bluuebunny/crossref_metadata_2025_split huggingface dataset:
Excitation and ionization of OCS molecules in strong UV and NIR laser fields
Authors: Shi 师 Huijun 慧军 , Liu 刘 Yang 洋 , Sun 孙 Tian 添 , Lv 吕 Hang 航 , Xu 徐 Haifeng 海峰 
Published: March 2024

Abstract
Rydberg state excitation (RSE) is a highly non-linear physical phenomenon that is induced by the ionization of atoms or molecules in strong femtosecond laser fields. Here we observe that both parent and fragments (S, C, OC) of the tri-atomic molecule carbonyl sulfide (OCS) can survive strong 800 nm or 400 nm laser fields in high Rydberg states. The dependence of parent and fragment RSE yields on laser intensity and ellipticity is investigated in both laser fields, and the results are compared with those for strong-field ionization. Distinctly different tendencies for laser intensity and ellipticity are observed for fragment RSE compared with the corresponding ions. The mechanisms of RSE and strong-field ionization of OCS molecules in different laser fields are discussed based on the experimental results. Our study sheds some light on the strong-field excitation and ionization of molecules irradiated by femtosecond NIR and UV laser fields.
Upgrade of the ATLAS Level-0 TGC Endcap Muon Trigger for HL-LHC
Authors: Kawamoto C. ,   the ATLAS collaboration
Published: March 2024

Abstract
The Level-0 endcap muon trigger system for the ATLAS experiment at the HL-LHC, which performs a fast muon reconstruction using the Thin Gap Chamber (TGC), is being developed to cope with more than three times higher luminosity environment and achieve a better performance. The efficiency in the high-p
T region was found to be 9% higher than the current system. The TGC hit signals digitized at the frontend electronics are sent to the backend, and muon candidates are reconstructed using the hits. Then, the candidates are combined with information from other detectors to refine transverse momentum (p
T) reconstruction and reduce fake trigger candidates. The precise online estimation of p
T allows us to apply highly efficient trigger condition to select events that contains muons with high p
T.
The Sector Logic (SL) is responsible for the online fast reconstruction in the L0 Muon Trigger system, and the algorithms are implemented in a large-scale modern FPGA on the SL. Each step of the reconstruction algorithms is first implemented as individual modules, and all trigger algorithms run sequentially as a chain in a combined firmware. The trigger algorithms are being tested on the prototype trigger board, the SL. The resource usage of the FPGA is reasonable and the trigger latency is within the acceptable limit.
Study of cosmogenic activation in 76Ge enriched germanium detectors during fabrication and transportation above ground
Authors: Nie Qiyuan , Zeng Zhi , Ma Hao , Yang Litao , Yue Qian , Cheng Jianping 
Published: March 2024

Abstract
Rare event search experiments using germanium detectors are
operated in underground laboratories to minimize the background
induced by cosmic rays. However, the cosmogenic activation in
germanium crystals on the ground during fabrication and
transportation generates long half-life radionuclides and
contributes a considerable background. We simulated the production
rates of cosmogenic radionuclides in germanium and calculated the
specific activities of cosmogenic radionuclides according to the
scheduled fabrication and transportation processes of 76Ge
enriched germanium detectors. The impact of cosmogenic background in
germanium crystals for the next generation CDEX experiment was
assessed with the scheduled exposure history above ground.
From design and construction to operation of the APPLE undulator at TPS
Authors: Chung Ting-Yi , Chang Cheng-Hsing , Chen Hsiung , Chen Hui-Huang , Hwang Ching-Shiang 
Published: March 2024

Abstract
The APPLE type of Elliptically Polarized Undulator (EPU) not
only serves as a crucial circularly polarized light source in
existing accelerator facilities but also acts as a standard light
source for soft X-rays at the Taiwan Photon Source (TPS). Up to the
present, we have autonomously designed, constructed, and operated
various EPU configurations. The experience gleaned from the
construction of various designs and the choice of material will be
outlined in this paper. We also elaborate upon the actions taken to
address the adverse effects on the magnetic fields due to the
characteristics of non-identical magnets and mechanical
deformation. In particular, a method for correction of discrepancies
in the magnetic field of the EPU with operation in numerous phase
modes employing iron shims is described. In addition, we also
discuss the adverse effects on the storage ring that must be dealt
with for stable operation of the EPU at the TPS and optimization of
the magnetic field during the laboratory construction phase. This
paper will further explain management issues related to the
susceptibility of the EPU to radiation damage. The comprehensive
experience related to the EPU at the TPS, from design and
construction to operation will be presented in this paper.
The multi-sightline compact D-D neutron spectrometers based on CLYC7-scintillator for beam ion anisotropy study in LHD
Authors: Liao L.Y. , Ogawa K. , Isobe M. , Sangaroon S. , Kawamoto Y. , Zhong G.Q. , Fan T.S. 
Published: March 2024

