bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation-by-environment as a driver of genetic differentiation among populations of the only broad-leaved evergreen shrub Ammopiptanthus mongolicus in Asian temperate deserts
Authors: Jiang Shan , Luo Min-Xin , Gao Run-Hong , Zhang Wei , Yang Yong-Zhi , Li Ying-Jie , Liao Pei-Chun 
Published: August 2019

AbstractWhether the effect of migration-selection-drift equilibrium on population structure is governed by spatial or environmental differences is usually elucidated by isolation-by-distance (IBD), isolation-by-environment (IBE), and isolation-by-resistance (IBR) tests. The population structure of Ammopiptanthus mongolicus, a broad-leaved evergreen psammophyte in eastern Central Asia, was previously thought to follow an isolation by distance pattern. However, recent studies have emphasized the effects of environmental factors on its growth and distribution, suggesting an important influence of local adaptation on the genetic structure of the species. Using inter-simple sequence repeat (ISSR) markers, we verified the previously inferred low intra-population variation and high inter-population differentiation. However, in contrast to previous studies, the results of partial Mantel tests and a maximum likelihood population effects mixed model (MLPE) suggested that local climate differences, rather than geographic distances or resistance distances, are the main factor affecting population differentiation. Further analysis with removal of multicollinear climatic variables and univariate MLPE found that summer and winter precipitation were crucial for shaping the current population genetic structure. Since local precipitation is related to the regeneration, colonization, and overwintering survival of A. mongolicus, its influence on demographic change may explain its effect on the population genetic structure. In addition, precipitation is related to terrain despite westward decreases, which explains the independence of genetic difference and geographic distance. The identified role of IBE suggests that collecting germplasm resources from genetically differentiated populations could be a more effective strategy to preserve the overall genetic diversity of the species than the establishment of corridors to enhance gene flow among populations.
Fabrication of innocuous gold nanoparticles using plant cells in culture
Authors: Bhaskaran Sinilal , Sharma Nilesh , Tiwari Pooja , Singh Shree R. , Sahi Shivendra V. 
Published: August 2019

AbstractPlant extracts and their different growth phases have been manipulated for the fabrication of nanomaterials, which can be an eco-friendly alternative to the chemical methods that produce hazardous by-products. However, practical difficulties in isolation of the nanoparticles obtained through biological methods and the scanty control that these methods allow over their shapes and sizes impose limitations in their utility. For the first time, we report here a versatile system using cell suspension culture of Medicago sativa, which ensures control over the reaction to regulate size of the particles as well as their easier recovery afterwards. Isolated nanoparticles were characterized for their shape, size and functions. The particles varied in shapes from isodiametric spheres to exotic tetrahedrons, pentagons and pentagonal prisms. They clearly demonstrated catalytic activity in the reduction reaction of methylene blue by stannous chloride. Interestingly, the cell culture-derived particles were found less cytotoxic to healthy human cell line HEp-2 while more cytotoxic to the cancer cell line 4T-1 in comparison to those synthesized through citrate method. However, when administered in mice, these nanoparticles elicited similar inflammatory responses as those produced by chemically synthesized counterparts. These results envisage the utility of these particles for various biological applications.
Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients
Authors: Fernandes Sunjay Jude , Morikawa Hiromasa , Ewing Ewoud , Ruhrmann Sabrina , Joshi Rubin Narayan , Lagani Vincenzo , Karathanasis Nestoras , Khademi Mohsen , Planell Nuria , Schmidt Angelika , Tsamardinos Ioannis , Olsson Tomas , Piehl Fredrik , Kockum Ingrid , Jagodic Maja , Tegnér Jesper , Gomez-Cabrero David 
Published: August 2019

