bluuebunny/crossref_metadata_2025_split huggingface dataset:
pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis
Authors: Plantinga Anna M , Chen Jun , Jenq Robert R , Wu Michael C 
Published: February 2019

Abstract

Motivation
The human microbiome is notoriously variable across individuals, with a wide range of ‘healthy’ microbiomes. Paired and longitudinal studies of the microbiome have become increasingly popular as a way to reduce unmeasured confounding and to increase statistical power by reducing large inter-subject variability. Statistical methods for analyzing such datasets are scarce.

Results
We introduce a paired UniFrac dissimilarity that summarizes within-individual (or within-pair) shifts in microbiome composition and then compares these compositional shifts across individuals (or pairs). This dissimilarity depends on a novel transformation of relative abundances, which we then extend to more than two time points and incorporate into several phylogenetic and non-phylogenetic dissimilarities. The data transformation and resulting dissimilarities may be used in a wide variety of downstream analyses, including ordination analysis and distance-based hypothesis testing. Simulations demonstrate that tests based on these dissimilarities retain appropriate type 1 error and high power. We apply the method in two real datasets.

Availability and implementation
The R package pldist is available on GitHub at https://github.com/aplantin/pldist.

Supplementary information
Supplementary data are available at Bioinformatics online.
Protein model quality assessment using 3D oriented convolutional neural networks
Authors: Pagès Guillaume , Charmettant Benoit , Grudinin Sergei 
Published: February 2019

Abstract

Motivation
Protein model quality assessment (QA) is a crucial and yet open problem in structural bioinformatics. The current best methods for single-model QA typically combine results from different approaches, each based on different input features constructed by experts in the field. Then, the prediction model is trained using a machine-learning algorithm. Recently, with the development of convolutional neural networks (CNN), the training paradigm has changed. In computer vision, the expert-developed features have been significantly overpassed by automatically trained convolutional filters. This motivated us to apply a three-dimensional (3D) CNN to the problem of protein model QA.

Results
We developed Ornate (Oriented Routed Neural network with Automatic Typing)—a novel method for single-model QA. Ornate is a residue-wise scoring function that takes as input 3D density maps. It predicts the local (residue-wise) and the global model quality through a deep 3D CNN. Specifically, Ornate aligns the input density map, corresponding to each residue and its neighborhood, with the backbone topology of this residue. This circumvents the problem of ambiguous orientations of the initial models. Also, Ornate includes automatic identification of atom types and dynamic routing of the data in the network. Established benchmarks (CASP 11 and CASP 12) demonstrate the state-of-the-art performance of our approach among single-model QA methods.

Availability and implementation
The method is available at https://team.inria.fr/nano-d/software/Ornate/. It consists of a C++ executable that transforms molecular structures into volumetric density maps, and a Python code based on the TensorFlow framework for applying the Ornate model to these maps.

Supplementary information
Supplementary data are available at Bioinformatics online.
UnfairDuelMerge: Merging with Even Fewer Moves
Authors: Mergen Sergio L S 
Published: February 2019

Abstract
The merging problem consists of forming an ordered sequence with n elements from two ordered sequences with n1 and n2 elements (where n=n1+n2). One recent development in in-place merging is a minimum storage algorithm (DuelMerge) that requires half the number of moves in average, when compared to other partition-based algorithms. The reduction is achieved by limiting the exchange to blocks with equal sizes, and using a particularly suited exchange method. The algorithm proposed in this paper (UnfairDuelMerge) reduces the number of moves even further, by limiting the exchange to blocks where the left side is one element larger than the right side, and using the floating hole technique to perform the exchange. As its predecessor, the algorithm is stable, in-place and the merge is asymptotically performed with a O(nlognn) runtime. A formal description of the method is provided, as well as an analysis of stability, memory cost and time complexity. Experimental results show that the proposed algorithm outperforms other partition-based solutions when applied directly to merge ordered sequences and when used within MergeSort.
Modular hierarchical and power-law small-world networks bear structural optima for minimal first passage times and cover time
Authors: Maier Benjamin F , Huepe Cristián , Brockmann Dirk 
Published: February 2019

