bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flow estimation solely from image data through persistent homology analysis
Authors: Suzuki Anna , Miyazawa Miyuki , Minto James M. , Tsuji Takeshi , Obayashi Ippei , Hiraoka Yasuaki , Ito Takatoshi 
Published: September 2021

AbstractTopological data analysis is an emerging concept of data analysis for characterizing shapes. A state-of-the-art tool in topological data analysis is persistent homology, which is expected to summarize quantified topological and geometric features. Although persistent homology is useful for revealing the topological and geometric information, it is difficult to interpret the parameters of persistent homology themselves and difficult to directly relate the parameters to physical properties. In this study, we focus on connectivity and apertures of flow channels detected from persistent homology analysis. We propose a method to estimate permeability in fracture networks from parameters of persistent homology. Synthetic 3D fracture network patterns and their direct flow simulations are used for the validation. The results suggest that the persistent homology can estimate fluid flow in fracture network based on the image data. This method can easily derive the flow phenomena based on the information of the structure.
Development of an automated system to measure ion channel currents using a surface-modified gold probe
Authors: Hirano Minako , Tomita Masahisa , Takahashi Chikako , Kawashima Nobuyuki , Ide Toru 
Published: September 2021

AbstractArtificial lipid bilayer single-channel recording technique has been employed to determine the biophysical and pharmacological properties of various ion channels. However, its measurement efficiency is very low, as it requires two time-consuming processes: preparation of lipid bilayer membranes and incorporation of ion channels into the membranes. In order to address these problems, we previously developed a technique based on hydrophilically modified gold probes on which are immobilized ion channels that can be promptly incorporated into the bilayer membrane at the same time as the membrane is formed on the probes’ hydrophilic area. Here, we improved further this technique by optimizing the gold probe and developed an automated channel current measurement system. We found that use of probes with rounded tips enhanced the efficiency of channel current measurements, and introducing a hydrophobic area on the probe surface, beside the hydrophilic one, further increased measurement efficiency by boosting membrane stability. Moreover, we developed an automated measurement system using the optimized probes; it enabled us to automatically measure channel currents and analyze the effects of a blocker on channel activity. Our study will contribute to the development of high-throughput devices to identify drug candidates affecting ion channel activity.
Atomic-resolution STEM-EDS studies of cation ordering in Ti-Nb oxide crystals
Authors: Iijima Sumio , Ohnishi Ichiro , Liu Zheng 
Published: September 2021

AbstractTernary metal oxide compounds, such as Ti-Nb and Nb-W oxides, have renewed research interest in energy storage materials because these oxides contain multivalent metal ions that may be able to control the ion transport in solid lithium batteries. One of these oxides is Ti2Nb10O29, which is composed of metal–oxygen octahedra connected through corner-sharing and edge-sharing to form “block structures”. In the early 1970s Von Dreele and Cheetham proposed a metal-atoms ordering in this oxide crystal using Rietveld refined neutron powder diffraction method. Most recent studies on these oxides, however, have not considered cation ordering in evaluating the battery electrode materials. In this paper, by utilizing the latest scanning transmission electron microscopy combined with energy dispersive X-ray spectroscopy imaging technology, the cation chemical ordering in those oxide crystals was directly revealed at atomic resolution.
The gastric microbiota in patients with Crohn’s disease; a preliminary study
Authors: Ostrowski Jerzy , Kulecka Maria , Zawada Iwona , Żeber-Lubecka Natalia , Paziewska Agnieszka , Graca-Pakulska Katarzyna , Dąbkowski Krzysztof , Skubisz Karolina , Cybula Patrycja , Ambrożkiewicz Filip , Urasińska Elżbieta , Mikula Michał , Starzyńska Teresa 
Published: September 2021

