bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens
Authors: Gonçalves Ana Teresa , Collipal-Matamal Rayen , Valenzuela-Muñoz Valentina , Nuñez-Acuña Gustavo , Valenzuela-Miranda Diego , Gallardo-Escárate Cristian 
Published: February 2020

AbstractCaligus rogercresseyi is a copepod ectoparasite with a high prevalence in salmon farms in Chile, causing severe welfare and economic concerns to the sector. Information on the parasite’s underpinning mechanisms to support its life strategy is recently being investigated. Due to the critical role of microbiota, this study aimed to characterize the microbiota community associated with C. rogercresseyi from different regions with salmon aquaculture in Chile. Using third-generation sequencing with Nanopore technology (MinION) the full 16S rRNA gene from sea lice obtained from 8 areas distributed over the three main aquaculture regions were sequenced. Microbiota of the parasite is mainly comprised of members of phyla Proteobacteria and Bacteroidetes, and a core microbiota community with 147 taxonomical features was identified, and it was present in sea lice from the three regions. This community accounted for 19% of total identified taxa but more than 70% of the total taxonomical abundance, indicating a strong presence in the parasite. Several taxa with bioactive compound secretory capacity were identified, such as members of genus Pseudoalteromonas and Dokdonia, suggesting a possible role of the lice microbiota during the host infestation processes. Furthermore, the microbiota community was differentially associated with the salmon production, where several potential pathogens such as Vibrio, Tenacibaculum, and Aeromonas in Los Lagos, Aysén, and Magallanes region were identified. Notably, the Chilean salmon industry was initially established in the Los Lagos region but it’s currently moving to the south, where different oceanographic conditions coexist with lice populations. The results originated by this study will serve as foundation to investigate putative role of sea lice as vectors for fish pathogens and also as reservoirs for antibiotic-resistant genes.
Genome-wide association mapping for dominance effects in female fertility using real and simulated data from Danish Holstein cattle
Authors: Mao Xiaowei , Sahana Goutam , Johansson Anna Maria , Liu Aoxing , Ismael Ahmed , Løvendahl Peter , De Koning Dirk-Jan , Guldbrandtsen Bernt 
Published: February 2020

AbstractExploring dominance variance and loci contributing to dominance variation is important to understand the genetic architecture behind quantitative traits. The objectives of this study were i) to estimate dominance variances, ii) to detect quantitative trait loci (QTL) with dominant effects, and iii) to evaluate the power and the precision of identifying loci with dominance effect through post-hoc simulations, with applications for female fertility in Danish Holstein cattle. The female fertility records analyzed were number of inseminations (NINS), days from calving to first insemination (ICF), and days from the first to last insemination (IFL), covering both abilities to recycle and to get pregnant in the female reproductive cycle. There were 3,040 heifers and 4,483 cows with both female fertility records and Illumina BovineSNP50 BeadChip genotypes (35,391 single nucleotide polymorphisms (SNP) after quality control). Genomic best linear unbiased prediction (BLUP) models were used to estimate additive and dominance genetic variances. Linear mixed models were used for association analyses. A post-hoc simulation study was performed using genotyped heifers’ data. In heifers, estimates of dominance genetic variances for female fertility traits were larger than additive genetic variances, but had large standard errors. The variance components for fertility traits in cows could not be estimated due to non-convergence of the statistical model. In total, five QTL located on chromosomes 9, 11 (2 QTL), 19, and 28 were identified and all of them showed both additive and dominance genetic effects. Among them, the SNP rs29018921 on chromosome 9 is close to a previously identified QTL in Nordic Holstein for interval between first and last insemination. This SNP is located in the 3’ untranslated region of gene peptidylprolyl isomerase like 4 (PPIL4), which was shown to be associated with milk production traits in US Holstein cattle but not known for fertility-related functions. Simulations indicated that the current sample size had limited power to detect QTL with dominance effects for female fertility probably due to low QTL variance. More females need to be genotyped to achieve reliable mapping of QTL with dominance effects for female fertility.
Oceanic vortex mergers are not isolated but influenced by the β-effect and surrounding eddies
Authors: de Marez Charly , Carton Xavier , L’Hégaret Pierre , Meunier Thomas , Stegner Alexandre , Le Vu Briac , Morvan Mathieu 
Published: February 2020

