bluuebunny/crossref_metadata_2025_split huggingface dataset:
Great strides of China's space programmes
Authors: Qiu Jane ,   writes for NSR from Beijing.
Published: January 2017

Abstract
While China's almost flawless space endeavours—such as its space lab Tiangong-2, launched last year, and the 2012 mission that sent a rover to the surface of the Moon—have long impressed the world, space-science missions were not among its priorities until recently. The situation improved in 2011 when the Chinese Academy of Sciences won government support for a 10-year Strategic Pioneering Programme on Space Science—with a total budget of nearly 1 billion dollars. Since then, China has launched satellites to probe dark matter, detect black holes and conduct quantum experiments from space. This year will see the launch of an astronomy satellite and a highly anticipated mission to bring back rocks from the Moon.
In a forum chaired by National Science Review's Executive Associate Editor Mu-ming Poo, space scientists discussed different types of Chinese space programmes, the science missions already launched or in development, the importance and challenges of international collaboration, and the uncertain future of the country's space-science development.
Chunlai Li Deputy Director, National Astronomical Observatories, Chinese Academy of Sciences, Beijing Ji Wu Director, National Centre of Space Science, Chinese Academy of Sciences, Beijing Jianyu Wang Deputy Director, Chinese Academy of Sciences Shanghai Branch Shuangnan Zhang Institute of High-Energy Physics, Chinese Academy of Sciences, Beijing Yifang Wang Director, Institute of High-Energy Physics, Chinese Academy of Sciences, Beijing Mu-ming Poo (Chair) Director, Institute of Neuroscience, Institute of High-Energy Physics, Chinese Academy of Sciences, Shanghai
Perinatal Biochemical Confirmation of Smoking Status by Trimester
Authors: Ashford Kristin , Wiggins Amanda , Rayens Emily , Assef Sara , Fallin Amanda , Rayens Mary Kay 
Published: January 2017

Abstract

Introduction:
Tobacco use during pregnancy is the most modifiable risk factor associated with poor pregnancy outcomes. Self-reported tobacco use has been demonstrated to have high misclassification rates. The aims were to examine misclassification rates of perinatal tobacco use during each trimester of pregnancy and 8 weeks postpartum, and to evaluate characteristics associated with misclassification of tobacco use status.

Methods:
This is secondary analysis of a prospective, multicenter trial of pregnant women, and it includes participants who were biochemically identified as tobacco users during their first trimester (N = 103). Each trimester and once postpartum, tobacco use was assessed via self-report and validated using a cutoff of 100 ng/mL for urine cotinine via NicAlert test strips to indicate current use. Those who self-reported as nonusers but were identified as users via urine cotinine were considered misclassified; misclassification rates were determined for each time period. Logistic regression assessed maternal factors associated with misclassification status.

Results:
Misclassification rates declined from 35.0% at first trimester to 31.9% and 26.6% at the second and third; the postpartum rate was 30.4%. These rates did not differ significantly from each other at the 0.05 level. Race/ethnicity was associated with misclassification status; white/non-Hispanic women were 87% less likely to be misclassified (p &lt; .001).

Conclusion:
Misclassification of prenatal smoking status decreases as pregnancy progresses, though the observed rate change was not significant. Minority women may be at particular risk for non-disclosure of tobacco use. Biochemical validation should be considered when assessing perinatal tobacco use via self-report, given high misclassification rates throughout the perinatal period.

Implications:
These results demonstrate that regardless of trimester, more than one-quarter of tobacco-using pregnant women may not disclose tobacco use throughout pregnancy and early postpartum. Although the rate of misclassification decreased from first to third trimester and then increased in the immediate postpartum, these changes in misclassification rates were not significant. Minority groups may be at particular risk of misclassification compared with white/non-Hispanic women. Biochemical validation is warranted throughout pregnancy to encourage cessation as tobacco use is one of the most easily-modified risk factors for poor birth outcomes.
Leveraging Lotteries for School Value-Added: Testing and Estimation*
Authors: Angrist Joshua D. , Hull Peter D. , Pathak Parag A. , Walters Christopher R. 
Published: January 2017

