bluuebunny/crossref_metadata_2025 huggingface dataset:
Secretome analysis of diarrhea‐inducing strains of Escherichia coli
Authors: Nirujogi Raja Sekhar , Muthusamy Babylakshmi , Kim Min‐Sik , Sathe Gajanan J. , Lakshmi P.T.V. , Kovbasnjuk Olga N. , Prasad T.S. Keshava , Wade Mary , Jabbour Rabih E.
Published: January 2017

Secreted proteins constitute a major part of virulence factors that are responsible for pathogenesis caused by Gram‐negative bacteria. Enterohemorrhagic Escherichia coli, O157:H7, is the major pathogen often causing outbreaks. However, studies have reported that the significant outbreaks caused by non‐O157:H7 E. coli strains, also known as “Big‐Six” serogroup strains, are increasing. There is no systematic study describing differential secreted proteins from these non‐O157:H7 E. coli strains. In this study, we carried out MS‐based differential secretome analysis using tandem mass tags labeling strategy of non‐O157:H7 E. coli strains, O103, O111, O121, O145, O26, and O45. We identified 1241 proteins, of which 565 proteins were predicted to be secreted. We also found that 68 proteins were enriched in type III secretion system and several of them were differentially expressed across the strains. Additionally, we identified several strain‐specific secreted proteins that could be used for developing potential markers for the identification and strain‐level differentiation. To our knowledge, this study is the first comparative proteomic study on secretome of E. coli Big‐Six serogroup and the several of these strain‐specific secreted proteins can be further studied to develop potential markers for identification and strain‐level differentiation. Moreover, the results of this study can be utilized in several applications, including food safety, diagnostics of E. coli outbreaks, and detection and identification of bio threats in biodefense.
Optical, spectral, and thermal analyses of InGaN/GaN near‐ultraviolet flip‐chip light‐emitting diodes with different package structures
Authors: Lee Soo Hyun , Guan Xiang‐Yu , Yu Jae Su
Published: January 2017

We analyzed and compared the optical, spectral, and thermal characteristics of InGaN/GaN near‐ultraviolet (NUV) flip‐chip (FC) light‐emitting diodes (LEDs) packaged on the board with dielectric/metal layers (DMB package), board with ceramic/metal layers (CMB package), and board with ceramic/metal layers and thermal tape (CMBT package) in the injection current range of 0–800 mA at 298 and 358 K. For the DMB packaged LED, the relatively high junction temperature was observed due to the inefficient heat dissipation, leading to the more optical output power drop and spectral shift. For the CMBT packaged device, it further dissipated heat at high currents where the performance of CMB packaged device was degraded. In comparison with the experimental results, the theoretically calculated temperature and stress distributions of the NUV FC LEDs with the DMB and CMB packages were also investigated by finite element method‐based simulations.
On Cost‐effective Reuse of Components in the Design of Complex Reconfigurable Systems
Authors: Aizpurua J. I. , Papadopoulos Y. , Muxika E. , Chiacchio F. , Manno G.
Published: January 2017

Design strategies that benefit from the reuse of system components can reduce costs while maintaining or increasing dependability—we use the term dependability to tie together reliability and availability. D3H2 (aDaptive Dependable Design for systems with Homogeneous and Heterogeneous redundancies) is a methodology that supports the design of complex systems with a focus on reconfiguration and component reuse. D3H2 systematizes the identification of heterogeneous redundancies and optimizes the design of fault detection and reconfiguration mechanisms, by enabling the analysis of design alternatives with respect to dependability and cost. In this paper, we extend D3H2 for application to repairable systems. The method is extended with analysis capabilities allowing dependability assessment of complex reconfigurable systems. Analysed scenarios include time‐dependencies between failure events and the corresponding reconfiguration actions. We demonstrate how D3H2 can support decisions about fault detection and reconfiguration that seek to improve dependability while reducing costs via application to a realistic railway case study. Copyright © 2017 John Wiley & Sons, Ltd.
The influence of memory, sample size effects, and filter paper material on online laser‐based plant and soil water isotope measurements
Authors: Cui Jiangpeng , Tian Lide , Gerlein‐Safdi Cynthia , Qu Dongmei
Published: January 2017

Rationale

The recent development of isotope ratio infrared spectroscopy (IRIS) was quickly followed by the addition of online extraction and analysis systems, making it faster and easier to measure soil and plant water isotopes. However, memory and sample size effects limit the efficiency and accuracy of these new setups. In response, this study presents a scheme dedicated to estimating and eliminating these two effects.

Methods

Memory effect was determined by injecting two standard waters alternately. Each standard was injected nine times in a row and analyzed using induction module cavity ring‐down spectroscopy (IM‐CRDS). Memory coefficients were calculated using a new “multistage jump” algorithm. Sample size effects were evaluated by injecting water volumes ranging from 1 μL to 6 μL. Finally, the influence of cellulose filter paper on the isotopic measurements, the memory, and the sample size effect was evaluated by comparing it with glass filter paper.

Results

Memory effects were detected for both δ18O and δ2H values, with the latter being stronger. Isotopic differences between replicates of the same plant or soil sample showed a clear decrease after memory correction. A small water volume effect was found only when the injected water volume was larger than 3 μL. However, while the correction method performed well for laboratory‐made samples, it did not for field samples, due to the heterogeneity of the isotopic composition of the samples. Stronger memory and water volume effects were found for cellulose filter paper.