AbstractThe gastric microbiota in Crohn’s disease (CD) has not been studied. The purpose of the study was to evaluate differences of stomach microbiota between CD patients and controls. DNA was extracted from gastric mucosal and fluid samples, from 24 CD patients and 19 controls. 16S rRNA gene sequencing identified 1511 operational taxonomic units (OTUs), of which 239 passed the low abundance and low variance filters. All but one CD patients were HP negative. Fifteen bacterial phyla were identified in at least one mucosal or fluid site. Of these, Bacteroidota and Firmicutes accounted for 70% of all phyla. Proteobacteria, Actinobacteriota, and Fusobacteriota combined accounted for 27%. There was significant difference in the relative abundance of Bacteroidota, Proteobacteria, Fusobacteriota, and Campilobacterota between CD patients and controls only in gastric corpus samples. In gastric liquid, there was a significant difference only in Actinobacteriota. Pairwise comparison identified 67 differentially abundant OTUs in at least one site. Of these, 13 were present in more than one comparison, and four differentiating OTUs (Neisseriaceae, Neisseria, Absconditabacteriales, and Microbacteriaceae) were identified at all tested sites. The results reveal significant changes in gastric microbial profiles (beta diversity, phylum, and individual taxa levels) between H. pylori-negative CD patients and controls.
TLR4-interactor with leucine-rich repeats (TRIL) is involved in diet-induced hypothalamic inflammation
Authors: Moura-Assis Alexandre , Nogueira Pedro A. S. , de-Lima-Junior Jose C. , Simabuco Fernando M. , Gaspar Joana M. , Donato Jr Jose , Velloso Licio A. 
Published: September 2021

AbstractObesity and high-fat diet (HFD) consumption result in hypothalamic inflammation and metabolic dysfunction. While the TLR4 activation by dietary fats is a well-characterized pathway involved in the neuronal and glial inflammation, the role of its accessory proteins in diet-induced hypothalamic inflammation remains unknown. Here, we demonstrate that the knockdown of TLR4-interactor with leucine-rich repeats (Tril), a functional component of TLR4, resulted in reduced hypothalamic inflammation, increased whole-body energy expenditure, improved the systemic glucose tolerance and protection from diet-induced obesity. The POMC-specific knockdown of Tril resulted in decreased body fat, decreased white adipose tissue inflammation and a trend toward increased leptin signaling in POMC neurons. Thus, Tril was identified as a new component of the complex mechanisms that promote hypothalamic dysfunction in experimental obesity and its inhibition in the hypothalamus may represent a novel target for obesity treatment.
Pleiotropic effects between cardiovascular disease risk factors and measures of cognitive and physical function in long-lived adults
Authors: Yudkovicz Julia J. , Minster Ryan L. , Barinas-Mitchell Emma , Christensen Kaare , Feitosa Mary , Barker Megan S. , Newman Anne B. , Kuipers Allison L. 
Published: September 2021

AbstractCardiovacular disease (CVD) is the leading cause of death among older adults and is often accompanied by functional decline. It is unclear what is driving this co-occurrence, but it may be behavioral, environmental and/or genetic. We used a family-based study to estimate the phenotypic and shared genetic correlation between CVD risk factors and physical and cognitive functional measures. Participants (n = 1,881) were from the Long Life Family Study, which enrolled families based on their exceptional longevity (sample mean age = 69.4 years, 44% female). Cardiovascular disease risk factors included carotid vessel measures [intima-media thickness and inter-adventitial diameter], obesity [body mass index (BMI) and waist circumference], and hypertension [systolic and diastolic blood pressures]. Function was measured in the physical [gait speed, grip strength, chair stand] and cognitive [digital symbol substitution test, retained and working memory, semantic fluency, and trail making tests] domains. We used SOLAR to estimate the genetic, environmental, and phenotypic correlation between each pair adjusting for age, age2, sex, field center, smoking, height, and weight. There were significant phenotypic correlations (range |0.05–0.22|) between CVD risk factors and physical and cognitive function (all P < 0.05). Most significant genetic correlations (range |0.21–0.62|) were between CVD risk factorsand cognitive function, although BMI and waist circumference had significant genetic correlation with gait speed and chair stand time (range |0.29–0.53|; all P < 0.05). These results suggest that CVD risk factors may share a common genetic-and thus, biologic-basis with both cognitive and physical function. This is particularly informative for research into the genetic determinants of chronic disease.
Differentially expressed genes in the femur cartilage transcriptome clarify the understanding of femoral head separation in chickens
Authors: Hul Ludmila Mudri , Ibelli Adriana Mércia Guaratini , Savoldi Igor Ricardo , Marcelino Débora Ester Petry , Fernandes Lana Teixeira , Peixoto Jane Oliveira , Cantão Maurício Egídio , Higa Roberto Hiroshi , Giachetto Poliana Fernanda , Coutinho Luiz Lehmann , Ledur Mônica Corrêa 
Published: September 2021

