bluuebunny/crossref_metadata_2025_split huggingface dataset:
snpAD: An ancient DNA genotype caller
Authors: Prüfer Kay 
Published: March 2018

AbstractMotivationThe study of ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling.ResultsI describe an expectation-maximization algorithm that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals.AvailabilityThe C++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/Contactpruefer@eva.mpg.deSupplementary informationSupplementary data are available at Bioinformatics online.
A Machine Learning Approach Predicts Tissue-Specific Drug Adverse Events
Authors: Madhukar Neel S. , Gayvert Kaitlyn , Gilvary Coryandar , Elemento Olivier 
Published: March 2018

ABSTRACTOne of the main causes for failure in the drug development pipeline or withdrawal post approval is the unexpected occurrence of severe drug adverse events. Even though such events should be detected by in vitro, in vivo, and human trials, they continue to unexpectedly arise at different stages of drug development causing costly clinical trial failures and market withdrawal. Inspired by the “moneyball” approach used in baseball to integrate diverse features to predict player success, we hypothesized that a similar approach could leverage existing adverse event and tissue-specific toxicity data to learn how to predict adverse events. We introduce MAESTER, a data-driven machine learning approach that integrates information on a compound’s structure, targets, and phenotypic effects with tissue-wide genomic profiling and our toxic target database to predict the probability of a compound presenting with different types of tissue-specific adverse events. When tested on 6 different types of adverse events MAESTER maintains a high accuracy, sensitivity, and specificity across both the training data and new test sets. Additionally, MAESTER scores could flag a number of drugs that were approved, but later withdrawn due to unknown adverse events – highlighting its potential to identify events missed by traditional methods. MAESTER can also be used to identify toxic targets for each tissue type. Overall MAESTER provides a broadly applicable framework to identify toxic targets and predict specific adverse events and can accelerate the drug development pipeline and drive the design of new safer compounds.
ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules
Authors: Silverbush Dana , Cristea Simona , Yanovich Gali , Geiger Tamar , Beerenwinkel Niko , Sharan Roded 
Published: March 2018

AbstractThe identification of molecular pathways driving cancer progression is a fundamental unsolved problem in tumorigenesis, which can substantially further our understanding of cancer mechanisms and inform the development of targeted therapies. Most current approaches to address this problem use primarily somatic mutations, not fully exploiting additional layers of biological information. Here, we describe ModulOmics, a method to de novo identify cancer driver pathways, or modules, by integrating multiple data types (protein-protein interactions, mutual exclusivity of mutations or copy number alterations, transcriptional co-regulation, and RNA co-expression) into a single probabilistic model. To efficiently search the exponential space of candidate modules, ModulOmics employs a two-step optimization procedure that combines integer linear programming with stochastic search. Across several cancer types, ModulOmics identifies highly functionally connected modules enriched with cancer driver genes, outperforming state-of-the-art methods. For breast cancer subtypes, the inferred modules recapitulate known molecular mechanisms and suggest novel subtype-specific functionalities. These findings are supported by an independent patient cohort, as well as independent proteomic and phosphoproteomic datasets.
Exacerbation of atopic dermatitis symptoms by ustekinumab in psoriatic patients with elevated serum immunoglobulin E levels: Report of two cases
Authors: Ishiuji Yozo , Umezawa Yoshinori , Asahina Akihiko , Fukuta Hirotaka , Aizawa Norie , Yanaba Koichi , Nakagawa Hidemi 
Published: March 2018

