bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated whole slide image analysis for a translational quantification of liver fibrosis
Authors: Serdjebi Cindy , Bertotti Karine , Huang Pinzhu , Wei Guangyan , Skelton-Badlani Disha , Leclercq Isabelle A. , Barbes Damien , Lepoivre Bastien , Popov Yury V. , Julé Yvon 
Published: November 2022

AbstractCurrent literature highlights the need for precise histological quantitative assessment of fibrosis which cannot be achieved by conventional scoring systems, inherent to their discontinuous values and reader-dependent variability. Here we used an automated image analysis software to measure fibrosis deposition in two relevant preclinical models of liver fibrosis, and established correlation with other quantitative fibrosis descriptors. Longitudinal quantification of liver fibrosis was carried out during progression of post-necrotic (CCl4-induced) and metabolic (HF-CDAA feeding) models of chronic liver disease in mice. Whole slide images of picrosirius red-stained liver sections were analyzed using a fully automated, unsupervised software. Fibrosis was characterized by a significant increase of collagen proportionate area (CPA) at weeks 3 (CCl4) and 8 (HF-CDAA) with a progressive increase up to week 18 and 24, respectively. CPA was compared to collagen content assessed biochemically by hydroxyproline assay (HYP) and by standard histological staging systems. CPA showed a high correlation with HYP content for CCl4 (r = 0.8268) and HF-CDAA (r = 0.6799) models. High correlations were also found with Ishak score or its modified version (r = 0.9705) for CCl4 and HF-CDAA (r = 0.9062) as well as with NASH CRN for HF-CDAA (r = 0.7937). Such correlations support the use of automated digital analysis as a reliable tool to evaluate the dynamics of liver fibrosis and efficacy of antifibrotic drug candidates in preclinical models.
Developmental trajectories of eye movements in oral and silent reading for beginning readers: a longitudinal investigation
Authors: Kim Young-Suk Grace , Little Callie , Petscher Yaacov , Vorstius Christian 
Published: November 2022

AbstractEye movements provide a sensitive window into cognitive processing during reading. In the present study, we investigated beginning readers’ longitudinal changes in temporal and spatial measures of eye movements during oral versus silent reading, the extent to which variation in eye movements is attributable to individual differences and text differences, and the functional form of growth trajectories of eye-movement variables. Data were from 363 English-speaking children (52% male; 59.8% White) in the US who were followed longitudinally from Grade 1 to Grade 3. Results showed a rapid decrease in temporal eye-movement measures (e.g., first fixation) and an increase in spatial eye-movement measures (initial landing position) in both oral and silent reading. The majority of variance in eye movements was attributable to individual differences whereas some variance in initial landing position was due to text differences. Most eye-movement measures had nonlinear growth trajectories where fast development tapered off near the end of Grade 3 while initial fixation count and total gaze count in silent reading had a linear growth trajectory. The findings provide a first large-scale look into the developmental progression of eye movements during oral and silent reading during a critical period when reading skills rapidly develop.
The influence of bone marrow edema for the assessment of the boundaries of necrotic lesions in patients with osteonecrosis of the femoral head
Authors: Ikemura Satoshi , Motomura Goro , Yamaguchi Ryosuke , Utsunomiya Takeshi , Hamai Satoshi , Fujii Masanori , kawahara Shinya , Sato Taishi , Hara Daisuke , shiomoto Kyohei , Yamamoto Takuaki , Nakashima Yasuharu 
Published: November 2022

