bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simple capacitor-switch model of excitatory and inhibitory neuron with all parts biologically explained allows input fire pattern dependent chaotic oscillations
Authors: Cejnar Pavel , Vyšata Oldřich , Kukal Jaromír , Beránek Martin , Vališ Martin , Procházka Aleš 
Published: April 2020

AbstractDue to known information processing capabilities of the brain, neurons are modeled at many different levels. Circuit theory is also often used to describe the function of neurons, especially in complex multi-compartment models, but when used for simple models, there is no subsequent biological justification of used parts. We propose a new single-compartment model of excitatory and inhibitory neuron, the capacitor-switch model of excitatory and inhibitory neuron, as an extension of the existing integrate-and-fire model, preserving the signal properties of more complex multi-compartment models. The correspondence to existing structures in the neuronal cell is then discussed for each part of the model. We demonstrate that a few such inter-connected model units are capable of acting as a chaotic oscillator dependent on fire patterns of the input signal providing a complex deterministic and specific response through the output signal. The well-known necessary conditions for constructing a chaotic oscillator are met for our presented model. The capacitor-switch model provides a biologically-plausible concept of chaotic oscillator based on neuronal cells.
Exploring the fitness benefits of genome reduction in Escherichia coli by a selection-driven approach
Authors: Vernyik Viktor , Karcagi Ildikó , Tímár Edit , Nagy István , Györkei Ádám , Papp Balázs , Györfy Zsuzsanna , Pósfai György 
Published: April 2020

AbstractArtificial simplification of bacterial genomes is thought to have the potential to yield cells with reduced complexity, enhanced genetic stability, and improved cellular economy. Of these goals, economical gains, supposedly due to the elimination of superfluous genetic material, and manifested in elevated growth parameters in selected niches, have not yet been convincingly achieved. This failure might stem from limitations of the targeted genome reduction approach that assumes full knowledge of gene functions and interactions, and allows only a limited number of reduction trajectories to interrogate. To explore the potential fitness benefits of genome reduction, we generated successive random deletions in E. coli by a novel, selection-driven, iterative streamlining process. The approach allows the exploration of multiple streamlining trajectories, and growth periods inherent in the procedure ensure selection of the fittest variants of the population. By generating single- and multiple-deletion strains and reconstructing the deletions in the parental genetic background, we showed that favourable deletions can be obtained and accumulated by the procedure. The most reduced multiple-deletion strain, obtained in five deletion cycles (2.5% genome reduction), outcompeted the wild-type, and showed elevated biomass yield. The spectrum of advantageous deletions, however, affecting only a few genomic regions, appears to be limited.
Identification of Isopeptides Between Human Tissue Transglutaminase and Wheat, Rye, and Barley Gluten Peptides
Authors: Lexhaller Barbara , Ludwig Christina , Scherf Katharina Anne 
Published: May 2020

AbstractCeliac disease (CD) is a chronic immune-mediated enteropathy of the small intestine, which is triggered by the ingestion of storage proteins (gluten) from wheat, rye, and barley in genetically predisposed individuals. Human tissue transglutaminase (TG2) plays a central role in the pathogenesis of CD, because it is responsible for specific gluten peptide deamidation and covalent crosslinking, resulting in the formation of Nε-(γ-glutamyl)-lysine isopeptide bonds. The resulting TG2-gluten peptide complexes are assumed to cause the secretion of anti-TG2 autoantibodies, but the underlying mechanisms are only partly known. To gain more insight into the structures of these complexes, the aim of our study was to identify TG2-gluten isopeptides. With the use of discovery-driven as well as targeted nanoscale liquid chromatography tandem mass spectrometry, we detected 29 TG2-gluten isopeptides in total, involving seven selected TG2 lysine residues (K205, K265, K429, K468, K590, K600, K677). Several gluten peptides carried known B-cell epitopes and/or T-cell epitopes, either intact 9-mer core regions or partial sequences, as well as sequences bearing striking similarities to already known epitopes. These novel insights into the molecular structures of TG2-gluten peptide complexes may help clarify their physiological relevance in the initiation of CD autoimmunity and the role of anti-TG2 autoantibodies.
Validity and Reliability of Three Commercially Available Smart Sports Bras during Treadmill Walking and Running
Authors: Navalta James W. , Ramirez Gabriela Guzman , Maxwell Crystal , Radzak Kara N. , McGinnis Graham R. 
Published: April 2020

