bluuebunny/crossref_metadata_2025_split huggingface dataset:
NREM sleep in the rodent neocortex and hippocampus reflects excitable dynamics
Authors: Levenstein Daniel , Buzsáki György , Rinzel John 
Published: June 2019

AbstractDuring non-rapid eye movement (NREM) sleep, neuronal populations in the mammalian forebrain alternate between periods of spiking and inactivity. Termed the slow oscillation in the neocortex and sharp wave-ripples in the hippocampus, these alternations are often considered separately but are both crucial for NREM functions. By directly comparing experimental observations of naturally-sleeping rats with a mean field model of an adapting, recurrent neuronal population, we find that the neocortical alternations reflect a dynamical regime in which a stable active state is interrupted by transient inactive states (slow waves) while the hippocampal alternations reflect a stable inactive state interrupted by transient active states (sharp waves). We propose that during NREM sleep in the rodent, hippocampal and neocortical populations are excitable: each in a stable state from which internal fluctuations or external perturbation can evoke the stereotyped population events that mediate NREM functions.
The footprint of column collapse regimes on pyroclastic flow temperatures and plume heights
Authors: Trolese Matteo , Cerminara Matteo , Esposti Ongaro Tomaso , Giordano Guido 
Published: June 2019

AbstractThe gravitational collapse of eruption columns generates ground-hugging pyroclastic density currents (PDCs) with highly variable temperatures, high enough to be a threat for communities surrounding volcanoes. The reasons for such great temperature variability are debated in terms of eruptive versus transport and emplacement processes. Here, using a three-dimensional multiphase model, we show that the initial temperature of PDCs linearly correlates to the percentage of collapsing mass, with a maximum temperature decrease of 45% in the case of low percentages of collapse (10%), owing to an efficient entrainment of air into the jet structure. Analyses also demonstrate that column collapse limits the dispersal capabilities of volcanic plumes, reducing their maximum height by up to 45%. Our findings provide quantitative insights into the mechanism of turbulent mixing, and suggest that temperatures of PDC deposits may serve as a marker for determining column collapse conditions, which are of primarily importance in hazard studies.
Hypervirulent Listeria monocytogenes clones’ adaption to mammalian gut accounts for their association with dairy products
Authors: Maury Mylène M. , Bracq-Dieye Hélène , Huang Lei , Vales Guillaume , Lavina Morgane , Thouvenot Pierre , Disson Olivier , Leclercq Alexandre , Brisse Sylvain , Lecuit Marc 
Published: June 2019

AbstractListeria monocytogenes (Lm) is a major human and animal foodborne pathogen. Here we show that hypervirulent Lm clones, particularly CC1, are strongly associated with dairy products, whereas hypovirulent clones, CC9 and CC121, are associated with meat products. Clone adaptation to distinct ecological niches and/or different food products contamination routes may account for this uneven distribution. Indeed, hypervirulent clones colonize better the intestinal lumen and invade more intestinal tissues than hypovirulent ones, reflecting their adaption to host environment. Conversely, hypovirulent clones are adapted to food processing environments, with a higher prevalence of stress resistance and benzalkonium chloride tolerance genes and a higher survival and biofilm formation capacity in presence of sub-lethal benzalkonium chloride concentrations. Lm virulence heterogeneity therefore reflects the diversity of the ecological niches in which it evolves. These results also have important public health implications and may help in reducing food contamination and improving food consumption recommendations to at-risk populations.
Loci for human leukocyte telomere length in the Singaporean Chinese population and trans-ethnic genetic studies
Authors: Dorajoo Rajkumar , Chang Xuling , Gurung Resham Lal , Li Zheng , Wang Ling , Wang Renwei , Beckman Kenneth B. , Adams-Haduch Jennifer , M Yiamunaa , Liu Sylvia , Meah Wee Yang , Sim Kar Seng , Lim Su Chi , Friedlander Yechiel , Liu Jianjun , van Dam Rob M. , Yuan Jian-Min , Koh Woon-Puay , Khor Chiea Chuen , Heng Chew-Kiat 
Published: June 2019