Abstract
Conventional value-added models (VAMs) compare average test scores across schools after regression-adjusting for students’ demographic characteristics and previous scores. This article tests for VAM bias using a procedure that asks whether VAM estimates accurately predict the achievement consequences of random assignment to specific schools. Test results from admissions lotteries in Boston suggest conventional VAM estimates are biased, a finding that motivates the development of a hierarchical model describing the joint distribution of school value-added, bias, and lottery compliance. We use this model to assess the substantive importance of bias in conventional VAM estimates and to construct hybrid value-added estimates that optimally combine ordinary least squares and lottery-based estimates of VAM parameters. The hybrid estimation strategy provides a general recipe for combining nonexperimental and quasi-experimental estimates. While still biased, hybrid school value-added estimates have lower mean squared error than conventional VAM estimates. Simulations calibrated to the Boston data show that, bias notwithstanding, policy decisions based on conventional VAMs that control for lagged achievement are likely to generate substantial achievement gains. Hybrid estimates that incorporate lotteries yield further gains.
Labor Markets and Poverty in Village Economies*
Authors: Bandiera Oriana , Burgess Robin , Das Narayan , Gulesci Selim , Rasul Imran , Sulaiman Munshi 
Published: January 2017

Abstract
We study how women's choices over labor activities in village economies correlate with poverty and whether enabling the poorest women to take on the activities of their richer counterparts can set them on a sustainable trajectory out of poverty. To do this we conduct a large-scale randomized control trial, covering over 21,000 households in 1,309 villages surveyed four times over a seven-year period, to evaluate a nationwide program in Bangladesh that transfers livestock assets and skills to the poorest women. At baseline, the poorest women mostly engage in low return and seasonal casual wage labor while wealthier women solely engage in livestock rearing. The program enables poor women to start engaging in livestock rearing, increasing their aggregate labor supply and earnings. This leads to asset accumulation (livestock, land, and business assets) and poverty reduction, both sustained after four and seven years. These gains do not crowd out the livestock businesses of noneligible households while the wages these receive for casual jobs increase as the poor reduce their labor supply. Our results show that (i) the poor are able to take on the work activities of the nonpoor but face barriers to doing so, and, (ii) one-off interventions that remove these barriers lead to sustainable poverty reduction.
Salt acclimation process: a comparison between a sensitive and a tolerant Olea europaea cultivar
Authors: Pandolfi Camilla , Bazihizina Nadia , Giordano Cristiana , Mancuso Stefano , Azzarello Elisa 
Published: January 2017

Abstract
Saline soils are highly heterogeneous in time and space, and this is a critical factor influencing plant physiology and productivity. Temporal changes in soil salinity can alter plant responses to salinity, and pre-treating plants with low NaCl concentrations has been found to substantially increase salt tolerance in different species in a process called acclimation. However, it still remains unclear whether this process is common to all plants or is only expressed in certain genotypes. We addressed this question by assessing the physiological changes to 100 mM NaCl in two contrasting olive cultivars (the salt-sensitive Leccino and the salt-tolerant Frantoio), following a 1-month acclimation period with 5 or 25 mM NaCl. The acclimation improved salt tolerance in both cultivars, but activated substantially different physiological adjustments in the tolerant and the sensitive cultivars. In the tolerant Frantoio the acclimation with 5 mM NaCl was more effective in increasing plant salt tolerance, with a 47% increase in total plant dry mass compared with non-acclimated saline plants. This enhanced biomass accumulation was associated with a 50% increase in K+ retention ability in roots. On the other hand, in the sensitive Leccino, although the acclimation process did not improve performance in terms of plant growth, pre-treatment with 5 and 25 mM NaCl substantially decreased salt-induced leaf cell ultrastructural changes, with leaf cell relatively similar to those of control plants. Taken together these results suggest that in the tolerant cultivar the acclimation took place primarily in the root tissues, while in the sensitive they occurred mainly at the shoot level.
Evolution of a wild-plant tobamovirus passaged through an exotic host: Fixation of mutations and increased replication
Authors: Koh Shu Hui , Li Hua , Sivasithamparam Krishnapillai , Admiraal Ryan , Jones Michael G.K. , Wylie Stephen J. 
Published: January 2017