AbstractNetworks that are organized as a hierarchy of modules have been the subject of much research, mainly focusing on algorithms that can extract this community structure from data. The question of why modular hierarchical (MH) organizations are so ubiquitous in nature, however, has received less attention. One hypothesis is that MH topologies may provide an optimal structure for certain dynamical processes. We revisit a MH network model that interpolates, using a single parameter, between two known network topologies: from strong hierarchical modularity to an Erdős–Rényi random connectivity structure. We show that this model displays a similar small-world effect as the Kleinberg model, where the connection probability between nodes decays algebraically with distance. We find that there is an optimal structure, in both models, for which the pair-averaged first passage time (FPT) and mean cover time of a discrete-time random walk are minimal, and provide a heuristic explanation for this effect. Finally, we show that analytic predictions for the pair-averaged FPT based on an effective medium approximation fail to reproduce these minima, which implies that their presence is due to a network structure effect.
Clinical impact of native T1 mapping for detecting myocardial impairment in takotsubo cardiomyopathy
Authors: Aikawa Yukio , Noguchi Teruo , Morita Yoshiaki , Tateishi Emi , Kono Atsushi , Miura Hiroyuki , Komori Yoshiaki , Asaumi Yasuhide , Fukuda Tetsuya , Yasuda Satoshi 
Published: February 2019

Abstract

Aims
To investigate the clinical impact of T1 mapping for detecting myocardial impairment in takotsubo cardiomyopathy (TTC) over time.

Methods and results
In 23 patients with the apical ballooning type of TTC, the following 3T magnetic resonance (MR) examinations were performed at baseline and 3 months after TTC onset: T2-weighted imaging, T2 mapping, native T1 mapping, extracellular volume fraction (ECV), and late gadolinium enhancement. Eight healthy controls underwent the same MR examinations. Serial echocardiography was performed daily for ≥7 days and monthly until 3 months after onset. The median time from onset to MR examination was 7 days. During the acute phase, patients had, relative to controls, higher native T1 (1438 ± 162 vs. 1251 ± 90 ms, P < 0.001), ECV (35 ± 5% vs. 29 ± 4%, P < 0.001), and T2 (90 ± 34 vs. 68 ± 12 ms, P < 0.001) for the entire heart. Per-region analysis showed that higher native T1 and T2 in the basal region were correlated with lower left ventricular ejection fraction (r = −0.599, P = 0.004 and r = −0.598, P = 0.003, respectively). Receiver operator characteristic analysis showed that the area under the curve for native T1 (0.96) was significantly larger than that for T2 (0.86; P = 0.005) but similar to that for ECV (0.92; P = 0.104). At 3-month follow-up, native T1, ECV, and T2 in the apical region remained significantly elevated in all patients with TTC. The number of left ventricular (LV) segments with elevated native T1 (cut-off value 1339 ms) was significantly correlated with prolonged LV wall motion recovery time (r = 0.494, P = 0.027).

Conclusion
Characterization of myocardium with native T1 mapping is a promising method for predicting LV wall motion restoration in TTC.
Famine on the Coast: The Royal Navy and the Relief of Ireland, 1846–1847
Authors: McLean David 
Published: February 2019