Abstract
Three compact neutron emission spectrometers (CNESs) based
on the novel inorganic scintillator Cs2LiYCl6:Ce with 99%
7Li-enrichment (CLYC7) were newly installed in different lines
of sight in the Large Helical Device (LHD) to study the anisotropy
of the velocity distribution of the beam ions. Neutron energy
spectra measurements using multi-sightline CNESs were performed
under neutral-beam (NB)-heated deuterium plasma. A significant
Doppler shift of the deuterium-deuterium (D-D) neutron energy
induced by different NB heating and different lines of sight was
observed. The measured peak neutron energies were nearly consistent
with those calculated by the simple two-body kinematics of the D-D
reaction using the tangency radii of CNESs and NBs. These results
demonstrated the capabilities of the CNESs for neutron energy
spectra measurements and the study of fast-ion physics in magnetic
confinement fusion research.
Search algorithm on strongly regular graph by lackadaisical quantum walk
Authors: Peng Fangjie , Li Meng , Sun Xiaoming 
Published: March 2024

Abstract
Quantum walk is a widely used method in designing quantum algorithms. In this article, we consider the lackadaisical discrete-time quantum walk (DTQW) on strongly regular graphs (SRG). When there is a single marked vertex in a SRG, we prove that lackadaisical DTQW can find the marked vertex with asymptotic success probability 1, with a quadratic speedup compared to classical random walk. This paper deals with any parameter family of SRG and argues that, by adding self-loops with proper weights, the asymptotic success probability can reach 1. The running time and asymptotic success probability matches the result of continuous-time quantum walk, and improves the result of DTQW.
Bioreactor-based stem cell therapy for liver fibrosis
Authors: Yan Mengchao , Yao Jia , Xie Ye , Jiang Pan , Yan Jun , Li Xun 
Published: March 2024

Abstract
Stem cell therapy, achieved using mesenchymal stem cells (MSCs), has been highlighted for the treatment of liver fibrosis. Infusion into the circulatory system is a traditional application of MSCs; however, this approach is limited by phenotypic drift, stem cell senescence, and vascular embolism. Maintaining the therapeutic phenotype of MSCs while avoiding adverse infusion-related reactions is the key to developing next-generation stem cell therapy technologies. Here, we propose a bioreactor-based MSCs therapy to avoid cell infusion. In this scheme, 5% liver fibrosis serum was used to induce the therapeutic phenotype of MSCs, and a fluid bioreactor carrying a co-culture system of hepatocytes and MSCs was constructed to produce the therapeutic medium. In a rat model of liver fibrosis, the therapeutic medium derived from the bioreactor significantly alleviated liver fibrosis. Therapeutic mechanisms include immune regulation, inhibition of hepatic stellate cell activation, establishment of hepatocyte homeostasis, and recovery of liver stem cell subsets. Overall, the bioreactor-based stem cell therapy (scheme) described here represents a promising new strategy for the treatment of liver fibrosis and will be beneficial for the development of ‘cell-free’ stem cell therapy.
Rapid fiber-detection technique by artificial intelligence in phase-contrast microscope images of simulated atmospheric samples
Authors: Yamamoto Takashi , Iwasaki Kazuharu , Iida Yukiko , Yuki Ken-ichi , Nakaji Fumihiro , Yamashiro Hayato , Toyoguchi Toshiyuki , Terazono Atsushi 
Published: March 2024

Abstract
Since the manufacture, import, and use of asbestos products have been completely abolished in Japan, the main cause of asbestos emissions into the atmosphere is the demolition and removal of buildings built with asbestos-containing materials. To detect and correct asbestos emissions from inappropriate demolition and removal operations at an early stage, a rapid method to measure atmospheric asbestos fibers is required. The current rapid measurement method is a combination of short-term atmospheric sampling and phase-contrast microscopy counting. However, visual counting takes a considerable amount of time and is not sufficiently fast. Using artificial intelligence (AI) to analyze microscope images to detect fibers may greatly reduce the time required for counting. Therefore, in this study, we investigated the use of AI image analysis for detecting fibers in phase-contrast microscope images. A series of simulated atmospheric samples prepared from standard samples of amosite and chrysotile were observed using a phase-contrast microscope. Images were captured, and training datasets were created from the counting results of expert analysts. We adopted 2 types of AI models—an instance segmentation model, namely the mask region-based convolutional neural network (Mask R-CNN), and a semantic segmentation model, namely the multi-level aggregation network (MA-Net)—that were trained to detect asbestos fibers. The accuracy of fiber detection achieved with the Mask R-CNN model was 57% for recall and 46% for precision, whereas the accuracy achieved with the MA-Net model was 95% for recall and 91% for precision. Therefore, satisfactory results were obtained with the MA-Net model. The time required for fiber detection was less than 1 s per image in both AI models, which was faster than the time required for counting by an expert analyst.
Tackling reference bias in genotyping by using founder sequences with PanVC 3
Authors: Norri Tuukka , Mäkinen Veli 
Published: March 2024

