bluuebunny/crossref_metadata_2025 huggingface dataset:
Lessons learned from the testing of RC frames with masonry infills and proposals for new solutions / Untersuchungen an mit Mauerwerk ausgefachten Stahlbetonrahmen und neue Lösungsvorschläge
Authors: Lourenço Paulo B. , Vasconcelos Graça , Leite João , Pereira Paulo
Published: April 2016

Past experience has shown that inadequate design of unreinforced masonry walls (URM) or inadequate selection of materials can lead to significant economic losses and fatalities in the case of a strong earthquake. In this context, this paper presents the experimental research that has been carried out with the aim of gaining a better insight into the traditional masonry infill walls commonly built in Portugal. The experimental research includes: (1) shaking table tests on reduced‐scale reinforced concrete (RC) buildings with masonry infills with distinct typologies, from traditional solutions to those with enhanced properties and solutions to improve the seismic behaviour; (2) in‐plane static cyclic tests on a representative one‐storey, one‐bay RC frame with masonry infills with distinct typologies but similar to the ones tested in the RC building models.

It was concluded that the typology of masonry walls influences the global behaviour of RC buildings, particularly when there is no connection between masonry infill and RC frame. An appropriate design is necessary to prevent an unforeseen failure mechanism due to shear stresses in the RC columns induced by the infill.

The in‐plane cyclic tests showed that render plays a central role in the lateral strength and stiffness. Additionally, it was observed that bed joint reinforcement and reinforced render are important measures for controlling damage but do not significantly influence the in‐plane lateral strength and stiffness.
Introducing Tetrel Zintl Ions to N‐Heterocyclic Carbenes – Synthesis of Coinage Metal NHC Complexes of [Ge9{Si(SiMe3)3}3]–
Authors: Geitner Felix S. , Fässler Thomas F.
Published: April 2016

Reaction of the functionalized tetrel cluster [Ge9R3]– {R = Si(SiMe3)3} with coinage metal N‐heterocyclic carbene (NHC) complexes affords the first Zintl cluster transition metal complexes coordinated by NHC molecules. In [(η3‐Ge9R3)M(NHCDipp)], the D3d‐symmetric cluster polyhedron coordinates with a triangular Ge3 face to the coinage metals M = Cu, Ag, Au, which themselves also bind to the NHC. The role of fine tuning of electronic properties by using an NHC ligand is discussed for the transformation reaction of [(η3‐Ge9R3)Ag(NHCDipp)] to yield [Ag(η3‐Ge9R3)2][Ag(NHCDipp)2]. All complexes are fully characterized including single‐crystal X‐ray structure analyses.
Complex refractive index of normal and malignant human colorectal tissue in the visible and near‐infrared
Authors: Giannios Panagiotis , Koutsoumpos Spyridon , Toutouzas Konstantinos G. , Matiatou Maria , Zografos George C. , Moutzouris Konstantinos
Published: April 2016

A multi‐wavelength prism coupling refractometer is utilized to measure the angular reflectance of freshly excised human intestinal tissue specimens. Based on reflectance data, the real and imaginary part of the refractive index is calculated via Fresnel analysis for three visible (blue, green, red) and two near‐infrared (963 nm and 1551 nm) wavelengths. Averaged values of the complex refractive index and corresponding Cauchy dispersion fits are given for the mucosa, submucosa and serosa layers of the colorectal wall at the normal state. The refractive constants of tumorous and normal mucosa are then cross‐compared for the indicative cases of one patient diagnosed with a benign polyp and three patients diagnosed with adenocarcinomas of different phenotype. Significant index contrast exists between the normal and diseased states, indicating the potential use of refractive index as a marker of colorectal dysplasia.

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On the Number of k‐Dominating Independent Sets
Authors: Nagy Zoltán Lóránt
Published: April 2016

We study the existence and the number of k‐dominating independent sets in certain graph families. While the case namely the case of maximal independent sets—which is originated from Erdős and Moser—is widely investigated, much less is known in general. In this paper we settle the question for trees and prove that the maximum number of k‐dominating independent sets in n‐vertex graphs is between and if , moreover the maximum number of 2‐dominating independent sets in n‐vertex graphs is between and . Graph constructions containing a large number of k‐dominating independent sets are coming from product graphs, complete bipartite graphs, and finite geometries. The product graph construction is associated with the number of certain Maximum Distance Separable (MDS) codes.
Variation in prevalence and patterns of peripherally inserted central catheter use in adults hospitalized with pneumonia
Authors: Chopra Vineet , Priya Aruna , Pekow Penelope S. , Thompson Rachel , Flanders Scott A. , Lindenauer Peter K.
Published: April 2016

BACKGROUND

Although peripherally inserted central catheters (PICCs) are often used in adults hospitalized with pneumonia, patterns related to PICC use in this context are unknown.

METHODS

Premier's inpatient database was used to identify patients hospitalized with pneumonia between July 1, 2007 and November 30, 2011. PICC placement was identified via billing codes. Generalized estimating equations were used to identify factors associated with PICC placement. Hospital risk‐standardized rates of PICC insertion were estimated using hierarchical generalized linear models.

