bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overdose History is associated with Postdetoxification Treatment Preference for Persons with Opioid use Disorder
Authors: Stein Michael D. , Flori Jessica N. , Risi Megan M. , Conti Micah T. , Anderson Bradley J. , Bailey Genie L. 
Published: July 2017

Background Without aftercare treatment, persons discharged from short-term inpatient detoxification for opioid use disorder are at high risk of relapse. In previous work, those who were recently homeless or had pending legal problems were more likely to prefer residential treatment for aftercare. Here, based on clinical experience, the authors hypothesize that a particular clinical factor, surviving an opioid overdose, will be associated with aftercare preference. Methods Between May and December 2015, the authors surveyed consecutive persons seeking inpatient opioid detoxification. To assess aftercare treatment preference, participants were asked, “If you had unlimited treatment options and all were free, which one would work best for you when you leave here?” To assess overdose history, participants were asked about overdose “since your first drug use,” and “in the last year.” Results Participants’ ( N = 440) mean age was 32.3 (± 8.7) years; 70.7% were male. More than half (51.1%) of participants expressed an aftercare preference for medication-assisted treatment (MAT), 12.7% for outpatient counseling only, 10.7% for residential treatment,18.6% for no formal treatment (Narcotics Anonymous/Alcoholics Anonymous only or a halfway house), and 6.8% did not want any postdetoxification treatment. About 40% reported a history of overdose, and 24.8% reported past year overdose. In the multivariate model, treatment preference was associated with sex ( P < .001), homelessness ( P = .01), and history of drug overdose ( P = .02). Conclusions Although MAT was preferred by the majority of participants, the experience of a nonfatal overdose was associated with the choice of residential treatment as postdetoxification treatment.
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study
Authors: Poux Sylvain , Arighi Cecilia N , Magrane Michele , Bateman Alex , Wei Chih-Hsuan , Lu Zhiyong , Boutet Emmanuel , Bye-A-Jee Hema , Famiglietti Maria Livia , Roechert Bernd , UniProt Consortium The 
Published: July 2017

Abstract

Motivation
Biological knowledgebases, such as UniProtKB/Swiss-Prot, constitute an essential component of daily scientific research by offering distilled, summarized and computable knowledge extracted from the literature by expert curators. While knowledgebases play an increasingly important role in the scientific community, their ability to keep up with the growth of biomedical literature is under scrutiny. Using UniProtKB/Swiss-Prot as a case study, we address this concern via multiple literature triage approaches.

Results
With the assistance of the PubTator text-mining tool, we tagged more than 10 000 articles to assess the ratio of papers relevant for curation. We first show that curators read and evaluate many more papers than they curate, and that measuring the number of curated publications is insufficient to provide a complete picture as demonstrated by the fact that 8000–10 000 papers are curated in UniProt each year while curators evaluate 50 000–70 000 papers per year. We show that 90% of the papers in PubMed are out of the scope of UniProt, that a maximum of 2–3% of the papers indexed in PubMed each year are relevant for UniProt curation, and that, despite appearances, expert curation in UniProt is scalable.

Availability and implementation
UniProt is freely available at http://www.uniprot.org/.

Supplementary information
Supplementary data are available at Bioinformatics online.
cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations
Authors: Faustino Ignacio , Marrink S J 
Published: July 2017

Abstract

Summary
We introduce cgHeliParm, a python program that provides the conformational analysis of Martini-based coarse-grained double strand DNA molecules. The software calculates the helical parameters such as base, base pair and base pair step parameters. cgHeliParm can be used for the analysis of coarse grain Martini molecular dynamics trajectories without transformation into atomistic models.

Availability and implementation
This package works with Python 2.7 on MacOS and Linux. The program is freely available for download from https://github.com/ifaust83/cgheliparm. Together with the main script, the base reference files CG_X_std.lib, a number of examples and R scripts are also available from the same website. A tutorial on the use and application is also available at http://cgmartini.nl/index.php/tutorials-general-introduction/tutorial-martini-dna.