AbstractMultiple Sclerosis (MS) is an autoimmune disease of the central nervous system with prominent neurodegenerative components. The triggering and progression of MS is associated with transcriptional and epigenetic alterations in several tissues, including peripheral blood. The combined influence of transcriptional and epigenetic changes associated with MS has not been assessed in the same individuals. Here we generated paired transcriptomic (RNA-seq) and DNA methylation (Illumina 450 K array) profiles of CD4+ and CD8+ T cells (CD4, CD8), using clinically accessible blood from healthy donors and MS patients in the initial relapsing-remitting and subsequent secondary-progressive stage. By integrating the output of a differential expression test with a permutation-based non-parametric combination methodology, we identified 149 differentially expressed (DE) genes in both CD4 and CD8 cells collected from MS patients. Moreover, by leveraging the methylation-dependent regulation of gene expression, we identified the gene SH3YL1, which displayed significant correlated expression and methylation changes in MS patients. Importantly, silencing of SH3YL1 in primary human CD4 cells demonstrated its influence on T cell activation. Collectively, our strategy based on paired sampling of several cell-types provides a novel approach to increase sensitivity for identifying shared mechanisms altered in CD4 and CD8 cells of relevance in MS in small sized clinical materials.
Coupled Ionic-Electronic Equivalent Circuit to Describe Asymmetric Rise and Decay of Photovoltage Profile in Perovskite Solar Cells
Authors: Ebadi Firouzeh , Aryanpour Masoud , Mohammadpour Raheleh , Taghavinia Nima 
Published: August 2019

AbstractIn this research, we employed transient photo-voltage rise and decay measurements to investigate the origin of slow unsymmetrical rise and decay profiles in single and triple cation perovskite solar cells. Drastic changes in photo-voltage decay profile were observed upon insertion of Br−, Cs+ and FA+ ions into perovskite structures. In order to explain our observations, the activation energy for ionic defects was measured and an equivalent circuit model was proposed containing both electrical and ionic components. The electrical branch consists of a diode, the bulk capacitance and resistances for charge transport and recombination. In parallel we introduced an ionic branch describing the ionic response by a resistance for ionic charge transport and a capacitance describing ion accumulation at the interface to the charge transport layer. To reproduce the asymmetry of photo-voltage rise and decay, a diode with a parallel resistor is introduced leading to a belayed backflow of the accumulated ions. The results revealed that the activation energy of ionic defects became larger upon insertion of either halides or cations. There is larger amount of ionic defects in the case of MAPbI3 while the de-accumulation process of ions happens in much larger time scale in triple cation perovskite. The presence of ions at the interfaces results in band bending generating a potential barrier restraining electrons and holes from recombination; so the loss of built-in potential is delayed until de-accumulation of ionic double layer happens. Our model proposes that the loss of built-in potential depends on electrostatic potential drop, suggesting coupled electronic-ionic phenomenon in perovskite solar cells.
An Innovative Harmonic Radar to Track Flying Insects: the Case of Vespa velutina
Authors: Maggiora Riccardo , Saccani Maurice , Milanesio Daniele , Porporato Marco 
Published: August 2019

AbstractOver the last 30 years, harmonic radars have been effective only in tracking insects flying at low altitude and over flat terrain. We developed an innovative harmonic radar, implementing the most advanced radar techniques, which covers a large field of view in elevation (with an angular aperture of about 24°) and can track insects up to a range of 500 m. We show all the components of this new harmonic radar and its first application, the tracking of Vespa velutina (yellow-legged Asian hornet). This is an invasive species which, although indigenous to South-East Asia, is spreading quickly to other regions of the world. Because of its fast diffusion and the serious threat it poses to both honeybee colonies and to humans, control measures are mandatory. When equipped with a small passive transponder, this radar system can track the flight trajectory of insects and locate nests to be destroyed. This tool has potential not only for monitoring V. velutina but also for tracking other larger insects and small size vertebrates.
Biotic Versus Abiotic Control of Primary Production Identified in a Common Garden Experiment
Authors: Belovsky Gary E. , Slade Jennifer B. 
Published: August 2019