RESULTS

There were 545,250 patients (median age: 71 years; range: 57–82 years) included. A total of 41,849 (7.7%) patients received a PICC during hospitalization (median receipt: hospital day 4). PICC recipients were younger (median age: 69 years), had higher levels of comorbidity (Gagne score median: 4 vs 2) and were more often diagnosed with healthcare‐associated pneumonia (43.1% vs 29.9%) than those who did not receive PICCs. The 3 patient variables most associated with PICC receipt included weight loss (odds ratio [OR]: 2.03, 95% confidence interval [CI]: 1.97‐2.10), sepsis on admission (OR: 1.80, 95%CI: 1.75‐1.85), and intensive care unit status on hospital day 1 or 2 (OR: 1.70, 95%CI: 1.64‐1.75). Compared to internal medicine, admission by geriatricians and critical care physicians was associated with PICC placement (OR: 1.81, 95% CI: 1.62‐2.03 and OR: 1.14, 95% CI: 1.05‐1.24, respectively). Risk‐standardized rates of PICC utilization varied from 0.3% to 41.7%. Nearly 70% of the variability in PICC use could not be explained by available data.

CONCLUSIONS

In adults hospitalized with pneumonia, PICC use appears directed towards those with severe illness and varies substantially between hospitals. Journal of Hospital Medicine 2016;11:568–575. © 2016 Society of Hospital Medicine
Association of hospital admission service structure with early transfer to critical care, hospital readmission, and length of stay
Authors: Smith G. Randy , Ma Madeleine , Hansen Luke O. , Christensen Nick , O'Leary Kevin J.
Published: April 2016

BACKGROUND

Hospital medical groups use various staffing models that may systematically affect care continuity during the admission process.

OBJECTIVE

To compare the effect of 2 hospitalist admission service models (“general” and “admitter‐rounder”) on patient disposition and length of stay.

DESIGN

Retrospective observational cohort study with difference‐in‐difference analysis.

SETTING

Large tertiary academic medical center in the United States.

PARTICIPANTS

Patients (n = 19,270) admitted from the emergency department to hospital medicine and medicine teaching services from July 2010 to June 2013.

INTERVENTIONS

Admissions to hospital medicine staffed by 2 different service models, compared to teaching service admissions.

MEASUREMENTS

Incidence of transfer to critical care within the first 24 hours of hospitalization, hospital and emergency department length of stay, and hospital readmission rates ≤30 days postdischarge.

RESULTS

The change of hospitalist services to an admitter‐rounder model was associated with no significant change in transfer to critical care or hospital length of stay compared to the teaching service (difference‐in‐difference P = 0.32 and P = 0.87, respectively). The admitter‐rounder model was associated with decreased readmissions compared to the teaching service on difference‐in‐difference analysis (odds ratio difference: −0.21, P = 0.01). Adoption of the hospitalist admitter‐rounder model was associated with an increased emergency department length of stay compared to the teaching service (difference of +0.49 hours, P < 0.001).

CONCLUSIONS

Rates of transfer to intensive care and overall hospital length of stay between the hospitalist admission models did not differ significantly. The hospitalist admitter‐rounder admission service structure was associated with extended emergency department length of stay and a decrease in readmissions. Journal of Hospital Medicine 2016;11:669–674. © 2016 Society of Hospital Medicine
Writing Conferences in a Second Language Writing Classroom: Instructor and Student Perspectives
Authors: Maliborska Veronika , You Yunjung
Published: April 2016

Teacher–student writing conferences are considered a valuable teaching method in composition courses, used mostly with the purpose of discussing students’ progress in their writing. This article presents an exploratory study on student and instructor expectations and perceptions of writing conferences in a semester‐long writing course for multilingual students. The sample consists of 100 students who were enrolled in this course and eight instructors who were teaching it. The course examined here was designed to offer one lecture and one writing conference per week to each student, resulting in two writing conferences for each of the five writing tasks. The factors examined are teacher preparation time and strategy, format (individual and group writing conferences), length, frequency, topics discussed, and overall satisfaction. The authors collected data through extensive surveys that included Likert‐type scales, item ranking, and open‐ended questions. The results show that the students and their instructors regarded individual conferences of 10 minutes to be more effective than longer group conferences; however, participants voiced weaknesses of both types of conferences. The results and implications inform writing instructors and administrators about possible uses of such a course design and potential improvements for the use of writing conferences in second language writing courses.
Single‐Port Surgery in Inflammatory Bowel Disease: A Review of Current Evidence
Authors: de Groof E. Joline , Buskens Christianne J. , Bemelman Willem A.
Published: April 2016

The majority of patients with Crohn’s disease and up to 35 % of patients with ulcerative colitis will ultimately require surgery during the course of their disease. Over the past few years, surgical techniques and experience in minimal invasive surgery have evolved resulting in single‐incision laparoscopic surgery. The aim of this approach is to diminish the surgical trauma by reducing the number of incision sites. This review discusses the benefits and disadvantages of single‐port surgery in various procedures in patients with inflammatory bowel disease (IBD). Short‐term postoperative results, functional outcome, and costs available in the literature will be discussed. Single‐port surgery in IBD has several benefits when compared to multi‐port laparoscopic surgery. By using fewer incisions, a potential reduction of postoperative pain with less morphine use can be accomplished. In addition, accelerated postoperative recovery can result in a shorter hospital stay. Furthermore, a superior cosmesis can be reached with placement of the port at the future ostomy site or at the umbilicus. Literature on single‐port surgery in IBD consists mainly of case series and a few matched case series. These studies demonstrated that single‐port surgery seems to be a safe and feasible approach for the surgical treatment of IBD patients.
RemakingThe Making: E.P. Thompson’s Reception in Argentina and the Shaping of Labor Historiography
Authors: Poy Lucas
Published: April 2016

