bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics
Authors: Bergauer Kristin , Fernandez-Guerra Antonio , Garcia Juan A. L. , Sprenger Richard R. , Stepanauskas Ramunas , Pachiadaki Maria G. , Jensen Ole N. , Herndl Gerhard J. 
Published: December 2017

Significance
Circumstantial evidence indicates that especially deep-ocean heterotrophic microbes rely on particulate organic matter sinking through the oceanic water column and being solubilized to dissolved organic matter (DOM) prior to utilization rather than on direct uptake of the vast pool of DOM in the deep ocean. Comparative metaproteomics allowed us to elucidate the vertical distribution and abundance of microbially mediated transport processes and thus the uptake of solutes throughout the oceanic water column. Taken together, our data suggest that, while the phylogenetic composition of the microbial community is depth stratified, the composition and substrate specificities of transporters considered in this study are ubiquitous while their relative abundance changes with depth.
Remote electrochemical modulation of pK
a
in a rotaxane by co-conformational allostery
Authors: Ragazzon Giulio , Schäfer Christian , Franchi Paola , Silvi Serena , Colasson Benoit , Lucarini Marco , Credi Alberto 
Published: December 2017

Significance
Rotaxanes are species in which a macrocyclic molecule—the ring—is interlocked with a dumbbell-shaped component—the axle. The translational motion of the ring along the axle provides the basis for constructing molecular machinery. In this paper we show that such a dynamic process enables the transfer of chemical information between two distant sites; as a result, the acidity of one site can be reversibly modulated by redox switching at the other site. Possibilities emerge not only for the rational design of species with tailor-made acid–base properties but also for the development of model systems to understand some of Nature’s most effective regulatory mechanisms—namely, allostery and proton-coupled electron transfer.
Controlled molecular self-assembly of complex three-dimensional structures in soft materials
Authors: Huang Changjin , Quinn David , Suresh Subra , Hsia K. Jimmy 
Published: December 2017

Significance
We demonstrate a unique growth mode to form complex 3D shapes in hydrogels by invoking the bottom-up approach analogous to cell enlargement and proliferation found in living animal tissues and plants. For this purpose, we control the oxygen concentration to modulate polymerization of monomers in porous hydrogel, wherein postgelation networks continue to expand––a process similar to the growth of living tissues in nature. The applicability of this experimental technique to a variety of situations in biology is demonstrated with several examples of the formation of complex 3D architectures through successful biomimetics of tissue morphogenesis in both animals and plants. These results offer possibilities for a diverse set of applications in tissue engineering, soft robotics, and flexible electronics.
Hydrodynamics of electrons in graphene
Authors: Lucas Andrew , Fong Kin Chung 
Published: December 2017

Abstract
Generic interacting many-body quantum systems are believed to behave as classical fluids on long time and length scales. Due to rapid progress in growing exceptionally pure crystals, we are now able to experimentally observe this collective motion of electrons in solid-state systems, including graphene. We present a review of recent progress in understanding the hydrodynamic limit of electronic motion in graphene, written for physicists from diverse communities. We begin by discussing the ‘phase diagram’ of graphene, and the inevitable presence of impurities and phonons in experimental systems. We derive hydrodynamics, both from a phenomenological perspective and using kinetic theory. We then describe how hydrodynamic electron flow is visible in electronic transport measurements. Although we focus on graphene in this review, the broader framework naturally generalizes to other materials. We assume only basic knowledge of condensed matter physics, and no prior knowledge of hydrodynamics.
BS-virus-finder: virus integration calling using bisulfite sequencing data
Authors: Gao Shengjie , Hu Xuesong , Xu Fengping , Gao Changduo , Xiong Kai , Zhao Xiao , Chen Haixiao , Zhao Shancen , Wang Mengyao , Fu Dongke , Zhao Xiaohui , Bai Jie , Mao Likai , Li Bo , Wu Song , Wang Jian , Li Shengbin , Yang Huangming , Bolund Lars , Pedersen Christian N S 
Published: December 2017

Abstract

Background
DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data.

Findings
We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR_015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF.

Conclusions
BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data.
Draft genome of the milu (Elaphurus davidianus)
Authors: Zhang Chenzhou , Chen Lei , Zhou Yang , Wang Kun , Chemnick Leona G , Ryder Oliver A , Wang Wen , Zhang Guojie , Qiu Qiang 
Published: December 2017

Abstract

Background
Milu, also known as Père David's deer (Elaphurus davidianus), was widely distributed in East Asia but recently experienced a severe bottleneck. Only 18 survived by the end of the 19th century, and the current population of 4500 individuals was propagated from just 11 kept by the 11th British Duke of Bedford. This species is known for its distinguishable appearance, the driving force behind which is still a mystery. To aid efforts to explore these phenomena, we constructed a draft genome of the species.

