bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling and docking antibody structures with Rosetta
Authors: Weitzner Brian D. , Jeliazkov Jeliazko R. , Lyskov Sergey , Marze Nicholas , Kuroda Daisuke , Frick Rahel , Biswas Naireeta , Gray Jeffrey J. 
Published: August 2016

ABSTRACTWe describe Rosetta-based computational protocols for predicting the three-dimensional structure of an antibody from sequence and then docking the antibody–protein-antigen complexes. Antibody modeling leverages canonical loop conformations to graft large segments from experimentally-determined structures as well as (1) energetic calculations to minimize loops, (2) docking methodology to refine the VL–VHrelative orientation, and (3)de novoprediction of the elusive complementarity determining region (CDR) H3 loop. To alleviate model uncertainty, antibody–antigen docking resamples CDR loop conformations and can use multiple models to represent an ensemble of conformations for the antibody, the antigen or both. These protocols can be run fully-automated via the ROSIE web server or manually on a computer with user control of individual steps. For best results, the protocol requires roughly 2,500 CPU-hours for antibody modeling and 250 CPU-hours for antibody–antigen docking. Tasks can be completed in under a day by using public supercomputers.
A Distinct Pathway for Polar Exocytosis in Plant Cell Wall Formation
Authors: Wang Hao , Zhuang Xiaohong , Wang Xiangfeng , Law Angus Ho Yin , Zhao Teng , Du Shengwang , Loy Michael M.T. , Jiang Liwen 
Published: August 2016

Abstract
Post-Golgi protein sorting and trafficking to the plasma membrane (PM) is generally believed to occur via the trans-Golgi network (TGN). In this study using Nicotiana tabacum pectin methylesterase (NtPPME1) as a marker, we have identified a TGN-independent polar exocytosis pathway that mediates cell wall formation during cell expansion and cytokinesis. Confocal immunofluorescence and immunogold electron microscopy studies demonstrated that Golgi-derived secretory vesicles (GDSVs) labeled by NtPPME1-GFP are distinct from those organelles belonging to the conventional post-Golgi exocytosis pathway. In addition, pharmaceutical treatments, superresolution imaging, and dynamic studies suggest that NtPPME1 follows a polar exocytic process from Golgi-GDSV-PM/cell plate (CP), which is distinct from the conventional Golgi-TGN-PM/CP secretion pathway. Further studies show that ROP1 regulates this specific polar exocytic pathway. Taken together, we have demonstrated an alternative TGN-independent Golgi-to-PM polar exocytic route, which mediates secretion of NtPPME1 for cell wall formation during cell expansion and cytokinesis and is ROP1-dependent.
Behavioral Activation Treatment for Smoking (BATS) in smokers with depressive symptomatology
Authors: MacPherson Laura , Collado Anahi , Lejuez Carl W. , Brown Richard A. , Tull Matthew T. 
Published: August 2016

Purpose
Cigarette smoking remains the primary preventable cause of mortality and morbidity globally. The overarching goal of the paper is to disseminate the Behavioral Activation Treatment for Smoking (BATS), which integrates behavioral activation principles with standard treatment guidelines to assist individuals in achieving short- and long-term smoking cessation. Through a series of sequential steps, BATS guides individuals who wish to quit smoking to increase their engagement in healthy, pleasurable, and value-consistent activities.

Design/methodology/approach
The document provides the BATS rationale and contains an abridged manual for use by clinicians and/or researchers in the context of clinical trials. Findings: BATS is accruing empirical evidence that suggests its ability to promote successful smoking cessation outcomes while decreasing any associated depressive symptoms.

Findings
BATS is accruing empirical evidence that suggests its ability to promote successful smoking cessation outcomes while decreasing any associated depressive symptoms.

Practical implications
A description of key components, forms, and strategies to address common treatment barriers are included.

Originality/value
BATS’s strong roots in learning theories and its idiographic nature allow for the intervention to be implemented flexibly across a wide range of settings and smoking populations. The treatment may also be combined seamlessly with pharmacotherapies. BATS targets both cigarette smoking and depressive symptoms, which constitute a significant barrier to cessation, through a common pathway: increasing rewarding activities. The treatment offers a parsimonious complement to standard smoking cessation treatments.
Non-decision making in the reform of equal pay policy
Authors: Koskinen Sandberg Paula 
Published: August 2016

Purpose
The purpose of this paper is to analyse an example of non-decision making in the Nordic tripartite policy process, namely, the reform of the Finnish gender equality legislation and the law for equal pay comparisons.

Design/methodology/approach
The paper uses non-decision making as a conceptual framework for qualitative analysis of the documentation of the working group that drafted the law for equal pay comparisons. The analysis focuses on the strategic responses used by the participants in order to defend the status quo and resist change in legislation.

