bluuebunny/crossref_metadata_2025 huggingface dataset:
A graphene integrated highly transparent resistive switching memory device
Authors: Dugu Sita , Pavunny Shojan P. , Limbu Tej B. , Weiner Brad R. , Morell Gerardo , Katiyar Ram S.
Published: April 2018

We demonstrate the hybrid fabrication process of a graphene integrated highly transparent resistive random-access memory (TRRAM) device. The indium tin oxide (ITO)/Al2O3/graphene nonvolatile memory device possesses a high transmittance of >82% in the visible region (370-700 nm) and exhibits stable and non-symmetrical bipolar switching characteristics with considerably low set and reset voltages (<±1 V). The vertical two-terminal device shows an excellent resistive switching behavior with a high on-off ratio of ∼5 × 103. We also fabricated a ITO/Al2O3/Pt device and studied its switching characteristics for comparison and a better understanding of the ITO/Al2O3/graphene device characteristics. The conduction mechanisms in high and low resistance states were analyzed, and the observed polarity dependent resistive switching is explained based on electro-migration of oxygen ions.
Dynamics of quality as a strategic variable in complex food supply chain network competition: The case of fresh produce
Authors: Nagurney Anna , Besik Deniz , Yu Min
Published: April 2018

In this paper, we construct a competitive food supply chain network model in which the profit-maximizing producers decide not only as to the volume of fresh produce produced and distributed using various supply chain network pathways, but they also decide, with the associated costs, on the initial quality of the fresh produce. Consumers, in turn, respond to the various producers' product outputs through the prices that they are willing to pay, given also the average quality associated with each producer or brand at the retail outlets. The quality of the fresh produce is captured through explicit formulae that incorporate time, temperature, and other link characteristics with links associated with processing, shipment, storage, etc. Capacities on links are also incorporated as well as upper bounds on the initial product quality of the firms at their production/harvesting sites. The governing concept of the competitive supply chain network model is that of Nash Equilibrium, for which alternative variational inequality formulations are derived, along with existence results. An algorithmic procedure, which can be interpreted as a discrete-time tatonnement process, is then described and applied to compute the equilibrium produce flow patterns and accompanying link Lagrange multipliers in a realistic case study, focusing on peaches, which includes disruptions.
An analytical drain current model for symmetric double-gate MOSFETs
Authors: Yu Fei , Huang Gongyi , Lin Wei , Xu Chuanzhong
Published: April 2018

An analytical surface-potential-based drain current model of symmetric double-gate (sDG) MOSFETs is described as a SPICE compatible model in this paper. The continuous surface and central potentials from the accumulation to the strong inversion regions are solved from the 1-D Poisson’s equation in sDG MOSFETs. Furthermore, the drain current is derived from the charge sheet model as a function of the surface potential. Over a wide range of terminal voltages, doping concentrations, and device geometries, the surface potential calculation scheme and drain current model are verified by solving the 1-D Poisson’s equation based on the least square method and using the Silvaco Atlas simulation results and experimental data, respectively. Such a model can be adopted as a useful platform to develop the circuit simulator and provide the clear understanding of sDG MOSFET device physics.
From coherent quasi-irreversible quantum dynamics towards the second law of thermodynamics: The model boron rotor B13+
Authors: Jia Dongming , Manz Jörn , Yang Yonggang
Published: April 2018

The planar boron cluster B13+ provides a model to investigate the microscopic origin of the second law of thermodynamics in a small system. It is a molecular rotor with an inner wheel that rotates in an outer bearing. The cyclic reaction path of B13+ passes along thirty equivalent global minimum structures (GMi, i = 1, 2, ..., 30). The GMs are embedded in a cyclic thirty-well potential. They are separated by thirty equivalent transition states with potential barrier Vb. If the boron rotor B13+ is prepared initially in one of the thirty GMs, with energy below Vb, then it tunnels sequentially to its nearest, next-nearest etc. neighbors (520 fs per step) such that all the other GMs get populated. As a consequence, the entropy of occupying the GMs takes about 6 ps to increases from zero to a value close to the maximum value for equi-distribution. Perfect recurrences are practically not observable.
Fluoxetine treatment of prepubertal male rats uniformly diminishes sex hormone levels and, in a subpopulation of animals, negatively affects sperm quality
Authors: Ayala María E. , Gonzáles Ayari , Olivarez Rodrigo M. , Aragón-Martínez Andrés
Published: April 2018

