bluuebunny/crossref_metadata_2025_split huggingface dataset:
The mining and construction of a knowledge base for gene-disease association in mitochondrial diseases
Authors: Wang Wei , Song Junying , Chuai Yunhai , Chen Fu , Song Chunlan , Shu Mingming , Wang Yayun , Li Yunfei , Zhai Xinyu , Han Shujie , Yao Shun , Shen Kexin , Shang Wei , Zhang Lei 
Published: December 2021

AbstractMitochondrial diseases are a group of heterogeneous genetic metabolic diseases caused by mitochondrial DNA (mtDNA) or nuclear DNA (nDNA) gene mutations. Mining the gene-disease association of mitochondrial diseases is helpful for understanding the pathogenesis of mitochondrial diseases, for carrying out early clinical diagnosis for related diseases, and for formulating better treatment strategies for mitochondrial diseases. This project researched the relationship between genes and mitochondrial diseases, combined the Malacards, Genecards, and MITOMAP disease databases to mine the knowledge on mitochondrial diseases and genes, used database integration and the sequencing method of the phenolyzer tool to integrate disease-related genes from different databases, and sorted the disease-related candidate genes. Finally, we screened 531 mitochondrial related diseases, extracted 26,723 genes directly or indirectly related to mitochondria, collected 24,602 variant sites on 1474 genes, and established a mitochondrial disease knowledge base (MitDisease) with a core of genes, diseases, and variants. This knowledge base is helpful for clinicians who want to combine the results of gene testing for diagnosis, to understand the occurrence and development of mitochondrial diseases, and to develop corresponding treatment methods.
Developing and evaluating non-invasive healthcare technologies for a group of female participants from a socioeconomically disadvantaged area
Authors: Awad Eman , Ramji Rathi , Cirovic Stefan , Rämgård Margareta , Kottorp Anders , Shleev Sergey 
Published: December 2021

AbstractWhen compared to the general population, socioeconomically disadvantaged communities frequently experience compromised health. Monitoring the divide is challenging since standardized biomedical tests are linguistically and culturally inappropriate. The aim of this study was to develop and test a unique mobile biomedical testbed based on non-invasive analysis, as well as to explore the relationships between the objective health measures and subjective health outcomes, as evaluated with the World Health Organization Quality of Life survey. The testbed was evaluated in a socioeconomically disadvantaged neighborhood in Malmö, which has been listed as one of the twelve most vulnerable districts in Sweden. The study revealed that compared to conventional protocols the less intrusive biomedical approach was highly appreciated by the participants. Surprisingly, the collected biomedical data illustrated that the apparent health of the participants from the ethnically diverse low-income neighborhood was comparable to the general Swedish population. Statistically significant correlations between perceived health and biomedical data were disclosed, even though the dependences found were complex, and recognition of the manifest complexity needs to be included in further research. Our results validate the potential of non-invasive technologies in combination with advanced statistical analysis, especially when combined with linguistically and culturally appropriate healthcare methodologies, allowing participants to appreciate the significance of the different parameters to evaluate and monitor aspects of health.
Quantum random number generator using a cloud superconducting quantum computer based on source-independent protocol
Authors: Li Yuanhao , Fei Yangyang , Wang Weilong , Meng Xiangdong , Wang Hong , Duan Qianheng , Ma Zhi 
Published: December 2021

AbstractQuantum random number generator (QRNG) relies on the intrinsic randomness of quantum mechanics to produce true random numbers which are important in information processing tasks. Due to the presence of the superposition state, a quantum computer can be used as a true random number generator. However, in practice, the implementation of the quantum computer is subject to various noise sources, which affects the randomness of the generated random numbers. To solve this problem, we propose a scheme based on the quantum computer which is motivated by the source-independent QRNG scheme in optics. By using a method to estimate the upper bound of the superposition state preparation error, the scheme can provide certified randomness in the presence of readout errors. To increase the generation rate of random bits, we also provide a parameter optimization method with a finite data size. In addition, we experimentally demonstrate our scheme on the cloud superconducting quantum computers of IBM.
Short-chain aurachin D derivatives are selective inhibitors of E. coli cytochrome bd-I and bd-II oxidases
Authors: Radloff Melanie , Elamri Isam , Grund Tamara N. , Witte Luca F. , Hohmann Katharina F. , Nakagaki Sayaka , Goojani Hojjat G. , Nasiri Hamid , Hideto Miyoshi  , Bald Dirk , Xie Hao , Sakamoto Junshi , Schwalbe Harald , Safarian Schara 
Published: December 2021