Findings
The key findings are that the suggested law for conducting equal pay comparisons as part of gender equality planning in Finnish organisations changed dramatically in the tripartite policy process. Employer organisations successfully prevented the most relevant features from being implemented in the reformed law.

Research limitations/implications
The findings of this research indicate that there is a need for more research on the tripartite policy process and its implication on developing policy.

Social implications
This paper shows what kind of power employer and employee organisations use in Finnish policy making. As a result, the reformed gender equality legislation is a compromise reflecting the vested interests of different stakeholders. The findings highlight the challenges of developing policy in tripartite policy process.

Originality/value
The tripartite policy process and its implications have rarely been studied. The value of this paper lies in both originality of the topic and approach, and the societal importance of the findings.
Facing the shortage in Benin: a strategy for information and documentation access at the Université d’Abomey-Calavi
Authors: Mêgnigbêto Eustache , Osseni Bachabi Khadidjath Kouboura 
Published: August 2016

Purpose
This paper aims to describe the response of students to the shortage of materials at the Université d’Abomey-Calavi (Republic of Benin).

Design/methodology/approach
A survey was conducted with over 2,000 students of the Université d’Abomey-Calavi in 2014, and the data were analysed. The paper deals with two questions related to the university library services they use.

Findings
To satisfy their information and documentation needs, students visit several university library services even on different campuses.

Practical implications
The study recommends the setting up and the implementation of a long-term development plan for the University of Abomey-Calavi libraries.

Originality/value
The study describes the behaviour of students of a developing country when faced with a lack of relevant information and documentation resources.
Bank leverage and stock liquidity: evidence from BRICS countries
Authors: Umar Muhammad , Sun Gang 
Published: August 2016

Purpose
The purpose of the study is to explore the relationship between bank leverage and stock liquidity.

Design/methodology/approach
A simultaneous equations model and a two-stage least squares method were used to find the above-mentioned relationship, using data from all the listed banks of the BRICS countries, for the years 2007-2014.

Findings
A decrease in leverage results in lower stock liquidity of the banks. Bank leverage is a significant determinant of stock liquidity, but changes in stock liquidity do not explain the variation in bank leverage. However, in the case of small banks, an increase in stock liquidity results in lower leverage. In the case of large banks, bank leverage and stock liquidity are significant determinants of each other, and the relationship between them is positive.

Practical implications
An increase in high quality capital, as required by the Basel III accord, will result in lower stock liquidity of the banks in emerging markets. However, stock liquidity shocks do not affect the leverage of banks.

Originality/value
To the best of the authors’knowledge, this study is the first one to explore the relationship between leverage and stock liquidity of financial firms. It contributes to the existing literature on bank liquidity and capital structure and helps managers and policy makers to formulate better policies.
Ownership, risk-taking and performance of banks in emerging economies
Authors: Haque Faizul , Shahid Rehnuma 
Published: August 2016

PurposeThis paper examines the effect of ownership structure on bank risk-taking and performance in emerging economies by using India as a case study.Design/methodology/approachWe use generalised method of moments (GMM) estimation technique to analyse an unbalanced panel data set covering 217 bank-year observations from 2008 to 2011.FindingsOverall, our study results suggest that government ownership is positively associated with default risk and negatively related to bank profitability. Interestingly, we find foreign ownership having a positive effect on default risk and a negative effect on profitability among the listed commercial banks. The effect of ownership concentration on bank risk-taking and profitability appears to be statistically insignificant.Originality/valueThis study is among the first to consider the impact of ownership on bank risk-taking and profitability from an emerging economy perspective. It also addresses the problem of endogenous relationships among ownership, risk-taking and performance of a bank. This study is likely to have implications for policymakers in undertaking regulatory reforms relating to ownership, risk management and banking sector stability.
Exchange rate risks in a small open economy
Authors: Nakamura Chikafumi 
Published: August 2016

PurposeThis study aims to analyze exchange rate risks and the choice of exchange rate policies in a small open economy indebted in foreign currency, incorporating the financial accelerator mechanism.Design/methodology/approachTo examine discussions on the fear of floating, this study develops a dynamic stochastic general equilibrium model in which a small open economy model has an open economy financial accelerator mechanism as the external borrowing restriction. The author then compares and analyzes the macroeconomic dynamics in response to an exchange rate shock under different exchange rate systems.FindingsThe most interesting finding is that the currency peg for a foreign currency used in borrowing is more efficient than the trade-weighted currency basket policy, regardless of trade openness or trade share.Practical implicationsThe result implies that in discussions on the fear of floating, more attention needs to be paid to exchange rate risks in finance. It also suggests that exchange rate policy used to mitigate exchange rate risks in finance stabilizes macroeconomic volatility more efficiently.Originality/valueThe paper provides an answer to the question: which is the more serious problem in the fear of floating and to what would the regime be anchored.
Individual determinants of punitive attitudes towards sexual and domestic abuse offenders
Authors: Palasinski Marek , Shortland Neil 
Published: August 2016

Purpose
The purpose of this paper is to address individual factors predicting punitive attitudes towards sexual and domestic offences and offenders have received little attention.

