bluuebunny/crossref_metadata_2025_split huggingface dataset:
A task-unified network with transformer and spatial–temporal convolution for left ventricular quantification
Authors: Li Dapeng , Peng Yanjun , Sun Jindong , Guo Yanfei 
Published: August 2023

AbstractQuantification of the cardiac function is vital for diagnosing and curing the cardiovascular diseases. Left ventricular function measurement is the most commonly used measure to evaluate the function of cardiac in clinical practice, how to improve the accuracy of left ventricular quantitative assessment results has always been the subject of research by medical researchers. Although considerable efforts have been put forward to measure the left ventricle (LV) automatically using deep learning methods, the accurate quantification is yet a challenge work as a result of the changeable anatomy structure of heart in the systolic diastolic cycle. Besides, most methods used direct regression method which lacks of visual based analysis. In this work, a deep learning segmentation and regression task-unified network with transformer and spatial–temporal convolution is proposed to segment and quantify the LV simultaneously. The segmentation module leverages a U-Net like 3D Transformer model to predict the contour of three anatomy structures, while the regression module learns spatial–temporal representations from the original images and the reconstruct feature map from segmentation path to estimate the finally desired quantification metrics. Furthermore, we employ a joint task loss function to train the two module networks. Our framework is evaluated on the MICCAI 2017 Left Ventricle Full Quantification Challenge dataset. The results of experiments demonstrate the effectiveness of our framework, which achieves competitive cardiac quantification metric results and at the same time produces visualized segmentation results that are conducive to later analysis.
Socioeconomic and environmental determinants of foot and mouth disease incidence: an ecological, cross-sectional study across Iran using spatial modeling
Authors: Nazari Ashani Mahdi , Alesheikh Ali Asghar , Neisani Samani Zeinab , Lotfata Aynaz , Bayat Sayeh , Alipour Siamak , Hoseini Benyamin 
Published: August 2023

AbstractFoot-and-mouth disease (FMD) is a highly contagious animal disease caused by a ribonucleic acid (RNA) virus, with significant economic costs and uneven distribution across Asia, Africa, and South America. While spatial analysis and modeling of FMD are still in their early stages, this research aimed to identify socio-environmental determinants of FMD incidence in Iran at the provincial level by studying 135 outbreaks reported between March 21, 2017, and March 21, 2018. We obtained 46 potential socio-environmental determinants and selected four variables, including percentage of population, precipitation in January, percentage of sheep, and percentage of goats, to be used in spatial regression models to estimate variation in spatial heterogeneity. In our analysis, we employed global models, namely ordinary least squares (OLS), spatial error model (SEM), and spatial lag model (SLM), as well as local models, including geographically weighted regression (GWR) and multiscale geographically weighted regression (MGWR). The MGWR model yielded the highest adjusted $${R}^{2}$$

R

2

of 90%, outperforming the other local and global models. Using local models to map the effects of environmental determinants (such as the percentage of sheep and precipitation) on the spatial variability of FMD incidence provides decision-makers with helpful information for targeted interventions. Our findings advocate for multiscale and multidisciplinary policies to reduce FMD incidence.
The effectiveness of isometric protocols using an external load or voluntary effort on jump height enhancement in trained females
Authors: Koźlenia Dawid , Domaradzki Jarosław 
Published: August 2023

AbstractThis study aimed to examine the effectiveness of isometric post-activation performance enhancement protocols using an external load (EXL) or voluntary effort (VE) on jump height (JH) in trained females divided into EXL (n = 15), VE (n = 14), and control (CON; n = 12) groups. JH was assessed using countermovement jumps at baseline and the third, fifth, seventh, and ninth minutes after the protocols. The EXL performed three sets of back squats with a 70%-repetition maximum load for four seconds, with one-minute breaks. The VE performed three sets of pushing against an immovable bar in the back squat position for five seconds, with one-minute breaks. The CON group ran on a treadmill at 6 km/h for four minutes. A RM-ANOVA showed a significant interaction for group-time (p < 0.01). The EXL protocol provided JH improvement at the third minute compared to baseline (p = 0.01), though it decreased in subsequent minutes (p < 0.05). JH declined in the VE group at the third and fifth minutes (p < 0.05), then peaked, surpassing baseline, after nine minutes (p = 0.04). No significant differences were found between the protocols in the relative effect (best—baseline) (p = 0.09), though the EXL group appeared to gain more (effect size [ES] = 0.76). Both protocols improved JH, but caution is required due to peak performance time and potential JH reduction.
El Niño and La Niña asymmetry in short-term predictability on springtime initial condition
Authors: Chen Hui , Jin Yishuai , Shen Xingchen , Lin Xiaopei , Hu Ruikun 
Published: August 2023

