bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate Filtering of Privacy-Sensitive Information in Raw Genomic Data
Authors: Decouchant Jérémie , Fernandes Maria , Völp Marcus , Couto Francisco M , Esteves-Veríssimo Paulo 
Published: March 2018

AbstractSequencing thousands of human genomes has enabled breakthroughs in many areas, among them precision medicine, the study of rare diseases, and forensics. However, mass collection of such sensitive data entails enormous risks if not protected to the highest standards. In this article, we follow the position and argue that post-alignment privacy is not enough and that data should be automatically protected as early as possible in the genomics workflow, ideally immediately after the data is produced. We show that a previous approach for filtering short reads cannot extend to long reads and present a novel filtering approach that classifies raw genomic data (i.e., whose location and content is not yet determined) into privacy-sensitive (i.e., more affected by a successful privacy attack) and non-privacy-sensitive information. Such a classification allows the fine-grained and automated adjustment of protective measures to mitigate the possible consequences of exposure, in particular when relying on public clouds. We present the first filter that can be indistinctly applied to reads of any length, i.e., making it usable with any recent or future sequencing technologies. The filter is accurate, in the sense that it detects all known sensitive nucleotides except those located in highly variable regions (less than 10 nucleotides remain undetected per genome instead of 100,000 in previous works). It has far less false positives than previously known methods (10% instead of 60%) and can detect sensitive nucleotides despite sequencing errors (86% detected instead of 56% with 2% of mutations). Finally, practical experiments demonstrate high performance, both in terms of throughput and memory consumption.
A human pathogenic bacteriumShigellaproliferates in the plant through the adoption of type III effectors for Shigellosis
Authors: Jo Sung Hee , Lee Jiyoung , Park Eunsook , Kim Dong Wook , Lee Dae Hee , Ryu Choong Min , Choi Doil , Park Jeong Mee 
Published: March 2018

AbstractHuman enteropathogenic bacteria has been reported to be transmitted by fresh vegitables.Shigella, which infects primates, is reportedly transmitted by fresh vegetables; however, its molecular interactions with plants have not been elucidated. Here, we show that fourShigellastrains,S. boydii(S. b),S. sonnei,S. flexneri2a (S. f2a), andS. flexneri5a (S. f5a), proliferated at different levels inArabidopsis thaliana. Microscopic studies revealed that these bacteria were present inside leaves and damaged plant cells. Green fluorescent protein (GFP)-taggedS. bandS. f5a colonized in leaves only, andS. f2a colonized both leaves and roots. Using mutants lacking type III secretion systems (T3SS), we found that T3SS ofShigellathat regulate the pathogenesis of Shigellosis in humans also play a central role in proliferation inArabidopsis.Strikingly, the immunosuppressive activity of two T3S effectors, OspF and OspG, were needed for the proliferation ofShigellainArabidopsis. Of note, delivery of OspF or OspG effectors inside of plant cells uponShigellainoculation was confirmed by using a split GFP system, respectively. These findings demonstrate that the human pathogenShigellacan proliferate in plants by adoption of immunosuppressive machinery for its original host human.
Internal model recalibration does not deteriorate with age while motor adaptation does
Authors: Vandevoorde Koenraad , de Xivry Jean-Jacques Orban 
Published: March 2018

AbstractA wide range of motor function declines with aging. Motor adaptation, which occurs when participants learn to reach accurately to a target despite a perturbation, does not deviate from this rule. There are currently three major hypotheses that have been put forward to explain this age-related decline in adaptation: deterioration of internal model recalibration due to age-related cerebellar degeneration, impairment of the cognitive component of motor adaptation, and deficit in the retention of the learned movement. In the present study, we systematically investigated these three hypotheses in a large sample of older women and men. We demonstrate that age-related deficits in motor adaptation are not due to impaired internal model recalibration or impaired retention of motor memory. Rather, we found that the cognitive component was reduced in older people. Therefore, our study suggests the interesting possibility that cerebellar-based mechanisms do not deteriorate with age despite cerebellar degeneration. In contrast, internal model recalibration appears to compensate for deficits in the cognitive component of this type of learning.
Holographic optical trapping Raman micro-spectroscopy of interacting live cells
Authors: Sinjab F. , Elsheikha H. M. , Awuah D. , Gibson G. , Padgett M. , Ghaemmaghami A. M. , Notingher I. 
Published: March 2018