Conclusions

The memory coefficients and the water volume–isotope relationship improved the consistency and accuracy of both laboratory and field data. Our results indicate that cellulose filter paper may not be a suitable medium to measure standard waters and evaluate memory and water volume effects. Finally, a detailed correction and calibration protocol is suggested, along with notes on best practices to obtain good‐quality IM‐CRDS data. Copyright © 2017 John Wiley & Sons, Ltd.
Boosting the precision of mediation analyses of randomised experiments through covariate adjustment
Authors: Vandenberghe S. , Vansteelandt S. , Loeys T.
Published: January 2017

Analyses of randomised experiments frequently include attempts to decompose the intention‐to‐treat effect into a direct and indirect effect, mediated by given intermediaries, with the aim to shed light onto the treatment mechanism. Methods from causal mediation analysis have facilitated this by allowing for arbitrary models for the outcome and the mediator. They thereby generalise the traditional approach to direct and indirect effects, which is essentially limited to linear models. The default maximum likelihood methods make use of a model for the conditional distribution of the mediator, given treatment and baseline covariates, but are prone to bias when that model is misspecified. In randomised experiments, specification of such model can be easily avoided, but at the expense of a sometimes major efficiency loss when those baseline covariates are predictive of the mediator. In this article, we develop a compromise approach: it makes use of a model for the mediator to optimally extract information from the baseline covariate data but is insulated from the impact of misspecification of that model; it achieves this by exploiting the known randomisation probabilities. Simulation studies and the analysis of a randomised study show major efficiency gains and confirm our theoretical findings that the default methods from causal mediation analysis are sometimes, although not always, reasonably robust to model misspecification. Copyright © 2017 John Wiley & Sons, Ltd.
Early-life status epilepticus induces long-term deficits in anxiety and spatial learning in mice
Authors: Smith Gregory , Ahmed Nowrin , Arbuckle Erin , Lugo Joaquin
Published: January 2017

Background One of the most devastating aspects of developmental epilepsy is the long-term impact on behavior. Children with epilepsy show a high co-morbidity with anxiety disorders and autism.

Methods To examine whether early-life status epilepticus results in altered anxiety, repetitive behavior, social behavior, and learning and memory, we induced status epilepticus in male C57BL/6 mice on postnatal day (PD) 10. The mice received intraperitoneal injections of either kainic acid (2 mg/kg) or 0.9% normal saline. We also included a nontreated control group. Kainic acid induced status epilepticus for approximately 1.5 h. At PD60, the adult mice were then tested in a battery of behavioral tasks, including open field activity, elevated-plus maze, light-dark test, marble burying, social chamber, social partition, conditioned fear, novel object recognition, and Morris water maze.

Results The early-life seizure group showed consistent increases in anxiety in the open field test (p < 0.05), elevated plus maze (p < 0.05), and light-dark task (p < 0.01). The seizure group showed significant (p < 0.01) impairment in the Morris water maze. There were no differences observed in marble burying, social partition, social chamber, novel object recognition, or delay fear conditioning tasks.

Conclusions These results demonstrate that a single insult of status epilepticus during the neonatal period is sufficient to cause specific, long-term impairments in anxiety and spatial learning.
Death Anxiety, Perfectionism and Disordered Eating
Authors: Le Marne Kristina M. , Harris Lynne M.
Published: January 2017

Recently, death anxiety, or dread of death, has been proposed as a key transdiagnostic process underlying the anxiety disorders, depressive disorders, somatic disorders, and trauma and stressor-related disorders. In fact, it has been argued that death anxiety underlies all psychopathology, and is more fundamental than perfectionism, a process which was previously considered the root of mental illness. However, there has been a paucity of research examining the relationship between death anxiety and the eating disorders, although these conditions have been found to be strongly related to perfectionism. The present study therefore aimed to examine whether death anxiety is related to disordered eating, and whether death anxiety is a better predictor of disordered eating than perfectionism. A sample of 164 participants (132 female), average age 33.55 years (SD= 15.45 years), completed an online survey comprising background questions (age, sex, diagnosed psychiatric disorder), the Eating Attitudes Test — 26 item version (EAT-26), the Almost Perfect Scale — Revised (APS-R), the Rosenberg Self-Esteem Scale (RSES), and the Death Anxiety Scale (DAS). The findings of a hierarchical multiple regression analysis with EAT-26 as the dependent variable, age entered at Step 1, the RSES and APS-R entered at Step 2, and the DAS entered at Step 3 showed that only death anxiety and self-esteem were independent predictors of disordered eating at Step 3. A simultaneous multiple regression analysis was subsequently run with age and the APS-R alone as predictors of EAT-26 scores. This analysis showed that perfectionism was only a predictor of disordered eating when death anxiety and self-esteem were not included in the regression model. Death anxiety and self-esteem both appear to be important transdiagnostic processes.
Treatment Outcomes in 1p19q Co-deleted/Partially Deleted Gliomas
Authors: McNamara Mairéad G. , Jiang Haiyan , Lim-Fat Mary Jane , Sahebjam Solmaz , Kiehl Tim-Rasmus , Karamchandani Jason , Coire Claire , Chung Caroline , Millar Barbara-Ann , Laperriere Normand , Mason Warren P.
Published: January 2017