AbstractCytochrome bd-type oxidases play a crucial role for survival of pathogenic bacteria during infection and proliferation. This role and the fact that there are no homologues in the mitochondrial respiratory chain qualify cytochrome bd as a potential antimicrobial target. However, few bd oxidase selective inhibitors have been described so far. In this report, inhibitory effects of Aurachin C (AurC-type) and new Aurachin D (AurD-type) derivatives on oxygen reductase activity of isolated terminal bd-I, bd-II and bo3 oxidases from Escherichia coli were potentiometrically measured using a Clark-type electrode. We synthesized long- (C10, decyl or longer) and short-chain (C4, butyl to C8, octyl) AurD-type compounds and tested this set of molecules towards their selectivity and potency. We confirmed strong inhibition of all three terminal oxidases for AurC-type compounds, whereas the 4(1H)-quinolone scaffold of AurD-type compounds mainly inhibits bd-type oxidases. We assessed a direct effect of chain length on inhibition activity with highest potency and selectivity observed for heptyl AurD-type derivatives. While Aurachin C and Aurachin D are widely considered as selective inhibitors for terminal oxidases, their structure–activity relationship is incompletely understood. This work fills this gap and illustrates how structural differences of Aurachin derivatives determine inhibitory potency and selectivity for bd-type oxidases of E. coli.
Identification of fractures in tight-oil reservoirs: a case study of the Da'anzhai member in the central Sichuan Basin, SW China
Authors: Tian Jie , Liu Hongqi , Wang Liang , Sima Liqiang , Liu Shiqiong , Liu Xiangjun 
Published: December 2021

AbstractThe Da'anzhai Member of the Jurassic Ziliujing formation in central Sichuan is a typical tight-oil reservoir with porosity and permeability less than 2% and 0.1 × 10–3 μm2, respectively. Fractures in this formation are well developed in micro- and nano-scale. However, the factors that control the fracture distribution are unclear. Additionally, the uncomprehensive and ineffective identification and evaluation of fractures in the early stage of tight-oil development makes it difficult to meet the requirements of tight-oil development. In our work, we used cores, thin sections, and a scanning electron microscope (SEM) to study the influence of the microscopic rock composition, including the shelly grains, calcite grains, and clastic grains, on the fracture development. We found that the microscopic composition of shelly grains and calcite grains separately control the development of inter-shelly fractures and shelly fractures, and intergranular fractures, and tectonic fractures. Except for a small number of dissolution fractures found in mudstone, the fractures are not well developed in the formations with clastic grains. According to the characteristics of the development degree of fracture and the resolution of the well-logs, the fractures are divided into large scale, small scale, and micro-scale. By a newly established level-by-level constraints method, we systematically identified the scale, occurrence, filling characteristics, and development degree of fractures in the Da'anzhai member by well-logs. Moreover, a quantitative model is also proposed for identifying the angles and development degree of fractures. The results show that the scale of fractures can be effectively identified by the shapes and values of resistivity logs; the occurrence, development, and filling characteristics of fractures can be semi-quantitatively evaluated by the relative amplitude difference between the matrix resistivity (Rb) and formation resistivity (RT). The results are consistent with the interpretation results by formation micro-resistivity imaging (FMI) log, which further demonstrates that the level-by-level constraint method by conventional well-logs can be used to systematically and effectively predict the fracture characteristics in tight-oil reservoirs.
Estimating and predicting snakebite risk in the Terai region of Nepal through a high-resolution geospatial and One Health approach
Authors: Ochoa Carlos , Pittavino Marta , Babo Martins Sara , Alcoba Gabriel , Bolon Isabelle , Ruiz de Castañeda Rafael , Joost Stéphane , Sharma Sanjib Kumar , Chappuis François , Ray Nicolas 
Published: December 2021