Fluoxetine (Flx) is a selective serotonin reuptake inhibitor that alters the male reproductive system when administered at the adult stage or after maternal exposure. In the present study we evaluated the effects of Flx administration on reproductive parameters during juvenile–peripubertal development when treated male rats reached adulthood. Groups of rats were treated daily with Flx (5 mg kg−1, i.p.) or saline (0.9% NaCl), or were left untreated. Rats were treated between 30 and 53 days of age and were killed at 65 days of age. Serotonin concentrations were determined in the hypothalamus, hypophysis and testis. Gonadotrophins, sex steroids and sperm quality (membrane integrity, sperm with functional mitochondria, sperm density, sperm motility and morphological abnormalities) were also evaluated. Flx did not affect bodyweight, but significantly diminished LH, FSH, progesterone and testosterone serum concentrations. After graphical analysis, a subgroup of rats was identified whose sperm quality parameters were greatly affected by Flx. In the present study we show that Flx administered to juvenile rats disrupts the hypothalamic–hypophyseal–testicular axis and its effects on sperm quality are not homogeneous in adults. In contrast, Flx altered concentrations of gonadotrophins and sexual steroids in all treated rats. These results suggest caution should be exercised in the prescription of Flx to prepubertal males.
Less immune activation following social stress in rural vs. urban participants raised with regular or no animal contact, respectively
Authors: Böbel Till S. , Hackl Sascha B. , Langgartner Dominik , Jarczok Marc N. , Rohleder Nicolas , Rook Graham A. , Lowry Christopher A. , Gündel Harald , Waller Christiane , Reber Stefan O.
Published: April 2018

Significance

Our results show that a standardized laboratory psychosocial stressor causes a greater inflammatory response in young healthy participants with an urban upbringing in the absence of pets, relative to young healthy participants with a rural upbringing in the presence of farm animals. In view of the known links between persistent inflammatory states and psychiatric disturbances, and considering that many stress-associated physical and mental disorders are more prevalent in environments offering a narrow range of microbial exposures, we feel that our findings are of general interest and significance. Moreover, we feel our study is timely, as urbanization and the associated socioeconomic consequences are increasing.
Gravisensors in plant cells behave like an active granular liquid
Authors: Bérut Antoine , Chauvet Hugo , Legué Valérie , Moulia Bruno , Pouliquen Olivier , Forterre Yoël
Published: April 2018

Significance

The sensor of gravity in plants consists of tiny starch-rich grains called statoliths that sediment and form miniature granular piles at the bottom of the gravisensing cells. How such a sensor could be a reliable clinometer is unclear, as granular materials are known to display jamming and finite avalanche angles. Here we address this issue by comparing statolith avalanches in plant cells to microfluidic avalanches of Brownian particles in biomimetic cells. We reveal that statoliths behave like a liquid, not a granular material, due to the cell activity that strongly agitates statoliths. Our study elucidates the physical grounds of the high sensitivity of plants to gravity and bridges the active microrheology of statoliths to the macroscopic response of the plant.
Strengthening mechanisms in polycrystalline nickel-based superalloys
Authors: Goodfellow A. J.
Published: April 2018

Nickel-based superalloys are currently the material of choice for use in high-temperature applications due to their excellent high-temperature strength. It is understood that many mechanisms contribute to this property, but debate exists regarding how to model these mechanisms and predict the overall strength. This review covers the different strengthening mechanisms occurring in polycrystalline Ni-based superalloys and how these may be modelled, with the aim of revealing the gaps in the literature. It is found that models for precipitation and coherency strengthening are particularly controversial, and a unified model for the yield strength of superalloys is missing from the literature. This is of commercial importance for the design of new alloys with superior mechanical properties to those currently available.

This review was submitted as part of the 2018 Materials Literature Review Prize of the Institute of Materials, Minerals and Mining run by the Editorial Board of MST. Sponsorship of the prize by TWI Ltd is gratefully acknowledged.
Impact-induced acceleration by obstacles
Authors: Corbin N A , Hanna J A , Royston W R , Singh H , Warner R B
Published: April 2018

We explore a surprising phenomenon in which an obstruction accelerates, rather than decelerates, a moving flexible object. It has been claimed that the right kind of discrete chain falling onto a table falls faster than a free-falling body. We confirm and quantify this effect, reveal its complicated dependence on angle of incidence, and identify multiple operative mechanisms. Prior theories for direct impact onto flat surfaces, which involve a single constitutive parameter, match our data well if we account for a characteristic delay length that must impinge before the onset of excess acceleration. Our measurements provide a robust determination of this parameter. This supports the possibility of modeling such discrete structures as continuous bodies with a complicated constitutive law of impact that includes angle of incidence as an input.
Spearfishing modulates flight initiation distance of fishes: the effects of protection, individual size, and bearing a speargun
Authors: Sbragaglia Valerio , Morroni Lorenzo , Bramanti Lorenzo , Weitzmann Boris , Arlinghaus Robert , Azzurro Ernesto
Published: April 2018

In a landscape of fear, humans are altering key behaviours of wild-living animals, including those related to foraging, reproduction, and survival. When exposed to potentially lethal human actions, such as hunting or fishing, fish, and wildlife are expected to behaviourally respond by becoming shyer and learning when to be cautious. Using a rich dataset collected in temperate rocky reefs, we provide evidence of spearfishing-induced behavioural changes in five coastal fish taxa, exposed to different levels of spearfishing exploitation, by using flight initiation distance (FID) as a proxy of predator avoidance. We detected a significant increase of mean and size effects of FID when the observer was equipped with a speargun. Such effects were more evident outside marine protected areas where spearfishing was allowed and was commensurate to the historically spearfishing pressure of each investigated taxon. Our results demonstrate the ability of fish to develop fine-tuned antipredator responses and to recognize the risks posed by spearfishers as human predators. This capacity is likely acquired by learning, but harvest-induced truncation of the behavioural diversity and fisheries-induced evolution may also play a role and help to explain the increased timidity shown by the exploited fishes in our study.
Stretching Convex Domains to Capture Many Lattice Points
Authors: Marshall Nicholas F
Published: April 2018

