnA/SseK2/NleB2 DxD motifs form Asx-turns, which are unable to bind Mn2+. Interestingly, methionine of the NleB2 DMD motif forms triple Met–aromatic interactions, as found in age-associated diseases and tumor necrosis factor (TNF) ligand-receptor complexes. The NleB1 A222M mutation induces triple Met–aromatic interactions to steeply attenuate glycosylation activity to 3% of that in the wild type. Thus, the characteristic conformation of the DxD motif is essential for binding Mn2+, donors, and glycosylate targets. This explains why SseK2/NleB2 effectors with the DxD motif caged in the Asp-/Asn-turn (Asx-turn) and triple Met–aromatic interactions have lower glycosyltransferase activity than that of other fatal NleB1/SseK1/SseK3 toxins.
Capturing SARS-CoV-2 from patient samples with low viral abundance: a comparative analysis
Authors: Pipoli da Fonseca Juliana , Kornobis Etienne , Turc Elodie , Enouf Vincent , Lemée Laure , Cokelaer Thomas , Monot Marc 
Published: November 2022

AbstractSince the beginning of the SARS-CoV-2 coronavirus pandemic, genome sequencing is essential to monitor viral mutations over time and by territory. This need for complete genetic information is further reinforced by the rapid spread of variants of concern. In this paper, we assess the ability of the hybridization technique, Capture-Seq, to detect the SARS-CoV-2 genome, either partially or in its integrity on patients samples. We studied 20 patient nasal swab samples broken down into five series of four samples of equivalent viral load from CT25 to CT36+ . For this, we tested 3 multi-virus panel as well as 2 SARS-CoV-2 only panels. The panels were chosen based on their specificity, global or specific, as well as their technological difference in the composition of the probes: ssRNA, ssDNA and dsDNA. The multi-virus panels are able to capture high-abundance targets but fail to capture the lowest-abundance targets, with a high percentage of off-target reads corresponding to the abundance of the host sequences. Both SARS-CoV-2-only panels were very effective, with high percentage of reads corresponding to the target. Overall, capture followed by sequencing is very effective for the study of SARS-CoV-2 in low-abundance patient samples and is suitable for samples with CT values up to 35.
Autonomic and circulatory alterations persist despite adequate resuscitation in a 5-day sepsis swine experiment
Authors: Carrara Marta , Antenucci Pietro , Liu Shengchen , Kohler Andreas , Langer Rupert , Jakob Stephan M. , Ferrario Manuela 
Published: November 2022

AbstractAutonomic and vascular failures are common phenotypes of sepsis, typically characterized by tachycardia despite corrected hypotension/hypovolemia, vasopressor resistance, increased arterial stiffness and decreased peripheral vascular resistance. In a 5-day swine experiment of polymicrobial sepsis we aimed at characterizing arterial properties and autonomic mechanisms responsible for cardiovascular homeostasis regulation, with the final goal to verify whether the resuscitation therapy in agreement with standard guidelines was successful in restoring a physiological condition of hemodynamic profile, cardiovascular interactions and autonomic control. Twenty pigs were randomized to polymicrobial sepsis and protocol-based resuscitation or to prolonged mechanical ventilation and sedation without sepsis. The animals were studied at baseline, after sepsis development, and every 24 h during the 3-days resuscitation period. Beat-to-beat carotid blood pressure (BP), carotid blood flow, and central venous pressure were continuously recorded. The two-element Windkessel model was adopted to study carotid arterial compliance, systemic vascular resistance and characteristic time constant τ. Effective arterial elastance was calculated as a simple estimate of total arterial load. Cardiac baroreflex sensitivity (BRS) and low frequency (LF) spectral power of diastolic BP were computed to assess autonomic activity. Sepsis induced significant vascular and autonomic alterations, manifested as increased arterial stiffness, decreased vascular resistance and τ constant, reduced BRS and LF power, higher arterial afterload and elevated heart rate in septic pigs compared to sham animals. This compromised condition was persistent until the end of the experiment, despite achievement of recommended resuscitation goals by administered vasopressors and fluids. Vascular and autonomic alterations persist 3 days after goal-directed resuscitation in a clinically relevant sepsis model. We hypothesize that the addition of these variables to standard clinical markers may better profile patients’ response to treatment and this could drive a more tailored therapy which could have a potential impact on long-term outcomes.
Texture analysis and artificial neural networks for identification of cereals—case study: wheat, barley and rape seeds
Authors: Gierz Ł. , Przybył K. 
Published: November 2022