Abstract

Summary
Overcoming reference bias and calling insertions and deletions are major challenges in genotyping. We present PanVC 3, a set of software that can be utilized as part of various variant calling workflows. We show that, by incorporating known genetic variants to a set of founder sequences to which reads are aligned, reference bias is reduced and precision of calling insertions and deletions is improved.

Availability and implementation
PanVC 3 and its source code are freely available at https://github.com/tsnorri/panvc3 and at https://anaconda.org/tsnorri/panvc3 under the MIT licence. The experiment scripts are available at https://github.com/algbio/panvc3-experiments.
Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning
Authors: Cappelletti Luca , Rekerle Lauren , Fontana Tommaso , Hansen Peter , Casiraghi Elena , Ravanmehr Vida , Mungall Christopher J , Yang Jeremy J , Spranger Leonard , Karlebach Guy , Caufield J Harry , Carmody Leigh , Coleman Ben , Oprea Tudor I , Reese Justin , Valentini Giorgio , Robinson Peter N 
Published: March 2024

Abstract

Motivation
Graph representation learning is a family of related approaches that learn low-dimensional vector representations of nodes and other graph elements called embeddings. Embeddings approximate characteristics of the graph and can be used for a variety of machine-learning tasks such as novel edge prediction. For many biomedical applications, partial knowledge exists about positive edges that represent relationships between pairs of entities, but little to no knowledge is available about negative edges that represent the explicit lack of a relationship between two nodes. For this reason, classification procedures are forced to assume that the vast majority of unlabeled edges are negative. Existing approaches to sampling negative edges for training and evaluating classifiers do so by uniformly sampling pairs of nodes.

Results
We show here that this sampling strategy typically leads to sets of positive and negative examples with imbalanced node degree distributions. Using representative heterogeneous biomedical knowledge graph and random walk-based graph machine learning, we show that this strategy substantially impacts classification performance. If users of graph machine-learning models apply the models to prioritize examples that are drawn from approximately the same distribution as the positive examples are, then performance of models as estimated in the validation phase may be artificially inflated. We present a degree-aware node sampling approach that mitigates this effect and is simple to implement.

Availability and implementation
Our code and data are publicly available at https://github.com/monarch-initiative/negativeExampleSelection.
Cross-context behavioural correlations and signals of aggression in females of a livebearing fish
Authors: Kolluru Gita R , Akky Yasmine J , Weissman Alana , Poore Hilary , Weiner Dana , Earley Ryan L 
Published: March 2024

Abstract
Behaviours can be adaptively correlated with each other and with other aspects of phenotype. We investigated behaviour across foraging, mating, and risk contexts in females of the poeciliid fish, Girardinus metallicus. We quantified relationships between these behaviours and aggression signals, body size, and reproductive output. Behaviours describing aggression and boldness, some of which were repeatable, were correlated in females. Aggression was signalled by the darkening of a black spot on the extended dorsal fin or by fin flaring. Spot darkening occurred during intra- and intersexual interactions and was positively correlated with interfemale aggression and negatively correlated with the time females spent following males, suggesting that it is an honest indicator of motivational state. In contrast, fin flaring was directed only at females and occurred more frequently in the foraging context. Larger females had fewer offspring and received fewer courtship displays, possibly because they were more aggressive to males. In contrast to studies of males, we found a negative relationship between rank order of boldness and aggression, consistent with either a trade-off or with selection favouring the negative relationship. Our results highlight the importance of studying females in model systems to uncover novel patterns and potentially meaningful departures from what is typically seen in males.
Morphological divergence of domatia in ant-free populations of the widespread Neotropical myrmecophyte Miconia tococa (Melastomataceae)
Authors: Bartimachi Alessandra , Pimenta Thais B , Telles Francismeire J , Vieira-Neto Ernane H M , Cardoso João C F , Vasconcelos Heraldo L , Costa Alan N 
Published: March 2024

