bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality Assessment of High-throughput DNA Sequencing Data via Range analysis
Authors: Külekci M. Oğuzhan , Fotouhi Ali , Majidi Mina 
Published: January 2017

AbstractIn the recent literature there appeared a number of studies for the quality assessment of sequencing data. These efforts, to a great extent, focused on reporting the statistical parameters regarding to the distribution of the quality scores and/or the base-calls in a FASTQ file. We investigate another dimension for the quality assessment motivated with the fact that reads including long intervals having fewer errors improve the performances of the post-processing tools in the down-stream analysis. Thus, the quality assessment procedures proposed in this study aim to analyze the segments on the reads that are above a certain quality. We define an interval of a read to be of desired quality when there are at mostkquality scores less than or equal to a threshold valuev, for somevandkprovided by the user. We present the algorithm to detect those ranges and introduce new metrics computed from their lengths. These metrics include the mean values for thelongest, shortest, average, cubic average, and average variation coefficientof the fragment lengths that are appropriate according to thevandkinput parameters. We provide a new software tool QASDRA for quality assessment of sequencing data via range analysis. QASDRA, implemented in Python, and publicly available athttps://github.com/ali-cp/QASDRA.git, creates the quality assessment report of an input FASTQ file according to the user specifiedkandvparameters. It also has the capabilities to filter out the reads according to the metrics introduced.
The seasonal climate niche predicts phenology and distribution of an ephemeral annual plant, Mollugo verticillata
Authors: Hereford Joe , Schmitt Johanna , Ackerly David D. 
Published: January 2017

Summary

Many short‐lived species complete their life cycles during brief seasonal windows of favourable environmental conditions. Such species may persist in the face of climate warming by migration to track their seasonal climate niche in space and/or by phenological shifts to track favourable conditions in time within the year. To describe the seasonal climate niche of the short‐lived annual Mollugo verticillata in California, we used data from herbarium specimens and historic climate records to estimate environmental conditions at the location, month and year of each collection.

We used these data in a MaxEnt framework to construct a seasonal species distribution model (SDM) of the species’ climate niche within the total climate space available across all seasons and locations in California. The model provides fine‐scale spatial and temporal predictions of habitat suitability, predicting both where and when the species should be observed.

We compared the predictions of the model to those from a conventional SDM based on mean annual climate data. Both models showed that M. verticillata is limited to warm environments within California. However, the seasonal SDM also predicted phenology by mapping climate suitability across the state for each month of the year. Mollugo verticillata is limited to warm months, and its seasonal climate niche shifts in space across California in the course of the year.

We used the seasonal SDM to map the predicted future species distribution for each month of the year under three warming scenarios. The species is predicted to expand its range and occur earlier in the year in most locations; in the warmest locations, seasonal suitability is predicted to decline in the warmest months, which may result in bimodal phenology with a mid‐summer gap.

Synthesis. We developed a novel species distribution model using herbarium records and monthly weather data, which predicts not only where a short‐lived species should be found but also when during the year it is predicted to occur in those areas. This model can be used to predict how climate change will affect the species distribution in space as well as seasonal phenology across the landscape.
Some Lessons of the SDP for Labour's Present Predicament
Authors: Liddle Roger 
Published: January 2017

AbstractJeremy Corbyn's election and re‐election as Labour leader, together with the emergence of a new Conservative Prime Minister committed to Brexit, has led to renewed speculation about the possibility of a new party appealing to the ‘politically homeless’ in the centre and centre‐left of British politics. This article draws lessons from the SDP experience in the early 1980s. Are the structural conditions more favourable to the progressive centre‐left now than they were then? Is there the sociological, electoral and ideological space for a new party? Does first past the post remain an insuperable barrier to an electoral breakthrough? From whom and in what circumstances might the leadership for a new party come? For all the depth of Labour's current problems, a new party seems an unlikely immediate prospect. In 1981, the SDP made a major miscalculation about the irreversibility of Labour's decline. However, the process of fragmentation in British politics seems set to continue.
Wild Lactobacillus strains: Technological characterisation and design of Coalho cheese lactic culture
Authors: Bruno Laura Maria , Briggiler Marcó Mariángeles , Capra Maria Luján , Carvalho Juliane Döering Gasparin , Meinardi Carlos , Quiberoni Andrea 
Published: January 2017

To design a specific lactic culture for the controlled manufacture of coalho cheese, 13 Lactobacillus rhamnosus, two Lactobacillus fermentum and one Lactobacillus plantarum strains isolated from artisanal coalho cheeses were identified and characterised. Two Lb. rhamnosus, one Lb. plantarum and one Lb. fermentum were selected and grouped in pairs designing four different culture formulations that demonstrated a good performance in cheesemaking experiments at pilot scale. Further studies to adjust the balance of strains used are necessary to attain adequate sensorial and technological attributes as expected for artisanal cheeses.
Functional analysis of the circadian clock gene timeless in Tribolium castaneum
Authors: Li Cheng‐Jun , Yun Xiao‐Pei , Yu Xiao‐Juan , Li Bin 
Published: January 2017

