bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting cell identity via network inference and in silico gene perturbation
Authors: Kamimoto Kenji , Stringa Blerta , Hoffmann Christy M. , Jindal Kunal , Solnica-Krezel Lilianna , Morris Samantha A. 
Published: February 2023

AbstractCell identity is governed by the complex regulation of gene expression, represented as gene-regulatory networks1. Here we use gene-regulatory networks inferred from single-cell multi-omics data to perform in silico transcription factor perturbations, simulating the consequent changes in cell identity using only unperturbed wild-type data. We apply this machine-learning-based approach, CellOracle, to well-established paradigms—mouse and human haematopoiesis, and zebrafish embryogenesis—and we correctly model reported changes in phenotype that occur as a result of transcription factor perturbation. Through systematic in silico transcription factor perturbation in the developing zebrafish, we simulate and experimentally validate a previously unreported phenotype that results from the loss of noto, an established notochord regulator. Furthermore, we identify an axial mesoderm regulator, lhx1a. Together, these results show that CellOracle can be used to analyse the regulation of cell identity by transcription factors, and can provide mechanistic insights into development and differentiation.
The cellular coding of temperature in the mammalian cortex
Authors: Vestergaard M. , Carta M. , Güney G. , Poulet J. F. A. 
Published: February 2023

AbstractTemperature is a fundamental sensory modality separate from touch, with dedicated receptor channels and primary afferent neurons for cool and warm1–3. Unlike for other modalities, however, the cortical encoding of temperature remains unknown, with very few cortical neurons reported that respond to non-painful temperature, and the presence of a ‘thermal cortex’ is debated4–8. Here, using widefield and two-photon calcium imaging in the mouse forepaw system, we identify cortical neurons that respond to cooling and/or warming with distinct spatial and temporal response properties. We observed a representation of cool, but not warm, in the primary somatosensory cortex, but cool and warm in the posterior insular cortex (pIC). The representation of thermal information in pIC is robust and somatotopically arranged, and reversible manipulations show a profound impact on thermal perception. Despite being positioned along the same one-dimensional sensory axis, the encoding of cool and that of warm are distinct, both in highly and broadly tuned neurons. Together, our results show that pIC contains the primary cortical representation of skin temperature and may help explain how the thermal system generates sensations of cool and warm.
High-throughput computation of Raman spectra from first principles
Authors: Bagheri Mohammad , Komsa Hannu-Pekka 
Published: February 2023

AbstractRaman spectroscopy is a widely-used non-destructive material characterization method, which provides information about the vibrational modes of the material and therefore of its atomic structure and chemical composition. Interpretation of the spectra requires comparison to known references and to this end, experimental databases of spectra have been collected. Reference Raman spectra could also be simulated using atomistic first-principles methods but these are computationally demanding and thus the existing databases of computational Raman spectra are fairly small. In this work, we developed an optimized workflow to calculate the Raman spectra efficiently and taking full advantage of the phonon properties found in existing material databases. The workflow was benchmarked and validated by comparison to experiments and previous computational methods for select technologically relevant material systems. Using the workflow, we performed high-throughput calculations for a large set of materials (5099) belonging to many different material classes, and collected the results to a database. Finally, the contents of database are analyzed and the calculated spectra are shown to agree well with the experimental ones.
Gridded Datasets for Japan: Total, Male, and Female Populations from 2001–2020
Authors: Li Chao , Managi Shunsuke 
Published: February 2023

AbstractJapan is a highly urbanized and severely aging society. In an aging society, chronic disease and disability are prevalent, and the population is sensitive to environmental issues and climate change. To identify the effects of population changes, formulate population and public health policies, and assist environmental projects, a high-resolution and accurate gridded population dataset is highly desirable. To provide basic data for research in these areas, we created an open access annual dataset from 2001 to 2020 containing the total, male, and female population counts in each grid at a resolution of 500 m. A random forest method was employed to fill the gaps in Japan’s nationwide census data collected in 2005, 2010, 2015, and 2020. The yearly population dataset was based on the 4th-level mesh data from the Statistics Bureau of Japan to make it easy to use. The dataset is provided here along with descriptions of the data and methods used in the fitting, cross-validation, and prediction processes.
Combating cholera by building predictive capabilities for pathogenic Vibrio cholerae in Yemen
Authors: Usmani Moiz , Brumfield Kyle D. , Magers Bailey M. , Chaves-Gonzalez Juan , Ticehurst Helen , Barciela Rosa , McBean Fergus , Colwell Rita R. , Jutla Antarpreet 
Published: February 2023