We consider an optimal stretching problem for strictly convex domains in $\mathbb{R}^d$ that are symmetric with respect to each coordinate hyperplane, where stretching refers to transformation by a diagonal matrix of determinant 1. Specifically, we prove that the stretched convex domain which captures the most positive lattice points in the large volume limit is balanced: the (d − 1)-dimensional measures of the intersections of the domain with each coordinate hyperplane are equal. Our results extend those of Antunes and Freitas, van den Berg, Bucur and Gittins, Ariturk and Laugesen, van den Berg and Gittins, and Gittins and Larson. The approach is motivated by the Fourier analysis techniques used to prove the classical $\#\{(i,j) \in \mathbb{Z}^2 : i^2 +j^2 \le r^2 \} =\pi r^2 + \mathcal{O}(r^{2/3})$ result for the Gauss circle problem.
Magnetic Resonance-Guided Laser-Induced Thermal Therapy for the Treatment of Progressive Enhancing Inflammatory Reactions Following Stereotactic Radiosurgery, or PEIRs, for Metastatic Brain Disease
Authors: Hernandez R Nick , Carminucci Arthur , Patel Purvee , Hargreaves Eric L , Danish Shabbar F
Published: April 2018

BACKGROUND

In patients who have previously undergone maximum radiation for metastatic brain tumors, a progressive enhancing inflammatory reaction (PEIR) that represents either tumor recurrence or radiation necrosis, or a combination of both, can occur. Magnetic resonance-guided laser-induced thermal therapy (LITT) offers a minimally invasive treatment option for this problem.

OBJECTIVE

To report our single-center experience using LITT to treat PEIRs after radiosurgery for brain metastases.

METHODS

Patients with progressive, enhancing reactions at the site of prior radiosurgery for metastatic brain tumors and who had a Karnofsky performance status of ≥70 were eligible for LITT. The primary endpoint was local control. Secondary end points included dexamethasone use and procedure-related complications.

RESULTS

Between 2010 and 2017, 59 patients who underwent 74 LITT procedures for 74 PEIRs met inclusion criteria. The mean pre-LITT PEIR size measured 3.4 ± 0.4 cm3. At a median follow-up of 44.6 wk post-LITT, the local control rate was 83.1%. Most patients were weaned off steroids post-LITT. Patients experiencing a post-LITT complication were more likely to remain on steroids indefinitely. The rate of new permanent neurological deficit was 3.4%.

CONCLUSION

LITT is an effective treatment for local control of PEIRs after radiosurgery for metastatic brain disease. When possible, we recommend offering LITT once PEIRs are identified and prior to the initiation of high-dose steroids for symptom relief.
Using a Genome-Based PCR Primer Prediction Pipeline to Develop Molecular Diagnostics for the Turfgrass Pathogen Acidovorax avenae
Authors: Giordano Paul R. , Wang Jie , Vargas Joseph M. , Jacobs Janette , Chilvers Martin I. , Zeng Quan
Published: April 2018

Acidovorax avenae is the causal agent of bacterial etiolation and decline (BED) of creeping bentgrass, a poorly understood and often misdiagnosed disease that can result in considerable aesthetic and functional damage to golf course putting greens. Current diagnostics of BED are based on laborious culture-based methods. In this work, we employed a novel alignment-free primer prediction pipeline to design diagnostic primers for turfgrass-pathogenic A. avenae using 15 draft genomes of closely related target and nontarget Acidovorax spp. as input. Twenty candidate primer sets specific to turfgrass-pathogenic A. avenae were designed. The specificity and sensitivity of these primer sets were validated via a traditional polymerase chain reaction (PCR) and a real-time PCR assay. Primer sets 0017 and 0019 coupled with an internal oligo probe showed optimal sensitivity and specificity when evaluated with the target pathogen, closely related bacterial species, and microorganisms that inhabit the same host and soil environment. Finally, the accuracy of the newly developed real-time PCR assay was evaluated to detect BED pathogens from BED-symptomatic and asymptomatic turfgrass samples. The diagnostic results produced by the real-time PCR assay were consistent with results of a cultural-based method. This assay will allow quicker and more effective detection of the BED pathogen, thus potentially reducing misdiagnoses and unnecessary usage of fungicides.
Cucumber mosaic virus Isolates from Greek Legumes are Associated with Satellite RNAs that are Necrogenic for Tomato
Authors: Giakountis Antonis , Tsarmpopoulos Iason , Chatzivassiliou Elisavet K.
Published: April 2018

