bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrio coralliilyticus infection triggers a behavioural response and perturbs nutritional exchange and tissue integrity in a symbiotic coral
Authors: Gibbin E , Gavish A , Krueger T , Kramarsky-Winter E , Shapiro O , Guiet R , Jensen L , Vardi A , Meibom A 
Published: December 2018

Abstract
Under homoeostatic conditions, the relationship between the coral Pocillopora damicornis and Vibrio coralliilyticus is commensal. An increase in temperature, or in the abundance of V. coralliilyticus, can turn this association pathogenic, causing tissue lysis, expulsion of the corals’ symbiotic algae (genus Symbiodinium), and eventually coral death. Using a combination of microfluidics, fluorescence microscopy, stable isotopes, electron microscopy and NanoSIMS isotopic imaging, we provide insights into the onset and progression of V. coralliilyticus infection in the daytime and at night, at the tissue and (sub-)cellular level. The objective of our study was to connect the macro-scale behavioural response of the coral to the micro-scale nutritional interactions that occur between the host and its symbiont. In the daytime, polyps enhanced their mucus production, and actively spewed pathogens. Vibrio infection primarily resulted in the formation of tissue lesions in the coenosarc. NanoSIMS analysis revealed infection reduced 13C-assimilation in Symbiodinium, but increased 13C-assimilation in the host. In the night incubations, no mucus spewing was observed, and a mucus film was formed on the coral surface. Vibrio inoculation and infection at night showed reduced 13C-turnover in Symbiodinium, but did not impact host 13C-turnover. Our results show that both the nutritional interactions that occur between the two symbiotic partners and the behavioural response of the host organism play key roles in determining the progression and severity of host-pathogen interactions. More generally, our approach provides a new means of studying interactions (ranging from behavioural to metabolic scales) between partners involved in complex holobiont systems, under both homoeostatic and pathogenic conditions.
Local mutational diversity drives intratumoral immune heterogeneity in non-small cell lung cancer
Authors: Jia Qingzhu , Wu Wei , Wang Yuqi , Alexander Peter B. , Sun Chengdu , Gong Zhihua , Cheng Jia-Nan , Sun Huaibo , Guan Yanfang , Xia Xuefeng , Yang Ling , Yi Xin , Wan Yisong Y. , Wang Haidong , He Ji , Futreal P. Andrew , Li Qi-Jing , Zhu Bo 
Published: December 2018

AbstractCombining whole exome sequencing, transcriptome profiling, and T cell repertoire analysis, we investigate the spatial features of surgically-removed biopsies from multiple loci in tumor masses of 15 patients with non-small cell lung cancer (NSCLC). This revealed that the immune microenvironment has high spatial heterogeneity such that intratumoral regional variation is as large as inter-personal variation. While the local total mutational burden (TMB) is associated with local T-cell clonal expansion, local anti-tumor cytotoxicity does not directly correlate with neoantigen abundance. Together, these findings caution against that immunological signatures can be predicted solely from TMB or microenvironmental analysis from a single locus biopsy.
The propagation of active-passive interfaces in bacterial swarms
Authors: Patteson Alison E. , Gopinath Arvind , Arratia Paulo E. 
Published: December 2018

AbstractPropagating interfaces are ubiquitous in nature, underlying instabilities and pattern formation in biology and material science. Physical principles governing interface growth are well understood in passive settings; however, our understanding of interfaces in active systems is still in its infancy. Here, we study the evolution of an active-passive interface using a model active matter system, bacterial swarms. We use ultra-violet light exposure to create compact domains of passive bacteria within Serratia marcescens swarms, thereby creating interfaces separating motile and immotile cells. Post-exposure, the boundary re-shapes and erodes due to self-emergent collective flows. We demonstrate that the active-passive boundary acts as a diffuse interface with mechanical properties set by the flow. Intriguingly, interfacial velocity couples to local swarm speed and interface curvature, raising the possibility that an active analogue to classic Gibbs-Thomson-Stefan conditions may control this boundary propagation.
Hartman effect for spin waves in exchange regime
Authors: Kłos Jarosław W. , Dadoenkova Yuliya S. , Rychły Justyna , Dadoenkova Nataliya N. , Lyubchanskii Igor L. , Barnaś Józef 
Published: December 2018