Background:Radiotherapy with procarbazine, lomustine, and vincristine improves overall survival (OS) in patients with 1p19q co-deleted anaplastic oligodendroglioma/anaplastic oligoastrocytoma.Methods:This retrospective analysis investigated outcomes in patients with 1p19q co-deleted/partially deleted oligodendroglioma, oligoastrocytoma, anaplastic oligodendroglioma, or anaplastic oligoastrocytoma. OS and progression-free survival (PFS) were analyzed using the Kaplan-Meier method and prognostic factors using the Cox proportional hazard model.Results:A total of 106 patients (between December 1997 and December 2013) were included. Median age was 40 years (19-66), 58 were male (55%), Eastern Cooperative Oncology Group performance status was 0 in 80 patients (75%). 1p19q status was co-deleted in 66 (62%), incompletely co-deleted in 27 (25%), and 1p or 19q loss alone in four (4%) and nine (8%) patients, respectively. Isocitrate dehydrogenase-1 R132H mutation was found in 67 of 85 patients with sufficient material. Upfront treatment was given in 72 (68%) patients and temozolomide alone in 52 (49%). Median time to radiotherapy in 47 patients (44%) was 34.7 months and 41.2 months in 9 patients with co-deleted/incompletely co-deleted anaplastic oligodendroglioma/anaplastic oligoastrocytoma who received upfront temozolomide alone. Median OS was not reached and 5-year OS was 91% for all groups (median follow-up, 5.1 years). On multivariable analysis for all patients, receipt of therapy upfront versus none (p=0.04), PS 1 versus 0 (p<0.001) and 1p19q co-deletion/incomplete deletion versus 1p or 19q loss alone (p=0.005) were prognostic for PFS. Isocitrate dehydrogenase-1 status was not prognostic for PFS.Conclusions:With similar survival patterns in low-grade/anaplastic gliomas, molecular characteristics may be more important than histological grade. Longer follow-up and results of prospective trials are needed for definitive guidance on treatment of these patients.
A Practical Tool for Surveillance of Surgical-Site Infections: A 5-Year Experience in Orthopedic Surgeries
Authors: Benenson Shmuel , Moses Allon E. , Cohen Matan J. , Brezis Meir , Minster Naomi , Schwartz Carmela , Kandel Leonid , Liebergall Meir , Mattan Yoav
Published: January 2017

Continuous surveillance of surgical-site infection (SSI) is labor intensive. We developed a semiautomatic surveillance system partly assisted by surgeons. Most patients who developed postdischarge SSI were readmitted, which allowed us to limit postdischarge surveillance to this group. This procedure significantly reduced workload while maintaining high sensitivity and specificity for SSI diagnosis.

Infect Control Hosp Epidemiol 2017;38:610–613
Separating viewpoint from mode of representation in iconic co-speech gestures: insights from Danish narratives
Authors: FREDERIKSEN ANNE THERESE
Published: January 2017

abstract

During narrative retelling, speakers shift between different viewpoints to reflect how they conceptualize the events that unfolded. These viewpoints can be indicated through gestural means as well as through verbal ones. Studies of co-speech gestures have inferred viewpoint from gesture form, i.e., how entities are mapped onto the (primarily manual) articulators, but the merits of this approach have not been discussed. The present study argues that viewpoint is more than gestural form. Despite connections between the two, many other factors may influence a gesture’s form. Assessing viewpoint from gesture form alone limits the applicability of gestural viewpoint as a window onto speakers’ event conceptualization and introduces unnecessary differences in the categorization of viewpoint across gestures types. The present study examines iconic co-speech gestures in Danish narratives, and makes explicit the means used to infer gestural viewpoint. The approach advocated here ensures that the notion of viewpoint can be applied in a principled way to all or most iconic gestures.
WOMEN’S EMPOWERMENT AND FAMILY PLANNING: A REVIEW OF THE LITERATURE
Authors: Prata Ndola , Fraser Ashley , Huchko Megan J. , Gipson Jessica D. , Withers Mellissa , Lewis Shayna , Ciaraldi Erica J. , Upadhyay Ushma D.
Published: January 2017

This paper reviews the literature examining the relationship between women’s empowerment and contraceptive use, unmet need for contraception and related family planning topics in developing countries. Searches were conducted using PubMed, Popline and Web of Science search engines in May 2013 to examine literature published between January 1990 and December 2012. Among the 46 articles included in the review, the majority were conducted in South Asia (n=24). Household decision-making (n=21) and mobility (n=17) were the most commonly examined domains of women’s empowerment. Findings show that the relationship between empowerment and family planning is complex, with mixed positive and null associations. Consistently positive associations between empowerment and family planning outcomes were found for most family planning outcomes but those investigations represented fewer than two-fifths of the analyses. Current use of contraception was the most commonly studied family planning outcome, examined in more than half the analyses, but reviewed articles showed inconsistent findings. This review provides the first critical synthesis of the literature and assesses existing evidence between women’s empowerment and family planning use.
DO THE SEX COMPOSITION OF LIVING CHILDREN AND THE DESIRE FOR ADDITIONAL CHILDREN AFFECT FUTURE INTENTION TO USE CONTRACEPTION IN ETHIOPIA?
Authors: Rai Rajesh Kumar
Published: January 2017