AbstractMost efforts to understand snakebite burden in Nepal have been localized to relatively small areas and focused on humans through epidemiological studies. We present the outcomes of a geospatial analysis of the factors influencing snakebite risk in humans and animals, based on both a national-scale multi-cluster random survey and, environmental, climatic, and socio-economic gridded data for the Terai region of Nepal. The resulting Integrated Nested Laplace Approximation models highlight the importance of poverty as a fundamental risk-increasing factor, augmenting the snakebite odds in humans by 63.9 times. For animals, the minimum temperature of the coldest month was the most influential covariate, increasing the snakebite odds 23.4 times. Several risk hotspots were identified along the Terai, helping to visualize at multiple administrative levels the estimated population numbers exposed to different probability risk thresholds in 1 year. These analyses and findings could be replicable in other countries and for other diseases.
Visceral adiposity index performed better than traditional adiposity indicators in predicting unhealthy metabolic phenotype among Chinese children and adolescents
Authors: Dong Yangyang , Bai Ling , Cai Rongrong , Zhou Jinyu , Ding Wenqing 
Published: December 2021

AbstractThe relationship between visceral adiposity index (VAI) and unhealthy metabolic phenotype remained unclear in children and adolescents. This study aimed to investigate their association and compared the ability of VAI and traditional adiposity indicators (body mass index, waist circumference and waist-to-height ratio) to predict metabolically unhealthy phenotype among normal-weight, overweight and obese children and adolescents. In this cross-sectional study, 1722 children and adolescents aged 12–18 years were selected by cluster random sampling, underwent a questionnaire survey, physical examination and biochemical tests. Participants were divided into four phenotypes according to the combination of the weight status determined by body mass index (BMI) and metabolic syndrome components. Receiver operating characteristic (ROC) analysis and multivariate logistic regression were used to compare the predictive capacity between VAI and traditional adiposity indicators and their relationship with metabolically unhealthy phenotype. We found that VAI had better performance in predicting metabolically unhealthy phenotype than traditional adiposity indicators, the area under the receiver-operating characteristic curve (AUC) were 0.808 and 0.763 for boys and girls with normal-weight, 0.829 and 0.816 for boys and girls with overweight and obese (all P < 0.001). VAI was most strongly related to metabolically unhealthy phenotype whether or not to adjust the age, the adjusted OR and 95%CI was 6.15 (4.13–9.14) in boys with normal weight, and 5.90 (3.06–11.36), 4.95 (2.35–10.41) in boys and girls with overweight and obese, respectively (all P < 0.001). Our findings suggested VAI could be used as a comprehensive predictor to identify unhealthy metabolic phenotype in children and adolescents.
Multipopulational transcriptome analysis of post-weaned beef cattle at arrival further validates candidate biomarkers for predicting clinical bovine respiratory disease
Authors: Scott Matthew A. , Woolums Amelia R. , Swiderski Cyprianna E. , Perkins Andy D. , Nanduri Bindu , Smith David R. , Karisch Brandi B. , Epperson William B. , Blanton John R. 
Published: December 2021

AbstractBovine respiratory disease (BRD) remains the leading infectious disease in post-weaned beef cattle. The objective of this investigation was to contrast the at-arrival blood transcriptomes from cattle derived from two distinct populations that developed BRD in the 28 days following arrival versus cattle that did not. Forty-eight blood samples from two populations were selected for mRNA sequencing based on even distribution of development (n = 24) or lack of (n = 24) clinical BRD within 28 days following arrival; cattle which developed BRD were further stratified into BRD severity cohorts based on frequency of antimicrobial treatment: treated once (treated_1) or treated twice or more and/or died (treated_2+). Sequenced reads (~ 50 M/sample, 150 bp paired-end) were aligned to the ARS-UCD1.2 bovine genome assembly. One hundred and thirty-two unique differentially expressed genes (DEGs) were identified between groups stratified by disease severity (healthy, n = 24; treated_1, n = 13; treated_2+, n = 11) with edgeR (FDR ≤ 0.05). Differentially expressed genes in treated_1 relative to both healthy and treated_2+ were predicted to increase neutrophil activation, cellular cornification/keratinization, and antimicrobial peptide production. Differentially expressed genes in treated_2+ relative to both healthy and treated_1 were predicted to increase alternative complement activation, decrease leukocyte activity, and increase nitric oxide production. Receiver operating characteristic (ROC) curves generated from expression data for six DEGs identified in our current and previous studies (MARCO, CFB, MCF2L, ALOX15, LOC100335828(akaCD200R1),andSLC18A2) demonstrated good-to-excellent (AUC: 0.800–0.899; ≥ 0.900) predictability for classifying disease occurrence and severity. This investigation identifies candidate biomarkers and functional mechanisms in at arrival blood that predicted development and severity of BRD.
Cy3-ATP labeling of unfixed, permeabilized mouse hair cells
Authors: Pacentine Itallia V. , Barr-Gillespie Peter G. 
Published: December 2021