AbstractThis study aimed to investigate the influence of bone marrow edema (BME) for the assessment of the boundaries of necrotic lesions using unenhanced and contrast-enhanced (CE) magnetic resonance (MR) images in patients with osteonecrosis of the femoral head (ONFH). We retrospectively reviewed 72 consecutive hips in 55 patients of ONFH that were Association Research Circulation Osseous (ARCO) stage III or higher and underwent both unenhanced and contrast-enhanced MR imaging between January 2005 and February 2016. The degree of extension of BMEs, and the boundaries of the necrotic lesions were compared using unenhanced and CE MR images on both mid coronal and mid oblique-axial slices. Forty-two percent of the coronal T1 images, 40% of the coronal fat-saturated T2 images, and 48% of the oblique-axial T1 images showed differences in the boundaries of necrotic lesion, by comparison with those of CET1-weighted MR images. The boundaries of necrotic lesions were clearly detected in all hips on CE coronal slices and 97% of all hips on CE oblique-axial slices. The BME grade in the difference group was significantly higher than in the non-difference group on the coronal plane (P = 0.0058). There were significant differences between the BME grade and duration from the onset of hip pain to MR imaging examination. Multivariate analyses revealed that the duration from the onset to MR imaging examination in both coronal (P = 0.0008) and oblique-axial slices (P = 0.0143) were independently associated with differences in the boundary of necrotic lesion between T1 and CET1-weighted MR images. Our findings suggest that unenhanced MR image may be insufficient for a precise assessment of the boundaries of the necrotic lesions for ONFH cases in the early phase of subchondral collapse due to the diffuse BME.
Insights from ozone and particulate matter pollution control in New York City applied to Beijing
Authors: Zhang Jie , Wang Junfeng , Sun Yele , Li Jingyi , Ninneman Matthew , Ye Jianhuai , Li Ke , Crandall Brian , Mao Jingbo , Xu Weiqi , Schwab Margaret J. , Li Weijun , Ge Xinlei , Chen Mindong , Ying Qi , Zhang Qi , Schwab James J. 
Published: November 2022

AbstractStrict emission control policies implemented in two megacities of New York City (NYC) and Beijing show impacts on the non-linear relationship of their ozone (O3) and fine particulate matter (PM2.5) during summertime. Here we show these non-linear O3-PM2.5 relationships including a positive linear part reflecting the O3/PM2.5 co-occurrence and a negative power function part reflecting the O3 formation suppression by PM2.5 based on the multiyear surface observations. The control policies targeting sulfur dioxide and PM2.5, then volatile organic compounds and nitrogen oxides, changed the PM2.5 chemical composition which resulted in an increased linear slope that indicates a weaker O3 control effect than occurred for PM2.5. These policies also enhanced the relative PM2.5 suppression effect as shown by an increase in the power function coefficient. Model simulations suggest that regional equal percentage emission reductions for Beijing and other Chinese megacities will be necessary to avoid further increase in the O3/PM2.5 linear slope and continuing occurrences of high levels of ozone.
Cloning the Dirac cones of bilayer graphene to the zone center by selenium adsorption
Authors: Lin Meng-Kai , Zhao Jun , Hlevyack Joseph A. , Chiang T.-C. 
Published: November 2022

AbstractDirac cones can foster extraordinary electronic effects, as exemplified by the case of graphene layers. Angle-resolved photoemission reveals that adsorption of selenium (Se) vapor on bilayer graphene creates a symmetric hybrid clone of the Dirac cones at the zone center. A detailed analysis aided by first-principles calculations shows that the adsorbed layer consists of an ordered array of Se8 molecules. The uncovered cloning mechanism illustrates a method to generate electronic features of scientific and technological interests by gentle surface modification via van der Waals adsorption.
Exploring two-dimensional van der Waals heavy-fermion material: Data mining theoretical approach
Authors: Jang Bo Gyu , Lee Changhoon , Zhu Jian-Xin , Shim Ji Hoon 
Published: November 2022

AbstractThe discovery of two-dimensional (2D) van der Waals (vdW) materials often provides interesting playgrounds to explore novel phenomena. One of the missing components in 2D vdW materials is the intrinsic heavy-fermion systems, which can provide an additional degree of freedom to study quantum critical point (QCP), unconventional superconductivity, and emergent phenomena in vdW heterostructures. Here, we investigate 2D vdW heavy-fermion candidates through the database of experimentally known compounds based on dynamical mean-field theory calculation combined with density functional theory (DFT+DMFT). We have found that the Kondo resonance state of CeSiI does not change upon exfoliation and can be easily controlled by strain and surface doping. Our result indicates that CeSiI is an ideal 2D vdW heavy-fermion material and the quantum critical point can be identified by external perturbations.
Representational ethical model calibration
Authors: Carruthers Robert , Straw Isabel , Ruffle James K. , Herron Daniel , Nelson Amy , Bzdok Danilo , Fernandez-Reyes Delmiro , Rees Geraint , Nachev Parashkev 
Published: November 2022