AbstractCircadian rhythms are endogenous oscillations with a period of about 24 h driven by a circadian clock. So far, variable oscillators have been found in insects. To explore the circadian clock of Tribolium castaneum, we cloned the clock gene timeless (Tctimeless). Its open reading frame is 3240 bp in length and consists of 10 exons. Tctimeless is highly expressed in the late pupal stage. Tissue‐specific expression analysis in late adult stages revealed high expression of Tctimeless in the head, epidermis, fat body and accessory glands. Silencing of Tctimeless by RNA interference (RNAi) at the late larval stages caused a failure to initiate eclosion. Tctimeless knockdown in late pupal stages led to a gender‐independent decline in egg production and progeny survival. As a core clock gene, Tctimeless exhibited one expression peak in the middle of the circadian day. Knockdown of Tctimeless disrupted daily expression patterns of Tccycle, Tcclock, Tcperiod and itself, while Tctimeless and Tcperiod expression patterns over the circadian day were also perturbed when Tccycle or Tcclock is suppressed by RNAi. This study identified a complex transcriptional relationship among circadian clock genes in T. castaneum.
Resprouting of woody species encroaching temperate European grasslands after cutting and burning
Authors: Michielsen Mathias , Szemák László , Fenesi Annamária , Nijs Ivan , Ruprecht Eszter 
Published: January 2017

AbstractQuestionsAre there interspecific differences in resprouting after cutting and burning among woody species encroaching temperate grasslands? Are alien woody species more successful than natives in their resprouting after the two treatments proposed to control shrub encroachment? Is resprouting influenced by age of the individuals? Does resprouting differ between cutting and burning?LocationTemperate grasslands encroached by shrubs, Transylvania, Romania.MethodsWe investigated the resprouting after cutting or burning of four shrub species (Cornus sanguinea, Crataegus monogyna, Prunus spinosa and Rosa canina) encroaching grasslands in field sites 3 yr following treatments. We compared the resprouting ability of shrubs between species and treatments and analysed the relationship between the number of resprouts and stump diameter, as a proxy for age. In a common garden experiment on 1‐yr‐old individuals we compared resprouting after cutting and burning between three native (C. sanguinea, C. monogyna and P. spinosa) and three alien woody species (Ailanthus altissima, Elaeagnus angustifolia and Hippophae rhamnoides) during one growing season.ResultsC. monogyna produced the largest number of resprouts in the field study, and H. rhamnoides in the experimental study. Overall, resprouting ability of alien woody species did not differ from that of natives. In the field study, we found an increasing number of resprouts with increasing stump diameter, and the rate of increase in the number of resprouts was highest in C. monogyna. We detected no difference in the resprouting of woody species between cutting and burning treatments either in the field or in the experimental study.ConclusionsOur study suggests that the success of encroachment control in grasslands does not depend on treatment type, but on the woody species composition and age of individuals. Grasslands encroached by C. monogyna or H. rhamnoides will be more labour‐intensive to restore and maintain free of shrubs. Restoration measures should be implemented in the early stage of shrub encroachment since younger shrubs have lower resprouting ability. Burning and cutting may be equally effective in controlling shrub encroachment, but treatments should be more intensive than in the current study in order to damage the resprouting buds and arrest resprouting.
The role of shame in people with a diagnosis of schizophrenia
Authors: Keen Nadine , George Darren , Scragg Peter , Peters Emmanuelle 
Published: January 2017

ObjectivesTo examine the role of shame and its relationship to depression in schizophrenia. It was predicted that individuals with a diagnosis of schizophrenia would exhibit higher levels of shame due to the stigma associated with their diagnosis, independently of depression levels, compared with psychiatric and medical control groups.DesignCross‐sectional design with three groups: individuals with a diagnosis of (1) schizophrenia, (2) depression, and (3) rheumatoid arthritis.MethodsSixty individuals participated in the study (20 per group). Groups were compared on questionnaires assessing external shame, trait shame and guilt, and depression.ResultsThe pattern of group differences depended on the type of shame measure used. Both the schizophrenia and depression groups exhibited higher levels of external shame, or seeing others as shaming, than the medical group. For individuals with schizophrenia, seeing others as shaming was associated with higher levels of depression, a relationship not found in either control group. They also showed lower levels of trait guilt and shame (at trend level), compared with both control groups. No difference was found between the groups on depression, suggesting that the observed differences were not attributable to differences in levels of depression.ConclusionsThe findings highlight the importance of shame in schizophrenia, especially the link between seeing other people as shaming and depression, which was unique to this group. These results suggest that stigma associated with a diagnosis of mental illness, and schizophrenia in particular, has negative emotional consequences that may impede recovery, and should be addressed by psychological and social interventions.Practitioner points

Clinical implications

Individuals with a diagnosis of mental illness (schizophrenia or depression) are more likely to experience others as shaming than those diagnosed with a physical illness, irrespective of current levels of depression and proneness to shame.