Worldwide, Cucumber mosaic virus (CMV) is the causal agent of many economically important diseases. Based on immunological or molecular analysis, three distinct subgroups of CMV isolates can be identified (IA, IB, and II). In addition, some CMV isolates are associated with satellite RNAs (satRNAs), a type of noncoding transcript that may alter the symptoms of CMV infections. This study presents an analysis of CMV isolates occurring in legumes in Greece in respect to their genetic diversity, and the presence and diversity of their satRNA. Phylogenetic analysis of the CMV coat protein sequence of 18 legume and 5 tomato CMV isolates collected throughout Greece classified them within subgroups IA and IB, with a limited genetic diversity. The CMV satRNAs found in nine field legumes exhibiting mild symptoms and in one tomato with a necrotic syndrome contained a functional necrogenic motif; therefore, they were grouped within the necrogenic group of CMV-satRNAs. The necrotic phenotype was expressed in all legume CMV isolates containing necrogenic satRNAs when mechanically inoculated onto tomato plants. To our knowledge, this is the first observation that legumes host necrogenic CMV-satRNAs. The possible role of legumes in the epidemiology of CMV and necrogenic satRNA complex is discussed.
Reduction of Gray Mold with Preharvest Applications of Potassium Tetraborate in Greenhouse Tomato
Authors: Ahmed Firas A. , Alvarez Anne M.
Published: April 2018

Potassium tetraborate tetrahydrate, K2B4O7⋅4H2O (PTB), was assessed as a preharvest spray in the greenhouse for reducing gray mold of tomato fruit caused by Botrytis cinerea. Efficacy of PTB was compared with a natural proprietary product formulated by Agrichem, which was previously shown to inhibit mycelial growth of B. cinerea in vitro and was used as a positive control for greenhouse studies. Mycelial growth and spore germination of B. cinerea were completely inhibited in vitro by PTB at 25 mM. Phytotoxicity was not observed on treated tomato plants with PTB at 25 mM. Preharvest sprays were applied at three ripening stages: turning, pink, and light red. After fruit reached the final ripening stage, all fruits were harvested and stored for 10 days at either 4 or 25°C. Disease severity was reduced compared with controls after storage at either temperature when PTB was applied at the turning stage. Preharvest applications of PTB improved the marketable quality of postharvest tomato fruit and significantly reduced the incidence of gray mold in comparison with inoculated control plants, which received no preharvest fungicidal treatment.
First Report of the 16SrIV-D Phytoplasma Associated with Decline of a Bismarck Palm (Bismarckia nobilis)
Authors: Dey K. K. , Jeyaprakash A. , Hansen J. , Jones D. , Smith T. , Davison D. , Srivastava P. , Bahder B. , Li C. , Sun X.
Published: April 2018

The Bismarck palm (Bismarckia nobilis Hildebr. & H. Wendl), with blue-gray leaves, is an important ornamental palm commonly planted along the highways in central and south Florida. During May of 2017, severe discoloration of the younger leaves of a Bismarck palm was observed in a roadside landscape in Manatee County, Florida. Symptoms of Texas Phoenix palm decline can include premature fruit drop, death of inflorescences, more than usual discoloration of the oldest leaves, and death of the spear leaf. The presence of the 16SrIV-D phytoplasma was confirmed on Bismarck palm.
Advancing national climate change risk assessment to deliver national adaptation plans
Authors: Warren R. F. , Wilby R. L. , Brown K. , Watkiss P. , Betts Richard A. , Murphy James M. , Lowe Jason A.
Published: April 2018

A wide range of climate vulnerability and risk assessments have been implemented using different approaches at different scales, some with a broad multi-sectoral scope and others focused on single risks or sectors. This paper describes the novel approach to vulnerability and risk assessment which was designed and put into practice in the United Kingdom's Second Climate Change Risk Assessment (CCRA2) so as to build upon its earlier assessment (CCRA1). First, we summarize and critique the CCRA1 approach, and second describe the steps taken in the CCRA2 approach in detail, providing examples of how each was applied in practice. Novel elements of the approach include assessment of both present day and future vulnerability, a focus on the urgency of adaptation action, and a structure focused around systems of receptors rather than conventional sectors. Both stakeholders and reviewers generally regarded the approach as successful in providing advice on current risks and future opportunities to the UK from climate change, and the fulfilment of statutory duty. The need for a well-supported and open suite of impact indicators going forward is highlighted.

This article is part of the theme issue ‘Advances in risk assessment for climate change adaptation policy'.
Assessing climate change risks to the natural environment to facilitate cross-sectoral adaptation policy
Authors: Brown Iain
Published: April 2018

Climate change policy requires prioritization of adaptation actions across many diverse issues. The policy agenda for the natural environment includes not only biodiversity, soils and water, but also associated human benefits through agriculture, forestry, water resources, hazard alleviation, climate regulation and amenity value. To address this broad agenda, the use of comparative risk assessment is investigated with reference to statutory requirements of the UK Climate Change Risk Assessment. Risk prioritization was defined by current adaptation progress relative to risk magnitude and implementation lead times. Use of an ecosystem approach provided insights into risk interactions, but challenges remain in quantifying ecosystem services. For all risks, indirect effects and potential systemic risks were identified from land-use change, responding to both climate and socio-economic drivers, and causing increased competition for land and water resources. Adaptation strategies enhancing natural ecosystem resilience can buffer risks and sustain ecosystem services but require improved cross-sectoral coordination and recognition of dynamic change. To facilitate this, risk assessments need to be reflexive and explicitly assess decision outcomes contingent on their riskiness and adaptability, including required levels of human intervention, influence of uncertainty and ethical dimensions. More national-scale information is also required on adaptation occurring in practice and its efficacy in moderating risks.

