bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noncoding RNAs in Atrial Fibrillation: Current Status and Prospect
Authors: Zhou Dongchen , Yang Kun , Hu Jingjing , Shi Jiaran , Hu Xiaosheng 
Published: October 2019

Abstract:
Atrial fibrillation (AF) is an important cause of cardiovascular morbidity and mortality. Current therapies for AF are ineffective, mainly due to incomplete understanding of the pathogenesis of AF. Atrial remodeling contributes to the occurrence and progression of AF, but molecular mechanisms underlying AF remain unclear. Noncoding RNAs, including microRNAs, long noncoding RNAs and circular RNAs, are now considered to play an important role in the pathophysiology of AF. In this review, we summarize recent evidence supporting the role of noncoding RNAs in AF and highlight their diagnostic and prognostic applications as potential biomarkers and therapeutic strategies.
Association between soft drink consumption and osteoporotic fractures among postmenopausal women: the Women's Health Initiative
Authors: Kremer Pedro A. , Laughlin Gail A. , Shadyab Aladdin H. , Crandall Carolyn J. , Masaki Kamal , Orchard Tonya , LaCroix Andrea Z. 
Published: October 2019

Abstract

Objective:
High consumption of soft drinks has been associated with lower bone mineral density among postmenopausal women. This study explores the association of soft drink consumption, osteoporosis, and incidental fractures in this population.

Methods:
Cross-sectional (at baseline) and cohort combined designs, over 11.9 years of median follow-up for 72,342 postmenopausal women participating in the Women's Health Initiative Observational Study. Multiple linear regression models were used to examine the cross-sectional associations between soft drink consumption and hip and lumbar spine bone mineral density. Cox proportional hazards regression models were used to examine the association of soft drink consumption with incident hip fractures.

Results:
There were no associations between soft drink consumption and hip or lumbar spine t scores. During 700,388 person-years of follow-up, 2,578 hip fractures occurred. Adjusted hazard ratios for incident hip fracture for the highest consumption category compared with no consumption were 1.26 (95% confidence interval [CI] 1.01-1.56) for total soda and 1.32 (95% CI 1.00-1.75) for caffeine-free soda. There was no association between caffeinated soda and incident hip fracture (hazard ratio = 1.16; 95% CI 0.86-1.57). There was no apparent linear trend in the risk of hip fracture across categories of soda consumption in the fully adjusted models, suggesting a threshold effect. A sensitivity analysis using adjudicated hip fractures showed significant associations for all three soda exposures in the highest intake groups.

Conclusions:
Consuming more than two servings of soft drinks per day on average showed potential associations with higher risk of hip fracture among postmenopausal women.
Characterizing Insertion Pressure Profiles During Cochlear Implantation: Simultaneous Fluoroscopy and Intracochlear Pressure Measurements
Authors: Gonzalez Joseph R. , Cass Nathan D. , Banakis Hartl Renee M. , Peacock John , Cass Stephen P. , Greene Nathaniel T. 
Published: October 2019

Background:
Combined electrical-acoustical stimulation (EAS) has gained popularity as patients with residual hearing are increasingly undergoing cochlear implantation. Preservation of residual hearing correlates with hearing outcomes, but loss of hearing occurs in a subset of these patients. Several mechanisms have been proposed as causing this hearing loss; we have previously described high amplitude pressure transients, equivalent to high-level noise exposures, in the inner ear during electrode insertion. The source of these transients has not been identified.

Methods:
Cadaveric human heads were prepared with an extended facial recess. Fiber-optic pressure sensors were inserted into the scala vestibuli and scala tympani to measure intracochlear pressures. Two cochlear implant (CI) electrode styles (straight and perimodiolar) were inserted during time-synced intracochlear pressures and video fluoroscopy measurements.

Results:
CI electrode insertions produced pressure transients in the cochlea up to 160 to 170 dB pSPL equivalent for both styles, consistent with previous results. However, the position of the electrode within the cochlea when transients were generated differed (particularly contact with the medial or lateral walls).

