bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toroidal modelling of RMP response in ASDEX Upgrade: coil phase scan, q95 dependence, and toroidal torques
Authors: Liu Yueqiang , Ryan D. , Kirk A. , Li Li , Suttrop W. , Dunne M. , Fischer R. , Fuchs J.C. , Kurzan B. , Piovesan P. , Willensdorfer M. 
Published: April 2016

Abstract
The plasma response to the vacuum resonant magnetic perturbation (RMP) fields, produced by the ELM control coils in ASDEX Upgrade experiments, is computationally modelled using the MARS-F/K codes (Liu et al 2000 Phys. Plasmas

7

3681, Liu et al 2008 Phys. Plasmas

15

112503). A systematic investigation is carried out, considering various plasma and coil configurations as in the ELM control experiments. The low q plasmas, with

q

95

∼
3.8

(q
95 is the safety factor q value at 95% of the equilibrium poloidal flux), responding to low n (n is the toroidal mode number) field perturbations from each single row of the ELM coils, generates a core kink amplification effect. Combining two rows, with different toroidal phasing, thus leads to either cancellation or reinforcement of the core kink response, which in turn determines the poloidal location of the peak plasma surface displacement. The core kink response is typically weak for the n  =  4 coil configuration at low q, and for the n  =  2 configuration but only at high q (

q

95

∼
5.5

). A phase shift of around 60 degrees for low q plasmas, and around 90 degrees for high q plasmas, is found in the coil phasing, between the plasma response field and the vacuum RMP field, that maximizes the edge resonant field component. This leads to an optimal coil phasing of about 100 (−100) degrees for low (high) q plasmas, that maximizes both the edge resonant field component and the plasma surface displacement near the X-point of the separatrix. This optimal phasing closely corresponds to the best ELM mitigation observed in experiments. A strong parallel sound wave damping moderately reduces the core kink response but has minor effect on the edge peeling response. For low q plasmas, modelling shows that both the resonant electromagnetic torque and the neoclassical toroidal viscous (NTV) torque (due to the presence of 3D magnetic field perturbations) contribute to the toroidal flow damping, in particular near the plasma edge region. For high q plasmas, however, significant amount of torque is also produced in the bulk plasma region, and the contributions from the electromagnetic, the NTV, and the torque associated with the Reynolds stress, all play significant roles.
State‐Level Cooperative Extension Spending and Farmer Exits
Authors: Goetz Stephan J. , Davlasheridze Meri 
Published: April 2016

AbstractNumerous studies have evaluated the impact of Extension on farm productivity and related outcomes. Here we use annual data from 1983 to 2010 covering the 50 U.S. states to examine the impact of Extension on net changes in the number of farmers. The historical transition of farmers out of U.S. agriculture raises the question of whether Cooperative Extension and underlying Hatch‐funded research spending keeps farmers in agriculture or accelerates their exit. On balance, nearly 500,000 more farmers left than entered agriculture over the period studied. We estimate that without Extension, as many as 137,700 (or 28%) additional farmers would have disappeared on net. Overall, Extension programs are a remarkably cost effective way of keeping farmers in agriculture. Alternatively, shifting just 1.5% of federal farm program payments to Extension would have reduced net exits over this period by an estimated 11%, or 55,000 farmers.
OxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA
Authors: Houseman E. Andres , Johnson Kevin C. , Christensen Brock C. 
Published: April 2016

Abstract
Summary: The use of sodium bisulfite (BS) treatment followed by hybridization to an Illumina Infinium BeadChip (HumanMethylation450 and MethylationEPIC) is a common method for interrogating 5-methylcytosine (5mC) at single nucleotide resolution. However, standard treatment of DNA with BS does not allow disambiguation of 5mC from an additional cytosine modification, 5-hydroxymethylcytosine (5hmC). Recently, it has been demonstrated that paired BS and oxidative bisulfite (oxBS) treatment on the same sample followed by hybridization to an Infinium microarray permits the differentiation of 5hmC from 5mC. Nevertheless, estimation of 5hmC and 5mC from tandem-treated arrays has been shown to produce irregular estimates of cytosine modifications.
Results: We present a novel method using maximum likelihood estimation to accurately estimate the parameters of unmethylated cytosine (5C), 5mC and 5hmC from Infinium microarray data given the signal intensities from the oxBS and BS replicates.
Availability and Implementation: OxyBS is an R package available on CRAN.
Contact: Andres.Houseman@oregonstate.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Shape complementarity and hydrogen bond preferences in protein–protein interfaces: implications for antibody modeling and protein–protein docking
Authors: Kuroda Daisuke , Gray Jeffrey J. 
Published: April 2016

