bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bipolar lophotrichous Helicobacter suis combine extended and wrapped flagella bundles to exhibit multiple modes of motility
Authors: Constantino Maira A. , Jabbarzadeh Mehdi , Fu Henry C. , Shen Zeli , Fox James G. , Haesebrouck Freddy , Linden Sara K. , Bansil Rama 
Published: September 2018

AbstractThe swimming strategies of unipolar flagellated bacteria are well known but little is known about how bipolar bacteria swim. Here we examine the motility of Helicobacter suis, a bipolar gastric-ulcer-causing bacterium that infects pigs and humans. Phase-contrast microscopy of unlabeled bacteria reveals flagella bundles in two conformations, extended away from the body (E) or flipped backwards and wrapped (W) around the body. We captured videos of the transition between these two states and observed three different swimming modes in broth: with one bundle rotating wrapped around the body and the other extended (EW), both extended (EE), and both wrapped (WW). Only EW and WW modes were seen in porcine gastric mucin. The EW mode displayed ballistic trajectories while the other two displayed superdiffusive random walk trajectories with slower swimming speeds. Separation into these two categories was also observed by tracking the mean square displacement of thousands of trajectories at lower magnification. Using the Method of Regularized Stokeslets we numerically calculate the swimming dynamics of these three different swimming modes and obtain good qualitative agreement with the measurements, including the decreased speed of the less frequent modes. Our results suggest that the extended bundle dominates the swimming dynamics.
Psychological Profile in Coronary Artery By-Pass Graft Patients vs. Valve Replacement Patients Entering Cardiac Rehabilitation after Surgery
Authors: Modica Maddalena , Castiglioni Paolo , Minotti Anna , Faini Andrea , Racca Vittorio , Ferratini Maurizio 
Published: September 2018

AbstractAnxiety and depression are thought to influence the genesis of ischemic diseases and not of valvular diseases, but little is known on the psychological profile of cardiac patients after surgery. Aim of this study was to investigate differences in disease experience and mood between patients undergoing cardiac rehabilitation after coronary artery by-pass graft (CABG) or after valve replacement (VR). We studied 1,179 CABG and 737 VR patients who completed the Illness Behaviour Questionnaire and the Hospital Anxiety and Depression Scale after surgery. We tested the independent effect of the type of surgery by multivariate analysis and between-group differences in prevalence of clinically relevant scores. Relevant scores in the psychosomatic concern scale were more frequent in CABG than in VR patients. After correction by age, sex, education and marital status, scores of disease conviction and psychosomatic concern were higher in CABG patients, scores of denial were higher in VR patients. Unexpectedly, anxiety and depression scores did not differ between groups. Results suggest providing psychological support for anxiety and depression to both VR and CABG patients during cardiac rehabilitation, and planning differentiated interventions of cardiac rehabilitation and secondary prevention tailored to the specific psychological reactions of CABG and VR patients.
Micropatterning of planar metal electrodes by vacuum filling microfluidic channel geometries
Authors: Chatzimichail Stelios , Supramaniam Pashiini , Ces Oscar , Salehi-Reyhani Ali 
Published: September 2018

AbstractWe present a simple, facile method to micropattern planar metal electrodes defined by the geometry of a microfluidic channel network template. By introducing aqueous solutions of metal into reversibly adhered PDMS devices by desiccation instead of flow, we are able to produce difficult to pattern “dead end” or discontinuous features with ease. We characterize electrodes fabricated using this method and perform electrical lysis of mammalian cancer cells and demonstrate their use as part of an antibody capture assay for GFP. Cell lysis in microwell arrays is achieved using the electrodes and the protein released is detected using an antibody microarray. We show how the template channels used as part of the workflow for patterning the electrodes may be produced using photolithography-free methods, such as laser micromachining and PDMS master moulding, and demonstrate how the use of an immiscible phase may be employed to create electrode spacings on the order of 25–50 μm, that overcome the current resolution limits of such methods. This work demonstrates how the rapid prototyping of electrodes for use in total analysis systems can be achieved on the bench with little or no need for centralized facilities.
Biolistic-delivery-based transient CRISPR/Cas9 expression enables in planta genome editing in wheat
Authors: Hamada Haruyasu , Liu Yuelin , Nagira Yozo , Miki Ryuji , Taoka Naoaki , Imai Ryozo 
Published: September 2018