Information on future intention to use contraceptives is a potential programme indicator for family planning services. Using three consecutive rounds of Ethiopian Demographic and Health Survey (EDHS) data collected in 2000, 2005 and 2011, this study examined whether the sex composition of living children and future desire for additional children were associated with the intention to use contraceptives among Ethiopian women aged 15–49 years who were not using any method of contraception at the time of the survey. The pooled multivariate binary logistic regression analysis indicated that between 2000 and 2011, the intentions of non-users to use contraceptives in the future increased significantly. Women who had at least one child (with an equal number of boys and girls, more boys than girls or more girls than boys) who did not want any more children, and those who were unsure about their desire for additional children, showed an increased intention to use contraceptives in the future, compared with those with an equal number of boys and girls who expressed a desire for additional children. Women with no children and who did not want children, or those who were unclear about their future desire, showed a lower intention to use contraceptives, compared with women with an equal number of boys and girls who wanted a child in the future.
A note on pragmatic constraints on syntax
Authors: TROTZKE ANDREAS
Published: January 2017

This note comments on Szendrői’s (2017) claim that some of the pragmatic constraints on syntactic operations proposed in Trotzke (2015a) are not supported by convincing empirical evidence. Szendrői objects to two empirical points made by Trotzke. I will deal with these points in turn: Section 1 focuses on the syntactic flexibility of idioms discussed by Szendrői, and Section 2 replies to her comments in the domain of island effects.
Cyclotron auto resonance maser and free electron laser devices: a unified point of view
Authors: Di Palma E. , Sabia E. , Dattoli G. , Licciardi S. , Spassovsky I.
Published: January 2017

We take advantage of previous research in the field of cyclotron auto resonance maser (CARM) and undulator-based free electron laser (U-FEL) sources to establish a common formalism for the relevant description of the underlying physical mechanisms. This strategy is aimed at stressing the deep analogies between the two devices and at providing a practical tool for their study based on the use of well-tested scaling formulae developed independently for the two systems.
AFRICAN DIGITAL RESEARCH REPOSITORIES: SURVEY REPORT
Authors: de Mutiis Anna , Kitchen Stephanie
Published: January 2017

Institutional repositories are an increasingly significant component in the provision of academic publication and information resources. They are being developed throughout the world as a consequence of the availability of scholarly resources in digital formats, and in response to Open Access policies and mandates.
Effects of Recombinant Human Growth Hormone for Osteoporosis: Systematic Review and Meta-Analysis
Authors: Atkinson Hayden F. , Moyer Rebecca F. , Yacoub Daniel , Coughlin Dexter , Birmingham Trevor B.
Published: January 2017

Notre objectif était d’évaluer l’efficacité de l’hormone de croissance humaine recombinante (HCH) sur la densité minérale osseuse (DMO) chez les personnes âgées de 50 ans et plus, ayant une fonction pituitaire normale, qui risquent de développer l’ostéoporose. Nous avons passé en revue systématiquement les essais cliniques randomisés (ECR), examinant six bases de données, et ont réalisé des méta-analyses pour examiner les effets de la HCH sur la DMO dans la colonne lombaire et le col du fémur. Les données au sujet de l’incidence des fractures, les biomarqueurs du métabolisme osseux et les événements indésirables ont également été extraites et analysées. Treize ECR ont rempli les critères d’admissibilité. Effets de mise en commun de différentes tailles ne suggèrent aucun effet significatif de la HCH sur la DMO. Les valeurs de l’effet de mise en commun étaient plus grandes, mais insignifiantes, comparativement au placebo. La HCH a eu un effet significatif sur plusieurs marqueurs pour le métabolisme osseux. On a observé un taux significativement plus élevé d’évènements indésirables dans les groupes HCH. La méta-analyse des ECR suggère que le traitement par la HCH pour personnes ayant ou à risque de développer l’ostéoporose entraîne des augmentations très petites et insignifiantes de la DMO.
Places of Encounter: Relational Ontologies, Animal Depiction and Ritual Performance at Göbekli Tepe
Authors: Busacca Gesualdo
Published: January 2017

Archaeologists have long debated the potential role of iconographic repertoires in reconstructing prehistoric ontologies and symbolic systems. The rich and complex imagery unearthed at Pre-Pottery Neolithic Göbekli Tepe (Turkey) has offered a promising ground to address this issue further. Previous interpretations have focused on the symbolic meaning of the depictions, often highlighting their male-centred and violent connotations, while overlooking the spatial and performative contexts of the depictions. This paper engages with this scholarly work in order to propose a new interpretation based on the anthropological framework of relational ontologies and on the analysis of some stylistic and contextual aspects of the iconography. Based on these premises, the curvilinear enclosures of Göbekli Tepe are interpreted as places of encounter devoted to interpersonal relationships among human and non-human agents, enabled by the intermediary role of images. The use of particular techniques of visual representation—including cues of motion and an emphasis on three-dimensionality—along with the centripetal orientation of the animal figures contributed to the animation of the depicted animals and to a sense of convergence of human and non-human beings in the social space of the enclosures.
Development and evaluation of a Nutrition Transition-FFQ for adolescents in South India
Authors: Shaikh Nida I , Frediani Jennifer K , Ramakrishnan Usha , Patil Shailaja S , Yount Kathryn M , Martorell Reynaldo , Narayan KM Venkat , Cunningham Solveig A
Published: January 2017

Objective

To develop and evaluate a Nutrition Transition-FFQ (NT-FFQ) to measure nutrition transition among adolescents in South India.

