bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precision of diamond turning sinusoidal structures as measurement standards used to assess topography fidelity
Authors: Hüser Dorothee , Meeß Rudolf , Dai Gaoliang , Felgner André , Hahm Kai , Verhülsdonk Stefan , Feist Carsten , Gao Sai 
Published: February 2024

Abstract
In optical surface metrology, it is crucial to assess the fidelity of the topography measuring signals. One parameter to quantify this is the small-scale fidelity limit T
FIL defined in ISO 25 178-600:2019. To determine this parameter, sinusoidal structures are generated, where the wavelengths are modulated according to a discrete chirp series. The objects are produced by means of ultra-precision diamond face turning. Planar areas and regions with slopes below 4° could be produced with form deviations of ≲10 nm. An initial estimate of the cutting tool’s nose radius resulted in a deviation that caused the ridges of the structures to be too narrow by approximately 150 nm, while the trenches were too wide. At the bottom of narrow trenches, deviations are observed in the form of elevations with heights of about 20 to 100 nm. The measurement standard investigated in this study has also been used to characterise optical instruments in a round-robin test within the European project TracOptic, which requires precise knowledge of the geometry of all structures. The geometry of the topography, cosine structures superimposed with form deviations, was measured using the Met. LR-AFM metrological long-range atomic force microscope of the German National Metrology Institute.
Assessment of the literature about Be-W mixed material layer formation in the fusion reactor environment
Authors: Lasa Ane , Dasgupta Dwaipayan , Baldwin Matthew J , Cusentino Mary Alice , Hatton Peter , Perez Danny , Uberuaga Blas P , Yang Li , Wirth Brian D 
Published: February 2024

Abstract
All plasma facing surfaces in a fusion reactor, whether initially pure or an alloy, will rapidly evolve into a mixed material due to plasma-induced erosion, migration and redeposition. Beryllium (Be) erosion from the main chamber, and its transport and deposition on to a tungsten (W) divertor results in the growth of mixed Be-W layers, which can evolve to form beryllides. These Be-W mixed materials exhibit generally less desirable properties than pure tungsten or pure beryllium, such as lower melting points. In order to better understand the parameter space for growth of these alloys, this paper reviews the literature on Be-W mixed material formation experiments—in magnetically confined fusion reactors, in linear plasma test stands, and during thin-film deposition—and on computational modeling of Be-W interactions, as well as briefly assesses the Be-W growth kinetics. We conclude that the following kinetic steps drive the material mixing: adsorption of the implanted/deposited ion on the metal surface; diffusion of the implanted/deposited ion from surface into the bulk, which is accelerated by defects; and loss of deposited material through erosion. Adsorption dominates (or prevents) material mixing in thin-film deposition experiments, whereas diffusion drives material mixing in plasma exposures due to the energetic ion implantation.
Tin-antimony/carbon composite porous fibers: electrospinning synthesis and application in sodium-ion batteries
Authors: Chen Xiong , Huang Yusen , Zhang Maobin , Yu Yunlong , Li Xiaoyan , Chen Dagui , Hong Jinquan , Du Shaowu , Guan Xiangfeng 
Published: February 2024

Abstract
In this work, tin-antimony/carbon composites porous fibers were successfully synthesized by an electrospinning method combined with two-step heat treatment processes, in which SnCl2 and SbCl3 were used as tin and antimony sources, and polyacrylonitrile (PAN) and polymethyl methacrylate (PMMA) were used as binders and pore-forming agents. The as-synthesized tin-antimony/carbon composites were systematically characterized by x-ray Diffraction (XRD), Transmission Electron Microscope (TEM), Scanning Electron Microscope (SEM), Energy-Dispersive Spectrometer (EDS), x-ray Photoelectron Spectroscopy (XPS), and Thermogravimetric Analysis-Differential Scanning Calorimetry (TG-DSC). The results indicate that the composite material consists of one-dimensional nitrogen-doped carbon porous fibers as the main matrix, with a three-dimensional network structure in which Sn, SnO2, and SnSb particles are encapsulated. Furthermore, the tin-antimony/carbon composites porous fibers were utilized as self-supported negative electrode for sodium-ion batteries. The results showed that the SNbM-2 sample electrode calcined at 800 °C demonstrated the best cycling stability and rate capability among all the sample electrodes, with a discharge capacity of 319.5 mAh·g−1 maintained after 100 cycles at a current density of 0.1 A·g−1. The excellent electrochemical performance of the SNbM-2 sample electrode is benefited from its unique porous structure and the carbon fiber network structure encapsulating Sn, SnO2, and SnSb particles, which could effectively shorten the Na+ ion transport distance and mitigate electrode volume expansion.
Recent advances of silicate materials for wastewater treatment: a review
Authors: Xu Meng , Wang Jinshu , Wu Junshu 
Published: February 2024