This article is part of the theme issue ‘Advances in risk assessment for climate change adaptation policy’.
How normative interpretations of climate risk assessment affect local decision-making: an exploratory study at the city scale in Cork, Ireland
Authors: McDermott T. K. J. , Surminski S.
Published: April 2018

Urban areas already suffer substantial losses in both economic and human terms from climate-related disasters. These losses are anticipated to grow substantially, in part as a result of the impacts of climate change. In this paper, we investigate the process of translating climate risk data into action for the city level. We apply a commonly used decision-framework as our backdrop and explore where in this process climate risk assessment and normative political judgements intersect. We use the case of flood risk management in Cork city in Ireland to investigate what is needed for translating risk assessment into action at the local city level. Evidence presented is based on focus group discussions at two stakeholder workshops, and a series of individual meetings and phone-discussions with stakeholders involved in local decision-making related to flood risk management and adaptation to climate change, in Ireland. Respondents were chosen on the basis of their expertise or involvement in the decision-making processes locally and nationally. Representatives of groups affected by flood risk and flood risk management and climate adaptation efforts were also included. The Cork example highlights that, despite ever more accurate data and an increasing range of theoretical approaches available to local decision-makers, it is the normative interpretation of this information that determines what action is taken. The use of risk assessments for decision-making is a process that requires normative decisions, such as setting ‘acceptable risk levels' and identifying ‘adequate’ protection levels, which will not succeed without broader buy-in and stakeholder participation. Identifying and embracing those normative views up-front could strengthen the urban adaptation process—this may, in fact, turn out to be the biggest advantage of climate risk assessment: it offers an opportunity to create a shared understanding of the problem and enables an informed evaluation and discussion of remedial action.

This article is part of the theme issue ‘Advances in risk assessment for climate change adaptation policy’.
Turning risk assessment and adaptation policy priorities into meaningful interventions and governance processes
Authors: Brown Kathryn , DiMauro Manuela , Johns Daniel , Holmes Gemma , Thompson David , Russell Andrew , Style David
Published: April 2018

The UK is one of the first countries in the world to have set up a statutory system of national climate risk assessments followed by a national adaptation programme. Having this legal framework has been essential for enabling adaptation at the government level in a challenging political environment. However, using this framework to create an improvement in resilience to climate change across the country requires more than publishing a set of documents; it requires careful thought about what interventions work, how they can be enabled and what level of risk acceptability individuals, organizations and the country should be aiming for.

This article is part of the theme issue ‘Advances in risk assessment for climate change adaptation policy'.
Evidence of an Unusual Poly(A) RNA Signature Detected by High-throughput Chemical Mapping
Authors: Wellington-Oguri Roger , Fisker Eli , Zada Mat , Wiley Michelle ,   Eterna Players
Published: April 2018

Homopolymeric adenosine RNA plays numerous roles in both cells and non-cellular genetic material, and for lack of evidence to the contrary, it is generally accepted to form a random coil under physiological conditions. However, chemical mapping data generated by the Eterna Massive Open Laboratory indicates that a poly (A) sequence of length seven or more, at pH 8.0 and MgCl concentrations of 10 mM, develops unexpected protection to selective 2’-hydroxyl acylation read out by primer extension (SHAPE) and dimethyl sulfate (DMS) chemical probing. This protection first appears in poly(A) sequences of length 7 and grows to its maximum strength at length ~10. In a long poly(A) sequence, substitution of a single A by any other nucleotide disrupts the protection, but only for the 6 or so nucleotides on the 5’ side of the substitution. The authors are grateful for pre-publication comments; please use https://docs.google.com/document/d/14972Q36IDTYMglwMXTOrqd4P9orQ6-P3bPbCuITdv6A.
Genetic regulatory mechanisms of smooth muscle cells map to coronary artery disease risk loci
Authors: Liu Boxiang , Pjanic Milos , Wang Ting , Nguyen Trieu , Gloudemans Michael , Rao Abhiram , Castano Victor G. , Nurnberg Sylvia , Rader Daniel J. , Elwyn Susannah , Ingelsson Erik , Montgomery Stephen B. , Miller Clint L. , Quertermous Thomas
Published: April 2018

Coronary artery disease (CAD) is the leading cause of death globally. Genome-wide association studies (GWAS) have identified more than 95 independent loci that influence CAD risk, most of which reside in non-coding regions of the genome. To interpret these loci, we generated transcriptome and whole-genome datasets using human coronary artery smooth muscle cells (HCASMC) from 52 unrelated donors, as well as epigenomic datasets using ATAC-seq on a subset of 8 donors. Through systematic comparison with publicly available datasets from GTEx and ENCODE projects, we identified transcriptomic, epigenetic, and genetic regulatory mechanisms specific to HCASMC. We assessed the relevance of HCASMC to CAD risk using transcriptomic and epigenomic level analyses. By jointly modeling eQTL and GWAS datasets, we identified five genes (SIPA1, TCF21, SMAD3, FES, and PDGFRA) that modulate CAD risk through HCASMC, all of which have relevant functional roles in vascular remodeling. Comparison with GTEx data suggests that SIPA1 and PDGFRA influence CAD risk predominantly through HCASMC, while other annotated genes may have multiple cell and tissue targets. Together, these results provide new tissue-specific and mechanistic insights into the regulation of a critical vascular cell type associated with CAD in human populations.
Diversity of Culturable Endophytic bacteria from Wild and Cultivated Rice showed potential Plant Growth Promoting activities
Authors: Borah Madhusmita , Das Saurav , Baruah Himangshu , Boro Robin C. , Barooah Madhumita
Published: April 2018

