bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reference values for body composition in healthy urban Mexican children and adolescents
Authors: Desiree Lopez-Gonzalez , C Wells Jonathan , Armando Partida-Gaytan , Mario Cortina-Borja , Patricia Clark 
Published: October 2023

Abstract
Introduction
Given the increasing incidence of chronic degenerative diseases related to changes in tissues, the availability of diagnostic tools with greater accuracy in the estimation of body composition (BC) has become necessary. Interpreting the BC values of individuals requires reference data obtained from a healthy population with the same ethnicity, to identify individuals at risk for the development of negative health outcomes.

Objective
Generate reference values (RV) of body composition (BC) for Mexican children and adolescents.

Methods
This was an urban-population-based cross-sectional study of healthy Mexican children and adolescents. BC estimations by anthropometry, multifrequency bioimpedance analysis (MF-BIA) and dual-energy X-ray absorptiometry (DXA) where used to create sex- and age-specific RV by means of generalized additive models for location, scale and shape (GAMLSS).

Results
We assessed 2104 subjects, and after confirming a clinically and metabolically healthy status, we measured 1659 subjects aged 5–20 years, [806 females (49%) and 853 males (51%)] by anthropometry, MF-BIA and DXA to create sex- and age- smoothed reference centiles, lambda (L), mu (M), and sigma (S) values. We also built sex- and age-smoothed graphic curves for each variable of interest.

Conclusions
We present valid RV and curves for BC variables estimated by anthropometry, MF-BIA and DXA from clinically and metabolically healthy urban Mexican children and adolescents. These RV are different from those reported for other populations, and therefore, should be used for clinical and research purposes involving urban Mexican children and adolescents.
A case of Marfanoid-progeroid-lipodystrophy syndrome: experimental proof of skipping exons and escaping nonsense-mediated decay
Authors: Moriwaki Takahito , Masuno Mitsuo , Nagata Miho , Ishihara Yasuki , Miyashita Yohei , Asano Yoshihiro , Takao Kayo , Tawa Kazumi , Yamanouchi Yasuko , Miki Atsushi , Otomo Takanobu 
Published: October 2023

AbstractWe report a Japanese patient with tall stature, dolichocephaly, prominent forehead, narrow nasal ridge, mild retrognathia, subcutaneous fat reduction, bilateral entropion of both eyelids, high arched palate, long fingers, and mild hyperextensible finger joints as a case of Marfanoid-progeroid-lipodystrophy syndrome. Genetic investigation revealed a heterozygous variant NC_000015.10(NM_000138.5):c.8226+5G>A in the FBN1 gene. Skipping of exon 65 and escaping nonsense-mediated decay followed by frameshift were experimentally confirmed in the proband’s mRNA.
Machine learning assisted derivation of minimal low-energy models for metallic magnets
Authors: Sharma Vikram , Wang Zhentao , Batista Cristian D. 
Published: October 2023

AbstractWe consider the problem of extracting a low-energy spin Hamiltonian from a triangular Kondo Lattice Model (KLM). The non-analytic dependence of the effective spin-spin interactions on the Kondo exchange excludes the use of perturbation theory beyond the second order. We then introduce a Machine Learning (ML) assisted protocol to extract effective two- and four-spin interactions. The resulting spin model reproduces the phase diagram of the original KLM as a function of magnetic field and single-ion anisotropy and reveals the effective four-spin interactions that stabilize the field-induced skyrmion crystal phase. Moreover, this model enables the computation of static and dynamical properties with a much lower numerical cost relative to the original KLM. A comparison of the dynamical spin structure factor in the fully polarized phase computed with both models reveals a good agreement for the magnon dispersion even though this information was not included in the training data set.
Population-based prevalence and mutational landscape of von Willebrand disease using large-scale genetic databases
Authors: Seidizadeh Omid , Cairo Andrea , Baronciani Luciano , Valenti Luca , Peyvandi Flora 
Published: October 2023