AbstractOceanic vortices are ubiquitous in the ocean. They dominate the sub-inertial energy spectrum, and their dynamics is key for the evolution of the water column properties. The merger of two like-signed coherent vortices, which ultimately results in the formation of a larger vortex, provides an efficient mechanism for the lateral mixing of water masses in the ocean. Understanding the conditions of such interaction in the ocean is thus essential. Here, we use a merger detection algorithm to draw a global picture of this process in the ocean. We show that vortex mergers are not isolated, contrary to the hypothesis made in most earlier studies. Paradoxically, the merging distance is well reproduced by isolated vortex merger numerical simulations, but it is imperative to consider both the β-effect and the presence of neighbouring eddies to fully understand the physics of oceanic vortex merger.
Analysis of Circulating Waves in Tissue Rings derived from Human Induced Pluripotent Stem Cells
Authors: Zhang Lu , Li Junjun , Liu Li , Tang Chao 
Published: February 2020

AbstractDeveloping more mature cardiomyocytes derived from human induced pluripotent stem cells is essential for cell transplantation and drug screening. In a previous study, we described a platform on which cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) formed three-dimensional self-organized tissue rings. Within these rings, traveling waves of action potentials spontaneously originate and propagate for a long time. In order to understand the dynamic behavior of these waves, we developed a mathematical model for the circulation of the electrical signal in such rings. By using the restitution curves of the action potential and the conduction velocity we demonstrated the mechanisms underlying the steady circulation and the features dependent on velocity. The analytic result agreed well with the experimental data in the origination, propagation, and long-term behavior of traveling waves within self-organized tissue rings. The theoretical analysis of traveling waves may also provide a reference to the analysis of reentrant rhythms in hearts.
Semi-quantitative versus quantitative assessments of late gadolinium enhancement extent for predicting spontaneous ventricular tachyarrhythmia events in patients with hypertrophic cardiomyopathy
Authors: Park Young Jun , Park Seung-Jung , Kim Eun-Kyung , Park Kyoung Min , Lee Sang-Cheol , On Young Keun , Kim June Soo 
Published: February 2020

AbstractExtent of late gadolinium enhancement (LGE) quantified by cardiac magnetic resonance was reportedly helpful for predicting the risk of ventricular tachyarrhythmias (VTA) in hypertrophic cardiomyopathy (HCM) patients. However, only a few data exist on the clinical implication of semi-quantitative assessment LGE extent in this patient population. The extent of left ventricular (LV) LGE was measured in 310 consecutive HCM patients using semi-quantitative (summing the LV segments with LGE, spatial extent) and quantitative (calculating the LGE volume percentage [vol% of LGE] against the total LV myocardial volume) methods, respectively. LV LGE was detected in 255 (82%) patients, most frequently in the mid-LV septum (n = 160, 52%). During the 49 ± 45 month follow-up, spontaneous VTA events were observed in 48 patients (16%) including aborted sudden cardiac death (SCD), appropriate defibrillator shock, and non-sustained VTA. The extent of LGE assessed by the two different methods showed a strong positive correlation (Spearman’s r = 0.63, P < 0.001). Moreover, there was a graded increase in the rates of VTA with the LGE extent evaluated semi-quantitatively and quantitatively. The extent of LGE was identified as an independent predictor of VTA events and more extensive LGE (positive ≥ 4 segments) significantly raised the risk of VTA, irrespective of the presence of conventional risk factors for SCD including family history, unexplained syncope, LV wall thickness ≥30 mm. The extent of LGE, whether assessed by semi-quantitative or quantitative methods, was closely associated with an increased risk of spontaneous VTA events in HCM patients.
Extreme rainfall events pulse substantial nutrients and sediments from terrestrial to nearshore coastal communities: a case study from French Polynesia
Authors: Fong Caitlin R. , Gaynus Camille J. , Carpenter Robert C. 
Published: February 2020