In this paper, we report the endophytic microbial diversity of cultivated and wild Oryza sativa plants including their functional traits related to multiple traits that promote plant growth and development. Around 255 bacteria were isolated out of which 70 isolates were selected for further studies based on their morphological differences. The isolates were characterized both at biochemical and at the molecular level by 16s rRNA gene sequencing. Based on 16S rRNA gene sequencing the isolates were categorized into three major phyla, viz, Firmicutes (57.1 %), Actinobacteria (20.0 %) and Proteobacteria (22.8 %). Firmicutes was the dominant group of bacteria of which the most abundant genus was Bacillus. The isolates were further screened in vitro for plant growth promoting activities which revealed a hitherto unreported endophytic bacterial isolate, Microbacteriaceae bacterium RS01 11 as the highest secretor of a phytohormone, IAA (28.39 ± 1.39 μg/ml) and GA (67.23 ± 1.83 μg/ml). Bacillus subtilis RHS 01 displayed highest phosphate solubilizing activity (81.70 ± 1.98 μg/ml) while, Microbacterium testaceum MK LS01, and Microbacterium trichothecenolyticum MI03 L05 exhibited highest potassium solubilizing activity (53.42±0.75μg/ml) and zinc solubilizing efficiency (157.50%) respectively. Bacillus barbaricus LP20 05 produced highest siderophore units (64.8 %). Potential plant growth promoting isolated were tested in vivo in pot culture under greenhouse conditions. A consortium consisting of Microbacteriaceae bacterium RS01 11, Bacillus testaceum MK LS01 and Bacillus subtilis RHS promoted plant growth and increased the yield 3.4 fold in rice when compared to control T0 when tested in pot culture and reduce application rates of chemical fertilizer to half the recommended dose. Our study confirms the potentiality of the rice endophytes isolated as good plant growth promoter and effective biofertilizer.
Super-enhancers are transcriptionally more active and cell-type-specific than stretch enhancers
Authors: Khan Aziz , Mathelier Anthony , Zhang Xuegong
Published: April 2018

Background

Super-enhancers and stretch enhancers represent classes of transcriptional enhancers that have been shown to control the expression of cell identity genes and carry disease- and trait-associated variants. Specifically, super-enhancers are clusters of enhancers defined based on the binding occupancy of master transcription factors (TFs), chromatin regulators, or chromatin marks, while stretch enhancers are large chromatin-defined regulatory regions of at least 3,000 base pairs. Several studies have characterized these regulatory regions in numerous cell types and tissues to decipher their functional importance. However, the differences and similarities between these regulatory regions have not been fully assessed.

Results

We integrated genomic, epigenomic, and transcriptomic data from ten human cell types to perform a comparative analysis of super and stretch enhancers with respect to their chromatin profiles, cell-type-specificity, and ability to control gene expression. We found that stretch enhancers are more abundant, more distal to transcription start sites, cover twice as much the genome and are significantly less conserved than super-enhancers. In contrast, super-enhancers are significantly more enriched for active chromatin marks and cohesin complex and transcriptionally active than stretch enhancers. Importantly, a vast majority of superenhancers (85%) overlap with only a small subset of stretch enhancers (13%), which are enriched for cell-type-specific biological functions, and control cell identity genes.

Conclusions

These results suggest that super-enhancers are transcriptionally more active and cell-type-specific than stretch enhancers, and importantly, most of the stretch enhancers that are distinct from superenhancers do not show an association with cell identity genes, are less active, and more likely to be poised enhancers.
Biogenesis of a young, 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation
Authors: Fei Qili , Yu Yu , Liu Li , Zhang Yu , Baldrich Patricia , Dai Qing , Chen Xuemei , Meyers Blake C.
Published: April 2018

Phased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22 nt miRNAs. Most 22 nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21 nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerousNB-LRRs, previously described as 21 nt in its mature form, primarily accumulates as a 22 nt isoform via monouridylation. We demonstrate that in Arabidopsis, this uridylation is performed by HESO1. Biochemical experiments showed that the 3’ terminus of miR1510 is only partially 2’-O-methylated, because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ~41 to 42 MYA with a conserved precursor structure yielding a 22 nt monouridylated form, yet a variant in mung bean is processed directly in a 22 nt mature form. This analysis of miR1510 yields two observations: (1) plants can utilize post-processing modification to generate abundant 22 nt miRNA isoforms to more efficiently regulate target mRNA abundances; (2) comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.
To B or not to B: Arsenophonus as a source of B-vitamins in whiteflies
Authors: Santos-Garcia Diego , Juravel Ksenia , Freilich Shiri , Zchori-Fein Einat , Latorre Amparo , Moya Andrés , Morin Shai , Silva Francisco J.
Published: April 2018

