bluuebunny/crossref_metadata_2025_split huggingface dataset:
A primer set for the rapid isolation of scFv fragments against cell surface antigens from immunised rats
Authors: Nannini Francesco , Parekh Farhaan , Wawrzyniecka Patrycja , Mekkaoui Leila , Righi Matteo , Dastjerdi Fatemeh V. , Yeung Jenny , Roddie Claire , Bai Yuchen , Ma Biao , Ferrari Mathieu , Onuoha Shimobi , Chester Kerry , Pule Martin 
Published: November 2020

AbstractAntibody phage display is a powerful platform for discovery of clinically applicable high affinity monoclonal antibodies against a broad range of targets. Libraries generated from immunized animals offer the advantage of in vivo affinity-maturation of V regions prior to library generation. Despite advantages, few studies have described isolation of antibodies from rats using immune phage display. In our study, we describe a novel primer set, covering the full rat heavy chain variable and kappa light chain variable regions repertoire for the generation of an unbiased immune libraries. Since the immune repertoire of rats is poorly understood, we first performed a deep sequencing analysis of the V(D)J regions of VH and VLK genes, demonstrating the high abundance of IGVH2 and IGVH5 families for VH and IGVLK12 and IGVLK22 for VLK. The comparison of gene’s family usage in naïve rats have been used to validate the frequency’s distribution of the primer set, confirming the absence of PCR-based biases. The primers were used to generate and assemble a phage display library from human CD160-vaccinated rats. CD160 represents a valid therapeutic target as it has been shown to be expressed on chronic lymphocytic leukaemia cells and on the surface of newly formed vessels. We utilised a novel phage display panning strategy to isolate a high affinity pool (KD range: 0.399–233 nM) of CD160 targeting monoclonal antibodies. Subsequently, identified binders were tested for function as third generation Chimeric Antigen Receptors (CAR) T cells demonstrating specific cytolytic activity. Our novel primer set coupled with a streamlined strategy for phage display panning enable the rapid isolation and identification of high affinity antibodies from immunised rats. The therapeutic utility of these antibodies was demonstrated in CAR format.
Plasma extracellular vesicle miRNAs as potential biomarkers of superstimulatory response in cattle
Authors: Gad Ahmed , Sánchez José María , Browne John A. , Nemcova Lucie , Laurincik Jozef , Prochazka Radek , Lonergan Pat 
Published: November 2020

AbstractThe ability to predict superstimulatory response would be a beneficial tool in assisted reproduction. Using small RNAseq technology, we profiled extracellular vesicle microRNA (EV-miRNA) abundance in the blood plasma of heifers exhibiting variable responses to superstimulation. Estrous synchronized crossbred beef heifers (n = 25) were superstimulated and blood samples were collected from each heifer on Day 7 of consecutive unstimulated (U) and superstimulated (S) cycles. A subset of high (H) and low (L) responders was selected depending on their response to superstimulation and EV-miRNA profiles were analysed at both time-points in each heifer. Approximately 200 known miRNAs were detected in each sample with 144 commonly detected in all samples. A total of 12 and 14 miRNAs were dysregulated in UH vs. UL and in SH vs. SL heifers, respectively. Interestingly, miR-206 and miR-6517 exhibited the same differential expression pattern in H compared to L heifers both before and after superstimulation. Pathway analysis indicated that circadian rhythm and signaling pathways were among the top pathways enriched with genes targeted by dysregulated miRNAs in H vs. L responding heifers. In conclusion, heifers with divergent ovarian responses exhibited differential expression of plasma EV-miRNAs which may be used as a potential biomarker to predict superstimulation response.
Fabrication of silane-grafted graphene oxide and its effect on the structural, thermal, mechanical, and hysteretic behavior of polyurethane
Authors: Lee Joo Hyung , Kim Seong Hun 
Published: November 2020