AbstractUnderstanding drivers of ecosystem primary production is a foundational question in ecology that grows in importance with anthropogenic stresses (e.g., climate change). Traditionally, ecosystem production is considered to be abiotically controlled at large spatial scales (e.g., precipitation, temperature, etc.), which underlies forecasting climate change impacts. Using a “common garden” experiment over 10 years at two sites with the same plant and grasshopper species, we show that primary production is strongly influenced by biotic factors (herbivory and plant adaptations to it) at finer spatial scales by creating positive feedbacks, which reverse relative productivity of ecosystems expected from abiotic conditions alone. Our results without herbivory indicate that one site has 26% less annual net primary production (ANPP) than the other site. With herbivory, the sites reverse in ANPP, so the site with lower ANPP without herbivory now is 15% greater than the site with higher ANPP without herbivory, as they respectively increase by 6% and decline by 33%. This reversal is due to changing nitrogen availability (N), as N becomes 16% greater at the higher ANPP site with herbivory, respectively a 3% increase and 41% decline in N. The ANPP and N changes are observed, even though the sites are a few kilometers apart and have the same grasshopper and plant species.
Whole-body cryotherapy does not augment adaptations to high-intensity interval training
Authors: Broatch James R. , Poignard Mathilde , Hausswirth Christophe , Bishop David J. , Bieuzen François 
Published: August 2019

AbstractThe aim of this study was to investigate the effects of regular post-exercise whole-body cryotherapy (WBC) on physiological and performance adaptations to high-intensity interval training (HIT). In a two-group parallel design, twenty-two well-trained males performed four weeks of cycling HIT, with each session immediately followed by 3 min of WBC (−110 °C) or a passive control (CON). To assess the effects of WBC on the adaptive response to HIT, participants performed the following cycling tests before and after the training period; a graded exercise test (GXT), a time-to-exhaustion test (Tmax), a 20-km time trial (20TT), and a 120-min submaximal test (SM120). Blood samples were taken before and after training to measure changes in basal adrenal hormones (adrenaline, noradrenaline, and cortisol). Sleep patterns were also assessed during training via wrist actigraphy. As compared with CON, the administration of WBC after each training session during four weeks of HIT had no effect on peak oxygen uptake ($$\dot{{\rm{V}}}$$

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O2peak) and peak aerobic power (Ppeak) achieved during the GXT, Tmax duration and work performed (WTmax), 20TT performance, substrate oxidation during the SM120, basal adrenaline/noradrenaline/cortisol concentrations, or sleep patterns (P > 0.05). These findings suggest that regular post-exercise WBC is not an effective strategy to augment training-induced aerobic adaptations to four weeks of HIT.
Organic contaminants as an ecological tool to explore niche partitioning: a case study using three pelagic shark species
Authors: Lyons Kady , Kacev Dovi , Preti Antonella , Gillett David , Dewar Heidi 
Published: August 2019

AbstractChemical contaminant profiles are linked to an animal’s niche, providing a potential tool by which to assess resource partitioning in pelagic species. As proof of concept, we examined contaminant signatures in three species of sharks (Isurus oxyrinchus, Prionace glauca, and Alopias vulpinus) known to overlap in both space and time. Since these sharks comprise a predatory guild within the Southern California Bight (SCB), we predicted that species may partition spatial and dietary resources to limit the extent of competitive exclusion. Indeed, species were distinguishable by both total contaminant loads and their contaminant fingerprint, as random forest analysis found that species could be correctly classified 96% of the time. Our results demonstrate the utility of chemical analyses for ecological studies, and how contaminant tracers can be used in combination with traditional methods to elucidate how species may undergo niche partitioning to reduce competition for overlapping resources within predatory guilds.
Burst statistics in an early biofilm quorum sensing model: the role of spatial colony-growth heterogeneity
Authors: Kindler Oliver , Pulkkinen Otto , Cherstvy Andrey G. , Metzler Ralf 
Published: August 2019