Findings
In total, we generated 321.86 gigabases (Gb) of raw DNA sequence from whole-genome sequencing of a male milu deer using an Illumina HiSeq 2000 platform. Assembly yielded a final genome with a scaffold N50 size of 3.03 megabases (Mb) and a total length of 2.52 Gb. Moreover, we identified 20 125 protein-coding genes and 988.1 Mb of repetitive sequences. In addition, homology-based searches detected 280 rRNA, 1335 miRNA, 1441 snRNA, and 893 tRNA sequences in the milu genome. The divergence time between E. davidianus and Bos taurus was estimated to be about 28.20 million years ago (Mya). We identified 167 species-specific genes and 293 expanded gene families in the milu lineage.

Conclusions
We report the first reference genome of milu, which will provide a valuable resource for studying the species' demographic history of severe bottleneck and the genetic mechanism(s) of special phenotypic evolution.
Identification of high-mass X-ray binaries selected from XMM–Newton observations of the LMC
Authors: van Jaarsveld N , Buckley D A H , McBride V A , Haberl F , Vasilopoulos G , Maitra C , Udalski A , Miszalski B 
Published: December 2017

Abstract
The Large Magellanic Cloud (LMC) currently hosts around 23 high-mass X-ray binaries (HMXBs) of which most are Be/X-ray binaries. The LMC XMM–Newton survey provided follow-up observations of previously known X-ray sources that were likely HMXBs, as well as identifying new HMXB candidates. In total, 19 candidate HMXBs were selected based on their X-ray hardness ratios. In this paper we present red and blue optical spectroscopy, obtained with Southern African Large Telescope and the South African Astronomical Observatory 1.9-m telescope, plus a timing analysis of the long-term optical light curves from OGLE to confirm the nature of these candidates. We find that nine of the candidates are new Be/X-ray binaries, substantially increasing the LMC Be/X-ray binary population. Furthermore, we present the optical properties of these new systems, both individually and as a group of all the BeXBs identified by the XMM–Newton survey of the LMC.
Cosmic homogeneity: a spectroscopic and model-independent measurement
Authors: Gonçalves R S , Carvalho G C , Bengaly Jr C A P , Carvalho J C , Bernui A , Alcaniz J S , Maartens R 
Published: December 2017

Abstract
Cosmology relies on the Cosmological Principle, i.e. the hypothesis that the Universe is homogeneous and isotropic on large scales. This implies in particular that the counts of galaxies should approach a homogeneous scaling with volume at sufficiently large scales. Testing homogeneity is crucial to obtain a correct interpretation of the physical assumptions underlying the current cosmic acceleration and structure formation of the Universe. In this letter, we use the Baryon Oscillation Spectroscopic Survey to make the first spectroscopic and model-independent measurements of the angular homogeneity scale θh. Applying four statistical estimators, we show that the angular distribution of galaxies in the range 0.46 &lt; z &lt; 0.62 is consistent with homogeneity at large scales, and that θh varies with redshift, indicating a smoother Universe in the past. These results are in agreement with the foundations of the standard cosmological paradigm.
Social Innovation Excubator
Authors: Castro-Spila Javier 
Published: December 2017

Purpose
The purpose of this paper is to propose a new framework for developing social innovation competencies in social sciences within the agenda of the Relational University. It explores the educational strategy promoted by the Social Innovation Excubator (SIE), an experimental social sciences lab that provides students with a work-based learning scenario focusing on the solution of social problems.

Design/methodology/approach
This conceptual paper explores a new learning strategy to promote the Relational University. This exploration designs an experimental infrastructure named SIE. This infrastructure promotes the link between work-based learning and social innovation to develop four key competencies: heuristic, epistemic, relational and experimental skills.

Findings
There is little attention in the literature about work-based learning and social innovation. The conceptual framework provides a program on Social Innovation Capitalization (SIC) in the framework of the SIE. This framework provides a process of four phases to prototype social innovations: exploration, experimentation, exploitation and evaluation as a process to boost social innovation skills.

Research limitations/implications
The conceptual framework of Relational University is an innovative and integrative model (companies, social organizations, public sector and civil society) that develops a work-based learning strategy through SIE infrastructure. The SIE has a strong implication for social sciences developing an experimental space to explore, exploit and evaluate local social problems.

Practical implications
The SIE infrastructure and the SIC program promotes a new strategy in social sciences to boost employability (new competencies), entrepreneurship (pilot social organizations) and intra-entrepreneurship (social innovation in organizations).