AbstractATP-utilizing enzymes play key roles in hair bundles, the mechanically sensitive organelles of sensory hair cells in the inner ear. We used a fluorescent ATP analog, EDA-ATP-Cy3 (Cy3-ATP), to label ATP-binding proteins in two different preparations of unfixed hair-cell stereocilia of the mouse. In the first preparation, we lightly permeabilized dissected cochleas, then labeled them with Cy3-ATP. Hair cells and their stereocilia remained intact, and stereocilia tips in rows 1 and 2 were labeled particularly strongly with Cy3-ATP. In many cases, vanadate (Vi) traps nucleotides at the active site of myosin isoforms and presents nucleotide dissociation. Co-application with Vi enhanced the tip labeling, which is consistent with myosin isoforms being responsible. By contrast, the actin polymerization inhibitors latrunculin A and cytochalasin D had no effect, suggesting that actin turnover at stereocilia tips was not involved. Cy3-ATP labeling was substantially reduced—but did not disappear altogether—in mutant cochleas lacking MYO15A; by contrast, labeling remained robust in cochleas lacking MYO7A. In the second preparation, used to quantify Cy3-ATP labeling, we labeled vestibular stereocilia that had been adsorbed to glass, which demonstrated that tip labeling was higher in longer stereocilia. We found that tip signal was reduced by ~ 50% in Myo15ash2/sh2 stereocilia as compared to Myo15ash2/+stereocilia. These results suggest that MYO15A accounts for a substantial fraction of the Cy3-ATP tip labeling in vestibular hair cells, and so this novel preparation could be utilized to examine the control of MYO15A ATPase activity in situ.
Client Service Receipt Inventory as a standardised tool for measurement of socio-economic costs in the rare genetic disease population (CSRI-Ra)
Authors: Chung Claudia C. Y. , Fung Jasmine L. F. , Lui Adrian C. Y. , Chan Marcus C. Y. , Ng Yvette N. C. , Wong Wilfred H. S. , Lee So Lun , Knapp Martin , Chung Brian H. Y. 
Published: December 2021

AbstractThe measurement of costs is fundamental in healthcare decision-making, but it is often challenging. In particular, standardised methods have not been developed in the rare genetic disease population. A reliable and valid tool is critical for research to be locally meaningful yet internationally comparable. Herein, we sought to develop, contextualise, translate, and validate the Client Service Receipt Inventory for the RAre disease population (CSRI-Ra) to be used in cost-of-illness studies and economic evaluations for healthcare planning. Through expert panel discussions and focus group meetings involving 17 rare disease patients, carers, and healthcare and social care professionals from Hong Kong, we have developed the CSRI-Ra. Rounds of forward and backward translations were performed by bilingual researchers, and face validity and semantic equivalence were achieved through interviews and telephone communications with focus group participants and an additional of 13 healthcare professional and university students. Intra-class correlation coefficient (ICC) was used to assess criterion validity between CSRI-Ra and electronic patient record in a sample of 94 rare disease patients and carers, with overall ICC being 0.69 (95% CI 0.56–0.78), indicating moderate to good agreement. Following rounds of revision in the development, contextualisation, translation, and validation stages, the CSRI-Ra is ready for use in empirical research. The CSRI-Ra provides a sufficiently standardised yet adaptable method for collecting socio-economic data related to rare genetic diseases. This is important for near-term and long-term monitoring of the resource consequences of rare diseases, and it provides a tool for use in economic evaluations in the future, thereby helping to inform planning for efficient and effective healthcare. Adaptation of the CSRI-Ra to other populations would facilitate international research.
Intercellular interactions between mast cells and stromal fibroblasts obtained from canine cutaneous mast cell tumours
Authors: Pulz Lidia H. , Cordeiro Yonara G. , Huete Greice C. , Cadrobbi Karine G. , Rochetti Arina L. , Xavier Pedro L. P. , Nishiya Adriana Tomoko , de Freitas Silvio Henrique , Fukumasu Heidge , Strefezzi Ricardo F. 
Published: December 2021