This article traces the reception of E.P. Thompson’s work in Argentina over the past three decades. It explores the context in which Thompson was read by labor historians as a means to analyse the way in which the country’s labor historiography was shaped over this period. It argues that, in the 1980s and the 1990s, against a context characterized by a crisis of the political left and a downturn in the labor movement, Thompson’s appropriation was focused on his critique of Marxist “determinism”. While this corresponded to similar developments in other countries, Argentinian labor historiography started to show a different path in the early 2000s, when a tremendous social, political, and economic crisis shook the country. The article concludes that recent developments in labor historiography in Argentina show a different pattern to those seen in the “Global North”.
E.P. Thompson in South Africa: The Practice and Politics of Social History in an Era of Revolt and Transition, 1976–2012
Authors: Hyslop Jonathan
Published: April 2016

The work of E.P. Thompson has had an enormous impact on the writing of history in South Africa since the 1970s. This article traces the rise of this historiographical trend, focusing especially on the History Workshop at Wits University (Johannesburg). It outlines how a South African version of Thompsonian historical practice was theorized, and sketches some of the ways in which Thompson’s ideas were utilized by South African historians. The article shows how the History Workshop attempted to popularize their research, and examines the political projects behind these activities. Finally, the article suggests that although the influence of Thompson-style South African social historians has declined, their work has had a lasting impact on the country’s literary culture, well beyond the academy.
A criterion for compactness in Lp(ℝ) of the resolvent of the maximal general form Sturm–Liouville operator
Authors: Chernyavskaya N. A. , Shuster L. A.
Published: April 2016

We consider the equation

where and

We assume that this equation is correctly solvable in Lp(ℝ). Under these assumptions, we study the problem of compactness of the resolvent of the maximal continuously invertible Sturm–Liouville operator . Here

In the case p = 2, for the compact operator , we obtain two-sided sharp-by-order estimates of the maximal eigenvalue.
Developing Navigation Competencies to Care for Older Rural Adults with Advanced Illness
Authors: Duggleby Wendy , Robinson Carole A. , Kaasalainen Sharon , Pesut Barbara , Nekolaichuk Cheryl , MacLeod Roderick , Keating Norah C. , Santos Salas Anna , Hallstrom Lars K. , Fraser Kimberly D. , Williams Allison , Struthers-Montford Kelly , Swindle Jennifer
Published: April 2016

Les navigateurs aident les adultes ruraux âgés avec des maladies avancées, ainsi que leurs familles, de se connecter aux ressources, à l’information, et aux gens qui peuvent améliorer leur qualité de vie. Cet article décrit le processus utilisé pour engager des experts—en vieillissement en milieu rural, les soins palliatifs en milieu rural, et la navigation—ainsi que les intervenants dans les collectivités rurales, d’élaborer une définition conceptuelle d’une telle navigation et de délimiter les compétences pertinentes pour la prise en charge de cette population. Un document de discussion sur les considérations importantes pour la navigation dans cette population a été développé, suivi d’un processus Delphi en quatre étapes avec 30 membres invités experts. Les résultats de l’étude ont abouti à cinq compétences générales de navigation pour les fournisseurs de soins de santé qui prennent soin des personnes âgées rurales et de leurs familles à la fin de vie: la capacité de fournir le dépistage des patients / famille; à préconiser pour le patient / famille; de faciliter les relations avec la communauté; de coordonner l’accès aux services et aux ressources; et de promouvoir l’engagement actif. Les compétences particulières ont également été développées. Ces compétences constituent la base pour la recherche et le développement de programmes d’études en navigation.
Gene expression profiling of microbial activities and interactions in sediments under haloclines of E. Mediterranean deep hypersaline anoxic basins
Authors: Edgcomb Virginia P , Pachiadaki Maria G , Mara Paraskevi , Kormas Konstantinos A , Leadbetter Edward R , Bernhard Joan M
Published: April 2016

Deep-sea hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea are considered some of the most polyextreme habitats on Earth. In comparison to microbial activities occurring within the haloclines and brines of these unusual water column habitats near the Mediterranean seafloor, relatively little is known about microbial metabolic activities in the underlying sediments. In addition, it is not known whether activities are shaped by the unique chemistries of the different DHAB brines and whether evidence exists for active microbial eukaryotes in those sediments. Metatranscriptome analysis was applied to sediment samples collected using ROV Jason from underneath the haloclines of Urania, Discovery and L’Atalante DHABs and a control site. We report on expression of genes associated with sulfur and nitrogen cycling, putative osmolyte biosynthetic pathways and ion transporters, trace metal detoxification, selected eukaryotic activities (particularly of fungi), microbe–microbe interactions, and motility in sediments underlying the haloclines of three DHABs. Relative to our control sediment sample collected outside of Urania Basin, microbial communities (including eukaryotes) in the Urania and Discovery DHAB sediments showed upregulation of expressed genes associated with nitrogen transformations, osmolyte biosynthesis, heavy metals resistance and metabolism, eukaryotic organelle functions, and cell–cell interactions. Sediments underlying DHAB haloclines that have cumulative physico-chemical stressors within the limits of tolerance for microoorganisms can therefore be hotspots of activity in the deep Mediterranean Sea.
High Resolution Dissection of Reactive Glial Nets in Alzheimer’s Disease
Authors: Bouvier David S. , Jones Emma V. , Quesseveur Gaël , Davoli Maria Antonietta , A. Ferreira Tiago , Quirion Rémi , Mechawar Naguib , Murai Keith K.
Published: April 2016