AbstractA variety of wearable technology devices report heart rate. Heart rate sensing smart bras are manufactured for females who participate in activity, however accuracy has not been determined. The purpose was to determine the validity of heart rate measures in three commercially available sports bras during walking and running. Twenty-four healthy females completed bouts of treadmill exercise. The Adidas Smart sports bra, Berlei sports bra, and Sensoria Fitness biometric sports bra were tested. Participant perception of each garment was obtained immediately after the participant divested the sports bra. The Adidas Smart sports bra was valid only during rest (Intraclass correlation Coefficient [ICC] = 0.79, mean absolute percentage error [MAPE] = 4.5%, Limits of Agreement [LoA]=−8 to 8). The Berlei sports bra was valid across all conditions (ICC = 0.99, MAPE = 0.66%, LoA = −19 to 19), and the Sensoria biometric bra was valid during rest and walking (ICC = 0.96, MAPE = 1.9%, LoA = −15 to 12). Perception of the smart sports bras was higher for the Adidas Smart sports bra and Sensoria Fitness sports bra, and lower for the Berlei sports bra. Sports bra manufacturers designing wearable technology garments must consider the ability of returning accurate biometric data while providing necessary function and comfort to females engaging in physical activity.
Comparison of Biaxial Biomechanical Properties of Post-menopausal Human Prolapsed and Non-prolapsed Uterosacral Ligament
Authors: Danso Elvis K. , Schuster Jason D. , Johnson Isabella , Harville Emily W. , Buckner Lyndsey R. , Desrosiers Laurephile , Knoepp Leise R. , Miller Kristin S. 
Published: April 2020

AbstractUterosacral ligaments (USLs) provide structural support to the female pelvic floor, and a loss of USL structural integrity or biomechanical function may induce pelvic organ prolapse (POP). Alterations in extracellular matrix composition and organization dictate USL mechanical function. Changes in USL microstructure and corresponding mechanical properties, however, are not fully understood, nor is it understood how microstructure and mechanics change with onset and progression of POP. This is due, in part, as USL properties are primarily characterized along a single direction (uniaxial test), whereas the USL is loaded in multiple directions simultaneously within the body. Biaxial testing permits the acquisition of biomechanical data from two axes simultaneously, and thus simulates a more physiologic assessment compared to the traditional uniaxial testing. Therefore, the objective of this study was to quantify the biaxial biomechanical properties and histological composition of the USL in post-menopausal women with and without POP at various stages. Potential correlations between tissue microstructural composition and mechanical function were also examined. Tangential modulus was lower and peak stretch higher in POP III/IV compared to non-POP and POP I/II in the main in vivo loading direction; however, no significant differences in mechanical properties were observed in the perpendicular loading direction. Collagen content positively correlated to tangential modulus in the main in vivo loading direction (r = 0.5, p = 0.02) and negatively correlated with the peak stretch in both the main in vivo (r = −0.5, p = 0.02) and perpendicular loading directions (r = −0.3, p = 0.05). However, no statistically significant differences in USL composition were observed, which may be due to the small sample size and high variability of small sections of human tissues. These results provide first step towards understanding what microstructural and mechanical changes may occur in the USL with POP onset and progression. Such information may provide important future insights into the development of new surgical reconstruction techniques and graft materials for POP treatment.
Population history in Okinawa based on JC virus and ALDH2 genotypes
Authors: Miyamori Daisuke , Tanaka Yuka , Ishikawa Noboru , Kitamura Tadaichi , Ikegaya Hiroshi 
Published: April 2020