Design

We developed an interviewer-administered NT-FFQ comprising a 125-item semi-quantitative FFQ and a twenty-seven-item eating behaviour survey. The reproducibility and validity of the NT-FFQ were assessed using Spearman correlations, intra-class correlation coefficients (ICC), and levels of agreement using Bland–Altman and cross-classification over 2 months (NT-FFQ1 and NT-FFQ2). Validity of foods was evaluated against three 24-h dietary recalls (24-HR). Face validity of eating behaviours was evaluated through semi-structured cognitive interviews. The reproducibility of eating behaviours was assessed using weighted kappa (κw) and cross-classification analyses.

Setting

Vijayapura, India.

Subjects

A representative sample of 198 adolescents aged 14–18 years.

Results

Reproducibility of NT-FFQ: Spearman correlations ranged from 0·33 (pulses) to 0·80 (red meat) and ICC from 0·05 (fruits) to 1·00 (tea). On average, concordance (agreement) was 60 % and discordance was 7 % for food groups. For eating behaviours,κwranged from 0·24 (eating snacks while watching television) to 0·67 (eating lunch at home) with a mean of 0·40. Validity of NT-FFQ: Spearman correlations ranged from 0·11 (fried traditional foods) to 0·70 (tea) and ICC ranged from 0·02 (healthy global foods) to 1·00 (grains). The concordance and discordance were 48 % and 8 %, respectively. Bland–Altman plots showed acceptable agreement between NT-FFQ2 and 24-HR. The eating behaviours had acceptable face validity.

Conclusions

The NT-FFQ has good reproducibility and acceptable validity for food intake and eating behaviours. The NT-FFQ can quantify the nutrition transition among Indian adolescents.
Can Latino food trucks (loncheras) serve healthy meals? A feasibility study
Authors: Cohen Deborah A , Colaiaco Ben , Martinez-Wenzl Mary , Montes Monica , Han Bing , Berry Sandy H
Published: January 2017

Objective

To conduct a pilot study to assess the feasibility of modifying food truck meals to meet the My Plate guidelines as well as the acceptability of healthier meals among consumers.

Design

We recruited the owners of Latino food trucks (loncheras) in 2013–2014 and offered an incentive for participation, assistance with marketing and training by a bilingual dietitian. We surveyed customers and we audited purchases to estimate sales of the modified meals.

Setting

City of Los Angeles, CA, USA.

Subjects

Owners or operators of Latino food trucks (loncheras) and their customers.

Results

We enrolled twenty-two lonchera owners and eleven completed the intervention, offering more than fifty new menu items meeting meal guidelines. Sales of the meals comprised 2 % of audited orders. Customers rated the meals highly; 97 % said they would recommend and buy them again and 75 % of participants who completed the intervention intended to continue offering the healthier meals. However, adherence to guidelines drifted after several months of operation and participant burden was cited as a reason for dropout among three of eleven lonchera owners who dropped out.

Conclusions

Lonchera owners/operators who participated reported minimal difficulty in modifying menu items. Given the difficulty in enrolment, expanding this programme and ensuring adherence would likely need to be accomplished through regulatory requirements, monitoring and feedback, similar to the methods used to achieve compliance with sanitary standards. A companion marketing campaign would be helpful to increase consumer demand.
Developments in the Study of Rock Physics
Authors: Adam Ludmila , Schmitt Douglas
Published: January 2017

AGU/SEG Joint Meeting on Rock Physics of the Upper Crust; Hilo, Hawaii, 11–14 July 2016
Topologically protected modes in non-equilibrium stochastic systems
Authors: Murugan Arvind , Vaikuntanathan Suriyanarayanan
Published: January 2017

Non-equilibrium driving of biophysical processes is believed to enable their robust functioning despite the presence of thermal fluctuations and other sources of disorder. Such robust functions include sensory adaptation, enhanced enzymatic specificity and maintenance of coherent oscillations. Elucidating the relation between energy consumption and organization remains an important and open question in non-equilibrium statistical mechanics. Here we report that steady states of systems with non-equilibrium fluxes can support topologically protected boundary modes that resemble similar modes in electronic and mechanical systems. Akin to their electronic and mechanical counterparts, topological-protected boundary steady states in non-equilibrium systems are robust and are largely insensitive to local perturbations. We argue that our work provides a framework for how biophysical systems can use non-equilibrium driving to achieve robust function.
A manifesto for reproducible science
Authors: Munafò Marcus R. , Nosek Brian A. , Bishop Dorothy V. M. , Button Katherine S. , Chambers Christopher D. , Percie du Sert Nathalie , Simonsohn Uri , Wagenmakers Eric-Jan , Ware Jennifer J. , Ioannidis John P. A.
Published: January 2017