Conclusions:
These results begin to elucidate the insertion pressure profiles of CI electrodes, which can be used to improve CI electrode designs and facilitate “silent-insertions” to improve chances of hearing preservation.
Characterizing Iranian Pediatric Patients With Relapsed Acute Lymphoblastic Leukemia Through Gene Expression Profiling of Common ATP Binding Cassette Transporters Subfamily C
Authors: Mehrvar Narjes , Abolghasemi Hassan , Rezvany Mohammad R. , Akbari Mohammad E. , Saberynejad Javad , Mehrvar Azim , Movafagh Abolfazl 
Published: October 2019

Background:
The correlation between gene expression of ABCC transporters and recurrence as a treatment failure in pediatric patients with acute lymphoblastic leukemia (ALL) is an unsolved problem in scientific associations. The aim of this study was to evaluate the predictive value of ABCC1-6 gene expression pattern for estimating recurrence in Iranian pediatric patients with ALL.

Materials and Methods:
Iranian pediatric patients with approved ALL enrolled in this study as 2 groups of case (relapsed ALL) and control (treated individuals who lasted for >3 years following their final treatment). Real-time polymerase chain reaction was done with GAPDH for expressing ABCC1-6 transporter genes. Cumulative doses of Vincristine, Daunorubicin, and L-Asparginase were checked for each patient. Gathered data analyzed with SPSS version 22 and REST 2009 software.

Results:
Thirty-nine samples as 23 relapsed ALL and 16 controls enrolled. High expression of ABCC2-6 and low expression of ABCC1 were detected in pediatric patients with relapse. ABCC3 and ABCC4 had significant relation with high-risk patients of NCI group. Also, ABCC4 and ABCC6 had more expression with high doses of Daunorubicin and L-Asparginase.

Conclusions:
Designed expression pattern have the predictive value for estimating of conferring relapse in Iranian pediatric patients with diagnosed ALL. The authors suggest of designing a multiple childhood malignancy center project to evaluate this pattern in a cohort study.
Mechanistic insights into heterogeneous radiofrequency ablation effects at the left atrial posterior wall during pulmonary vein isolation
Authors: Tomlinson David R. 
Published: October 2019

AbstractBackgroundIndependent investigations demonstrate greater radiofrequency (RF) ablation effects at left- sided left atrial posterior wall (LAPW) sites.ObjectiveTo investigate mechanisms underlying RF ablation heterogeneity during contact-force (CF) and VISITAG™ Module (Biosense Webster)-guided pulmonary vein isolation (PVI).MethodsConsecutive patients undergoing PVI during atrial overdrive pacing comprised 2 cohorts: intermittent positive pressure ventilation (IPPV, 14-16/min, 6-8ml/kg); high frequency jet ventilation (HFJV, 150/min, Monsoon III, Acutronic). Temperature-controlled (17ml/min, 48°C) RF data was retrospectively assessed at first-annotated (target 15s) LAPW sites: 30W during IPPV; 20W at left-sided sites during HFJV.ResultsTwenty-five and 15 patients underwent PVI during IPPV and HFJV, respectively. During IPPV, left versus right-sided median impedance drop (ImpD) was 13.6Ω versus 9.9Ω (p<0.0001) respectively and mean time to pure R unipolar electrogram (UE) morphology change 4.9s versus 6.7s (p=0.007) respectively. During HFJV, ImpD was greater at left-sided sites (9.7Ω versus 7.4Ω, p=0.21) and time to pure R UE significantly shorter: 4.3s versus 6.1s (p=0.02). Minimum case impedance subtracted from pre-RF baseline impedance (BI) generated site-specific ΔBI. Left-sided sites demonstrated significantly greater ΔBI, correlating strongly with Ln(ImpD) – IPPV r=0.84 (0.65 – 0.93), HFJV r=0.77 (0.35 – 0.93).At right-sided sites, ΔBI and Ln(ImpD) were without correlation during IPPV, but correlation was modest during HFJV (r=0.54, -0.007 – 0.84).ConclusionsΔBI may usefully indicate catheter-tissue contact surface area (SA). Consequently, greater left-sided LAPW RF effect may result from greater contact SA and in-phase catheter-tissue motion; HFJV may reduce right-sided out-of-phase catheter-tissue motion. Modifying RF delivery based on ΔBI may improve PVI safety and efficacy.
A Chemoenzymatic Method for Glycoproteomic N-glycan Type Quantitation
Authors: Li Henghui , Li Leyuan , Cheng Kai , Ning Zhibin , Mayne Janice , Zhang Xu , Walker Krystal , Chen Rui , Twine Susan , Li Jianjun , Figeys Daniel 
Published: October 2019