AbstractThe current application of genome editing to crop plants is limited to cultivars that are amenable to in vitro culture and regeneration. Here, we report an in planta genome-editing which does not require callus culture and regeneration. Shoot apical meristems (SAMs) contain a subepidermal cell layer, L2, from which germ cells later develop during floral organogenesis. The biolistic delivery of gold particles coated with plasmids expressing CRISPR/Cas9 components designed to target TaGASR7 were bombarded into SAM-exposed embryos of imbibed seeds. Bombarded embryos showing transient GFP expression within SAM were selected and grown into adult plants. Mutations in the target gene were assessed in fifth-leaf tissue by cleaved amplified polymorphic sequence analysis. Eleven (5.2%) of the 210 bombarded plants carried mutant alleles, and the mutations of three (1.4%) of these were inherited in the next generation. Genotype analysis of T1 plants identified plants homozygous for the three homeologous genes, which were all derived from one T0 plant. These plants showed no detectable integration of the Cas9 and guide RNA genes, indicating that transient expression of CRISPR/Cas9 introduced the mutations. Together, our current method can be used to achieve in planta genome editing in wheat using CRISPR/Cas9 and suggests possible applications to other recalcitrant plant species and variations.
Climate change to severely impact West African basin scale irrigation in 2 °C and 1.5 °C global warming scenarios
Authors: Sylla Mouhamadou Bamba , Pal Jeremy S. , Faye Aissatou , Dimobe Kangbeni , Kunstmann Harald 
Published: September 2018

AbstractWest Africa is in general limited to rainfed agriculture. It lacks irrigation opportunities and technologies that are applied in many economically developed nations. A warming climate along with an increasing population and wealth has the potential to further strain the region’s potential to meet future food needs. In this study, we investigate West Africa’s hydrological potential to increase agricultural productivity through the implementation of large-scale water storage and irrigation. A 23-member ensemble of Regional Climate Models is applied to assess changes in hydrologically relevant variables under 2 °C and 1.5 °C global warming scenarios according to the UNFCCC 2015 Conference of Parties (COP 21) agreement. Changes in crop water demand, irrigation water need, water availability and the difference between water availability and irrigation water needs, here referred as basin potential, are presented for ten major river basins covering entire West Africa. Under the 2 °C scenario, crop water demand and irrigation water needs are projected to substantially increase with the largest changes in the Sahel and Gulf of Guinea respectively. At the same time, irrigation potential, which is directly controlled by the climate, is projected to decrease even in regions where water availability increases. This indicates that West African river basins will likely face severe freshwater shortages thus limiting sustainable agriculture. We conclude a general decline in the basin-scale irrigation potential in the event of large-scale irrigation development under 2 °C global warming. Reducing the warming to 1.5 °C decreases these impacts by as much as 50%, suggesting that the region of West Africa clearly benefits from efforts of enhanced mitigation.
Theoretical predicted high-thermal-conductivity cubic Si3N4 and Ge3N4: promising substrate materials for high-power electronic devices
Authors: Xiang Huimin , Feng Zhihai , Li Zhongping , Zhou Yanchun 
Published: September 2018

AbstractCeramic substrates play key roles in power electronic device technology through dissipating heat, wherein both high thermal conductivity and mechanical strength are required. The increased power of new devices has led to the replacement of Al2O3 by high thermal conducting AlN and further β-Si3N4 based substrates. However, the low mechanical strength and/or anisotropic mechanical/thermal properties are still the bottlenecks for the practical applications of these materials in high power electronic devices. Herein, using a combination of density functional theory and modified Debye-Callaway model, two new promising substrate materials γ-Si3N4 and γ-Ge3N4 are predicted. Our results demonstrate for the first time that both compounds exhibit higher room temperature thermal conductivity but less anisotropy in expansion and heat conduction compared to β-Si3N4. The mechanism underpins the high RT κ is identified as relatively small anharmonicity, high phonon velocity and frequency. The suitability of these two nitrides as substrate materials was also discussed.
Assessing cortical plasticity after spinal cord injury by using resting-state functional magnetic resonance imaging in awake adult mice
Authors: Matsubayashi Kohei , Nagoshi Narihito , Komaki Yuji , Kojima Kota , Shinozaki Munehisa , Tsuji Osahiko , Iwanami Akio , Ishihara Ryosuke , Takata Norio , Matsumoto Morio , Mimura Masaru , Okano Hideyuki , Nakamura Masaya 
Published: September 2018

