bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variation in space and time: a long-term examination of density-dependent dispersal in a woodland rodent
Authors: Denomme-Brown Simon T. , Cottenie Karl , Falls J. Bruce , Falls E. Ann , Brooks Ronald J. , McAdam Andrew G. 
Published: January 2019

AbstractDispersal is a fundamental ecological process that can be affected by population density, yet studies report contrasting effects of density on propensity to disperse. Additionally, the relationship between dispersal and density is seldom examined using densities measured at different spatial scales or over extensive time-series. We used 51-years of trapping data to examine how dispersal by wild deer mice (Peromyscus maniculatus) was affected by changes in both local and regional population densities. We examined these patterns over both the entire time-series and also in ten-year shifting windows to determine whether the nature and strength of the relationship changed through time. Probability of dispersal decreased with increased local and regional population density, and the negative effect of local density on dispersal was more pronounced in years with low regional densities. Additionally, the strength of negative density-dependent dispersal changed through time, ranging from very strong in some decades to absent in other periods of the study. Finally, while females were less likely to disperse, female dispersal was more density-dependent than male dispersal. Our study shows that the relationship between density and dispersal is not temporally static and that investigations of density-dependent dispersal should consider both local and regional population densities.
Geographic Patterns of Bacterioplankton among Lakes of the Middle and Lower Reaches of the Yangtze River Basin, China
Authors: Bai Chengrong , Cai Jian , Zhou Lei , Jiang Xingyu , Hu Yang , Dai Jiangyu , Shao Keqiang , Tang Xiangming , Yang Xiangdong , Gao Guang 
Published: January 2019

AbstractIn aquatic ecosystems, microbial biogeography research is critical for unveiling the mechanisms of microbial community succession. However, little is known about the microbial biogeography among interconnected lakes. To address this deficit, we used high-throughput sequencing to explore geographic patterns and the relative importance of ecological processes that shape these patterns in abundant and rare bacterial subcommunities from 25 lakes across the middle and lower reaches of Yangtze River basin (MLYB, located in southeast China), where most of the lakes are interconnected by river networks. We found that there were significant differences in both abundant and rare bacterial subcommunities between the two lake groups that were far from each other, while were no difference among the nearby lakes in each group. Both abundant and rare bacteria followed a strong distance-decay relationship, especially for rare bacteria. These findings suggest that although the interconnectivity between lakes breaks the geographical isolation of bacteria, the dispersal capability of bacterial taxa was still limited by geographic distance. We also found that although deterministic processes and stochastic processes together drive the bacterial subcommunities assembly, the stochastic processes (based on adjusted R2 in redundancy analysis) exhibited a greater influence on bacterial subcommunities. Our results implied that bacterial dispersal among interconnected lakes was more stochastically.ImportanceUnraveling the relative importance of ecological processes regulating microbial community structure is a central goal in microbial ecology. In aquatic ecosystems, microbial communities often occur in spatially structured habitats, where connectivity directly affects dispersal and metacommunity processes. Recent theoretical work suggests that directional dispersal among connected habitats leads to higher variability in local diversity and among-community composition. However, the study of microbial biogeography among natural interconnected habitats is still lacking. The findings of this study revealed interesting phenomena of microbial biogeography among natural interconnected habitats, suggested that the high interconnectivity reduced the spatial heterogeneity of bacteria, and caused the dispersal of bacteria to be more stochastically. This study has provided a deeper understanding of the biogeographic patterns of rare and abundant bacterial taxa and their determined processes among interconnected aquatic habitats.
Comparison of expression profiling through microarray and RNA-seq analysis for Nipah virus
Authors: Rajput Akanksha , Kumar Manoj 
Published: January 2019