AbstractHeavy metal ions and organic pollutants cause irreversible damage to water environment, thereby posing significant threats to the well-being of organisms. The techniques of adsorption and photocatalytic degradation offer versatile solutions for addressing water pollution challenges, attributed to their inherent sustainability and adaptability. Silicates exhibit exceptional practicality in the realm of environmental protection owing to their structural integrity and robust chemical/thermal stability during hybridization and application process. Furthermore, the abundance of silicate reserves, coupled with their proven effectiveness, has garnered significant attention in recent years. This detailed review compiles and analyzes the extensive body of literature spanning the past six years (2018–2023), emphasizing the pivotal discoveries associated with employing silicates as water purification materials. This review article provides a comprehensive overview of the structure, classification, and chemical composition of diverse silicates and offers a thorough descriptive analysis of their performance in eliminating pollutants. Additionally, the utilization of diatomite as either precursors or substrates for silicates, along with the exploration of their corresponding purification mechanisms is discussed. The review unequivocally verifies the efficiency of silicates and their composites in the effective elimination of various toxic pollutants. However, the development of novel silicates capable of adapting to diverse environmental conditions to enhance pollution control, remains an urgent necessity.
ABAG-docking benchmark: a non-redundant structure benchmark dataset for antibody–antigen computational docking
Authors: Zhao Nan , Han Bingqing , Zhao Cuicui , Xu Jinbo , Gong Xinqi 
Published: February 2024

Abstract
Accurate prediction of antibody–antigen complex structures is pivotal in drug discovery, vaccine design and disease treatment and can facilitate the development of more effective therapies and diagnostics. In this work, we first review the antibody–antigen docking (ABAG-docking) datasets. Then, we present the creation and characterization of a comprehensive benchmark dataset of antibody–antigen complexes. We categorize the dataset based on docking difficulty, interface properties and structural characteristics, to provide a diverse set of cases for rigorous evaluation. Compared with Docking Benchmark 5.5, we have added 112 cases, including 14 single-domain antibody (sdAb) cases and 98 monoclonal antibody (mAb) cases, and also increased the proportion of Difficult cases. Our dataset contains diverse cases, including human/humanized antibodies, sdAbs, rodent antibodies and other types, opening the door to better algorithm development. Furthermore, we provide details on the process of building the benchmark dataset and introduce a pipeline for periodic updates to keep it up to date. We also utilize multiple complex prediction methods including ZDOCK, ClusPro, HDOCK and AlphaFold-Multimer for testing and analyzing this dataset. This benchmark serves as a valuable resource for evaluating and advancing docking computational methods in the analysis of antibody–antigen interaction, enabling researchers to develop more accurate and effective tools for predicting and designing antibody–antigen complexes. The non-redundant ABAG-docking structure benchmark dataset is available at https://github.com/Zhaonan99/Antibody-antigen-complex-structure-benchmark-dataset.
Language model enables end-to-end accurate detection of cancer from cell-free DNA
Authors: Shen Hongru , Liu Jilei , Chen Kexin , Li Xiangchun 
Published: February 2024