AbstractLocomotor problems are among one of the main concerns in the current poultry industry, causing major economic losses and affecting animal welfare. The most common bone anomalies in the femur are dyschondroplasia, femoral head separation (FHS), and bacterial chondronecrosis with osteomyelitis (BCO), also known as femoral head necrosis (FHN). The present study aimed to identify differentially expressed (DE) genes in the articular cartilage (AC) of normal and FHS-affected broilers by RNA-Seq analysis. In the transcriptome analysis, 12,169 genes were expressed in the femur AC. Of those, 107 genes were DE (FDR < 0.05) between normal and affected chickens, of which 9 were downregulated and 98 were upregulated in the affected broilers. In the gene-set enrichment analysis using the DE genes, 79 biological processes (BP) were identified and were grouped into 12 superclusters. The main BP found were involved in the response to biotic stimulus, gas transport, cellular activation, carbohydrate-derived catabolism, multi-organism regulation, immune system, muscle contraction, multi-organism process, cytolysis, leukocytes and cell adhesion. In this study, the first transcriptome analysis of the broilers femur articular cartilage was performed, and a set of candidate genes (AvBD1,AvBD2,ANK1,EPX,ADA,RHAG) that could trigger changes in the broiler´s femoral growth plate was identified. Moreover, these results could be helpful to better understand FHN in chickens and possibly in humans.
Global analysis of lysine acetylation in soybean leaves
Authors: Li Geng , Zheng Bin , Zhao Wei , Ren Tinghu , Zhang Xinghui , Ning Tangyuan , Liu Peng 
Published: September 2021

AbstractProtein lysine acetylation (Kac) is an important post-translational modification in both animal and plant cells. Global Kac identification has been performed at the proteomic level in various species. However, the study of Kac in oil and resource plant species is relatively limited. Soybean is a globally important oil crop and resouce plant. In the present study, lysine acetylome analysis was performed in soybean leaves with proteomics techniques. Various bioinformatics analyses were performed to illustrate the structure and function of these Kac sites and proteins. Totally, 3148 acetylation sites in 1538 proteins were detected. Motif analysis of these Kac modified peptides extracted 17 conserved motifs. These Kac modified protein showed a wide subcellular location and functional distribution. Chloroplast is the primary subcellular location and cellular component where Kac proteins were localized. Function and pathways analyses indicated a plenty of biological processes and metabolism pathways potentially be influenced by Kac modification. Ribosome activity and protein biosynthesis, carbohydrate and energy metabolism, photosynthesis and fatty acid metabolism may be regulated by Kac modification in soybean leaves. Our study suggests Kac plays an important role in soybean physiology and biology, which is an available resource and reference of Kac function and structure characterization in oil crop and resource plant, as well as in plant kingdom.
Tracking of the biochemical changes upon pleomorphic adenoma progression using vibrational microspectroscopy
Authors: Paluszkiewicz Czesława , Roman Maciej , Piergies Natalia , Pięta Ewa , Woźniak Monika , Guidi Mariangela Cestelli , Miśkiewicz-Orczyk Katarzyna , Marków Magdalena , Ścierski Wojciech , Misiołek Maciej , Drozdzowska Bogna , Kwiatek Wojciech M. 
Published: September 2021

AbstractHead and neck tumors can be very challenging to treat because of the risk of problems or complications after surgery. Therefore, prompt and accurate diagnosis is extremely important to drive appropriate treatment decisions, which may reduce the chance of recurrence. This paper presents the original research exploring the feasibility of Fourier transform infrared (FT-IR) and Raman spectroscopy (RS) methods to investigate biochemical alterations upon the development of the pleomorphic adenoma. Principal component analysis (PCA) was used for a detailed assessment of the observed changes and to determine the spectroscopic basis for salivary gland neoplastic pathogenesis. It is implied that within the healthy margin, as opposed to the tumoral tissue, there are parts that differ significantly in lipid content. This observation shed new light on the crucial role of lipids in tissue physiology and tumorigenesis. Thus, a novel approach that eliminates the influence of lipids on the elucidation of biochemical changes is proposed. The performed analysis suggests that the highly heterogeneous healthy margin contains more unsaturated triacylglycerols, while the tumoral section is rich in proteins. The difference in protein content was also observed for these two tissue types, i.e. the healthy tissue possesses more proteins in the anti-parallel β-sheet conformation, whereas the tumoral tissue is dominated by proteins rich in unordered random coils. Furthermore, the pathogenic tissue shows a higher content of carbohydrates and reveals noticeable differences in nucleic acid content. Finally, FT-IR and Raman spectroscopy methods were proposed as very promising methods in the discrimination of tumoral and healthy tissues of the salivary gland.
Occupational exposure and markers of genetic damage, systemic inflammation and lung function: a Danish cross-sectional study among air force personnel
Authors: Andersen Maria Helena Guerra , Saber Anne Thoustrup , Frederiksen Marie , Clausen Per Axel , Sejbaek Camilla Sandal , Hemmingsen Caroline Hallas , Ebbehøj Niels E. , Catalán Julia , Aimonen Kukka , Koivisto Joonas , Loft Steffen , Møller Peter , Vogel Ulla 
Published: September 2021