Design/methodology/approach
In Study 1,137 participants completed a 25-item online questionnaire exploring individual factors hypothesised to predict punitive attitudes towards four sexual crimes: rape, paedophilia, incest and bestiality. In Study 2,100 participants completed a similar questionnaire exploring individual factors hypothesised to predict punitive attitudes towards male and female emotional, physical and sexual abusers.

Findings
The standard multiple regression models of Study 1 found that age (i.e. being older), belief in a just world and gender (i.e. being female) were predictors of harsher punitive attitudes. The models of Study 2 found that the low score on the social dominance scale was the most common predictor.

Research limitations/implications
This survey-based project presents a nuanced picture that could be complemented by the inclusion of a wider range of more complex factors and follow-on qualitative studies.

Practical implications
The key message from this study is to inform the public on the role of personality factors in developing punitive attitudes.

Social implications
It is vital to increase the legislators’ and the people’ awareness of the factors shaping the public impressions of criminal justice processes and evidence-based treatment effectiveness.

Originality/value
This relatively modest paper offers insight of personality factors into people’s punitive attitudes shaping actual legislation.
Alien and native plant establishment in grassland communities is more strongly affected by disturbance than above‐ and below‐ground enemies
Authors: Müller Gregor , Horstmeyer Lena , Rönneburg Tilman , van Kleunen Mark , Dawson Wayne 
Published: August 2016

SummaryUnderstanding the factors that drive commonness and rarity of plant species and whether these factors differ for alien and native species are key questions in ecology. If a species is to become common in a community, incoming propagules must first be able to establish. The latter could be determined by competition with resident plants, the impacts of herbivores and soil biota, or a combination of these factors.We aimed to tease apart the roles that these factors play in determining establishment success in grassland communities of 10 alien and 10 native plant species that are either common or rare in Germany, and from four families. In a two‐year multisite field experiment, we assessed the establishment success of seeds and seedlings separately, under all factorial combinations of low vs. high disturbance (mowing vs mowing and tilling of the upper soil layer), suppression or not of pathogens (biocide application) and, for seedlings only, reduction or not of herbivores (net‐cages).Native species showed greater establishment success than alien species across all treatments, regardless of their commonness. Moreover, establishment success of all species was positively affected by disturbance. Aliens showed lower establishment success in undisturbed sites with biocide application. Release of the undisturbed resident community from pathogens by biocide application might explain this lower establishment success of aliens. These findings were consistent for establishment from either seeds or seedlings, although less significantly so for seedlings, suggesting a more important role of pathogens in very early stages of establishment after germination. Herbivore exclusion did play a limited role in seedling establishment success.Synthesis: In conclusion, we found that less disturbed grassland communities exhibited strong biotic resistance to establishment success of species, whether alien or native. However, we also found evidence that alien species may benefit weakly from soilborne enemy release, but that this advantage over native species is lost when the latter are also released by biocide application. Thus, disturbance was the major driver for plant species establishment success and effects of pathogens on alien plant establishment may only play a minor role.
Plant mutualisms with rhizosphere microbiota in introduced versus native ranges
Authors: Shelby Natasha , Duncan Richard P. , van der Putten Wim H. , McGinn Kevin J. , Weser Carolin , Hulme Philip E. 
Published: August 2016

Summary

The performance of introduced plants can be limited by the availability of soil mutualists outside their native range, but how interactions with mutualists differ between ranges is largely unknown. If mutualists are absent, incompatible or parasitic, plants may compensate by investing more in root biomass, adapting to be more selective or by maximizing the benefits associated with the mutualists available.

We tested these hypotheses using seven non‐agricultural species of Trifolium naturalized in New Zealand (NZ). We grew seeds from two native (Spain, UK) and one introduced (NZ) provenance of each species in glasshouse pots inoculated with rhizosphere microbiota collected from conspecifics in each region.

We compared how plant biomass, degree of colonization by rhizobia and arbuscular mycorrhizal fungi (AMF), and the growth benefit associated with each mutualist differed between provenances (native and introduced populations) when grown with soil microbiota from each region. We also tested whether the growth benefit of colonization by mutualists was correlated with the extent to which alien plants were distributed in the introduced range.

Rhizobia colonization was generally lower among introduced relative to native provenances. In NZ soils, 9% of all plants lacked rhizobia and 16% hosted parasitic nodules, whereas in native‐range soils, there was no evidence of parasitism and all but one plant hosted rhizobia. Growth rates as a factor of rhizobia colonization were always highest when plants were grown in soil from their home range. Colonization by AMF was similar for all provenances in all soils but for four out of seven species grown in NZ soils, the level of AMF colonization was negatively correlated with growth rate. In general, introduced provenances did not compensate for lower growth rates or lower mutualist associations by decreasing shoot–root ratios.