AbstractRainfall mobilizes and transports anthropogenic sources of sediments and nutrients from terrestrial to coastal marine ecosystems, and episodic but extreme rainfall may drive high fluxes to marine communities. Between January 13th and January 22nd, 2017, the South Pacific Island of Moorea, French Polynesia experienced an extreme rainfall event. ~57 cm of rain was delivered over a 10-day storm. We quantified pulsed sediments and nutrients transported to nearshore reefs. We determined the spatial and temporal extent of the sediment pulse with estimates of water transparency. We quantified pulsed nutrients at multiple spatial and temporal scales. To determine if terrestrial nutrients were incorporated into the benthic community, we collected macroalgae over 10 days following the storm and measured tissue nutrient concentrations and δN15. Pulsed sediments impacted water clarity for 6 days following the storm, with greatest impacts closest to the river mouth. Nitrite +nitrate concentrations were >100 times the average while phosphate was >25 times average. Macroalgal tissue nutrients were elevated, and δN15 implicates sewage as the source, demonstrating transported nutrients were transferred to producer communities. Future climate change predictions suggest extreme rainfall will become more common in this system, necessitating research on these pulses and their ramifications on marine communities.
Optimal Multi-Stage Arrhythmia Classification Approach
Authors: Zheng Jianwei , Chu Huimin , Struppa Daniele , Zhang Jianming , Yacoub Sir Magdi , El-Askary Hesham , Chang Anthony , Ehwerhemuepha Louis , Abudayyeh Islam , Barrett Alexander , Fu Guohua , Yao Hai , Li Dongbo , Guo Hangyuan , Rakovski Cyril 
Published: February 2020

AbstractArrhythmia constitutes a problem with the rate or rhythm of the heartbeat, and an early diagnosis is essential for the timely inception of successful treatment. We have jointly optimized the entire multi-stage arrhythmia classification scheme based on 12-lead surface ECGs that attains the accuracy performance level of professional cardiologists. The new approach is comprised of a three-step noise reduction stage, a novel feature extraction method and an optimal classification model with finely tuned hyperparameters. We carried out an exhaustive study comparing thousands of competing classification algorithms that were trained on our proprietary, large and expertly labeled dataset consisting of 12-lead ECGs from 40,258 patients with four arrhythmia classes: atrial fibrillation, general supraventricular tachycardia, sinus bradycardia and sinus rhythm including sinus irregularity rhythm. Our results show that the optimal approach consisted of Low Band Pass filter, Robust LOESS, Non Local Means smoothing, a proprietary feature extraction method based on percentiles of the empirical distribution of ratios of interval lengths and magnitudes of peaks and valleys, and Extreme Gradient Boosting Tree classifier, achieved an F1-Score of 0.988 on patients without additional cardiac conditions. The same noise reduction and feature extraction methods combined with Gradient Boosting Tree classifier achieved an F1-Score of 0.97 on patients with additional cardiac conditions. Our method achieved the highest classification accuracy (average 10-fold cross-validation F1-Score of 0.992) using an external validation data, MIT-BIH arrhythmia database. The proposed optimal multi-stage arrhythmia classification approach can dramatically benefit automatic ECG data analysis by providing cardiologist level accuracy and robust compatibility with various ECG data sources.
Characteristics and outcomes of bacteremia among ICU-admitted patients with severe sepsis
Authors: Komori Akira , Abe Toshikazu , Kushimoto Shigeki , Ogura Hiroshi , Shiraishi Atsushi , Saitoh Daizoh , Fujishima Seitaro , Mayumi Toshihiko , Naito Toshio , Hifumi Toru , Shiino Yasukazu , Nakada Taka-aki , Tarui Takehiko , Otomo Yasuhiro , Okamoto Kohji , Umemura Yutaka , Kotani Joji , Sakamoto Yuichiro , Sasaki Junichi , Shiraishi Shin-ichiro , Takuma Kiyotsugu , Tsuruta Ryosuke , Hagiwara Akiyoshi , Yamakawa Kazuma , Masuno Tomohiko , Takeyama Naoshi , Yamashita Norio , Ikeda Hiroto , Ueyama Masashi , Fujimi Satoshi , Gando Satoshi ,   JAAM FORECAST group, Tasaki Osamu , Mizobata Yasumitsu , Funakoshi Hiraku , Okuyama Toshiro , Yamashita Iwao , Kanai Toshio , Yamada Yasuo , Aibiki Mayuki , Sato Keiji , Yamashita Susumu , Yoshida Kenichi , Kasaoka Shunji , Kon Akihide , Rinka Hiroshi , Kato Hiroshi , Okudera Hiroshi , Narimatsu Eichi , Fujiwara Toshifumi , Sugita Manabu , Shichinohe Yasuo , Nakae Hajime , Iiduka Ryouji , Nakamura Mitsunobu , Murata Yuji , Sato Yoshitake , Ishikura Hiroyasu , Myojo Yasuhiro , Tsujita Yasuyuki , Kinoshita Kosaku , Yamaguchi Hiroyuki , Sakurai Toshihiro , Miyatake Satoru , Saotome Takao , Yasuda Susumu , Mizushima Yasuaki 
Published: February 2020