Originality/value
This paper proposes a conceptual and empirical framework to develop the Relational University through a new learning strategy linking work-based learning and social innovation. This practical framework covers a lack in the work-based learning perspective opening a new line of research linked to social innovation.
Integrated sustainability reporting at HNE Eberswalde – a practice report
Authors: Kräusche Kerstin , Pilz Stefanie 
Published: December 2017

Purpose
The purpose of this paper is to present the development of an integrated sustainability reporting. In this paper success criteria are named and empirical values when dealingwith specific challenges are formulated. The focus is on the development of criteria for reporting, the involvement of university members and quality assurance.

Design/methodology/approach
The voluntary and compulsory reporting requirements of German universities are presented, and the concept for integrated reporting is developed from them. Possible criteria catalogues for the evaluation of sustainable development are presented and evaluated. However, the focus is on the practical experience that the university has made in the launch and implementation of an integrated sustainability reporting – both in terms of content and organisation.

Findings
A prerequisite for the preparation of a sustainability reporting is that the university develops a common understanding of sustainability and formulates objectives. This results in a structure for the reporting which is self-explanatory. For the project management before, during and after the reporting, it is indispensable to structure the work sequence (data collection, data analysis, text editor, etc) and to ensure a process-accompanying communication. Participation by all university groups in reporting is necessary.

Practical implications
Universities have a special responsibility for the sustainable development of society. To be accountable for their activities in the field of sustainability, the practical report provides a handbook on which universities can set up their own sustainability reporting.

Originality/value
At German universities, there is a lively discussion on how to define a criteria catalogue to report objectively on sustainability. The Eberswalde University for Sustainable Development is involved in the discussion and, at the same time, sets a good example. This article describes the practical implementation of the Sustainability Report.
A spatial and organisational analysis of Asian panethnic association in Perth, Western Australia
Authors: Stevens Catriona 
Published: December 2017

Purpose“Asian” is an aggregating descriptive term commonly used in Australian media, politics and everyday speech to describe people of diverse backgrounds. The purpose of this paper is to question the extent to which “Asian” Australian residents living in Perth, Western Australia demonstrate spatial or organisational panethnic association.Design/methodology/approachThe paper analyses quantitative population data from the 2011 Census using GIS to visualise the spatial residential distribution of individuals born in Asian countries and individuals with Chinese ancestry within the Perth metropolitan area. The paper further uses qualitative data drawn from fieldwork conducted in Perth to consider evidence of organisational panethnic association.FindingsFor first generation migrants there is currently little spatial or organisation evidence of “Asian” panethnic association in Perth. Migrants from different ethno-national backgrounds exhibit very different residential patterns. Incipient ethnoburbs are developing that appear to be based on ethnicity rather than panethnicity. Migrant organisation in Perth is likewise arranged primarily on the basis of ethnicity although some panethnic work is observed.Research limitations/implicationsFindings indicate trends towards ethnic residential segregation. Further longitudinal research could expand upon these findings. Qualitative research could determine causes of segregation and implications of (pan)ethnic identities, and explore how individuals from Asian countries respond to the dominant linguistic aggregation of “Asians”.Originality/valueThis paper offers an original analysis of a common frame of reference that has received little critical attention in the Australian context. It applies the framework of Asian panethnicity developed in the USA and finds it wanting, highlighting an inconsistency between the racialised language used in Australia to describe migrants from Asia and the ways these migrants associate.
Young-adults NEET in Italy: orientations and strategies toward the future
Authors: Gaspani Fabio 
Published: December 2017

PurposeThe purpose of this paper is to examine the relation with the future of young-adults Not in Education, Employment or Training (NEET) in Italy. The study of temporal experiences allows to understand how subjects represent their own condition and construct their biographies in an age of uncertainty.Design/methodology/approachThe study follows a qualitative approach to allow participants to express their own experiences and representations through narratives. The 12 cases considered are illustrative of the different orientations detected in the group of 36 young people involved in the research.FindingsYoung-adults NEET have problems in acquiring a recognized social status and in designing future orientations. The difficulties to project themselves in time hinder the attainment of a sense of biographical continuity as well as the process of identity construction, which tends to be increasingly detached from the planning sphere.Originality/valueThe study adds to the literature on the issue of young people NEET, contributing to differentiate the social conditions of this group by referring to their experiences, social belongings and resources. The analysis sheds new light on the agency of young people, that conceive biographical strategies in relation to the scenarios they envisage.
Multiple sexual violence prevention tools: doses and boosters
Authors: Banyard Victoria , Potter Sharyn J. , Cares Alison C. , Williams Linda M. , Moynihan Mary M. , Stapleton Jane G. 
Published: December 2017

Purpose
Sexual violence prevention programs on college campuses have proliferated in recent years. While research has also increased, a number of questions remain unanswered that could assist campus administrators in making evidence-based decisions about implementation of prevention efforts. To that end, the field of prevention science has highlighted the need to examine the utility of booster sessions for enhancing prevention education. The purpose of this paper is to examine how two methods of prevention delivery – small group educational workshops and a community-wide social marketing campaign (SMC) – worked separately and together to promote attitude change related to sexual violence among college students.

