bluuebunny/crossref_metadata_2025 huggingface dataset:
Laser-driven two-electron quantum dot in plasmas
Authors: Bahar M. K. , Soylu A.
Published: June 2018

We have investigated the energies of two-electron parabolic quantum dots (TEPQdots) embedded in plasmas characterized by more general exponential cosine screened Coulomb (MGECSC) potential under the action of a monochromatic, linearly polarized laser field by solving the corresponding Schrödinger equation numerically via the asymptotic iteration method. The four different cases of the MGECSC potential constituted by various sets of the potential parameters are reckoned in modeling of the interactions in the plasma environments which are Debye and quantum plasmas. The plasma environment is a remarkable experimental argument for the quantum dots and the interactions in plasma environments are different compared to the interactions in an environment without plasma and the screening specifications of the plasmas can be controlled through the plasma parameters. These findings constitute our major motivation in consideration of the plasma environments. An appreciable confinement effect is made up by implementing the laser field on the TEPQdot. The influences of the laser field on the system are included by using the Ehlotzky approximation, and then Kramers-Henneberger transformation is carried out for the corresponding Schrödinger equation. The influences of the ponderomotive force on two-electron quantum dots embedded in plasmas are investigated. The behaviours, the similarities and the functionalities of the laser field, the plasma environment, and the quantum dot confinement are also scrutinized. In addition, the role of the plasma environments in the mentioned analysis is also discussed in detail.
Y-type three-blade bluff body for wind energy harvesting
Authors: Liu Feng-Rui , Zou Hong-Xiang , Zhang Wen-Ming , Peng Zhi-Ke , Meng Guang
Published: June 2018

A three-blade bluff body for wind energy harvesting is proposed and designed. The bluff body with a Y-type cross-section is formed by three rigid thin blades and fixed at the free end of a piezoelectric cantilever beam. Simulations and experiments confirmed that this three-blade structure can achieve much higher energy output than a square prism. The output voltages of horizontal harvesters with different half-angles between the two front blades of the bluff body were measured first. The half-angle dramatically affected the performance of the energy harvester. Half-angles between 60° and 80° are found to be the optimal values for generating a high output voltage. In addition, the performance of the harvester can be enhanced when the length ratio of the rear blade to the front blade is in the range of 4/3–5/3. Interestingly, the output voltage of the vertical three-blade harvester was higher than that of the horizontal one and the optimal half-angle in this case was also between 60° and 80°.
Influence of catalyst packing configuration on the discharge characteristics of dielectric barrier discharge reactors: A numerical investigation
Authors: Gadkari Siddharth , Gu Sai
Published: June 2018

A two-dimensional numerical fluid model is developed for studying the influence of packing configurations on dielectric barrier discharge (DBD) characteristics. Discharge current profiles and time averaged electric field strength, electron number density, and electron temperature distributions are compared for the three DBD configurations, plain DBD with no packing, partially packed DBD, and fully packed DBD. The results show that a strong change in discharge behaviour occurs when a DBD is fully packed as compared to partial packing or no packing. While the average electric field strength and electron temperature of a fully packed DBD are higher relative to the other DBD configurations, the average electron density is substantially lower and may impede the DBD reactor performance under certain operating conditions. Possible scenarios of the synergistic effect of the combination of plasma with catalysis are also discussed.
Determination of band alignment at two-dimensional MoS2/Si van der Waals heterojunction
Authors: Goel Neeraj , Kumar Rahul , Mishra Monu , Gupta Govind , Kumar Mahesh
Published: June 2018

To understand the different mechanism occurring at the MoS2-silicon interface, we have fabricated a MoS2/Si heterojunction by exfoliating MoS2 on top of the silicon substrate. Raman spectroscopy and atomic force microscopy (AFM) measurement expose the signature of few-layers in the deposited MoS2 flake. Herein, the temperature dependence of the energy barrier and carrier density at the MoS2/Si heterojunction has been extensively investigated. Furthermore, to study band alignment at the MoS2/Si interface, we have calculated a valence band offset of 0.66 ± 0.17 eV and a conduction band offset of 0.42 ± 0.17 eV using X-ray and Ultraviolet photoelectron spectroscopy. We determined a type-II band alignment at the interface which is very conducive for the transport of photoexcited carriers. As a proof-of-concept application, we extend our analysis of the photovoltaic behavior of the MoS2/Si heterojunction. This work provides not only a comparative study between MoS2/p-Si and MoS2/n-Si heterojunctions but also paves the way to engineer the properties of the interface for the future integration of MoS2 with silicon.
Extraordinary SEAWs under influence of the spin-spin interaction and the quantum Bohm potential
Authors: Andreev Pavel A.
Published: June 2018