AbstractIt is widely known that people in Okinawa originated from the Jomon people, and are generally tolerant to alcohol. However, some individuals in mainland Japan lack alcohol tolerance due to a mutation in the human mitochondrial aldehyde dehydrogenase 2 (ALDH2) gene. Furthermore, the JC virus (JCV) genotype MY, which is related to the Jomon people, has not been found in Okinawa. In this study, to analyze the origin of the Okinawan people, we investigated the relationship between the JCV genotype and ALDH2 genotype. We collected 108 JCV positive samples from Okinawa. Only CY genotype JCV, and not the MY genotype, was detected. Among JCV-positive samples, a variant of ALDH2 (Glu/Lys heterozygote) was detected in 31 samples (29%) and wild-type ALDH2 (Glu/Glu homozygote) was detected in 77 samples (71%). Another variant of ALDH2 (Lys/Lys homozygote) was not detected. Among carriers of CY genotype JCV, wild-type ALDH2 was much more frequent in people living in Okinawa than in mainland Japan (P < 0.05). Our results suggested that the original inhabitants of Okinawa were people who carried MY genotype JCV and wild-type ALDH2; and that after the extinction of these original inhabitants, people who carried CY genotype JCV and wild-type ALDH2 migrated to the area. Due to the founder effect, CY genotype JCV and wild-type ALDH2 became dominant. Over a long period, many people with the variant ALDH2 migrated to Okinawa; the variant allele increased in frequency, but other JCV genotypes were eliminated.
Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations
Authors: Pierini Federica , Nutsua Marcel , Böhme Lisa , Özer Onur , Bonczarowska Joanna , Susat Julian , Franke Andre , Nebel Almut , Krause-Kyora Ben , Lenz Tobias L. 
Published: April 2020

AbstractThe highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.
Performance targets defined by retro-techno-economic analysis for the use of soybean protein as saccharification additive in an integrated biorefinery
Authors: Brondi Mariana G. , Elias Andrew M. , Furlan Felipe F. , Giordano Roberto C. , Farinas Cristiane S. 
Published: April 2020

AbstractThe use of additives in the enzymatic saccharification of lignocellulosic biomass can have positive effects, decreasing the unproductive adsorption of cellulases on lignin and reducing the loss of enzyme activity. Soybean protein stands out as a potential lignin-blocking additive, but the economic impact of its use has not previously been investigated. Here, a systematic evaluation was performed of the process conditions, together with a techno-economic analysis, for the use of soybean protein in the saccharification of hydrothermally pretreated sugarcane bagasse in the context of an integrated 1G-2G ethanol biorefinery. Statistical experimental design methodology was firstly applied as a tool to select the process variable solids loading at 15% (w/w) and soybean protein concentration at 12% (w/w), followed by determination of enzyme dosage at 10 FPU/g and hydrolysis time of 24 h. The saccharification of sugarcane bagasse under these conditions enabled an increase of 26% in the amount of glucose released, compared to the control without additive. The retro-techno-economic analysis (RTEA) technique showed that to make the biorefinery economically feasible, some performance targets should be reached experimentally such as increasing biomass conversion to ideally 80% and reducing enzyme loading to 5.6 FPU/g in the presence of low-cost soybean protein.
N,N-Dimethylaminopyrene as a fluorescent affinity mass tag for ligand-binding mode analysis
Authors: Arai Atsushi , Watanabe Rei , Hattori Atsunori , Iio Keita , Hu Yaping , Yoneda Kozo , Kigoshi Hideo , Kita Masaki 
Published: April 2020

AbstractElucidation of the binding mode of protein–ligand interactions provides insights for the design of new pharmacological tools and drug leads. Specific labeling of target proteins with chemical probes, in which the ligands are conjugated with reacting and detecting groups, can establish the binding positions of ligands. Label-assisted laser desorption/ionization mass spectrometry (LA-LDI MS) is a promising detection method to selectively detect labeled molecules. However, previous LDI MS tags, such as nitrogen-substituted pyrenes, had problems with low sensitivity and stability. Here we show 6-N,N-dimethylaminopyrene (dmpy) as a versatile mass tag, which was detected at an amount of 0.1 fmol by LA-LDI MS and applicable for MS/MS analysis. By using ligand-dissociation-type dmpy probes and affinity purification with a polystyrene gel, we demonstrated that dmpy-labeled peptides were predominantly detected by MALDI MS. Our dmpy-probe-labeling method might be highly useful for determining the target biomacromolecules of various ligands and their binding sites.
Synthesis and evaluation of polyamine carbon quantum dots (CQDs) in Litopenaeus vannamei as a therapeutic agent against WSSV
Authors: Huang Huai-Ting , Lin Han-Jia , Huang Hui-Ju , Huang Chih-Ching , Lin John Han-You , Chen Li-Li 
Published: April 2020