AbstractNeural connectivity has recently been shown to be altered after spinal cord injury (SCI) not only in the spinal cord but also in the brain. However, to date, no studies have analyzed the functional alterations after SCI in various areas of the cerebral cortex over time. To examine the plasticity of the neural connectivity in the brain after SCI, we performed resting-state functional magnetic resonance imaging (rs-fMRI) in awake adult mice pre- and post-SCI. After a complete thoracic SCI, the functional connectivity between the primary motor (MOp) and primary sensory (SSp) areas was significantly decreased during the chronic phase. In contrast, the connectivity between the MOp and motivation area was increased. Thus, impairments in sensory and motor connections after SCI led to a time-dependent compensatory upregulation of “motor functional motivation”. Moreover, the functional connectivity between the SSp and pain-related areas, such as the caudoputamen (CP) and the anterior cingulate area (ACA), was strengthened during the chronic phase, thus suggesting that rs-fMRI can indicate the presence of neuropathic pain after SCI. Therefore, rs-fMRI is a useful tool for revealing the pathological changes that occur in the brain after SCI.
Effects of Social Exclusion on Effortful Control and Mentalizing in relation to Borderline Personality Features
Authors: Sato Momoko , Fonagy Peter , Luyten Patrick 
Published: September 2018

AbstractThe current study investigated the effects of social interactions on effortful control (EC) and mentalizing in individuals with borderline personality disorder (BPD) features. 123 nonclinical participants completed the emotional Stroop task to assess EC and the modified Reading the Mind in the Eyes Test (RMET) to assess mentalizing capacities before and after having social interactions. The Cyberball paradigm was used to generate socially inclusive and exclusive interactions. Results indicated the high BPD group made more errors on the Stroop task following exclusive social interactions than the low BPD group. The high BPD group, compared to the low BPD group, associated fewer emotional words with facial cues following inclusive social interactions but overanalysed facial cues (hypermentalizing) following the exclusive social interaction. Exclusive social interactions hindered the inhibitory capacities in individuals with high BPD features, but inclusive social interactions facilitated. Individuals with high BPD features responded to exclusive social interactions by hypermentalizing. Thus, it was found social rejection could activate cognitive-affective processes which led to hypermentalizing and impairments in EC which in combination could explain the disruptive effects on social interactions in people with BPD features.
MicroRNA Expression Profiles in Gastric Carcinogenesis
Authors: Hwang Jinha , Min Byung-Hoon , Jang Jiryeon , Kang So Young , Bae Hyunsik , Jang Se Song , Kim Jong-Il , Kim Kyoung-Mee 
Published: September 2018

AbstractIntestinal-type gastric carcinoma exhibits a multistep carcinogenic sequence from adenoma to carcinoma with a gradual increase in genomic alterations. But the roles of microRNAs (miRNA) in this multistage cascade are not fully explored. To identify differentially expressed miRNA (DEM) during early gastric carcinogenesis, we performed miRNA microarray profiling with 24 gastric cancers and precursor lesions (7 early gastric cancer [EGC], 3 adenomas with high-grade dysplasia, 4 adenomas with low-grade dysplasia, and 10 adjacent normal tissues). Alterations in the expression of 132 miRNA were detected; these were categorized into three groups based on their expression patterns. Of these, 42 miRNAs were aberrantly expressed in EGC. Five miRNA (miR-26a, miR-375, miR-574-3p, miR-145, and miR-15b) showed decreased expression since adenoma. Expression of two miRNA, miR-200C and miR-29a, was down-regulated in EGCs compared to normal mucosa or adenomas. Six miRNA (miR-601, miR-107, miR-18a, miR-370, miR-300, and miR-96) showed increased expression in gastric cancer compared to normal or adenoma samples. Five representative miRNAs were further validated with RT-qPCR in independent 77 samples. Taken together, these results suggest that the dysregulated miRNA show alterations at the early stages of gastric tumorigenesis and may be used as a candidate biomarker.
Ahnak promotes tumor metastasis through transforming growth factor-β-mediated epithelial-mesenchymal transition
Authors: Sohn Mira , Shin Sunmee , Yoo Jung-Yeon , Goh Yookyung , Lee In Hye , Bae Yun Soo 
Published: September 2018