The separate spin evolution (SSE) of electrons causes the existence of the spin-electron acoustic wave. Extraordinary spin-electron acoustic waves (SEAWs) propagating perpendicular to the external magnetic field have a large contribution of the transverse electric field. Its spectrum has been studied in the quasi-classical limit at the consideration of the separate spin evolution. The spin-spin interaction and the quantum Bohm potential give contribution in the spectrum extraordinary SEAWs. This contribution is studied in this paper. Moreover, it is demonstrated that the spin-spin interaction leads to the existence of the extraordinary SEAWs if the SSE is neglected. It has been found that the SSE causes the instability of the extraordinary SEAW at the large wavelengths, but the quantum Bohm potential leads to the full stabilization of the spectrum.
Communication: An efficient and accurate perturbative correction to initiator full configuration interaction quantum Monte Carlo
Authors: Blunt Nick S.
Published: June 2018

We present a perturbative correction within initiator full configuration interaction quantum Monte Carlo (i-FCIQMC). In the existing i-FCIQMC algorithm, a significant number of spawned walkers are discarded due to the initiator criteria. Here we show that these discarded walkers have a form that allows the calculation of a second-order Epstein-Nesbet correction, which may be accumulated in a trivial and inexpensive manner, yet substantially improves i-FCIQMC results. The correction is applied to the Hubbard model and the uniform electron gas and molecular systems.
Seed-dormancy depth is partitioned more strongly among habitats than among species in tropical ephemerals
Authors: Cross Adam T. , Barrett Matthew D. , Turner Shane R. , Dixon Kingsley W. , Merritt David J.
Published: June 2018

Seed biology in the annual herbaceous flora of ecologically stressful, seasonally wet habitats remains largely unexplored. Temporal and spatial species turnover among these habitats is often high, yet little is known about how fine-scale habitat variation drives intraspecific variability in seed dormancy depth and seed germination requirements. The present study characterised seed dormancy and investigated the germination biology of six closely related herbaceous annual species of Byblis from northern Australia. We assessed variation in the response of seeds of all species to temperature cues, as well as light and the naturally occurring germination stimulants karrikinolide (KAR1) and ethylene. We also examined intraspecific variation in germination response and seed-dormancy depth for three widely distributed species with overlapping distribution occurring in habitats with differing soil thermal and hydrological conditions. Seed germination in all six species was significantly increased by exposure to either KAR1 or ethylene, with this effect being amplified in two species (B. filifolia and B. rorida) following a period of warm, dry after-ripening. Seed-dormancy depth and the germination response of seeds to both KAR1 and ethylene were partitioned more strongly among habitats than among species. Populations on shallow (<20-cm soil depth) sandy soils produced less dormant seeds than did populations of the same species on deeper sandy soils (40+ cm) or on heavy cracking clays. The upper soil profile of shallow soil habitats was exposed to higher average temperatures, greater diurnal temperature fluctuation and greatly reduced moisture persistence compared with deeper soils. Fine-scale differences in the thermal and hydrological conditions of seasonally wet habitats appear to be strong drivers of dormancy depth in seeds of tropical Byblis. Widely distributed species exhibit high levels of plasticity in seed-dormancy depth and germination response among different habitats, with similar responses being observed for sympatric species. So as to fully understand species turnover in tropical ephemerals, future studies should examine phenotypic plasticity and the rate of local adaptation of seed traits in greater detail.
Towards a structural ownership condition on moral responsibility
Authors: Matheson Benjamin
Published: June 2018

In this paper, I propose and defend a structural ownership condition on moral responsibility. According to the condition I propose, an agent owns a mental item if and only if it is part of or is partly grounded by a coherent set of psychological states. As I discuss, other theorists have proposed or alluded to conditions like psychological coherence, but each proposal is unsatisfactory in some way. My account appeals to narrative explanation to elucidate the relevant sense of psychological coherence.
3DPatch: fast 3D structure visualization with residue conservation
Authors: Jakubec David , Vondrášek Jiří , Finn Robert D
Published: June 2018

Amino acid residues showing above background levels of conservation are often indicative of functionally significant regions within a protein. Understanding how the sequence conservation profile relates in space requires projection onto a protein structure, a potentially time-consuming process. 3DPatch is a web application that streamlines this task by automatically generating multiple sequence alignments (where appropriate) and finding structural homologs, presenting the user with a choice of structures matching their query, annotated with residue conservation scores in a matter of seconds.

Availability and implementation

3DPatch is written in JavaScript and is freely available at http://www.skylign.org/3DPatch/. Mozilla Firefox, Google Chrome, and Safari web browsers are supported. Source code is available under MIT license at https://github.com/davidjakubec/3DPatch.

Supplementary information

Supplementary data are available at Bioinformatics online.
The stringent response and Mycobacterium tuberculosis pathogenesis
Authors: Prusa Jerome , Zhu Dennis X , Stallings Christina L
Published: June 2018

During infection, the host restrains Mycobacterium tuberculosis (Mtb) from proliferating by imposing an arsenal of stresses. Despite this onslaught of attacks, Mtb is able to persist for the lifetime of the host, indicating that this pathogen has substantial molecular mechanisms to resist host-inflicted damage. The stringent response is a conserved global stress response in bacteria that involves the production of the hyperphosphorylated guanine nucleotides ppGpp and pppGpp (collectively called (p)ppGpp). (p)ppGpp then regulates a number of cellular processes to adjust the physiology of the bacteria to promote survival in different environments. Survival in the presence of host-generated stresses is an essential quality of successful pathogens, and the stringent response is critical for the intracellular survival of a number of pathogenic bacteria. In addition, the stringent response has been linked to virulence gene expression, persistence, latency and drug tolerance. In Mtb, (p)ppGpp synthesis is required for survival in low nutrient conditions, long term culture and during chronic infection in animal models, all indicative of a strict requirement for (p)ppGpp during exposure to stresses associated with infection. In this review we discuss (p)ppGpp metabolism and how this functions as a critical regulator of Mtb virulence.
An Extension of Polynomial Integrability to Dual Quermassintegrals
Authors: Yaskin Vladyslav
Published: June 2018