AbstractIncorporation of nanofillers into polyurethane (PU) is a promising technique for enhancing its thermal and mechanical properties. Silane grafting has been used as a surface treatment for the functionalization of graphene oxide (GO) with numerous reactive sites dispersed on its basal plane and edge. In this study, amine-grafted GO was prepared using silanization of GO with (3-aminopropyl)triethoxysilane. The functionalized graphene oxide (fGO) was characterized by Fourier transform infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy. Next, it was introduced in PU fabricated using polycaprolactone diol, castor oil, and hexamethylene diisocyanate. The fGO–PU nanocomposites were in turn characterized by FT-IR, X-ray diffraction, scanning electron microscopy, differential scanning calorimetry, thermogravimetric analysis, and a universal testing machine. The results obtained from these analyses showed changes in structural thermal properties, as well as improved thermal stability and mechanical properties because of the strong interfacial adhesion between the fGO and the PU matrix.
Mapping the genetic basis of diabetes mellitus in the Australian Burmese cat (Felis catus)
Authors: Samaha Georgina , Wade Claire M. , Beatty Julia , Lyons Leslie A. , Fleeman Linda M. , Haase Bianca 
Published: November 2020

AbstractDiabetes mellitus, a common endocrinopathy affecting domestic cats, shares many clinical and pathologic features with type 2 diabetes in humans. In Australia and Europe, diabetes mellitus is almost four times more common among Burmese cats than in other breeds. As a genetically isolated population, the diabetic Australian Burmese cat provides a spontaneous genetic model for studying diabetes mellitus in humans. Studying complex diseases in pedigreed breeds facilitates tighter control of confounding factors including population stratification, allelic frequencies and environmental heterogeneity. We used the feline SNV array and whole genome sequence data to undertake a genome wide-association study and runs of homozygosity analysis, of a case–control cohort of Australian and European Burmese cats. Our results identified diabetes-associated haplotypes across chromosomes A3, B1 and E1 and selective sweeps across the Burmese breed on chromosomes B1, B3, D1 and D4. The locus on chromosome B1, common to both analyses, revealed coding and splice region variants in candidate genes,ANK1, EPHX2andLOXL2,implicated in diabetes mellitus and lipid dysregulation. Mapping this condition in Burmese cats has revealed a polygenic spectrum, implicating loci linked to pancreatic beta cell dysfunction, lipid dysregulation and insulin resistance in the pathogenesis of diabetes mellitus in the Burmese cat.
Increase in temperature enriches heat tolerant taxa in Aedes aegypti midguts
Authors: Onyango Gorreti Maria , Bialosuknia M. Sean , Payne F. Anne , Mathias Nicholas , Ciota T. Alexander , Kramer D. Laura 
Published: November 2020

AbstractInsect midgut microbial symbionts have been considered as an integral component in thermal adaptation due to their differential thermal sensitivity. Altered midgut microbial communities can influence both insect physiology and competence for important vector-borne pathogens. This study sought to gain insights into how Aedes aegypti midgut microbes and life history traits are affected by increase in baseline diurnal temperature. Increase in temperature resulted in the enrichment of specific taxa with Bacillus being the most enriched. Bacillus is known to be heat tolerant. It also resulted in a dissimilar microbial assemblage (Bray–Curtis Index, PERMANOVA, F = 2.2063; R2 = 0.16706; P = 0.002) and reduced survivorship (Log-rank [Mantel-Cox] test, Chi-square = 35.66 df = 5, P < 0.0001). Blood meal intake resulted in proliferation of pathogenic bacteria such as Elizabethkingia in the midgut of the mosquitoes. These results suggest that alteration of temperature within realistic parameters such as 2 °C for Ae. aegypti in nature may impact the midgut microbiome favoring specific taxa that could alter mosquito fitness, adaptation and vector–pathogen interactions.
Genetic and comparative mapping of Lupinus luteus L. highlight syntenic regions with major orthologous genes controlling anthracnose resistance and flowering time
Authors: Lichtin Nicole , Salvo-Garrido Haroldo , Till Bradley , Caligari Peter D. S. , Rupayan Annally , Westermeyer Fernando , Olivos Marcos 
Published: November 2020