ABSTRACTWe present a combined holographic optical tweezers and confocal Raman spectroscopy instrument which allows fast, flexible, and interactive manipulation with molecular measurement of interacting live cell systems. Multiple laser foci created using a spatial light modulator are simultaneously used for optical trapping and spontaneous Raman spectroscopy. To enable confocal Raman measurements with high spectral resolution, a digital micro-mirror device was used to generate reflective pinholes which are matched to each laser trap. We demonstrate this unique capability by initiating complex interactions between multiple live cells whilst non-invasively acquiring Raman spectra of the processes with high spatial, spectral, and temporal resolution.
Mass spectra alignment using virtual lock-masses
Authors: Brochu Francis , Plante Pier-Luc , Drouin Alexandre , Gagnon Dominic , Richard Dave , Durocher Francine , Diorio Caroline , Marchand Mario , Corbeil Jacques , Laviolette François 
Published: March 2018

ABSTRACTMass spectrometry is a valued method to evaluate the metabolomics content of a biological sample. The recent advent of rapid ionization technologies such as Laser Diode Thermal Desorption (LDTD) and Direct Analysis in Real Time (DART) has rendered high-throughput mass spectrometry possible. It is used for large-scale comparative analysis of populations of samples. In practice, many factors resulting from the environment, the protocol, and even the instrument itself, can lead to minor discrepancies between spectra, rendering automated comparative analysis difficult. In this work, a sequence/pipeline of algorithms to correct variations between spectra is proposed. The algorithms correct multiple spectra by identifying peaks that are common to all and, from those, computes a spectrum-specific correction. We show that these algorithms increase comparability within large datasets of spectra, facilitating comparative analysis, such as machine learning.
Widespread noncoded amino acids in human proteome
Authors: Yang Jing-Hua , Chen Xinjun , Gong Jing , Lv Xin , Zhao Han , Li Cuiling , Bi Baibing , Wang Fengqin , Sun Shengnan , Wang Xingyuan , Zhang Haobo , Huang Tao , Azadzoi Kazem , Shi Feng , Kong Xianglong , Shu Minglei , Wang Yinglong , Huang Wan , Chin Y. Eugene , Chen Zhinan , Chen Zi-Jiang 
Published: March 2018

SUMMARYProteins are usually deciphered by translation of the coding genome; however, their amino acid residues are seldom determined directly across the proteome. Herein, we describe a systematic workflow for identifying all possible protein residues that differ from the coding genome, termed noncoded amino acids (ncAAs). By measuring the mass differences between the coding amino acids and the actual protein residues in human spermatozoa, over a million nonzero delta masses were detected, fallen into 424 high-quality Gaussian clusters and 571 high-confidence ncAAs spanning 29,053 protein sites. Most ncAAs are novel with unresolved side-chains and discriminative between healthy individuals and patients with oligoasthenospermia. For validation, 40 out of 98 ncAAs that matched with amino acid substitutions were confirmed by exon sequencing. This workflow revealed the widespread existence of previously unreported ncAAs in the sperm proteome, which represents a new dimension on the understanding of amino acid polymorphisms at the proteomic level.Highlights571 ncAAs spanning 108,000 protein sites were identified in human sperm proteome.Most ncAAs are novel with unresolved sidechains and found at unreported protein sites.Exon sequencing confirmed 40 of 98 ncAAs that matched with amino acid substitutions.Many ncAAs are linked with disease and have potential for diagnosis and targeting.eTOC BlurbWe describe a systematic identification of all possible protein residues that were not encoded by their genomic sequences. A total of 571 high-confidence most novel noncoded amino acids were identified in human sperm proteome, corresponding to over 108,000 ncAA-containing protein sites. For validation, 40 out of 98 ncAAs that matched to amino acid substitutions were confirmed by exon sequencing. These ncAAs are discriminative between individuals and expand our understanding of amino acid polymorphisms in human proteomes and diseases.
Effective bulk modulus of the pore fluid at patchy saturation
Authors: Wollner Uri , Dvorkin Jack 
Published: March 2018

