bluuebunny/crossref_metadata_2025_split huggingface dataset:
Participation in Rural Land Rental Markets in Sub‐Saharan Africa: Who Benefits and by How Much? Evidence from Malawi and Zambia
Authors: Chamberlin Jordan , Ricker‐Gilbert Jacob 
Published: July 2016

AbstractWe use nationally representative household‐level panel survey data in two neighboring countries in Southern Africa—Zambia and Malawi—to characterize the current status of rural land rental market participation by smallholder farmers, and their subsequent welfare impacts. Rural rental market participation is much higher in densely‐populated Malawi than in lower‐density Zambia, reflecting the role of land scarcity in driving rental market development. Consistent with previous literature, we find evidence that rental markets contribute to efficiency gains within the smallholder sector by facilitating the transfer of land from less‐able to more‐able producers, on average, in both countries. Furthermore, we find that rental markets serve to re‐allocate land from relatively land‐rich to land‐poor households. We examine the impacts of participation on a number of welfare outcomes and find evidence for generally positive returns to renting in land in both countries, on average. However, our analysis also indicates that the returns to renting in land vary strongly with scale of production: tenants who produce more have larger returns to renting in, and many of the smaller producers who rent in do so at an economic loss. The impacts of renting out (i.e., participating in markets as landlords) are decidedly more mixed, with overall negative returns to landlords in Malawi and negligible returns to landlords in Zambia. The findings in this article highlight the need for researchers and policymakers in sub‐Saharan Africa to stay attuned to how land rental market participation and its impacts evolve in the near future.
Psychosocial Correlates of Nocturnal Blood Pressure Dipping in African Americans: The Jackson Heart Study
Authors: Spruill Tanya M. , Shallcross Amanda J. , Ogedegbe Gbenga , Chaplin William F. , Butler Mark , Palfrey Amy , Shimbo Daichi , Muntner Paul , Sims Mario , Sarpong Daniel F. , Agyemang Charles , Ravenell Joseph 
Published: July 2016

Abstract

BACKGROUND
African Americans exhibit a lower degree of nocturnal blood pressure (BP) dipping compared with Whites, but the reasons for reduced BP dipping in this group are not fully understood. The aim of this study was to identify psychosocial factors associated with BP dipping in a population-based cohort of African Americans.

METHODS
This cross-sectional study included 668 Jackson Heart Study (JHS) participants with valid 24-hour ambulatory BP data and complete data on psychosocial factors of interest including stress, negative emotions, and psychosocial resources (e.g., perceived support). The association of each psychosocial factor with BP dipping percentage and nondipping status (defined as &lt;10% BP dipping) was assessed using linear and Poisson regression models, respectively, with progressive adjustment for demographic, socioeconomic, biomedical, and behavioral factors.

RESULTS
The prevalence of nondipping was 64%. Higher depressive symptoms, higher hostility, and lower perceived social support were associated with a lower BP dipping percentage in unadjusted models and after adjustment for age, sex, body mass index, and mean 24-hour systolic BP ( P &lt; 0.05). Only perceived support was associated with BP dipping percentage in fully adjusted models. Also, after full multivariable adjustment, the prevalence ratio for nondipping BP associated with 1 SD (7.1 unit) increase in perceived support was 0.93 (95% CI: 0.88–0.99). No other psychosocial factors were associated with nondipping status.

CONCLUSIONS
Lower perceived support was associated with reduced BP dipping in this study. The role of social support as a potentially modifiable determinant of nocturnal BP dipping warrants further investigation.
Aldosterone Antagonists or Renin-Guided Therapy for Treatment-Resistant
Hypertension: A Comparative Effectiveness Pilot Study in Primary Care
Authors: Egan Brent M. , Laken Marilyn A. , Sutherland Susan E. , Qanungo Suparna , Fleming Douglas O. , Cook Anne G. , Hester William H. , Jones Kelly W. , Jebaily Gerard C. , Valainis Gregory T. , Way Charles F. , Wright Mary Beth , Davis Robert A. 
Published: July 2016

Abstract

BACKGROUND
Uncontrolled treatment-resistant hypertension (TRH), i.e., blood pressure (BP, mm Hg) ≥140/≥90mm Hg in and out of office on ≥3 different BP medications at optimal doses, is common and has a poor prognosis. Aldosterone antagonist (AA) and renin-guided therapy (RGT) are effective strategies for improving BP control in TRH but have not been compared.