Abstract
Motivations: Characterizing protein–protein interfaces and the hydrogen bonds is a first step to better understand proteins’ structures and functions toward high-resolution protein design. However, there are few large-scale surveys of hydrogen bonds of interfaces. In addition, previous work of shape complementarity of protein complexes suggested that lower shape complementarity in antibody–antigen interfaces is related to their evolutionary origin.
Results: Using 6637 non-redundant protein–protein interfaces, we revealed peculiar features of various protein complex types. In contrast to previous findings, the shape complementarity of antibody–antigen interfaces resembles that of the other interface types. These results highlight the importance of hydrogen bonds during evolution of protein interfaces and rectify the prevailing belief that antibodies have lower shape complementarity.
Contact: jgray@jhu.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Beta-Poisson model for single-cell RNA-seq data analyses
Authors: Vu Trung Nghia , Wills Quin F. , Kalari Krishna R. , Niu Nifang , Wang Liewei , Rantalainen Mattias , Pawitan Yudi 
Published: April 2016

Abstract
Motivation: Single-cell RNA-sequencing technology allows detection of gene expression at the single-cell level. One typical feature of the data is a bimodality in the cellular distribution even for highly expressed genes, primarily caused by a proportion of non-expressing cells. The standard and the over-dispersed gamma-Poisson models that are commonly used in bulk-cell RNA-sequencing are not able to capture this property.
Results: We introduce a beta-Poisson mixture model that can capture the bimodality of the single-cell gene expression distribution. We further integrate the model into the generalized linear model framework in order to perform differential expression analyses. The whole analytical procedure is called BPSC. The results from several real single-cell RNA-seq datasets indicate that ∼90% of the transcripts are well characterized by the beta-Poisson model; the model-fit from BPSC is better than the fit of the standard gamma-Poisson model in &gt; 80% of the transcripts. Moreover, in differential expression analyses of simulated and real datasets, BPSC performs well against edgeR, a conventional method widely used in bulk-cell RNA-sequencing data, and against scde and MAST, two recent methods specifically designed for single-cell RNA-seq data.
Availability and Implementation: An R package BPSC for model fitting and differential expression analyses of single-cell RNA-seq data is available under GPL-3 license at https://github.com/nghiavtr/BPSC .
Contact: yudi.pawitan@ki.se or mattias.rantalainen@ki.se
Supplementary information: Supplementary data are available at Bioinformatics online.
e23D: database and visualization of A-to-I RNA editing sites mapped to 3D protein structures
Authors: Solomon Oz , Eyal Eran , Amariglio Ninette , Unger Ron , Rechavi Gidi 
Published: April 2016

Abstract
Summary: e23D, a database of A-to-I RNA editing sites from human, mouse and fly mapped to evolutionary related protein 3D structures, is presented. Genomic coordinates of A-to-I RNA editing sites are converted to protein coordinates and mapped onto 3D structures from PDB or theoretical models from ModBase. e23D allows visualization of the protein structure, modeling of recoding events and orientation of the editing with respect to nearby genomic functional sites from databases of disease causing mutations and genomic polymorphism.
Availability and Implementation: http://www.sheba-cancer.org.il/e23D
Contact: oz.solomon@live.biu.ac.il or Eran.Eyal@sheba.health.gov.il
Discard ban and balanced harvest: a contradiction?
Authors: Borges Lisa , Cocas Luis , Nielsen Kåre Nolde 
Published: April 2016

