bluuebunny/crossref_metadata_2025_split huggingface dataset:
The EU's New Approach To the Two-State Solution in the Israeli-Palestinian Conflict: A Paradigm Shift or PR Exercise?
Authors: HARPAZ GUY 
Published: April 2017

AbstractThe EU's consistent policy towards the Israeli-Palestinian conflict has been that Israel's presence in the West Bank, East Jerusalem, the Gaza Strip (prior to the 2005 disengagement) and the Golan Heights is subject to the laws of belligerent occupation, that any purported Israeli annexation is illegal and null and void, that Israel's settlements in the Territories are in breach of public international law and constitute a serious obstacle to peace, and that Israel and Palestine should settle their conflict on the basis of public international law and through the two-state solution. In recent years the EU attempted to concretize this policy through its trade and trade-related agreements with Israel, withholding the benefits of EU-Israeli co-operation from companies and research institutions based in the Territories or operating therein, as well as from products produced therein (the New Approach). Thus, from the EU perception, the New Approach towards the long-standing conflict and its reliance on international law may be seen as an instrument to reinforce internal and external legitimacy, buttress identity cohesiveness and as a manifestation of its more robust effectiveness. But this article seeks to conduct a more careful and balanced analysis of the New Approach and in doing so to reveal that the EU's (almost) exclusive focus on non-governmental entities, such as corporations situated in the Territories, and on Territories’ products, is misplaced in terms of public international law and effectiveness. The New Approach's deficiencies,in abstractoandin concreto, as evaluated in this article, are likely to prevent it from serving as a paradigm shift in EU-Israel relations.
Maternal mind–mindedness and toddler behavior problems: The moderating role of maternal trauma and posttraumatic stress
Authors: Easterbrooks M. Ann , Crossman Molly K. , Caruso Alessandra , Raskin Maryna , Miranda-Julian Claudia 
Published: April 2017

AbstractMaternal mind–mindedness (MM) reflects a caregiver's tendency to view a child as an individual with an independent mind. Research has linked higher MM with more favorable parenting and child adaptation. The aim of this study was to examine whether MM was associated with toddlers’ behavior problems and competence, and the moderating role of trauma and posttraumatic stress disorder (PTSD) in a sample (N = 212) of adolescent mothers and their toddlers. MM was coded from maternal utterances during free play; mothers completed the University of California at Los Angeles Trauma and Posttraumatic Stress Disorder Reaction Index and reported on children's behavior problems and competence using the Brief Infant–Toddler Social and Emotional Assessment. The majority of mothers (84%) experienced trauma; 45% of these mothers met criteria for partial or full PTSD. Trauma was related to greater behavior problems, and PTSD moderated MM–child functioning relations. When mothers experienced full PTSD, there was no relation between MM and behavior problems. With child competence, when compared to children of mothers with no trauma exposure, children of mothers experiencing partial PTSD symptoms were more likely to have delays in competence when mothers made more MM comments. Results are discussed in light of how MM, in the context of trauma and PTSD, may affect parenting.
Paediatric-onset coronary artery anomalies in pregnancy: a single-centre experience and systematic literature review
Authors: Keir Michelle , Bhagra Catriona , Vatenmakher Debra , Arancibia-Galilea Francisca , Jansen Katrijn , Toh Norihisa , Silversides Candice K. , Colman Jack , Siu Samuel C. , Sermer Mathew , Crean Andrew M. , Wald Rachel M. 
Published: April 2017