AbstractEquity is widely held to be fundamental to the ethics of healthcare. In the context of clinical decision-making, it rests on the comparative fidelity of the intelligence – evidence-based or intuitive – guiding the management of each individual patient. Though brought to recent attention by the individuating power of contemporary machine learning, such epistemic equity arises in the context of any decision guidance, whether traditional or innovative. Yet no general framework for its quantification, let alone assurance, currently exists. Here we formulate epistemic equity in terms of model fidelity evaluated over learnt multidimensional representations of identity crafted to maximise the captured diversity of the population, introducing a comprehensive framework forRepresentational Ethical Model Calibration. We demonstrate the use of the framework on large-scale multimodal data from UK Biobank to derive diverse representations of the population, quantify model performance, and institute responsive remediation. We offer our approach as a principled solution to quantifying and assuring epistemic equity in healthcare, with applications across the research, clinical, and regulatory domains.
Disorganized functional architecture of amygdala subregional networks in obsessive-compulsive disorder
Authors: Cao Lingxiao , Li Hailong , Liu Jing , Jiang Jiaxin , Li Bin , Li Xue , Zhang Suming , Gao Yingxue , Liang Kaili , Hu Xinyue , Bao Weijie , Qiu Hui , Lu Lu , Zhang Lianqing , Hu Xinyu , Gong Qiyong , Huang Xiaoqi 
Published: November 2022

AbstractA precise understanding of amygdala-centered subtle networks may help refine neurocircuitry models of obsessive-compulsive disorder (OCD). We applied connectivity-based parcellation methodology to segment the amygdala based on resting-state fMRI data of 92 medication-free OCD patients without comorbidity and 90 matched healthy controls (HC). The amygdala was parcellated into two subregions corresponding to basolateral amygdala (BLA) and centromedial amygdala (CMA). Amygdala subregional functional connectivity (FC) maps were generated and group differences were evaluated with diagnosis-by-subregion flexible factorial ANOVA. We found significant diagnosis × subregion FC interactions in insula, supplementary motor area (SMA), midcingulate cortex (MCC), superior temporal gyrus (STG) and postcentral gyrus (PCG). In HC, the BLA demonstrated stronger connectivity with above regions compared to CMA, whereas in OCD, the connectivity pattern reversed to stronger CMA connectivity comparing to BLA. Relative to HC, OCD patients exhibited hypoconnectivity between left BLA and left insula, and hyperconnectivity between right CMA and SMA, MCC, insula, STG, and PCG. Moreover, OCD patients showed reduced volume of left BLA and right CMA compared to HC. Our findings characterized disorganized functional architecture of amygdala subregional networks in accordance with structural defects, providing direct evidence regarding the specific role of amygdala subregions in the neurocircuitry models of OCD.
Discovery of small molecule agonists of the Relaxin Family Peptide Receptor 2
Authors: Esteban-Lopez Maria , Wilson Kenneth J. , Myhr Courtney , Kaftanovskaya Elena M. , Henderson Mark J. , Southall Noel T. , Xu Xin , Wang Amy , Hu Xin , Barnaeva Elena , Ye Wenjuan , George Emmett R. , Sherrill John T. , Ferrer Marc , Morello Roy , Agoulnik Irina U. , Marugan Juan J. , Agoulnik Alexander I. 
Published: November 2022

AbstractThe relaxin/insulin-like family peptide receptor 2 (RXFP2) belongs to the family of class A G-protein coupled receptors (GPCRs) and it is the only known target for the insulin-like factor 3 peptide (INSL3). The importance of this ligand-receptor pair in the development of the gubernacular ligament during the transabdominal phase of testicular descent is well established. More recently, RXFP2 has been implicated in maintaining healthy bone formation. In this report, we describe the discovery of a small molecule series of RXFP2 agonists. These compounds are highly potent, efficacious, and selective RXFP2 allosteric agonists that induce gubernacular invagination in mouse embryos, increase mineralization activity in human osteoblasts in vitro, and improve bone trabecular parameters in adult mice. The described RXFP2 agonists are orally bioavailable and display favorable pharmacokinetic properties, which allow for future evaluation of the therapeutic benefits of modulating RXFP2 activation in disease models.
Chromosome-scale assemblies of the male and female Populus euphratica genomes reveal the molecular basis of sex determination and sexual dimorphism
Authors: Zhang Shanhe , Wu Zhihua , Ma De , Zhai Juntuan , Han Xiaoli , Jiang Zhenbo , Liu Shuo , Xu Jingdong , Jiao Peipei , Li Zhijun 
Published: November 2022