AbstractDiscard bans have been proposed as part of management policies aimed at balanced harvest (BH). Nationwide discard bans exist in several countries, including Chile, the European Union, Norway, and New Zealand. We analysed experiences from these countries to determine whether or not discard bans are in contradiction with BH, based on six aspects: policy objectives, species/sizes applicability, accompanying technical measures, at-sea monitoring and control, and possible impacts. When discard bans are fully implemented, fishing operations change to more selective fishing, typically targeting bigger individuals of main commercial species. This is consistent with the primary objective of many discard policies, i.e. to reduce unwanted catch. In contrast, proponents of BH argue that broader catch diversity, a product of a widespread harvest strategy, should be sought to avoid major impacts on the ecosystem. Our analysis demonstrates that the scope of discard bans is often limited to main commercial species, although usually they can be extended to include more ecosystem components. Some of the policies examined also prohibit the use of unwanted catches for human consumption, thus limiting their effective use. However, the implementation of discard bans requires high levels of at-sea monitoring and effective control, and/or strong incentives to fish more selectively, neither of which applied in most cases examined. We conclude that if discard bans were set differently, they could contribute to fishery management policies aiming at BH. Their goals should be in line with BH, i.e. to reach a wider global harvest pattern, or at least be established within management regimes that promote high compliance. Finally, the extent to which a discard ban contributes to achieve BH depends also on the relative importance of the ecosystem benthic and megafauna components.
Fracture of the patella treated by percutaneous cerclage wiring
Authors: Yang Jun , Zhang Guang-ming , Ruan Zhiyong 
Published: April 2016

Background:
To investigate the efficacy of percutaneous cerclage wiring of selective patellar fracture cases.

Methods:
Twenty-eight closed patellar fractures were treated with closed reduction and fixation using the Pyrford percutaneous tension band wiring technique.

Results:
The surgical time ranged from 1 to 2 hr. All the patients were followed postoperatively from 9 to 53 mo, 21 mo on average. The fracture healed without complications except wire breakage in two patients. Infection, nonunion, and migration did not occur in any patient. Böstman score was 30-28 in 27 patients and 24 in one patient. Visual analog score was 3 in 23 patients and 4-6 in five patients.

Conclusions:
Patellar fractures fixed with the Pyrford percutaneous cerclage wiring technique were successful; the technique is minimally invasive and the clinical workflow was acceptable.
Cutaneous Adenomyoepithelioma: Report of a Case and Review of the Literature
Authors: González Iván , Gonzalez Manuel Lora , Kroh Jan-Marie , Fraga Garth R. 
Published: April 2016

Abstract:
Adenomyoepithelioma (AME) is a biphasic neoplasm of epithelial and myoepithelial cells. It is most commonly found in the breast, although rare cases have been reported from the lung, salivary glands, and skin. There are 5 well-documented cases of cutaneous AME in the literature. We report a new case of cutaneous AME. Our case was commingled with apocrine hidrocystoma. This is the first report of cutaneous AME in a male patient and the first to describe SOX10 immunostaining in cutaneous AME. We review the literature on cutaneous AME and note the greater than chance colocalization with other adnexal tumors. We speculate that AME may represent localized overgrowth of myoepithelial cells within a pre-existent sweat gland tumor. Histopathologists should be aware of the potential of SOX10-positive myoepithelial neoplasms to mimic nodular melanocytic proliferations.
Eosinophil-Rich Acute Febrile Neutrophilic Dermatosis in a Patient With Enteropathy-Associated T-cell Lymphoma, Type 1
Authors: Soon Christopher W. , Kirsch Ilan R. , Connolly Andrew J. , Kwong Bernice Y. , Kim Jinah 
Published: April 2016

Abstract:
The presence of eosinophils within the neutrophilic infiltrates of acute febrile neutrophilic dermatosis (Sweet syndrome) is documented in the literature. Here, the authors describe a case of eosinophil-rich acute febrile neutrophilic dermatosis in the setting of new onset enteropathy-associated T-cell lymphoma (EATL), type 1. Histopathologic evaluation of the skin biopsies demonstrated a mixed superficial perivascular and inflammatory infiltrate composed of neutrophils, lymphocytes, and abundant eosinophils. EATL, type 1 is an aggressive although rare primary intestinal lymphoma that may be associated with celiac disease. This lymphoma is associated with a poor prognosis due to treatment resistance or bowel perforation. To the authors' knowledge, Sweet syndrome has not been reported in a patient with EATL.
Normative Fecal Calprotectin Concentrations in Guatemalan Preschoolers Are High Relative to Children Reported Elsewhere
Authors: Soto‐Méndez María‐José , Romero‐Abal María‐Eugenia , Schümann Klaus , Gil Ángel , Solomons Noel W. 
Published: April 2016