ABSTRACTWe explore a package of parallel porous layers, each filled with a different fluid. Assume that this package is sampled by an elastic wave with the wavelength much larger than the thickness of an individual layer. Also assume that the layers are hydraulically isolated from each other, meaning that the diffusion length is smaller than that of the individual layer. This assumption is relevant to a patchy saturation scenario. Suppose that we wish to conduct the fluid substitution operation on this package treated as a single porous elastic body. What is the effective bulk modulus of the pore fluid to be used in this operation that will result in the same elastic modulus as computed by Backus averaging the individual moduli of the layers? We address this question analytically by assuming that the porosity, dry frame, and the mineral matrix properties of the individual layers are the same for all layers. The only difference between the layers is the pore fluid. We find that the resulting effective bulk modulus of the fluid thus derived falls between the arithmetic and harmonic averages of the fluid bulk moduli in the layers. It can be approximated by a linear combination of these two bounds where the weights are 0.50 and 0.50 or 0.75 for the arithmetic average and 0.25 for the harmonic average, depending on the elastic moduli of the dry frame, the mineral, and the pore fluids. This solution also provides a relation between the effective bulk modulus of the pore fluid in the system under examination and water saturation to be used in the fluid substitution operation at a coarse spatial scale.
Relationships between vital rates and ecological traits in an avian community
Authors: Bellier Edwige , Kéry Marc , Schaub Michael 
Published: March 2018

AbstractComparative studies about the relationships between vital rates and ecological traits at the community level are conspicuously lacking for most taxa because estimating vital rates requires detailed demographic data. Identifying relationships between vital rates and ecological traits could help to better understand ecological and evolutionary demographic mechanisms that lead to interspecific differences in vital rates.We use novel dynamicN‐mixture models for counts to achieve this for a whole avian community comprising 53 passerine species, while simultaneously accounting for density dependence and environmental stochasticity in recruitment and survival and, importantly, correcting our inferences for imperfect detection. Demographic stochasticity is taken into account in the form of the binomial and Poisson distributions describing survival events and number of recruits. We then explore relationships between estimated demographic parameters (i.e., vital rates) and ecological traits related to migration patterns, diet, habitat and nesting location of each species.The relative importance of recruitment and adult survival as contributors to population growth varied greatly among species, and interspecific differences in vital rates partly reflected differences in ecological traits. Migratory mode was associated with interspecific differences in population growth and density dependence. Resident species had higher population growth rates than long‐ and short‐distance migrants. We found no relationships between diet and population growth rate. Habitat differences were associated with different growth rates: alpine, wetland and farmland species had lower population growth rates than forest species. Differences in population growth rates among nesting locations showed that breeding habitat is essential for population dynamics.Our study reveals relationships between ecological traits and contributions of vital rates to population growth and suggests ways in which patterns of population growth fluctuations in a community might be determined by life history.
Parents, migrant domestic workers and children's speaking of a second language: Evidence from Hong Kong
Authors: Tang Sam Hak Kan 
Published: March 2018