Fixed human brain samples in tissue repositories hold great potential for unlocking complexities of the brain and its alteration with disease. However, current methodology for simultaneously resolving complex three-dimensional (3D) cellular anatomy and organization, as well as, intricate details of human brain cells in tissue has been limited due to weak labeling characteristics of the tissue and high background levels. To expose the potential of these samples, we developed a method to overcome these major limitations. This approach offers an unprecedented view of cytoarchitecture and subcellular detail of human brain cells, from cellular networks to individual synapses. Applying the method to AD samples, we expose complex features of microglial cells and astrocytes in the disease. Through this methodology, we show that these cells form specialized 3D structures in AD that we refer to as reactive glial nets (RGNs). RGNs are areas of concentrated neuronal injury, inflammation and tauopathy and display unique features around β-amyloid plaque types. RGNs have conserved properties in an AD mouse model and display a developmental pattern coinciding with the progressive accumulation of neuropathology. The method provided here will help reveal novel features of the healthy and diseased human brain and aid experimental design in translational brain research.
Phase 2 Randomised Controlled Trial and Feasibility Study of Future Care Planning in Patients with Advanced Heart Disease
Authors: Denvir Martin A. , Cudmore Sarah , Highet Gill , Robertson Shirley , Donald Lisa , Stephen Jacqueline , Haga Kristin , Hogg Karen , Weir Christopher J. , Murray Scott A. , Boyd Kirsty
Published: April 2016

Future Care Planning (FCP) rarely occurs in patients with heart disease until close to death by which time the potential benefits are lost. We assessed the feasibility, acceptability and tested a design of a randomised trial evaluating the impact of FCP in patients and carers. 50 patients hospitalised with acute heart failure or acute coronary syndrome and with predicted 12 month mortality risk of >20% were randomly allocated to FCP or usual care for 12 weeks upon discharge and then crossed-over for the next 12 weeks. Quality of life, symptoms and anxiety/distress were assessed by questionnaire. Hospitalisation and mortality events were documented for 6 months post-discharge. FCP increased implementation and documentation of key decisions linked to end-of-life care. FCP did not increase anxiety/distress (Kessler score -E 16.7 (7.0) vs D 16.8 (7.3), p = 0.94). Quality of life was unchanged (EQ5D: E 0.54(0.29) vs D 0.56(0.24), p = 0.86) while unadjusted hospitalised nights was lower (E 8.6 (15.3) vs D 11.8 (17.1), p = 0.01). Qualitative interviews indicated that FCP was highly valued by patients, carers and family physicians. FCP is feasible in a randomised clinical trial in patients with acute high risk cardiac conditions. A Phase 3 trial is needed urgently.
Orthogonal NGS for High Throughput Clinical Diagnostics
Authors: Chennagiri Niru , White Eric J. , Frieden Alexander , Lopez Edgardo , Lieber Daniel S. , Nikiforov Anastasia , Ross Tristen , Batorsky Rebecca , Hansen Sherry , Lip Va , Luquette Lovelace J. , Mauceli Evan , Margulies David , Milos Patrice M. , Napolitano Nichole , Nizzari Marcia M. , Yu Timothy , Thompson John F.
Published: April 2016

Next generation sequencing is a transformative technology for discovering and diagnosing genetic disorders. However, high-throughput sequencing remains error-prone, necessitating variant confirmation in order to meet the exacting demands of clinical diagnostic sequencing. To address this, we devised an orthogonal, dual platform approach employing complementary target capture and sequencing chemistries to improve speed and accuracy of variant calls at a genomic scale. We combined DNA selection by bait-based hybridization followed by Illumina NextSeq reversible terminator sequencing with DNA selection by amplification followed by Ion Proton semiconductor sequencing. This approach yields genomic scale orthogonal confirmation of ~95% of exome variants. Overall variant sensitivity improves as each method covers thousands of coding exons missed by the other. We conclude that orthogonal NGS offers improvements in variant calling sensitivity when two platforms are used, better specificity for variants identified on both platforms, and greatly reduces the time and expense of Sanger follow-up, thus enabling physicians to act on genomic results more quickly.
Nucleation processes of nanobubbles at a solid/water interface
Authors: Fang Chung-Kai , Ko Hsien-Chen , Yang Chih-Wen , Lu Yi-Hsien , Hwang Ing-Shouh
Published: April 2016

Experimental investigations of hydrophobic/water interfaces often return controversial results, possibly due to the unknown role of gas accumulation at the interfaces. Here, during advanced atomic force microscopy of the initial evolution of gas-containing structures at a highly ordered pyrolytic graphite/water interface, a fluid phase first appeared as a circular wetting layer ~0.3 nm in thickness and was later transformed into a cap-shaped nanostructure (an interfacial nanobubble). Two-dimensional ordered domains were nucleated and grew over time outside or at the perimeter of the fluid regions, eventually confining growth of the fluid regions to the vertical direction. We determined that interfacial nanobubbles and fluid layers have very similar mechanical properties, suggesting low interfacial tension with water and a liquid-like nature, explaining their high stability and their roles in boundary slip and bubble nucleation. These ordered domains may be the interfacial hydrophilic gas hydrates and/or the long-sought chemical surface heterogeneities responsible for contact line pinning and contact angle hysteresis. The gradual nucleation and growth of hydrophilic ordered domains renders the original homogeneous hydrophobic/water interface more heterogeneous over time, which would have great consequence for interfacial properties that affect diverse phenomena, including interactions in water, chemical reactions, and the self-assembly and function of biological molecules.
Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors
Authors: Wang Jianwei , Zhang Yong
Published: April 2016