AbstractCholera remains a global public health threat in regions where social vulnerabilities intersect with climate and weather processes that impact infectious Vibrio cholerae. While access to safe drinking water and sanitation facilities limit cholera outbreaks, sheer cost of building such infrastructure limits the ability to safeguard the population. Here, using Yemen as an example where cholera outbreak was reported in 2016, we show how predictive abilities for forecasting risk, employing sociodemographical, microbiological, and climate information of cholera, can aid in combating disease outbreak. An epidemiological analysis using Bradford Hill Criteria was employed in near-real-time to understand a predictive model’s outputs and cholera cases in Yemen. We note that the model predicted cholera risk at least four weeks in advance for all governorates of Yemen with overall 72% accuracy (varies with the year). We argue the development of anticipatory decision-making frameworks for climate modulated diseases to design intervention activities and limit exposure of pathogens preemptively.
Piecewise-potential-field-based path planning method for fixed-wing UAV formation
Authors: Fang Yuxuan , Yao Yiping , Zhu Feng , Chen Kai 
Published: February 2023

AbstractThe multi-UAV path planning method based on artificial potential field (APF) has the advantage of rapid processing speed and the ability to deal with dynamic obstacles, though some problems remain—such as a lack of consideration of the initial heading constraint of the UAVs, making it easy to fall into a local minimum trap, and the path not being sufficiently smooth. Consequently, a fixed-wing UAV formation path planning method based on piecewise potential field (PPF) is proposed, where the problem of UAV formation flight path planning in different states can be solved by suitable design of the PPF function. Firstly, the potential field vector can be used to represent the potential field functions of obstacles and target points to meet the kinematic constraints of the UAV. Secondly, the local minimum region can be detected, the additional potential field vector being set to break away from this region. Finally, the change rules of the potential field vector of a UAV in the formation reconstruction scene can be designed, a smooth formation flight track being assured by adjusting the corresponding speed of each UAV track point. Considering the path planning of a five-UAV formation as an example, we conducted simulation experiments. The results showed that—compared with the existing methods based on APF—the results obtained using the PPF-based method considered the initial heading limits of the UAVs, the planned path being considerably smoother. Moreover, the proposed method could plan multiple UAV tracks, satisfying the known constraints without conflict in complex scenarios.
Ecological successions throughout the desiccation of Tirez lagoon (Spain) as an astrobiological time-analog for wet-to-dry transitions on Mars
Authors: Fairén Alberto G. , Rodríguez Nuria , Sánchez-García Laura , Rojas Patricia , Uceda Esther R. , Carrizo Daniel , Amils Ricardo , Sanz José L. 
Published: February 2023

AbstractTirez was a small and seasonal endorheic athalassohaline lagoon that was located in central Spain. In recent years, the lagoon has totally dried out, offering for the first time the opportunity to analyze its desiccation process as a “time-analog” to similar events occurred in paleolakes with varying salinity during the wet-to-dry transition on early Mars. On the martian cratered highlands, an early period of water ponding within enclosed basins evolved to a complete desiccation of the lakes, leading to deposition of evaporitic sequences during the Noachian and into the Late Hesperian. As Tirez also underwent a process of desiccation, here we describe (i) the microbial ecology of Tirez when the lagoon was still active 20 years ago, with prokaryotes adapted to extreme saline conditions; (ii) the composition of the microbial community in the dried lake sediments today, in many case groups that thrive in sediments of extreme environments; and (iii) the molecular and isotopic analysis of the lipid biomarkers that can be recovered from the sediments today. We discuss the implications of these results to better understanding the ecology of possible Martian microbial communities during the wet-to-dry transition at the end of the Hesperian, and how they may inform about research strategies to search for possible biomarkers in Mars after all the water was lost.
Pleural fluid microbiota as a biomarker for malignancy and prognosis
Authors: Kwok Benjamin , Wu Benjamin G. , Kocak Ibrahim F. , Sulaiman Imran , Schluger Rosemary , Li Yonghua , Anwer Raheel , Goparaju Chandra , Ryan Daniel J. , Sagatelian Marla , Dreier Matthew S. , Murthy Vivek , Rafeq Samaan , Michaud Gaetane C. , Sterman Daniel H. , Bessich Jamie L. , Pass Harvey I. , Segal Leopoldo N. , Tsay Jun-Chieh J. 
Published: February 2023

