bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound-guided localization of the radial nerve along the humerus: providing reference points for safer upper arm surgery
Authors: Da Silva T. , Mueck D. , Knop C. , Merkle T. 
Published: July 2024

Abstract
Purpose
The close proximity of the radial nerve to the humerus poses a risk during upper arm surgery. Although the general course of the radial nerve is well-known, its exact position in relation to anatomical reference points remains poorly investigated. This study aimed to develop a standardized protocol for the sonographic and clinical identification of the radial nerve in the upper arm. The ultimate goal is to assist surgeons in avoiding iatrogenic radial nerve palsy.

Methods
A total of 76 measurements were performed in 38 volunteers (both sides). Ultrasound measurements were performed using a linear transducer (10 MHz) to identify the radial nerve at two key points: RD (where the radial nerve crosses the dorsal surface of the humerus) and RL (where the radial nerve crosses the lateral aspect of the humerus). Distances from specific reference points (acromion, lateral epicondyle, medial epicondyle, olecranon fossa) to RD and RL were measured, and the angle between the course of the nerve and the humeral axis was recorded. Humeral length was defined as the distance between the posterodorsal corner of the acromion and the lateral epicondyle.

Results
The distance from the lateral epicondyle to RD was on average 15.5 cm ± 1.3, corresponding to 50% of the humeral length. The distance from the lateral epicondyle to RL was on average 6.7 cm ± 0.8, corresponding to 21% of the humeral length. The course of the nerve between RD and RL showed an average angulation of 37° to the anatomical axis of the humerus. Gender, BMI, dominant hand, and arm thickness did not correlate with the distances to RD or RL. Measurements were consistent between the left and right side.

Conclusion
The radial nerve can typically be identified by employing a 1/2 and 1/5 ratio on the dorsal and lateral aspects of the humerus. Due to slight variations in individual anatomy, the utilization of ultrasound-assisted visualization presents a valuable and straightforward approach to mitigate the risk of iatrogenic radial nerve palsy during upper arm surgery. This study introduces an easy and fast protocol for this purpose.
Analyzing Covid-19 Pandemic Through Cases and Spillover Effect: Cross Wavelet Transformation of Mobility in the Countries
Authors: Dogan Ibrahim , Dogan Aydan , Gurbuz Suleyman , Cirakli Umit 
Published: July 2024

AbstractThis research examines the relationship between daily Covid-19 cases and public mobility for six different places, where mobility can be high, in Brazil, the UK, and the USA. We tried to show how the spreading effect of infectious diseases occurs in places where human mobility is intense. The data consists of daily data covering the periods from 28/02/2020 to 08/02/2021, which includes the database of Our World in Data and Google Mobility Reports. Basically, there is a positive correlation between mobility and case numbers. Results in the paper differ from country to country. That is to say, mobility in grocery stores and pharmacies can be said to have an impact on the number of cases in all three countries. Brazil is the country where mobility in parks has the strongest impact. The country which has the lowest frequency in retail outlets is America.
(Levamisole Adulterated) Cocaine-Induced Vasculitis: What Is Known/Current Evidence
Authors: Donkers Johan W. J. , Feijen Robert A. , Rutgers Abraham 
Published: July 2024

Abstract
Purpose of review
(Levamisole adulterated) cocaine can cause a number of symptoms. One of the most severe is cocaine-induced vasculitis, which is hard to both diagnose and treat. We conducted a review to summarize the most recent findings on symptomatology, treatment options, anti-neutrophil cytoplasmic antibodies (ANCA) positivity and pathophysiology.

Recent findings
In the past years multiple large cohort studies have been published extensively describing the symptomology and rates of ANCA positivity in patients with (levamisole-adulterated) cocaine-induced vasculitis. These studies also give more insight into the effects of different treatment strategies.