Abstract
We present a language model Affordable Cancer Interception and Diagnostics (ACID) that can achieve high classification performance in the diagnosis of cancer exclusively from using raw cfDNA sequencing reads. We formulate ACID as an autoregressive language model. ACID is pretrained with language sentences that are obtained from concatenation of raw sequencing reads and diagnostic labels. We benchmark ACID against three methods. On testing set subjected to whole-genome sequencing, ACID significantly outperforms the best benchmarked method in diagnosis of cancer [Area Under the Receiver Operating Curve (AUROC), 0.924 versus 0.853; P &lt; 0.001] and detection of hepatocellular carcinoma (AUROC, 0.981 versus 0.917; P &lt; 0.001). ACID can achieve high accuracy with just 10 000 reads per sample. Meanwhile, ACID achieves the best performance on testing sets that were subjected to bisulfite sequencing compared with benchmarked methods. In summary, we present an affordable, simple yet efficient end-to-end paradigm for cancer detection using raw cfDNA sequencing reads.
Hound: a novel tool for automated mapping of genotype to phenotype in bacterial genomes assembled de novo
Authors: Reding Carlos , Satapoomin Naphat , Avison Matthew B 
Published: February 2024

Abstract
Increasing evidence suggests that microbial species have a strong within species genetic heterogeneity. This can be problematic for the analysis of prokaryote genomes, which commonly relies on a reference genome to guide the assembly process. Differences between reference and sample genomes will therefore introduce errors in final assembly, jeopardizing the detection from structural variations to point mutations—critical for genomic surveillance of antibiotic resistance. Here we present Hound, a pipeline that integrates publicly available tools to assemble prokaryote genomes de novo, detect user-given genes by similarity to report mutations found in the coding sequence, promoter, as well as relative gene copy number within the assembly. Importantly, Hound can use the query sequence as a guide to merge contigs, and reconstruct genes that were fragmented by the assembler. To showcase Hound, we screened through 5032 bacterial whole-genome sequences isolated from farmed animals and human infections, using the amino acid sequence encoded by blaTEM-1, to detect and predict resistance to amoxicillin/clavulanate which is driven by over-expression of this gene. We believe this tool can facilitate the analysis of prokaryote species that currently lack a reference genome, and can be scaled either up to build automated systems for genomic surveillance or down to integrate into antibiotic susceptibility point-of-care diagnostics.
ZSCAN10 deficiency causes a neurodevelopmental disorder with characteristic oto-facial malformations
Authors: Laugwitz Lucia , Cheng Fubo , Collins Stephan C , Hustinx Alexander , Navarro Nicolas , Welsch Simon , Cox Helen , Hsieh Tzung-Chien , Vijayananth Aswinkumar , Buchert Rebecca , Bender Benjamin , Efthymiou Stephanie , Murphy David , Zafar Faisal , Rana Nuzhat , Grasshoff Ute , Falb Ruth J , Grimmel Mona , Seibt Annette , Zheng Wenxu , Ghaedi Hamid , Thirion Marie , Couette Sébastien , Azizimalamiri Reza , Sadeghian Saeid , Galehdari Hamid , Zamani Mina , Zeighami Jawaher , Sedaghat Alireza , Ramshe Samira Molaei , Zare Ali , Alipoor Behnam , Klee Dirk , Sturm Marc , Ossowski Stephan , Houlden Henry , Riess Olaf , Wieczorek Dagmar , Gavin Ryan , Maroofian Reza , Krawitz Peter , Yalcin Binnaz , Distelmaier Felix , Haack Tobias B 
Published: February 2024