Abstract
While the significance of private charity, local organisation and government policy have all been evaluated with respect to Irish famine relief, the role of the Royal Navy in distributing food and assisting ashore has been overlooked within the existing historical literature. Operating from its base at Cork and receiving provisions from Plymouth and Portsmouth, the navy battled against Atlantic storms throughout the winter of 1846–7, and for months thereafter, to supply coastal food depots. It had also to confront a growing lawlessness which placed merchant craft at sea and the movement of aid on shore in peril. Yet the navy was not only a vital means of transport. To assist with medical care, the Admiralty sent surgeons to Ireland who reported at length on the extent of starvation and the worst effects of disease—an initiative which brought the Admiralty into conflict with the authorities in Dublin. Furthermore, naval activities had always to be co-ordinated with the Treasury in London, which had overall responsibility for Irish relief yet often far less understanding of the practicalities of distribution along the south and west coasts of Ireland. The unexplored archival material used allows an original perspective on the efforts made to alleviate the worst effects of Black ’47 and the calamity which overwhelmed so much of Ireland.
The association between self-harm and area-level characteristics in Northern Ireland: an ecological study
Authors: Griffin Eve , Bonner Brendan , Dillon Christina B , O’Hagan Denise , Corcoran Paul 
Published: February 2019

Abstract

Background
Factors contributing to suicidal behaviour are complex and multi-faceted. This study took an ecological approach to examine the association between area-level factors and rates of self-harm in Northern Ireland.

Methods
Data on self-harm presentations to emergency departments (EDs) were obtained from the Northern Ireland Self-harm Registry. The study included residents of Northern Ireland aged 16–64 years. Deprivation was measured using the Northern Ireland Multiple Deprivation Measure 2017. Population density and social fragmentation were calculated using measures from the 2011 census. Associations between area-level factors and self-harm rates were explored using negative binomial regression.

Results
Between 2013 and 2015, 14 477 individuals aged 16–64 years presented to EDs in Northern Ireland following self-harm. The rate of self-harm was 472 per 100 000 and was higher for male residents (478 vs. 467). Self-harm rates were highest in urban areas—680 per 100 000 in Belfast City and 751 per 100 000 in Derry City. Rates of self-harm in Northern Ireland were more than four times higher in the most deprived areas. A positive association with rates of self-harm held for the deprivation domains of employment, crime, education, health and income. There was a moderate association with population density. Some gender differences emerged, with associations with male rates of self-harm more pronounced.

Conclusion
These findings indicate that self-harm rates are highest for those residing in highly deprived areas, where unemployment, crime and low level of education are challenges. Community interventions tailored to meet the needs of specific areas may be effective in reducing suicidal behaviour.
The Application of a Self-Labeling Approach among Military-Connected Adolescents in a Public School Setting
Authors: Kranke Derrick , Barmak Shant , Weiss Eugenia , Dobalian Aram 
Published: February 2019

AbstractThe contextual factors and individual responses to the labeling of military-connected adolescents as “being in a military family” is an understudied yet important phenomenon. Minimal research construes the experience of being in a military family as a label applied to military-connected populations by people in society. However, social environmental factors associated with school setting among military-connected adolescents being in a military family have common components to the process of self-labeling. This article seeks to explore the concept and application of self-labeling by (a) providing a literature review of self-labeling among military-connected adolescents and (b) relying on modified labeling theory to identify any consistencies or potential nuances. The analysis of the process is strictly hypothetical, but could help to account for widely varying responses, sequence of events, and underlying reasons for the behaviors among some military-connected adolescents identified in the literature review and in light of the U.S. protracted military involvement in Iraq and Afghanistan. Authors conclude by highlighting the need for future research to assess the adequacy of this self-labeling framework to ensure the healthy development of military-connected youths.
To jump or not to jump? A multicentre propensity-matched study of sequential vein grafting of the heart
Authors: Skov Jens K , Kimose Hans-Henrik , Greisen Jacob , Jakobsen Carl-Johan 
Published: February 2019