AbstractMalignant pleural effusions (MPE) complicate malignancies and portend worse outcomes. MPE is comprised of various components, including immune cells, cancer cells, and cell-free DNA/RNA. There have been investigations into using these components to diagnose and prognosticate MPE. We hypothesize that the microbiome of MPE is unique and may be associated with diagnosis and prognosis. We compared the microbiota of MPE against microbiota of pleural effusions from non-malignant and paramalignant states. We collected a total of 165 pleural fluid samples from 165 subjects; Benign (n = 16), Paramalignant (n = 21), MPE-Lung (n = 57), MPE-Other (n = 22), and Mesothelioma (n = 49). We performed high throughput 16S rRNA gene sequencing on pleural fluid samples and controls. We showed that there are compositional differences among pleural effusions related to non-malignant, paramalignant, and malignant disease. Furthermore, we showed differential enrichment of bacterial taxa within MPE depending on the site of primary malignancy. Pleural fluid of MPE-Lung and Mesothelioma were associated with enrichment with oral and gut bacteria that are commonly thought to be commensals, including Rickettsiella, Ruminococcus, Enterococcus, and Lactobacillales. Mortality in MPE-Lung is associated with enrichment in Methylobacterium, Blattabacterium, and Deinococcus. These observations lay the groundwork for future studies that explore host-microbiome interactions and their influence on carcinogenesis.
Prevalence and influencing factors of wheeze and asthma among preschool children in Urumqi city: a cross-sectional survey
Authors: Wang Tingting , Shi Haonan , Wan Guangsheng , Zhao Zhuohui , Norback Dan , Pu Guiping , Ma Shaowei , Dong Huijuan , Yao Jian , Lu Junwen , Wang Yue , Yan Qi , Qi Huizhen , Ma Qi , Shi Yufeng 
Published: February 2023

AbstractTo investigate the prevalence and indoor environmental influencing factors of wheeze and asthma among preschool children in Urumqi, Xinjiang, China to provide a strong basis for prevention and control. In August 2019, a cross-sectional study involving 8153 preschool children was conducted in 60 kindergartens in Urumqi. The ALLHOME-2 questionnaire was used for childhood wheeze and asthma survey, and the dampness in buildings and health (DBH) questionnaire was used for the childhood home dwelling and living environment survey. Multivariate unconditional logistic regression was then used to analyze the potential influencing factors of childhood asthma and wheeze. The prevalence of wheeze and asthma in children was 4.7% and 2.0%, respectively. Multivariate unconditional logistic regression results suggested that ethnicity other than the Han Chinese (odds ratio (OR) 1.39, 95% confidence interval (CI) 1.05–1.84), caesarean section (OR 1.24, 95% CI 1.00–1.53), family history of asthma (OR 5.00, 95% CI 3.36–7.44), carpet or floor bedding at home (OR 1.40, 95% CI 1.05–1.87), purchasing new furniture in the mother’s residence during pregnancy (OR 1.58, 95% CI 1.06–2.36), pet keeping in the residence at aged 0–1 year (OR 1.55, 95% CI 1.13–2.13), passive smoking by child in the current residence (OR 1.35, 95% CI 1.01–1.80), and having mould or hygroma in the child's residence at aged 0–1 year (OR 1.72, 95% CI 1.12–2.64) were risk factors for wheeze. In addition, Girls (OR 0.73, 95% CI 0.59–0.90) was a protective factor for wheeze. Caesarean section (OR 1.46, 95% CI 1.06–2.00), family history of asthma (OR 7.06, 95% CI 4.33–11.53), carpet or floor bedding at home (OR 2.20, 95% CI 1.50–3.23), and pet keeping in the residence at aged 0–1 year (OR 1.64, 95% CI 1.04–1.83) were risk factors for asthma, whereas Girls (OR 0.58, 95% CI 0.42–0.80) was a protective factor for asthma. This survey indicates that the purchase of new furniture, the placement of carpet or floor bedding in the child's residence, the pets keeping, room dampness or moldy phenomena, and passive smoking may all contribute to an elevated risk of wheeze or asthma in children.
Three-dimensional visualization of dentine occlusion based on FIB-SEM tomography
Authors: Chen Xinye , Ryan Kaleigh M. , Hines Deon , Pan Long , Du Ke , Xu Shiyou 
Published: February 2023