AbstractHartman effect for spin waves tunnelling through a barrier in a thin magnetic film is considered theoretically. The barrier is assumed to be created by a locally increased magnetic anisotropy field. The considerations are focused on a nanoscale system operating in the exchange-dominated regime. We derive the formula for group delay τgr of a spin wave packet and show that τgr saturates with increasing barrier width, which is a signature of the Hartman effect predicted earlier for photonic and electronic systems. In our calculations, we consider the general boundary conditions which take into account different strength of exchange coupling between the barrier and its surrounding. As a system suitable for experimental observation of the Hartman effect we propose a CoFeB layer with perpendicular magnetic anisotropy induced by a MgO overlayer.
HAI Peptide and Backbone Analogs—Validation and Enhancement of Biostability and Bioactivity of BBB Shuttles
Authors: Arranz-Gibert Pol , Prades Roger , Guixer Bernat , Guerrero Simón , Araya Eyleen , Ciudad Sonia , Kogan Marcelo J. , Giralt Ernest , Teixidó Meritxell 
Published: December 2018

AbstractLow effectiveness and resistance to treatments are commonplace in disorders of the central nervous system (CNS). These issues concern mainly the blood-brain barrier (BBB), which preserves homeostasis in the brain and protects this organ from toxic molecules and biohazards by regulating transport through it. BBB shuttles—short peptides able to cross the BBB—are being developed to help therapeutics to cross this barrier. BBB shuttles can be discovered by massive exploration of chemical diversity (e.g. computational means, phage display) or rational design (e.g. derivatives from a known peptide/protein able to cross). Here we present the selection of a peptide shuttle (HAI) from several candidates and the subsequent in-depth in vitro and in vivo study of this molecule. In order to explore the chemical diversity of HAI and enhance its biostability, and thereby its bioactivity, we explored two new protease-resistant versions of HAI (i.e. the retro-D-version, and a version that was N-methylated at the most sensitive sites to enzymatic cleavage). Our results show that, while both versions of HAI are resistant to proteases, the retro-D-approach preserved better transport properties.
The effects of a human food additive, titanium dioxide nanoparticles E171, on Drosophila melanogaster - a 20 generation dietary exposure experiment
Authors: Jovanović Boris , Jovanović Nikola , Cvetković Vladimir J. , Matić Sanja , Stanić Snežana , Whitley Elizabeth M. , Mitrović Tatjana Lj. 
Published: December 2018

AbstractIn this study, fruit flies (Drosophila melanogaster) were exposed to an estimated daily human E171 consumption concentration for 20 generations. Exposure to E171 resulted in: a change in normal developmental and reproductive dynamics, reduced fecundity after repetitive breeding, increased genotoxicity, the appearance of aberrant phenotypes and morphologic changes to the adult fat body. Marks of adaptive evolution and directional selection were also exhibited. The larval stages were at a higher risk of sustaining damage from E171 as they had a slower elimination rate of TiO2 compared to the adults. This is particularly worrisome, since among the human population, children tend to consume higher daily concentrations of E171 than do adults. The genotoxic effect of E171 was statistically higher in each subsequent generation compared to the previous one. Aberrant phenotypes were likely caused by developmental defects induced by E171, and were not mutations, since the phenotypic features were not transferred to any progeny even after 5 generations of consecutive crossbreeding. Therefore, exposure to E171 during the early developmental period carries a higher risk of toxicity. The fact that the daily human consumption concentration of E171 interferes with and influences fruit fly physiological, ontogenetic, genotoxic, and adaptive processes certainly raises safety concerns.
An Automatic Classification Method on Chronic Venous Insufficiency Images
Authors: Shi Qiang , Chen Weiya , Pan Ye , Yin Shan , Fu Yan , Mei Jiacai , Xue Zhidong 
Published: December 2018

AbstractChronic venous insufficiency (CVI) affect a large population, and it cannot heal without doctors’ interventions. However, many patients do not get the medical advisory service in time. At the same time, the doctors also need an assistant tool to classify the patients according to the severity level of CVI. We propose an automatic classification method, named CVI-classifier to help doctors and patients. In this approach, first, low-level image features are mapped into middle-level semantic features by a concept classifier, and a multi-scale semantic model is constructed to form the image representation with rich semantics. Second, a scene classifier is trained using an optimized feature subset calculated by the high-order dependency based feature selection approach, and is used to estimate CVI’s severity. At last, classification accuracy, kappa coefficient, F1-score are used to evaluate classification performance. Experiments on the CVI images from 217 patients’ medical records demonstrated superior performance and efficiency for CVI-classifier, with classification accuracy up to 90.92%, kappa coefficient of 0.8735 and F1score of 0.9006. This method also outperformed doctors’ diagnosis (doctors rely solely on images to make judgments) with accuracy, kappa and F1-score improved by 9.11%, 0.1250 and 0.0955 respectively.
Fast oxygen dynamics as a potential biomarker for epilepsy
Authors: Farrell Jordan S. , Greba Quentin , Snutch Terrance P. , Howland John G. , Teskey G. Campbell 
Published: December 2018