AbstractThe Nipah virus is responsible various outbreaks among countries of south east Asia, most recent is in Kerala, India. It is considered to be highly contagious and having a range of vectors for transmission. The condition worsens due to the lack of effective inhibitors. This study is first study, which focused to detect the differentially expressed genes among two different NiV studies from 2012 and 2017. The transcriptomic profiling data were retrieved from the sequence archives. The multivariate gene enrichment analyses were performed on the log transformed data from them using pathway, gene ontology, disease, reactome, etc. The comparison study suggests that the down regulated differentially expressed genes are common among them as compared to up regulated ones with statistical significance. However, among the diseased category the upregulated genes are mostly from metabolic pathways and diseased category like metabolic pathways, heart failure, cholesterol metabolism while the downregulated genes linked to various cancers, and viral diseases like hepatitis, dengue, influenza, etc. We found various small molecules mapped in the pathways which are differentially expressed among the studies, which could be targeted so as to control the Nipah infection. In order to design the inhibitors, our study would be useful to extract the effective and broad-spectrum drug targets.
Neuronal differentiation affects tissue mechanics and progenitor arrangement in the vertebrate neuroepithelium
Authors: Guerrero Pilar , Perez-Carrasco Ruben , Zagorski Marcin , Page David , Kicheva Anna , Briscoe James , Page Karen M. 
Published: January 2019

ABSTRACTCell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube where neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we use experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates inter-kinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube.
Bright near-infrared genetically encoded voltage indicator for all-optical electrophysiology
Authors: Monakhov Mikhail V. , Matlashov Mikhail E. , Colavita Michelangelo , Song Chenchen , Shcherbakova Daria M. , Antic Srdjan D. , Verkhusha Vladislav V. , Knöpfel Thomas 
Published: January 2019

AbstractWe developed genetically encoded voltage indicators (GEVIs) using bright near-infrared (NIR) fluorescent proteins from bacterial phytochromes. These new NIR GEVIs are optimized for combination of voltage imaging with simultaneous blue light optogenetic actuator activation. Iterative optimizations led to a GEVI here termed nirButterfly, which reliably reports neuronal activities including subthreshold membrane potential depolarization and hyperpolarization, as well as spontaneous spiking, or electrically- and optogenetically-evoked action potentials. This enables largely improved all-optical causal interrogations of physiology.
Identification of a Type IV CRISPR-Cas system located exclusively on IncHI1B/IncFIB plasmids in Enterobacteriaceae
Authors: Newire Enas , Aydin Alp , Juma Samina , Enne Virve I , Roberts Adam P. 
Published: January 2019

AbstractDuring an investigation of CRISPR carriage in clinical, multi-drug resistant, Klebsiella pneumoniae, a novel CRISPR-Cas system (which we have designated Type IV-B) was detected on plasmids from two K. pneumoniae isolates from Egypt (isolated in 2002-2003) and a single K. pneumoniae isolate from the UK (isolated in 2017). Sequence analysis of other genomes available in GenBank revealed that this novel Type IV-B CRISPR-Cas system was present on 28 other plasmids from various Enterobacteriaceae hosts and was never found on the chromosome. Type IV-B is found exclusively on IncHI1B/IncFIB plasmids and is associated with multiple putative transposable elements. Type IV-B has a single repeat-spacer array (CRISPR1) upstream of the cas loci with some spacers matching regions of conjugal transfer genes of IncFIIK/IncFIB(K) plasmids suggesting a role in plasmid incompatibility. Expression of the cas loci was confirmed in available clinical isolates by RT-PCR; indicating the system is active. To our knowledge, this is the first report describing a new subtype within Type IV CRISPR-Cas systems exclusively associated with IncHI1B/IncFIB plasmids.ImportanceHere, we report the identification of a novel subtype of Type IV CRISPR-Cas that is expressed and exclusively carried by IncHI1B/IncFIB plasmids in Enterobacteriaceae, demonstrating unique evolutionarily juxtaposed connections between CRISPR-Cas and mobile genetic elements (MGEs). Type IV-B encodes a variety of spacers showing homology to DNA from various sources, including plasmid specific spacers and is therefore thought to provide specific immunity against plasmids of other incompatible groups (IncFIIK/IncFIB(K)). The relationship between Type IV-B CRISPR-Cas and MGEs that surround and interrupt the system is likely to promote rearrangement and be responsible for the observed variability of this type. Finally, the Type IV-B CRISPR-Cas is likely to co-operate with other cas loci within the bacterial host genome during spacer acquisition.
The synergistic antitumor effect of combined Anti-Human Epidermal Growth Factor Receptor 2 (HER2) antibody and Gamma Interferon therapy to Ab resistant breast cancer cells
Authors: Gocho Toshihiko , Tsuchiya Hiromichi , Kamijo Shotaro , Yamazaki Yoshitaka , Akita Yui , Sasaki Akiko , Kiuchi Yuji 
Published: January 2019