AbstractPsoriasis is a chronic inflammatory skin disease mainly mediated by a T‐helper cell subset, Th17 cells. Recently, increased levels of total serum immunoglobulin (Ig)E have been reported in a subset of psoriatic patients. Ustekinumab (UST) is one of the most commonly used biologic agents for the treatment of moderate to severe plaque psoriasis, and a previous report also documented effectiveness of UST for psoriatic patients with high serum IgE levels. We experienced two psoriatic patients with high serum IgE levels, in whom UST completely improved psoriasis but paradoxically provoked or exacerbated atopic dermatitis (AD)‐like symptoms. This reciprocal phenomenon suggests the shift of Th balance toward Th2, along with altered profiles of inflammatory cytokines. It appears prudent to consider the possibility of such adverse effects when treating psoriatic patients with UST with concomitant AD symptoms, a history of AD or high serum IgE levels.
Related plant species respond similarly to chronic anthropogenic disturbance: Implications for conservation decision‐making
Authors: Martínez‐Blancas Alejandra , Paz Horacio , Salazar Gerardo A. , Martorell Carlos 
Published: March 2018

Abstract

Many developing countries harbour large numbers of species that face little‐understood, gradual changes in their environment, including chronic anthropogenic disturbance (CAD), a high frequency but low intensity form of disturbance. These countries also lack the resources to study each species, so conservation practices have been generalized, assuming that complete taxonomic groups may be managed in the same ways. This approach could be justified if closely related species respond similarly to threats. We assessed if related species respond similarly to CAD, whether this affects phylogenetic diversity and if such patterns occur in different systems.

Species’ identity and abundance was recorded in 59 sites differing in CAD intensity in a semi‐arid grassland and a tropical dry forest in Mexico. Disturbance response indices were calculated for each species. Nested analysis of variance coupled with null models were applied to determine if generalizations within taxa are justified and which taxonomic level explained the most variation in disturbance response among species. We obtained phylogenetic trees using molecular data for the grassland and published data for the tropical forest. Phylogenetic signal was measured with Pagel's λ. Community mean phylogenetic distance was regressed on CAD.

Higher taxonomic levels explained more variation than expected by chance, indicating that related species respond similarly to CAD. However, only species in the same genus behaved similarly enough to make generalizations reliable. This is the result of an underlying, if modest, phylogenetic signal in CAD responses. Mean phylogenetic distance decreased with CAD in the grassland but not the tropical dry forest. This suggests that CAD was a stronger environmental filter in the grassland but weak in the tropical dry forest, where it was less intense.

Policy implications. Species inform us how their relatives respond to chronic anthropogenic disturbance (CAD), supporting the idea that generalizations in management are possible. However, this procedure is seemingly reliable only within genera, which explain over 80% of the accumulated variance in species’ CAD responses, and not within orders or families. CAD may reduce phylogenetic diversity, perhaps leading to ecosystem function loss.
Spatial variation in herbivory, climate and isolation predicts plant height and fruit phenotype in Plectritis congesta populations on islands
Authors: Skaien Cora L. , Arcese Peter 
Published: March 2018

Abstract

Climate and herbivory can each drive natural selection on plant traits but may interact to give rise to different patterns in trait distributions when surveyed across island populations. These different patterns may arise because the occurrence of ungulate herbivores often varies across archipelagos, potentially leading to strong and abrupt spatial heterogeneity in the direction or intensity of natural selection. In contrast, climate tends to vary gradually and thus is more likely to lead to gradual clines in trait values.

Population isolation may also affect trait values, given that random genetic drift may fix alleles or traits in the absence of gene flow or because gene flow between populations with similar or opposing selection pressures may augment or swamp the effects of selection.

Here, we estimate the independent and interactive effects of deer, climate and isolation on fruit phenotype and plant height in 285 Plectritis congesta populations at 77 island and 44 mainland sites in western North America.

Plectritis congesta is a palatable winter annual with two fruit phenotypes based on a simple Mendelian locus with clear dominance and heritable variation in height as a polygenic trait. Fruit phenotype and plant height were well predicted by deer occurrence; plants in populations with resident deer were short (15.0 ± 1.1 cm) and mainly expressed wingless fruits (73.0 ± 4.0%), whereas plants in populations without deer were 2.6 times taller (38.9 ± 5.3 cm) and only 9.0 ± 1.6% expressed wingless fruits.