A bounded domain $K$ is called polynomially integrable if its parallel section function $V_{n-1}(K\cap \{\xi ^\perp +t\xi \})$ is a polynomial of $t$ (on its support) for every $\xi $. A complete characterization of such domains was given recently. Here we obtain a generalization of these results in the setting of dual quermassintegrals. We also address the associated smoothness issues.
Obesity, Diabetes, and the Risk of Invasive Group B Streptococcal Disease in Nonpregnant Adults in the United States
Authors: Pitts Samantha I , Maruthur Nisa M , Langley Gayle E , Pondo Tracy , Shutt Kathleen A , Hollick Rosemary , Schrag Stephanie J , Thomas Ann , Nichols Megin , Farley Monica , Watt James P , Miller Lisa , Schaffner William , Holtzman Corinne , Harrison Lee H
Published: June 2018

Background

Rates of invasive group B Streptococcus (GBS) disease, obesity, and diabetes have increased in US adults. We hypothesized that obesity would be independently associated with an increased risk of invasive GBS disease.

Methods

We identified adults with invasive GBS disease within Active Bacterial Core surveillance during 2010–2012 and used population estimates from the Behavioral Risk Factor Surveillance System to calculate invasive GBS incidence rates. We estimated relative risks (RRs) of invasive GBS using Poisson analysis with offset denominators, with obesity categorized as class I/II (body mass index [BMI] = 30–39.9 kg/m2) and class III (BMI ≥ 40.0 kg/m2).

Results

In multivariable analysis of 4281 cases, the adjusted RRs of invasive GBS disease were increased for obesity (class I/II: RR, 1.52; 95% confidence interval [CI], 1.14–2.02; and class III: RR, 4.87; 95% CI, 3.50–6.77; reference overweight) and diabetes (RR, 6.04; 95% CI, 4.77–7.65). The adjusted RR associated with class III obesity was 3-fold among persons with diabetes (95% CI, 1.38–6.61) and nearly 9-fold among persons without diabetes (95% CI, 6.41–12.46), compared with overweight. The adjusted RRs associated with diabetes varied by age and BMI, with the highest RR in young populations without obesity. Population attributable risks of invasive GBS disease were 27.2% for obesity and 40.1% for diabetes.

Conclusions

Obesity and diabetes were associated with substantially increased risk of infection from invasive GBS. Given the population attributable risks of obesity and diabetes, interventions that reduce the prevalence of these conditions would likely reduce the burden of invasive GBS infection.
Infectious Diseases Physicians’ Perspectives Regarding Injection Drug Use and Related Infections, United States, 2017
Authors: Rapoport Alison B , Fischer Leah S , Santibanez Scott , Beekmann Susan E , Polgreen Philip M , Rowley Christopher F
Published: June 2018

Background

In the context of the opioid epidemic, injection drug use (IDU)–related infections are an escalating health issue for infectious diseases (ID) physicians in the United States.

Methods

We conducted a mixed methods survey of the Infectious Diseases Society of America’s Emerging Infections Network between February and April 2017 to evaluate perspectives relating to care of persons who inject drugs (PWID). Topics included the frequency of and management strategies for IDU-related infection, the availability of addiction services, and the evolving role of ID physicians in substance use disorder (SUD) management.

Results

More than half (53%, n = 672) of 1273 network members participated. Of these, 78% (n = 526) reported treating PWID. Infections frequently encountered included skin and soft tissue (62%, n = 324), bacteremia/fungemia (54%, n = 281), and endocarditis (50%, n = 263). In the past year, 79% (n = 416) reported that most IDU-related infections required ≥2 weeks of parenteral antibiotics; strategies frequently employed for prolonged treatment included completion of the entire course in the inpatient unit (41%, n = 218) or at another supervised facility (35%, n = 182). Only 35% (n = 184) of respondents agreed/strongly agreed that their health system offered comprehensive SUD management; 46% (n = 242) felt that ID providers should actively manage SUD.