AbstractObjectivesIndividuals with childhood-onset coronary artery anomalies are at increased risk of lifelong complications. Although pregnancy is thought to confer additional risk, a few data are available regarding outcomes in this group of women. We sought to define outcomes of pregnancy in this unique population.MethodsWe performed a retrospective survey of women with paediatric-onset coronary anomalies and pregnancy in our institution, combined with a systematic review of published cases. We defined paediatric-onset coronary artery anomalies as congenital coronary anomalies and inflammatory arteriopathies of childhood that cause coronary aneurysms. Major cardiovascular events were defined as pulmonary oedema, sustained arrhythmia requiring treatment, stroke, myocardial infarction, cardiac arrest, or death.ResultsA total of 25 surveys were mailed, and 20 were returned (80% response rate). We included 46 articles from the literature, which described cardiovascular outcomes in 82 women (138 pregnancies). These data were amalgamated for a total of 102 women and 194 pregnancies; 59% of women were known to have paediatric-onset coronary artery anomalies before pregnancy. In 23%, the anomaly was unmasked during or shortly after pregnancy. The remainder, 18%, was diagnosed later in life. Major cardiovascular events occurred in 14 women (14%) and included heart failure (n=5, 5%), myocardial infarction (n=7, 7%), maternal death (n=2, 2%), cardiac arrest secondary to ventricular fibrillation (n=1, 1%), and stroke (n=1, 1%). The majority of maternal events (13/14, 93%) occurred in women with no previous diagnosis of coronary disease.ConclusionsWomen with paediatric-onset coronary artery anomalies have a 14% risk of adverse cardiovascular events in pregnancy, indicating the need for careful assessment and close follow-up. Prospective, multicentre studies are required to better define risk and predictors of complications during pregnancy.
Unit cost of common illness management: a comparison between a primary care unit and a community pharmacy in Thailand
Authors: Saramunee Kritsanee , Ploylearmsang Chanuttha , Chaiyasong Surasak , Phimarn Wiraphol , Sookaneknun Phayom 
Published: April 2017

AimThis study was to perform unit cost analysis of managing common illnesses comparing between a primary care unit (PCU) and a community pharmacy.BackgroundPCU is a key point of access for primary care in Thailand. Although a community pharmacy is an ideal setting, it has not been successfully incorporated in Thailand's health service. Common illnesses are encountered everyday by community pharmacists, an appropriate compensation for this service has not been established.MethodsA primary care service of one educational institution was a study site. Eight common illnesses were emphasised. Patient visits were observed, prospectively at community pharmacy and retrospectively at PCU, during August to October 2013. Labour and material costs related to management of common illnesses were recorded. Total cost divided by total patient visits determined the unit cost. For the community pharmacy, patients were followed up after 3–14 days of visit to evaluate the effectiveness. Sensitivity analysis was performed by varying direct medical cost at ±10–30%.FindingsAt the community pharmacy, community pharmacists performed multiple tasks including interviewing and assessing patients, choosing an appropriate treatment and dispensing. Of 9141 visits, 775 (8.5%) with common illnesses were included. Upper respiratory disorder was found the highest 41.9% (325/755). Unit cost of treatment ranged from 54.16 baht (£1.18) for pain to 82.71 baht (£1.80) for skin disorder. Two-thirds of pharmacy visits (77.9%, 539/692) reported complete recovery. Managing common illnesses at the PCU was performed by nurse assistants, nurses, doctors and pharmacists. Of 6701 patient visits to the PCU, 1545 (23.1%) visits were at least one of the eight illnesses. Upper respiratory disorder was the majority, 53.0% (771/1454). Unit cost of treatment ranged from 85.39 baht (£1.86) for eye/ear to 245.93 baht (£5.36) for sexual health. Managing common illness at a community pharmacy shows satisfactory effectiveness with lower unit cost.
Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis
Authors: Hao Xiaoke , Li Chanxiu , Yan Jingwen , Yao Xiaohui , Risacher Shannon L , Saykin Andrew J , Shen Li , Zhang Daoqiang ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: April 2017

Abstract

Motivation
Neuroimaging genetics identifies the relationships between genetic variants (i.e., the single nucleotide polymorphisms) and brain imaging data to reveal the associations from genotypes to phenotypes. So far, most existing machine-learning approaches are widely used to detect the effective associations between genetic variants and brain imaging data at one time-point. However, those associations are based on static phenotypes and ignore the temporal dynamics of the phenotypical changes. The phenotypes across multiple time-points may exhibit temporal patterns that can be used to facilitate the understanding of the degenerative process. In this article, we propose a novel temporally constrained group sparse canonical correlation analysis (TGSCCA) framework to identify genetic associations with longitudinal phenotypic markers.

Results
The proposed TGSCCA method is able to capture the temporal changes in brain from longitudinal phenotypes by incorporating the fused penalty, which requires that the differences between two consecutive canonical weight vectors from adjacent time-points should be small. A new efficient optimization algorithm is designed to solve the objective function. Furthermore, we demonstrate the effectiveness of our algorithm on both synthetic and real data (i.e., the Alzheimer’s Disease Neuroimaging Initiative cohort, including progressive mild cognitive impairment, stable MCI and Normal Control participants). In comparison with conventional SCCA, our proposed method can achieve strong associations and discover phenotypic biomarkers across multiple time-points to guide disease-progressive interpretation.