Synthesis. Despite differences between introduced and native provenances in their associations with soil mutualists and substantial evidence of parasitism in the introduced range, neither level of colonization by mutualists nor the growth benefit associated with colonization was correlated with the extent of species’ distributions in the introduced range, suggesting mutualist associations are not predictive of invasion success for these species.
Do fine motor skills contribute to early reading development?
Authors: Suggate Sebastian , Pufke Eva , Stoeger Heidrun 
Published: August 2016

BackgroundLittle is known about how fine motor skills (FMS) relate to early literacy skills, especially over and above cognitive variables. Moreover, a lack of distinction between FMS, grapho‐motor and writing skills may have hampered previous work.MethodIn Germany, kindergartners (n = 144, aged 6;1) were recruited before beginning formal reading instruction and were administered a host of FMS, early reading skills and cognitive measures.ResultsAnalyses indicate that FMS related less strongly than grapho‐motor skills to emergent literacy skills. Controlling for grapho‐motor and cognitive skills, FMS did not generally explain unique variance in emergent literacy skills.ConclusionsThe link between reading and motor skills is highly differential. Findings did not suggest that pure FMS played a significant role in early reading development, however, its close cousin grapho‐motor skills – even when devoid of the cognitive knowledge of letters – did.Implications for practiceWhat is already known about this topic

Fine motor skills (FMS) are considered an important school readiness indicator
FMS play a role in cognition and language development
Some research suggests that FMS might be important for reading
What this paper adds

First study to look differentially at FMS and emergent literacy
FMS was considered separately from grapho‐motor and handwriting skill
Links between these motor skills and a broad range of emergent literacy and cognitive skills were investigated
Implications for practice and/or policy

FMS may be important in the development of grapho‐motor skills
Grapho‐motor skills appear, in turn, linked to reading
Fostering children's grapho‐motor skills may be important in kindergarten
Malchish‐Kibalchish: cultural factors in a clinical case
Authors: Tsivinsky Vladimir 
Published: August 2016

AbstractIn this paper, a Jungian understanding of cultural factors influencing individual analysis is illustrated with the case of a patient suffering from panic attacks. The analysis revealed that, in addition to the patient's personal background, the collectivistic attitudes of the Soviet culture, which had a moulding effect on the patient in his childhood and obstructed his individuation, should be taken into account. The concepts of the totalitarian object and the Russian cultural complex encompassing a grandiosity pole and an inferiority pole are used to explore the patient's condition, and the crucial role of creating mutual language with the patient is outlined.
‘You were not born here, so you are classless, you are free!’ Social class and cultural complex in analysis
Authors: Kiehl Emilija 
Published: August 2016

AbstractThe unconscious impact of differences in culture and social class is discussed from the perspective of an analyst practising in London whose ‘foreign accent’ prevents patients from placing her within the social stratifications by which they feel confined. Because she is seen by them as an analyst from both ‘inside’ and ‘outside’ the British psycho‐social fabric and cultural complex, this opens a space in the transference that enables fuller exploration of the impact of the British social class system on patients’ experience of themselves and their world. The paper considers this impact as a trans‐generational trauma of living in a society of sharp socio‐economic divisions based on material property. This is illustrated with the example of a patient who, at the point of moving towards the career to which he aspired, was unable to separate a sense of personal identity from the social class he so desperately wanted to leave behind and walk the long avenue of individuation. The dearth of literature on the subject of class is considered, and the paper concludes that not enough attention is given to class identification in training.
A different gut microbial community between larvae and adults of a wild bumblebee nest (Bombus pascuorum)
Authors: Parmentier Anneleen , Meeus Ivan , Van Nieuwerburgh Filip , Deforce Dieter , Vandamme Peter , Smagghe Guy 
Published: August 2016

AbstractAlthough the gut microbial communities in adult bumblebees and their associated functionalities are widely studied, descriptive data on the larval gut microbiota are still limited. The gut microbiota of a fully sampled wild Bombus pascuorum nest has been characterized, using the multiplexed Illumina MiSeq 16S ribosomal RNA amplicon sequencing technique. The nesters and foragers inhabiting the same nest showed the typical core bacterial sequences and only marginal differences in their characterized gut microbiota. The gut microbial communities within the adult and larval specimens differed strongly, as the typical core gut bacteria in the adult bumblebees are absent in the larval bumblebees. The bacterial communities within the larval gut are dominated by bacterial phylotypes of Enterobacteriaceae and Lactobacillaceae, supplemented with genera belonging to Corynebacteriales and Bacillales. The function of this larval gut microbiota, being different from the adult, remains to be determined.