AbstractAnti-HER2 antibody is molecular targeted antibody for cancer therapy. Approximately 20% of breast cancers are characterized by overexpression of HER2 protein. However, the recurrence rate was 30% and the metastasis rate was 18% one year after treatment of Anti-HER2 antibody for HER2 positive breast cancer. The resistance to antibody treatment is a major problem for patients. We previously reported that Anti-HER2 antibody and Gamma Interferon (IFN-γ) combined therapy showed higher anti-tumor effect than usual therapy in vitro and in vivo mouse experiments.In this study, we evaluated whether anti-HER2 antibody and IFN-γ combined therapy shows good synergistic effect against drug resistant HER2 positive breast cancer cells and higher antitumor effect than conventional clinical treatment. The resistant cell lines were made under the continuous presence of antibody until cell growth was not affected by the drug. We divided the resistant cells into the appropriate number of groups, which we and treated with anti-cancer therapy. We evaluated the antitumor effect for both in vitro study and in vivo mouse xenograft model prepared with the same immunogenicity. And we investigated the differences of immunofluorescence staining of CD8, Gr-1 and PDL-1 in tissues, especially related to immunity system.The combined therapy showed significantly higher anti-tumor effect than other groups in vitro and in vivo experiments. The combined therapy affects anti-tumor immunity in this immunofluorescence experiment. Taken together, we showed the possibility that combined therapy could be an effective treatment option for anti-HER2 antibody resistant breast cancer, helping patients suffering from cancer progression after developing treatment resistance.
Information recovery following a retrospective cue decreases with time
Authors: Nouri Asal , Ester Edward F. 
Published: January 2019

AbstractWorking memory (WM) performance can be enhanced by an informative cue presented during storage. This effect, termed a retrocue benefit, can be used to explore how observers prioritize information stored in WM to guide behavior. Recent studies have demonstrated that neural representations of task-relevant memoranda are strengthened following the appearance of a retrocue, suggesting that participants can consult alternative information stores to supplement active memory traces. Here, we sought to better understand the nature of these memory store(s) by asking whether they are subject to the same temporal degradation seen in active memory representations. We reconstructed and quantified representations of remembered positions from alpha-band EEG activity recorded while participants performed a retrospectively cued spatial WM task, and varied the temporal interval separating the encoding display and retrocue. Although we observed a partial recovery of location information in all cue conditions, the magnitude of recovery was linearly and inversely related to the timing of the retrocue. This suggests that participants’ ability to supplement active memory representations with information from additional memory stores is not static: the information maintained in these stores may be subject to temporal degredation, or the stores themselves may become more difficult to access with time.
What kind of video gamer are you?
Authors: Jimenez Nadia , San-Martin Sonia , Camarero Carmen , San Jose Cabezudo Rebeca 
Published: January 2019