AbstractEl Niño-Southern Oscillation (ENSO) asymmetry in predictability on springtime initial condition remains unclear. From the perspective of the spring predictability barrier (SPB), this paper investigates the ENSO asymmetry in SPB and explores the potential factors that may lead to this asymmetry. Both the observation and 29 Coupled Model Intercomparison Project Phase 6 (CMIP6) models show that the spring sea surface temperature (SST) persistence is significantly higher in El Niño years than that in La Niña years, and the SPB intensity is stronger in La Niña years than that in El Niño years. Through the recharge oscillator model, observation and CMIP6 models, we demonstrate that the nonlinear wind stress response to SST anomalies in spring is the main cause of the asymmetric SPB intensity. By the mixed-layer heat budget of the tropical Pacific in the spring, we further identify that a stronger response of zonal wind stress in El Niño events can cause a stronger zonal advection feedback, which finally leads to a weaker SPB and enhances the predictability of El Niño. In contrast, the cooling SST in the spring only leads to weak easterly anomalies, the zonal advection feedback is relatively weaker, thus SPB is stronger and the predictability of La Niña is lower. From the perspective of SPB, we suggest that El Niño is more predictable than La Niña.
Possible factors for the recent changes in frequency of central Indian Summer Monsoon precipitation extremes during 2005–2020
Authors: Bajrang C. , Attada Raju , Goswami B. N. 
Published: August 2023

AbstractThe transitions of short-term trends of Indian Summer Monsoon daily precipitation extremes remain poorly understood. Here, we show a short-term declination of temporal frequency of monsoonal precipitation extremes over Central India for the last 15 years starting from 2005 to 2020 while the low and moderate events show increasing trends. The possible dynamical and thermodynamical factors for the observed decline in precipitation extremes include depletion in moisture transport to Central India via cross-equatorial flow and the low-level Somali jet, caused by reduced evaporation from the regional moisture sources. In addition, the vertical gradient of the moist static energy exhibits favorable conditions for increased lower atmospheric stability, supporting the declining trends. Lastly, the Atlantic Zonal Mode seems to be a potential large-scale climate driver for the less frequent central Indian extreme rainfall events during 2005–2020.
Tumor-associated macrophage-related strategies for glioma immunotherapy
Authors: Tang Fansong , Wang Yuelong , Zeng Yunhui , Xiao Anqi , Tong Aiping , Xu Jianguo 
Published: August 2023

AbstractHigh-grade glioma is one of the deadliest primary tumors of the central nervous system. Despite the many novel immunotherapies currently in development, it has been difficult to achieve breakthrough results in clinical studies. The reason may be due to the suppressive tumor microenvironment of gliomas that limits the function of specific immune cells (e.g., T cells) which are currently the primary targets of immunotherapy. However, tumor-associated macrophage, which are enriched in tumors, plays an important role in the development of GBM and is becoming a research hotspot for immunotherapy. This review focuses on current research advances in the use of macrophages as therapeutic targets or therapeutic tools for gliomas, and provides some potential research directions.
Molecular disparities in colorectal cancers of White Americans, Alabama African Americans, and Oklahoma American Indians
Authors: Yamada Hiroshi Y. , Xu Chao , Jones Kenneth L. , O’Neill Philip H. , Venkateshwar Madka , Chiliveru Srikanth , Kim Hyung-Gyoon , Doescher Mark , Morris Katherine T. , Manne Upender , Rao Chinthalapally V. 
Published: August 2023