AbstractChanges in brain activity can entrain cerebrovascular dynamics, though this has not been extensively investigated in pathophysiology. We assessed whether pathological network activation (i.e. seizures) in the Genetic Absence Epilepsy Rat from Strasbourg (GAERS) could alter dynamic fluctuations in local oxygenation. Spontaneous absence seizures in an epileptic rat model robustly resulted in brief dips in cortical oxygenation and increased spectral oxygen power at frequencies greater than 0.08 Hz. Filtering oxygen data for these fast dynamics was sufficient to distinguish epileptic vs. non-epileptic rats. Furthermore, this approach distinguished brain regions with seizures from seizure-free brain regions in the epileptic rat strain. We suggest that fast oxygen dynamics may be a useful biomarker for seizure network identification and could be translated to commonly used clinical tools that measure cerebral hemodynamics.
Association between diabetes mellitus and poor patient outcomes after out-of-hospital cardiac arrest: A systematic review and meta-analysis
Authors: Voruganti Dinesh Chandra , Chennamadhavuni Adithya , Garje Rohan , Shantha Ghanshyam Palamaner Subash , Schweizer Marin L. , Girotra Saket , Giudici Michael 
Published: December 2018

AbstractDiabetes mellitus (DM) serves as an important prognostic indicator in patients with cardiac-related illness. Our objective is to compare survival and neurological outcomes among diabetic and non-diabetic patients who were admitted to the hospital after an out-of-hospital cardiac arrest (OHCA). We searched MEDLINE and EMBASE for relevant articles from database inception to July 2018 without any language restriction. Studies were included if they evaluated patients who presented with OHCA, included mortality and neurological outcome data separately for DM patients and Non-DM patients and reported crude data, odds ratio (OR), relative risk (RR) or hazard ratio (HR). Two investigators independently reviewed the retrieved citations and assessed eligibility. The quality of included studies was evaluated using Newcastle-Ottawa quality assessment scale for cohort studies. Random-effect models using the generic variance method were used to create pooled odds ratios (OR) and 95% confidence intervals (CI). Heterogeneity was assessed using theI2value. Survival and neurological outcomes (using modified rankin scale and cerebral performance category scale) after OHCA in hospitalized patients with DM compared with patients without DM. Out of 57 studies identified, six cohort studies met the inclusion criteria. In an analysis of unadjusted data, patients with DM had lower odds of survival, pooled OR 0.64; 95% CI, 0.52–0.78, [I2 = 90%]. When adjusted ORs were pooled, the association between DM and survival after OHCA was still significantly reduced, pooled OR 0.78, 95% CI, 0.68–0.89 [I2 = 55%]. Unadjusted pooled OR revealed poor neurological outcomes in patients with DM, pooled OR 0.55, 95% CI, 0.38–0.80 [I2 = 90%]. The result demonstrates significant poor outcomes of in-hospital survival and neurological outcomes among DM patients after OHCA.
Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene
Authors: Cocker Jonathan M. , Wright Jonathan , Li Jinhong , Swarbreck David , Dyer Sarah , Caccamo Mario , Gilmartin Philip M. 
Published: December 2018

AbstractPrimula vulgaris(primrose) exhibits heterostyly: plants produce self-incompatible pin- or thrum-form flowers, with anthers and stigma at reciprocal heights. Darwin concluded that this arrangement promotes insect-mediated cross-pollination; later studies revealed control by a cluster of genes, or supergene, known as theS(Style length) locus. TheP.vulgaris Slocus is absent from pin plants and hemizygous in thrum plants (thrum-specific); mutation ofSlocus genes produces self-fertile homostyle flowers with anthers and stigma at equal heights. Here, we present a 411 Mb P.vulgarisgenome assembly of a homozygous inbred long homostyle, representing ~87% of the genome. We annotate over 24,000 P.vulgarisgenes, and reveal more genes up-regulated in thrum than pin flowers. We show reduced genomic read coverage across theSlocus in otherPrimulaspecies, includingP.veris, where we define the conserved structure and expression of theSlocus genes in thrum. Further analysis reveals theSlocus has elevated repeat content (64%) compared to the wider genome (37%). Our studies suggest conservation ofSlocus genetic architecture inPrimula, and provide a platform for identification and evolutionary analysis of theSlocus and downstream targets that regulate heterostyly in diverse heterostylous species.
Self-Similarity and the Dynamics of Coarsening in Materials
Authors: Sun Yue , Andrews W. Beck , Thornton Katsuyo , Voorhees Peter W. 
Published: December 2018