AbstractGenetic factors underlying leukocyte telomere length (LTL) may provide insights into telomere homeostasis, with direct links to disease susceptibility. Genetic evaluation of 23,096 Singaporean Chinese samples identifies 10 genome-wide loci (P < 5 × 10−8). Several of these contain candidate genes (TINF2, PARP1, TERF1, ATM and POT1) with potential roles in telomere biology and DNA repair mechanisms. Meta-analyses with additional 37,505 European individuals reveals six more genome-wide loci, including associations at MPHOSPH6, NKX2-3 and TYMS. We demonstrate that longer LTL associates with protection against respiratory disease mortality [HR = 0.854(0.804–0.906), P = 1.88 × 10−7] in the Singaporean Chinese samples. We further show that the LTL reducing SNP rs7253490 associates with respiratory infections (P = 7.44 × 10−4) although this effect may not be strongly mediated through LTL. Our data expands on the genetic basis of LTL and may indicate on a potential role of LTL in immune competence.
Two-dimensional semiconducting covalent organic frameworks via condensation at arylmethyl carbon atoms
Authors: Bi Shuai , Yang Can , Zhang Wenbei , Xu Junsong , Liu Lingmei , Wu Dongqing , Wang Xinchen , Han Yu , Liang Qifeng , Zhang Fan 
Published: June 2019

AbstractConstruction of organic semiconducting materials with in-plane π-conjugated structures and robustness through carbon-carbon bond linkages, alternatively as organic graphene analogs, is extremely desired for powerfully optoelectrical conversion. However, the poor reversibility forsp2carbon bond forming reactions makes them unavailable for building high crystalline well-defined organic structures through a self-healing process, such as covalent organic frameworks (COFs). Here we report a scalable solution-processing approach to synthesize a family of two-dimensional (2D) COFs withtrans-disubstituted C = C linkages via condensation reaction at arylmethyl carbon atoms on the basis of 3,5-dicyano-2,4,6-trimethylpyridine and linear/trigonal aldehyde (i.e., 4,4″-diformyl-p-terphenyl, 4,4′-diformyl-1,1′-biphenyl, or 1,3,5-tris(4-formylphenyl)benzene) monomers. Suchsp2carbon-jointed-pyridinyl frameworks, featuring crystalline honeycomb-like structures with high surface areas, enable driving two half-reactions of water splitting separately under visible light irradiation, comparable to graphitic carbon nitride (g-C3N4) derivatives.
Probing the formation and degradation of chemical interactions from model molecule/metal oxide to buried polymer/metal oxide interfaces
Authors: Pletincx Sven , Fockaert Laura Lynn I. , Mol Johannes M. C. , Hauffman Tom , Terryn Herman 
Published: June 2019

AbstractThe mechanisms governing coating/metal oxide delamination are not fully understood, although adhesive interactions at the interface are considered to be an important prerequisite for excellent durability. This review aims to better understand the formation and degradation of these interactions. Developments in adhesion science made it clear that physical and chemical interfacial interactions are key factors in hybrid structure durability. However, it is very challenging to get information directly from the hidden solid/solid interface. This review highlights approaches that allow the (in situ) investigation of the formation and degradation of molecular interactions at the interface under (near-)realistic conditions. Over time, hybrid interfaces tend to degrade when exposed to environmental conditions. The culprits are predominantly water, oxygen, and ion diffusion resulting in bond breakage due to changing acid–base properties or leading to the onset of corrosive de-adhesion processes. Therefore, a thorough understanding on local bond interactions is required, which will lead to a prolonged durability of hybrid systems under realistic environments.
Cheese whey to biohydrogen and useful organic acids: A non-pathogenic microbial treatment by L. acidophilus
Authors: Pandey Anjana , Srivastava Saumya , Rai Priya , Duke Mikel 
Published: June 2019

AbstractThe burgeoning organic waste and continuously increasing energy demands have resulted in significant environmental pollution concerns. To address this issue, the potential of different bacteria to produce biogas/biohydrogen from organic waste can be utilized as a source of renewable energy, however these pathogenic bacteria are not safe to use without strict contact isolation. In this study the role of safe food grade lactic acid bacteria (Lactobacillus spp.) was investigated for production of biogas from cheese waste with starting hexose concentration 32 g/L. The bacterium Lactobacillus acidophilus was identified as one of the major biogas producers at optimum pH of 6.5. Further the optimum inoculum conditions were found to be 12.5% at inoculum age of 18 h. During the investigation the maximum biogas production was observed to be 1665 mL after 72 hours of incubation at pH 6.5. The biogas production was accompanied with production of other valuable metabolites in the form of organic acids including pyruvate, propionate, acetate, lactate, formate and butyrate. Thus this research is paving way for nonpathogenic production of biohydrogen from food waste.
The vertical distribution and biological transport of marine microplastics across the epipelagic and mesopelagic water column
Authors: Choy C. Anela , Robison Bruce H. , Gagne Tyler O. , Erwin Benjamin , Firl Evan , Halden Rolf U. , Hamilton J. Andrew , Katija Kakani , Lisin Susan E. , Rolsky Charles , S. Van Houtan Kyle 
Published: June 2019