Summary
The mainstay of treatment is abstinence of cocaine supported by antibiotics in case of concomitant infections and/or immunosuppressive medication depending on symptoms. ANCA positivity is a hallmark of more extensive disease and is a characteristic of immune system activation. In cocaine-induced vasculitis, dual positivity for both proteinase 3(PR3)- and myeloperoxidase (MPO)-ANCA is described and some patients are found to have human elastase type (HNE-)ANCA. HNE-ANCA positivity varies in patients with cocaine-induced midline destruction (CIMDL) from 28-84%, but has not been researched thoroughly in patients with cocaine-induced vasculitis. We present our hypothesis of a “sliding-scale” by which CIMDL turns into cocaine-induced systemic vasculitis based upon recent literature and we describe the mechanisms by which cocaine-induced vasculitis develops.
Deep Learning Models for Aorta Segmentation in Computed Tomography Images: A Systematic Review And Meta-Analysis
Authors: Wang Ting-Wei , Tzeng Yun-Hsuan , Hong Jia-Sheng , Liu Ho-Ren , Wu Kuan-Ting , Fu Hao-Neng , Lee Yung-Tsai , Yin Wei-Hsian , Wu Yu-Te 
Published: July 2024

Abstract
Purpose
This systematic review and meta-analysis was conducted to evaluate the usefulness of deep learning (DL) models for aorta segmentation in computed tomography (CT) images.

Methods
Adhering to 2020 PRISMA guidelines, we systematically searched PubMed, Embase, and Web of Science for studies published up to March 13, 2024, that used DL models for aorta segmentation in adults’ chest CT images. We excluded studies that did not use DL models, involved nonhuman subjects or aortic diseases (aneurysms and dissections), or lacked essential data for meta-analysis. Segmentation performance was evaluated primarily in terms of Dice scores. Subgroup analyses were performed to identify variations related to geographical location and methodology.

Results
Our review of 16 studies indicated that DL models achieve high segmentation accuracy, with a pooled Dice score of 96%. We further noted geographical variations in model performance but no significant publication bias, according to the Egger test.

Conclusion
DL models facilitate aorta segmentation in CT images, and they can therefore guide accurate, efficient, and standardized diagnosis and treatment planning for cardiovascular diseases. Future studies should address the current challenges to enhance model generalizability and evaluate clinical benefits and thus expand the application of DL models in clinical practice.
Magnesium Isotopes Archive the Initial Carbonate Abundances of Metasedimentary Rocks Prior to Thermal Decarbonation
Authors: Shi Qingshang , He Yongsheng , Zhao Zhidan , Rolfo Franco , Groppo Chiara , Harris Nigel , Wu Hongjie , Qi Ningyuan , Ke Shan 
Published: July 2024

AbstractInvestigating the carbonate preservation efficiency (CPE) of continental crust is crucial to understand the global carbon cycle, which requires constraints on initial carbonate abundances (ICAs) of crustal rocks. To link Mg isotopes to ICAs, we present elemental and Mg isotopic data for Himalayan carbonate‐bearing and carbonate‐free metasedimentary rocks. Given no evident melt extraction or external‐fluid infiltration, ICAs of these samples can be independently estimated by elemental data. Despite different carbonate species in the protoliths, all the samples show congruent relationship between their δ26Mg and ICAs, owing to the elevated carbonate δ26Mg and Mg/Ca in protoliths of calcite‐rich samples resulting from diagenetic processes. When collated with literature data, we suggest the observed correlation here can be applied to most carbonate‐bearing (meta‐)sedimentary rocks. Based on a steady state box‐model, we constrained the modern net carbonate accretion flux ( Tmol/year) and the average time‐integrated CPE (∼%) for continental crust.
Solar Radiation Triggers the Bimodal Leaf Phenology of Central African Evergreen Broadleaved Forests
Authors: Liu Liyang , Ciais Philippe , Maignan Fabienne , Zhang Yuan , Viovy Nicolas , Peaucelle Marc , Kearsley Elizabeth , Hufkens Koen , Bauters Marijn , Chapman Colin A. , Fu Zheng , Lin Shangrong , Lu Haibo , Ren Jiashun , Yang Xueqin , He Xianjin , Chen Xiuzhi 
Published: July 2024