AbstractThe occlusion of dentinal tubules has become a rapid and effective method for treating dentin hypersensitivity. Accurate evaluation of dentin occlusion is critical to illustrate the efficacy of oral care products and to optimize dental therapy in the clinics, which is limited by the conventional two-dimensional (2-D) characterization methods. Here, we demonstrate the visualization of the dentin occlusion via three-dimensional (3-D) characterization using a focused ion beam-scanning electron microscopy (FIB-SEM) tomography. Using the “Slice and View” approach, the material used for occluding dentin tubules is imaged with a very high-resolution voxel (10 nm × 10 nm × 20 nm) from 2-D SEM images and then reconstructed into a 3-D volume, which presents the mode of action of toothpaste for treating dentin hypersensitivity. Meanwhile, quantitative analysis of the depth of occlusion is successfully obtained. This work validates the feasibility of FIB-SEM tomography in the analysis of dentin occlusion within the complicated networks of dentine tubules at the nanoscale, and provides a novel approach to facilitate the research and development of oral care products.
Improving red-color performance, immune response and resistance to Vibrio parahaemolyticus on white shrimp Penaeus vannamei by an engineered astaxanthin yeast
Authors: Lin Yu-Ju , Chang Jui-Jen , Huang Huai-Ting , Lee Chih-Ping , Hu Yeh-Fang , Wu Mao-Lun , Huang Chih-Yang , Nan Fan-Hua 
Published: February 2023

AbstractAstaxanthin (AST), a super antioxidant with coloring and medical properties, renders it a beneficial feed additive for shrimp. This study conducted a white shrimp feeding trial of 3S, 3’S isoform AST, which was derived from metabolic-engineered Kluyveromyces marxianus fermented broth (TB) and its extract (TE) compared to sources from two chemically synthetic ASTs (Carophyll Pink [CP] and Lucantin Pink [LP]), which contain 3S, 3’S, 3R, 3’S (3S, 3’R) and 3R, 3’R isoforms ratio of 1:2:1. The effects on red coloration, immune parameters and resistance to Vibrio infection were evaluated. Four AST sources were incorporated into the diets at concentrations of 0 (control), 100 mg kg−1 (TB100, TE100, CP100, and LP100), and 200 mg kg−1 (TB200, TE200, CP200, and LP200). Results revealed that in week 4, shrimps that received AST-supplemented feeds, especially TB100, TB200, and TE200, significantly increased redness (a*) values. Immune responses including phagocytosis activity, superoxide-anion production, phenoloxidase activity, and immune-related genes were examined on days 0, 1, 2, 4, 7, 14, 21, and 28. Generally, shrimps that received AST-supplemented feeds exhibited higher immune responses on days 7 and 14 than the control feed. Gene expression levels of superoxide dismutase and glutathione peroxidase were significantly upregulated on days 7 and 14 in shrimps that received AST-supplemented feeds, while genes of penaeidins, antilipopolysaccharide factor, and lysozyme were upregulated on days 4, 7, and 14, especially received TB200 and TE200. Furthermore, shrimps that received TB100, TE100, CP100, and LP100 7 days were then challenged with Vibrio parahaemolyticus and the result demonstrated higher survival rates especially TB100 at 168 h than the control feed. In conclusion, incorporating AST into the diets enhanced shrimp red coloration, immune parameters, and resistance against V. parahaemolyticus infection. The K. marxianus-derived AST exhibited higher performance than did chemical AST to be a potential feed additive in shrimp aquaculture.
Breaking the hard-sphere model with fluorite and antifluorite solid solutions
Authors: Vauchy Romain , Hirooka Shun , Watanabe Masashi , Kato Masato 
Published: February 2023

AbstractUsing the hard-sphere model with the existing tabulated values of ionic radii to calculate the lattice parameters of minerals does not always match experimental data. An adaptation of this crystallographic model is proposed by considering the cations and anions as hard and soft close-packed spheres, respectively. We demonstrate the relevance of this “hybrid model” by combining Pauling’s first rule with experimental unit-cell parameters of fluorite and antifluorite-structured systems to revise the ionic radii of their constitutive species.
A long-term retrospective analysis of the haemorrhagic fever with renal syndrome epidemic from 2005 to 2021 in Jiangxi Province, China
Authors: Liu Shiwen , Zhang Tianchen 
Published: February 2023