AbstractMast cell tumours (MCTs) are the most frequent malignant skin neoplasm in dogs. Due to the difficulty in purifying large numbers of canine neoplastic mast cells, relatively little is known about their properties. A reproducible in vitro model is needed to increase the understanding about the phenotype and functional properties of neoplastic mast cells. In the present study, we describe the establishment of primary cocultures of neoplastic mast cells from canine cutaneous MCTs and cancer-associated fibroblasts. We confirmed the inability of canine neoplastic mast cells to remain viable for long periods in vitro without the addition of growth factors or in vivo passages in mice. Using a transwell system, we observed that mast cell viability was significantly higher when there is cell-to-cell contact in comparison to non-physical contact conditions and that mast cell viability was significantly higher in high-grade than in low-grade derived primary cultures. Moreover, the use of conditioned medium from co-cultured cells led to a significantly higher tumoral mast cell viability when in monoculture. Signalling mechanisms involved in these interactions might be attractive therapeutic targets to block canine MCT progression and deserve more in-depth investigations.
Metabolic profiling reveals nutrient preferences during carbon utilization in Bacillus species
Authors: Chang James D. , Vaughan Ellen E. , Liu Carmen Gu , Jelinski Joseph W. , Terwilliger Austen L. , Maresso Anthony W. 
Published: December 2021

AbstractThe genus Bacillus includes species with diverse natural histories, including free-living nonpathogenic heterotrophs such as B. subtilis and host-dependent pathogens such as B. anthracis (the etiological agent of the disease anthrax) and B. cereus, a cause of food poisoning. Although highly similar genotypically, the ecological niches of these three species are mutually exclusive, which raises the untested hypothesis that their metabolism has speciated along a nutritional tract. Here, we developed a pipeline for quantitative total assessment of the use of diverse sources of carbon for general metabolism to better appreciate the “culinary preferences” of three distinct Bacillus species, as well as related Staphylococcus aureus. We show that each species has widely varying metabolic ability to utilize diverse sources of carbon that correlated to their ecological niches. This approach was applied to the growth and survival of B. anthracis in a blood-like environment and find metabolism shifts from sugar to amino acids as the preferred source of energy. Finally, various nutrients in broth and host-like environments are identified that may promote or interfere with bacterial metabolism during infection.
Prediction of glaucoma severity using parameters from the electroretinogram
Authors: Sarossy Marc , Crowston Jonathan , Kumar Dinesh , Weymouth Anne , Wu Zhichao 
Published: December 2021

AbstractGlaucoma is an optic neuropathy that results in the progressive loss of retinal ganglion cells (RGCs), which are known to exhibit functional changes prior to cell loss. The electroretinogram (ERG) is a method that enables an objective assessment of retinal function, and the photopic negative response (PhNR) has conventionally been used to provide a measure of RGC function. This study sought to examine if additional parameters from the ERG (amplitudes of the a-, b-, i-wave, as well the trough between the b- and i-wave), a multivariate adaptive regression splines (MARS; a non-linear) model and achromatic stimuli could better predict glaucoma severity in 103 eyes of 55 individuals with glaucoma. Glaucoma severity was determined using standard automated perimetry and optical coherence tomography imaging. ERGs targeting the PhNR were recorded with a chromatic (red-on-blue) and achromatic (white-on-white) stimulus with the same luminance. Linear and MARS models were fitted to predict glaucoma severity using the PhNR only or all ERG markers, derived from chromatic and achromatic stimuli. Use of all ERG markers predicted glaucoma severity significantly better than the PhNR alone (P ≤ 0.02), and the MARS performed better than linear models when using all markers (P = 0.01), but there was no significant difference between the achromatic and chromatic stimulus models. This study shows that there is more information present in the photopic ERG beyond the conventional PhNR measure in characterizing RGC function.