AbstractWhite spot syndrome virus (WSSV) is the causative agent of white spot syndrome (WSS), a disease that has led to severe mortality rates in cultured shrimp all over the world. The WSSV is a large, ellipsoid, enveloped double-stranded DNA virus with a wide host range among crustaceans. Currently, the main antiviral method is to block the receptor of the host cell membrane using recombinant viral proteins or virus antiserum. In addition to interference with the ligand-receptor binding, disrupting the structure of the virus envelope may also be a means to combat the viral infection. Carbon quantum dots (CQDs) are carbonaceous nanoparticles that have many advantageous characteristics, including small size, low cytotoxicity, cheap, and ease of production and modification. Polyamine-modified CQDs (polyamine CQDs) with strong antibacterial ability have been identified, previously. In this study, polyamine CQDs are shown to attach to the WSSV envelope and inhibit the virus infection, with a dose-dependent effect. The results also show that polyamine CQDs can upregulate several immune genes in shrimp and reduce the mortality upon WSSV infection. This is first study to identify that polyamine CQDs could against the virus. These results, indeed, provide a direction to develop effective antiviral strategies or therapeutic methods using polyamine CQDs in aquaculture.
Discovery of seven novel mutations of gyrB, parC and parE in Salmonella Typhi and Paratyphi strains from Jiangsu Province of China
Authors: Qian Huimin , Cheng Siyun , Liu Guoye , Tan Zhongming , Dong Chen , Bao Jinfeng , Hong Jie , Jin Dazhi , Bao Changjun , Gu Bing 
Published: April 2020

AbstractObjective: To investigate the prevalence of Salmonella Typhi and Paratyphi resistance to quinolones and characterize the underlying mechanism in Jiangsu Province of China. Methods: Antimicrobial susceptibility testing was performed using Kirby-Bauer disc diffusion system. Quinolone resistance-determining region (QRDR), plasmid-mediated quinolone resistance (PMQR) determinant genes were detected by PCR and sequencing. Results: Out of 239 Salmonella isolates, 164 were S. Typhi and 75 were S. Paratyphi. 128 (53.6%) Salmonella isolates were resistant to nalidixic acid; 11 (4.6%) isolates to ciprofloxacin and 66 (27.6%) isolates were intermediate to ciprofloxacin. QRDR were present in 69 S. Typhi isolates, among which mutation at codon 83 (n = 45) and 133 (n = 61) predominated. In S. Paratyphi, the most common mutations were detected in gyrA at codon 83(n = 24) and parC: T57S (n = 8). Seven mutations were first reported in Salmonella isolates including gyrB: S426G, parC: D79G and parE: [S498T, E543K, V560G, I444S, Y434S]. PMQR genes including qnrD1, qnrA1, qnrB4, aac (6′)-Ib-cr4 and qnrS1 were detected in 1, 2, 3, 7 and 9 isolates, relatively. Conclusions: High resistance to quinolones in Salmonella remains a serious problem in Jiangsu, China. The presence of the novel mutations increases the complexity of quinolone-resistant genotypes and poses a threat to public health. Subject terms: Salmonella Typhi, Salmonella Paratyphi, antimicrobial resistance, QRDR, PMQR.
The diagnostic accuracy of lung auscultation in adult patients with acute pulmonary pathologies: a meta-analysis
Authors: Arts Luca , Lim Endry Hartono Taslim , van de Ven Peter Marinus , Heunks Leo , Tuinman Pieter R. 
Published: April 2020