Abstract
Neurodevelopmental disorders are major indications for genetic referral and have been linked to more than 1500 loci including genes encoding transcriptional regulators. The dysfunction of transcription factors often results in characteristic syndromic presentations; however, at least half of these patients lack a genetic diagnosis. The implementation of machine learning approaches has the potential to aid in the identification of new disease genes and delineate associated phenotypes.
Next generation sequencing was performed in seven affected individuals with neurodevelopmental delay and dysmorphic features. Clinical characterization included reanalysis of available neuroimaging datasets and 2D portrait image analysis with GestaltMatcher. The functional consequences of ZSCAN10 loss were modelled in mouse embryonic stem cells (mESCs), including a knockout and a representative ZSCAN10 protein truncating variant. These models were characterized by gene expression and western blot analyses, chromatin immunoprecipitation and quantitative PCR (ChIP-qPCR) and immunofluorescence staining. Zscan10 knockout mouse embryos were generated and phenotyped.
We prioritized bi-allelic ZSCAN10 loss-of-function variants in seven affected individuals from five unrelated families as the underlying molecular cause. RNA-sequencing analyses in Zscan10−/− mESCs indicated dysregulation of genes related to stem cell pluripotency. In addition, we established in mESCs the loss-of-function mechanism for a representative human ZSCAN10 protein truncating variant by showing alteration of its expression levels and subcellular localization, interfering with its binding to DNA enhancer targets. Deep phenotyping revealed global developmental delay, facial asymmetry and malformations of the outer ear as consistent clinical features. Cerebral MRI showed dysplasia of the semicircular canals as an anatomical correlate of sensorineural hearing loss. Facial asymmetry was confirmed as a clinical feature by GestaltMatcher and was recapitulated in the Zscan10 mouse model along with inner and outer ear malformations.
Our findings provide evidence of a novel syndromic neurodevelopmental disorder caused by bi-allelic loss-of-function variants in ZSCAN10.
Health care utilization and the associated costs attributable to cardiovascular disease in Ireland: a cross-sectional study
Authors: Stamenic Danko , Fitzgerald Anthony P , Gajewska Katarzyna A , O'Neill Kate N , Bermingham Margaret , Cronin Jodi , Lynch Brenda M , O'Brien Sarah M , McHugh Sheena M , Buckley Claire M , Kavanagh Paul M , Kearney Patricia M , O'Keeffe Linda M 
Published: February 2024

Abstract

Background
Cardiovascular disease (CVD) is the leading cause of mortality and disability globally. We examined healthcare service utilization and costs attributable to CVD in Ireland in the period before the introduction of a major healthcare reform in 2016.

Methods
Secondary analysis of data from 8113 participants of the first wave of The Irish Longitudinal Study on Ageing. Cardiovascular disease was defined as having a self-reported doctor's diagnosis of myocardial infarction, angina, heart failure, stroke, atrial fibrillation, or transient ischaemic attack. Participants self-reported the utilization of healthcare services in the year preceding the interview. Negative binomial regression with average marginal effects (AMEs) was used to estimate the incremental number of general practitioner (GP) and outpatient department (OPD) visits, accident and emergency department attendances and hospitalizations in population with CVD relative to population without CVD. We calculated the corresponding costs at individual and population levels, by gender and age groups.

Results
The prevalence of CVD was 18.2% (95% CI: 17.3, 19.0) Participants with CVD reported higher utilization of all healthcare services. In adjusted models, having CVD was associated with incremental 1.19 [95% confidence interval (CI): 0.99, 1.39] GP and 0.79 (95% CI: 0.65, 0.93) OPD visits. There were twice as many incremental hospitalizations in males with CVD compared to females with CVD [AME (95% CI): 0.20 (0.16, 0.23) vs. 0.10 (0.07, 0.14)]. The incremental cost of healthcare service use in population with CVD was an estimated €352.2 million (95% CI: €272.8, €431.7), 93% of which was due to use of secondary care services.

Conclusion
We identified substantially increased use of healthcare services attributable to CVD in Ireland. Continued efforts aimed at CVD primary prevention and management are required.
Design and performance analysis of thermal assisted reverse osmosis (RO)
Authors: Almatrafi Eydhah 
Published: February 2024