AbstractOBJECTIVESIn this propensity-matched study we investigated the outcome after grafting with either a single vein or a sequential vein grafting strategy. Outcomes were primarily risk of reintervention and death in the short, intermediate and long term (10 years).MATERIALSIn the period from 2000 to 2016, data from 24 742 patients undergoing coronary artery bypass grafting were extracted from the Western Denmark Heart Registry, where data are registered perioperatively. We used a propensity-matched study in which the study groups were matched on parameters primarily from the EuroSCORE. The numbers of patients in both groups after matching were 3380.RESULTSSingle grafts resulted in significantly more postoperative bleeding and were more time-consuming. No differences were seen regarding in-hospital events such as stroke, acute myocardial infarction, dialysis or arrhythmias. After 30 days, patients in the jump graft group showed an increased rate of reintervention due to ischaemia after adjusting for confounding factors [hazard ratio (HR) 2.08, 95% confidence interval 1.01–4.34]. In addition, after adjusting for known confounders, sequential grafts were found to increase the risk of mortality at 6 months (HR 1.51, 95% confidence limits 1.07–2.11) and 5 years (HR 1.23, 95% confidence limits 1.04–1.46).CONCLUSIONSThis propensity-matched analysis suggested, although discretely, that a jump graft as a grafting strategy is associated with a slightly increased risk of mortality and early graft failure and that a single grafting strategy to the coronary arteries should be preferred when feasible.
Variations in 𝔸1 on a Theme of Mohan Kumar
Authors: Wendt Matthias 
Published: February 2019

Abstract
For every prime $p$, Mohan Kumar constructed examples of stably free modules of rank $p$ on suitable $p+1$-dimensional smooth affine varieties. This note discusses how to detect the corresponding unimodular rows by an explicit motivic cohomology group. Using the recent developments in the $\mathbb{A}^1$-obstruction classification of vector bundles, this provides an alternative proof of non-triviality of Mohan Kumar’s stably free modules. The reinterpretation of Mohan Kumar’s examples also allows to produce interesting examples of stably trivial torsors for other algebraic groups.
Data-driven modeling of diabetes care teams using social network analysis
Authors: Ostovari Mina , Steele-Morris Charlotte-Joy , Griffin Paul M , Yu Denny 
Published: February 2019

AbstractObjectiveWe assess working relationships and collaborations within and between diabetes health care provider teams using social network analysis and a multi-scale community detection.Materials and MethodsRetrospective analysis of claims data from a large employer over 2 years was performed. The study cohort contained 827 patients diagnosed with diabetes. The cohort received care from 2567 and 2541 health care providers in the first and second year, respectively. Social network analysis was used to identify networks of health care providers involved in the care of patients with diabetes. A multi-scale community detection was applied to the network to identify groups of health care providers more densely connected. Social network analysis metrics identified influential providers for the overall network and for each community of providers.ResultsCentrality measures identified medical laboratories and mail-order pharmacies as the central providers for the 2 years. Seventy-six percent of the detected communities included primary care physicians, and 97% of the communities included specialists. Pharmacists were detected as central providers in 24% of the communities.DiscussionSocial network analysis measures identified the central providers in the network of diabetes health care providers. These providers could be considered as influencers in the network that could enhance the implication of promotion programs through their access to a large number of patients and providers.ConclusionThe proposed framework provides multi-scale metrics for assessing care team relationships. These metrics can be used by implementation experts to identify influential providers for care interventions and by health service researchers to determine impact of team relationships on patient outcomes.
The Cost of Use of the Emergency Department by Persons With Inflammatory Bowel Disease Living in a Canadian Health Region: A Retrospective Population-Based Study
Authors: Bernstein Charles N , Nugent Zoann , Targownik Laura E , Singh Harminder , Snider Carolyn , Witt Julia 
Published: February 2019

Abstract

Background
We aimed to determine the costs of emergency department (ED) attendance by persons with inflammatory bowel disease (IBD) not admitted to hospital from the ED.

Methods
This was a population-based administrative database study linking the University of Manitoba IBD Epidemiology Database with the Winnipeg Regional Health Authority (WRHA) ED Information Service database. We identified persons with IBD who presented to the ED and were not admitted between January 1, 2009 and March 31, 2012. We then applied costs in Canadian dollars for these visits including an average ED visit cost plus 26% for overhead (total = $508), an average estimated cost of laboratory investigations ($50), and costs for each of radiographic imaging, lower endoscopy and consultation with an internist/gastroenterologist or a surgeon. We tallied the costs of each unique ED presentation. We determined average costs for visits associated with specific consultations or investigations.