AbstractThe stethoscope is used as first line diagnostic tool in assessment of patients with pulmonary symptoms. However, there is much debate about the diagnostic accuracy of this instrument. This meta-analysis aims to evaluate the diagnostic accuracy of lung auscultation for the most common respiratory pathologies. Studies concerning adult patients with respiratory symptoms are included. Main outcomes are pooled estimates of sensitivity and specificity with 95% confidence intervals, likelihood ratios (LRs), area under the curve (AUC) of lung auscultation for different pulmonary pathologies and breath sounds. A meta-regression analysis is performed to reduce observed heterogeneity. For 34 studies the overall pooled sensitivity for lung auscultation is 37% and specificity 89%. LRs and AUC of auscultation for congestive heart failure, pneumonia and obstructive lung diseases are low, LR− and specificity are acceptable. Abnormal breath sounds are highly specific for (hemato)pneumothorax in patients with trauma. Results are limited by significant heterogeneity. Lung auscultation has a low sensitivity in different clinical settings and patient populations, thereby hampering its clinical utility. When better diagnostic modalities are available, they should replace lung auscultation. Only in resource limited settings, with a high prevalence of disease and in experienced hands, lung auscultation has still a role.
Long-term consequences of one anastomosis gastric bypass on esogastric mucosa in a preclinical rat model
Authors: Siebert Matthieu , Ribeiro-Parenti Lara , Nguyen Nicholas D. , Hourseau Muriel , Duchêne Belinda , Humbert Lydie , Jonckheere Nicolas , Nuel Grégory , Chevallier Jean-Marc , Duboc Henri , Rainteau Dominique , Msika Simon , Kapel Nathalie , Couvelard Anne , Bado André , Le Gall Maude 
Published: April 2020

AbstractAlthough bariatric surgery is proven to sustain weight loss in morbidly obese patients, long-term adverse effects have yet to be fully characterized. This study compared the long-term consequences of two common forms of bariatric surgery: one-anastomosis gastric bypass (OAGB) and Roux-en-Y Gastric Bypass (RYGB) in a preclinical rat model. We evaluated the influence of biliopancreatic limb (BPL) length, malabsorption, and bile acid (BA) reflux on esogastric mucosa. After 30 weeks of follow-up, Wistar rats operated on RYGB, OAGB with a short BPL (15 cm, OAGB-15), or a long BPL (35 cm, OAGB-35), and unoperated rats exhibit no cases of esogastric cancer, metaplasia, dysplasia, or Barrett’s esophagus. Compared to RYGB, OAGB-35 rats presented higher rate of esophagitis, fundic gastritis and perianastomotic foveolar hyperplasia. OAGB-35 rats also revealed the greatest weight loss and malabsorption. On the contrary, BA concentrations were the highest in the residual gastric pouch of OAGB-15 rats. Yet, no association could be established between the esogastric lesions and malabsorption, weight loss, or gastric bile acid concentrations. In conclusion, RYGB results in a better long-term outcome than OAGB, as chronic signs of biliary reflux or reactional gastritis were reported post-OAGB even after reducing the BPL length in a preclinical rat model.
Ultrasound Molecular Imaging of Renal Cell Carcinoma: VEGFR targeted therapy monitored with VEGFR1 and FSHR targeted microbubbles
Authors: Ingels Alexandre , Leguerney Ingrid , Cournède Paul-Henry , Irani Jacques , Ferlicot Sophie , Sébrié Catherine , Benatsou Baya , Jourdain Laurène , Pitre-Champagnat Stephanie , Patard Jean-Jacques , Lassau Nathalie 
Published: April 2020

AbstractRecent treatment developments for metastatic renal cell carcinoma offer combinations of immunotherapies or immunotherapy associated with tyrosine kinase inhibitors (TKI). There is currently no argument to choose one solution or another. Easy-to-use markers to assess longitudinal responses to TKI are necessary to determine when to switch to immunotherapies. These new markers will enable an earlier adaptation of therapeutic strategy in order to prevent tumor development, unnecessary toxicity and financial costs. This study evaluates the potential of ultrasound molecular imaging to track the response to sunitinib in a clear cell renal carcinoma model (ccRCC). We used a patient-derived xenograft model for this imaging study. Mice harboring human ccRCC were randomized for sunitinib treatment vs. control. The tumors were imaged at days 0, 7, 14 and 28 with ultrasound molecular imaging. Signal enhancement was quantified and compared between the two groups after injections of non-targeted microbubbles and microbubbles targeting VEGFR1 and FSHR. The tumor growth of the sunitinib group was significantly slower. There was a significantly lower expression of both VEGFR-1 and FSHR molecular ultrasound imaging signals in the sunitinib group at all times of treatment (Days 7, 14 and 28). These results confirm the study hypothesis. There was no significant difference between the 2 groups for the non-targeted microbubble ultrasound signal. This study demonstrated for the first time the potential of VEGFR1 and FSHR, by ultrasound-based molecular imaging, to follow-up the longitudinal response to sunitinib in ccRCC. These results should trigger developments for clinical applications.