When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN and ZnO on the tensile strain side, Ge, Si and GaP on the compressive strain side.
Somatic embryogenesis and enhanced shoot organogenesis in Metabriggsia ovalifolia W. T. Wang
Authors: Ouyang Yao , Chen Yulu , Lü Jinfeng , Teixeira da Silva Jaime A. , Zhang Xinhua , Ma Guohua
Published: April 2016

An efficient protocol providing a dual regeneration pathway via direct shoot organogenesis and somatic embryogenesis for an endangered species, Metabriggsia ovalifolia W. T. Wang, was established from leaf explants. When applied at 2.5 μM, the cytokinins 6-benzyladenine (BA) or thidiazuron (TDZ) and the auxins indole-3-butyric acid (IBA), α-naphthaleneacetic acid (NAA) and indole-3-acetic acid (IAA) could induce shoots when on basal Murashige and Skoog (MS) medium. BA and TDZ could induce more adventitious shoots (19.1 and 31.2/explant, respectively) than NAA (4.6/explant), IBA (5.7/explant) or IAA (6.4/explant). BA and TDZ at 5–10 μM could induce both shoots and somatic embryos. A higher concentration of TDZ (25 μM) induced only somatic embryos (39.8/explant). The same concentration of BA induced both adventitious shoots (23.6/explant) and somatic embryos (9.7/explant). Thus, somatic embryogenesis in this plant needs a high cytokinin concentration (BA; TDZ), as evidenced by histology. Somatic embryos germinated easily when left on the same media, but formed adventitious roots in two weeks on MS supplemented with 0.5 μM NAA, 0.5 μM IBA and 0.1% activated charcoal. Over 93% of plantlets survived following acclimatization and transfer to a mixture of sand and vermiculite (1:1, v/v) in trays.
Leveraging family-specific signatures for AMP discovery and high-throughput annotation
Authors: Waghu Faiza Hanif , Barai Ram Shankar , Idicula-Thomas Susan
Published: April 2016

Antimicrobial peptides (AMPs) are diverse, biologically active, essential components of the innate immune system. As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance. They are widely researched for their therapeutic potential, especially against multi-drug resistant pathogens. AMPs are known to have family-specific sequence composition, which can be mined for their discovery and rational design. Here, we present a detailed family-based study on AMP families. The study involved the use of sequence signatures represented by patterns and hidden Markov models (HMMs) present in experimentally studied AMPs to identify novel AMPs. Along with AMPs, peptides hitherto lacking antimicrobial annotation were also retrieved and wet-lab studies on randomly selected sequences proved their antimicrobial activity against Escherichia coli. CAMPSign, a webserver has been created for researchers to effortlessly exploit the use of AMP family signatures for identification of AMPs. The webserver is available online at www.campsign.bicnirrh.res.in. In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.
Mitigating methane emission from paddy soil with rice-straw biochar amendment under projected climate change
Authors: Han Xingguo , Sun Xue , Wang Cheng , Wu Mengxiong , Dong Da , Zhong Ting , Thies Janice E. , Wu Weixiang
Published: April 2016

Elevated global temperatures and increased concentrations of carbon dioxide (CO2) in the atmosphere associated with climate change will exert profound effects on rice cropping systems, particularly on their greenhouse gas emitting potential. Incorporating biochar into paddy soil has been shown previously to reduce methane (CH4) emission from paddy rice under ambient temperature and CO2. We examined the ability of rice straw-derived biochar to reduce CH4 emission from paddy soil under elevated temperature and CO2 concentrations expected in the future. Adding biochar to paddy soil reduced CH4 emission under ambient conditions and significantly reduced emissions by 39.5% (ranging from 185.4 mg kg−1 dry weight soil, dws season−1 to 112.2 mg kg−1 dws season−1) under simultaneously elevated temperature and CO2. Reduced CH4 release was mainly attributable to the decreased activity of methanogens along with the increased CH4 oxidation activity and pmoA gene abundance of methanotrophs. Our findings highlight the valuable services of biochar amendment for CH4 control from paddy soil in a future that will be shaped by climate change.
Prioritizing functional phosphorylation sites based on multiple feature integration
Authors: Xiao Qingyu , Miao Benpeng , Bi Jie , Wang Zhen , Li Yixue
Published: April 2016