AbstractPreviously, we reported a molecular mechanism by which Ahnak potentiates transforming growth factor-β (TGFβ) signaling during cell growth. Here, we show that Ahnak induces epithelial-mesenchymal transition (EMT) in response to TGFβ. EMT phenotypes, including altered in cell morphology, and expression patterns of various EMT marker genes were detected in HaCaT keratinocytes transfected with Ahnak-specific siRNA. Knockdown of Ahnak expression in HaCaT keratinocytes resulted in attenuated cell migration and invasion. We found that Ahnak activates TGFβ signaling via Smad3 phosphorylation, leading to enhanced Smad3 transcriptional activity. To validate function of Ahnak in EMT of B16F10 cells having high metastatic and tumorigenic properties, we established B16F10 cells with stable knockdown of Ahnak. N-cadherin expression and Smad3 phosphorylation were significantly decreased in B16F10-shAhnak cells, compared to B16F10-shControl cells after treatment of TGFβ. Moreover, TGFβ failed to induce cell migration and cell invasion in B16F10-shAhnak cells. To determine whether Ahnak regulates the metastatic activity of B16F10 cells, we established a lung metastasis model in C57BL/6 mice via tail vein injection of B16F10-shAhnak cells. Lung metastasis was significantly suppressed in mice injected with B16F10-shAhnak cells, compared to those injected with B16F10-shControl cells. Taken together, we propose that TGFβ-Ahnak signaling axis regulates EMT during tumor metastasis.
A Toolbox for Diverse Oxyfunctionalisation of Monoterpenes
Authors: Hernandez-Ortega Aitor , Vinaixa Maria , Zebec Ziga , Takano Eriko , Scrutton Nigel S. 
Published: September 2018

AbstractThe successful implementation of synthetic biology for chemicals biosynthesis relies on the availability of large libraries of well-characterized enzymatic building blocks. Here we present a scalable pipeline that applies the methodology of synthetic biology itself to bootstrap the creation of such a library. By designing and building a cytochrome P450 enzyme collection and testing it in a custom-made untargeted GC/MS-metabolomics-based approach, we were able to rapidly create and characterize a comprehensive enzyme library for the controlled oxyfunctionalisation of terpene scaffolds with a wide range of activities and selectivities towards several monoterpenes. This novel resource can now be used to access the extensive chemical diversity of terpenoids by pathway engineering and the assembly of biocatalytic cascades to subsequently produce libraries of oxygenated terpenoids and their derivatives for diverse applications, including drug discovery.
Meta-analysis of data from spaceflight transcriptome experiments does not support the idea of a common bacterial “spaceflight response”
Authors: Morrison Michael D. , Nicholson Wayne L. 
Published: September 2018

AbstractSeveral studies have been undertaken with the goal of understanding how bacterial transcriptomes respond to the human spaceflight environment. However, these experiments have been conducted using a variety of organisms, media, culture conditions, and spaceflight hardware, and to date no cross-experiment analyses have been performed to uncover possible commonalities in their responses. In this study, eight bacterial transcriptome datasets deposited in NASA’s GeneLab Data System were standardized through a common bioinformatics pipeline then subjected to meta-analysis to identify among the datasets (i) individual genes which might be significantly differentially expressed, or (ii) gene sets which might be significantly enriched. Neither analysis resulted in identification of responses shared among all datasets. Principal Component Analysis of the data revealed that most of the variation in the datasets derived from differences in the experiments themselves.
A meta-analysis of bovine viral diarrhoea virus (BVDV) prevalences in the global cattle population
Authors: Scharnböck Bettina , Roch Franz-Ferdinand , Richter Veronika , Funke Carsten , Firth Clair L. , Obritzhauser Walter , Baumgartner Walter , Käsbohrer Annemarie , Pinior Beate 
Published: September 2018