AbstractJiangxi is one of the provinces in China most seriously affected by the haemorrhagic fever with renal syndrome (HFRS) epidemic. The aim of this paper was to systematically explore the HFRS epidemic in Jiangxi from the perspective of Hantavirus (HV) prevalence in rodents and humans and virus molecular characteristics. Individual information on all HFRS cases in Jiangxi from 2005 to 2021 was extracted from the China Information System for Disease Control and Prevention. All S and M fragment sequences of the Seoul virus and Hantan virus strains uploaded by Jiangxi and its neighbouring provinces and some representative sequences from provinces in China or some countries of Southeast Asia with the highest HV prevalence were retrieved and downloaded from NCBI GenBank. Periodogram and spatial autocorrelation were adopted for temporal periodicity and spatial clustering analysis of the HFRS epidemic. Joinpoint regression was utilized to explore the changing morbidity trend patterns of HFRS. Multiple sequence alignment and amino acid variation analysis were used to explore the homology and variation of strain prevalence in Jiangxi. Based on monthly morbidity time series, the periodogram analysis showed that the prevalence of HFRS had periodicities of 6 months and 12 months. Spatial autocorrelation analysis showed that HFRS distributed in Jiangxi was not random, with a “High-High” clustering area around Gaoan County. HFRS morbidity among the 0 ~ 15-year-old and ~ 61-year-old or older populations in Jiangxi increased significantly during the period of 2008–2015. Generally, HFRS morbidity was significantly positively correlated with the index of rat with virus (IRV) (r = 0.742) in the counties surrounding Gaoan from 2005 to 2019. HTNV strains in Jiangxi were in one independent branch, while the SEOV strains in Jiangxi were relatively more diverse. Both the YW89-15 and GAW30/2021 strains shared approximately 85% nucleotide homology and approximately 97% amino acid homology with their corresponding standard strains and vaccine strains. GAW30/2021 and YW89-15 had some amino acid site variations in nucleoprotein, glycoprotein precursor and RNA-dependent polymerase with their corresponding vaccine strains Z10 (HTNV) and Z37 (SEOV). The HFRS epidemic in Jiangxi has obvious temporal periodicity and spatial clustering, and the significant increase in the non-Immunization Expanded Program (EPI) targeted population (children and elderly) suggests that HFRS vaccination in this population needs to be considered. Although applying the EPI played a certain role in curbing the incidence of HFRS in Jiangxi from the perspective of ecological epidemiology, HTNV and SEOV strains prevalent in Jiangxi have some amino acid site variations compared to their corresponding vaccine strains, suggesting that HV variation needs to be continuously monitored in the future to observe vaccine protective efficiency.
Translation and psychometric assessment of a Persian version of medication safety competence scale (MSCS) for clinical nurses
Authors: Mohammadi Fateme , Kouhpayeh Seyed Amin , Bijani Mostafa , Farjam Mojtaba , Faghihi Amir , Badiyepeymaiejahromi Zohreh 
Published: February 2023

AbstractNurses play a key role in medication safety and, by extension, patient safety. Evaluation of medication safety competence in nurses requires valid, specific, and comprehensive instruments. The present study was conducted to translate and psychometric assessment a Persian version of medication safety competence scale (MSCS) for clinical nurses in Iran. This is a cross-sectional and multi-centric work of research with a methodological design. A total of 1080 clinical nurses were selected from 5 cities located in Iran. The original version of the MSCS was translated into Persian and the psychometric properties of MSCS were assessed using COSMIN criteria. The exploratory factor analysis (EFA) showed that the factor loading of the 36 items was between 0.72–0.87, all of which were significant. The confirmatory factor analysis (CFA) fitted the data well (χ2/df = 7, RMSEA = 0.01, CFI = 0.96, NFI = 0.95, and TLI = 0.97). The reliability of the instrument was assessed in terms of its internal homogeneity where the Cronbach's alpha of the whole instrument was found to be 0.96. The Persian version of MSCS for nurses possesses satisfactory validity and reliability. Thus, nurse managers can use this instrument to measure medication safety competence in nurses.