Supplementary information
Supplementary data are available at Bioinformatics online.
MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor
Authors: Ding Jun , Bar-Joseph Ziv 
Published: July 2017

Abstract

Motivation
Profiling of genome wide DNA methylation is now routinely performed when studying development, cancer and several other biological processes. Although Whole genome Bisulfite Sequencing provides high-quality methylation measurements at the resolution of nucleotides, it is relatively costly and so several studies have used alternative methods for such profiling. One of the most widely used low cost alternatives is MeDIP-Seq. However, MeDIP-Seq is biased for CpG enriched regions and thus its results need to be corrected in order to determine accurate methylation levels.

Results
Here we present a method for correcting MeDIP-Seq results based on Random Forest regression. Applying the method to real data from several different tissues (brain, cortex, penis) we show that it achieves almost 4 fold decrease in run time while increasing accuracy by as much as 20% over prior methods developed for this task.

Availability and implementation
MethRaFo is freely available as a python package (with a R wrapper) at https://github.com/phoenixding/methrafo.

Supplementary information
Supplementary data are available at Bioinformatics online.
Common continuum polarization properties: a possible link between proto-planetary nebulae and Type Ia Supernova progenitors
Authors: Cikota Aleksandar , Patat Ferdinando , Cikota Stefan , Spyromilio Jason , Rau Gioia 
Published: July 2017

Abstract
The lines of sight to highly reddened SNe Ia show peculiar continuum polarization curves, growing towards blue wavelengths and peaking at $\lambda _{\text{max}} \lesssim 0.4 \,\mu \mathrm{m}$, like no other sightline to any normal Galactic star. We examined continuum polarization measurements of a sample of asymptotic giant branch (AGB) and post-AGB stars from the literature, finding that some proto-planetary nebulae (PPNe) have polarization curves similar to those observed along SN Ia sightlines. These polarization curves are produced by scattering on circumstellar dust. We discuss the similarity and the possibility that at least some SNe Ia might explode during the post-AGB phase of their binary companion. Furthermore, we speculate that the peculiar SN Ia polarization curves might provide observational support to the core-degenerate progenitor model.
Additive Dose Response Models: Explicit Formulations and the Loewe Additivity Consistency Condition
Authors: Lederer Simone , Dijkstra Tjeerd M. H. , Heskes Tom 
Published: July 2017

AbstractHigh-throughput techniques allow for massive screening of drug combinations. To find combinations that exhibit an interaction effect, one filters for promising compound combinations by comparing to a response without interaction. A common principle for no interaction is Loewe Additivity which is based on the assumption that no compound interacts with itself and that doses of both compounds for a given effect are equivalent. For the model to be consistent, the doses of both compounds have to be proportional. We call this restriction the Loewe Additivity Consistency Condition (LACC). We derive explicit and implicit null reference models from the Loewe Additivity principle that are equivalent when the LACC holds. Of these two formulations, the implicit formulation is the known General Isobole Equation [1], whereas the explicit one is the novel contribution. The LACC is violated in a significant number of cases. In this scenario the models make different predictions. We analyze two data sets of drug screening that are non-interactive [2, 3] and show that the LACC is mostly violated and Loewe Additivity not defined. Further, we compare the measurements of the non-interactive cases of both data sets to the theoretical null reference models in terms of bias and mean squared error. We demonstrate that the explicit formulation of the null reference model leads to smaller mean squared errors than the implicit one and is much faster to compute.
Precision genome editing using synthesis-dependent repair of Cas9-induced DNA breaks
Authors: Paix Alexandre , Folkmann Andrew , Goldman Daniel H , Kulaga Heather , Grzelak Michael , Rasoloson Dominique , Paidemarry Supriya , Green Rachel , Reed Randall , Seydoux Geraldine 
Published: July 2017