AbstractCentral African evergreen broadleaved forests around the equator exhibit a double annual cycle for canopy phenology and carbon uptake seasonality. The underlying drivers of this behavior are poorly understood and the double seasonality is not captured by land surface models (LSM). In this study, we developed a new leaf phenology module into the ORCHIDEE LSM (hereafter ORCHIDEE‐AFP), which utilizes short‐wave incoming radiation (SWd) as the main driver of leaf shedding and partial rejuvenation of the canopy, to simulate the double seasonality of central African forests. The ORCHIDEE‐AFP model has been evaluated by using field data from two forest sites and satellite observations of the enhanced vegetation index (EVI), which is a proxy of young leaf area index (LAIYoung) with leafage less than 6 months, as well as six products of GPP or GPP proxies. Results demonstrate that ORCHIDEE‐AFP successfully reproduces observed leaf turnover (R = 0.45) and young leaf abundance (R = 0.74), and greatly improve the representation of the bimodal leaf phenology. The proportion of grid cells with a significant positive correlation between the seasonality of modeled LAIYoung and observed EVI increased from 0.2% in the standard model to 27% in the new model. For photosynthesis, the proportions of grid cells with significant positive correlations between modeled and observed seasonality range from 26% to 65% across the six GPP evaluation products. The improved performance of the ORCHIDEE‐AFP model in simulating leaf phenology and photosynthesis of central African forests will allow a more accurate assessment of the impacts of climate change in tropical forests.
A Hydrochemical Method for Identifying Orbital Imprints of Dust in Paleofluvial Sequences
Authors: Yan Zhongyi , Yang Yibo , Han Wenxia , Liu Yudong , Liu Xiaoming , Fang Xiaomin 
Published: July 2024

AbstractMineral dust plays an important role in Earth's climate system, yet it is difficult to identify dust imprints in paleofluvial sediments, especially on orbital timescales. Here, we present high‐resolution authigenic carbonate Ca–Mg–Sr compositions in a fluvial sequence under the transport pathway of Asian dust. The Mg/Ca, Sr/Ca, and Mg/Sr ratios exhibit distinct transitions in both secular trends and orbital cycles at ∼8 Ma. Before ∼8 Ma, given similar Mg and Sr partitioning behaviors during carbonate formation, hydroclimate changes yielded strong orbital signals in the Sr/Ca and Mg/Ca ratios but no detectable signals in the Mg/Sr ratios. After ∼8 Ma, given the strengthened input of Mg‐rich dust during cold‒dry periods, the Mg/Sr and Mg/Ca ratios clearly exhibited orbital signals, but the Sr/Ca ratio did not. Such transitions in carbonate composition corroborate the dust‐induced changes in fluvial hydrochemistry, offering an innovative methodology for detecting orbital dust cycles in paleofluvial systems.
The Spatial Variation of Large‐ and Meso‐Scale Plasma Flow Vorticity Statistics in the High‐Latitude Ionosphere and Implications for Ionospheric Plasma Flow Models
Authors: Chisham G. , Freeman M. P. 
Published: July 2024

AbstractThe ability to understand and model ionospheric plasma flow on all spatial scales has important implications for operational space weather models. This study exploits a recently developed method to statistically separate large‐scale and meso‐scale contributions to probability density functions (PDFs) of ionospheric flow vorticity measured by the Super Dual Auroral Radar Network (SuperDARN). The SuperDARN vorticity data are first sub‐divided depending on the Interplanetary Magnetic Field (IMF) direction, and the separation method is applied to PDFs of vorticity compiled in spatial regions of size 1° of geomagnetic latitude by 1 hr of magnetic local time, covering much of the high‐latitude ionosphere in the northern hemisphere. The resulting PDFs are fit by model functions using maximum likelihood estimation (MLE) and the spatial variations of the MLE estimators for both the large‐scale and meso‐scale components are presented. The spatial variations of the large‐scale vorticity estimators are ordered by the average ionospheric convection flow, which is highly dependent on the IMF direction. The spatial variations of the meso‐scale vorticity estimators appear independent of the senses of vorticity and IMF direction, but have a different character in the polar cap, the cusp, the auroral region, and the sub‐auroral region. The paper concludes by discussing the sources of the vorticity components in the different regions, and the consequences for the fidelity of ionospheric plasma flow models.
Changes in the Direct Climate Effect of Black Carbon Aerosols in East Asia Under the “Dual Carbon” Goal of China
Authors: Gao Peng , Gao Yiman , Zhou Yinan , Cao Heng , Hu Yaxin , Li Shu , Liang Shanrong , Wang Tijian , Xie Min , Li Mengmeng , Zhuang Bingliang 
Published: July 2024