ABSTRACTBackground:Calprotectin is a fecal marker of intraintestinal inflammation derived from activated enteric neutrophils and macrophages. It is useful as a clinical marker in inflammatory bowel diseases; furthermore, it may have a role in public health epidemiology.Objectives:The aim of the study was to describe the distribution of fecal calprotectin in Guatemalan preschool children sharing a common institutional diet; to relate it collectively to pediatric distributions in other geographic settings, and individually to concomitant indicators of intestinal infection or colonization and other descriptive features of the child.Methods:Fecal samples were collected in 87 subjects, ages 2 to 7 years across 3 daycare centers sharing a common institutional menu, but from different ecological settings. Stools were examined, variously by routine light microscopy, quantitative egg counts, and a Giardia antigen test, for microbiological diagnosis, and an ELISA assay for fecal calprotectin (CalproLab).Results:The median fecal calprotectin value was 58 mg/kg, with a mean of 98 ± 136 mg/kg and a range from 10 to 950 mg/kg; 61% of values were above the manufacturer's cut‐off for elevated concentration and 51% exceeded an age‐adjusted criterion. There were no associations between sex, age, growth indicators, or fecal microbiological findings by microscopy or ELISA assays, alone or in combination. The central tendency (mean or median) and distribution were generally shifted to the right in relation to comparable reports from children across the world literature.Conclusions:Although specific, low‐grade intestinal infections do not define calprotectin subgroups, right‐shifted fecal calprotectin status in this population may reflect a general and diffuse stress of adverse environmental sanitation.
LEM2 recruits CHMP7 for ESCRT-mediated nuclear envelope closure in fission yeast and human cells
Authors: Gu Mingyu , LaJoie Dollie , Chen Opal S. , Von Appen Alexander , Ladinsky Mark S. , Redd Michael J. , Nikolova Linda , Bjorkman Pamela J. , Sundquist Wesley I. , Ullman Katharine S. , Frost Adam 
Published: April 2016

AbstractESCRT-III proteins have been implicated in sealing the nuclear envelope in mammals, spindle pole body dynamics in fission yeast, and surveillance of defective nuclear pore complexes in budding yeast. Here, we report that Lem2p (LEM2), a member of the LEM (Lap2-Emerin-Man1) family of inner nuclear membrane proteins, and the ESCRT-II/ESCRT-III hybrid protein Cmp7p (CHMP7), work together to recruit additional ESCRT-III proteins to holes in the nuclear membrane. InS. pombe, deletion of the ATPasevps4leads to severe defects in nuclear morphology and integrity. These phenotypes are suppressed by loss-of-function mutations that arise spontaneously inlem2orcmp7,implying that these proteins may function upstream in the same pathway. Building on these genetic interactions, we explored the role of LEM2 during nuclear envelope reformation in human cells. We found that CHMP7 and LEM2 enrich at the same region of the chromatin disc periphery during this window of cell division, and that CHMP7 can bind directly to the C-terminal domain of LEM2in vitro. We further found that, during nuclear envelope formation, recruitment of the ESCRT factors CHMP7, CHMP2A and IST1/CHMP8 all depend on LEM2 in human cells. We conclude that Lem2p/LEM2 is a conserved nuclear site-specific adaptor that recruits Cmp7p/CHMP7 and downstream ESCRT factors to the nuclear envelope.
Ten simple rules for managing high-throughput nucleotide sequencing data
Authors: Vos Rutger A. 
Published: April 2016

AbstractThe challenges posed by large data volumes produced by high-throughput nucleotide sequencing technologies are well known. This document establishes ten simple rules for coping with these challenges. At the level of master data management, (1) data triage reduces data volumes; (2) some lossless data representations are much more compact than others; (3) careful management of data replication reduces wasted storage space. At the level of data analysis, (4) automated analysis pipelines obviate the need for storing work files; (5) virtualization reduces the need for data movement and bandwidth consumption; (6) tracking of data and analysis provenance will generate a paper trail to better understand how results were produced. At the level of data access and sharing, (7) careful modeling of data movement patterns reduces bandwidth consumption and haphazard copying; (8) persistent, resolvable identifiers for data reduce ambiguity caused by data movement; (9) sufficient metadata enables more effective collaboration. Finally, because of rapid developments in HTS technologies, (10) agile practices that combine loosely coupled modules operating on standards-compliant data are the best approach for avoiding lock-in. A generalized scenario is presented for data management from initial raw data generation to publication of result data.
Here’s one for the next show
Authors: Hegner Sabrina M , Beldad Ardion D. , Klein Langenhorst Nienke 
Published: April 2016