AbstractVon Willebrand disease (VWD) is a common bleeding disorder caused by mutations in the von Willebrand factor gene (VWF). The true global prevalence of VWD has not been accurately established. We estimated the worldwide and within-population prevalence of inherited VWD by analyzing exome and genome data of 141,456 individuals gathered by the genome Aggregation Database (gnomAD). We also extended our data deepening by mining the main databases containingVWFvariants i.e., the Leiden Open Variation Database (LOVD) and the Human Gene Mutation Database (HGMD) with the goal to explore the global mutational spectrum of VWD. A total of 4,313VWFvariants were identified in the gnomAD population, of which 505 were predicted to be pathogenic or already reported to be associated with VWD. Among the 282,912 alleles analyzed, 31,785 were affected by the aforementioned variants. The global prevalence of dominant VWD in 1000 individuals was established to be 74 for type 1, 3 for 2A, 3 for 2B and 6 for 2M. The global prevalences for recessive VWD forms (type 2N and type 3) were 0.31 and 0.7 in 1000 individuals, respectively. This comprehensive analysis provided a global mutational landscape ofVWFby means of 927 already reported variants in the HGMD and LOVD datasets and 287 novel pathogenic variants identified in the gnomAD. Our results reveal that there is a considerably higher than expected prevalence of putative disease alleles and variants associated with VWD and suggest that a large number of VWD patients are undiagnosed.
Deterministic Bell state measurement with a single quantum memory
Authors: Kamimaki Akira , Wakamatsu Keidai , Mikata Kosuke , Sekiguchi Yuhei , Kosaka Hideo 
Published: October 2023

AbstractEntanglements serve as a resource for any quantum information system and are deterministically generated or swapped by a joint measurement called complete Bell state measurement (BSM). The determinism arises from a quantum nondemolition measurement of two coupled qubits with the help of readout ancilla, which inevitably requires extra physical qubits. We here demonstrate a deterministic and complete BSM with only a nitrogen atom in a nitrogen-vacancy (NV) center in diamond as a quantum memory without relying on any carbon isotopes, which are the extra qubits, by exploiting electron‒nitrogen (14N) double qutrits at a zero magnetic field. The degenerate logical qubits within the subspace of qutrits on the electron and nitrogen spins are holonomically controlled by arbitrarily polarized microwave and radiofrequency pulses via zero-field-split states as the ancilla, thus enabling the complete BSM deterministically. Since the system works under an isotope-free and field-free environment, the demonstration paves the way to realize high-fidelity quantum repeaters for long-haul quantum networks and quantum interfaces for large-scale distributed quantum computers.
Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton
Authors: You Jiaqi , Liu Zhenping , Qi Zhengyang , Ma Yizan , Sun Mengling , Su Ling , Niu Hao , Peng Yabing , Luo Xuanxuan , Zhu Mengmeng , Huang Yuefan , Chang Xing , Hu Xiubao , Zhang Yuqi , Pi Ruizhen , Liu Yuqi , Meng Qingying , Li Jianying , Zhang Qinghua , Zhu Longfu , Lin Zhongxu , Min Ling , Yuan Daojun , Grover Corrinne E. , Fang David D. , Lindsey Keith , Wendel Jonathan F. , Tu Lili , Zhang Xianlong , Wang Maojun 
Published: October 2023

AbstractPolyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic regulation of gene expression between coresident subgenomes in polyploids remains to be understood. Here we document the genetic regulation of fiber development in allotetraploid cotton Gossypium hirsutum by sequencing 376 genomes and 2,215 time-series transcriptomes. We characterize 1,258 genes comprising 36 genetic modules that control staged fiber development and uncover genetic components governing their partitioned expression relative to subgenomic duplicated genes (homoeologs). Only about 30% of fiber quality-related homoeologs show phenotypically favorable allele aggregation in cultivars, highlighting the potential for subgenome additivity in fiber improvement. We envision a genome-enabled breeding strategy, with particular attention to 48 favorable alleles related to fiber phenotypes that have been subjected to purifying selection during domestication. Our work delineates the dynamics of gene regulation during fiber development and highlights the potential of subgenomic coordination underpinning phenotypes in polyploid plants.
Trimodal single-cell profiling reveals a novel pediatric CD8αα+ T cell subset and broad age-related molecular reprogramming across the T cell compartment
Authors: Thomson Zachary , He Ziyuan , Swanson Elliott , Henderson Katherine , Phalen Cole , Zaim Samir Rachid , Pebworth Mark-Phillip , Okada Lauren Y. , Heubeck Alexander T. , Roll Charles R. , Hernandez Veronica , Weiss Morgan , Genge Palak C. , Reading Julian , Giles Josephine R. , Manne Sasikanth , Dougherty Jeanette , Jasen C. J. , Greenplate Allison R. , Becker Lynne A. , Graybuck Lucas T. , Vasaikar Suhas V. , Szeto Gregory L. , Savage Adam K. , Speake Cate , Buckner Jane H. , Li Xiao-jun , Bumol Thomas F. , Wherry E.John , Torgerson Troy R. , Vella Laura A. , Henrickson Sarah E. , Skene Peter J. , Gustafson Claire E. 
Published: October 2023