AbstractThis paper explores the effects of different language home environments provided by English‐speaking and non‐English‐speaking migrant domestic workers (MDW) on Hong Kong children's ability to speak English. Results show that English‐speaking MDW in working‐mother households increase children's likelihood of speaking English by 12% if the mother in the household does not speak English but by 25% if the mother in the household is capable of speaking English. Non‐English‐speaking MDW, however, are found to have little such effects. Age and education are two qualities of English‐speaking MDW that are significantly associated with improvements in children's English‐speaking ability and their English school subject.
Undiagnosed Congenital Heart Defects as a Cause of Sudden, Unexpected Death in Children
Authors: Serinelli Serenella , Arunkumar Ponni , White Steven 
Published: March 2018

AbstractDespite advances in the diagnosis and treatment of congenital heart defects (CHDs), these defects are still an important cause of sudden, unexpected death in young children. This retrospective study identified 64 cases of CHDs presenting as a cause of sudden, unexpected death in a busy, urban Medical Examiner's Office pediatric population between 2006 and 2016. The majority of cases (52 of 64, 81%) were infants. Interestingly, 52% of cases were undiagnosed prior to autopsy. Ventricular septal defects and atrioventricular septal defects were the most common simple (14%) and complex (17%) malformations observed, respectively. In many cases, there were coexistent simple and/or complex defects. Most of the cases diagnosed with CHD prior to autopsy (48%) had undergone some type of surgical repair. This study highlights the importance of considering undiagnosed CHDs as a cause of sudden, unexpected death, particularly in young children.
Compositional Analysis of Coronary Artery Calcification in Dialysis Patients in vivo by Dual‐Energy Computed Tomography Angiography
Authors: Nishizawa Yoko , Higuchi Chieko , Nakaoka Takashi , Omori Hisako , Ogawa Tetsuya , Sakura Hiroshi , Nitta Kosaku 
Published: March 2018

AbstractWhile vascular calcification is an important factor regulating prognosis in dialysis patients, its components have not been adequately studied. We analyzed in vivo components of calcification in the coronary arteries of dialysis patients using the effective atomic number from dual‐energy computed tomography. In dialysis patients (hemodialysis, N = 10; peritoneal dialysis, N = 12), average of median effective atomic number was 13.8 in the hemodialysis group, and 13.7 in the peritoneal dialysis group. No significant differences were seen between groups, with calcium oxalate monohydrate identified as the most common component in each. To confirm the accuracy of this method, we investigated the composition of surgically removed calcified tissues using already established methods. Comparison with the effective atomic number from dual‐energy computed tomography showed that the results of calcification analysis were the same. We concluded that calcium oxalate monohydrate might be one of the major components of coronary artery calcification in dialysis patients.
Maintenance of Continuity in Older Adulthood: Concept Analysis
Authors: Lim SoYeun , Song Jun‐Ah 
Published: March 2018

PURPOSEThis article aims to define the concept of maintenance of continuity in older adulthood (MCOA) and assist nurses to better understand the concept of MCOA.METHODSThe method by Walker and Avant was used for this concept analysis.FINDINGSIn the literature, MCOA is defined as a psychosocial adaptation strategy by searching for preference and familiarity, making a sense of connection, and creating coherence.CONCLUSIONSMCOA has potential to improve psychosocial adjustment to difficult life transitions as a coping mechanism.IMPLICATION FOR NURSING PRACTICEInsights about MCOA in nursing may contribute to improved patient care outcomes by assisting nurses to understand the elderly's experience during age‐related challenges from a life course perspective.
Appendicectomy during pregnancy and the risk of preterm birth: A population data linkage study
Authors: Ibiebele Ibinabo , Schnitzler Margaret , Nippita Tanya , Ford Jane B. 
Published: March 2018