There is a specific association between external shame and depression in individuals diagnosed with schizophrenia, suggesting the need for interventions levelled both at the individual's illness appraisals, and at social stigma relating to schizophrenia.

Limitations of the study

The participant numbers were low in each group.

The three groups could not be matched on all variables.

No additional internalized‐stigma measure was used.
Editorial: CAMHS goes mainstream
Authors: Fonagy Peter , Pugh Kathryn 
Published: January 2017

Over the last 2 years the world has woken up to something that we in the world of children and young people's mental health have known for a very long time – the best correlate of adult life satisfaction is not income but physical and mental health, and we can predict adult life satisfaction best, not from academic qualifications but from the emotional health of 16‐year olds (Clark, Fleche, Layard, Powdthavee, & Ward, 2016). The overwhelming burden of disease associated with mental ill health suggests that early intervention focused on child mental health is probably the most effective social investment any government could make both from economic and ethical perspectives. We are now at the moment of national insight – so how will we translate this into real goals and action, and drive our own effective strategies?
Associations between participation in family activities and adolescent school problems
Authors: Goldfarb S. S. , Locher J. L. , Preskitt J. , Becker D. , Davies S. L. , Sen B. 
Published: January 2017

SummaryIntroductionAdolescent risk outcomes related to school issues are widespread, with about 20% parents reporting poor school engagement amongst their youth. Previous literature suggests that adolescents who report strong bonds with their parents are often identified as being less likely to engage in risky behaviours, such as substance use. The current study sought to examine the association between the frequencies of selected family activities and school problems amongst adolescents after adjustments for family connectedness and other characteristics.MethodsData were drawn from the National Longitudinal Survey of Youth, 1997. Of the 8984 youth interviewed, 3855 also had a sibling interviewed who met the selection criteria. School problem outcomes measured were suspension occurrence, poor grades and highest grade completed low for age. Independent variables of interest were self‐reported frequency of family dinner, fun and religious activities in a typical week. Multivariable logistic models were estimated for each outcome, and multivariable linear probability models were estimated adjusting for family fixed effects.ResultsAdjusting for family connectedness, there were significant associations between certain family activities and adolescent school problem measures. However, these results did not remain significant in models with family fixed effects, suggesting that associations could be driven by family‐level confounders.DiscussionThis study did not find strong evidence of a protective relationship between family activities and school problems. Therefore, it suggested that programme and policymakers be cautious in overstating the importance of family activities in preventing adolescent risk outcomes until true causal relationships can be determined.
An evaluation of the quality of evidence available to inform current bone conducting hearing device national policy
Authors: Mandavia R. , Carter A.W. , Haram N. , Mossialos E. , Schilder A.G.M. 
Published: January 2017

ObjectivesIn 2016, NHS England published the commissioning policy on Bone Conducting Hearing Devices (BCHDs). This policy was informed by updated evidence on the clinical and cost‐effectiveness of BCHDs as well as by the 2013 Bone Anchored Hearing Aid (BAHA) policy. Commissioning policies set the criteria for service delivery and therefore have a major impact on the care received by patients. It is important that stakeholders have a good appreciation of the available evidence informing policy, as this will promote engagement both with the policy and with future research leading on from the policy. In this article, we provide stakeholders with a transparent and pragmatic assessment of the quality of the body of evidence available to inform current BCHD national policy.Method(i) A systematic review of the literature on BCHDs published since the development of the 2013 policy was performed in September 2016, adhering to PRISMA recommendations. The search terms used were as follows bone conduction; bone conducting; bone anchor; BAHA; Bone Anchored Hearing Aid; Bone Conducting Hearing Device; BCHD; Bone Conducting Hearing Implant; BCHI; Sophono; Bonebridge; Soundbite; Ponto; Hearing aid; implant; device; hearing device. Publications that could inform current BCHD policy were included. The quality of included articles was assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) system. (ii) The quality of evidence referenced by the 2013 BAHA policy was assessed using the GRADE system.Results(i) Of the 2576 publications on BCHDs identified by the systematic search, 39 met the inclusion criteria for further analysis. Using the GRADE criteria, the quality of evidence was classified as of ‘very low quality’. (ii) The 2013 BAHA policy was informed by 14 references. The GRADE system classifies the quality of evidence that informed the policy as of ‘very low quality’.ConclusionsThe GRADE system defines the body of evidence available to inform current national BCHD policy as of ‘very low quality’. There is an urgent need for high‐quality research to help make informed policy decisions about the care of patients with hearing loss. An (inter)national registry of BCHDs could address this need.
Early exposure to predation risk carries over metamorphosis in two distantly related freshwater insects
Authors: FONTANA‐BRIA LAIA , SELFA JESÚS , TUR CARLES , FRAGO ENRIC 
Published: January 2017