Abstract
Co-evolving organisms experience multiple selection pressures that may lead to trait mismatches among different populations and sites. In defensive ant–plant mutualisms, host plants (myrmecophytes) produce specialized shelters (domatia) to harbour specialized ant-partners in exchange for protection against enemies. Although populations of myrmecophytes without ants occur in some locations, there are no records of changes in domatia morphology—at the population level—due to the absence of symbiotic ants. We conducted broad-scale samplings of Miconia tococa (Melastomataceae) populations across the Brazilian Cerrado and a 2-year transplant experiment to test whether domatia morphology changes when symbiotic ants are naturally absent. Domatia were 33.9% smaller in ant-free populations than in ant-inhabited populations. Transplants revealed that host plants from ant-inhabited sites still developed larger domatia than those from ant-free sites, even in the absence of ant-partners. These findings point to a change of M. tococa traits associated with biotic defences where symbiotic ants are absent. What may have begun as a plastic adjustment to ant-free environments appears to have been transformed into fixed (genetic) interpopulation differences over time, indicating a potential local destabilization of the mutualism or a mechanism to stabilize the interaction at the landscape scale.
The role of the skin microbiome in wound healing
Authors: Yang Yuyan , Huang Jiuzuo , Zeng Ang , Long Xiao , Yu Nanze , Wang Xiaojun 
Published: March 2024

Abstract
The efficient management of skin wounds for rapid and scarless healing represents a major clinical unmet need. Nonhealing skin wounds and undesired scar formation impair quality of life and result in high healthcare expenditure worldwide. The skin-colonizing microbiota contributes to maintaining an intact skin barrier in homeostasis, but it also participates in the pathogenesis of many skin disorders, including aberrant wound healing, in many respects. This review focuses on the composition of the skin microbiome in cutaneous wounds of different types (i.e. acute and chronic) and with different outcomes (i.e. nonhealing and hypertrophic scarring), mainly based on next-generation sequencing analyses; furthermore, we discuss the mechanistic insights into host–microbe and microbe–microbe interactions during wound healing. Finally, we highlight potential therapeutic strategies that target the skin microbiome to improve healing outcomes.
Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2024 Update by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM)
Authors: Miller J Michael , Binnicker Matthew J , Campbell Sheldon , Carroll Karen C , Chapin Kimberle C , Gonzalez Mark D , Harrington Amanda , Jerris Robert C , Kehl Sue C , Leal Sixto M , Patel Robin , Pritt Bobbi S , Richter Sandra S , Robinson-Dunn Barbara , Snyder James W , Telford Sam , Theel Elitza S , Thomson Richard B , Weinstein Melvin P , Yao Joseph D 
Published: March 2024

Abstract
The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the healthcare team. This document, developed by experts in both adult and pediatric laboratory and clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract Infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including arboviral Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also addressed. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.
Taxonomic, phylogenetic, and functional nestedness of mammal assemblages in the Zhoushan Archipelago, China
Authors: Zhan Chengxiu , Li Bicheng , Chen Chuanwu , Wang Yanping 
Published: March 2024

Abstract
Nestedness is an important part of the theoretical framework of island biogeography and community ecology. However, most previous studies focused on taxonomic dimension and overlooked functional and phylogenetic nestedness. Here, we simultaneously investigated taxonomic, functional, and phylogenetic nestedness of terrestrial mammals on 39 land-bridge islands in the Zhoushan Archipelago, China. As mammals’ response to the environment may depend on their body size, we performed analyses for three mammal assemblages separately: overall species, large and medium-sized species, and small species. The taxonomic nestedness was quantified by organizing the species incidence matrix, while the functional and phylogenetic nestedness were estimated by combining the similarity of their ecological traits and phylogeny. Island characteristics (island area, three isolation indices, land use intensity, and habitat diversity) and species traits (body size, litter size, habitat specificity, geographic range size, and minimum area requirement) were used as predictors of nestedness. Overall and small species were significantly nested in 3 facets of nestedness, and results supported the selective extinction, selective colonization, and habitat nestedness hypotheses. Large and medium-sized species were functionally and phylogenetically nested when matrices were ordered by increasing distance to mainland, supporting the selective colonization hypothesis. Overall, differences in nestedness and its underlying mechanisms were detected not only in 3 facets of nestedness but also in the 3 mammal assemblages. Therefore, frameworks that incorporate taxonomic, phylogenetic, and functional nestedness can contribute to a more comprehensive understanding of nestedness processes. Additionally, it also improves our ability to understand the divergent responses of mammal assemblages to the insular environment.