AbstractThe clinical implications of bacteremia among septic patients remain unclear, although a vast amount of data have been accumulated on sepsis. We aimed to compare the clinical characteristics and outcomes of severe sepsis patients with and without bacteremia. This secondary analysis of a multicenter, prospective cohort study included 59 intensive care units (ICUs) in Japan between January 2016 and March 2017. The study cohort comprised 1,184 adults (aged ≥ 16 years) who were admitted to an ICU with severe sepsis and diagnosed according to the Sepsis-2 criteria. Of 1,167 patients included in the analysis, 636 (54.5%) had bacteremia. Those with bacteremia had significantly higher rates of septic shock (66.4% vs. 58.9%, p = 0.01) and higher sepsis severity scores, including the Acute Physiology and Chronic Health Evaluation (APACHE) II and the Sequential Organ Failure Assessment (SOFA). No significant difference in in-hospital mortality was seen between patients with and without bacteremia (25.6% vs. 21.0%, p = 0.08). In conclusion, half of severe sepsis patients in ICUs have bacteremia. Although patients with bacteremia had more severe state, between-group differences in patient-centered outcomes, such as in-hospital mortality, have not been fully elucidated.
Evaluating the significance of contact maps in low-homology protein modeling using contact-assisted threading
Authors: Bhattacharya Sutanu , Bhattacharya Debswapna 
Published: February 2020

AbstractThe development of improved threading algorithms for remote homology modeling is a critical step forward in template-based protein structure prediction. We have recently demonstrated the utility of contact information to boost protein threading by developing a new contact-assisted threading method. However, the nature and extent to which the quality of a predicted contact map impacts the performance of contact-assisted threading remains elusive. Here, we systematically analyze and explore this interdependence by employing our newly-developed contact-assisted threading method over a large-scale benchmark dataset using predicted contact maps from four complementary methods including direct coupling analysis (mfDCA), sparse inverse covariance estimation (PSICOV), classical neural network-based meta approach (MetaPSICOV), and state-of-the-art ultra-deep learning model (RaptorX). Experimental results demonstrate that contact-assisted threading using high-quality contacts having the Matthews Correlation Coefficient (MCC) ≥ 0.5 improves threading performance in nearly 30% cases, while low-quality contacts with MCC <0.35 degrades the performance for 50% cases. This holds true even in CASP13 dataset, where threading using high-quality contacts (MCC ≥ 0.5) significantly improves the performance of 22 instances out of 29. Collectively, our study uncovers the mutual association between the quality of predicted contacts and its possible utility in boosting threading performance for improving low-homology protein modeling.
Nonlinear dynamic stability of piezoelectric thermoelastic electromechanical resonators
Authors: SoltanRezaee Masoud , Bodaghi Mahdi 
Published: February 2020

AbstractThis research work deals with analyzing instability and nonlinear behaviors of piezoelectric thermal nano-bridges. An adjustable thermo-elastic model with the ability to control stability conditions is developed to examine the system behavior at different temperatures. To increase the performance range and improve system characteristics, a piezovoltage is applied and a spring is connected to the sliding end of the deformable beam as design parameters. The partial differential equations (PDEs) are derived using the extended Hamilton’s principle and Galerkin decomposition is implemented to discretize the nonlinear equations, which are solved via a computational method called the step-by-step linearization method (SSLM). To improve the accuracy of the solution, the number of mode shapes and the size of voltage increments are analyzed and sufficient values are employed in the solution. The validity of the formulation and solution method is verified with experimental, analytical, and numerical data for several cases. Finally, the vibration and eigenvalue problem of the actuated nano-manipulator subjected to electrostatic and Casimir attractions are investigated. It is concluded that the fringing-fields correction changes the system frequency, static equilibrium, and pull-in characteristics significantly. The results are expected to be instrumental in the analysis, design, and operation of numerous adjustable advanced nano-systems.
A genetic analysis identifies a haplotype at adiponectin locus: Association with obesity and type 2 diabetes
Authors: Palit Sayantani Pramanik , Patel Roma , Jadeja Shahnawaz D. , Rathwa Nirali , Mahajan Ankit , Ramachandran A. V. , Dhar Manoj K. , Sharma Swarkar , Begum Rasheedunnisa 
Published: February 2020