AbstractAnthracnose susceptibility and ill-adapted flowering time severely affect Lupinus luteus yield, which has high seed protein content, is excellent for sustainable agriculture, but requires genetic improvement to fulfil its potential. This study aimed to (1) develop a genetic map; (2) define collinearity and regions of synteny with Lupinus angustifolius; and (3) map QTLs/candidate genes for anthracnose resistant and flowering time. A few linkage groups/genomic regions tended to be associated with segregation distortion, but did not affect the map. The developed map showed collinearity, and syntenic regions with L. angustifolius. Major QTLs were mapped in syntenic regions. Alleles from the wild parent and cultivar, explained 75% of the phenotypic variance for anthracnose resistance and 83% for early flowering, respectively. Marker sequences flanking the QTLs showed high homology with the Lanr1 gene and Flowering-locus-T of L. angustifolius. This suggests orthologous genes for both traits in the L. luteus genome. The findings are remarkable, revealing the potential to combine early flowering/anthracnose resistant in fulfilling yield capacity in L. luteus, and can be a major strategy in the genetic improvement and usage of this species for sustainable protein production. Allele sequences and PCR-marker tagging of these genes are being applied in marker assisted selection.
Deep learning approach for predicting functional Z-DNA regions using omics data
Authors: Beknazarov Nazar , Jin Seungmin , Poptsova Maria 
Published: November 2020

AbstractComputational methods to predict Z-DNA regions are in high demand to understand the functional role of Z-DNA. The previous state-of-the-art method Z-Hunt is based on statistical mechanical and energy considerations about B- to Z-DNA transition using sequence information. Z-DNA CHiP-seq experiment results showed little overlap with Z-Hunt predictions implying that sequence information only is not sufficient to explain emergence of Z-DNA at different genomic locations. Adding epigenetic and other functional genomic mark-ups to DNA sequence level can help revealing the functional Z-DNA sites. Here we take advantage of the deep learning approach that can analyze and extract information from large volumes of molecular biology data. We developed a machine learning approach DeepZ that aggregates information from genome-wide maps of epigenetic markers, transcription factor and RNA polymerase binding sites, and chromosome accessibility maps. With the developed model we not only verify the experimental Z-DNA predictions, but also generate the whole-genome annotation, introducing new possible Z-DNA regions, which have not yet been found in experiments and can be of interest to the researchers from various fields.
Inhibition of inflammatory signaling in Pax5 mutant cells mitigates B-cell leukemogenesis
Authors: Isidro-Hernández Marta , Mayado Andrea , Casado-García Ana , Martínez-Cano Jorge , Palmi Chiara , Fazio Grazia , Orfao Alberto , Ribera Jordi , Ribera Josep Maria , Zamora Lurdes , Raboso-Gallego Javier , Blanco Oscar , Alonso-López Diego , De Las Rivas Javier , Jiménez Rafael , García Criado Francisco Javier , García Cenador María Begoña , Ramírez-Orellana Manuel , Cazzaniga Giovanni , Cobaleda César , Vicente-Dueñas Carolina , Sánchez-García Isidro 
Published: November 2020

AbstractPAX5 is one of the most frequently mutated genes in B-cell acute lymphoblastic leukemia (B-ALL), and children with inherited preleukemic PAX5 mutations are at a higher risk of developing the disease. Abnormal profiles of inflammatory markers have been detected in neonatal blood spot samples of children who later developed B-ALL. However, how inflammatory signals contribute to B-ALL development is unclear. Here, we demonstrate that Pax5 heterozygosis, in the presence of infections, results in the enhanced production of the inflammatory cytokine interleukin-6 (IL-6), which appears to act in an autocrine fashion to promote leukemia growth. Furthermore, in vivo genetic downregulation of IL-6 in these Pax5 heterozygous mice retards B-cell leukemogenesis, and in vivo pharmacologic inhibition of IL-6 with a neutralizing antibody in Pax5 mutant mice with B-ALL clears leukemic cells. Additionally, this novel IL–6 signaling paradigm identified in mice was also substantiated in humans. Altogether, our studies establish aberrant IL6 expression caused by Pax5 loss as a hallmark of Pax5-dependent B-ALL and the IL6 as a therapeutic vulnerability for B-ALL characterized by PAX5 loss.
Spatial accessibility of general inpatient care in Germany: an analysis of surgery, internal medicine and neurology
Authors: Bauer Jan , Klingelhöfer Doris , Maier Werner , Schwettmann Lars , Groneberg David A. 
Published: November 2020

