bluuebunny/crossref_metadata_2025_split huggingface dataset:
The STROMICS genome study: deep whole-genome sequencing and analysis of 10K Chinese patients with ischemic stroke reveal complex genetic and phenotypic interplay
Authors: Cheng Si , Xu Zhe , Bian Shengzhe , Chen Xi , Shi Yanfeng , Li Yanran , Duan Yunyun , Liu Yang , Lin Jinxi , Jiang Yong , Jing Jing , Li Zixiao , Wang Yilong , Meng Xia , Liu Yaou , Fang Mingyan , Jin Xin , Xu Xun , Wang Jian , Wang Chaolong , Li Hao , Liu Siyang , Wang Yongjun 
Published: July 2023

AbstractIschemic stroke is a leading cause of global mortality and long-term disability. However, there is a paucity of whole-genome sequencing studies on ischemic stroke, resulting in limited knowledge of the interplay between genomic and phenotypic variations among affected patients. Here, we outline the STROMICS design and present the first whole-genome analysis on ischemic stroke by deeply sequencing and analyzing 10,241 stroke patients from China. We identified 135.59 million variants, > 42% of which were novel. Notable disparities in allele frequency were observed between Chinese and other populations for 89 variants associated with stroke risk and 10 variants linked to response to stroke medications. We investigated the population structure of the participants, generating a map of genetic selection consisting of 31 adaptive signals. The adaption of the MTHFR rs1801133-G allele, which links to genetically evaluated VB9 (folate acid) in southern Chinese patients, suggests a gene-specific folate supplement strategy. Through genome-wide association analysis of 18 stroke-related traits, we discovered 10 novel genetic-phenotypic associations and extensive cross-trait pleiotropy at 6 lipid-trait loci of therapeutic relevance. Additionally, we found that the set of loss-of-function and cysteine-altering variants present in the causal gene NOTCH3 for the autosomal dominant stroke disorder CADASIL displayed a broad neuro-imaging spectrum. These findings deepen our understanding of the relationship between the population and individual genetic layout and clinical phenotype among stroke patients, and provide a foundation for future efforts to utilize human genetic knowledge to investigate mechanisms underlying ischemic stroke outcomes, discover novel therapeutic targets, and advance precision medicine.
Mapping diversity in African trypanosomes using high resolution spatial proteomics
Authors: Moloney Nicola M. , Barylyuk Konstantin , Tromer Eelco , Crook Oliver M. , Breckels Lisa M. , Lilley Kathryn S. , Waller Ross F. , MacGregor Paula 
Published: July 2023

AbstractAfrican trypanosomes are dixenous eukaryotic parasites that impose a significant human and veterinary disease burden on sub-Saharan Africa. Diversity between species and life-cycle stages is concomitant with distinct host and tissue tropisms within this group. Here, the spatial proteomes of two African trypanosome species, Trypanosoma brucei and Trypanosoma congolense, are mapped across two life-stages. The four resulting datasets provide evidence of expression of approximately 5500 proteins per cell-type. Over 2500 proteins per cell-type are classified to specific subcellular compartments, providing four comprehensive spatial proteomes. Comparative analysis reveals key routes of parasitic adaptation to different biological niches and provides insight into the molecular basis for diversity within and between these pathogen species.
Optofluidic memory and self-induced nonlinear optical phase change for reservoir computing in silicon photonics
Authors: Gao Chengkuan , Gaur Prabhav , Almutairi Dhaifallah , Rubin Shimon , Fainman Yeshaiahu 
Published: July 2023