PurposeThis paper aims to attempt to understand the extent to which the effect of motivations on purchase intention varies for diverse segments of video gamers (depending on their personality).Design/methodology/approachInformation was collected from 511 Spanish video game consumers. Structural equation modeling, clustering and multi-group analysis were then conducted to compare results between segments of gamers.FindingsResults show that hedonic, social and mainly addiction motivations lead to purchase intention of game-related products. Moreover, the authors identify a typology of gamer that gives rise to differences in motivations-purchase intention links: Analysts include individuals who are essentially conscientious, prefer inventive or cognitive and simulation games and whose behavior is more influenced by hedonic and social motivations to play; socializers comprise individuals who are mainly extrovert and emotionally stable gamers and who prefer sports and strategy games. The motivations to play that affect their purchase intentions are mainly social; and sentinels include individuals that are unmindful and introvert, prefer inventive, cognitive, sports and simulation games, and whose social motivations drive their purchase intentions.Originality/valueThere are 2,200 million video gamers around the world, although it is assumed that this vast market is not homogeneous, which has implications for consumer motivations and purchase intention. However, the currently available classifications that address this challenge are rather limited. In this sense, the present paper provides valuable insights into understanding how personality offers a useful variable to segment consumers in the video game industry and how it moderates the effect of motivations on purchase behavior.
Regulation of reproductive processes with dynamic energy budgets
Authors: Muller Erik B. , Lika Konstadia , Nisbet Roger M. , Schultz Irvin R. , Casas Jérôme , Gergs André , Murphy Cheryl A. , Nacci Diane , Watanabe Karen H. 
Published: January 2019

Abstract

Linking organismal‐level processes to underlying suborganismal mechanisms at the molecular, cellular and organ level constitutes a major challenge for predictive ecological risk assessments. This challenge can be addressed with the simple bioenergetic models in the family of dynamic energy budget (DEB), which consist of a small number of state equations quantifying universal processes, such as feeding, maintenance, development, reproduction and growth.

Motivated by the need for process‐based models to evaluate the impact of endocrine disruptors on ecologically relevant endpoints, this paper develops and evaluates two general modelling modules describing demand‐driven feedback mechanisms within the DEB modelling framework exerted by gonads on the allocation of resources to production of reproductive matter.

These modules describe iteroparous, semelparous and batch‐mode reproductive strategies. The modules have a generic form with both positive and negative feedback components; species‐ and sex‐specific attributes of endocrine regulation can be added without changing the core of the modules.

We demonstrate that these modules successfully describe time‐resolved measurements of wet weight of body, ovaries and liver, egg diameter and plasma content of vitellogenin and oestradiol in rainbow trout (Oncorynchus mykiss) by fitting these models to published and new data, which require the estimation of less than two parameters per data type.

We illustrate the general applicability of the concept of demand‐driven allocation of resources to reproduction by evaluating one of the modules with data on growth and seed production of an annual plant, the common bean (Phaseolis vulgaris).

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Three‐dimensional geophysical characterization of the La Rambla and Zafra de Záncara anticlines (Loranca Basin, Central Spain)
Authors: Ayala C. , Rubio F.M. , Rey‐Moral C. , Reguera M.I. , Biete C. 
Published: January 2019

ABSTRACTThe Zafra de Záncara anticline (also known as the El Hito anticline), located in the Loranca Cenozoic Basin (part of the Tagus Basin, Central Spain), had been studied by several oil companies during the late 1960s and early 1970s. In 2009, within the ‘Plan for selection and characterization of suitable structures of CO2 geological storage’, this anticline was selected as a potential CO2 storage site. A preliminary three‐dimensional geological model, based on five geological cross sections that were constrained with the interpretation of the available seismic profiles (that are rather old and do not have very good quality), was created. With the aim of improving the geological knowledge of the Zafra de Záncara anticline and helping to investigate the suitability of a nearby anticline, namely La Rambla, as another structural closure that might make it a possible CO2 storage site, a local gravity survey (1 station every km2) was carried out in the area, seven new geological cross sections, based on these existing seismic profiles and field geology, were build, and a new three‐dimensional geological model that included both anticlines, improved through three‐dimensional stochastic gravity inversion, was constructed. The densities needed for the geological formations of the model come from the analysis of rock samples, logging data from El Hito‐1 drillhole and petrophysical information from Instituto Geológico y Minero de España database. The inversion has improved the knowledge about the geometry of the anticlines’ traps and seals as well as the geometry of the basement relief and the structural relationship between basement and cover.
Association of Vitamin D Receptor Gene Polymorphism With the Risk of Nephrolithiasis
Authors: Yang Shi‐Kun , Song Na , Wang Yang‐Yang , Li Ai‐Mei , Liu Jun , Deng Fei , Zhan Ming , Zhang Wei , Han Ya‐Chun , Zhang Hao 
Published: January 2019