AbstractQuorum-sensing bacteria in a growing colony of cells send out signalling molecules (so-called “autoinducers”) and themselves sense the autoinducer concentration in their vicinity. Once—due to increased local cell density inside a “cluster” of the growing colony—the concentration of autoinducers exceeds a threshold value, cells in this clusters get “induced” into a communal, multi-cell biofilm-forming mode in a cluster-wide burst event. We analyse quantitatively the influence of spatial disorder, the local heterogeneity of the spatial distribution of cells in the colony, and additional physical parameters such as the autoinducer signal range on the induction dynamics of the cell colony. Spatial inhomogeneity with higher local cell concentrations in clusters leads to earlier but more localised induction events, while homogeneous distributions lead to comparatively delayed but more concerted induction of the cell colony, and, thus, a behaviour close to the mean-field dynamics. We quantify the induction dynamics with quantifiers such as the time series of induction events and burst sizes, the grouping into induction families, and the mean autoinducer concentration levels. Consequences for different scenarios of biofilm growth are discussed, providing possible cues for biofilm control in both health care and biotechnology.
Eight new freshwater mussels (Unionidae) from tropical Asia
Authors: Bolotov Ivan N. , Konopleva Ekaterina S. , Vikhrev Ilya V. , Lopes-Lima Manuel , Bogan Arthur E. , Lunn Zau , Chan Nyein , Win Than , Aksenova Olga V. , Gofarov Mikhail Yu , Tomilova Alena A. , Kondakov Alexander V. 
Published: August 2019

AbstractFreshwater mussels are sensitive to habitat and water quality, revealing the fastest rates of human-mediated global extinction among aquatic animals. These animals are especially diverse in tropical Asia, the faunas of which are characterized by high levels of endemism. Here we describe four new species and four new subspecies of freshwater mussels from Myanmar. Leoparreysia whittenisp. nov., the smallest representative of this genus, was discovered from the Ayeyarwady and Chindwin rivers. Radiatula myitthanensissp. nov. and R. chindwinensissp. nov. were recorded from the Chindwin Basin, and R. mouhoti haungthayawensisssp. nov. has been discovered from the Haungthayaw River. Indochinella pugio has been revised with a description of three subspecies: I. pugio viridissimassp. nov. from the Sittaung, Bilin and Bago rivers, I. pugio daweiensisssp. nov. from the Dawei River, and I. pugio paradoxassp. nov. from the Haungthayaw River. Yaukthwa elongatulasp. nov., a peculiar species, conchologically resembling representatives of the genus Solenaia (Gonideinae) with ultra-elongated shell was found in the Chindwin Basin. Our records highlight that tropical Asia harbors numerous, but still overlooked local endemic lineages of freshwater bivalves, which may be on the brink of extinction due to the high anthropogenic and climate change impacts.
Postoperative bleeding and biliary leak after liver resection: A cohort study between two different fibrin sealant patches
Authors: López-Guerra Diego , Santos-Naharro Jesús , Rojas-Holguín Adela , Jaen-Torrejimeno Isabel , Prada-Villaverde Aranzazu , Blanco-Fernández Gerardo 
Published: August 2019

AbstractDifferent topical products have been tested in liver resection to get a control of bleeding. This study compares the effectiveness and complications between two haemostatic agents Tachosil versus Hemopatch. A cohort study including patients who underwent liver resection since November 2014 to April 2016 was conducted. The study was performed in a single institution. Demographic variables, intraoperative characteristics and postoperative complications were analysed. A total of 92 patients (50 in Tachosil group and 42 in Hemopatch group) were included. No differences were found in patients who required intraoperative (Tachosil 6 (12%) vs Hemopatch 2 (4.8%); p = 0.28) and postoperative (Tachosil 4 (8%) vs Hemopatch 3 (7.1%); p = 0.87) blood transfusion. There were no differences in length of hospital stay (Tachosil 7.02 ± 4.1 days vs Hemopatch 7.63 ± 9.1; p = 0.67). Overall postoperative complications were similar between both patches (Tachosil 21 (42%) vs Hemopatch 14 (33%); p = 0.48). No differences were found in specific complications, however Hemopatch showed a higher incidence of intraabdominal abscess 5 (11.9%) and vs 0 (0%) p = 0.01.In this study no differences have been found between Hemopatch and Tachosil in the effectiveness and overall postoperative complication after liver resection, although Hemopatch shows a higher incidence of intraabdominal abscess. Further studies are necessary to confirm these findings.
A comprehensive computational study of amino acid interactions in membrane proteins
Authors: Mbaye Mame Ndew , Hou Qingzhen , Basu Sankar , Teheux Fabian , Pucci Fabrizio , Rooman Marianne 
Published: August 2019