METHODS
A comparative effectiveness TRH pilot study of AA vs. RGT was conducted in 4 primary care clinics with 2 each randomized to AA or RGT. The primary outcome was change in clinic BP defined by means of 5 automated office BP values. Eighty-nine patients with apparent TRH were screened and 44 met criteria for true TRH.

RESULTS
Baseline characteristics of 20 patients in the AA (70% Black, 45% female, mean age: 57.4 years) and 24 patients in RGT (79% Black, 50% female, 57.8 years) arms were similar with baseline BP 162±5/90±3 vs. 153±3/84±3, respectively, P = 0.11/0.20. BP declined to 144±5/86±4 in AA vs. 132±4/75±3 in RGT, P = 0.07/0.01; BP was controlled to JNC7 (Seventh Joint National Committee Report) goal in 25% vs. 62.5%, respectively, P &lt; 0.01. Although BP changes from baseline, the primary outcome, were not different (−17.6±5.1/−4.0±3.0 AA vs. −20.4±3.8/−9.7±2.0 RGT, P = 0.65/0.10.), more BP medications were added with AA than RGT (+0.9±0.1 vs. +0.4±0.1 per patient, P &lt; 0.01).

CONCLUSIONS
In this TRH pilot study, AA and RGT lowered BP similarly, although fewer additional medications were required with RGT. A larger comparative effectiveness study could establish the utility of these treatment strategies for lowering BP of uncontrolled TRH patients in primary care.
samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files
Authors: Stupnikov Alexey , Tripathi Shailesh , de Matos Simoes Ricardo , McArt Darragh , Salto-Tellez Manuel , Glazko Galina , Dehmer Matthias , Emmert-Streib Frank 
Published: July 2016

Abstract
Motivation: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (i) a cost efficient and (ii) an optimal experimental design leading to a compromise, e.g. in the sequencing depth of experiments.
Results: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.
Availability and Implementation: samExploreR is available as an R package from Bioconductor.
Contact: v@bio-complexity.com
Supplementary information: Supplementary data are available at Bioinformatics online.
New quality measure for SNP array based CNV detection
Authors: Macé A. , Tuke M.A. , Beckmann J.S. , Lin L. , Jacquemont S. , Weedon M.N. , Reymond A. , Kutalik Z. 
Published: July 2016

Abstract
Motivation: Only a few large systematic studies have evaluated the impact of copy number variants (CNVs) on common diseases. Several million individuals have been genotyped on single nucleotide variation arrays, which could be used for genome-wide CNVs association studies. However, CNV calls remain prone to false positives and only empirical filtering strategies exist in the literature. To overcome this issue, we defined a new quality score (QS) estimating the probability of a CNV called by PennCNV to be confirmed by other software.
Results: Out-of-sample comparison showed that the correlation between the consensus CNV status and the QS is twice as high as it is for any previously proposed CNV filters. ROC curves displayed an AUC higher than 0.8 and simulations showed an increase up to 20% in statistical power when using QS in comparison to other filtering strategies. Superior performance was confirmed also for alternative consensus CNV definition and through improving known CNV-trait associations.
Availability and Implementation: http://goo.gl/T6yuFM
Contact: zoltan.kutalik@unil.ch or aurelien@mace@unil.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
The
Affaire des placards
, Polemical Humour, and The Sardonic Laugh
Authors: Hayes Bruce 
Published: July 2016