AbstractThe RNA-guided DNA endonuclease Cas9 has emerged as a powerful new tool for genome engineering. Cas9 creates targeted double-strand breaks (DSBs) in the genome. Knock-in of specific mutations (precision genome editing) requires homology-directed repair (HDR) of the DSB by synthetic donor DNAs containing the desired edits, but HDR has been reported to be variably efficient. Here, we report that linear DNAs (single and double-stranded) engage in a high-efficiency HDR mechanism that requires only ∼35 nucleotides of homology with the targeted locus to introduce edits ranging from 1 to 1000 nucleotides. We demonstrate the utility of linear donors by introducing fluorescent protein tags in human cells and mouse embryos using PCR fragments. We find that repair is local, polarity-sensitive, and prone to template switching, characteristics that are consistent with gene conversion by synthesis-dependent strand-annealing (SDSA). Our findings enable rational design of synthetic donor DNAs for efficient genome editing.SignificanceGenome editing, the introduction of precise changes in the genome, is revolutionizing our ability to decode the genome. Here we describe a simple method for genome editing that takes advantage of an efficient mechanism for DNA repair called synthesis-dependent strand annealing. We demonstrate that synthetic linear DNAs (ssODNs and PCR fragments) with ∼35bp homology arms function as efficient donors for SDSA repair of Cas9-induced double-strand breaks. Edits from 1 to 1000 base pairs can be introduced in the genome without cloning or selection.
A typology of social venture business model configurations
Authors: Margiono Ari , Zolin Roxanne , Chang Artemis 
Published: July 2017

Purpose
Social ventures are unique and important for society; yet, we know very little about their business models. The purpose of this paper is to: re-conceptualize extant business model frameworks so that they can analyze social ventures; identify the key characteristics of social ventures; and identify the typology of effective social venture business model configurations.

Design/methodology/approach
The paper uses resource dependence theory to make sense of extant business models and borrows from public administration literature to identify key characteristics and different configurations of social venture business models.

Findings
The paper re-conceptualizes business model frameworks as inter-organizational arrangements to cope with external resource dependence; this paper also identifies four key characteristics of social ventures, and develops a social venture business model typology based on these unique key characteristics and extant business model dimensions.

Research limitations/implications
The typology may guide further social venture research, e.g. research on social venture business model creation, on social venture business model innovation, and on social change. Limitations and boundary conditions are discussed in the paper.

Practical implications
The research may further help social entrepreneurs to develop effective business models that meet the social and financial objectives.

Originality/value
The paper offers a novel reconceptualization of traditional business model frameworks, a unique set of key characteristics of social ventures, and a theoretical typology of effective social venture business model configurations.
Misinformation in a riot: a two-step flow view
Authors: Pang Natalie , Ng Joshua 
Published: July 2017

Purpose
Misinformation can have lasting impacts in the management and control of a public emergency. The purpose of this paper is to demonstrate how misinformation flows and how user characteristics can shape such flows in the context of a violent riot in Singapore.

Design/methodology/approach
The authors apply the two-step flow theory and discuss the mixed methods approach involving wrangling Twitter data and descriptive analysis to develop and analyse two corpuses of misinformation related to the riot.

Findings
The findings are mostly consistent with the two-step flow theory, in that misinformation flows to the masses from opinion leaders (as indicated by higher measures such as online social influence and followers/following ratio). In the presence of misinformation, tweets opposing such misinformation may not always come from opinion leaders.

Practical implications
The authors work furthers knowledge about how misinformation goes viral, which provides practical implications to help policymakers and scholars in understanding and managing the dynamics and pitfalls of misinformation during an emergency.