1

Insect lineages feeding on nutritionally restricted diets such as phloem, xylem, or blood, were able to diversify by acquiring bacterial species that complemented the missing nutrients. These bacteria, considered obligate/primary endosymbionts, share a long evolutionary history with their hosts. In some cases, however, these endosymbionts are not able to fulfill all the nutritional requirements of their host, driving the acquisition of additional symbiotic species. Whiteflies, which feed on phloem, established an obligate relationship with Candidatus Portiera aleyrodidarum, who provides essential amino acids and carotenoids to the host. As many Whiteflies species harbor additional endosymbionts, they could provide their hosts with missing nutrients. To test this hypothesis, genomes of several endosymbionts from the whiteflies Aleurodicus dispersus, A. floccissimus and Trialeurodes vaporariorum were sequenced and analyzed. All three species were found to harbor an endosymbiont from the genus Arsenophonus, and the two former also host Wolbachia. A comparative analysis of the three Arsenophonus genomes revealed that although all of them are capable of synthesizing B-vitamins and cofactors, such as pyridoxal, riboflavin, or folate, their genomes and phylogenetic relationship vary greatly. Arsenophonus of A. floccissimus and T. vaporariorum belong to the same clade and display characteristics of facultative endosymbionts, such as large genomes (3 Mb) with thousands of genes, many pseudogenes, intermediate GC content, and mobile genetic elements (MGEs). In contrast, Arsenophonus of A. dispersus belongs to a different lineage and displays the characteristics of a primary endosymbiont, such as a reduced genome (670 kb) with 400 genes, 32% GC content, and no MGEs. However, the presence of 274 pseudogenes suggests that this symbiotic association is more recent than other reported hemipteran’s primary endosymbionts. Arsenophonus of A. dispersus gene repertoire is completely integrated in the symbiotic consortia, and the biosynthesis of most vitamins occurs in shared pathways with its host. In addition, Wolbachia have also retained the ability to produce riboflavin, FAD, and folate, and may have a nutritional contribution. Taken together, our results show that Arsenophonus have a pivotal place in whiteflies nutrition by their ability to produce B-vitamins, even if they diverge and/or go through a genome reduction process.
Diagnosis of Human Leptospirosis: High Resolution Melting Analysis for Direct Detection ofLeptospirain the Early Stage of the Disease in a Clinical Setting
Authors: Esteves Lisa M. , Bulhões Sara M. , Branco Claudia C. , Carreira Teresa , Vieira Maria L. , Gomes-Solecki Maria , Mota-Vieira Luisa
Published: April 2018

Currently, the direct detection ofLeptospirainfection can be done in clinical laboratories by a conventional nested polymerase chain reaction method (nested PCR), which is labourious and time-consuming. To overcome these drawbacks, we tested a set of paired samples of serum and urine from 202 patients presenting at a hospital located in an area endemic for leptospirosis using high resolution melting (HRM). The results were compared with those obtained by nested PCR for direct detection of the pathogen in both specimens and with the gold standard test used for indirect detection of anti-Leptospiraantibodies in serum (the microscopic agglutination test, MAT). The HRM assay results were positive for 46/202 (22.7%) samples, whereas 47/202 (23.3%) samples were positive by nested PCR. As expected in recently infected febrile patients, MAT results were positive in only 3/46 (6.5%) HRM-positive samples. We did a unique comparative analysis using a robust biobank of paired samples of serum and urine from the same patient to validate the HRM assay for molecular diagnosis of human leptospirosis in a clinical setting. This assay fills a void unmet by serologic assays as it can detect the presence ofLeptospirain biological samples even before development of antibody takes place.
A functional different immune capacity in cattle is associated with higher mastitis incidence
Authors: Lutterberg Karina , Kleinwort Kristina J. H. , Hobmaier Bernhard F. , Hauck Stefanie M. , Nüske Stefan , Scholz Armin M. , Deeg Cornelia A.
Published: April 2018

Bovine neonatal pancytopenia (BNP) was a deadly disease transferred by antibodies from 5-10% of cows given a novel BVD vaccine. Disease was lethal in 90% of calves receiving colostrum with BNP antibodies. The cause of BNP is not fully understood to date. We revealed a profound difference in immune capacities between BNP dams and non-responders. Significant differences were detectable in response toin vitrostimulation of peripheral blood derived lymphocytes to several mitogens and IL-2. BNP cows regulated their immune proteomes completely different from controls with other immune response master regulators. Since we detected this response pattern also in 22% of cows that were never vaccinated at all, this immune deviant (ID) phenotype is still present in cattle and probably inherited. Immune response pattern of these cows was stable over an observation period of 38 months. Importantly, ID have a significant increased prevalence of mastitis underscoring the clinical importance.
Automated Segmentation of Epithelial Tissue Using Cycle-Consistent Generative Adversarial Networks
Authors: Häring Matthias , Großhans Jörg , Wolf Fred , Eule Stephan
Published: April 2018