Conclusions

The majority of physicians surveyed treated PWID and reported myriad obstacles to providing care. Public health and health care systems should consider ways to support ID physicians caring for PWID, including (1) guidelines for providing complex care, including safe provision of multiweek parenteral antibiotics; (2) improved access to SUD management; and (3) strategies to assist those interested in roles in SUD management.
Pulmonary Disease Associated With Nonencapsulated Streptococcus pneumoniae
Authors: Martin Caleb S , Bradshaw Jessica L , Pipkins Haley R , McDaniel Larry S
Published: June 2018

We discuss 3 patients presenting with pneumonia associated with nonencapsulated Streptococcus pneumoniae (NESp), an emerging pathogen commonly causing upper respiratory infections. Clinical isolates obtained from these patients were characterized to evaluate their respective antibiotic resistance and virulence mechanisms. We demonstrate that NESp resistant to classical drug treatments are isolated during pneumonia.
An Innovative Network Approach to Coordinating a National Effort to Improve Cardiovascular Health: The Case of Million Hearts
Authors: Varda Danielle M. , Williams Malcolm V. , Schooley Michael , Duplantier Daniel , Newman Kayleigh , Lowe Beasley Kincaid , Lucido Briana , Marshall Ashley
Published: June 2018

Objective:

To assess the structure, content, quality, and quantity of partnerships that developed in response to a national cardiovascular health initiative, Million Hearts.

Design:

This study used a social network analysis (SNA) approach to assess the Million Hearts initiative network partnerships and identify potential implications for policy and practice.

Setting/Participants:

The Million Hearts network comprised a core group of federal and private sector partners that participate in Million Hearts activities and align with initiative priorities. To bound the network for the SNA, we used a list of 58 organizations (74% response rate) from a previously completed qualitative analysis of Million Hearts partnerships.

Main Outcome Measures:

We used the online PARTNER (Program to Analyze Record and Track Networks to Enhance Relationships—www.partnertool.net) survey to collect data on individual organizational characteristics and relational questions that asked organizations to identify and describe their relationships with other partners in the network. Key SNA measures include network density, centralizations, value, and trust.

Results:

Our analyses show a network that is decentralized, has strong perceptions of trust and value among its members, and strong agreement on intended outcomes. Interestingly, partners report a desire and ability to contribute resources to Million Hearts; however, the perceptions between partners are that resources are not being contributed at the level they potentially could be. The majority of partners reported that being in the network helped them achieve their goals related to cardiovascular disease prevention. The largest barrier to successful activities within the network was cited as lack of targeted funding and staff to support participation in the network.

Conclusions:

The Million Hearts network described in this article is unique in its membership at the national level, agreement on outcomes, its powerful information-sharing abilities that require few resources, and its decentralized structure. We identified strategies that could be implemented to strengthen the network and its activities. By examining a national-level public-private partnership formed to address a public health issue, we can identify ways to strengthen the network and provide a framework for developing other initiatives.
Synonym-Based Word Frequency Analysis to Support the Development and Presentation of a Public Health Quality Improvement Taxonomy
Authors: Pina Jamie , Massoudi Barbara L. , Chester Kelley , Koyanagi Mark
Published: June 2018

Context:

Researchers and analysts have not completely examined word frequency analysis as an approach to creating a public health quality improvement taxonomy.

Objective:

To develop a taxonomy of public health quality improvement concepts for an online exchange of quality improvement work.

Design:

We analyzed documents, conducted an expert review, and employed a user-centered design along with a faceted search approach to make online entries searchable for users. To provide the most targeted facets to users, we used word frequency to analyze 334 published public health quality improvement documents to find the most common clusters of word meanings. We then reviewed the highest-weighted concepts and categorized their relationships to quality improvement details in our taxonomy. Next, we mapped meanings to items in our taxonomy and presented them in order of their weighted percentages in the data. Using these methods, we developed and sorted concepts in the faceted search presentation so that online exchange users could access relevant search criteria.

Results:

We reviewed 50 of the top synonym clusters and identified 12 categories for our taxonomy data. The final categories were as follows: Summary; Planning and Execution Details; Health Impact; Training and Preparation; Information About the Community; Information About the Health Department; Results; Quality Improvement (QI) Staff; Information; Accreditation Details; Collaborations; and Contact Information of the Submitter.

Conclusion:

Feedback about the elements in the taxonomy and presentation of elements in our search environment from users has been positive. When relevant data are available, the word frequency analysis method may be useful in other taxonomy development efforts for public health.
Pay to Play? State Laws Related to High School Sports Participation Fees
Authors: Eyler Amy A. , Piekarz-Porter Elizabeth , Serrano Natalicio H.
Published: June 2018

Context:

Participation in high school sports can impact the physical and mental health of students and influence other positive social and economic outcomes. To maintain sports programs amidst school budget deficits, many districts are implementing sports participation fee policies. Although locally implemented, these district policies can be guided by state law.

Objective:

The main objective of this study was to assess state laws and regulations related to high school sports participation fees.

Design:

Codified statutes and administrative regulations were compiled for all 50 states and the District of Columbia using subscription-based services from LexisNexis and WestlawNext. A content assessment tool was developed to identify key components of school sports participation fee laws and used for summarization. Key components identified included legislation summarization, years in effect, whether it allows fees, whether there is any fee waiver, qualifications needed for fee waiver, whether there is a tax credit, and whether there is disclosure of implementation. State information was aggregated and doubled-coded to ensure reliability.

Results:

As of December 31, 2016, 18 states had laws governing sports participation fees; 17 of these states' laws allowed for such fees, whereas 1 state prohibited them. Most laws give authority to local school boards to set and collect fees. The laws in 9 states have provisions for a waiver program for students who cannot pay the fees, although they do not all mandate the existence of these waivers. Other content within laws included tax credits and disclosure.