Protein phosphorylation is an important type of post-translational modification that is involved in a variety of biological activities. Most phosphorylation events occur on serine, threonine and tyrosine residues in eukaryotes. In recent years, many phosphorylation sites have been identified as a result of advances in mass-spectrometric techniques. However, a large percentage of phosphorylation sites may be non-functional. Systematically prioritizing functional sites from a large number of phosphorylation sites will be increasingly important for the study of their biological roles. This study focused on exploring the intrinsic features of functional phosphorylation sites to predict whether a phosphosite is likely to be functional. We found significant differences in the distribution of evolutionary conservation, kinase association, disorder score, and secondary structure between known functional and background phosphorylation datasets. We built four different types of classifiers based on the most representative features and found that their performances were similar. We also prioritized 213,837 human phosphorylation sites from a variety of phosphorylation databases, which will be helpful for subsequent functional studies. All predicted results are available for query and download on our website (Predict Functional Phosphosites, PFP,http://pfp.biosino.org/pfp).
Properties of Two Enterovirus Antibodies that are Utilized in Diabetes Research
Authors: Maccari Giuseppe , Genoni Angelo , Sansonno Silvia , Toniolo Antonio
Published: April 2016

Human enteroviruses (EVs) comprise >100 different types. Research suggests a non-chance association between EV infections and type 1 diabetes. Immunohistochemical studies with the anti-EV antibody 5D-8.1 have shown that the EV capsid antigen is present in pancreatic islet cells of diabetic subjects. When it was noticed that 5D-8.1 may cross-react with human proteins, doubt was casted on the significance of the above histopathologic findings. To address this issue, properties of EV antibodies 5D-8.1 and 9D5 have been investigated using peptide microarrays, peptide substitution scanning, immunofluorescence of EV-infected cells, EV neutralization assays, bioinformatics analysis. Evidence indicates that the two antibodies bind to distinct non-neutralizing linear epitopes in VP1 and are specific for a vast spectrum of EV types (not for other human viruses). However, their epitopes may align with a few human proteins at low expected values. When tested by immunofluorescence, high concentrations of 5D-8.1 yelded faint cytoplasmic staining in uninfected cells. At reduced concentrations, both antibodies produced dotted staining only in the cytoplasm of infected cells and recognized both acute and persistent EV infection. Thus, the two monoclonals represent distinct and independent probes for hunting EVs in tissues of patients with diabetes or other endocrine conditions.
Understanding of HLA-conferred susceptibility to chronic hepatitis B infection requires HLA genotyping-based association analysis
Authors: Nishida Nao , Ohashi Jun , Khor Seik-Soon , Sugiyama Masaya , Tsuchiura Takayo , Sawai Hiromi , Hino Keisuke , Honda Masao , Kaneko Shuichi , Yatsuhashi Hiroshi , Yokosuka Osamu , Koike Kazuhiko , Kurosaki Masayuki , Izumi Namiki , Korenaga Masaaki , Kang Jong-Hon , Tanaka Eiji , Taketomi Akinobu , Eguchi Yuichiro , Sakamoto Naoya , Yamamoto Kazuhide , Tamori Akihiro , Sakaida Isao , Hige Shuhei , Itoh Yoshito , Mochida Satoshi , Mita Eiji , Takikawa Yasuhiro , Ide Tatsuya , Hiasa Yoichi , Kojima Hiroto , Yamamoto Ken , Nakamura Minoru , Saji Hiroh , Sasazuki Takehiko , Kanto Tatsuya , Tokunaga Katsushi , Mizokami Masashi
Published: April 2016

Associations of variants located in the HLA class II region with chronic hepatitis B (CHB) infection have been identified in Asian populations. Here, HLA imputation method was applied to determine HLA alleles using genome-wide SNP typing data of 1,975 Japanese individuals (1,033 HBV patients and 942 healthy controls). Together with data of an additional 1,481 Japanese healthy controls, association tests of six HLA loci including HLA-A, C, B, DRB1, DQB1, and DPB1, were performed. Although the strongest association was detected at a SNP located in the HLA-DP locus in a SNP-based GWAS using data from the 1,975 Japanese individuals, HLA genotyping-based analysis identified DQB1*06:01 as having the strongest association, showing a greater association with CHB susceptibility (OR = 1.76, P = 6.57 × 10−18) than any one of five HLA-DPB1 alleles that were previously reported as CHB susceptibility alleles. Moreover, HLA haplotype analysis showed that, among the five previously reported HLA-DPB1 susceptibility and protective alleles, the association of two DPB1 alleles (DPB1*09:01, and *04:01) had come from linkage disequilibrium with HLA-DR-DQ haplotypes, DRB1*15:02-DQB1*06:01 and DRB1*13:02-DQB1*06:04, respectively. The present study showed an example that SNP-based GWAS does not necessarily detect the primary susceptibility locus in the HLA region.
A de novo self-assembling peptide hydrogel biosensor with covalently immobilised DNA-recognising motifs
Authors: King Patrick J. S. , Saiani Alberto , Bichenkova Elena V. , Miller Aline F.
Published: April 2016

The conjugate co-assemblies within the peptide-rich fibres leaving oligonucleotide recognition elements exposed on the external surface of the peptide fibre to ‘fish out’ DNA/RNA sequences, leading to a fluorescence response.
HaloTag mediated artificial cellulosome assembly on a rolling circle amplification DNA template for efficient cellulose hydrolysis
Authors: Sun Qing , Chen Wilfred
Published: April 2016

We report here the generation of artificial cellulosomes onto a DNA scaffold using the self-labeling HaloTag for DNA conjugation. Rolling circle amplification multiplexing templates were used to increase the complexity of this system with higher efficiency observed.
Sweet supramolecular elastomers from α,ω-(β-cyclodextrin terminated) PDMS
Authors: Rambarran Talena , Bertrand Arthur , Gonzaga Ferdinand , Boisson Fernande , Bernard Julien , Fleury Etienne , Ganachaud François , Brook Michael A.
Published: April 2016