Originality/value
This paper tackles the problem of misinformation in public emergencies using a mixed methods approach and contributes to ongoing theoretical work on managing online misinformation especially in public emergencies and crises.
Large-size color models visualization under 3D paper-based printing
Authors: Yuan Jiangping , Yu Zhaohui , Chen Guangxue , Zhu Ming , Gao Yanfei 
Published: July 2017

Purpose
The purpose of this paper is to study a feasible visualization of large-size three-dimension (3D) color models which are beyond the maximum print size of newest paper-based 3D printer used 3D cutting-bonding frame (3D-CBF) and evaluate the effects of cutting angle and layout method on printing time of designed models.

Design/methodology/approach
Sixteen models, including cuboid model, cylinder model, hole model and sphere model with different shape features, were divided into two symmetric parts and printed by the Mcor IRIS HD 3D printer. Before printing, two sub-parts were rearranged in one of three layout methods. Nine scaled sizes of original models were printed to find the quantitative relationship between printing time and scale values in each type. For the 0.3 times of original models, six cutting angles were evaluated in detail.

Findings
The correlation function about colorization time and printed pages was proposed. Based on 3D-CBF, the correlation between printing time and scale size is statistically defined. Optimization parameters of designed parts visualization about cutting angel and layout method were found, even if their statistical results were difficult to model their effects on printing time of specimens.

Research limitations/implications
The research is comparative and limited to the special models and used procedures.

Originality/value
The paper provides a feasible visualization and printing speed optimization methods for the further industrialization of 3D paper-based printing technology in cultural creative field.
Twin-wire welding based additive manufacturing (TWAM): manufacture of functionally gradient objects
Authors: M. Adinarayanappa Somashekara , Simhambhatla Suryakumar 
Published: July 2017

Purpose
Twin-wire welding-based additive manufacturing (TWAM) is a unique process which uses gas metal arc welding (GMAW)-based twin-wire weld-deposition to create functionally gradient materials (FGMs). Presented study aims to focus on creating metallic objects with a hardness gradient using GMAW of twin-wire weld deposition setup.

Design/methodology/approach
By using dissimilar filler wires in twin-wire weld-deposition, it is possible to create metallic objects with varying hardness. This is made possible by individually controlling the proportion of each filler wire used. ER70S-6 and ER110S-G are the two filler wires used for the study; the former has lower hardness than the latter. In the current study, methodology and various experiments carried out to identify the suitable process parameters at a given location for a desired variation of hardness have been presented. A predictive model for obtaining the wire speed of the filler wires required for a desired value of hardness was also created. Subsequently, sample parts with gradient in various directions have been fabricated.

Findings
For dissimilar twin-wire weld-deposition used here, it is observed that the resultant hardness is in the volumetric proportion of the hardness of the individual filler wires. This aids the fabrication of FGMs using arc based weld-deposition with localized control of hardness, achieved through the control of the ratio of wire speeds of the individual filler wires. Four sample parts were fabricated to demonstrate the concept of realizing FGMs through TWAM. The fabricated parts showed good match with the desired hardness variation.

Research limitations/implications
This paper successfully presents the capability of TWAM for creating gradient metallic objects with varying hardness. Although developed using ER70S-6 and ER110S-G filler wire combination, the methodology can be extended for other filler wire combinations too for creating FGMs

Originality/value
GMAW-based twin-wire welding for additive manufacturing is a novel process which uses dissimilar filler wires for creating FGMs. This paper describes methodology of the same followed by illustration of parts created with bi-directional hardness gradient.
The comprehensibility of pantomimes produced by people with aphasia
Authors: van Nispen Karin , Mieke W.M.E. , van de Sandt‐Koenderman E. , Krahmer Emiel 
Published: July 2017