Conclusion:

This analysis shows that states with laws related to school sports participation fees varied in scope and content. Little is known about the implementation or impact of these laws at the local level and the effect of fees on different student population groups. This warrants future investigation.
Contextual Influences on Value-based Choice
Authors: Man Vincent , Kovacheff Chloe , Cunningham William A.
Published: June 2018

Biases in choice behavior are shaped by both immediately encountered cues as well as the background context in which these cues are embedded. Here we examine the mechanisms that underlie the integration of contextual and cue information, and the manner in which these sources of information shape behavior. We demonstrate contextual influence on choice dissociated from cue information using a value-based multi-alternative choice task while recording neural activity using electroencephalography. Consistent with work on negativity biases, we show that contextual attributes related to loss, reflected along central-parietal sites in the gamma (30-59 Hz) frequency range, are prioritized and drive behavior to prevent loss. We employ a multi-alternative sequential sampling computational model to show that contextual and cue information are integrated through the decision process to shape choice responses, and link this integrative process to a neural signature in the gamma frequency band.
Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network
Authors: Zeng Wanwen , Wang Yong , Jiang Rui
Published: June 2018

Motivation

Interactions among such cis-regulatory elements as enhancers and promoters are main driving forces shaping context-specific chromatin structure and gene expression. Although there have been computational methods for predicting gene expression from genomic and epigenomic information, most of them overlook long-range enhancer-promoter interactions, due to the difficulty in precisely linking regulatory enhancers to target genes. Recently, a novel high-throughput experimental approach named HiChIP has been developed and generating comprehensive data on high-resolution interactions between promoters and distal enhancers. On the other hand, plenty of studies have suggested that deep learning achieves state-of-the-art performance in epigenomic signal prediction, and thus promoting the understanding of regulatory elements. In consideration of these two factors, we integrate proximal promoter sequences and HiChIP distal enhancer-promoter interactions to accurately model gene expression.

Results

We propose DeepExpression, a densely connected convolutional neural network to predict gene expression using both promoter sequences and enhancer-promoter interactions. We demonstrate that our model consistently outperforms baseline methods not only in the classification of binary gene expression status but also in the regression of continuous gene expression levels, in both cross-validation experiments and cross-cell lines predictions. We show that sequential promoter information is more informative than experimental enhancer information while enhancer-promoter interactions are most beneficial from those within ±100 kbp around the TSS of a gene. We finally visualize motifs in both promoter and enhancer regions and show the match of identified sequence signatures and known motifs. We expect to see a wide spectrum of applications using HiChIP data in deciphering the mechanism of gene regulation.

Availability

DeepExpression is freely available at https://github.com/wanwenzeng/DeepExpression.

Contact

ruijiang@tsinghua.edu.cn, ywang@amss.ac.cn

Supplementary information

Supplementary data are available at Bioinformatics online.
Role of DCP1-DCP2 complex regulated by viral and host microRNAs in DNA virus infection
Authors: Sun Yuechao , Zhang Xiaobo
Published: June 2018

The DCP1-DCP2 complex can regulate the animal antiviral immunity by the decapping of retrovirus RNAs and the suppression of RNAi pathway. However, the influence of DCP1-DCP2 complex on DNA virus infection and the regulation of DCP1-DCP2 complex by microRNAs (miRNAs) remain unclear. In this study, we investigated the role of miRNA-regulated DCP1-DCP2 complex in DNA virus infection. Our results suggested that the DCP1-DCP2 complex played a positive role in the infection of white spot syndrome virus (WSSV), a DNA virus of shrimp. The N-terminal regulatory domain of DCP2 was interacted with the EVH1 domain of DCP1, forming the DCP1-DCP2 complex. Furthermore, a host shrimp miRNA (miR-87) inhibited WSSV infection by targeting the host DCP2 gene and a viral miRNA (WSSV-miR-N46) took a negative effect on WSSV replication by targeting the host DCP1 gene. Therefore, our study provided novel insights into the underlying mechanism of DCP1-DCP2 complex and its regulation by miRNAs in virus-host interactions.

The DCP1-DCP2 complex can regulate the animal antiviral immunity by the decapping of retrovirus RNAs and the suppression of RNAi pathway. In the present study, the findings indicated that the silencing of the DCP1-DCP2 complex inhibited the infection of WSSV, a DNA virus of shrimp, suggesting that the DCP1-DCP2 complex facilitated DNA virus infection. Due to the suppressive role of the DCP1-DCP2 complex in RNAi pathway against virus infection, the DCP1-DCP2 complex could promote WSSV infection in shrimp. In this context, our study contributed a novel aspect of the DCP1-DCP2 complex in virus-host interactions. Our study revealed that the host and viral miRNAs could regulate the DCP1-DCP2 complex to affect virus infection. Therefore, our study provided novel insights into the miRNA-mediated regulation of DCP1-DCP2 complex took great effects on RNAi immunity of invertebrates against virus infection.
Demographic features and mortality risks in smallholder poultry farms of the Mekong river delta region
Authors: Delabouglise Alexis , Nguyen-Van-Yen Benjamin , Nguyen Thanh Thi Le , Huynh Xuyen Thi Ai , Phuong Tuyet Ngoc , Ha Lam Minh , Boni Maciej Filip
Published: June 2018