AbstractReference-quality genomes of both sexes are essential for studying sex determination and sex-chromosome evolution, as their gene contents and expression profiles differ. Here, we present independent chromosome-level genome assemblies for the female (XX) and male (XY) genomes of desert poplar (Populus euphratica), resolving a 22.7-Mb X and 24.8-Mb Y chromosome. We also identified a relatively complete 761-kb sex-linked region (SLR) in the peritelomeric region on chromosome 14 (Y). Within the SLR, recombination around the partial repeats for the feminizing factor ARR17 (ARABIDOPSIS RESPONSE REGULATOR 17) was potentially suppressed by flanking palindromic arms and the dense accumulation of retrotransposons. The inverted small segments S1 and S2 of ARR17 exhibited relaxed selective pressure and triggered sex determination by generating 24-nt small interfering RNAs that induce male-specific hyper-methylation at the promoter of the autosomal targeted ARR17. We also detected two male-specific fusion genes encoding proteins with NB-ARC domains at the breakpoint region of an inversion in the SLR that may be responsible for the observed sexual dimorphism in immune responses. Our results show that the SLR appears to follow proposed evolutionary dynamics for sex chromosomes and advance our understanding of sex determination and the evolution of sex chromosomes in Populus.
Reassessing a cryptic history of early trilobite evolution
Authors: Holmes James D. , Budd Graham E. 
Published: November 2022

AbstractTrilobites are an iconic Paleozoic group of biomineralizing marine euarthropods that appear abruptly in the fossil record (c. 521 million years ago) during the Cambrian ‘explosion’. This sudden appearance has proven controversial ever since Darwin puzzled over the lack of pre-trilobitic fossils in theOrigin of Species, and it has generally been assumed that trilobites must have an unobserved cryptic evolutionary history reaching back into the Precambrian. Here we review the assumptions behind this model, and suggest that a cryptic history creates significant difficulties, including the invocation of rampant convergent evolution of biomineralized structures and the abandonment of the synapomorphies uniting the clade. We show that a vicariance explanation for early Cambrian trilobite palaeobiogeographic patterns is inconsistent with factors controlling extant marine invertebrate distributions, including the increasingly-recognized importance of long-distance dispersal. We suggest that survivorship bias may explain the initial rapid diversification of trilobites, and conclude that the group’s appearance at c. 521 Ma closely reflects their evolutionary origins.
Use of temporal contact graphs to understand the evolution of COVID-19 through contact tracing data
Authors: Wu Mincheng , Li Chao , Shen Zhangchong , He Shibo , Tang Lingling , Zheng Jie , Fang Yi , Li Kehan , Cheng Yanggang , Shi Zhiguo , Sheng Guoping , Liu Yu , Zhu Jinxing , Ye Xinjiang , Chen Jinlai , Chen Wenrong , Li Lanjuan , Sun Youxian , Chen Jiming 
Published: November 2022