Results
One thousand six hundred and eighty-two persons with IBD (4,853 individual visits) attended the ED and did not get hospitalized. The average cost per ED visit by a person with IBD who did not get hospitalized was $650. This resulted in a total expenditure of $3,152,227 on these persons for their ED attendance or $969,916 per year. The visits with the highest mean costs were those associated with an abdominal computerized tomography scan ($979), those associated with surgical consultation ($1019), and those associated with an internist/gastroenterologist consultation ($942).

Conclusion
Better strategies for management of acute issues for persons with IBD that can reduce the use of an ED are needed and can be considerably cost saving.
State Responsibility for Complicity in the Internationally Wrongful Acts of Non-State Armed Groups
Authors: Mackenzie-Gray Scott Richard 
Published: February 2019

Abstract
Determining the responsibility of a state for complicity in the internationally wrongful act of a non-state armed group is an issue that requires analysis from a general international law standpoint. There are numerous ongoing conflicts throughout the world, which are fought by states and non-state armed groups. In the course of such violence, rules of international humanitarian law and international human rights law are breached. There is abundant practice of states rendering aid or assistance to non-state armed groups in their undertakings, whether through the provision of weapons, financial aid, logistical support, intelligence sharing, and/or otherwise. Therefore, when non-state armed groups commit internationally wrongful acts that have been helped by states through such avenues, complicity becomes a pertinent issue. This article addresses and answers the following question: how can the responsibility of a state be established for complicity in the unlawful act(s) of a non-state armed group?
The impact of highways on population redistribution: the role of land development restrictions
Authors: Levkovich Or , Rouwendal Jan , van Ommeren Jos 
Published: February 2019

Abstract
We study the role of land development restrictions for the effects of highway expansion on the spatial distribution of population for the Netherlands. Introducing an IV approach to address multiple endogenous interaction variables, our findings show that new highways accelerated population growth in peripheral areas, but had no apparent effect in suburban municipalities, in line with the presence of development restrictions. Highway expansions caused a ‘leapfrog’ pattern in which suburban growth skipped development-restricted areas and expanded into farther located peripheral areas.
Categories that Blind Us, Categories that Bind Them: The Deployment of the Notion of Vulnerability for Syrian Refugees in Turkey
Authors: Sözer Hande 
Published: February 2019

Abstract
In policy projects on refugees, the concept ‘vulnerable populations’ is treated as self-evident and any policy intervention about vulnerable refugees is seen as inherently positive. Before all else, such interest in ‘the most vulnerable of the vulnerable’ recalls the most virtuous aspects of heavily criticized humanitarianism. The category ‘vulnerable refugee’ has escaped from critical scrutiny by academic literature. The existing studies rely on preconceived notions of vulnerability in line with scholars’ normative predispositions, which makes us blind to already existing vulnerabilities on the ground. This article focuses on how the ‘vulnerable refugee’ category is constructed, appropriated and enacted by self-identified local humanitarian actors regarding Syrian refugees in Turkey. It argues, first, that various humanitarian actors’ notion of ‘vulnerable refugee’ is formed at the crosscurrents of various discourses (e.g. global securitization and global humanitarianism, and nationalism, Islamicism, secularism). Second, local humanitarian actors uniformly present Syrian ‘women and children’ as the most vulnerable; yet, their identification of particular ‘vulnerable women and children’ is informed by and enhances their own gendered, ethnonational, religious, political ideologies. This situation results in leaving out some refugees (as those whose vulnerabilities do not count) while exposing and binding the designated vulnerable into contradictory political ideologies and local faultlines. In the end, Syrian refugees may become not more resilient, but more vulnerable.