This study describes the demographic structure and dynamics of small scale poultry farms of the Mekong river delta region, one of the world's highest-risk regions for avian influenza outbreaks. Fifty farms were monitored over a 20-month period, with farm sizes, species, age, arrival/departure of poultry, and farm management practices recorded monthly. The history of poultry flocks in the sampled farms was recovered using a flock-matching algorithm. Median flock population sizes were 16 for chickens (IQR: 10 - 40), 32 for ducks (IQR: 18 - 101) and 11 for Muscovy ducks (IQR: 7 - 18); farm size distributions for the three species were heavily right-skewed. There was substantial flock overlap on almost all farms, with only one farm practicing an all-in-all-out management system. The rate of interspecific contacts was high, with two out of three farms housing at least two bird species. Among poultry species, demographic dynamics varied. Muscovy ducks were kept for long periods, in small numbers and outdoors, while chickens and ducks were farmed in larger numbers, indoors or in pens, with more rapid flock turnover. Most chicks were sold young to be fattened on other farms, and broiler and layer ducks had a short production period and higher degree of specialization. The rate of mortality due to disease did not differ much among species, with birds being less likely to die from disease at older ages, but frequency of disease symptoms differed by species. Time series of disease-associated mortality and population size were correlated for Muscovy ducks (Kendall's coefficient = 0.49, p value < 0.01).
What is the Best Available Science?: Conservation Status of Two California Desert Vertebrates
Authors: Clause Adam G. , Norment Christopher J. , Cunningham Laura , Emmerich Kevin , Buckmaster Nicholas G. , Nordin Erin , Hansen Robert W.
Published: June 2018

Scientific progress depends on evidence-based research, and reliance on accurate scholarship is essential when making management decisions for imperiled species. However, erroneous claims are sometimes perpetuated in the scientific and technical literature, which can complicate policy and regulatory judgments. The literature associated with two enigmatic California desert vertebrates, the Panamint alligator lizardElgaria panamintinaand the Inyo Mountains salamanderBatrachoseps campi, exemplifies this problem. We produced a comprehensive threat analysis and status assessment for these species, which are both under review for possible listing under the US Endangered Species Act (ESA). Despite uncertainties and limited data, we find that many sources contain factual errors about the status of these two species, particularly the original petition that advocated for ESA listing. Although localized declines may have gone undetected, no evidence exists of population declines, population extirpation, or population-scale habitat conversion forE. panamintina. However, there is evidence of recent flash flood damage to some occupiedB. campihabitat, which has possibly led to population declines at those localities. Contrary to inaccurate statements by some authors, all known populations of both species occur exclusively on federal lands, and numerous populations have likely benefited from recent federal management targeted at reducing known threats. Of the 12 threats that we identified for one or both species, only three currently appear to be serious: water diversions, climate change, and flash floods. The remaining threats are neither widespread nor severe, despite numerous contrary yet poorly supported statements in the literature. We thus evaluate the contemporary conservation status of both species as relatively secure, althoughB. campiis more at-risk compared toE. panamintina. This conclusion is independently supported by a recent review. Nonetheless, ongoing stewardship of these species in a multi-use context by federal agencies remains vital, and we identify several priority management actions and research needs for both species. We also recommend updated determinations on the IUCN Red List, and the Species of Conservation Concern list of the Inyo National Forest. To maximize the quality and effectiveness of conservation planning, we urge government agencies, non-governmental organizations, and individual scientists to maintain high standards of scholarship and decision-making.
Structure simulation of thrombopoietin receptor C-MPL with missense SNPs and its geographical distribution
Authors: Zheng Weizhong , Zeng Dongyu , Zhou Qi , Li Zhilan , Liang Haojian
Published: June 2018

Mpl is a key gene controlling the process of proliferation and differentiation of megakaryocyte and several studies reported that the mutation of mpl will even cause accurate megakaryocyte leukemia. By overlapping the missense mutation in NCBI and recorded SNP in 1000 genome database, we sorted out 4 SNPs(rs190983971, rs563996763, rs546510242, rs373621350) to find out its conformational changes. With Phyre v2.0, we simulated the secondary and tertiary structure change caused by the SNP and compared it with the original structure. The significant changes indicated its potential in leading to diseases associated with platelet reproduction. Finally, according to 1000 genome database, we constructed the geographically distribution of different populations and its SNPs carrying rate.
Novel Significant Stage-Specific Differentially Expressed Genes in Liver Hepatocellular Carcinoma
Authors: Sarathi Arjun , Palaniappan Ashok
Published: June 2018