ABSTRACTGlycosylation is one of the most important post-translational modifications in biological systems. Current glycoproteome methods mainly focus on qualitative identification of glycosylation sites or intact glycopeptides. However, the systematic quantitation of glycoproteins has remained largely unexplored. Here, we developed a chemoenzymatic method to quantitatively investigate N-glycoproteome based on the N-glycan types. Taking advantage of the specificity of different endoglycosidases and isotope dimethyl labeling, six N-glycan types of structures linked on each glycopeptide, including high-mannose/hybrid, bi-antennary and tri-antennary with/without core fucose, were quantified. As a proof of principle, the glycoproteomic N-glycan type quantitative (glyco-TQ) method was first used to determine the N-glycan type composition of immunoglobulin G1 (IgG1) Fc fragment. Then we applied the method to analyze the glycan type profile of proteins in the breast cancer cell line MCF7, and quantitatively revealed the N-glycan type micro-heterogeneity at both the glycopeptide and glycoprotein levels. The novel quantitative strategy to evaluate the relative intensity of the six states of N-glycan type glycosylation on each site provides a new avenue to investigate function of glycoproteins in broad areas, such as cancer biomarker research, pharmaceuticals characterization and anti-glycan vaccine development.
Probing the neural dynamics of mnemonic representations after the initial consolidation
Authors: Liu Wei , Kohn Nils , Fernández Guillén 
Published: October 2019

AbstractMemories are not stored as static engrams, but as dynamic representations affected by processes occurring after initial encoding. Previous studies revealed changes in activity and mnemonic representations in visual processing areas, parietal lobe, and hippocampus underlying repeated retrieval and suppression. However, these neural changes are usually induced by memory modulation immediately after memory formation. Here, we investigated 27 healthy participants with a two-day functional Magnetic Resonance Imaging design to probe how established memories are dynamically modulated by retrieval and suppression 24 hours after learning. Behaviorally, we demonstrated that established memories can still be strengthened by repeated retrieval. By contrast, repeated suppression had a modest negative effect, and suppression-induced forgetting was associated with individual suppression efficacy. Neurally, we demonstrated item-specific pattern reinstatements in visual processing areas, parietal lobe, and hippocampus. Then, we showed that repeated retrieval reduced activity amplitude in the ventral visual cortex and hippocampus, but enhanced the distinctiveness of activity patterns in the ventral visual cortex and parietal lobe. Critically, reduced activity was associated with enhanced representation of idiosyncratic memory traces in ventral visual cortex and precuneus. In contrast, repeated memory suppression was associated with the reduced lateral prefrontal activity, but relative intact mnemonic representations. Our results replicated most of the neural changes induced by memory retrieval and suppression immediately after learning and extended those findings to established memories after initial consolidation. Active retrieval seems to promote episode-unique mnemonic representations in the neocortex after initial encoding but also consolidation.HighlightsRepeated retrieval strengthened consolidated memories, while repeated suppression had a modest negative effect.Pattern reinstatements of individual memories were detected in the visual area, parietal lobe, and hippocampus after 24 hours.After repeated retrieval, reduced activity amplitude was associated with increased distinctiveness of activity patterns in the ventral visual cortex and right precuneus.Repeated suppression was associated with the reduced lateral prefrontal activity, but unchanged mnemonic representations.
Monitoring the prolonged TNF stimulation in space and time with topological-functional networks
Authors: Papoudas Stylianos Mavropoulos , Papanikolaou Nikolaos , Nikolaou Christoforos 
Published: October 2019