AbstractTwo-phase mixtures, from metallic alloys to islands on surfaces, undergo coarsening wherein the total interfacial area of the system decreases with time. Theory predicts that during coarsening the average size-scale of a two-phase mixture increases with time as t1/3 when the two-phase mixture is self-similar, or time independent when scaled by a time-dependent length. Here, we explain why this temporal power law is so robustly observed even when the microstructure is not self-similar. We show that there exists an upper limit to the length scales in the system that are kinetically active during coarsening, which we term the self-similar length scale. Length scales smaller than the self-similar length scale evolve, leading to the classical temporal power law for the coarsening dynamics of the system. Longer length scales are largely inactive, leading to a non-self-similar structure. This result holds for any two-phase mixture with a large distribution of morphological length scales.
Adult hippocampal neurogenesis occurs in the absence of Presenilin 1 and Presenilin 2
Authors: Dhaliwal Jagroop , Kannangara Timal S. , Vaculik Michael , Xue Yingben , Kumar Keren L. , Maione Amanda , Béïque Jean-Claude , Shen Jie , Lagace Diane C. 
Published: December 2018

AbstractMutations in the presenilin genes (PS1 and PS2) are a major cause of familial-Alzheimer’s disease (FAD). Presenilins regulate neurogenesis in the developing brain, with loss of PS1 inducing aberrant premature differentiation of neural progenitor cells, and additional loss of PS2 exacerbating this effect. It is unclear, however, whether presenilins are involved in adult neurogenesis, a process that may be impaired in Alzheimer’s disease within the hippocampus. To investigate the requirement of presenilins in adult-generated dentate granule neurons, we examined adult neurogenesis in the PS2−/− adult brain and then employ a retroviral approach to ablate PS1 selectively in dividing progenitor cells of the PS2−/− adult brain. Surprisingly, the in vivo ablation of both presenilins resulted in no defects in the survival and differentiation of adult-generated neurons. There was also no change in the morphology or functional properties of the retroviral-labeled presenilin-null cells, as assessed by dendritic morphology and whole-cell electrophysiology analyses. Furthermore, while FACS analysis showed that stem and progenitor cells express presenilins, inactivation of presenilins from these cells, using a NestinCreERT2 inducible genetic approach, demonstrated no changes in the proliferation, survival, or differentiation of adult-generated cells. Therefore, unlike their significant role in neurogenesis during embryonic development, presenilins are not required for cell-intrinsic regulation of adult hippocampal neurogenesis.
A 3D microvascular network model to study the impact of hypoxia on the extravasation potential of breast cell lines
Authors: Song Jiho , Miermont Agnès , Lim Chwee Teck , Kamm Roger D. 
Published: December 2018

AbstractHypoxia is a common feature of the tumor microenvironment. Accumulating evidence has demonstrated hypoxia to be an important trigger of tumor cell invasion or metastasizes via hypoxia-signaling cascades, including hypoxia-inducible factors (HIFs). Microfluidic model can be a reliable in vitro tool for systematically interrogating individual factors and their accompanying downstream effects, which may otherwise be difficult to study in complex tumor tissues. Here, we used an in vitro model of microvascular networks in a microfluidic chip to measure the extravasation potential of breast cell lines subjected to different oxygen conditions. Through the use of HIF-1α knock-down cell lines, we also validated the importance of HIF-1α in the transmigration ability of human breast cell lines. Three human breast cell lines derived from human breast tissues (MCF10A, MCF-7 and MDA-MB-231) were used in this study to evaluate the role of hypoxia in promoting metastasis at different stages of cancer progression. Under hypoxic conditions, HIF-1α protein level was increased, and coincided with changes in cell morphology, viability and an elevated metastatic potential. These changes were accompanied by an increase in the rate of extravasation compared to normoxia (21% O2). siRNA knockdown of HIF-1α in hypoxic tumors significantly decreased the extravasation rates of all the cell lines tested and may have an effect on the function of metastatic and apoptotic-related cellular processes.
Stimulatory effects of amino acids on γ-polyglutamic acid production by Bacillus subtilis
Authors: Zhang Chao , Wu Daoji , Qiu Xueliang 
Published: December 2018