AbstractAir force ground crew personnel are potentially exposed to fuels and lubricants, as raw materials, vapours and combustion exhaust emissions, during operation and maintenance of aircrafts. This study investigated exposure levels and biomarkers of effects for employees at a Danish air force military base. We enrolled self-reported healthy and non-smoking employees (n = 79) and grouped them by exposure based on job function, considered to be potentially exposed (aircraft engineers, crew chiefs, fuel operators and munition specialists) or as reference group with minimal occupational exposure (avionics and office workers). We measured exposure levels to polycyclic aromatic hydrocarbons (PAHs) and organophosphate esters (OPEs) by silicone bands and skin wipes (PAHs only) as well as urinary excretion of PAH metabolites (OH-PAHs). Additionally, we assessed exposure levels of ultrafine particles (UFPs) in the breathing zone for specific job functions. As biomarkers of effect, we assessed lung function, plasma levels of acute phase inflammatory markers, and genetic damage levels in peripheral blood cells. Exposure levels of total PAHs, OPEs and OH-PAHs did not differ between exposure groups or job functions, with low correlations between PAHs in different matrices. Among the measured job functions, the UFP levels were higher for the crew chiefs. The exposure level of the PAH fluorene was significantly higher for the exposed group than the reference group (15.9 ± 23.7 ng/g per 24 h vs 5.28 ± 7.87 ng/g per 24 h, p = 0.007), as was the OPE triphenyl phosphate (305 ± 606 vs 19.7 ± 33.8 ng/g per 24 h, p = 0.011). The OPE tris(1,3-dichlor-2-propyl)phosphate had a higher mean in the exposed group (60.7 ± 135 ng/g per 24 h) compared to the reference group (8.89 ± 15.7 ng/g per 24 h) but did not reach significance. No evidence of effects for biomarkers of systemic inflammation, genetic damage or lung function was found. Overall, our biomonitoring study show limited evidence of occupational exposure of air force ground crew personnel to UFPs, PAHs and OPEs. Furthermore, the OH-PAHs and the assessed biomarkers of early biological effects did not differ between exposed and reference groups.
Association between telomere length and hepatic fibrosis in non-alcoholic fatty liver disease
Authors: Shin Hee Kyung , Park Jeong Hwan , Yu Jung Hwan , Jin Young-Joo , Suh Young Ju , Lee Jin-Woo , Kim Won ,   The Korean Nonalcoholic Fatty Liver Study Group (KNSG)
Published: September 2021

AbstractTelomere length has been linked to the prevalence and progression of metabolic disease. However, clinical implications of telomere length in biopsy-proven non-alcoholic fatty liver disease (NAFLD) patients remain unclear. Therefore, this study aimed to investigate the association of telomere length with the histological severity of NAFLD. The cross-sectional data derived from the prospectively enrolled Boramae NAFLD registry (n = 91) were analyzed. The liver tissues and clinical information were obtained from both NAFLD patients and non-NAFLD subjects. Binary logistic regression was performed to identify the independent association between telomere length and the histological severity of NAFLD. A total of 83 subjects with or without biopsy-proven NAFLD were included for analysis: non-NAFLD in 23 (27.7%), non-alcoholic fatty liver in 15 (18.1%), and non-alcoholic steatohepatitis (NASH) in 45 (54.2%). Telomere length measured from liver tissues showed a strong negative correlation (p < 0.001) with age, regardless of NAFLD status. Therefore, telomere length was corrected for age. Age-adjusted telomere length than decreased gradually with an increasing severity of fibrosis in patients with NAFLD (p < 0.028). In multivariate analysis, age-adjusted telomere length (odds ratio [OR] 0.59; 95% CI 0.37–0.92; p = 0.019) and high-density lipoprotein cholesterol (OR 0.94; 95% CI 0.80–0.99; p = 0.039) were independently associated with significant fibrosis. The age-adjusted telomere length tends to decrease along with the fibrosis stage of NAFLD. In particular, among the histological components of NAFLD, fibrosis severity seems to be related to telomere length in the liver.
Population genetic structure of European wildcats inhabiting the area between the Dinaric Alps and the Scardo-Pindic mountains
Authors: Urzi Felicita , Šprem Nikica , Potočnik Hubert , Sindičić Magda , Konjević Dean , Ćirović Duško , Rezić Andrea , Duniš Luka , Melovski Dime , Buzan Elena 
Published: September 2021