AbstractGenes in linear proximity often share regulatory inputs, expression and evolutionary patterns, even in complex eukaryote genomes with extensive intergenic sequences. Gene regulation, on the other hand, is effected through the co-ordinated activation (or suppression) of genes participating in common biological pathways, which are often transcribed from distant loci. Existing approaches for the study of gene expression focus on the functional aspect, taking positional constraints into account only marginally.In this work we propose a novel concept for the study of gene expression, through the combination of topological and functional information into bipartite networks. Starting from genome-wide expression profiles, we define extended chromosomal regions with consistent patterns of differential gene expression and then associate these domains with enriched functional pathways. By analyzing the resulting networks in terms of size, connectivity and modularity we can draw conclusions on the way genome organization may underlie the gene regulation program.We implement our approach in a detailed RNASeq profiling of sustained TNF stimulation of mouse synovial fibroblasts. Bipartite network analysis suggests that the cytokine response set by TNF, progresses through two distinct transitions. An early generalization of the inflammatory response, marked by an increase in related functions and high connectivity of corresponding genomic loci, that is followed by a late shutdown of immune functions and the redistribution of expression to developmental and cell adhesion pathways and distinct chromosomal regions.Our results suggest that the incorporation of topological information may provide additional insights in the underlying topological constraints that are shaping gene expression.
Cell cycle-dependent active stress drives epithelia remodeling
Authors: Devany John , Sussman Daniel M. , Yamamoto Takaki , Manning M. Lisa , Gardel Margaret L. 
Published: October 2019

ABSTRACTEpithelia have distinct cellular architectures, which are established in development, re-established after wounding, and maintained during tissue homeostasis despite cell turnover and mechanical perturbations. In turn, cell shape also controls tissue function as a regulator of cell differentiation, proliferation, and motility. Here we investigate cell shape changes in a model epithelial monolayer. After the onset of confluence, cells continue to proliferate and change shape over time, eventually leading to a final architecture characterized by arrested motion and more regular cell shapes. Such monolayer remodeling is robust, with qualitatively similar evolution in cell shape and dynamics observed across disparate perturbations. Here we quantify differences in monolayer remodeling guided by the active vertex model to identify underlying order parameters controlling epithelial architecture. When monolayers are formed atop extracellular matrix with varied stiffness, we find the cell density at which motion arrests varies significantly but the cell shape remains constant, consistent with the onset of tissue rigidity. In contrast, pharmacological perturbations can significantly alter the cell shape at which tissue dynamics is arrested, consistent with varied amounts of active stress within the tissue. Across all experimental conditions the final cell shape is well correlated to the cell proliferation rate, and cell cycle inhibition immediately arrests cell motility. Finally, we demonstrate cell-cycle variation in junctional tension as a source of active stress within the monolayer. Thus, the architecture and mechanics of epithelial tissue can arise from an interplay between cell mechanics and stresses arising from cell cycle dynamics.SIGNIFICANCE STATEMENTThe morphology of biological tissue is determined by the shape and density of constituent cells. Here we measure the dynamics of cells in model epithelial tissues to study the evolution of their shape and density over time. Guided by a mathematical model, we find that cell shape is controlled by rigidity and active stresses within the tissue. We then show that cell cycle dynamics are the source of active stress that drives epithelial remodeling.
Net effects of field and landscape scale habitat on insect and bird damage to sunflowers
Authors: Kross Sara M. , Martinico Breanna L. , Bourbour Ryan P. , Townsend Jason M. , McColl Chris , Kelsey T. Rodd 
Published: October 2019

AbstractAgriculture-dominated landscapes harbor significantly diminished biodiversity, but are also areas in which significant gains in biodiversity can be achieved. Planting or retaining woody vegetation along field margins can provide farmers with valuable ecosystem services while simultaneously benefitting biodiversity. However, when crops are damaged by the biodiversity harbored in such vegetation, farmers are reluctant to incorporate field margin habitat onto their land and may even actively remove such habitats, at cost to both farmers and non-target wildlife. We investigated how damage by both insect pests (sunflower moth,Homoeosoma electellum) and avian pests to sunflower (Helianthus annuus) seed crops varied as a function of bird abundance and diversity, as well as by landscape-scale habitat. Surveys for insect damage, avian abundance, and bird damage were carried out over two years in 30 different fields on farms in California’s Sacramento Valley. The mean percentage of moth-damaged sunflowers sampled was nearly four times higher in fields that had bare or weedy margins (23.5%) compared to fields with woody vegetation (5.9%) and decreased in both field types as landscape-scale habitat complexity declined. Birds damaged significantly fewer sunflower seeds (2.7%) than insects, and bird damage was not affected by field margin habitat type, landscape-scale habitat variables, or avian abundance, but was significantly higher along field edges compared to ≥ 50m from the field edge. Avian species richness nearly doubled in fields with woody margin habitat compared to fields with bare/weedy margins in both the breeding season and in fall. These results indicate that the benefits of planting or retaining woody vegetation along sunflower field margins could outweigh the ecosystem disservices related to bird damage, while simultaneously increasing the biodiversity value of intensively farmed agricultural landscapes.
A thalamic reticular circuit for head direction cell tuning and spatial navigation
Authors: Vantomme Gil , Rovó Zita , Cardis Romain , Béard Elidie , Katsioudi Georgia , Guadagno Angelo , Perrenoud Virginie , Fernandez Laura MJ , Lüthi Anita 
Published: October 2019