AbstractPlastic waste has been documented in nearly all types of marine environments and has been found in species spanning all levels of marine food webs. Within these marine environments, deep pelagic waters encompass the largest ecosystems on Earth. We lack a comprehensive understanding of the concentrations, cycling, and fate of plastic waste in sub-surface waters, constraining our ability to implement effective, large-scale policy and conservation strategies. We used remotely operated vehicles and engineered purpose-built samplers to collect and examine the distribution of microplastics in the Monterey Bay pelagic ecosystem at water column depths ranging from 5 to 1000 m. Laser Raman spectroscopy was used to identify microplastic particles collected from throughout the deep pelagic water column, with the highest concentrations present at depths between 200 and 600 m. Examination of two abundant particle feeders in this ecosystem, pelagic red crabs (Pleuroncodes planipes) and giant larvaceans (Bathochordaeus stygius), showed that microplastic particles readily flow from the environment into coupled water column and seafloor food webs. Our findings suggest that one of the largest and currently underappreciated reservoirs of marine microplastics may be contained within the water column and animal communities of the deep sea.
α′ formation kinetics and radiation induced segregation in neutron irradiated 14YWT nanostructured ferritic alloys
Authors: Aydogan E. , Martinez E. , March K. , El-Atwani O. , Krumwiede D. L. , Hosemann P. , Saleh T. , Maloy S. A. 
Published: June 2019

AbstractNanostructured ferritic alloys are considered as candidates for structural components in advanced nuclear reactors due to a high density of nano-oxides (NOs) and ultrafine grain sizes. However, bimodal grain size distribution results in inhomogeneous NO distribution, or vice versa. Here, we report that density of NOs in small grains (<0.5 µm) is high while there are almost no NOs inside the large grains (>2 µm) before and after irradiation. After 6 dpa neutron irradiation at 385–430 °C, α′ precipitation has been observed in these alloys; however, their size and number densities vary considerably in small and large grains. In this study, we have investigated the precipitation kinetics of α′ particles based on the sink density, using both transmission electron microscopy and kinetic Monte Carlo simulations. It has been found that in the presence of a low sink density, α′ particles form and grow faster due to the existence of a larger defect density in the matrix. On the other hand, while α′ particles form far away from the sink interface when the sink size is small, Cr starts to segregate at the sink interface with the increase in the sink size. Additionally, grain boundary characteristics are found to determine the radiation-induced segregation of Cr.
Defective Zn2+ homeostasis in mouse and human platelets with α- and δ-storage pool diseases
Authors: Kiran Gotru Sanjeev , van Geffen Johanna P. , Nagy Magdolna , Mammadova-Bach Elmina , Eilenberger Julia , Volz Julia , Manukjan Georgi , Schulze Harald , Wagner Leonard , Eber Stefan , Schambeck Christian , Deppermann Carsten , Brouns Sanne , Nurden Paquita , Greinacher Andreas , Sachs Ulrich , Nieswandt Bernhard , Hermanns Heike M. , Heemskerk Johan W. M. , Braun Attila 
Published: June 2019