Availability and implementation
The Matlab code is available at https://sourceforge.net/projects/ibrain-cn/files/.
Direct AUC optimization of regulatory motifs
Authors: Zhu Lin , Zhang Hong-Bo , Huang De-Shuang 
Published: April 2017

Abstract

Motivation
The discovery of transcription factor binding site (TFBS) motifs is essential for untangling the complex mechanism of genetic variation under different developmental and environmental conditions. Among the huge amount of computational approaches for de novo identification of TFBS motifs, discriminative motif learning (DML) methods have been proven to be promising for harnessing the discovery power of accumulated huge amount of high-throughput binding data. However, they have to sacrifice accuracy for speed and could fail to fully utilize the information of the input sequences.

Results
We propose a novel algorithm called CDAUC for optimizing DML-learned motifs based on the area under the receiver-operating characteristic curve (AUC) criterion, which has been widely used in the literature to evaluate the significance of extracted motifs. We show that when the considered AUC loss function is optimized in a coordinate-wise manner, the cost function of each resultant sub-problem is a piece-wise constant function, whose optimal value can be found exactly and efficiently. Further, a key step of each iteration of CDAUC can be efficiently solved as a computational geometry problem. Experimental results on real world high-throughput datasets illustrate that CDAUC outperforms competing methods for refining DML motifs, while being one order of magnitude faster. Meanwhile, preliminary results also show that CDAUC may also be useful for improving the interpretability of convolutional kernels generated by the emerging deep learning approaches for predicting TF sequences specificities.

Availability and Implementation
CDAUC is available at: https://drive.google.com/drive/folders/0BxOW5MtIZbJjNFpCeHlBVWJHeW8.

Supplementary information
Supplementary data are available at Bioinformatics online.
Laboratory x-ray micro-computed tomography: a user guideline for biological samples
Authors: du Plessis Anton , Broeckhoven Chris , Guelpa Anina , le Roux Stephan Gerhard 
Published: April 2017

Abstract
Laboratory x-ray micro–computed tomography (micro-CT) is a fast-growing method in scientific research applications that allows for non-destructive imaging of morphological structures. This paper provides an easily operated “how to” guide for new potential users and describes the various steps required for successful planning of research projects that involve micro-CT. Background information on micro-CT is provided, followed by relevant setup, scanning, reconstructing, and visualization methods and considerations. Throughout the guide, a Jackson's chameleon specimen, which was scanned at different settings, is used as an interactive example. The ultimate aim of this paper is make new users familiar with the concepts and applications of micro-CT in an attempt to promote its use in future scientific studies.
Demixing sines and spikes: Robust spectral super-resolution in the presence of outliers
Authors: Fernandez-Granda Carlos , Tang Gongguo , Wang Xiaodong , Zheng Le 
Published: April 2017

AbstractWe consider the problem of super-resolving the line spectrum of a multisinusoidal signal from a finite number of samples, some of which may be completely corrupted. Measurements of this form can be modeled as an additive mixture of a sinusoidal and a sparse component. We propose to demix the two components and super-resolve the spectrum of the multisinusoidal signal by solving a convex program. Our main theoretical result is that—up to logarithmic factors—this approach is guaranteed to be successful with high probability for a number of spectral lines that is linear in the number of measurements, even if a constant fraction of the data are outliers. The result holds under the assumption that the phases of the sinusoidal and sparse components are random and the line spectrum satisfies a minimum-separation condition. We show that the method can be implemented via semi-definite programming, and explain how to adapt it in the presence of dense perturbations as well as exploring its connection to atomic-norm denoising. In addition, we propose a fast greedy demixing method that provides good empirical results when coupled with a local non-convex-optimization step.
Risk of Acute Liver Injury With Antiretroviral Therapy by Viral Hepatitis Status
Authors: Gowda Charitha , Newcomb Craig W. , Liu Qing , Carbonari Dena M. , Lewis James D. , Forde Kimberly A. , Goldberg David S. , Reddy K. Rajender , Roy Jason A. , Marks Amy R. , Schneider Jennifer L. , Kostman Jay R. , Tate Janet P. , Lim Joseph K. , Justice Amy C. , Goetz Matthew Bidwell , Corley Douglas A. , Lo Re Vincent 
Published: April 2017

Abstract

Background
The risk of hepatotoxicity with antiretroviral therapy (ART) remains unknown. We determined the comparative risk of acute liver injury (ALI) for antiretroviral drugs, classes, and regimens, by viral hepatitis status.