AbstractIn the context of China's “dual carbon” goal, emissions of air pollutants are expected to significantly decrease in the future. Thus, the direct climate effects of black carbon (BC) aerosols in East Asia are investigated under this goal using an updated regional climate and chemistry model. The simulated annual average BC concentration over East Asia is approximately 1.29 μg/m3 in the last decade. Compared to those in 2010–2020, both the BC column burden and instantaneous direct radiative forcing in East Asia decrease by more than 55% and 80%, respectively, in the carbon peak year (2030s) and the carbon neutrality year (2060s). Conversely, the BC effective radiative forcing (ERF) and regional climate responses to BC exhibit substantial nonlinearity to emission reduction, possibly resulting from different adjustments of thermal‐dynamic fields and clouds from BC‐radiation interactions. The regional mean BC ERF at the tropopause over East Asia is approximately +1.11 W/m2 in 2010–2020 while negative in the 2060s. BC‐radiation interactions in the present‐day impose a significant annual mean cooling of −0.2 to −0.5 K in central China but warming +0.3 K in the Tibetan Plateau. As China's BC emissions decline, surface temperature responses show a mixed picture compared to 2010–2020, with more cooling in eastern China and Tibet of −0.2 to −0.3 K in the 2030s, but more warming in central China of approximately +0.3 K by the 2060s. The Indian BC might play a more important role in East Asian climate with reduction of BC emissions in China.
Application of polygenic scores to a deeply phenotyped sample enriched for substance use disorders reveals extensive pleiotropy with psychiatric and somatic traits
Authors: Hartwell Emily E. , Jinwala Zeal , Milone Jackson , Ramirez Sarah , Gelernter Joel , Kranzler Henry R. , Kember Rachel L. 
Published: July 2024

AbstractCo-occurring psychiatric, medical, and substance use disorders (SUDs) are common, but the complex pathways leading to such comorbidities are poorly understood. A greater understanding of genetic influences on this phenomenon could inform precision medicine efforts. We used the Yale-Penn dataset, a cross-sectional sample enriched for individuals with SUDs, to examine pleiotropic effects of genetic liability for psychiatric and somatic traits. Participants completed an in-depth interview that provides information on demographics, environment, medical illnesses, and psychiatric and SUDs. Polygenic scores (PGS) for psychiatric disorders and somatic traits were calculated in European-ancestry (EUR; n = 5691) participants and, when discovery datasets were available, for African-ancestry (AFR; n = 4918) participants. Phenome-wide association studies (PheWAS) were then conducted. In AFR participants, the only PGS with significant associations was bipolar disorder (BD), all of which were with substance use phenotypes. In EUR participants, PGS for major depressive disorder (MDD), generalized anxiety disorder (GAD), post-traumatic stress disorder (PTSD), schizophrenia (SCZ), body mass index (BMI), coronary artery disease (CAD), and type 2 diabetes (T2D) all showed significant associations, the majority of which were with phenotypes in the substance use categories. For instance, PGSMDD was associated with over 200 phenotypes, 15 of which were depression-related (e.g., depression criterion count), 55 of which were other psychiatric phenotypes, and 126 of which were substance use phenotypes; and PGSBMI was associated with 138 phenotypes, 105 of which were substance related. Genetic liability for psychiatric and somatic traits is associated with numerous phenotypes across multiple categories, indicative of the broad genetic liability of these traits.
Human cytomegalovirus in breast milk is associated with milk composition and the infant gut microbiome and growth
Authors: Johnson Kelsey E. , Hernandez-Alvarado Nelmary , Blackstad Mark , Heisel Timothy , Allert Mattea , Fields David A. , Isganaitis Elvira , Jacobs Katherine M. , Knights Dan , Lock Eric F. , Rudolph Michael C. , Gale Cheryl A. , Schleiss Mark R. , Albert Frank W. , Demerath Ellen W. , Blekhman Ran 
Published: July 2024

AbstractHuman cytomegalovirus (CMV) is a highly prevalent herpesvirus that is often transmitted to the neonate via breast milk. Postnatal CMV transmission can have negative health consequences for preterm and immunocompromised infants, but any effects on healthy term infants are thought to be benign. Furthermore, the impact of CMV on the composition of the hundreds of bioactive factors in human milk has not been tested. Here, we utilize a cohort of exclusively breastfeeding full-term mother-infant pairs to test for differences in the milk transcriptome and metabolome associated with CMV, and the impact of CMV in breast milk on the infant gut microbiome and infant growth. We find upregulation of the indoleamine 2,3-dioxygenase (IDO) tryptophan-to-kynurenine metabolic pathway in CMV+ milk samples, and that CMV+ milk is associated with decreased Bifidobacterium in the infant gut. Our data indicate two opposing CMV-associated effects on infant growth; with kynurenine positively correlated, and CMV viral load negatively correlated, with infant weight-for-length at 1 month of age. These results suggest CMV transmission, CMV-related changes in milk composition, or both may be modulators of full-term infant development.
Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription
Authors: Shelansky Robert , Abrahamsson Sara , Brown Christopher R. , Doody Michael , Lenstra Tineke L. , Larson Daniel R. , Boeger Hinrich 
Published: July 2024