AbstractNanophotonics allows to employ light-matter interaction to induce nonlinear optical effects and realize non-conventional memory and computation capabilities, however to date, light-liquid interaction was not considered as a potential mechanism to achieve computation on a nanoscale. Here, we experimentally demonstrate self-induced phase change effect which relies on the coupling between geometric changes of thin liquid film to optical properties of photonic waveguide modes, and then employ it for neuromorphic computing. In our optofluidic silicon photonics system we utilize thermocapillary-based deformation of thin liquid film capable to induce nonlinear effect which is more than one order of magnitude higher compared to the more traditional heat-based thermo-optical effect, and allowing operation as a nonlinear actuator and memory element, both residing at the same compact spatial region. The resulting dynamics allows to implement Reservoir Computing at spatial region which is approximately five orders of magnitude smaller compared to state-of-the-art experimental liquid-based systems.
SHARPER-DOSY: Sensitivity enhanced diffusion-ordered NMR spectroscopy
Authors: Peat George , Boaler Patrick J. , Dickson Claire L. , Lloyd-Jones Guy C. , Uhrín Dušan 
Published: July 2023

AbstractSince its discovery in mid-20th century, the sensitivity of Nuclear Magnetic Resonance (NMR) has increased steadily, in part due to the design of new, sophisticated NMR experiments. Here we report on a liquid-state NMR methodology that significantly increases the sensitivity of diffusion coefficient measurements of pure compounds, allowing to estimate their sizes using a much reduced amount of material. In this method, the diffusion coefficients are being measured by analysing narrow and intense singlets, which are invariant to magnetic field inhomogeneities. The singlets are obtained through signal acquisition embedded in short (<0.5 ms) spin-echo intervals separated by non-selective 180° or 90° pulses, suppressing the chemical shift evolution of resonances and their splitting due to J couplings. The achieved 10−100 sensitivity enhancement results in a 100−10000-fold time saving. Using high field cryoprobe NMR spectrometers, this makes it possible to measure a diffusion coefficient of a medium-size organic molecule in a matter of minutes with as little as a few hundred nanograms of material.
Activation of brown adipose tissue by a low-protein diet ameliorates hyperglycemia in a diabetic lipodystrophy mouse model
Authors: Munoz Marcos David , Zamudio Alexa , McCann Maximilian , Gil Victoria , Xu Pingwen , Liew Chong Wee 
Published: July 2023

AbstractLong-term ad libitum dietary restrictions, such as low-protein diets (LPDs), improve metabolic health and extend the life span of mice and humans. However, most studies conducted thus far have focused on the preventive effects of LPDs on metabolic syndromes. To test the therapeutic potential of LPD, we treated a lipodystrophy mouse model IRFKO (adipose-specific insulin receptor knockout) in this study. We have previously shown that IRFKO mice have profound insulin resistance, hyperglycemia, and whitening of interscapular brown adipose tissue (BAT), closely mimicking the phenotypes in lipoatrophic diabetic patients. Here, we demonstrate that 14-day of LPD (5.1% kcal from protein) feeding is sufficient to reduce postprandial blood glucose, improve insulin resistance, and normalize glucose tolerance in the IRFKO mice. This profound metabolic improvement is associated with BAT activation and increase in whole body energy expenditure. To confirm, we showed that surgical denervation of BAT attenuated the beneficial metabolic effects of LPD feeding in IRFKO mice, including the ‘browning’ effects on BAT and the glucose-ameliorating results. However, BAT denervation failed to affect the body weight-lowering effects of LPD. Together, our results imply a therapeutic potential to use LPD for the treatment of lipoatrophic diabetes.
Forecasting consumer confidence through semantic network analysis of online news
Authors: Fronzetti Colladon Andrea , Grippa Francesca , Guardabascio Barbara , Costante Gabriele , Ravazzolo Francesco 
Published: July 2023

AbstractThis research studies the impact of online news on social and economic consumer perceptions through semantic network analysis. Using over 1.8 million online articles on Italian media covering four years, we calculate the semantic importance of specific economic-related keywords to see if words appearing in the articles could anticipate consumers’ judgments about the economic situation and the Consumer Confidence Index. We use an innovative approach to analyze big textual data, combining methods and tools of text mining and social network analysis. Results show a strong predictive power for the judgments about the current households and national situation. Our indicator offers a complementary approach to estimating consumer confidence, lessening the limitations of traditional survey-based methods.
Human PNPase causes RNA stabilization and accumulation of R-loops in the Escherichia coli model system
Authors: Falchi Federica A. , Forti Francesca , Carnelli Cristina , Genco Aurelia , Pizzoccheri Roberto , Manzari Caterina , Pavesi Giulio , Briani Federica 
Published: July 2023

AbstractPolyribonucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. In Escherichia coli, PNPase controls complex phenotypic traits like biofilm formation and growth at low temperature. In human cells, PNPase is located in mitochondria, where it is implicated in the RNA import from the cytoplasm, the mitochondrial RNA degradation and the processing of R-loops, namely stable RNA–DNA hybrids displacing a DNA strand. In this work, we show that the human PNPase (hPNPase) expressed in E. coli causes oxidative stress, SOS response activation and R-loops accumulation. Hundreds of E. coli RNAs are stabilized in presence of hPNPase, whereas only few transcripts are destabilized. Moreover, phenotypic traits typical of E. coli strains lacking PNPase are strengthened in presence of the human enzyme. We discuss the hypothesis that hPNPase expressed in E. coli may bind, but not degrade, the RNA, in agreement with previous in vitro data showing that phosphate concentrations in the range of those found in the bacterial cytoplasm and, more relevant, in the mitochondria, inhibit its activity.
SU-Net: pose estimation network for non-cooperative spacecraft on-orbit
Authors: Gao Hu , Li Zhihui , Wang Ning , Yang Jingfan , Dang Depeng 
Published: July 2023

AbstractThe estimation of spacecraft pose is crucial in numerous space missions, including rendezvous and docking, debris removal, and on-orbit maintenance. Estimating the pose of space objects is significantly more challenging than that of objects on Earth, primarily due to the widely varying lighting conditions, low resolution, and limited amount of data available in space images. Our main proposal is a new deep learning neural network architecture, which can effectively extract orbiting spacecraft features from images captured by inverse synthetic aperture radar (ISAR) for pose estimation of non-cooperative on orbit spacecraft. Specifically, our model enhances spacecraft imaging by improving image contrast, reducing noise, and using transfer learning to mitigate data sparsity issues via a pre-trained model. To address sparse features in spacecraft imaging, we propose a dense residual U-Net network that employs dense residual block to reduce feature loss during downsampling. Additionally, we introduce a multi-head self-attention block to capture more global information and improve the model’s accuracy. The resulting tightly interlinked architecture, named as SU-Net, delivers strong performance gains on pose estimation by spacecraft ISAR imaging. Experimental results show that we achieve the state of the art results, and the absolute error of our model is 0.128$$^{\circ }$$

∘

to 0.4491$$^{\circ }$$

∘

, the mean error is about 0.282$$^{\circ }$$

∘

, and the standard deviation is about 0.065$$^{\circ }$$

∘

. The code are released at https://github.com/Tombs98/SU-Net.
Development of cochlear spiral ligament fibrocytes of the common marmoset, a nonhuman model animal
Authors: Hosoya Makoto , Iwabu Kaho , Kitama Tsubasa , Nishiyama Takanori , Oishi Naoki , Okano Hideyuki , Ozawa Hiroyuki 
Published: July 2023

AbstractSpiral ligament fibrocytes generate potassium gradients, which hair cells require to convert mechanical sound waves into electrical palsy. Together with the stria vascularis, they regulate endolymph electrolyte homeostasis. Developing spiral ligament fibrocytes and generating endocochlear potential with an appropriate endolymph ion composition are essential for hearing. Understanding spiral ligament fibrocyte development is useful for studying age-related and genetic hearing loss, as well as for regenerative therapy and cochlear immunology. Despite interspecies differences, most studies of cochlear development have been conducted in rodent models due to the difficulty of using human fetal samples. This study investigated the cochlear development of spiral ligament fibrocytes in a small New World monkey species, the common marmoset (Callithrix jacchus). We examined the developmental expression of specific genes in spiral ligament fibrocytes, including those essential for the generation of endolymphatic potential. Our results showed that this animal model of spiral ligament fibrocyte development is similar to that of humans and is a suitable alternative for the analysis of human cochlear development. The time course established in this study will be useful for studying the primate-specific developmental biology of the inner ear, which may lead to novel treatment strategies for human hearing loss.
No association between genetic markers and hypertension control in multiple cross-sectional studies
Authors: Chekanova Valeriya , Vaucher Julien , Marques-Vidal Pedro 
Published: July 2023