Abstract
Tobamovirus is a group of viruses that have become serious pathogens of crop plants. As part of a study informing risk of wild plant virus spill over to crops, we investigated the capacity of a solanaceous-infecting tobamovirus from an isolated indigenous flora to adapt to new exotic hosts. Yellow tailflower mild mottle virus (YTMMV) (genus Tobamovirus, family Virgaviridae) was isolated from a wild plant of yellow tailflower (Anthocercis littoria, family Solanaceae) and initially passaged through a plant of Nicotiana benthamiana, then one of Nicotiana glutinosa where a single local lesion was used to inoculate a N. benthamiana plant. Sap from this plant was used as starting material for nine serial passages through three plant species. The virus titre was recorded periodically, and 85% of the virus genome was sequenced at each passage for each host. Six polymorphic sites were found in the YTMMV genome across all hosts and passages. At five of these, the alternate alleles became fixed in the viral genome until the end of the experiment. Of these five alleles, one was a non-synonymous mutation (U1499C) that occurred only when the virus replicated in tomato. The mutant isolate harbouring U1499C, designated YTMMV-δ, increased its titre over passages in tomato and outcompeted the wild-type isolate when both were co-inoculated to tomato. That YTMMV-δ had greater reproductive fitness in an exotic host than did the wild type isolate suggests YTMMV evolution is influenced by host changes.
Cash Transfers and Health: Evidence from Tanzania
Authors: Evans David K , Holtemeyer Brian , Kosec Katrina 
Published: January 2017

Abstract
How do cash transfers conditioned on health clinic visits and school attendance impact health-related outcomes? Examining the 2010 randomized introduction of a program in Tanzania, this paper finds nuanced impacts. An initial surge in clinic visits after 1.5 years—due to more visits by those already complying with program health conditions and by non-compliers—disappeared after 2.5 years, largely due to compliers reducing above-minimal visits. The study finds significant increases in take-up of health insurance and the likelihood of seeking treatment when ill. Health improvements were concentrated among children ages 0–5 years rather than the elderly, and took time to materialize; the study finds no improvements after 1.5 years, but 0.76 fewer sick days per month after 2.5 years, suggesting the importance of looking beyond short-term impacts. Reductions in sick days were largest in villages with more baseline health workers per capita, consistent with improvements being sensitive to capacity constraints. These results are robust to adjustments for multiple hypothesis testing.
Gender-Neutral Inheritance Laws, Family Structure, and Women’s Status in India
Authors: Mookerjee Sulagna 
Published: January 2017

Abstract
This paper examines whether economic empowerment of women improves their autonomy within their marital household, and investigates the mechanism, by exploiting variation from a legal reform aimed at improving women’s inheritance rights in India. Results suggest that the reform increased women’s participation in decision-making but at the expense of the older generation of household members and not at the expense of their husbands. Two channels are proposed to explain this phenomenon. First, this can be driven by a shift in the family structure from traditional joint families to nuclear households. Such a change is consistent both with the increase in women’s decision-making authority, which they can exert to move out of the joint household, as well as with men’s incentives, since men have weaker financial links with their parents post-reform. Second, even within joint families, the amendments empowered young couples at the expense of the older generation of household members.
Arabidopsis JASMONATE-INDUCED OXYGENASES down-regulate plant immunity by hydroxylation and inactivation of the hormone jasmonic acid
Authors: Caarls Lotte , Elberse Joyce , Awwanah Mo , Ludwig Nora R. , de Vries Michel , Zeilmaker Tieme , Van Wees Saskia C.M. , Schuurink Robert C. , Van den Ackerveken Guido 
Published: January 2017