AbstractIn the US, the majority of cancer samples analyzed are from white people, leading to biases in racial and ethnic treatment outcomes. Colorectal cancer (CRC) incidence and mortality rates are high in Alabama African Americans (AAs) and Oklahoma American Indians (AIs). We hypothesized that differences between racial groups may partially explain these disparities. Thus, we compared transcriptomic profiles of CRCs of Alabama AAs, Oklahoma AIs, and white people from both states. Compared to CRCs of white people, CRCs of AAs showed (a) higher expression of cytokines and vesicle trafficking toward modulated antitumor-immune activity, and (b) lower expression of the ID1/BMP/SMAD axis, IL22RA1, APOBEC3, and Mucins; and AIs had (c) higher expression of PTGS2/COX2 (an NSAID target/pro-oncogenic inflammation) and splicing regulators, and (d) lower tumor suppressor activities (e.g., TOB2, PCGF2, BAP1). Therefore, targeting strategies designed for white CRC patients may be less effective for AAs/AIs. These findings illustrate needs to develop optimized interventions to overcome racial CRC disparities.
Predicting HPV association using deep learning and regular H&E stains allows granular stratification of oropharyngeal cancer patients
Authors: Klein Sebastian , Wuerdemann Nora , Demers Imke , Kopp Christopher , Quantius Jennifer , Charpentier Arthur , Tolkach Yuri , Brinker Klaus , Sharma Shachi Jenny , George Julie , Hess Jochen , Stögbauer Fabian , Lacko Martin , Struijlaart Marijn , van den Hout Mari F.C.M. , Wagner Steffen , Wittekindt Claus , Langer Christine , Arens Christoph , Buettner Reinhard , Quaas Alexander , Reinhardt Hans Christian , Speel Ernst-Jan , Klussmann Jens Peter 
Published: August 2023

AbstractHuman Papilloma Virus (HPV)-associated oropharyngeal squamous cell cancer (OPSCC) represents an OPSCC subgroup with an overall good prognosis with a rising incidence in Western countries. Multiple lines of evidence suggest that HPV-associated tumors are not a homogeneous tumor entity, underlining the need for accurate prognostic biomarkers. In this retrospective, multi-institutional study involving 906 patients from four centers and one database, we developed a deep learning algorithm (OPSCCnet), to analyze standard H&E stains for the calculation of a patient-level score associated with prognosis, comparing it to combined HPV-DNA and p16-status. When comparing OPSCCnet to HPV-status, the algorithm showed a good overall performance with a mean area under the receiver operator curve (AUROC) = 0.83 (95% CI = 0.77-0.9) for the test cohort (n = 639), which could be increased to AUROC = 0.88 by filtering cases using a fixed threshold on the variance of the probability of the HPV-positive class - a potential surrogate marker of HPV-heterogeneity. OPSCCnet could be used as a screening tool, outperforming gold standard HPV testing (OPSCCnet: five-year survival rate: 96% [95% CI = 90–100%]; HPV testing: five-year survival rate: 80% [95% CI = 71–90%]). This could be confirmed using a multivariate analysis of a three-tier threshold (OPSCCnet: high HR = 0.15 [95% CI = 0.05–0.44], intermediate HR = 0.58 [95% CI = 0.34–0.98] p = 0.043, Cox proportional hazards model, n = 211; HPV testing: HR = 0.29 [95% CI = 0.15–0.54] p < 0.001, Cox proportional hazards model, n = 211). Collectively, our findings indicate that by analyzing standard gigapixel hematoxylin and eosin (H&E) histological whole-slide images, OPSCCnet demonstrated superior performance over p16/HPV-DNA testing in various clinical scenarios, particularly in accurately stratifying these patients.
Predicting labor onset relative to the estimated date of delivery using smart ring physiological data
Authors: Erickson Elise N. , Gotlieb Neta , Pereira Leonardo M. , Myatt Leslie , Mosquera-Lopez Clara , Jacobs Peter G. 
Published: August 2023