Improving the reliability and efficiency of scientific research will increase the credibility of the published scientific literature and accelerate discovery. Here we argue for the adoption of measures to optimize key elements of the scientific process: methods, reporting and dissemination, reproducibility, evaluation and incentives. There is some evidence from both simulations and empirical studies supporting the likely effectiveness of these measures, but their broad adoption by researchers, institutions, funders and journals will require iterative evaluation and improvement. We discuss the goals of these measures, and how they can be implemented, in the hope that this will facilitate action toward improving the transparency, reproducibility and efficiency of scientific research.
In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions
Authors: Mwaffo Violet , Butail Sachit , Porfiri Maurizio
Published: January 2017

Zebrafish is fast becoming a species of choice in biomedical research for the investigation of functional and dysfunctional processes coupled with their genetic and pharmacological modulation. As with mammals, experimentation with zebrafish constitutes a complicated ethical issue that calls for the exploration of alternative testing methods to reduce the number of subjects, refine experimental designs, and replace live animals. Inspired by the demonstrated advantages of computational studies in other life science domains, we establish an authentic data-driven modelling framework to simulate zebrafish swimming in three dimensions. The model encapsulates burst-and-coast swimming style, speed modulation, and wall interaction, laying the foundations for in-silico experiments of zebrafish behaviour. Through computational studies, we demonstrate the ability of the model to replicate common ethological observables such as speed and spatial preference, and anticipate experimental observations on the correlation between tank dimensions on zebrafish behaviour. Reaching to other experimental paradigms, our framework is expected to contribute to a reduction in animal use and suffering.
Effect of seed morph and light level on growth and reproduction of the amphicarpic plant Amphicarpaea edgeworthii (Fabaceae)
Authors: Zhang Keliang , Baskin Jerry M. , Baskin Carol C. , Yang Xuejun , Huang Zhenying
Published: January 2017

Amphicarpic plants produce aerial and subterranean fruits on an individual plant, and these heteromorphic diaspores give rise to plants that differ in growth and ecology. Amphicarpaea edgeworthii is a summer annual amphicarpic species that grows over a range of light levels. We aimed to compare the response to shading intensity of plants of A. edgeworthii grown throughout their life cycle from aerial seeds (ASP) and from subterranean seeds (SSP). We hypothesized that vegetative and reproductive growth of plants from ASP and SSP respond differently to light. Plants were grown from ASP and SSP under 0, 46, 71 and 90% shading intensities. With plant height as a covariate, vegetative biomass of ASP and SSP did not differ. Leaf area and seed production of SSP were greater and internode length less than they were for ASP in all shading intensities. Aerial and subterranean seed yield, seed mass and number for both ASP and SSP were highest in full light. Aerial seed yield was affected more than subterranean seed yield by shading intensity. The growth and reproductive responses of ASP and SSP of A. edgeworthii may be adaptive to the range of low to high light environments in which this species grows.
Ocular dominance plasticity: inhibitory interactions and contrast equivalence
Authors: Spiegel Daniel P. , Baldwin Alex S. , Hess Robert F.
Published: January 2017

Brief monocular occlusion results in a transient change in ocular dominance, such that the previously patched eye makes a stronger contribution to the binocular percept after occlusion. The previously unpatched eye therefore makes a correspondingly weaker contribution to the binocular sum. To shed light on the mechanism underlying this change we investigate how the relationship between the perception of fusion, suppression, and diplopia changes after short-term monocular deprivation. Results show that fusible stimuli seen by the unpatched eye are actively suppressed as a result of patching and that this can be reversed by an interocular contrast imbalance. This suggests that dichoptic inhibition plays an important role in ocular dominance changes due to short-term occlusion, possibly by altering the contrast gain prior to binocular summation. This may help explain why this form of plasticity affects the perception of both fusible and rivalrous stimuli.
Association between reductions in low-density lipoprotein cholesterol with statin therapy and the risk of new-onset diabetes: a meta-analysis
Authors: Wang Shaohua , Cai Rongrong , Yuan Yang , Varghese Zac , Moorhead John , Ruan Xiong Z.
Published: January 2017

A recent meta-analysis demonstrated that statin therapy was associated with a risk of diabetes. The present study investigated whether the relative reduction in low-density lipoprotein cholesterol (LDL-c) was a good indicator of the risk of new-onset diabetes. We searched the PubMed, Embase, Cochrane Central Register, Lilacs, Food and Drug Administration, and European Medicines Agency databases for randomized controlled trials of statins. Fourteen trials were included in the study. Eight trials with target LDL-c levels ≤100 mg/dL (2.6 mmol/L) or LDL-c reductions of at least 30% were extracted separately. The results showed that the overall risk of incident diabetes increased by 11% (OR = 1.11; 95% CI 1.03–1.20). The group with intensive LDL-c-lowering statin had an 18% increase in the likelihood of developing diabetes (OR = 1.18; 95% CI, 1.10–1.28). Furthermore, the risks of incident diabetes were 13% (OR = 1.13; 95% CI 1.01–1.26) and 29% (OR = 1.29; 95% CI 1.13–1.47) in the subgroups with 30–40% and 40–50% reductions in LDL-c, respectively, suggesting that LDL-c reduction may provide a dynamic risk assessment parameter for new-onset diabetes. In conclusion, LDL-c reduction is positively related to the risk of new-onset diabetes. When LDL-c is reduced by more than 30% during lipid-lowering therapy, blood glucose monitoring is suggested to detect incident diabetes in high-risk populations.
Benzyl Isothiocyanate potentiates p53 signaling and antitumor effects against breast cancer through activation of p53-LKB1 and p73-LKB1 axes
Authors: Xie Bei , Nagalingam Arumugam , Kuppusamy Panjamurthy , Muniraj Nethaji , Langford Peter , Győrffy Balázs , Saxena Neeraj K. , Sharma Dipali
Published: January 2017