AbstractImproving spatial accessibility to hospitals is a major task for health care systems which can be facilitated using recent methodological improvements of spatial accessibility measures. We used the integrated floating catchment area (iFCA) method to analyze spatial accessibility of general inpatient care (internal medicine, surgery and neurology) on national level in Germany determining an accessibility index (AI) by integrating distances, hospital beds and morbidity data. The analysis of 358 million distances between hospitals and population locations revealed clusters of lower accessibility indices in areas in north east Germany. There was a correlation of urbanity and accessibility up to r = 0.31 (p < 0.001). Furthermore, 10% of the population lived in areas with significant clusters of low spatial accessibility for internal medicine and surgery (neurology: 20%). The analysis revealed the highest accessibility for heart failure (AI = 7.33) and the lowest accessibility for stroke (AI = 0.69). The method applied proofed to reveal important aspects of spatial accessibility i.e. geographic variations that need to be addressed. However, for the majority of the German population, accessibility of general inpatient care was either high or at least not significantly low, which suggests rather adequate allocation of hospital resources for most parts of Germany.
Genetic profiling of Vietnamese population from large-scale genomic analysis of non-invasive prenatal testing data
Authors: Tran Ngoc Hieu , Vo Thanh Binh , Nguyen Van Thong , Tran Nhat-Thang , Trinh Thu-Huong Nhat , Pham Hong-Anh Thi , Dao Thi Hong Thuy , Nguyen Ngoc Mai , Van Yen-Linh Thi , Tran Vu Uyen , Vu Hoang Giang , Bui Quynh-Tram Nguyen , Vo Phuong-Anh Ngoc , Nguyen Huu Nguyen , Nguyen Quynh-Tho Thi , Do Thanh-Thuy Thi , Lam Nien Vinh , Ngoc Phuong Cao Thi , Truong Dinh Kiet , Nguyen Hoai-Nghia , Giang Hoa , Phan Minh-Duy 
Published: November 2020

AbstractThe under-representation of several ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in many populations. Cost and technology limitations remain the challenges in performing large-scale genome sequencing projects in many developing countries, including Vietnam. As one of the most rapidly adopted genetic tests, non-invasive prenatal testing (NIPT) data offers an alternative untapped resource for genetic studies. Here we performed a large-scale genomic analysis of 2683 pregnant Vietnamese women using their NIPT data and identified a comprehensive set of 8,054,515 single-nucleotide polymorphisms, among which 8.2% were new to the Vietnamese population. Our study also revealed 24,487 disease-associated genetic variants and their allele frequency distribution, especially 5 pathogenic variants for prevalent genetic disorders in Vietnam. We also observed major discrepancies in the allele frequency distribution of disease-associated genetic variants between the Vietnamese and other populations, thus highlighting a need for genome-wide association studies dedicated to the Vietnamese population. The resulted database of Vietnamese genetic variants, their allele frequency distribution, and their associated diseases presents a valuable resource for future genetic studies.
Force–velocity profile during vertical jump cannot be assessed using only bodyweight jump and isometric maximal voluntary contraction tasks
Authors: Šarabon Nejc , Kozinc Žiga , Marković Goran 
Published: November 2020

AbstractRecently, the two-point method of force–velocity (F–V) profiling of multi-joint human movements has been introduced and validated. In this study, we investigated the validity of estimating the jumping F–V profile using only bodyweight jump and isometric maximal voluntary contraction (MVC) task. Participants (n = 30) performed 3 repetitions of squat (SJ) and counter-movement jumps (CMJ), each at loads that were progressively increased by 10 kg increments, with the number of loads depending on the individual’s ability. Then, 3 isometric MVC trials were performed in 3 knee angles (30°, 60° and 90°). F–V profiling of SJ and CMJ were performed using the multiple-point method, the two-point method, and the novel Jump-MVC method. The results showed poor to fair validity of the novel Jump-MVC method for assessing jumping F–V profile (most ICC < 0.5, most CV > 10%, significant systematic bias present, and the presence of proportional bias). The exception was the estimation of theoretical maximal power, which was highly valid for both SJ and CMJ (ICC = 0.91–0.95; CV = 5.0–6.3%). In contrast, validity of the two-point method was excellent (all ICC > 0.90; CV = 2–6%). Although additional studies are needed, present results suggest that the F–V profiling of vertical jumps should be performed using the two-point method with distal loads.
Metabolite activity in the anterior cingulate cortex during a painful stimulus using functional MRS
Authors: Archibald J. , MacMillan E. L. , Graf C. , Kozlowski P. , Laule C. , Kramer J. L. K. 
Published: November 2020