SummaryTo navigate in space, an animal must refer to sensory cues to orient and move. Circuit and synaptic mechanisms that integrate cues with internal head-direction (HD) signals remain, however, unclear. We identify an excitatory synaptic projection from the presubiculum (PreS) and the multisensory-associative retrosplenial cortex (RSC) to the anterodorsal thalamic reticular nucleus (TRN), so far classically implied in gating sensory information flow. In vitro, projections to TRN involved AMPA/NMDA-type glutamate receptors that initiated TRN cell burst discharge and feedforward inhibition of anterior thalamic nuclei. In vivo, chemogenetic anterodorsal TRN inhibition modulated PreS/RSC-induced anterior thalamic firing dynamics, broadened the tuning of thalamic HD cells, and led to preferential use of allo-over egocentric search strategies in the Morris water maze. TRN-dependent thalamic inhibition is thus an integral part of limbic navigational circuits wherein it coordinates external sensory and internal HD signals to regulate the choice of search strategies during spatial navigation.
OdoBD: An online database for the dragonflies and damselflies of Bangladesh
Authors: Shah Md Nur Ahad , Khan Md Kawsar 
Published: October 2019

AbstractCombining scientific data over a long-time period is necessary to understand the diversity, population trends, and conservation importance of any taxa in a global and regional scale. Bangladesh is located in a biodiversity hotspot region, however, till date, only few animal groups has been extensively investigated at a nation-wide scale. Although being one of the earliest and well-known insect groups, the knowledge on Odonata of this region remains rudimentary and dispersed. To resolve this issue, we have developed an online database for the Odonata of Bangladesh. We have compiled data from our last four years field study, from previously published research articles, field guides, and also collected data from citizen scientists regarding Bangladeshi odonates. Odonata of Bangladesh database (http://www.odobd.org) contains information on morphology, abundance, gene and protein sequences, local and global distribution and conservation status of the Odonata of Bangladesh. The database also demonstrates gender specified photographs with descriptions for better understanding for the novice researchers and naturalists. Odonata of Bangladesh database provides a comprehensive source for meta-analyses in ecology, conservation biology, and genetic research.
GAIA: an integrated metagenomics suite
Authors: Paytuví A. , Battista E. , Scippacercola F. , Aiese Cigliano R. , Sanseverino W. 
Published: October 2019

AbstractIdentifying the biological diversity of a microbial population is of fundamental importance due to its implications in industrial processes, environmental studies and clinical applications. Today, there is still an outstanding need to develop new, easy-to-use bioinformatics tools to analyze both amplicon and shotgun metagenomics, including both prokaryotic and eukaryotic organisms, with the highest accuracy and the lowest running time. With the aim of overcoming this need, we introduce GAIA, an online software solution that has been designed to provide users with the maximum information whether it be 16S, 18S, ITS, or shotgun analysis. GAIA is able to obtain a comprehensive and detailed overview at any taxonomic level of microbiomes of different origins: human (e.g. stomach or skin), agricultural and environmental (e.g. land, water or organic waste). By using recently published benchmark datasets from shotgun and 16S experiments we compared GAIA against several available pipelines. Our results show that for shotgun metagenomics, GAIA obtained the highest F-measures at species level above all tested pipelines (CLARK, Kraken, LMAT, BlastMegan, DiamondMegan and NBC). For 16S metagenomics, GAIA also obtained excellent F-measures comparable to QIIME at family level. The overall objective of GAIA is to provide both the academic and industrial sectors with an integrated metagenomics suite that will allow to perform metagenomics data analysis easily, quickly and affordably with the highest accuracy.