Liver cancer is among the top deadly cancers worldwide with a very poor prognosis, and the liver is a particularly vulnerable site for metastasis of other cancers. In this study, we developed a novel computational framework for the stage-specific analysis of hepatocellular carcinoma initiation and progression. Using publicly available clinical and RNA-Seq data of cancer samples and controls, we annotated the gene expression matrix with sample stages. We performed a linear modelling analysis of gene expression across all stages and found significant genome-wide changes in gene expression in cancer samples relative to control. Using a contrast against the control, we were able to identify differentially expressed genes (log fold change >2) that were significant at an adjusted p-value < 10E-3. In order to identify genes that were specific to each stage without confounding differential expression in other stages, we developed a full set of pairwise stage contrasts and enforced a p-value threshold (<0.05) for each such contrast. Genes were specific for a stage if they passed all the significance filters for that stage. Our analysis yielded two stage-I specific genes (CA9, WNT7B), two stage-II specific genes (APOBEC3B, FAM186A), ten stage-III specific genes including DLG5, PARI and GNMT, and ten stage-IV specific genes including GABRD, PGAM2 and PECAM1. Of these, only APOBEC3B is an established cancer driver gene. DLG5 was found to be tumor-promoting contrary to the cancer literature on this gene. Further, GABRD, well studied in literature on other cancers, emerged as a stage-IV specific gene. Our findings could be validated using multiple sources of omics data as well as experimentally. The biomarkers identified herein could potentially underpin diagnosis as well as pinpoint drug targets.
Long-range chromatin interactions on the inactive X and atHoxclusters are regulated by the non-canonical SMC protein Smchd1
Authors: Jansz Natasha , Keniry Andrew , Trussart Marie , Bildsoe Heidi , Beck Tamara , Tonks Ian D. , Mould Arne W. , Hickey Peter , Breslin Kelsey , Iminitoff Megan , Ritchie Matthew E. , McGlinn Edwina , Kay Graham F. , Murphy James M. , Blewitt Marnie E.
Published: June 2018

The regulation of higher order chromatin structure is complex and dynamic; however we do not yet understand the full suite of mechanisms governing architecture. Here we reveal the non-canonical SMC protein Smchd1 as a novel regulator of long-range chromatin interactions, and add it to the canon of epigenetic proteins required forHoxgene regulation. The effect of losing Smchd1-dependent chromatin interactions has varying outcomes dependent on chromatin context. At autosomal targets transcriptionally sensitive to Smchd1 deletion, we find increased short-range interactions and ectopic enhancer activation. By contrast, the inactive X chromosome is transcriptionally refractive to Smchd1 ablation, despite chromosome-wide increases in short-range interactions. There we observe spreading of H3K27me3 domains into regions not normally decorated by this mark. Together these data suggest Smchd1 has the capacity to insulate the chromatin, thereby limiting access to other chromatin modifying proteins.
Functional Role of Annexins in Zebrafish Caudal Fin Regeneration – A Gene Knockdown Approach in Regenerating Tissue
Authors: Quoseena Mir , Vuppaladadium Sowmya , Hussain Shahid , Bharathi Swarna , Idris Mohammed M
Published: June 2018

Regeneration is an adaptive phenomenon with wide biological implications spread heterogeneously in almost all the organism including human beings. The ability of regeneration varies from species to species for its impediment. Epimorphic regeneration of zebrafish caudal fin tissue is most widely studied regeneration mechanism for its discrete and rapid regenerative capability. Several genes/proteins were found to be associated with zebrafish caudal fin tissue regeneration. Here, we have evaluated the functional role ofAnnexin 2aand2bgenes in adult zebrafish caudal fin tissue undergoing regeneration using a novel CRSISPR-Cas9 gene knock down approach. Knock down of both the genes individually elicited in decelerated regeneration and down regulation of target genes and its partner genes/proteins such as ANXA1a, ANXA5b and ANXA13. This study validates a novel gene targeting approach and the possible role of annexin in regeneration mechanism.
On identifying collective displacements in apo-proteins that reveal eventual binding pathways
Authors: Prakashchand Dube Dheeraj , Ahalawat Navjeet , Khandelia Himanshu , Mondal Jagannath , Sengupta Surajit
Published: June 2018

Binding of small molecules to proteins often involves large conformational changes in the latter, which open up pathways to the binding site. Observing and pinpointing these rare events in large scale, all-atom, computations of specific protein-ligand complexes, is expensive and to a great extent serendipitous. Further, relevant collective variables which characterise specific binding or un-binding scenarios are still difficult to identify despite the large body of work on the subject. Here, we show that possible primary and secondary binding pathways can be discovered from short simulations of the apo-protein without waiting for an actual binding event to occur. We use a projection formalism, introduced earlier to study deformation in solids, to analyse local atomic displacements into two mutually orthogonal subspaces — those which are “affine” i.e. expressible as a homogeneous deformation of the native structure, and those which are not. The susceptibility to non-affine displacements among the various residues in the apo-protein is then shown to correlate with typical binding pathways and sites crucial for allosteric modifications. We validate our observation with all-atom computations of three proteins, T4-Lysozyme, Src kinase and Cytochrome P450.
A synthetic system that senses Candida albicans and inhibits virulence factors
Authors: Tscherner Michael , Giessen Tobias W. , Markey Laura , Kumamoto Carol A. , Silver Pamela A.
Published: June 2018