Purpose
– Financial constraints recently confronting performing arts organizations propel them to employ various marketing tactics to not only win new visitors but also to maintain its current clientele. Fostering a long-term relationship with clients is regarded a vital solution to a survival-related predicament these organizations face. Hence, the purpose of this paper is to investigate the impact of four marketing tactics – personalization, two-way communication, preferential treatment, and rewarding – on the dimensions of customer relationship, namely, satisfaction, trust, and commitment.

Design/methodology/approach
– Data to test the various research hypotheses were collected through a survey with 252 clients of a performing arts venue in a Dutch city. Structural equation modeling was used to test the hypotheses.

Findings
– Results reveal that extension of rewards to and maintaining a two-way communication with clients of a performing arts venue positively influence their satisfaction with, trust in, and commitment to the performing arts venue. Personalization of services impacts commitment only. However, the effect of preferential treatment on the three relationship dimensions is not statistically significant. Additionally, analysis shows that satisfied customers are more likely to trust the performing arts venue, although clients’ satisfaction with and trust in the performing arts venue do not influence their commitment to the venue.

Originality/value
– Research into the ways to strengthen customer relationships in the performing arts is still scarce. The current research aims at investigating the impact of several marketing tactics on customer relationship measured in terms of satisfaction, trust, and commitment and shows how performing arts venues can strengthen their bonds with customers.
The effects of relatedness, number of partners, and learning on equity contributions in joint ventures
Authors: Sukoco Badri Munir 
Published: April 2016

Purpose– Equity contributions in joint ventures (JVs) formation are crucial and how firms decide to contribute its equity less has been explored. Based on the equity theory, the purpose of this paper is to argue that the perceived benefits-to-cost (B/C) ratio of their partners determines the level of contribution made by a focal firm. This study then argues that business relatedness, number of partners, and learning orientation in JVs are the determinants. The conditions that explain the moderating effects of business relatedness and number of partners on the likelihood of an equity contribution are also discussed.Design/methodology/approach– In total, 853 high tech industry ventures in USA spanning from 1995 to 2008 are used to test the developed hypotheses.Findings– A firm tends to employ disproportional equity contributions when their business highly related with its partners, which is similar to high number of partners dues to low B/C ratio. On the other hand, exploration JVs leads firms to employ proportional equity contributions. Further, this study shows that exploration learning positively moderates the effect of business relatedness on the likelihood of proportional equity contribution.Originality/value– This study extends the equity theory by integrating the logic of resource-based view and organizational learning into the formation of JVs.
Processing of product placements and brand persuasiveness
Authors: Chan Fanny Fong Yee , Lowe Ben , Petrovici Dan 
Published: April 2016

PurposeThis research contributes to literature on marketing communication by exploring the roles of depth of processing and the dispositional factor, need for cognition (NFC), on consumer perceptions of product placement.Design/methodology/approachA web-based experiment with a 2 (low versus high prominence) x2 (low versus high brand awareness) x2 (with versus without prior disclosure) between-subjects full factorial design was conducted.FindingsThe results indicate that prominent placements were found to elicit more extensive processing, which was negatively correlated with brand attitudes. A significant negative relationship between NFC and purchase intention towards a placed brand was also revealed.Practical implicationsThe study offers managerial and policy implications for practitioners and educators. It is suggested that brand practitioners should avoid placing brands too prominently or in film genres which are cognitively demanding. The low NFC group appears to be more vulnerable to covert marketing. Therefore it is suggested that media educators target this group and plan effective media literacy programs to guard youngsters from surreptitious selling.Originality/valueThis is the first study to empirically examine the role of prominence, brand awareness and prior disclosure in the processing of product placement information and their influence on product placement effectiveness.