AbstractWe aimed to assess whether genetic markers are associated with hypertension control using two cross-sectional surveys conducted in Lausanne, Switzerland. Management of hypertension was assessed as per ESC guidelines using the 140/90 or the 130/80 mm Hg thresholds. One genetic risk score (GRS) for hypertension (18 SNPs) and 133 individual SNPs related to response to specific antihypertensive drugs were tested. We included 1073 (first) and 1157 (second survey) participants treated for hypertension. The prevalence of controlled participants using the 140/90 threshold was 58.8% and 63.6% in the first and second follow-up, respectively. On multivariable analysis, only older age was consistently and negatively associated with hypertension control. No consistent associations were found between GRS and hypertension control (140/90 threshold) for both surveys: Odds ratio and (95% confidence interval) for the highest vs. the lowest quartile of the GRS: 1.06 (0.71–1.58) p = 0.788, and 1.11 (0.71–1.72) p = 0.657, in the first and second survey, respectively. Similar findings were obtained using the 130/80 threshold: 1.23 (0.79–1.90) p = 0.360 and 1.09 (0.69–1.73) p = 0.717, in the first and second survey, respectively. No association between individual SNPs and hypertension control was found. We conclude that control of hypertension is poor in Switzerland. No association between GRS or SNPs and hypertension control was found.
The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era
Authors: Wen Andrew , He Huan , Fu Sunyang , Liu Sijia , Miller Kurt , Wang Liwei , Roberts Kirk E. , Bedrick Steven D. , Hersh William R. , Liu Hongfang 
Published: July 2023

AbstractClinical phenotyping is often a foundational requirement for obtaining datasets necessary for the development of digital health applications. Traditionally done via manual abstraction, this task is often a bottleneck in development due to time and cost requirements, therefore raising significant interest in accomplishing this task via in-silico means. Nevertheless, current in-silico phenotyping development tends to be focused on a single phenotyping task resulting in a dearth of reusable tools supporting cross-task generalizable in-silico phenotyping. In addition, in-silico phenotyping remains largely inaccessible for a substantial portion of potentially interested users. Here, we highlight the barriers to the usage of in-silico phenotyping and potential solutions in the form of a framework of several desiderata as observed during our implementation of such tasks. In addition, we introduce an example implementation of said framework as a software application, with a focus on ease of adoption, cross-task reusability, and facilitating the clinical phenotyping algorithm development process.
Single-cell sequencing reveals the landscape of the human brain metastatic microenvironment
Authors: Song Qianqian , Ruiz Jimmy , Xing Fei , Lo Hui-Wen , Craddock Lou , Pullikuth Ashok K. , Miller Lance D. , Soike Michael H. , O’Neill Stacey S. , Watabe Kounosuke , Chan Michael D. , Su Jing 
Published: July 2023