1. Predation and competition play a central role in ecological communities, and it is increasingly recognised that animals use early warning cues to reduce the impact of these antagonistic interactions.2. Strategies to avoid risk can occur during embryo development through plasticity in egg hatching time. This strategy, and its associated costs and carryover effects on adults are little understood in insects. In this study, these are explored in two distantly related freshwater insects: the damselfly Ischnura elegans and the mosquito Aedes albopictus.3. As predicted, damselfly eggs hatched earlier in response to larval predators cues, a treatment that also affected adult size. Risk cues did not affect mosquito egg hatching time, but they did affect larval development time in a sex‐dependent manner.4. The results suggest that responses aimed at avoiding risks can be triggered during the egg stage, and although they can vary dramatically among species, they are likely to be widespread in insects. Early warning responses can be particularly important to understand the ecology of aquatic insects, some of them global vectors of human diseases.
The second Team Haemophilia Education Meeting, 2016, Frankfurt, Germany
Authors: Berntorp Erik , Dargaud Yesim , Hart Daniel , Lobet Sébastien , Mancuso Maria Elisa , d'Oiron Roseline , Perry David , Pollard Debra , van den Berg Marijke , Blatný Jan , Chambost Hervé , Doria Andrea S. , Holme Pål André , Kaczmarek Radoslaw , Mantovani Lorenzo , McLaughlin Paul , Nanayakkara Lochana , Petrini Pia , Sannié Thomas , Laane Edward , Maia Raquel , Dettoraki Athina , Farrell Anna , Halimeh Susan , Raza Sayma , Taylor Stephanie 
Published: January 2017

AbstractThe first Team Haemophilia Education (THE) Meeting was held on 7–8 May 2015 in Amsterdam, The Netherlands. It aimed to promote the optimal care of patients with haemophilia through education of the multidisciplinary treatment team. This was achieved by reviewing the latest developments in haemophilia management, considering how these can be implemented in the clinic to improve patient care and providing a platform for networking and debate for all haemophilia treatment team members. The second THE Meeting was held on 19–20 May in Frankfurt, Germany, and participants included doctors, nurses, physiotherapists, patient representatives and data management staff from 20 different countries. Topics covered the role of the multidisciplinary team in delivering the best haemophilia care, challenges in the management of haemophilia across Europe, available clotting factor treatments, future treatments and the use of genetics in advising carriers of haemophilia. This report is a summary of the key developments in haemophilia care presented by various investigators and healthcare professionals at THE Meeting 2016.
Microbial diversity and soil functions
Authors: Nannipieri P. , Ascher J. , Ceccherini M. T. , Landi L. , Pietramellara G. , Renella G. 
Published: January 2017

SummarySoil is a complex and dynamic biological system, and still in 2003 it is difficult to determine the composition of microbial communities in soil. We are also limited in the determination of microbially mediated reactions because present assays for determining the overall rate of entire metabolic processes (such as respiration) or specific enzyme activities (such as urease, protease and phosphomonoesterase activity) do not allow any identification of the microbial species directly involved in the measured processes. The central problem posed by the link between microbial diversity and soil function is to understand the relations between genetic diversity and community structure and between community structure and function. A better understanding of the relations between microbial diversity and soil functions requires not only the use of more accurate assays for taxonomically and functionally characterizing DNA and RNA extracted from soil, but also high‐resolution techniques with which to detect inactive and active microbial cells in the soil matrix.Soil seems to be characterized by a redundancy of functions; for example, no relationship has been shown to exist between microbial diversity and decomposition of organic matter. Generally, a reduction in any group of species has little effect on overall processes in soil because other microorganisms can take on its function.The determination of the composition of microbial communities in soil is not necessary for a better quantification of nutrient transformations. The holistic approach, based on the division of the systems in pools and the measurement of fluxes linking these pools, is the most efficient. The determination of microbial C, N, P and S contents by fumigation techniques has allowed a better quantification of nutrient dynamics in soil. However, further advances require determining new pools, such as active microbial biomass, also with molecular techniques. Recently investigators have separated 13C‐ and 12C‐DNA, both extracted from soil treated with a 13C source, by density‐gradient centrifugation. This technique should allow us to calculate the active microbial C pool by multiplying the ratio between labelled and total DNA by the microbial biomass C content of soil. In addition, the taxonomic and functional characterization of 13C‐DNA allows us to understand more precisely the changes in the composition of microbial communities affected by the C‐substrate added to soil.