BackgroundSuspected appendicitis is a common non‐obstetric indication for emergency abdominal surgery during pregnancy.AimsAssess the risk of preterm birth and other maternal and neonatal adverse birth outcomes following appendicectomy during pregnancy.Materials and MethodsPopulation‐based data linkage study of women with singleton births in New South Wales, Australia, 2002–2014. Pregnancies with appendicitis and appendicectomy were compared to pregnancies without appendicitis. Crude and adjusted hazard ratios (aHR) with 95% confidence intervals (CI) for preterm birth were estimated. Modified Poisson regression with robust variance was used to estimate crude and adjusted risk ratios (aRR) with 99% CI for other outcomes.ResultsOf 1 124 551 eligible pregnancies, 1024 (0.9/1000 pregnancies) had appendicitis and appendicectomy. Of these, 566 (55.3%) had laparoscopic and 458 (44.7%) had open appendicectomy. Appendicectomy at later gestational ages was associated with increasing rates of preterm birth. After adjustment for maternal and pregnancy factors, appendicectomy was associated with increased risk of preterm birth (overall aHR 1.73, 95% CI 1.42–2.09; planned aHR 2.08, 95% CI 1.60–2.72), maternal morbidity (aRR 2.68, 99% CI 1.88–3.83) and neonatal morbidity (aRR 1.42, 99% CI 1.03–1.94). However, there was no difference in perinatal mortality rates.ConclusionAppendicectomy during pregnancy is associated with increased risk of spontaneous and planned preterm birth, maternal and neonatal morbidity. Availability of resources to prevent or manage preterm labour should be considered when appendicectomy is performed at gestational ages of 20 weeks or more.
Electoral Effects of Biased Media: Russian Television in Ukraine
Authors: Peisakhin Leonid , Rozenas Arturas 
Published: March 2018

AbstractWe use plausibly exogenous variation in the availability of the Russian analog television signal in Ukraine to study how a media source with a conspicuous political agenda impacts political behavior and attitudes. Using highly disaggregated election data and an original survey, we estimate that Russian television substantially increased average electoral support for parties and candidates with a “pro‐Russian” agenda in the 2014 presidential and parliamentary elections. Evidence suggests that this effect is attributable to persuasion rather than differential mobilization. The effectiveness of biased media varied in a politically consequential way: Its impact was largest on voters with strong pro‐Russian priors but was less effective, and to some degree even counter‐effective, in persuading those with strong pro‐Western priors. Our finding suggests that exposing an already polarized society to a biased media source can result in even deeper polarization.
“To screen or not to screen”: Comparing the health and economic benefits of early peanut introduction strategies in five countries
Authors: Shaker M. , Stukus D. , Chan E. S. , Fleischer D. M. , Spergel J. M. , Greenhawt M. 
Published: March 2018

AbstractBackgroundEarly peanut introduction (EPI) in the first year of life is associated with reduced risk of developing peanut allergy in children with either severe eczema and/or egg allergy. However, EPI recommendations differ among countries with formal guidelines.MethodsUsing simulation and Markov modeling over a 20‐year horizon to attempt to explore optimal EPI strategies applied to the US population, we compared high‐risk infant‐specific IgE peanut screening (US/Canadian) with the Australiasian Society for Clinical Immunology and Allergy (Australia/New Zealand) (ASCIA) and the United Kingdom Department of Health (UKDOH)‐published EPI approaches.ResultsScreening peanut skin testing of all children with early‐onset eczema and/or egg allergy before in‐office peanut introduction was dominated by a no screening approach, in terms of number of cases of peanut allergy prevented, quality‐adjusted life years (QALY), and healthcare costs, although screening resulted in a slightly lower rate of allergic reactions to peanut per patient in high‐risk children. Considering costs of peanut allergy in high‐risk children, the per‐patient cost of early introduction without screening over the model horizon was $6556.69 (95%CI, $6512.76‐$6600.62), compared with a cost of $7576.32 (95%CI, $7531.38‐$7621.26) for skin test screening prior to introduction. From a US societal perspective, screening prior to introduction cost $654 115 322 and resulted in 3208 additional peanut allergy diagnoses. Both screening and nonscreening approaches dominated deliberately delayed peanut introduction.ConclusionsA no‐screening approach for EPI has superior health and economic benefits in terms of number of peanut allergy cases prevented, QALY, and total healthcare costs compared to screening and in‐office peanut introduction.