Due to a limited set of antifungals available and problems in early diagnosis invasive fungal infections caused by Candida species are among the most common hospital-acquired infections with staggering mortality rates. Here, we describe an engineered system able to sense and respond to the fungal pathogen Candida albicans, the most common cause of candidemia. In doing so, we identified hydroxyphenylacetic acid (HPA) as a novel molecule secreted by C. albicans. Furthermore, we engineered E. coli to be able to sense HPA produced by C. albicans. Finally, we constructed a sense-and-respond system by coupling the C. albicans sensor to the production of an inhibitor of hypha formation thereby reducing filamentation, virulence factor expression and fungal-induced epithelial damage. This system could be used as a basis for the development of novel prophylactic approaches to prevent fungal infections.
Storage of prescription veterinary medicines on UK dairy farms: a cross-sectional study
Authors: Rees Gwen M. , Barrett David C. , Buller Henry J. , Mills Harriet L. , Reyher Kristen K.
Published: June 2018

Prescription veterinary medicine (PVM) use in the United Kingdom is an area of increasing focus for the veterinary profession. While many studies measure antimicrobial use on dairy farms, none report the quantity of antimicrobials stored on farms, nor the ways in which they are stored. The majority of PVM treatments occur in the absence of the prescribing veterinarian, yet there is an identifiable knowledge gap surrounding PVM use and farmer decision making. To provide an evidence base for future work on PVM use, data were collected from 27 dairy farms in England and Wales in Autumn 2016. The number of different PVM stored on farms ranged from 9-35, with antimicrobials being the most common therapeutic group stored. Injectable antimicrobials comprised the greatest weight of active ingredient found while intramammary antimicrobials were the most frequent unit of medicine stored. Antimicrobials classed by the European Medicines Agency as critically-important to human health were present on most farms, and the presence of expired medicines and medicines not licensed for use in dairy cattle was also common. The medicine resources available to farmers are likely to influence their treatment decisions, therefore evidence of the PVM stored on farms can help inform understanding of medicine use.
CRISPR/Cas9-mediated gene knockin in the hydroid Hydractinia symbiolongicarpus
Authors: Sanders Steven M. , Ma Zhiwei , Hughes Julia M. , Riscoe Brooke M. , Gibson Gregory A. , Watson Alan M. , Flici Hakima , Frank Uri , Schnitzler Christine E. , Baxevanis Andreas D. , Nicotra Matthew L.
Published: June 2018

Background

Hydractinia symbiolongicarpus, a colonial cnidarian, is a tractable model system for many cnidarian-specific and general biological questions. Until recently, tests of gene function in Hydractinia have relied on laborious forward genetic approaches, randomly integrated transgenes, or transient knockdown of mRNAs.

Results

Here, we report the use of CRISPR/Cas9 genome editing to generate targeted genomic insertions in H. symbiolonigcarpus. We used CRISPR/Cas9 to promote homologous recombination of two fluorescent reporters, eGFP and tdTomato, into the Eukaryotic elongation factor 1 alpha (Eef1a) locus. We demonstrate that the transgenes are expressed ubiquitously and are stable over two generations of breeding. We further demonstrate that CRISPR/Cas9 genome editing can be used to mark endogenous proteins with FLAG or StrepII-FLAG affinity tags to enable in vivo and ex vivo protein studies.

Conclusions

This is the first account of CRISPR/Cas9 mediated knockins in Hydractinia and the first example of the germline transmission of a CRISPR/Cas9 inserted transgene in a cnidarian. The ability to precisely insert exogenous DNA into the Hydractinia genome will enable sophisticated genetic studies and further development of functional genomics tools in this understudied cnidarian model.
Machine learning techniques for classifying the mutagenic origins of point mutations
Authors: Zhu Yicheng , Ong Cheng Soon , Huttley Gavin A
Published: June 2018

There is increasing interest in developing diagnostics that discriminate individual mutagenic mechanisms in a range of applications that include identifying population specific mutagenesis and resolving distinct mutation signatures in cancer samples. Analyses for these applications assume that mutagenic mechanisms have a unique relationship with neighboring bases that allows them to be distinguished. Direct support for this assumption is limited to a small number of simple cases, e.g. CpG hypermutability. We have directly evaluated whether the mechanistic origin of a point mutation can be resolved using only sequence context for a more complicated case. We contrasted mutations originating from the multitude of mutagenic processes that normally operate in the mouse germline with those induced by the potent mutagen N-ethyl-N-nitrosourea (ENU). The considerable overlap in the mutation spectra of these two samples make this a challenging problem. Employing a new, robust log-linear modeling method, we demonstrate that neighboring bases contain information regarding point mutation direction that differs between the ENU-induced and spontaneous mutation classes. A logistic regression classifier proved to be substantially more powerful at discriminating between the different mutation classes than alternatives. Concordance between the feature set of the best classifier and information content analyses suggest our results can be generalized to other mutation classification problems. We conclude that machine learning can be used to build a practical classification tool to identify the mutation mechanism for individual genetic variants. Software implementing our approach is freely available under the BSD 3-clause license.