AbstractAdiponectin is a prime determinant of the status of insulin resistance. Association studies between adiponectin (ADIPOQ) gene single nucleotide polymorphisms (SNPs) and metabolic diseases have been reported earlier. However, results are ambiguous due to apparent contradictions. Hence, we investigated (1) the association between ADIPOQ SNPs: −11377C/G, +10211T/G, +45T/G and +276G/T for the risk towards type 2 diabetes (T2D) and, (2) genotype-phenotype association of these SNPs with various biochemical parameters in two cohorts. Genomic DNA of diabetic patients and controls from Gujarat and, Jammu and Kashmir (J&K) were genotyped using PCR-RFLP, TaqMan assay and MassArray. Transcript levels of ADIPOQ were assessed in visceral adipose tissue samples, and plasma adiponectin levels were estimated by qPCR and ELISA respectively. Results suggest: (i) reduced HMW adiponectin/total adiponectin ratio in Gujarat patients and its association with +10211T/G and +276G/T, and reduced ADIPOQ transcript levels in T2D, (ii) association of the above SNPs with increased FBG, BMI, TG, TC in Gujarat patients and (iii) increased GGTG haplotype in obese patients of Gujarat population and, (iv) association of −11377C/G with T2D in J&K population. Reduced HMW adiponectin, in the backdrop of obesity and ADIPOQ genetic variants might alter metabolic profile posing risk towards T2D.
Quantitative expansion microscopy for the characterization of the spectrin periodic skeleton of axons using fluorescence microscopy
Authors: Martínez Gaby F. , Gazal Nahir G. , Quassollo Gonzalo , Szalai Alan M. , Cid-Pellitero Esther Del , Durcan Thomas M. , Fon Edward A. , Bisbal Mariano , Stefani Fernando D. , Unsain Nicolas 
Published: February 2020

AbstractFluorescent nanoscopy approaches have been used to characterize the periodic organization of actin, spectrin and associated proteins in neuronal axons and dendrites. This membrane-associated periodic skeleton (MPS) is conserved across animals, suggesting it is a fundamental component of neuronal extensions. The nanoscale architecture of the arrangement (190 nm) is below the resolution limit of conventional fluorescent microscopy. Fluorescent nanoscopy, on the other hand, requires costly equipment and special analysis routines, which remain inaccessible to most research groups. This report aims to resolve this issue by using protein-retention expansion microscopy (pro-ExM) to reveal the MPS of axons. ExM uses reagents and equipment that are readily accessible in most neurobiology laboratories. We first explore means to accurately estimate the expansion factors of protein structures within cells. We then describe the protocol that produces an expanded specimen that can be examined with any fluorescent microscopy allowing quantitative nanoscale characterization of the MPS. We validate ExM results by direct comparison to stimulated emission depletion (STED) nanoscopy. We conclude that ExM facilitates three-dimensional, multicolor and quantitative characterization of the MPS using accessible reagents and conventional fluorescent microscopes.
Associations between brain inflammatory profiles and human neuropathology are altered based on apolipoprotein E ε4 genotype
Authors: Friedberg Jacob S. , Aytan Nurgul , Cherry Jonathan D. , Xia Weiming , Standring Oliver J. , Alvarez Victor E. , Nicks Raymond , Svirsky Sarah , Meng Gaoyuan , Jun Gyungah , Ryu Hoon , Au Rhoda , Stein Thor D. 
Published: February 2020

AbstractAlzheimer disease (AD) is a chronic neurodegenerative disease with a multitude of contributing genetic factors, many of which are related to inflammation. The apolipoprotein E (APOE) ε4 allele is the most common genetic risk factor for AD and is related to a pro-inflammatory state. To test the hypothesis that microglia and AD-implicated cytokines were differentially associated with AD pathology based on the presence of APOE ε4, we examined the dorsolateral frontal cortex from deceased participants within a community-based aging cohort (n = 154). Cellular density of Iba1, a marker of microglia, was positively associated with tau pathology only in APOE ε4 positive participants (p = 0.001). The cytokines IL-10, IL-13, IL-4, and IL-1α were negatively associated with tau pathology, independent of Aβ1–42 levels, only in APOE ε4 negative participants. Overall, the association of mostly anti-inflammatory cytokines with less tau pathology suggests a protective effect in APOE ε4 negative participants. These associations are largely absent in the presence of APOE ε4 where tau pathology was significantly associated with increased microglial cell density. Taken together, these results suggest that APOE ε4 mediates an altered inflammatory response and increased tau pathology independent of Aβ1–42 pathology.