AbstractAge-associated changes in the T cell compartment are well described. However, limitations of current single-modal or bimodal single-cell assays, including flow cytometry, RNA-seq (RNA sequencing) and CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing), have restricted our ability to deconvolve more complex cellular and molecular changes. Here, we profile >300,000 single T cells from healthy children (aged 11–13 years) and older adults (aged 55–65 years) by using the trimodal assay TEA-seq (single-cell analysis of mRNA transcripts, surface protein epitopes and chromatin accessibility), which revealed that molecular programming of T cell subsets shifts toward a more activated basal state with age. Naive CD4+T cells, considered relatively resistant to aging, exhibited pronounced transcriptional and epigenetic reprogramming. Moreover, we discovered a novel CD8αα+T cell subset lost with age that is epigenetically poised for rapid effector responses and has distinct inhibitory, costimulatory and tissue-homing properties. Together, these data reveal new insights into age-associated changes in the T cell compartment that may contribute to differential immune responses.
A Spitzoid Tumor dataset with clinical metadata and Whole Slide Images for Deep Learning models
Authors: Mosquera-Zamudio Andrés , Launet Laëtitia , del Amor Rocío , Moscardó Anaïs , Colomer Adrián , Naranjo Valery , Monteagudo Carlos 
Published: October 2023

AbstractSpitzoid tumors (ST) are a group of melanocytic tumors of high diagnostic complexity. Since 1948, when Sophie Spitz first described them, the diagnostic uncertainty remains until now, especially in the intermediate category known as Spitz tumor of unknown malignant potential (STUMP) or atypical Spitz tumor. Studies developing deep learning (DL) models to diagnose melanocytic tumors using whole slide imaging (WSI) are scarce, and few used ST for analysis, excluding STUMP. To address this gap, we introduce SOPHIE: the first ST dataset with WSIs, including labels as benign, malignant, and atypical tumors, along with the clinical information of each patient. Additionally, we explain two DL models implemented as validation examples using this database.
Fully resolved assembly of Fusarium proliferatum DSM106835 genome
Authors: Purayil Gouthaman P. , Almarzooqi Amal Y. , El-Tarabily Khaled A. , You Frank M. , AbuQamar Synan F. 
Published: October 2023

AbstractIn the United Arab Emirates, sudden decline syndrome (SDS) is a destructive disease of date palm caused by the soil-borne fungal pathogen Fusarium proliferatum (Fp) DSM106835. Here, a high-resolution genome assembly of Fp DSM106835 was generated using PacBio HiFi sequencing with Omni-C data to provide a high-quality chromatin-organised reference genome with 418 scaffolds, totalling 58,468,907 bp in length and an N50 value of 4,383,091 bp from which 15,580 genes and 16,321 transcripts were predicted. The assembly achieved a complete BUSCO score of 99.2% for 758 orthologous genes. Compared to seven other Fp strains, Fp DSM106835 exhibited the highest continuity with a cumulative size of 44.26 Mbp for the first ten scaffolds/contigs, surpassing the assemblies of all examined Fp strains. Our findings of the high-quality genome of Fp DSM106835 provide an important resource to investigate its genetics, biology and evolutionary history. This study also contributes to fulfill the gaps in fungal knowledge, particularly the genes/metabolites associated with pathogenicity during the plant-pathogen interaction responsible for SDS.
Mapping and targeting of C1ql1-expressing cells in the mouse
Authors: Moghimyfiroozabad Shayan , Paul Maëla A. , Sigoillot Séverine M. , Selimi Fekrije 
Published: October 2023