AbstractTransmembrane proteins play a fundamental role in a wide series of biological processes but, despite their importance, they are less studied than globular proteins, essentially because their embedding in lipid membranes hampers their experimental characterization. In this paper, we improved our understanding of their structural stability through the development of new knowledge-based energy functions describing amino acid pair interactions that prevail in the transmembrane and extramembrane regions of membrane proteins. The comparison of these potentials and those derived from globular proteins yields an objective view of the relative strength of amino acid interactions in the different protein environments, and their role in protein stabilization. Separate potentials were also derived from α-helical and β-barrel transmembrane regions to investigate possible dissimilarities. We found that, in extramembrane regions, hydrophobic residues are less frequent but interactions between aromatic and aliphatic amino acids as well as aromatic-sulfur interactions contribute more to stability. In transmembrane regions, polar residues are less abundant but interactions between residues of equal or opposite charges or non-charged polar residues as well as anion-π interactions appear stronger. This shows indirectly the preference of the water and lipid molecules to interact with polar and hydrophobic residues, respectively. We applied these new energy functions to predict whether a residue is located in the trans- or extramembrane region, and obtained an AUC score of 83% in cross validation, which demonstrates their accuracy. As their application is, moreover, extremely fast, they are optimal instruments for membrane protein design and large-scale investigations of membrane protein stability.
Factors affecting dural sinus density in non-contrast computed tomography of brain
Authors: Akhavan Reza , Abbasi Bita , Kheirollahi Moein , Ghamari Khameneh Afshar , Hashemi Jahanbakhsh , Khoei Samin , Darban Hosseini Amirkhiz Gisoo 
Published: August 2019

AbstractThe possibility of changing the intracranial vasculature computed tomography (CT) attenuation under the influence of variable factors is a long-held unestablished belief. The purpose of this study is to evaluate factors affecting dural sinus density in non-contrast computed tomography of the brain. Patients presented with acute neurologic symptoms to the emergency department were candidates to be enrolled in this study. A region of interest (ROI) measuring 1–2-mm2 recorder (base on sinus size) used to measure the attenuation of each sinus in Hounsfield Unit (HU) and then mean density calculated. CBC, BUN and Cr were extracted from patients’ records. Chi-square test, correlation analyze, independent sample unpaired student t-test and one-way ANOVA test and Multivariate logistic regression were used. Positive significant correlation (0.48) was found between the hematocrit level (HCT) and average attenuation in the four sinus segments (P value < 0.0001) and between the HCT and basilar artery attenuation (P value < 0.0001). There was no significant correlation between the age and average attenuation. There was a significant and negative correlation between the BUN/Cr and average attenuation. Using a multivariate analysis on a large sample volume, we conclude that Hgb and HCT are the only factors that have a significant correlation with average sinus attenuation. This correlation is relatively stronger for Hgb in comparison to HCT.
Calcium carbonate alters the functional response of coastal sediments to eutrophication-induced acidification
Authors: Drylie Tarn P. , Needham Hazel R. , Lohrer Andrew M. , Hartland Adam , Pilditch Conrad A. 
Published: August 2019

AbstractCoastal ocean acidification research is dominated by laboratory-based studies that cannot necessarily predict real-world ecosystem response given its complexity. We enriched coastal sediments with increasing quantities of organic matter in the field to identify the effects of eutrophication-induced acidification on benthic structure and function, and assess whether biogenic calcium carbonate (CaCO3) would alter the response. Along the eutrophication gradient we observed declines in macrofauna biodiversity and impaired benthic net primary productivity and sediment nutrient cycling. CaCO3 addition did not alter the macrofauna community response, but significantly dampened negative effects on function (e.g. net autotrophy occurred at higher levels of organic matter enrichment in +CaCO3 treatments than −CaCO3 (1400 vs 950 g dw m−2)). By identifying the links between eutrophication, sediment biogeochemistry and benthic ecosystem structure and function in situ, our study represents a crucial step forward in understanding the ecological effects of coastal acidification and the role of biogenic CaCO3 in moderating responses.