AbstractBrain metastases is the most common intracranial tumor and account for approximately 20% of all systematic cancer cases. It is a leading cause of death in advanced-stage cancer, resulting in a five-year overall survival rate below 10%. Therefore, there is a critical need to identify effective biomarkers that can support frequent surveillance and promote efficient drug guidance in brain metastasis. Recently, the remarkable breakthroughs in single-cell RNA-sequencing (scRNA-seq) technology have advanced our insights into the tumor microenvironment (TME) at single-cell resolution, which offers the potential to unravel the metastasis-related cellular crosstalk and provides the potential for improving therapeutic effects mediated by multifaceted cellular interactions within TME. In this study, we have applied scRNA-seq and profiled 10,896 cells collected from five brain tumor tissue samples originating from breast and lung cancers. Our analysis reveals the presence of various intratumoral components, including tumor cells, fibroblasts, myeloid cells, stromal cells expressing neural stem cell markers, as well as minor populations of oligodendrocytes and T cells. Interestingly, distinct cellular compositions are observed across different samples, indicating the influence of diverse cellular interactions on the infiltration patterns within the TME. Importantly, we identify tumor-associated fibroblasts in both our in-house dataset and external scRNA-seq datasets. These fibroblasts exhibit high expression of type I collagen genes, dominate cell-cell interactions within the TME via the type I collagen signaling axis, and facilitate the remodeling of the TME to a collagen-I-rich extracellular matrix similar to the original TME at primary sites. Additionally, we observe M1 activation in native microglial cells and infiltrated macrophages, which may contribute to a proinflammatory TME and the upregulation of collagen type I expression in fibroblasts. Furthermore, tumor cell-specific receptors exhibit a significant association with patient survival in both brain metastasis and native glioblastoma cases. Taken together, our comprehensive analyses identify type I collagen-secreting tumor-associated fibroblasts as key mediators in metastatic brain tumors and uncover tumor receptors that are potentially associated with patient survival. These discoveries provide potential biomarkers for effective therapeutic targets and intervention strategies.
Gapless fermionic excitation in the antiferromagnetic state of ytterbium zigzag chain
Authors: Hori Fumiya , Kinjo Katsuki , Kitagawa Shunsaku , Ishida Kenji , Mizutani Souichiro , Yamamoto Rikako , Ohmagari Yudai , Onimaru Takahiro 
Published: July 2023

AbstractThe emergence of charge-neutral fermionic excitations in magnetic systems is one of the unresolved issues in recent condensed matter physics. This type of excitations has been observed in various systems, such as low-dimensional quantum spin liquids, Kondo insulators, and antiferromagnetic insulators. Here, we report the presence of a pronounced gapless spin excitation in the low-temperature antiferromagnetic state of YbCuS2 semiconductor, where trivalent ytterbium atoms form a zigzag chain structure. We confirm the presence of this gapless excitations by a combination of experimental probes, namely 63/65Cu-nuclear magnetic resonance and nuclear quadrupole resonance, as well as specific heat measurements, revealing a linear low-temperature behavior of both the nuclear spin-lattice relaxation rate 1/T1 and the specific heat. This system provides a platform to investigate the origin of gapless excitations in spin chains and the relationship between emergent fermionic excitations and frustration.
Practices of climate responsibility
Authors: Moos Thorsten , Arndt Megan 
Published: July 2023

AbstractIn the context of climate protection, the notion of responsibility is regularly invoked to address individuals and collectives as liable to urgent climate action. The article argues for an understanding of responsibility not only as a normative (and counterfactual) concept but also as a social practice. As an analytical tool to examine the complex social reality of responsibility, the concept of responsibility practices is introduced. Following four constitutive dimensions of responsibility, this approach allows for studying how responsibility is negotiated between individual and collective subjects, how the scope of responsibility is adjusted between local and global foci, what values (e.g., economical, political, and moral norms) are invoked, and towards which internal, external or virtual authorities responsibility is addressed. As an example, carbon offsetting programs are analyzed as bundles of practices of attributing, negotiating, and refusing responsibility. This praxeological account is useful to complement psychological and behavioral economy approaches to the knowledge-action gap. Especially, it facilitates the empirical consideration of denying, avoiding, and delegating responsibility. It can be expected that research on responsibility practices will contribute to a more realistic concept of climate responsibility.
A large-area multi-finger β-Ga2O3 MOSFET and its self-heating effect
Authors: Zhou Xuanze , Xu Guangwei , Long Shibing 
Published: July 2023

Abstract
The self-heating effect severely limits device performance and reliability. Although some studies have revealed the heat distribution of β-Ga2O3 MOSFETs under biases, those devices all have small areas and have difficulty reflecting practical conditions. This work demonstrated a multi-finger β-Ga2O3 MOSFET with a maximum drain current of 0.5 A. Electrical characteristics were measured, and the heat dissipation of the device was investigated through infrared images. The relationship between device temperature and time/bias is analyzed.