ABSTRACTThe phytohormone jasmonic acid (JA) is vital in plant defense and development. Although biosynthesis of JA and activation of JA-responsive gene expression by the bioactive form JA-isoleucine (JA-Ile) have been well-studied, knowledge on JA metabolism is incomplete. In particular, the enzyme that hydroxylates JA to 12-OH-JA, an inactive form of JA that accumulates after wounding and pathogen attack, is unknown. Here, we report the identification of four paralogous 2-oxoglutarate/Fe(II)-dependent oxygenases inArabidopsis thalianaas JA hydroxylases and show that they down-regulate JA-dependent responses. As they are induced by JA we named themJASMONATE-INDUCED OXYGENASEs(JOXs). Concurrent mutation of the four genes in a quadruple Arabidopsis mutant resulted in increased defense gene expression and increased resistance to the necrotrophic fungusBotrytis cinereaand the caterpillarMamestra brassicae. In addition, root and shoot growth of the plants was inhibited. Metabolite analysis of leaves showed that loss of function of the four JOX enzymes resulted in over-accumulation of JA and in reduced turnover of JA into 12-OH-JA. Transformation of the quadruple mutant with eachJOXgene strongly reduced JA levels, demonstrating that all four JOXs inactivate JA in plants. Thein vitrocatalysis of 12-OH-JA from JA by recombinant enzyme could be confirmed for three JOXs. The identification of the enzymes responsible for hydroxylation of JA reveals a missing step in JA metabolism, which is important for the inactivation of the hormone and subsequent down-regulation of JA-dependent defenses.SIGNIFICANCE STATEMENTIn plants, the hormone jasmonic acid (JA) is synthesized in response to attack by pathogens and herbivores, leading to activation of defense responses. Rapidly following JA accumulation, the hormone is metabolized, presumably to prevent inhibitive effects of high JA levels on growth and development. The enzymes that directly inactivate JA were so far unknown. Here, we identify four jasmonate-induced oxygenases (JOXs) in Arabidopsis that hydroxylate jasmonic acid to form inactive 12-OH-JA. A mutant that no longer produces the four enzymes hyperaccumulates JA, exhibits reduced growth, and is highly resistant to attackers that are sensitive to JA-dependent defense. The JOX enzymes thus play an important role in determining the amplitude and duration of JA responses to balance the growth-defense tradeoff.
Semiparametric methods for estimation of a non-linear exposure–outcome relationship using instrumental variables with application to Mendelian randomization
Authors: Staley James R , Burgess Stephen 
Published: January 2017

AbstractMendelian randomization, the use of genetic variants as instrumental variables (IV), can test for and estimate the causal effect of an exposure on an outcome. Most IV methods assume that the function relating the exposure to the expected value of the outcome (the exposure-outcome relationship) is linear. However, in practice this assumption may not hold. Indeed, often the primary question of interest is to assess the shape of this relationship. We present two novel IV methods for investigating the shape of the exposure-outcome relationship: a fractional polynomial method and a piecewise linear method. We divide the population into strata using the exposure distribution, and estimate a causal effect, referred to as a localized average causal effect (LACE), in each stratum of population. The fractional polynomial method performs meta-regression on these LACE estimates. The piecewise linear method estimates a continuous piecewise linear function, the gradient of which is the LACE estimate in each stratum. Both methods were demonstrated in a simulation study to estimate the true exposure-outcome relationship well, particularly when the relationship was a fractional polynomial (for the fractional polynomial method) or was piecewise linear (for the piecewise linear method). The methods were used to investigate the shape of relationship of body mass index with systolic blood pressure and diastolic blood pressure.Availability and implementation:https://github.com/jrs95/nlmr
Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
Authors: Norton Scott , Vaquero-Garcia Jorge , Barash Yoseph 
Published: January 2017