CDs linked to PDMS vaturally phase separate and hydrogen bond to generate supramolecular elastomers.
Gas phase complexes of H3N⋯CuF and H3N⋯CuI studied by rotational spectroscopy and ab initio calculations: the effect of X (X = F, Cl, Br, I) in OC⋯CuX and H3N⋯CuX
Authors: Bittner Dror M. , Stephens Susanna L. , Zaleski Daniel P. , Tew David P. , Walker Nicholas R. , Legon Anthony C.
Published: April 2016

Complexes of H3N⋯CuF and H3N⋯CuI have been synthesised in the gas phase and characterized by microwave spectroscopy.
Investigation into atmospheric PM2.5-borne PAHs in Eastern cities of China: concentration, source diagnosis and health risk assessment
Authors: Li Ye , Liu Xinran , Liu Min , Li Xiaofei , Meng Fei , Wang Juan , Yan Wenjun , Lin Xianbiao , Zhu Junmin , Qin Yukun
Published: April 2016

PM2.5and PM2.5-borne PAHs pollution patterns were investigated simultaneously in three main cities (Beijing, Jinan and Shanghai) of China.
Migration behavior of anionic polyurethane dispersion during infiltration and redistribution in sand
Authors: Zang Yunxiao , Xie Hao , Gong Wei , Du Zechuan , Liu Bailing , Chen Hualin
Published: April 2016

The migration behavior of anionic polyurethane (APU) dispersion (APUD) was investigated by using a newly established method, which is based weight measurement.
Ductile-to-brittle transition and materials’ resistance to amorphization by irradiation damage
Authors: Wang Xin , Zhang Yu-Ting , Liu Peng-Chuang , Yan Jiawei , Mo Wenlin , Zhang Peng-Cheng , Chen Xing-Qiu
Published: April 2016

By summarizing over seven hundred elastic constants of materials with various crystal structures, we have found that ductile-to-brittle transition can be reflected by the change of G/B, an important indicator of bonding type.
Engineering peptide-based biomimetic enzymes for enhanced catalysis
Authors: Zhang Guohua , Huang Renliang , Qi Wei , Wang Yuefei , Su Rongxin , He Zhimin
Published: April 2016

Herein, we reported a novel hydrolase model by integrating the supramolecular self-assembly of Fmoc-FFH and electrostatic complexation (with PEI) at an aqueous liquid–liquid interface for the synthesis of peptide–polymer hybrid capsules.
One-pot preparation of pomegranate-like polydopamine stabilized small gold nanoparticles with superior stability for recyclable nanocatalysts
Authors: Ni Yunzhou , Tong Gangsheng , Wang Jie , Li Huimei , Chen Feng , Yu Chunyang , Zhou Yongfeng
Published: April 2016

A pre-mixing and post-polymerization strategy has been developed to fabricate polydopamine (PDA) stabilized small gold nanoparticles (size of AuNPs < 5 nm) with high stability for recyclable catalysis of 50 mM 4-nitrophenol with a TOF of 1006 h−1.
Inverted thermal annealing of perovskite films: a method for enhancing photovoltaic device efficiency
Authors: Dong Guohua , Yang Yulin , Sheng Li , Xia Debin , Su Ting , Fan Ruiqing , Shi Yan , Wang Junhai
Published: April 2016

A novel method called inverted thermal annealing was adopted to treat perovskite films for efficient PSCs.
ZnO nanorods decorated with metal sulfides as stable and efficient counter-electrode materials for high-efficiency quantum dot-sensitized solar cells
Authors: Gopi Chandu V. V. M. , Venkata-Haritha Mallineni , Lee Young-Seok , Kim Hee-Je
Published: April 2016

Metal sulfide decorated with ZnO NRs (ZnO/CoS, ZnO/NiS, ZnO/CuS and ZnO/PbS) were fabricated and used as efficient CEs for QDSSCs.
Air-stable and highly luminescent bismuth complex nanoparticles
Authors: Zhou Dan-Dan , Liu Bo-Mei , Zhou Yang , Chen Mu-Zi , Fang Yong-Zheng , Hou Jing-Shan , Li Li-Na , Sun Hong-Tao
Published: April 2016

We report, for the first time, the preparation of air-stable, solution-processed, luminescent Bi complex nanoparticles (NPs) through a one-pot wet chemical reaction method.
Perfusion Computed Tomography Study: A Utility Tool in Traumatic Cerebral Contusions
Authors: Velho Vernon , Valsangkar Shonali A. , Singh Jasmit , Survashe Pravin , Aher Sucheta , Kharosekar Hrushikesh U.
Published: April 2016

Aim To assess the usefulness of CT perfusion scans of the brain in patients with traumatic brain injury having cerebral contusion on CT scan.

Material and Methods This prospective study included 76 patients with cerebral contusion on plain CT of the brain, aged 5 to 86 years, admitted in our institution. They underwent perfusion CT as part of their admission CT survey and follow-up scan 48 hours later. Clinical data, unenhanced CT brain findings, and perfusion CT scans were evaluated with respect to the postoperative GCS (Glasgow Coma Score) and neurologic deficit.

Results Perfusion CT gave additional information when done with conventional unenhanced CT in the detection of cerebral contusions. Perfusion CT featured specific patterns with respect to patient outcome, patients with unfavorable outcome having significant decrease in cerebral perfusion. In patients having less GCS score, a significant decrease in cerebral blood flow and cerebral blood volume was detected.