AbstractHabitat fragmentation and loss have contributed significantly to the demographic decline of European wildcat populations and hybridization with domestic cats poses a threat to the loss of genetic purity of the species. In this study we used microsatellite markers to analyse genetic variation and structure of the wildcat populations from the area between the Dinaric Alps and the Scardo-Pindic mountains in Slovenia, Croatia, Serbia and North Macedonia. We also investigated hybridisation between populations of wildcats and domestic cats in the area. One hundred and thirteen samples from free-leaving European wildcats and thirty-two samples from domestic cats were analysed. Allelic richness across populations ranged from 3.61 to 3.98. The observed Ho values ranged between 0.57 and 0.71. The global FST value for the four populations was 0.080 (95% CI 0.056–0.109) and differed significantly from zero (P < 0.001). The highest FST value was observed between the populations North Macedonia and Slovenia and the lowest between Slovenia and Croatia. We also found a signal for the existence of isolation by distance between populations. Our results showed that wildcats are divided in two genetic clusters largely consistent with a geographic division into a genetically diverse northern group (Slovenia, Croatia) and genetically eroded south-eastern group (Serbia, N. Macedonia). Hybridisation rate between wildcats and domestic cats varied between 13% and 52% across the regions.
Plasmon resonances management of meta-mirror for combining radar cross section (RCS) reduction and specular reflection with frequency selectivity
Authors: Pesarakloo Ali , Oruji Alireza 
Published: September 2021

AbstractIn this paper using Plasmon Resonances Management (PRM), a bi-functional meta-mirror is proposed in which, the meta-mirror can obtain two opposite properties in two different frequency ranges. In this method, an anisotropic unit cell with polarization conversion property is modified to have two plasmon resonances in both symmetric and anti-symmetric planes in a specific frequency. This allows the unit cell to have the property of unchanged polarization in that frequency. The meta-mirror is composed of this modified unit cell and its mirror as a chessboard arrangement and the incident wave on the meta-mirror is reflected as in-phase in that specific frequency i.e. specular reflection, while as out-of-phase in other frequencies i.e. RCS reduction. The designed meta-mirror in this paper demonstrates the RCS reduction in two side-bands from 4 to 9 GHz and 10.8 to 14.8 GHz while behaving as a specular reflection in the frequency around 10 GHz.
Taxonomic bias in AMP prediction of invertebrate peptides
Authors: Rádai Zoltán , Kiss Johanna , Nagy Nikoletta A. 
Published: September 2021

AbstractInvertebrate antimicrobial peptides (AMPs) are at the forefront in the search for agents of therapeutic utility against multi-resistant microbial pathogens, and in recent years substantial advances took place in the in silico prediction of antimicrobial function of amino acid sequences. A yet neglected aspect is taxonomic bias in the performance of these tools. Owing to differences in the prediction algorithms and used training data sets between tools, and phylogenetic differences in sequence diversity, physicochemical properties and evolved biological functions of AMPs between taxa, notable discrepancies may exist in performance between the currently available prediction tools. Here we tested if there is taxonomic bias in the prediction power in 10 tools with a total of 20 prediction algorithms in 19 invertebrate taxa, using a data set containing 1525 AMP and 3050 non-AMP sequences. We found that most of the tools exhibited considerable variation in performance between tested invertebrate groups. Based on the per-taxa performances and on the variation in performances across taxa we provide guidance in choosing the best-performing prediction tool for all assessed taxa, by listing the highest scoring tool for each of them.