AbstractBackgroundPeople with aphasia (PWA) use pantomime, gesture in absence of speech, differently from non‐brain‐damaged people (NBDP).AimsTo evaluate through an exploratory study the comprehensibility of PWA's pantomimes and to find out whether they can compensate for information PWA are unable to convey in speech.Methods & ProceduresA total of 273 naïve observers participated in one of two judgement tasks: forced‐choice and open‐ended questions. These were used to determine the comprehensibility of pantomimes produced to depict objects by PWA as compared with NBDP. Furthermore, we compared the information conveyed in pantomime with the information in speech. We looked into factors influencing pantomime's comprehensibility: individual factors, manner of depiction and information needed to be depicted.Outcome & ResultsAlthough comprehensibility scores for PWA's pantomimes were lower than for those produced by NBDP, all PWA were able to convey information in pantomime that they could not convey in speech. Comprehensibility of pantomimes was predicted by apraxia. The inability to use the right hand related to slightly lower comprehensibility scores. Objects for which individuals depicted its use were best understood.Conclusion & ImplicationsOur findings highlight the potential benefit of pantomime for clinical practice. Pantomimes, even though sometimes impaired, can convey information that PWA cannot convey in speech. Clinical implications are discussed.
Response to Vogelstein: How the 2012 AAP Task Force on circumcision went wrong
Authors: Van Howe Robert S. 
Published: July 2017

AbstractVogelstein cautions medical organizations against jumping into the fray of controversial issues, yet proffers the 2012 American Academy of Pediatrics' Task Force policy position on infant male circumcision as ‘an appropriate use of position‐statements.’ Only a scratch below the surface of this policy statement uncovers the Task Force's failure to consider Vogelstein's many caveats. The Task Force supported the cultural practice by putting undeserved emphasis on questionable scientific data, while ignoring or underplaying the importance of valid contrary scientific data. Without any effort to quantitatively assess the risk/benefit balance, the Task Force concluded the benefits of circumcision outweighed the risks, while acknowledging that the incidence of risks was unknown. This Task Force differed from other Academy policy‐forming panels by ignoring the Academy's standard quality measures and by not appointing members with extensive research experience, extensive publications, or recognized expertise directly related to this topic. Despite nearly 100 publications available at the time addressing the substantial ethical issues associated with infant male circumcision, the Task Force chose to ignore the ethical controversy. They merely stated, with minimal justification, the opinion of one of the Task Force members that the practice of infant male circumcision is morally permissible. The release of the report has fostered an explosion of academic discussion on the ethics of infant male circumcision with a number of national medical organizations now decrying the practice as a human rights violation.
Gender differences in preferences for psychological treatment, coping strategies, and triggers to help‐seeking
Authors: Liddon Louise , Kingerlee Roger , Barry John A. 
Published: July 2017

ObjectiveThere is some evidence that men and women deal with stress in different ways; for example, a meta‐analysis found that women prefer to focus on emotions as a coping strategy more than men do. However, sex differences in preferences for therapy is a subject little explored.DesignA cross‐sectional online survey.MethodParticipants (115 men and 232 women) were recruited via relevant websites and social media. The survey described therapies and asked participants how much they liked each. Their coping strategies and help‐seeking behaviour were assessed too.ResultsSurvey data were analysed using multiple linear regression. After familywise adjustment of the alpha for multiple testing to p < .0125, and controlling for other relevant variables, men liked support groups more than women did (β = −.163, p < .010), used sex or pornography to cope with stress more than women did (Exp[B] = .280, p < .0002), and thought that there is a lack of male‐friendly options more than women did (Exp[B] = .264, p < .002). The majority of participants expressed no preference for the sex of their therapist, but of those who did, men were only slightly more likely to prefer a female therapist whereas women were much more likely to prefer females (p < .0004). Even after familywise adjustment, there were still more significant findings than would be expected by chance (p < .001, two‐tailed).ConclusionsAlthough there are many similarities in the preferences of men and women regarding therapy, our findings support the hypothesis that men and women show statistically significant differences of relevance to clinical psychologists.Practitioner points

Men are less inclined than women to seek help for psychological issues

This study demonstrates that men and women show significant differences in some aspects of therapy, coping behaviour, and help‐seeking

It is possible that men would be more inclined to seek help if therapies catered more for men's preferences

Practitioners can learn to improve the success of their practice by taking the gender of clients into account