Wingless fruits were less common in populations experiencing wetter conditions with more seasonal variability in temperatures, particularly in the absence of deer. In contrast, population isolation was unrelated to fruit phenotype, except in populations rarely exposed to deer, where plants expressed phenotypes more like those in populations without deer as isolation increased. Our results are consistent with the hypothesis that spatial variation in browsing by deer or other factors correlated with it contributes to population‐level variation in fruit phenotype and plant height in P. congesta and that climate leads to a modest spatial gradient in plant height.

Synthesis. The occurrence of deer at 285 island and mainland populations of Plectritis congesta predicted plant height and fruit phenotype, supporting the hypothesis that spatial variation in herbivory is a key factor affecting population‐level variation in the distribution of these heritable traits.
A pilot study evaluation of Marte Meo for divorced fathers
Authors: DeGarmo David S. , Jones Jeremy , Rains Laura A. 
Published: March 2018

AbstractA Marte Meo strengths‐based video feedback programme for improving divorced fathers' self‐conceptions and parenting was tested. By identifying and reinforcing fathers' skills in child communication, we hypothesized that fathers would exhibit pre‐post improvements in fathering self‐evaluations and behaviours. Therapists treated eleven divorced fathers with three to five home‐visit, video feedback sessions over twelve months. Data showed reductions in harsh discipline and inept parenting, and some evidence of improvements in efficacy and father involvement. Changes in fathering identity were significantly associated with changes in parental efficacy (r = .47), harsh parenting (r = −.64), and inept parenting (r = −.42). Programme acceptability was rated high on positive experiences and low on negative experiences. The data suggest promise for promoting fathers' effective parenting, quality involvement and self‐conceptions through video feedback.Practitioner points

Single fathers are relatively under‐represented in clinical treatment and evidence‐based science relative to practice with mothers and couples

This article shows evidence of promise for Marte Meo, a strengths‐based video feedback treatment, to improve parenting skills of at‐risk fathers

Reinforcing and building upon existing skills can be a complementary treatment component and/or an alternative to deficit‐based practice
‘Utterly Disgraceful’: Social Media and the Workplace
Authors: Barnes Alison , Balnave Nikola , Holland Peter 
Published: March 2018

AbstractSocial media use by Australian public servants has given rise to questions pertaining to their political rights, impartiality and privacy outside of work. Drawing on the recent case Starr v Department of Human Services these issues are explored. The findings suggest that social media use has heightened tensions around public servant's rights to comment on issues of the day, and its use by employees both inside and beyond the workplace remains contested terrain.
Toxic money or paid altruism: the meaning of payments for identity‐release gamete donors
Authors: Gilman Leah 
Published: March 2018

AbstractPublic discourses commonly frame gamete, organ and other forms of bodily donation as altruistic ‘gifts’. However, despite on‐going debates about the ethics of payments to donors, few studies have examined the views of donors themselves regarding the meaning of payments and their compatibility (or not) with understandings of these practices as gifts. This article addresses this issue, analysing 24 in‐depth interviews withUKidentity‐release gamete donors. It was crucial to all participants that their donation be viewed as fundamentally other‐oriented, motivated by the desire to help others. However, whilst egg donors often accommodated payment within this narrative, male participants explained that any money would taint the gift they had given. I argue that sperm donors faced particular challenges to incorporating payment within a gift narrative for two key reasons: first, sperm donors relied on a discourse of ‘pure altruism’, including absolute opposition between gifts and market exchange, in order to present their donation as other‐oriented. In contrast, egg donors were also able to mobilise a discourse of relational giving to present their donations as a personal gift. Second, according to a continued stereotype of sperm donors as financially motivated students, their payments have already been culturally earmarked as side‐line earnings.
Nurses’ elicitation of patient error as a practice in training end‐stage renal patients in automated home peritoneal dialysis
Authors: Larsen Tine 
Published: March 2018