AbstractThe C1Q complement protein C1QL1 is highly conserved in mammals where it is expressed in various tissues including the brain. This secreted protein interacts with Brain-specific Angiogenesis Inhibitor 3, BAI3/ADGRB3, and controls synapse formation and maintenance. C1ql1 is expressed in the inferior olivary neurons that send projections to cerebellar Purkinje cells, but its expression in the rest of the brain is less documented. To map C1ql1 expression and enable the specific targeting of C1ql1-expressing cells, we generated a knockin mouse model expressing the Cre recombinase under the control of C1ql1 regulatory sequences. We characterized the capacity for Cre-driven recombination in the brain and mapped Cre expression in various neuron types using reporter mouse lines. Using an intersectional strategy with viral particle injections, we show that this mouse line can be used to target specific afferents of Purkinje cells. As C1ql1 is also expressed in other regions of the brain, as well as in other tissues such as adrenal glands and colon, our mouse model is a useful tool to target C1ql1-expressing cells in a broad variety of tissues.
Integrated single-cell and bulk RNA sequencing in pancreatic cancer identifies disulfidptosis-associated molecular subtypes and prognostic signature
Authors: Wu Yunhao , Shang Jin , Ruan Qiang , Tan Xiaodong 
Published: October 2023

AbstractPancreatic cancer (PC) is known for its high degree of heterogeneity and exceptionally adverse outcome. While disulfidptosis is the most recently identified form of cell death, the predictive and therapeutic value of disulfidptosis-related genes (DRGs) for PC remains unknown. RNA sequencing data with the follow-up information, were retrieved from the TCGA and ICGC databases. Consensus clustering analysis was conducted on patient data using R software. Subsequently, the LASSO regression analysis was conducted to create a prognostic signature for foreseeing the outcome of PC. Differences in relevant pathways, mutational landscape, and tumor immune microenvironment were compared between PC samples with different risk levels. Finally, we experimentally confirmed the impact of DSG3 on the invasion and migration abilities of PC cells. All twenty DRGs were found to be hyperexpressed in PC tissues, and fourteen of them significantly associated with PC survival. Using consensus clustering analysis based on these DRGs, four DRclusters were identified. Additionally, altogether 223 differential genes were evaluated between clusters, indicating potential biological differences between them. Four gene clusters (geneClusters) were recognized according to these genes, and a 10-gene prognostic signature was created. High-risk patients were found to be primarily enriched in signaling pathways related to the cell cycle and p53. Furthermore, the rate of mutations was markedly higher in high-risk patients, besides important variations were present in terms of immune microenvironment and chemotherapy sensitivity among patients with different risk levels. DSG3 could appreciably enhance the invasion and migration of PC cells. This work, based on disulfidoptosis-related genes (DRGs), holds the promise of classifying PC patients and predicting their prognosis, mutational landscape, immune microenvironment, and drug therapy. These insights could boost an improvement in a better comprehension of the role of DRGs in PC as well as provide new opportunities for prognostic prediction and more effective treatment strategies.
Interaction force modeling and analysis of the human–machine kinematic chain based on the human–machine deviation
Authors: Zhou Xin , Duan Zhisheng 
Published: October 2023

AbstractA mechanical model for a human–machine interaction force based on the man–machine kinematic chain is established. This is combined with screw theory and a virtual rigid body model for the human–machine interaction force is proposed. This model interprets the basic principle model of the human–machine contact force. The deviation of the human–machine kinematic chain is calculated using the virtual model. In order to carry out the calibration simulation for the model, a 6-sps parallel mechanism is taken as an example to illustrate the construction principle of the human–machine interaction virtual rigid body model. This is calibrated by introducing finite element software. Finally, using the knee exoskeleton as an example, a numerical simulation is introduced. This illustrates the relationship between the driving force of the exoskeleton, the human–machine deviation as well as the virtual stiffness. The modeling method of this paper provides theoretical reference for controller design of human–machine interaction forces in the future.
Thermal-structural hybrid Lagrangian solver and numerical simulation-based correction of shape deformation of stainless-steel parts produced by laser powder bed fusion
Authors: Tsivilskiy Ilya , Shishkovsky Igor 
Published: October 2023