AbstractA random effect meta-analysis was performed to estimate the worldwide pooled bovine viral diarrhoea virus (BVDV) prevalences of persistently infected (PI), viraemic (VI) and antibody-positive (AB) animals and herds. The meta-analysis covered 325 studies in 73 countries that determined the presence or absence of BVDV infections in cattle from 1961 to 2016. In total, 6.5 million animals and 310,548 herds were tested for BVDV infections in the global cattle population. The worldwide pooled PI prevalences at animal level ranged from low (≤0.8% Europe, North America, Australia), medium (>0.8% to 1.6% East Asia) to high (>1.6% West Asia). The PI and AB prevalences in Europe decreased over time, while BVDV prevalence increased in North America. The highest mean pooled PI prevalences at animal level were identified in countries that had failed to implement any BVDV control and/or eradication programmes (including vaccination). Our analysis emphasizes the need for more standardised epidemiological studies to support decision-makers implementing animal health policies for non-globally-regulated animal diseases.
ANTH domain-containing proteins are required for the pollen tube plasma membrane integrity via recycling ANXUR kinases
Authors: Muro Keita , Matsuura-Tokita Kumi , Tsukamoto Ryoko , Kanaoka Masahiro M. , Ebine Kazuo , Higashiyama Tetsuya , Nakano Akihiko , Ueda Takashi 
Published: September 2018

AbstractDuring plant reproduction, sperm cells are delivered to ovules through growing pollen tubes. This process involves tip-localized receptor kinases regulating integrity and/or guidance of pollen tubes, whose localizations must be strictly regulated. However, the molecular basis for tip-localization of these molecules remains largely elusive. Here we show that a pair of AP180 N-terminal homology domain-containing proteins, PICALM5a and PICALM5b, is responsible for the tip-localization of ANXUR receptor kinases acting in an autocrine signaling pathway required for pollen tube integrity in Arabidopsis thaliana. The picalm5a picalm5b double mutant exhibits reduced fertility, and the double mutant pollen is defective in pollen tube integrity with premature bursts. The tip localization of ANXUR proteins is severely impaired in picalm5a picalm5b pollen tubes, whereas another receptor kinase PRK6 acting in pollen tube guidance is not affected. Based on these results, we propose that PICALM5 proteins serve as specific loading adaptors to recycle ANXUR proteins.
2D association and integrative omics analysis in rice provides systems biology view in trait analysis
Authors: Zhang Wenchao , Dai Xinbin , Xu Shizhong , Zhao Patrick X. 
Published: September 2018

AbstractThe interactions among genes and between genes and environment contribute significantly to the phenotypic variation of complex traits and may be possible explanations for missing heritability. However, to our knowledge no existing tool can address the two kinds of interactions. Here we propose a novel linear mixed model that considers not only the additive effects of biological markers but also the interaction effects of marker pairs. Interaction effect is demonstrated as a 2D association. Based on this linear mixed model, we developed a pipeline, namely PATOWAS. PATOWAS can be used to study transcriptome-wide and metabolome-wide associations in addition to genome-wide associations. Our case analysis with real rice recombinant inbred lines (RILs) at three omics levels demonstrates that 2D association mapping and integrative omics are able to provide a systems biology view into the analyzed traits, leading toward an answer about how genes, transcripts, proteins, and metabolites work together to produce an observable phenotype.
Fitness variation in isogenic populations leads to a novel evolutionary mechanism for crossing fitness valleys
Authors: Van Egeren Debra , Madsen Thomas , Michor Franziska 
Published: September 2018

AbstractIndividuals in a population often have different fitnesses even when they have identical genotypes, but the effect of this variation on the evolution of a population through complicated fitness landscapes is unknown. Here, we investigate how populations with non-genetic fitness variation cross fitness valleys, common barriers to adaptation in rugged fitness landscapes in which a population must pass through a deleterious intermediate to arrive at a final advantageous stage. We develop a stochastic computational model describing the dynamics of an asexually reproducing population crossing a fitness valley, in which individuals of the same evolutionary stage can have variable fitnesses. We find that fitness variation that persists over multiple generations increases the rate of valley crossing through a novel evolutionary mechanism different from previously characterized mechanisms such as stochastic tunneling. By reducing the strength of selection against deleterious intermediates, persistent fitness variation allows for faster adaptation through rugged fitness landscapes.