Design/methodology/approach
The two-part study was conducted at two universities. Participants were from successive cohorts of first year students and randomly assigned to participate in a bystander based in-person sexual violence prevention program or a control group. Participants were later exposed to a bystander based sexual violence prevention SMC either before or after a follow-up survey. Analyses investigated if attitudes varied by exposure group (program only, SMC only, both program and SMC, no prevention exposure).

Findings
Results revealed benefits of the SMC as a booster for attitude changes related to being an active bystander to prevent sexual violence. Further, students who first participated in the program showed enhanced attitude effects related to the SMC.

Originality/value
This is the first study to look at the combination of effects of different sexual violence prevention tools on student attitudes. It also showcases a method for how to investigate if prevention tools work separately and together.
Patients’ attitude toward diabetes mellitus screening in Thai dental clinics
Authors: Tantipoj Chanita , Hiransuthikul Narin , Supa-amornkul Sirirak , Lohsoonthorn Vitool , Piboonniyom Khovidhunkit Siribang-on 
Published: December 2017

Purpose
Diabetes mellitus (DM) is an important health problem throughout the world. Association between DM and oral diseases has been reported and dental clinic is indicated to be one of the suitable venues for the screening of DM. The purpose of this paper is to determine patients’ attitude toward DM screening in dental clinics.

Design/methodology/approach
The anonymous, self-administered questionnaires of five-point response scale questions were distributed to convenience samples of adult patients (⩾25 years) attending one of the dental settings. These dental settings were divided into the university/hospital-based dental clinics (encompassing two university-based and five hospital-based dental clinics) or the private dental clinics (encompassing two private, and one special (after office hour) clinic of a faculty of dentistry). The questions could be categorized into three groups regarding importance, willingness, and agreement of DM screening in dental settings. Results are presented as percentage by respondents based upon the number of responses for each question. The favorable outcomes which were defined as responses of either scale of 4 or 5 were also summarized according to dental settings. The χ2 test for comparison was used to compare the favorable outcomes between the two settings.

Findings
A total of 601 completed questionnaires were collected; 394 from university/hospital-based dental clinics and 207 from two private clinics and a special (after office hour) clinic of a faculty of dentistry. Overall, the majority of respondents in both university/hospital-based and private practice settings felt that it is important to have a dentist conduct a screening (84.8 vs 79.5 percent). The majority of patients in both groups were willing to receive blood pressure examination (95.0 vs 92.0 percent), weight and height measurements (94.7 vs 94.0 percent), saliva/oral fluid investigation (86.4 and 86.9 percent) and finger-stick blood test (83.8 vs 83.9 percent). More than 75 percent of all respondents agreed with diabetes screening in dental clinics.

Originality/value
The majority of respondents supported the screening of DM in dental settings and they were willing to have a screening test by the dentist. Patient acceptance is an important key to be successful in the screening of DM in dental settings.
Azathioprine monotherapy in autoimmune blistering diseases: A feasible option for mild to moderate cases
Authors: Kakuta Risa , Yamagami Jun , Funakoshi Takeru , Takahashi Hayato , Ohyama Manabu , Amagai Masayuki 
Published: December 2017

AbstractAzathioprine (AZP) is used as a corticosteroid (CS)‐sparing medication to treat autoimmune blistering diseases. In this study, we examined the efficacy of AZP and the feasibility of using AZP monotherapy (without CS) to treat pemphigus and pemphigoid. We performed a retrospective study of 10 Japanese patients (seven with pemphigus and three with pemphigoid) with mild to moderate disease activity who had been treated using AZP. The treatment efficacy was evaluated based on decreases in the disease activity scores and autoantibody titers. The results demonstrate that seven out of 10 cases (70%) were treated successfully using AZP monotherapy with no severe adverse effects. The disease activity scores of the successfully‐treated patients decreased to zero after 1–37.5 months (average, 11.9) and the average disease activity scores in these cases decreased significantly at 2 months (38.2 ± 36.6%) compared with the scores of the three patients who required additional systemic CS therapy (77.5 ± 3.5%) (P < 0.05). Additionally, the autoantibody titers of five cases treated successfully using AZP decreased by half at 6 months. In conclusion, our findings suggest that AZP monotherapy is a viable treatment option for mild to moderate pemphigus and pemphigoid.