AbstractAn efficient thermal-structural numerical solver for Additive Manufacturing has been developed based on a modified Lagrangian approach to solve the energy conservation equations in differential form. The heat transfer is modeled using the finite difference method applied to a deforming Lagrangian mesh. The structural solver has been enhanced with the proposed effective quasi-elastic differential approach for modeling the elastoplastic behavior of materials. The algorithm is relatively simple to implement yet is highly effective. The solver can predict shape deformations of metal parts printed using the laser powder bed fusion technique. The second key capability of the solver is the auto-compensation of distortions of 3D-printed parts by proposing a corrected geometry of a surface to be printed, in order to ensure minimal deviation of the actual printed part from the desired one, even under non-optimal operating conditions or for complex shapes. All the simulation results have been verified in real-life experiments for 3D parts of sizes ranging from 10 to 15 mm up to 40 mm.
Phase-shifted imaging on multi-directional induction thermography
Authors: Urtasun Benat , Andonegui Imanol , Gorostegui-Colinas Eider 
Published: October 2023

AbstractA novel multi-directional eddy current thermography (ECT) system is presented generating sets of directional phase images that have been fused with a processing pipeline allowing for an improved probability of detection (POD). Inhomogeneous electromagnetic Joule heating derived from the diversion of induced eddy currents provoked by cracks, altering its path around as well as under its bottom, is the principal phenomenon enabling its usage as a non-destructive-evaluation (NDE) technique. Most induction thermography systems employ inductors derived from old designs, optimized for localized heating with a fixed magnetic field direction. This provokes a directional detection blind-spot for surfaces with random crack orientations. In this paper we have observed that the pattern associated with the thermal response distribution can be geometrically correlated to the relative orientation of the magnetic field regarding the crack, conforming to a rotating feature that has not been described before. Extracting the apparent motion as an optical flow, with a phase-shifting interpolation of the intermediate orientations, generates a signal that enables a robust segmentation of a wide variety of defects in ferritic and austenitic alloys. Its performance has been evaluated with two ‘Hit/Miss’ POD studies TIG welds Inconel 718 and Haynes 282 alloys. Results show an increased detectability regarding the manual labelling of the defects in the same directional set, employing the same input.
Bio-inspired artificial somatic index for reflecting the travel experience of passenger agents under a flexible transportation scenario
Authors: Cabrera-Paniagua Daniel , Flores Diego , Rubilar-Torrealba Rolando , Cubillos Claudio 
Published: October 2023

AbstractThis work analyzes the implementation of an artificial mechanism inspired by a biological somatic marker that ables a passenger agent to both, react to changes in the service, as well as keep said reactions as a memory for future decisions. An artificial mental model was designed, and the passenger agent was implemented as an autonomous decision-making system, where both, the choice of the transport operator and the evaluation of the received service were fully delegated to the system. The evaluation of the service experience is not only based on rational aspects (such as the cost of the trip) but also on subjective aspects related to the satisfaction level derived from the passenger's experience. The experimental scenario considered 10,000 trip requests simulated within an artificial map that emulates characteristics that are usually present in a city, such as vehicular congestion, the unsafety of certain streets, or the benefits of an area with tourist interest. The results show that the option to travel under a transport operator with a touristic profile is a trend. Unlike current cases in the industry, this research work explores the scenario where the passenger can have as a client a trip profile with memory, differentiated from other clients, and can receive more than one trip proposal for the same trip request, according to the different conditions that the passenger is looking for.
Cross-reactivity and sequence similarity between microbial transglutaminase and human tissue antigens
Authors: Lerner Aaron , Benzvi Carina , Vojdani Aristo 
Published: October 2023

AbstractMicrobial transglutaminase (mTG) is a bacterial survival factor, frequently used as a food additive to glue processed nutrients. As a result, new immunogenic epitopes are generated that might drive autoimmunity. Presently, its contribution to autoimmunity through epitope similarity and cross-reactivity was investigated. Emboss Matcher was used to perform sequence alignment between mTG and various antigens implicated in many autoimmune diseases. Monoclonal and polyclonal antibodies made specifically against mTG were applied to 77 different human tissue antigens using ELISA. Six antigens were detected to share significant homology with mTG immunogenic sequences, representing major targets of common autoimmune conditions. Polyclonal antibody to mTG reacted significantly with 17 out of 77 tissue antigens. This reaction was most pronounced with mitochondrial M2, ANA, and extractable nuclear antigens. The results indicate that sequence similarity and cross-reactivity between mTG and various tissue antigens are possible, supporting the relationship between mTG and the development of autoimmune disorders 150W.