Methods
We followed a cohort of 10 083 human immunodeficiency virus (HIV)-infected persons in Kaiser Permanente Northern California (n = 2099) from 2004 to 2010 and the Veterans Aging Cohort Study (n = 7984) from 2004 to 2012. Within the first year of ART, we determined occurrence of (1) liver aminotransferases &gt;200 U/L and (2) severe ALI (coagulopathy with hyperbilirubinemia). We used Cox regression to determine hazard ratios (HRs) with 95% confidence intervals (CIs) of endpoints among initiators of nucleos(t)ide analogue combinations, antiretroviral classes, and ART regimens, all stratified by viral hepatitis status.

Results
Liver aminotransferases &gt;200 U/L developed in 206 (2%) persons and occurred more frequently among HIV/viral hepatitis-coinfected than HIV-monoinfected persons (116.1 vs 20.7 events/1000 person-years; P &lt; .001). No evidence of differential risk was found between initiators of abacavir/lamivudine versus tenofovir/emtricitabine among coinfected (HR, 0.68; 95% CI, .29–1.57) or HIV-monoinfected (HR, 1.19; 95% CI, .47–2.97) groups. Coinfected patients had a higher risk of aminotransferases &gt;200 U/L after initiation with a protease inhibitor than nonnucleoside reverse-transcriptase inhibitor (HR, 2.01; 95% CI, 1.36–2.96). Severe ALI (30 events; 0.3%) occurred more frequently in coinfected persons (15.9 vs 3.1 events/1000 person-years; P &lt; .001) but was too uncommon to evaluate in adjusted analyses.

Conclusions
Within the year after ART initiation, aminotransferase elevations were infrequently observed and rarely led to severe ALI. Protease inhibitor use was associated with a higher risk of aminotransferase elevations among viral hepatitis-coinfected patients.
Powerful Inference with the D-statistic on Low-Coverage Whole-Genome Data
Authors: Soraggi Samuele , Wiuf Carsten , Albrechtsen Anders 
Published: April 2017

ABSTRACTThe detection of ancient gene flow between human populations is an important issue in population genetics. A common tool for detecting ancient admixture events is the D-statistic. The D-statistic is based on the hypothesis of a genetic relationship that involves four populations, whose correctness is assessed by evaluating specific coincidences of alleles between the groups.When working with high throughput sequencing data calling genotypes accurately is not always possible, therefore the D-statistic currently samples a single base from the reads of one individual per population. This implies ignoring much of the information in the data, an issue especially striking in the case of ancient genomes.We provide a significant improvement to overcome the problems of the D-statistic by considering all reads from multiple individuals in each population. We also apply type-specific error correction to combat the problems of sequencing errors and show a way to correct for introgression from an external population that is not part of the supposed genetic relationship, and how this leads to an estimate of the admixture rate.We prove that the D-statistic is approximated by a standard normal. Furthermore we show that our method outperforms the traditional D-statistic in detecting admixtures. The power gain is most pronounced for low/medium sequencing depth (1-10X) and performances are as good as with perfectly called genotypes at a sequencing depth of 2X. We show the reliability of error correction on scenarios with simulated errors and ancient data, and correct for introgression in known scenarios to estimate the admixture rates.
Chemotaxonomic characterisation of the thaumarchaeal lipidome
Authors: Elling Felix J. , Könneke Martin , Nicol Graeme W. , Stieglmeier Michaela , Bayer Barbara , Spieck Eva , de la Torre José R. , Becker Kevin W. , Thomm Michael , Prosser James I. , Herndl Gerhard J. , Schleper Christa , Hinrichs Kai‐Uwe 
Published: April 2017