AbstractThe transition from pregnancy into parturition is physiologically directed by maternal, fetal and placental tissues. We hypothesize that these processes may be reflected in maternal physiological metrics. We enrolled pregnant participants in the third-trimester (n = 118) to study continuously worn smart ring devices monitoring heart rate, heart rate variability, skin temperature, sleep and physical activity from negative temperature coefficient, 3-D accelerometer and infrared photoplethysmography sensors. Weekly surveys assessed labor symptoms, pain, fatigue and mood. We estimated the association between each metric, gestational age, and the likelihood of a participant’s labor beginning prior to (versus after) the clinical estimated delivery date (EDD) of 40.0 weeks with mixed effects regression. A boosted random forest was trained on the physiological metrics to predict pregnancies that naturally passed the EDD versus undergoing onset of labor prior to the EDD. Here we report that many raw sleep, activity, pain, fatigue and labor symptom metrics are correlated with gestational age. As gestational age advances, pregnant individuals have lower resting heart rate 0.357 beats/minute/week, 0.84 higher heart rate variability (milliseconds) and shorter durations of physical activity and sleep. Further, random forest predictions determine pregnancies that would pass the EDD with accuracy of 0.71 (area under the receiver operating curve). Self-reported symptoms of labor correlate with increased gestational age and not with the timing of labor (relative to EDD) or onset of spontaneous labor. The use of maternal smart ring-derived physiological data in the third-trimester may improve prediction of the natural duration of pregnancy relative to the EDD.
VHH CDR-H3 conformation is determined by VH germline usage
Authors: Bahrami Dizicheh Zahra , Chen I-Ling , Koenig Patrick 
Published: August 2023

AbstractVHHs or nanobodies are single antigen binding domains originating from camelid heavy-chain antibodies. They are used as diagnostic and research tools and in a variety of therapeutic molecules. Analyzing variable domain structures from llama and alpaca we found that VHHs can be classified into two large structural clusters based on their CDR-H3 conformation. Extended CDR-H3 loops protrude into the solvent, whereas kinked CDR-H3 loops fold back onto framework regions. Both major families have distinct properties in terms of their CDR-H3 secondary structure, how their CDR-H3 interacts with the framework region and how they bind to antigens. We show that the CDR-H3 conformation of VHHs correlates with the germline from which the antibodies are derived: IGHV3-3 derived antibodies almost exclusively adopt a kinked CDR-H3 conformation while the CDR-H3 adopts an extended structure in most IGHV3S53 derived antibodies. We do not observe any bias stemming from V(D)J recombination in llama immune repertoires, suggesting that the correlation is the result of selection processes during B-cell development. Our findings demonstrate a previously undescribed impact of germline usage on antigen interaction and contribute to a better understanding on how properties of the antibody framework shape the immune repertoire.
Formation of turing patterns in strongly magnetized electric discharges
Authors: Menati Mohamad , Williams Stephen , Rasoolian Behnam , Thomas Edward , Konopka Uwe 
Published: August 2023

AbstractPattern formation and self-organization in many biological and non-biological systems can be explained through Turing’s activator-inhibitor model. Here we show how this model can be employed to describe the formation of filamentary structures in a low-pressure electric discharge exposed to a strong magnetic field. Theoretical investigation reveals that the fluid equations describing a magnetized plasma can be rearranged to take the mathematical form of Turing’s activator-inhibitor model. Numerical simulations based on the equations derived from this approach could reproduce the various patterns observed in the experiments. Also, it is shown that a density imbalance between electrons and ions exists in the bulk of the magnetized plasma that generates an electric field structure transverse to the applied magnetic field. This electric field is responsible for the stability of the filamentary patterns in the magnetized plasma over time scales much longer than the characteristic time scales of the electric discharge.
Refertilized continental root controls the formation of the Mianning–Dechang carbonatite-associated rare-earth-element ore system
Authors: Hou Zeng-Qian , Xu Bo , Zhang Haijiang , Zheng Yuan-Chuan , Wang Rui , Liu Yan , Miao Zhuang , Gao Lei , Zhao Zhidan , Griffin William L. , O’Reilly Suzanne Y. 
Published: August 2023