Functional reactivation of p53 pathway, although arduous, can potentially provide a broad-based strategy for cancer therapy owing to frequent p53 inactivation in human cancer. Using a phosphoprotein-screening array, we found that Benzyl Isothiocynate, (BITC) increases p53 phosphorylation in breast cancer cells and reveal an important role of ERK and PRAS40/MDM2 in BITC-mediated p53 activation. We show that BITC rescues and activates p53-signaling network and inhibits growth of p53-mutant cells. Mechanistically, BITC induces p73 expression in p53-mutant cells, disrupts the interaction of p73 and mutant-p53, thereby releasing p73 from sequestration and allowing it to be transcriptionally active. Furthermore, BITC-induced p53 and p73 axes converge on tumor-suppressor LKB1 which is transcriptionally upregulated by p53 and p73 in p53-wild-type and p53-mutant cells respectively; and in a feed-forward mechanism, LKB1 tethers with p53 and p73 to get recruited to p53-responsive promoters. Analyses of BITC-treated xenografts using LKB1-null cells corroborate in vitro mechanistic findings and establish LKB1 as the key node whereby BITC potentiates as well as rescues p53-pathway in p53-wild-type as well as p53-mutant cells. These data provide first in vitro and in vivo evidence of the integral role of previously unrecognized crosstalk between BITC, p53/LKB1 and p73/LKB1 axes in breast tumor growth-inhibition.
Temperature-dependent Schottky barrier in high-performance organic solar cells
Authors: Li Hui , He Dan , Zhou Qing , Mao Peng , Cao Jiamin , Ding Liming , Wang Jizheng
Published: January 2017

Organic solar cells (OSCs) have attracted great attention in the past 30 years, and the power conversion efficiency (PCE) now reaches around 10%, largely owning to the rapid material developments. Meanwhile with the progress in the device performance, more and more interests are turning to understanding the fundamental physics inside the OSCs. In the conventional bulk-heterojunction architecture, only recently it is realized that the blend/cathode Schottky junction serves as the fundamental diode for the photovoltaic function. However, few researches have focused on such junctions, and their physical properties are far from being well-understood. In this paper based on PThBDTP:PC71BM blend, we fabricated OSCs with PCE exceeding 10%, and investigated temperature-dependent behaviors of the junction diodes by various characterization including current-voltage, capacitance-voltage and impedance measurements between 70 to 290 K. We found the Schottky barrier height exhibits large inhomogeneity, which can be described by two sets of Gaussian distributions.
Lasing optical cavities based on macroscopic scattering elements
Authors: Consoli Antonio , López Cefe
Published: January 2017

Two major elements are required in a laser device: light confinement and light amplification. Light confinement is obtained in optical cavities by employing a pair of mirrors or by periodic spatial modulation of the refractive index as in photonic crystals and Bragg gratings. In random lasers, randomly placed nanoparticles embedded in the active material provide distributed optical feedback for lasing action. Recently, we demonstrated a novel architecture in which scattering nanoparticles and active element are spatially separated and random lasing is observed. Here we show that this approach can be extended to scattering media with macroscopic size, namely, a pair of sand grains, which act as feedback elements and output couplers, resulting in lasing emission. We demonstrate that the number of lasing modes depends on the surface roughness of the sand grains in use which affect the coherent feedback and thus the emission spectrum. Our findings offer a new perspective of material science and photonic structures, facilitating a novel and simple approach for the realization of new photonics devices based on natural scattering materials.
Covalent modification of pericardial patches for sustained rapamycin delivery inhibits venous neointimal hyperplasia
Authors: Bai Hualong , Lee Jung Seok , Chen Elizabeth , Wang Mo , Xing Ying , Fahmy Tarek M. , Dardik Alan
Published: January 2017

Prosthetic grafts and patches are commonly used in cardiovascular surgery, however neointimal hyperplasia remains a significant concern, especially under low flow conditions. We hypothesized that delivery of rapamycin from nanoparticles (NP) covalently attached to patches allows sustained site-specific delivery of therapeutic agents targeted to inhibit localized neointimal hyperplasia. NP were covalently linked to pericardial patches using EDC/NHS chemistry and could deliver at least 360 ng rapamycin per patch without detectable rapamycin in serum; nanoparticles were detectable in the liver, kidney and spleen but no other sites within 24 hours. In a rat venous patch angioplasty model, control patches developed robust neointimal hyperplasia on the patch luminal surface characterized by Eph-B4-positive endothelium and underlying SMC and infiltrating cells such as macrophages and leukocytes. Patches delivering rapamycin developed less neointimal hyperplasia, less smooth muscle cell proliferation, and had fewer infiltrating cells but retained endothelialization. NP covalently linked to pericardial patches are a novel composite delivery system that allows sustained site-specific delivery of therapeutics; NP delivering rapamycin inhibit patch neointimal hyperplasia. NP linked to patches may represent a next generation of tissue engineered cardiovascular implants.
Loss of Coupling Distinguishes GJB1 Mutations Associated with CNS Manifestations of CMT1X from Those Without CNS Manifestations
Authors: Abrams Charles K. , Goman Mikhail , Wong Sarah , Scherer Steven S. , Kleopa Kleopas A. , Peinado Alejandro , Freidin Mona M.
Published: January 2017