AbstractDigital contact tracing has been recently advocated by China and many countries as part of digital prevention measures on COVID-19. Controversies have been raised about their effectiveness in practice as it remains open how they can be fully utilized to control COVID-19. In this article, we show that an abundance of information can be extracted from digital contact tracing for COVID-19 prevention and control. Specifically, we construct a temporal contact graph that quantifies the daily contacts between infectious and susceptible individuals by exploiting a large volume of location-related data contributed by 10,527,737 smartphone users in Wuhan, China. The temporal contact graph reveals five time-varying indicators can accurately capture actual contact trends at population level, demonstrating that travel restrictions (e.g., city lockdown) in Wuhan played an important role in containing COVID-19. We reveal a strong correlation between the contacts level and the epidemic size, and estimate several significant epidemiological parameters (e.g., serial interval). We also show that user participation rate exerts higher influence on situation evaluation than user upload rate does, indicating a sub-sampled dataset would be as good at prediction. At individual level, however, the temporal contact graph plays a limited role, since the behavior distinction between the infected and uninfected individuals are not substantial. The revealed results can tell the effectiveness of digital contact tracing against COVID-19, providing guidelines for governments to implement interventions using information technology.
Integration of machine learning with neutron scattering for the Hamiltonian tuning of spin ice under pressure
Authors: Samarakoon Anjana , Tennant D. Alan , Ye Feng , Zhang Qiang , Grigera Santiago A. 
Published: November 2022

AbstractQuantum materials research requires co-design of theory with experiments and involves demanding simulations and the analysis of vast quantities of data, usually including pattern recognition and clustering. Artificial intelligence is a natural route to optimise these processes and bring theory and experiments together. Here, we propose a scheme that integrates machine learning with high-performance simulations and scattering measurements, covering the pipeline of typical neutron experiments. Our approach uses nonlinear autoencoders trained on realistic simulations along with a fast surrogate for the calculation of scattering in the form of a generative model. We demonstrate this approach in a highly frustrated magnet, Dy2Ti2O7, using machine learning predictions to guide the neutron scattering experiment under hydrostatic pressure, extract material parameters and construct a phase diagram. Our scheme provides a comprehensive set of capabilities that allows direct integration of theory along with automated data processing and provides on a rapid timescale direct insight into a challenging condensed matter system.
Robust liveness enforcement of Petri nets with uncontrollable and unobservable transitions based on structural analysis
Authors: Li Xiaoyang , Liu Gaiyun , Qin Meng , Li Zhiwu 
Published: November 2022

AbstractThis paper concentrates on robust deadlock control problems for an automated manufacturing system with uncontrollable, unobservable events and resource failures, which is modeled by a subclass of Petri nets. A recovery subnet is added to the holder of each unreliable resource to model resource failure and recovery. In order to prevent a strict minimal siphon in a Petri net model from being emptied, an extended constraint set is constructed based on the complementary set of a strict minimal siphon to obtain a robust liveness constraint. Due to the uncontrollability and unobservability of the transitions, an automated manufacturing system cannot enforce inadmissible robust liveness constraints. It is necessary to decide the admissibility of robust liveness constraints and transform the inadmissible constraints into admissible ones. To this end, a monitor is designed for each admissible robust liveness constraint such that it can be enforced. Finally, an iterative algorithm is developed to perform the above steps and a robust liveness controlled system is obtained. The feasibility of the control strategy is demonstrated by examples.
The Ecological Validity of Countermovement Jump to On-Court Asymmetry
in Basketball
Authors: Keogh Joshua A.J. , Ruder Matthew C , Masood Zaryan , Kobsar Dylan 
Published: November 2022

AbstractJump-based asymmetry is often used as an indicator of sport performance and may
be used to discern injury susceptibility. Due to task specificity, however,
countermovement jump asymmetry may not be representative of on-court asymmetry.
As such, we assessed the association between countermovement jump asymmetry and
on-court impact asymmetry metrics (n=3, and n=4, respectively)
using linear regressions (α=0.05). Fifteen female basketball
athletes completed countermovement jump and on-court sessions across a
competitive season. A significant negative association was found between peak
landing force asymmetry and both overall and medium acceleration on-court
asymmetry (b=–0.1, R2=0.08, p<0.001;
b=–0.1, R2 =0.11, p<0.001,
respectively), as well as between peak propulsive force asymmetry and on-court
medium acceleration asymmetry (b=–0.24,
R2=0.04, p=0.01). Alternatively, both peak landing
and peak propulsive force asymmetry were significantly positively associated
with on-court high acceleration asymmetry (b=0.17,
R2 =0.08, p<0.001; b=0.35,
R2=0.02, p=0.04, respectively). While some
overlap may exist, countermovement jump and on-court impact asymmetry appear to
be independent. Thus, sport-specific monitoring may be necessary to adequately
monitor injury susceptibility using asymmetry.