AbstractRare earth element ore deposits associated with carbonatite derived from Earth’s mantle supply half of the world’s rare earth element. However, the formation of carbonatite and initial enrichment and transport of rare earth element in the mantle, is unclear. Here, we image the lithospheric architecture of a Cenozoic rare earth element ore belt in southwestern China by integrating seismic tomography with geochemical data. The subduction of the Indian continent caused vertical upwelling and lateral flow of the asthenosphere, which triggered the melting of the overlying subcontinental lithospheric mantle to generate carbonatites. Such a mantle source that previously metasomatized by fluids from recycled marine sediments is a precursor process critical for forming a giant rare earth element system. For the studied ore belt, three key factors are prerequisites to generating ore-forming carbonatites: thick lithosphere with a continental root; prior fertilization of the subcontinental lithospheric mantle; and trans-lithospheric weakness for magma ascent.
Inter-comparison of marine microbiome sampling protocols
Authors: Pascoal Francisco , Tomasino Maria Paola , Piredda Roberta , Quero Grazia Marina , Torgo Luís , Poulain Julie , Galand Pierre E , Fuhrman Jed A , Mitchell Alex , Tinta Tinkara , Turk Dermastia Timotej , Fernandez-Guerra Antonio , Vezzi Alessandro , Logares Ramiro , Malfatti Francesca , Endo Hisashi , Dąbrowska Anna Maria , De Pascale Fabio , Sánchez Pablo , Henry Nicolas , Fosso Bruno , Wilson Bryan , Toshchakov Stephan , Ferrant Gregory Kevin , Grigorov Ivo , Vieira Fabio Rocha Jimenez , Costa Rodrigo , Pesant Stéphane , Magalhães Catarina 
Published: August 2023

Abstract
Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d’Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (&gt;0.22 µm, 0.22–3 µm, 3–20 µm and &gt;20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and “whole water” (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume.
Indices for dynamic evaluation of indoor humidity and thermal environment
Authors: Hu Jiale , Wang Yingying , Wang Dengjia , Du Hu , Fan Jianhua , Liu Yanfeng , Sun Xin 
Published: August 2023

AbstractMoisture sources release wet-components into indoor air, affecting the occupants’ health, air conditioning energy consumption, and building service-life. Wet-component evaporation and diffusion are dynamic processes, and yet existing indices are limited in their ability to accurately describe moisture sources dynamically influencing indoor air. Here we propose two indices CRIt(H), an index of the rate of humidity contribution change, and CRIt(c) as the rate of indoor climate contribution change. Taking a humidifier as the source, we use our indices to compare by experiment the impact of source parameters on a variety of ambient conditions over space and time. Our approach accurately reflects how the moisture source affect humidity and temperature, with identification of specific stages of dynamic influence. This study will be beneficial for the establishment of transient indoor environmental models, regulation of air-conditioning systems, and sustainable control of the indoor environment.
A novel broken-gap chemical-bonded SiC/Ti2CO2 heterojunction with band to band tunneling: first-principles investigation
Authors: Dai Zhuo-Ni , Sheng Wei , Zhou Xiao-Ying , Zhan Jie , Xu Ying 
Published: August 2023

Novel chemical-bonded SiC/Ti2CO2 heterojunction exists band-to-band tunneling from the valence band of SiC to the conduction band of Ti2CO2. The current–voltage characteristics of the device demonstrate a negative differential resistance effect.
Lactobacillus gasseriCKCC1913 mediated modulation of the gut–liver axis alleviated insulin resistance and liver damage induced by type 2 diabetes
Authors: Jiang Shuaiming , Liu Aijie , Ma Wenyao , Liu Xinlei , Luo Pengfei , Zhan Meng , Zhou Xiaoli , Chen Lihao , Zhang Jiachao 
Published: August 2023

Lactobacillus gasseri CKCC1913 regulated lipid metabolism and alleviated and liver damage induced by type 2 diabetes in mice.