AbstractThis study aimed to explore the relationship between vitamin D receptor (VDR) gene polymorphisms and the risk of nephrolithiasis. All relevant trials were searched from multiple databases according to predefined criteria, the pooled OR and corresponding 95% CI were analyzed using Stata software. Seventeen studies involving 2441 cases and 2296 controls were included. The pooled analysis showed that VDR BsmI, FokI, and ApaI gene polymorphisms were not associated with nephrolithiasis susceptibility either in Asian and in Caucasians populations. VDR TaqI gene polymorphism was associated with nephrolithiasis in the overall populations (T vs. t: OR = 0.84, 95% CI: 0.73–0.95, P = 0.006; TT vs. Tt + tt: OR = 0.79, 95% CI: 0.66–0.95, P = 0.010). In Asian population, VDR TaqI gene polymorphism also was associated with nephrolithiasis susceptibility (TT vs. Tt + tt: OR = 0.72, 95% CI: 0.55–0.93, P = 0.012; Tt vs. TT + tt: OR = 1.43, 95% CI: 1.00–2.05, P = 0.048). But TaqI gene polymorphism was not associated with nephrolithiasis risk in Caucasian populations (T vs. t: OR = 0.85, 95% CI: 0.72–1.00, P = 0.051; TT vs. Tt + tt: OR = 0.87, 95% CI: 0.68–1.10, P = 0.245; tt vs. Tt + TT: OR = 1.32, 95% CI: 0.86–2.01, P = 0.206; Tt vs. TT+ tt: OR = 0.98, 95% CI: 0.70–1.38, P = 0.931). VDR BsmI, FokI, and ApaI gene polymorphisms were not associated with the risk of nephrolithiasis either in Asian and Caucasians populations, but VDR TaqI gene polymorphism was associated with nephrolithiasis in the Asian subjects.
LlpB represents a second subclass of lectin‐like bacteriocins
Authors: Ghequire Maarten G. K. , De Mot René 
Published: January 2019

SummaryBacteriocins are secreted bacterial proteins that selectively kill related strains. Lectin‐like bacteriocins are atypical bacteriocins not requiring a cognate immunity factor and have been primarily studied in Pseudomonas. These so‐called LlpAs are composed of a tandem of B‐lectin domains. One domain interacts with d‐rhamnose residues in the common polysaccharide antigen of Pseudomonas lipopolysaccharide (LPS). The other lectin domain is crucial for interference with the outer membrane protein assembly machinery by interacting with surface‐exposed loops of its central component BamA. Via genome mining, we identified a second subclass of Pseudomonas lectin‐like proteins, termed LlpB, consisting of a single B‐lectin domain. We show that these proteins also display bactericidal activity. Among LlpB‐resistant transposon mutants of an LlpB‐susceptible Pseudomonas strain, a major subset was hit in an acyltransferase gene, predicted to be involved in LPS core modification, hereby suggesting that LlpBs equally attach to LPS for surface anchoring. This indicates that LPS binding and target strain specificity are condensed in a single B‐lectin domain. The identification of this second subclass of lectin‐like bacteriocins further expands the toolbox of antibacterial warfare deployed by bacteria and holds potential for their integration in biotechnological applications.