AbstractAs part of a reorganisation of the delivery of health care in Denmark therapies for chronic medical conditions are moved out of hospitals and disease‐specific patient education programmes instituted to train patients to assume responsibility for treating their disease at home, that is, perform tasks and functions traditionally done by healthcare professionals. Drawing on video‐recordings (90:25h) from a programme for self‐management of end‐stage renal disease through automated home peritoneal dialysis, the study employs conversation analysis to examine nurses’ instructional practices for providing patients with the necessary knowledge, skill and competences. Showing training to rely on an error‐based monitoring strategy, the study demonstrates that rather than solely waiting for random errors to emerge, nurses on occasion steer patients towards specific errors to bring about particular instructional opportunities. Surprising given the seriousness of the therapy, this elicitation of error is shown to reflect a deliberate instructional choice; nurses promote select errors to impart patients with an understanding of the procedural logic behind the therapy and medical technology. The study argues that training patients for chronic disease self‐management and providing them with a proficiency level, normally associated with certified professionals, necessitates pushing patients beyond what is strictly accurate and exposing them to medically delicate events.
Integrated and Person‐Centered Care for Community‐Living Older Adults: A Cost‐Effectiveness Study
Authors: Uittenbroek Ronald J. , van Asselt Antoinette D. I. , Spoorenberg Sophie L. W. , Kremer Hubertus P. H. , Wynia Klaske , Reijneveld Sijmen A. 
Published: March 2018

ObjectivesTo assess the cost‐effectiveness of Embrace, an integrated primary care service for older adults.Data SourcesCare and support claims from health care insurers, long‐term care administration, and municipalities for enrolled older adults between 2011 and 2013.Study DesignA total of 1,456 older adults, listed with 15 general practitioners practices in the Netherlands, were stratified into risk profiles (“Robust,” “Frail,” and “Complex care needs”) and randomized to Embrace or care‐as‐usual groups. Incremental costs were calculated per quality‐adjusted life year, per day able to age in place, and per percentage point risk profile improvement.Principal FindingsTotal average costs were higher for Embrace compared to care‐as‐usual. Differences in health‐associated outcomes were small and not statistically significant. Probabilities that Embrace is cost‐effective were below 80 percent, except for “risk profile improvements” within risk profile “Complex care needs.” Complete case analysis resulted in smaller differences in total average costs across conditions and differences in health‐associated outcomes remained small.ConclusionsAccording to current standards, Embrace is not considered cost effective after 12 months. However, it could be considered worthwhile in terms of “risk profile improvements” for older adults with “Complex care needs,” if society is willing to invest substantially.
Fundamental Limits of Shaking a Baby
Authors: Reimann Richard J. 
Published: March 2018

AbstractBasic physics places limits on the mechanics involved in shaking a baby. Fundamental definitions and practical limitations are used to compare shaking with car crashes and low‐level falls. First‐order mathematical considerations applied to a 6‐month‐old infant determine an angular velocity limit for head rotation around 75 rad/s and maximum angular acceleration less than 1600 rad/s2 without impact. By comparison, results from a low‐level fall of 0.76 m (30 inches) yield values of 83 rad/s and 13,000 rad/s2 in a practical worst‐case scenario.
Medication use in infants admitted with bronchiolitis
Authors: Oakley Ed , Brys Trusha , Borland Meredith , Neutze Jocelyn , Phillips Natalie , Krieser David , Dalziel Stuart R , Davidson Andrew , Donath Susan , Jachno Kim , South Mike , Williams Amanda , Babl Franz E ,   on behalf of the Paediatric Research in Emergency Departments International Collaborative (PREDICT)
Published: March 2018