SummaryThaumarchaeota are globally distributed and abundant microorganisms occurring in diverse habitats and thus represent a major source of archaeal lipids. The scope of lipids as taxonomic markers in microbial ecological studies is limited by the scarcity of comparative data on the membrane lipid composition of cultivated representatives, including the phylum Thaumarchaeota. Here, we comprehensively describe the core and intact polar lipid (IPL) inventory of ten ammonia‐oxidising thaumarchaeal cultures representing all four characterized phylogenetic clades. IPLs of these thaumarchaeal strains are generally similar and consist of membrane‐spanning, glycerol dibiphytanyl glycerol tetraethers with monoglycosyl, diglycosyl, phosphohexose and hexose‐phosphohexose headgroups. However, the relative abundances of these IPLs and their core lipid compositions differ systematically between the phylogenetic subgroups, indicating high potential for chemotaxonomic distinction of thaumarchaeal clades. Comparative lipidomic analyses of 19 euryarchaeal and crenarchaeal strains suggested that the lipid methoxy archaeol is synthesized exclusively by Thaumarchaeota and may thus represent a diagnostic lipid biomarker for this phylum. The unprecedented diversity of the thaumarchaeal lipidome with 118 different lipids suggests that membrane lipid composition and adaptation mechanisms in Thaumarchaeota are more complex than previously thought and include unique lipids with as yet unresolved properties.
Robustness of a model microbial community emerges from population structure among single cells of a clonal population
Authors: Thompson Anne W. , Turkarslan Serdar , Arens Christina E. , López García de Lomana Adrián , Raman Arjun V. , Stahl David A. , Baliga Nitin S. 
Published: April 2017

SummaryMicrobial populations can withstand, overcome and persist in the face of environmental fluctuation. Previously, we demonstrated how conditional gene regulation in a fluctuating environment drives dilution of condition‐specific transcripts, causing a population of Desulfovibrio vulgaris Hildenborough (DvH) to collapse after repeatedly transitioning from sulfate respiration to syntrophic conditions with the methanogen Methanococcus maripaludis. Failure of the DvH to successfully transition contributed to the collapse of this model community. We investigated the mechanistic basis for loss of robustness by examining whether conditional gene regulation altered heterogeneity in gene expression across individual DvH cells. We discovered that robustness of a microbial population across environmental transitions was attributable to the retention of cells in two states that exhibited different condition‐specific gene expression patterns. In our experiments, a population with disrupted conditional regulation successfully alternated between cell states. Meanwhile, a population with intact conditional regulation successfully switched between cell states initially, but collapsed after repeated transitions, possibly due to the high energy requirements of regulation. These results demonstrate that the survival of this entire model microbial community is dependent on the regulatory system's influence on the distribution of distinct cell states among individual cells within a clonal population.
Natural resource landscapes of a marine bacterium reveal distinct fitness‐determining genes across the genome
Authors: Takemura Alison F. , Corzett Christopher H. , Hussain Fatima , Arevalo Philip , Datta Manoshi , Yu Xiaoqian , Le Roux Frederique , Polz Martin F. 
Published: April 2017

SummaryHeterotrophic bacteria exploit diverse microhabitats in the ocean, from particles to transient gradients. Yet the degree to which genes and pathways can contribute to an organism's fitness on such complex and variable natural resource landscapes remains poorly understood. Here, we determine the gene‐by‐gene fitness of a generalist saprophytic marine bacterium (Vibrio sp. F13 9CS106) on complex resources derived from its natural habitats – copepods (Apocyclops royi) and brown algae (Fucus vesiculosus) – and as reference substrates, glucose and the polysaccharide alginate, derived from brown algal cell walls. We find that resource complexity strongly buffers fitness costs of mutations, and that anabolic rather than catabolic pathways are more stringently required, likely due to functional redundancy in the latter. Moreover, while carbohydrate‐rich algae requires several synthesis pathways, protein‐rich Apocyclops does not, suggesting this ancestral habitat for Vibrios is a replete medium with metabolically redundant substrates. We also identify a candidate fitness trade‐off for algal colonization: deletion of mshA increases mutant fitness. Our results demonstrate that gene fitness depends on habitat composition, and suggest that this generalist uses distinct resources in different natural habitats. The results further indicate that substrate replete conditions may lead to relatively relaxed selection on catabolic genes.