AbstractZinc (Zn2+) can modulate platelet and coagulation activation pathways, including fibrin formation. Here, we studied the (patho)physiological consequences of abnormal platelet Zn2+ storage and release. To visualize Zn2+ storage in human and mouse platelets, the Zn2+ specific fluorescent dye FluoZin3 was used. In resting platelets, the dye transiently accumulated into distinct cytosolic puncta, which were lost upon platelet activation. Platelets isolated from Unc13d−/− mice, characterized by combined defects of α/δ granular release, showed a markedly impaired Zn2+ release upon activation. Platelets from Nbeal2−/− mice mimicking Gray platelet syndrome (GPS), characterized by primarily loss of the α-granule content, had strongly reduced Zn2+ levels, which was also confirmed in primary megakaryocytes. In human platelets isolated from patients with GPS, Hermansky-Pudlak Syndrome (HPS) and Storage Pool Disease (SPD) altered Zn2+ homeostasis was detected. In turbidity and flow based assays, platelet-dependent fibrin formation was impaired in both Nbeal2−/− and Unc13d−/− mice, and the impairment could be partially restored by extracellular Zn2+. Altogether, we conclude that the release of ionic Zn2+ store from secretory granules upon platelet activation contributes to the procoagulant role of Zn2+ in platelet-dependent fibrin formation.
Biology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neurons
Authors: Kronman Hope , Richter Felix , Labonté Benoit , Chandra Ramesh , Zhao Shan , Hoffman Gabriel , Lobo Mary Kay , Schadt Eric E. , Nestler Eric J. 
Published: June 2019

AbstractSubcellular RNAseq promises to dissect transcriptional dynamics but is not well characterized. Furthermore, FACS may introduce bias but has not been benchmarked genome-wide. Finally, D1 and D2 dopamine receptor-expressing medium spiny neurons (MSNs) of the nucleus accumbens (NAc) are fundamental to neuropsychiatric traits but have only a short list of canonical surface markers. We address these gaps by systematically comparing nuclear-FACS, whole cell-FACS, and RiboTag affinity purification from D1- and D2-MSNs. Using differential expression, variance partitioning, and co-expression, we identify the following trade-offs for each method. RiboTag-seq best distinguishes D1- and D2-MSNs but has the lowest transcriptome coverage. Nuclear-FACS-seq generates the most differentially expressed genes and overlaps significantly with neuropsychiatric genetic risk loci, but un-annotated genes hamper interpretation. Whole cell-FACS is more similar to nuclear-FACS than RiboTag, but captures aspects of both. Using pan-method approaches, we discover that transcriptional regulation is predominant in D1-MSNs, while D2-MSNs tend towards cytosolic regulation. We are also the first to find evidence for moderate sexual dimorphism in these cell types at baseline. As these results are from 49 mice (nmale = 39, nfemale = 10), they represent generalizable ground-truths. Together, these results guide RNAseq methods selection, define MSN transcriptomes, highlight neuronal sex differences, and provide a baseline for D1- and D2-MSNs.
Topological Optimization of Phononic Crystal Thin Plate by a Genetic Algorithm
Authors: Han X. K. , Zhang Z. 
Published: June 2019

AbstractGenetic algorithm (GA) is used for the topological optimization of phononic crystal thin plate composed of aluminum and epoxy resin. Plane wave expansion (PWE) method is used for calculations of band gaps. Fourier displacement property is used to calculate the structure function in PWE. The crossover rate and the mutation rate are calculated according to the adaptive GA method. Results indicate that filling rates, symmetry, polymerization degree and material parameters are key factors for design of topological configurations. The relations between the key factors and different topologies are studied in detail.
QTL-seq identifies cooked grain elongation QTLs near soluble starch synthase and starch branching enzymes in rice (Oryza sativa L.)
Authors: Arikit Siwaret , Wanchana Samart , Khanthong Srisawat , Saensuk Chatree , Thianthavon Tripop , Vanavichit Apichart , Toojinda Theerayut 
Published: June 2019

AbstractGrain quality is one of the main targets that rice breeders focus on to improve elite rice varieties. Several characteristics are considered when determine rice grain quality, such as aroma, amylose content (AC), gelatinization temperature (GT) and, especially, lengthwise grain elongation (GE). GE is a desirable feature in premium rice of high quality, such as India and Pakistan’ Basmati. Inheritance of GE in rice has not been clearly elucidated due to its complex and inconsistent pattern. In this study, we identified QTLs for GE in rice using bulk-segregant analysis (BSA) and whole-genome sequencing based on an F2 population segregated for GE as well as AC and GT. We identified two QTLs on chromosome 6, qGE6.1 and qGE6.2, and another QTL on chromosome 4, qGE4.1. qGE6.1 and qGE6.2 were located near starch synthase IIa (SSIIa) and starch branching enzyme III (SBEIII), respectively, and qGE4.1 was located near starch branching enzyme IIa (SBEIIa). qGE6.1 was considered to be the major QTL for GE based on this population, and SSIIa was suggested to be the best candidate gene associated with the GE trait. The results of this study may be useful for breeding rice with increased grain elongation and different starch properties.
Contact-free determination of viscosity in multiple parallel samples
Authors: Sieben Michaela , Hanke René , Büchs Jochen 
Published: June 2019