Abstract
Today, the world is facing difficult challenges related to water scarcity and freshwater resources. Water desalination has become necessary to meet this great demand. The reverse osmosis desalination system is considered the dominant type of desalination, although the high amount of energy consumed is considered the main barrier to expanding seawater reverse osmosis (SWRO). The need for producing an environmentally friendly energy source is also one of the most important challenges in preserving the environment and reducing global warming. The coexistence of power plants that release waste heat energy through the condenser and reverse osmosis plant represents an opportunity for a synergy system. Therefore, research has shown that the low/ultralow grade heat from natural sources or industrial processes can assist the process of desalination. This paper reviews available process configurations, system design, and operating parameters, and discusses the performance of the RO process at high temperatures.
Feasibility and economic analysis of electric vehicle battery secondary utilization to reduce wind and photovoltaic abandonment
Authors: Shen Xiaowang 
Published: February 2024

Abstract
The Chinese government has been very supportive of electric vehicles (EVs); however, the disposal of retired batteries from EVs must be carefully considered. Renewable energy, such as photovoltaic (PV) and wind power, whose output cannot be controlled, often use batteries to smooth production. For this reason, using retired EV batteries in renewable energy applications such as PVs and wind power, rather than new batteries, is considered an up-and-coming solution because retired EV batteries have a lower cost. In this paper, we will analyze both its feasibility and economics. The Chinese government’s support for EVs and the requirement for renewable energy consumption rates make it feasible to apply retired EV batteries to renewable energy. For the cost of retired EV batteries, we give the cost variations with different module capacities, different sizes, and different failure rates; if the battery energy storage is used in low electricity price situations such as in the home, it is difficult to make a profit, but if it is used in high electricity price situations such as factories, it is perfect when the economic benefits are taken into account. If the price of electricity in factories is RMB 1/kWh, the retired battery can start to make a profit after about 400 cycles, which is only about 25% of its life cycle.
Noncommutative Poisson Boundaries, Ultraproducts, and Entropy
Authors: Zhou Shuoxing 
Published: February 2024

Abstract
We construct the noncommutative Poisson boundaries of tracial von Neumann algebras through the ultraproducts of von Neumann algebras. As an application of this result, we complete the proof of Kaimanovich-Vershik’s fundamental theorems regarding noncommutative entropy. We also prove the Amenability-Trivial Boundary equivalence and Choquet-Deny-Type I equivalence for tracial von Neumann algebras.
On Uniqueness in Steiner Problem
Authors: Basok Mikhail , Cherkashin Danila , Rastegaev Nikita , Teplitskaya Yana 
Published: February 2024

Abstract
We prove that the set of $n$-point configurations for which the solution to the planar Steiner problem is not unique has the Hausdorff dimension at most $2n-1$ (as a subset of $\mathbb{R}^{2n}$). Moreover, we show that the Hausdorff dimension of the set of $n$-point configurations for which at least two locally minimal trees have the same length is also at most $2n-1$. The methods we use essentially rely upon the theory of subanalytic sets developed in [ 1]. Motivated by this approach, we develop a general setup for the similar problem of uniqueness of the Steiner tree where the Euclidean plane is replaced by an arbitrary analytic Riemannian manifold $M$. In this setup, we argue that the set of configurations possessing two locally-minimal trees of the same length either has dimension equal to $n \dim M - 1$ or has a non-empty interior. We provide an example of a two-dimensional surface for which the last alternative holds. In addition to the above-mentioned results, we study the set of $n$-point configurations for which there is a unique solution to the Steiner problem in $\mathbb{R}^{d}$. We show that this set is path-connected.
Exploring Diverse Signaling Mechanisms of G Protein-Coupled Receptors through Structural Biology
Authors: Suno Ryoji 
Published: February 2024

Abstract
Recent advancements in structural biology have facilitated the elucidation of complexes involving G protein-coupled receptors (GPCRs) and their associated signal transducers, including G proteins and arrestins. A comprehensive analysis of these structures provides profound insights into the dynamics of signaling mechanisms. These structural revelations can potentially guide the development of drugs to minimize side effects through targeted and selective signaling. Understanding the binding modes of different signal-selective ligands is imperative for future drug research and development. Here, we conduct a comparative examination of the structural details of various GPCR–signal transducer complexes and delve into the molecular basis of the currently proposed signal selectivity.