AbstractThe scope of the research comprises an analysis and evaluation of samples of rape, barley and wheat seeds. The experiments were carried out using the author’s original research object. The air flow velocities to transport seeds, were set at 15, 20 and 25 m s−1. A database consisting of images was created, which allowed to determine 3 classes of kernels on the basis of 6 research variants, including their transportation way via pipe and the speed of sowing. The process of creating neural models was based on multilayer perceptron networks (MLPN) in Statistica (machine learning). It should be added that the use of MLPN also allowed identification of rape seeds, wheat seeds and barley seeds transported via pipe II at 20 m s−1, for which the lowest RMS was 0.05 and the coefficient of classification accuracy was 0.94.
Investigating the mechanisms by which selective attention affects subsequent preferences and choice
Authors: Egger Martin , Florack Arnd 
Published: November 2022

AbstractIn two experiments, we investigated two untested assumptions regarding the mechanism by which selective attention during search affects subsequent preferences for objects. First, we tested whether an increase in visual competition during search increases preferences for relevant objects and decreases preferences for irrelevant objects subsequent to search. Second, we tested whether searching for objects increases the perceived fluency to process relevant objects and decreases the perceived fluency to process irrelevant objects. Our results show that search can affect relevant and irrelevant objects differently. Selective attention increased preferences for target objects subsequent to search, whereas selective attention did not affect preferences for distractors. Furthermore, our results indicate that searching for a target object increased the perceived fluency for this target object during choice, whereas ignoring a distractor product blocked mere exposure effects. Contrary to assumptions made in previous research, we found no indication that the competition for visual resources during search is linked to preferences for targets or distractors.
Organic molecule functionalized lead sulfide hybrid system for energy storage and field dependent polarization performances
Authors: Ghosh Sarit K. , Waziri Ibrahim , Bo Maolin , Singh Harishchandra , Islam Rafique Ul , Mallick Kaushik 
Published: November 2022

AbstractA wet chemical route is reported for synthesising organic molecule stabilized lead sulfide nanoparticles. The dielectric capacitance, energy storage performances and field-driven polarization of the organic–inorganic hybrid system are investigated in the form of a device under varying temperature and frequency conditions. The structural analysis confirmed the formation of the monoclinic phase of lead sulfide within the organic network. The band structure of lead sulfide was obtained by density functional theory calculation that supported the semiconductor nature of the material with a direct band gap of 2.27 eV. The dielectric performance of the lead sulfide originated due to the dipolar and the space charge polarization. The energy storage ability of the material was investigated under DC-bias conditions, and the device exhibited the power density values 30 W/g and 340 W/g at 100 Hz and 10 kHz, respectively. The electric field-induced polarization study exhibited a fatigue-free behaviour of the device for 103 cycles with a stable dielectric strength. The study revealed that the lead sulfide-based system has potential in energy storage applications.
The spatial modification effect of predictors on household level food insecurity in Ethiopia
Authors: Dessie Zelalem G. , Zewotir Temesgen , North Delia 
Published: November 2022

AbstractHousehold food insecurity remains highly prevalent in developing countries (including in Ethiopia) and it has been recognized as a serious public health problem. Several factors such as demographic, economic, social, and clinical factors influence household food insecurity, and these vary geographically. In this work, we investigate the geographical modification of the effect of several factors on chronic food insecurity. The data is from the Ethiopia socioeconomic survey conducted by the Ethiopia Central Statistics Agency (ECSA) in collaboration with the World Bank. Ethiopia socioeconomic survey is a long-term project to collect nationally representative panel survey of over 6500 households. A geo-additive model which accounts the structured and unstructured special effect was adopted to estimate household food insecurity risk factors. The study also revealed significant spatial variations on household food insecurity among administrative zones. Mainly, household living in the Sidama, Gamo Gofa, Shinille, Basketo, Wolyita, Wag Hemira, Liben, Awi, Eastern Tigray and West Harerghe zones, having higher food insecurity than the other zones in Ethiopia. Moreover, the analysis also showed that availability of credit services, proximity to service centers, average years of schooling of members of the household, and household assets are negatively associated with household food insecurity, whereas shocks, age, and dependency ratio increase the odds of a household to be food insecured. The generalized geo-additive mixed-effects model enables simultaneous modeling of spatial correlation, heterogeneity and possible nonlinear effects of covariates. Our study investigated the spatial heterogeneity of household level food insecurity, and its association with shocks, age, dependency ratio, availability of credit services, average years of schooling, and household assets. Our findings have also an important implication for planning as well as in the search for the variables that might account for the residual spatial patterns.
Continental tapering of South America caused asymmetric non-uniform opening of the South Atlantic Ocean
Authors: Gao Dengliang 
Published: November 2022