AbstractFluctuations in the initiation rate of transcription, the first step in gene expression, ensue from the stochastic behavior of the molecular process that controls transcription. In steady state, the regulatory process is often assumed to operate reversibly, i.e., in equilibrium. However, reversibility imposes fundamental limits to information processing. For instance, the assumption of equilibrium is difficult to square with the precision with which the regulatory process executes its task in eukaryotes. Here we provide evidence — from microscopic analyses of the transcription dynamics at a single gene copy of yeast — that the regulatory process for transcription is cyclic and irreversible (out of equilibrium). The necessary coupling to reservoirs of free energy occurs via sequence-specific transcriptional activators and the recruitment, in part, of ATP-dependent chromatin remodelers. Our findings may help explain how eukaryotic cells reconcile the dual but opposing requirements for fast regulatory kinetics and high regulatory specificity.
The molecular basis underlying T cell specificity towards citrullinated epitopes presented by HLA-DR4
Authors: Loh Tiing Jen , Lim Jia Jia , Jones Claerwen M. , Dao Hien Thy , Tran Mai T. , Baker Daniel G. , La Gruta Nicole L. , Reid Hugh H. , Rossjohn Jamie 
Published: July 2024

AbstractCD4+ T cells recognising citrullinated self-epitopes presented by HLA-DRB1 bearing the shared susceptibility epitope (SE) are implicated in rheumatoid arthritis (RA). However, the underlying T cell receptor (TCR) determinants of epitope specificity towards distinct citrullinated peptide antigens, including vimentin-64cit59-71 and α-enolase-15cit10-22 remain unclear. Using HLA-DR4-tetramers, we examine the T cell repertoire in HLA-DR4 transgenic mice and observe biased TRAV6 TCR gene usage across these two citrullinated epitopes which matches with TCR bias previously observed towards the fibrinogen β−74cit69-81 epitope. Moreover, shared TRAV26-1 gene usage is evident in four α-enolase-15cit10-22 reactive T cells in three human samples. Crystal structures of mouse TRAV6+ and human TRAV26-1+ TCR-HLA-DR4 complexes presenting vimentin-64cit59-71 and α-enolase-15cit10-22, respectively, show three-way interactions between the TCR, SE, citrulline, and the basis for the biased selection of TRAV genes. Position 2 of the citrullinated epitope is a key determinant underpinning TCR specificity. Accordingly, we provide a molecular basis of TCR specificity towards citrullinated epitopes.
Mutational profiling of SARS-CoV-2 papain-like protease reveals requirements for function, structure, and drug escape
Authors: Wu Xinyu , Go Margareta , Nguyen Julie V. , Kuchel Nathan W. , Lu Bernadine G. C. , Zeglinski Kathleen , Lowes Kym N. , Calleja Dale J. , Mitchell Jeffrey P. , Lessene Guillaume , Komander David , Call Matthew E. , Call Melissa J. 
Published: July 2024

AbstractPapain-like protease (PLpro) is an attractive drug target for SARS-CoV-2 because it is essential for viral replication, cleaving viral poly-proteins pp1a and pp1ab, and has de-ubiquitylation and de-ISGylation activities, affecting innate immune responses. We employ Deep Mutational Scanning to evaluate the mutational effects on PLpro enzymatic activity and protein stability in mammalian cells. We confirm features of the active site and identify mutations in neighboring residues that alter activity. We characterize residues responsible for substrate binding and demonstrate that although residues in the blocking loop are remarkably tolerant to mutation, blocking loop flexibility is important for function. We additionally find a connected network of mutations affecting activity that extends far from the active site. We leverage our library to identify drug-escape variants to a common PLpro inhibitor scaffold and predict that plasticity in both the S4 pocket and blocking loop sequence should be considered during the drug design process.