AbstractMotivationA key component in many RNA-Seq based studies is contrasting multiple replicates from different experimental conditions. In this setup replicates play a key role as they allow to capture underlying biological variability inherent to the compared conditions, as well as experimental variability. However, what constitutes a “bad” replicate is not necessarily well defined. Consequently, researchers might discard valuable data or downstream analysis may be hampered by failed experiments.ResultsHere we develop a probability model to weigh a given RNA-Seq sample as a representative of an experimental condition when performing alternative splicing analysis. We demonstrate that this model detects outlier samples which are consistently and significantly different compared to other samples from the same condition. Moreover, we show that instead of discarding such samples the proposed weighting scheme can be used to downweight samples and specific splicing variations suspected as outliers, gaining statistical power. These weights can then be used for differential splicing (DS) analysis, where the resulting algorithm offers a generalization of the MAJIQ algorithm. Using both synthetic and real-life data we perform an extensive evaluation of the improved MAJIQ algorithm in different scenarios involving perturbed samples, mislabeled samples, no-signal groups, and different levels of coverage, showing it compares favorably to other tools. Overall, this work offers an outlier detection algorithm that can be combined with any splicing pipeline, a generalized and improved version of MAJIQ for differential splicing detection, and an evaluation pipeline researchers can use to evaluate which algorithm may work best for their needs.AvailabilityProgram is accessible viahttp://majiq.biociphers.org/norton_et_al_2017/Contacthttp://yosephb@upenn.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
Improving the performance of minimizers and winnowing schemes
Authors: Marçais Guillaume , Pellow David , Bork Daniel , Orenstein Yaron , Shamir Ron , Kingsford Carl 
Published: January 2017

AbstractThe minimizers scheme is a method for selectingk-mers from sequences. It is used in many bioinformatics software tools to bin comparable sequences or to sample a sequence in a deterministic fashion at approximately regular intervals, in order to reduce memory consumption and processing time. Although very useful, the minimizers selection procedure has undesirable behaviors (e.g., too manyk-mers are selected when processing certain sequences). Some of these problems were already known to the authors of the minimizers technique, and the natural lexicographic ordering ofk-mers used by minimizers was recognized as their origin. Many software tools using minimizers employ ad hoc variations of the lexicographic order to alleviate those issues.We provide an in-depth analysis of the effect ofk-mer ordering on the performance of the minimizers technique. By using small universal hitting sets (a recently defined concept), we show how to significantly improve the performance of minimizers and avoid some of its worse behaviors. Based on these results, we encourage bioinformatics software developers to use an ordering based on a universal hitting set or, if not possible, a randomized ordering, rather than the lexicographic order. This analysis also settles negatively a conjecture (by Schleimeret al.) on the expected density of minimizers in a random sequence.The software used for this analysis is available on GitHub:https://github.com/gmarcais/minimizers.git.Contact:gmarcais@cs.cmu.edu
THiCweed: fast, sensitive detection of sequence features by clustering big data sets
Authors: Agrawal Ankit , Sambare Snehal V. , Narlikar Leelavati , Siddharthan Rahul 
Published: January 2017

AbstractWe present THiCweed, a new approach to analyzing transcription factor binding data from high-throughput chromatin-immunoprecipitation-sequencing (ChIP-seq) experiments. THiCweed clusters bound regions based on sequence similarity using a divisive hierarchical clustering approach based on sequence similarity within sliding windows, while exploring both strands. ThiCweed is specially geared towards data containing mixtures of motifs, which present a challenge to traditional motif-finders. Our implementation is significantly faster than standard motif-finding programs, able to process 30,000 peaks in 1-2 hours, on a single CPU core of a desktop computer. On synthetic data containing mixtures of motifs it is as accurate or more accurate than all other tested programs.THiCweed performs best with large “window” sizes (≥ 50bp), much longer than typical binding sites (7-15 base pairs). On real data it successfully recovers literature motifs, but also uncovers complex sequence characteristics in flanking DNA, variant motifs, and secondary motifs even when they occur in < 5% of the input, all of which appear biologically relevant. We also find recurring sequence patterns across diverse ChIP-seq data sets, possibly related to chromatin architecture and looping. THiCweed thus goes beyond traditional motif-finding to give new insights into genomic TF binding complexity.