A central problem in biomedical imaging is the automated segmentation of images for further quantitative analysis. Recently, fully convolutional neural networks, such as the U-Net, were applied successfully in a variety of segmentation tasks. A downside of this approach is the requirement for a large amount of well-prepared training samples, consisting of image - ground truth mask pairs. Since training data must be created by hand for each experiment, this task can be very costly and time-consuming. Here, we present a segmentation method based on cycle consistent generative adversarial networks, which can be trained even in absence of prepared image - mask pairs. We show that it successfully performs image segmentation tasks on samples with substantial defects and even generalizes well to different tissue types.
Gating Mechanisms during Actin Filament Elongation by Formins
Authors: Aydin Fikret , Courtemanche Naomi , Pollard Thomas D. , Voth Gregory A.
Published: April 2018

Formins play an important role in the polymerization of unbranched actin filaments, and particular formins slow elongation by 5-95%. We studied the interactions between actin and the FH2 domains of formins Cdc12, Bni1 and mDia1 to understand the factors underlying their different rates of polymerization. All-atom molecular dynamics simulations revealed two factors that influence actin filament elongation and correlate with the rates of elongation. First, FH2 domains can sterically block the addition of new actin subunits. Second, FH2 domains flatten the helical twist of the terminal actin subunits, making the end less favorable for subunit addition. Coarse-grained simulations over longer time scales support these conclusions. The simulations show that filaments spend time in states that either allow or block elongation. The rate of elongation is a time-average of the degree to which the formin compromises subunit addition rather than the formin-actin complex literally being in ‘open’ or ‘closed’ states.
Molecular dissection of a natural transposable element invasion
Authors: Kofler Robert , Senti Kirsten-André , Nolte Viola , Tobler Ray , Schlötterer Christian
Published: April 2018

The first tracking of the dynamics of a natural invasion by a transposable element (TE) provides unprecedented details on the establishment of host defense mechanisms against TEs. We captured aD. simulanspopulation at an early stage of aP-elementinvasion and studied the spread of the TE in replicated experimentally evolving populations kept under hot and cold conditions. We analyzed the factors controlling the invasion by NGS, RNA-FISH, and gonadal dysgenesis assays. Under hot conditions, theP-elementspread rapidly for 20 generations, but no further spread was noted later on. This plateauing of the invasion was mediated by the rapid emergence ofP-element-specific piRNAs. Under cold conditions, we observed a lower expression of theP-elementand a slower emergence of the piRNA defense, resulting in a three times slower invasion that continued beyond 40 generations. We conclude that the environment is a major factor determining the evolution of TEs in their host.
Ionic scattering factors of atoms that compose biological molecules
Authors: Yonekura Koji , Matsuoka Rei , Yamashita Yoshiki , Yamane Tsutomu , Ikeguchi Mitsunori , Kidera Akinori , Maki-Yonekura Saori
Published: April 2018

Ionic scattering factors of atoms that compose biological molecules have been computed by the multi-configuration Dirac–Fock method. These ions are chemically unstable and their scattering factors had not been reported except for O−. Yet these factors are required for the estimation of partial charges in protein molecules and nucleic acids. The electron scattering factors of these ions are particularly important as the electron scattering curves vary considerably between neutral and charged atoms in the spatial-resolution range explored in structural biology. The calculated X-ray and electron scattering factors have then been parameterized for the major scattering curve models used in X-ray and electron protein crystallography and single-particle cryo-EM. The X-ray and electron scattering factors and the fitting parameters are presented for future reference.
Numerical and experimental analysis of rotating wheel in contact with the ground
Authors: Kulak Michal , Karczewski Maciej , Lesniewicz Pawel , Olasek Krzysztof , Hoogterp Bas , Spolaore Guillaume , Józwik Krzysztof
Published: April 2018

Purpose

This paper aims to provide the results of investigations concerning an influence of the tyre with longitudinal grooves on the car body aerodynamics. It is considered as an important aspect affecting the vehicle aerodynamic drag.

Design/methodology/approach

To investigate a contribution of grooved tyres to the overall vehicle drag, three wind tunnel experimental campaigns were performed (two by Peugeot Société Anonyme Peugeot Citroen, one at the Lodz University of Technology). In parallel, computational fluid dynamics (CFD) simulations were conducted with the ANSYS CFX software to enable formulation of wider conclusions.

Findings

The research shows that optimised tread patterns can be derived on a single tyre via a CFD study in combination with a controlled experiment to deliver designs actively lowering the overall vehicle aerodynamic drag.

Practical implications

A reduction in the aerodynamic drag is one of ways to decrease vehicle fuel consumption. Alternatively, it can be translated into an increase in the maximum travel velocity and the maximum distance driven (key factor in electric vehicles), as well as in a reduction of CO2 emissions. Finally, it can improve the vehicle driving and steering stability.

Originality/value

The tyre tread pattern analysis on isolated wheels provides an opportunity to cut costs of R&D and could be a step towards isolating aerodynamic properties of tyres, irrespective of the car body on which they are applied.