AbstractViscosity is an inherent characteristic of fluids and is therefore an important parameter in many different processes. Current methods to measure viscosity involve direct contact with the liquid sample, which is often undesirable. Here we present a simple, precise and robust contact-free method to determine viscosity, using a single drive motor, inexpensive components and disposable sample vessels. The measurement principle involves the detection of viscosity-dependent angular positions in a rotating liquid relative to the direction of centrifugal acceleration in an orbitally shaken vessel. The signal can be detected using different optical methods, as shown here using fluorescence and transmitted light. The sensitivity of the system can be adjusted over a wide range by varying the sample volume or the shaking diameter, and multiple samples can be analysed in parallel. This novel viscometer is also applicable to characterize non-Newtonian shear rate-dependent fluids.
The human glomerular endothelial cells are potent pro-inflammatory contributors in an in vitro model of lupus nephritis
Authors: Dimou Paraskevi , Wright Rachael D. , Budge Kelly L. , Midgley Angela , Satchell Simon C. , Peak Matthew , Beresford Michael W. 
Published: June 2019

AbstractJuvenile-onset lupus nephritis (LN) affects up to 80% of juvenile-onset systemic lupus erythematosus patients (JSLE). As the exact role of human renal glomerular endothelial cells (GEnCs) in LN has not been fully elucidated, the aim of this study was to investigate their involvement in LN. Conditionally immortalised human GEnCs (ciGEnCs) were treated with pro-inflammatory cytokines known to be involved in LN pathogenesis and also with LPS. Secretion and surface expression of pro-inflammatory proteins was quantified via ELISA and flow cytometry. NF-κΒ and STAT-1 activation was investigated via immunofluorescence. Serum samples from JSLE patients and from healthy controls were used to treat ciGEnCs to determine via qRT-PCR potential changes in the mRNA levels of pro-inflammatory genes. Our results identified TNF-α, IL-1β, IL-13, IFN-γ and LPS as robustin vitrostimuli of ciGEnCs. Each of them led to significantly increased production of different pro-inflammatory proteins, including; IL-6, IL-10, MCP-1, sVCAM-1, MIP-1α, IP-10, GM-CSF, M-CSF, TNF-α, IFN-γ, VCAM-1, ICAM-1, PD-L1 and ICOS-L. TNF-α and IL-1β were shown to activate NF-κB, whilst IFN-γ activated STAT-1. JSLE patient serum promoted IL-6 and IL-1β mRNA expression. In conclusion, ourin vitromodel provides evidence that human GEnCs play a pivotal role in LN-associated inflammatory process.
Filling the gap between collection, transport and storage of the human gut microbiota
Authors: Martínez Noelia , Hidalgo-Cantabrana Claudio , Delgado Susana , Margolles Abelardo , Sánchez Borja 
Published: June 2019

AbstractStool collection devices minimizing the exposure of gut bacteria to oxygen are critical for the standardization of further microbiota-based studies, analysis and developments. The aim of this work was to evidence that keeping anaerobiosis has a deep impact on the viability and diversity of the fecal microbiota that is recovered in the laboratory. Recovering certain microbial populations, such as obligate anaerobic bacteria, is particularly critical if the purpose of the study is to envisage personalized therapeutic purposes, such as autologous Fecal Microbiota Transplant. In this study the same fecal specimens were sampled in conventional stool containers and GutAlive, a disposable device that minimizes exposure of the gut microbiota to oxygen. Samples from five healthy donors were analysed and 150 differential colonies were recovered and identified by 16S rRNA gene sequencing. Globally, GutAlive maintained extremely oxygen sensitive (EOS) populations that were lost in conventional stool containers, and thus viability of species such as as Akkermansia muciniphila, Faecalibacterium prausnitzii and a novel member of the Clostridiales order was kept. These obligate anaerobes were not recovered using the conventional stool collection device. In conclusion, the use of GutAlive for stool collection and transport optimized the viability and recovery of EOS bacteria in the lab by diminishing oxygen toxicity.