AbstractBackgroundThere are no medications known that improve the outcome of infants with bronchiolitis. Studies have shown the management of bronchiolitis to be varied.ObjectivesTo describe medication use at the seven study hospitals from a recent multi‐centre randomised controlled trial on hydration in bronchiolitis (comparative rehydration in bronchiolitis [CRIB]).MethodsA retrospective analysis of extant data of infants between 2 months (corrected for prematurity) and 12 months of age admitted with bronchiolitis identified through the CRIB trial. CRIB study records, medical records, pathology and radiology databases were used to collect data using a standardised form and entered in a single site database. Medications investigated included salbutamol, adrenaline, steroids, ipratropium bromide, normal saline, hypertonic saline, steroids and antibiotics.ResultsThere were 3456 infants available for analysis, of which 42.0% received at least one medication during hospitalisation. Medication use varied by site between 27.0 and 48.7%. The most frequently used medication was salbutamol (25.5%). Medication use in general, and salbutamol use in particular, increased by 8.2 and 9.3%, respectively, per month after 4 months of age; from 22.9 and 3.6% at 4 months to 81.4 and 68.8% at 11 months. In infants admitted to the intensive care unit (ICU) compared with those not admitted to ICU 81.6 and 39.5%, respectively, received medication at one point during the hospital stay.ConclusionsMedication was used for infants with bronchiolitis frequently and variably in Australia and New Zealand. Medication use increased with age. Better strategies for translating evidence into practice are needed.
Methyl salicylate and trans‐anethole affect the pheromonal activity of homofarnesal, the female sex pheromone of azuki bean beetle
Authors: Chiluwal Kashinath , Kim Junheon , Bae Soon Do , Roh Gwang Hyun , Park Chung Gyoo 
Published: March 2018

AbstractPlant essential oils (EOs) exhibit an array of biological activities against insect pests. However, their negative influences on the pheromonal activity of azuki bean beetle (ABB), Callosobruchus chinensis L. have not received research attentions. ABB is a field‐to‐storage pest of legumes, and its female produces the sex pheromone known as homofarnesal with two isomeric components: 2E‐ and 2Z–homofarnesal, (2E,6E)‐7‐ethyl‐3,11‐dimethyl‐2,6,10‐dodecatrienals and (2Z,6E)‐7‐ethyl‐3,11‐dimethyl‐2,6,10‐dodecatrienals. We evaluated the effects of three EOs and their two major components on the attractiveness of male ABBs to synthetic homofarnesal (2E‐:2Z–homofarnesal = 6:4) using Y‐tube olfactometry in laboratory and rocket traps in the semi‐open polyhouse. Y‐tube olfactometry showed the significant negative effect of EOs of Illicium verum, Croton anisatum at 10 and 100 ng, and Gaultheria fragrantissima at 100 ng against homofarnesal (100 ng) in attracting male ABBs. Similarly trans‐anethole (at 10 and 100 ng) and methyl salicylate (at 100 ng) also ascertained significant negative effect against homofarnesal (100 ng) in Y‐tube olfactometry. When 10 mg of each of trans‐anethole and methyl salicylate was released at the downstream of 30 mg homofarnesal lure in rocket traps, highly significant effect was achieved against attractiveness of homofarnesal to ABB males. This study ascertained significant level of negative effect of the tested EOs and their major components to homofarnesal, tracing out a new opportunity of integrating them in ABB management programs both in field and storage.
Review of Leptocimbex formosanus group (Hymenoptera: Cimbicidae) with two new Chinese species
Authors: Yan Yuchen , Niu Gengyun , Lan Bocheng , Wei Meicai 
Published: March 2018

AbstractLeptocimbex formosanus group of Leptocimbex Semenov , Cimbicidae is defined and the relationships and characteristics are provided. Two new species of this group are described from Hunan and Yunnan Provinces in China: Leptocimbex shinoharai Yan & Wei sp. nov. and L. naitoi Yan & Wei sp. nov. Redescriptions of the three known species of L. formosanus group (L. formosanus Enslin , L. dendrobii Rohwer and L. nigropropodea Wei & Deng ) and a key to all known species of this group are provided.