CMT1X, an X-linked inherited neuropathy, is caused by mutations in GJB1, which codes for Cx32, a gap junction protein expressed by Schwann cells and oligodendrocytes. Many GJB1 mutations cause central nervous system (CNS) abnormality in males, including stable subclinical signs and, less often, short-duration episodes characterized by motor difficulties and altered consciousness. However, some mutations have no apparent CNS effects. What distinguishes mutations with and without CNS manifestations has been unclear. Here we studied a total of 14 Cx32 mutations, 10 of which are associated with florid episodic CNS clinical syndromes in addition to peripheral neuropathy. The other 4 mutations exhibit neuropathy without clinical or subclinical CNS abnormalities. These “PNS-only” mutations (Y151C, V181M, R183C and L239I) form gap junction plaques and produce levels of junctional coupling similar to those for wild-type Cx32. In contrast, mutants with CNS manifestations (F51L, E102del, V139M, R142Q, R142W, R164W T55I, R164Q and C168Y) either form no morphological gap junction plaques or, if they do, produce little or no detectable junctional coupling. Thus, PNS and CNS abnormalities may involve different aspects of connexin function.
Platelet to lymphocyte ratio in the prediction of adverse outcomes after acute coronary syndrome: a meta-analysis
Authors: Li Wenzhang , Liu Qianqian , Tang Yin
Published: January 2017

Recent studies have shown platelet to lymphocyte ratio (PLR) to be a potential inflammatory marker in cardiovascular diseases. We performed a meta-analysis to systematically evaluate the prognostic role of PLR in acute coronary syndrome (ACS). A comprehensive literature search up to May 18, 2016 was conducted from PUBMED, EMBASE and Web of science to identify related studies. The risk ratio (RR) with 95% confidence interval (CI) was extracted or calculated for effect estimates. Totally ten studies involving 8932 patients diagnosed with ACS were included in our research. We demonstrated that patients with higher PLR level had significantly higher risk of in-hospital adverse outcomes (RR = 2.24, 95%CI = 1.81–2.77) and long-term adverse outcomes (RR = 2.32, 95%CI = 1.64–3.28). Sensitivity analyses confirmed the stability of our results. We didn’t detect significant publication bias by Begg’s and Egger’s test (p > 0.05). In conclusion, our meta-analysis revealed that PLR is promising biomarker in predicting worse prognosis in ACS patients. The results should be validated by future large-scale, standard investigations.
Fatty acid synthase 2 contributes to diapause preparation in a beetle by regulating lipid accumulation and stress tolerance genes expression
Authors: Tan Qian-Qian , Liu Wen , Zhu Fen , Lei Chao-Liang , Wang Xiao-Ping
Published: January 2017

Diapause, also known as dormancy, is a state of arrested development that allows insects to survive unfavorable environmental conditions. Diapause-destined insects store large amounts of fat when preparing for diapause. However, the extent to which these accumulated fat reserves influence diapause remains unclear. To address this question, we investigated the function of fatty acid synthase (FAS), which plays a central role in lipid synthesis, in stress tolerance, the duration of diapause preparation, and whether insects enter diapause or not. In diapause-destined adult female cabbage beetles, Colaphellus bowringi, FAS2 was more highly expressed than FAS1 at the peak stage of diapause preparation. FAS2 knockdown suppressed lipid accumulation and subsequently affected stress tolerance genes expression and water content. However, silencing FAS2 had no significant effects on the duration of diapause preparation or the incidence of diapause. FAS2 transcription was suppressed by juvenile hormone (JH) and the JH receptor methoprene-tolerant (Met). These results suggest that the absence of JH-Met induces FAS2 expression, thereby promoting lipid storage in diapause-destined female beetles. These results demonstrate that fat reserves regulate stress tolerance genes expression and water content, but have no significant effect on the duration of diapause preparation or the incidence of diapause.
Efficient biosynthesis of a Cecropin A-melittin mutant in Bacillus subtilis WB700
Authors: Ji Shengyue , Li Weili , Baloch Abdul Rasheed , Wang Meng , Li Hengxin , Cao Binyun , Zhang Hongfu
Published: January 2017

The efficient production of antimicrobial peptides (AMPs) for clinical applications has attracted the attention of the scientific community. To develop a novel microbial cell factory for the efficient biosynthesis of a cecropin A-melittin mutant (CAM-W), a recombinant Bacillus subtilis WB700 expression system was genetically modified with a novel vector, including a fusion gene encoding CAM-W, the autoprotease EDDIE and the signal peptide SacB under the control of the maltose-inducible promoter Pglv. A total of 159 mg of CAM-W was obtained from 1 L of fermentation supernatant. The purified CAM-W showed a consistent size with the expected molecular weight of 3.2 kDa. Our findings suggest that this novel expression system can be used as a powerful tool for the efficient production of CAM-W.