AbstractThis paper is about study to increase the γ-PGA yield by developing new methods. The effect of various amino acids on production of γ-PGA by Bacillus subtilis Z15 was investigated. The γ-PGA yield was increased 23.18%, 12.15% and 31.46%, respectively, with 3 g/L aspartic acid (0 h), 1.5 g/L phenylalanine (0 h) and 7 g/L glutamic acid (24 h). Additonally, crude extract of glutamic acid after isoelectric crystallization (CEGA)could be a replacement for glutamate for γ-PGA production. Then, response surface methodology (RSM) was used for further optimization. The final media ingredient of amino acids were obtained as follow: CEGA 9 g/L, aspartic acid 4 g/L, phenylalanine 1.55 g/L. By applying this receipt in 5-L bioreactor, the γ-PGA yield reached 42.92 ± 0.23 g/L after 44 h, which is 63.1% higher than the control without amino acids for production. In addition, amino acids could shorten the lag phase and the average fermentation time (44 h versus 48 h). Fermentation with amino acids addition can be an positive option for γ-PGA production.
Environmental factors influencing mucilage accumulation of the endangered Brasenia schreberi in China
Authors: Xie Chun , Li Jiafeng , Pan Fan , Fu Junjie , Zhou Wenzong , Lu Shan , Li Pengfu , Zhou Changfang 
Published: December 2018

AbstractBrasenia schreberi J. F. Gmel. (Cabombaceae), a perennial freshwater macrophyte characterized by a thick mucilage on all underwater organs and especially young buds, has been widely cultivated as an aquatic vegetable in China for many years but is now listed as an endangered species due to anthropogenic impacts and habitat loss. Recent studies have demonstrated that different B. schreberi populations in China have low levels of genetic diversity but significantly different mucilage contents (MucC). Considering the importance of mucilage on both economic and ecological aspects, we examined mucilage-environment relationships in three B. schreberi cultivation sites. The results indicated that water permanganate index (CODMn), total N (TNw), electrical conductivity (ECw), dissolved oxygen (DOw), sediment organic carbon (SOC) and total N (TNs) were significant factors, which explained 82.2% of the variation in mucilage accumulation. The MucC and mucilage thickness (MucT) as well as single bud weight (SBW) of B. schreberi showed negative relationships with CODMn, TNw and ECw but positive relationships with SOC and TNs. Besides, high temperature may have a negative impact on mucilage accumulation of the species. Our study demonstrated that the mucilage accumulation of B. schreberi required good water quality and nutrient-enriched sediments, suggesting that habitat conservation, especially the quality of water, is important for maintaining B. schreberi populations.
Uncovering secondary metabolite evolution and biosynthesis using gene cluster networks and genetic dereplication
Authors: Theobald Sebastian , Vesth Tammi C. , Rendsvig Jakob Kræmmer , Nielsen Kristian Fog , Riley Robert , de Abreu Lucas Magalhães , Salamov Asaf , Frisvad Jens Christian , Larsen Thomas Ostenfeld , Andersen Mikael Rørdam , Hoof Jakob Blæsbjerg 
Published: December 2018

AbstractThe increased interest in secondary metabolites (SMs) has driven a number of genome sequencing projects to elucidate their biosynthetic pathways. As a result, studies revealed that the number of secondary metabolite gene clusters (SMGCs) greatly outnumbers detected compounds, challenging current methods to dereplicate and categorize this amount of gene clusters on a larger scale. Here, we present an automated workflow for the genetic dereplication and analysis of secondary metabolism genes in fungi. Focusing on the secondary metabolite rich genus Aspergillus, we categorize SMGCs across genomes into SMGC families using network analysis. Our method elucidates the diversity and dynamics of secondary metabolism in section Nigri, showing that SMGC diversity within the section has the same magnitude as within the genus. Using our genome analysis we were able to predict the gene cluster responsible for biosynthesis of malformin, a potentiator of anti-cancer drugs, in 18 strains. To proof the general validity of our predictions, we developed genetic engineering tools in Aspergillus brasiliensis and subsequently verified the genes for biosynthesis of malformin.