AbstractSouth Atlantic opening has been typically modelled as being related to symmetric and static thermal upwelling and seafloor spreading that drive divergent continental drift of South America and Africa. Comparative analyses, however, show that South Atlantic opening is asymmetric and non-uniform. For neither asymmetric nor non-uniform opening are the underlying mechanisms clear. Here I use geological and geophysical data to inform analytical modelling, revealing that westward drifting and southward tapering of the South American continent have controlled the asymmetry and the non-uniformity in South Atlantic opening. I interpret that the asymmetric non-uniform seafloor spreading caused the ridge and hotspots to migrate, leaving behind non-linear seamount trails that are indicative of the speed of hotspot migration rather than direction of plate movement. The findings point towards a chain reaction from continental drifting, through seafloor spreading to ridge-hotspot interaction, which is instrumental in understanding the geodynamics for global plate tectonics.
Assessment of Hearing-Related Lifestyle Based on the Common Sound Scenarios Framework
Authors: Lelic Dina , Wolters Florian , Herrlin Petra , Smeds Karolina 
Published: November 2022

Purpose:
Auditory lifestyle can play a role in hearing care needs, and, as such, it needs to be considered when treating people with hearing loss. In this study, we propose a questionnaire consisting of 24 listening situations based on the Common Sound Scenarios (CoSS) framework.

Method:
Seventeen experienced hearing aid (HA) users filled out the Hearing-Related Lifestyle Questionnaire four times: Days 1, 2, 15, and 29. The questionnaire consisted of 24 listening situations that participants rated on frequency of occurrence, importance to hear well, difficulty to hear, and HA satisfaction. Four questionnaire outcomes were extracted from these ratings: richness of hearing-related lifestyle, hearing demand, hearing difficulty, and HA satisfaction. Additionally, the participants were asked whether any listening situations are not understandable or relatable, whether any situations are missing from the questionnaire, and whether the number of questions is acceptable. Test–retest reliability analyses were done to assess whether the questionnaire outcomes are reliable across the four reports. Correlation analyses were done to assess whether there is a relationship between the questionnaire outcomes.

Results:
The questionnaire outcomes have excellent reliability. The listening situations in the questionnaire are generally complete and relatable, and the number of questions is acceptable. Correlation analyses revealed that the questionnaire outcomes are related to each other.

Conclusions:
Currently, there are no other hearing-related lifestyle questionnaires that purely assess listening situations. The proposed questionnaire has the potential to add to our understanding of hearing-related lifestyle of people needing or undergoing hearing care.

Supplemental Material:

https://doi.org/10.23641/asha.21514044
Video-Based Facial Movement Analysis in the Assessment of Bulbar Amyotrophic Lateral Sclerosis: Clinical Validation
Authors: Guarin Diego L. , Taati Babak , Abrahao Agessandro , Zinman Lorne , Yunusova Yana 
Published: November 2022

Purpose:Facial movement analysis during facial gestures and speech provides clinically useful information for assessing bulbar amyotrophic lateral sclerosis (ALS). However, current kinematic methods have limited clinical application due to the equipment costs. Recent advancements in consumer-grade hardware and machine/deep learning made it possible to estimate facial movements from videos. This study aimed to establish the clinical validity of a video-based facial analysis for disease staging classification and estimation of clinical scores.Method:Fifteen individuals with ALS and 11 controls participated in this study. Participants with ALS were stratified into early and late bulbar ALS groups based on their speaking rate. Participants were recorded with a three-dimensional (3D) camera (color + depth) while repeating a simple sentence 10 times. The lips and jaw movements were estimated, and features related to sentence duration and facial movements were used to train a machine learning model for multiclass classification and to predict the Amyotrophic Lateral Sclerosis Functional Rating Scale–Revised (ALSFRS-R) bulbar subscore and speaking rate.Results:The classification model successfully separated healthy controls, the early ALS group, and the late ALS group with an overall accuracy of 96.1%. Video-based features demonstrated a high ability to estimate the speaking rate (adjustedR2= .82) and a moderate ability to predict the ALSFRS-R bulbar subscore (adjustedR2= .55).Conclusions:The proposed approach based on a 3D camera and machine learning algorithms represents an easy-to-use and inexpensive system that can be included as part of a clinical assessment of bulbar ALS to integrate facial movement analysis with other clinical data seamlessly