AbstractTo understand neurochemical brain responses to pain, proton magnetic resonance spectroscopy (1H-MRS) is used in humans in vivo to examine various metabolites. Recent MRS investigations have adopted a functional approach, where acquisitions of MRS are performed over time to track task-related changes. Previous studies suggest glutamate is of primary interest, as it may play a role during cortical processing of noxious stimuli. The objective of this study was to examine the metabolic effect (i.e., glutamate) in the anterior cingulate cortex during noxious stimulation using fMRS. The analysis addressed changes in glutamate and glutamate + glutamine (Glx) associated with the onset of pain, and the degree by which fluctuations in metabolites corresponded with continuous pain outcomes. Results suggest healthy participants undergoing tonic noxious stimulation demonstrated increased concentrations of glutamate and Glx at the onset of pain. Subsequent reports of pain were not accompanied by corresponding changes in glutamate of Glx concentrations. An exploratory analysis on sex revealed large effect size changes in glutamate at pain onset in female participants, compared with medium-sized effects in male participants. We propose a role for glutamate in the ACC related to the detection of a noxious stimulus.
Anisotropic optical properties of single Si2Te3 nanoplates
Authors: Chen Jiyang , Bhattarai Romakanta , Cui Jingbiao , Shen Xiao , Hoang Thang 
Published: November 2020

AbstractWe report a combined experimental and computational study of the optical properties of individual silicon telluride (Si2Te3) nanoplates. The p-type semiconductor Si2Te3 has a unique layered crystal structure with hexagonal closed-packed Te sublattices and Si–Si dimers occupying octahedral intercalation sites. The orientation of the silicon dimers leads to unique optical and electronic properties. Two-dimensional Si2Te3 nanoplates with thicknesses of hundreds of nanometers and lateral sizes of tens of micrometers are synthesized by a chemical vapor deposition technique. At temperatures below 150 K, the Si2Te3 nanoplates exhibit a direct band structure with a band gap energy of 2.394 eV at 7 K and an estimated free exciton binding energy of 150 meV. Polarized reflection measurements at different temperatures show anisotropy in the absorption coefficient due to an anisotropic orientation of the silicon dimers, which is in excellent agreement with theoretical calculations of the dielectric functions. Polarized Raman measurements of single Si2Te3 nanoplates at different temperatures reveal various vibrational modes, which agree with density functional perturbation theory calculations. The unique structural and optical properties of nanostructured Si2Te3 hold great potential applications in optoelectronics and chemical sensing.
An iron corrosion-assisted H2-supplying system: a culture method for methanogens and acetogens under low H2 pressures
Authors: Kato Souichiro , Takashino Motoko , Igarashi Kensuke , Mochimaru Hanako , Mayumi Daisuke , Tamaki Hideyuki 
Published: November 2020

AbstractH2 is an important fermentation intermediate in anaerobic environments. Although H2 occurs at very low partial pressures in the environments, the culture and isolation of H2-utilizing microorganisms is usually carried out under very high H2 pressures, which might have hampered the discovery and understanding of microorganisms adapting to low H2 environments. Here we constructed a culture system designated the “iron corrosion-assisted H2-supplying (iCH) system” by connecting the gas phases of two vials (one for the iron corrosion reaction and the other for culturing microorganisms) to achieve cultures of microorganisms under low H2 pressures. We conducted enrichment cultures for methanogens and acetogens using rice paddy field soil as the microbial source. In the enrichment culture of methanogens under canonical high H2 pressures, only Methanobacterium spp. were enriched. By contrast, Methanocella spp. and Methanoculleus spp., methanogens adapting to low H2 pressures, were specifically enriched in the iCH cultures. We also observed selective enrichment of acetogen species by the iCH system (Acetobacterium spp. and Sporomusa spp.), whereas Clostridium spp. predominated in the high H2 cultures. These results demonstrate that the iCH system facilitates culture of anaerobic microorganisms under low H2 pressures, which will enable the selective culture of microorganisms adapting to low H2 environments.