Conclusion Perfusion CT provides independent useful information regarding functional outcome. In the acute phase of mild head injury, disturbed cerebral perfusion is seen in patients with normal noncontrast CT correlating with evolution, severity of injury, and outcome.
Effects of variations in electron thermal velocity on the whistler anisotropy instability: Particle-in-cell simulations
Authors: Hughes R. Scott , Wang Joseph , Decyk Viktor K. , Gary S. Peter
Published: April 2016

This paper investigates how the physics of the whistler anisotropy instability (WAI) is affected by variations in the electron thermal velocity vte, referred to here in terms of the ratio v̂te=vte/c, where c is the speed of light. The WAI is driven by the electron condition RT>1, where RT=Te⊥/Te∥ is the temperature anisotropy ratio and ⊥/∥ signify directions perpendicular/parallel to the background magnetic field B0. While a typical value of v̂te in the solar wind is ∼0.005, electromagnetic (EM) particle-in-cell (PIC) simulations often use a value near 0.1 in order to maximize the computational time step. In this study, a two-dimensional (2D) Darwin particle-in-cell (DPIC) code, MDPIC2, is used. The time step in the DPIC model is not affected by the choice of v̂te, making DPIC suited for this study. A series of simulations are carried out under the condition that the electron βe is held fixed, while v̂te is varied over the range 0.1≥v̂te≥0.025. The results show that, with βe held fixed, the linear dispersion properties and the nonlinear saturation amplitude and pitch angle scattering rates associated with the WAI are insensitive to the value of v̂te. A supplementary investigation is conducted which characterizes how the WAI model is affected at various values of v̂te by noise associated with the limited number of particles in a typical PIC simulation. It is found that the evolution of the WAI is more strongly influenced by electrostatic noise as v̂te is decreased. The electrostatic noise level is inversely proportional to the number of particles per computational cell (Nc); this implies that the number of particles required to remove nonphysical effects from the PIC simulation increases as v̂te decreases. It is concluded that PIC simulations of this instability which use an artificially large value of v̂te accurately reproduce the response of a cooler plasma as long as a realistic value of βe is used. Moreover, for a fixed number of particles, the quantitative accuracy of the model improves with increasing v̂te.
Suppression of phase synchronisation in network based on cat's brain
Authors: Lameu Ewandson L. , Borges Fernando S. , Borges Rafael R. , Iarosz Kelly C. , Caldas Iberê L. , Batista Antonio M. , Viana Ricardo L. , Kurths Jürgen
Published: April 2016

We have studied the effects of perturbations on the cat's cerebral cortex. According to the literature, this cortex structure can be described by a clustered network. This way, we construct a clustered network with the same number of areas as in the cat matrix, where each area is described as a sub-network with a small-world property. We focus on the suppression of neuronal phase synchronisation considering different kinds of perturbations. Among the various controlling interventions, we choose three methods: delayed feedback control, external time-periodic driving, and activation of selected neurons. We simulate these interventions to provide a procedure to suppress undesired and pathological abnormal rhythms that can be associated with many forms of synchronisation. In our simulations, we have verified that the efficiency of synchronisation suppression by delayed feedback control is higher than external time-periodic driving and activation of selected neurons of the cat's cerebral cortex with the same coupling strengths.
Elasticity of methane hydrate phases at high pressure
Authors: Beam Jennifer , Yang Jing , Liu Jin , Liu Chujie , Lin Jung-Fu
Published: April 2016

Determination of the full elastic constants (cij) of methane hydrates (MHs) at extreme pressure-temperature environments is essential to our understanding of the elastic, thermodynamic, and mechanical properties of methane in MH reservoirs on Earth and icy satellites in the solar system. Here, we have investigated the elastic properties of singe-crystal cubic MH-sI, hexagonal MH-II, and orthorhombic MH-III phases at high pressures in a diamond anvil cell. Brillouin light scattering measurements, together with complimentary equation of state (pressure-density) results from X-ray diffraction and methane site occupancies in MH from Raman spectroscopy, were used to derive elastic constants of MH-sI, MH-II, and MH-III phases at high pressures. Analysis of the elastic constants for MH-sI and MH-II showed intriguing similarities and differences between the phases′ compressional wave velocity anisotropy and shear wave velocity anisotropy. Our results show that these high-pressure MH phases can exhibit distinct elastic, thermodynamic, and mechanical properties at relevant environments of their respective natural reservoirs. These results provide new insight into the determination of how much methane exists in MH reservoirs on Earth and on icy satellites elsewhere in the solar system and put constraints on the pressure and temperature conditions of their environment.
Quasi-stationary fluid theory of the hole-boring process
Authors: Pei Zhikun , Shen Baifei , Shi Yin , Ji Liangliang , Wang Wenpeng , Zhang Xiaomei , Zhang Lingang , Xu Tongjun , Liu Chen
Published: April 2016

We present a quasi-stationary fluid theory to precisely describe the hole-boring process. The corresponding distributions of the electrostatic field and the particle density are theoretically obtained, which give more details than the previous stationary theory. The theoretical result is confirmed by one-dimensional particle-in-cell simulations. Such quasi-stationary fluid theory may help in understanding the basic mechanisms of ion acceleration in the radiation pressure acceleration.