Abstract

Working with Erasmus’s exploration of the sardonic laugh, this article begins with the placard of the notorious Affaire des placards of 17–18 October 1534. The aim is to uncover uses of polemical humour in pamphlets produced during the early years of religious conflict in France. Starting with Antoine Marcourt, the likely author of the placard, the article investigates Marcourt’s first known satirical pamphlet, the
Livre des marchans
. This is followed by a study of Jérome Hangest’s response to the affaire. Hangest was not only the person designated by the Sorbonne to produce a response to the placards, but also one of the first Catholics to attempt to counteract the effects of Protestant propaganda in France. Finally, this article examines Marcourt’s enigmatic co-religionist, Marie Dentière, whose work also contains illuminating examples of the sardonic laugh. In all of this, the goal is to uncover connections between humour and violence, as well as growing suspicions about the uses and dangers of laughter. As new, more vicious forms of satire are developed, suspicions about these also intensify, and, in an increasingly polarized society, there is little room left for laughter other than the sardonic laugh.
Impact of computerized provider order entry (CPOE) on length of stay and mortality
Authors: Lyons Ann M , Sward Katherine A , Deshmukh Vikrant G , Pett Marjorie A , Donaldson Gary W , Turnbull Jim 
Published: July 2016

Objective: To examine changes in patient outcome variables, length of stay (LOS), and mortality after implementation of computerized provider order entry (CPOE).Materials and Methods: A 5-year retrospective pre-post study evaluated 66 186 patients and 104 153 admissions (49 683 pre-CPOE, 54 470 post-CPOE) at an academic medical center. Generalized linear mixed statistical tests controlled for 17 potential confounders with 2 models per outcome.Results: After controlling for covariates, CPOE remained a significant statistical predictor of decreased LOS and mortality. LOS decreased by 0.90 days, P &lt; .0001. Mortality decrease varied by model: 1 death per 1000 admissions (pre = 0.006, post = 0.0005, P &lt; .001) or 3 deaths (pre = 0.008, post = 0.005, P &lt; .01). Mortality and LOS decreased in medical and surgical units but increased in intensive care units.Discussion: This study examined CPOE at multiple levels. Given the inability to randomize CPOE assignment, these results may only be applicable to the local setting. Temporal trends found in this study suggest that hospital-wide implementations may have impacted nursing staff and new residents. Differences in the results were noted at the patient care unit and room levels. These differences may partly explain the mixed results from previous studies.Conclusion: Controlling for confounders, CPOE implementation remained a statistically significant predictor of LOS and mortality at this site. Mortality appears to be a sensitive outcome indicator with regard to hospital-wide implementations and should be further studied.
Tyrosine receptor kinase B is a drug target in astrocytomas
Authors: Ni Jing , Xie Shaozhen , Ramkissoon Shakti H. , Luu Victor , Sun Yu , Bandopadhayay Pratiti , Beroukhim Rameen , Roberts Thomas M. , Stiles Charles D. , Segal Rosalind A. , Ligon Keith L. , Hahn William C. , Zhao Jean J. 
Published: July 2016

Abstract

Background.
Astrocytomas are the most common primary human brain tumors. Receptor tyrosine kinases (RTKs), including tyrosine receptor kinase B (TrkB, also known as tropomyosin-related kinase B; encoded by neurotrophic tyrosine kinase receptor type 2 [NTRK2]), are frequently mutated by rearrangement/fusion in high-grade and low-grade astrocytomas. We found that activated TrkB can contribute to the development of astrocytoma and might serve as a therapeutic target in this tumor type.

Methods.
To identify RTKs capable of inducing astrocytoma formation, a library of human tyrosine kinases was screened for the ability to transform murine Ink4a−/−/Arf−/− astrocytes. Orthotopic allograft studies were conducted to evaluate the effects of RTKs on the development of astrocytoma. Since TrkB was identified as a driver of astrocytoma formation, the effect of the Trk inhibitors AZD1480 and RXDX-101 was assessed in astrocytoma cells expressing activated TrkB. RNA sequencing, real-time PCR, western blotting, and enzyme-linked immunosorbent assays were conducted to characterize NTRK2 in astrocytomas.

Results.
Activated TrkB cooperated with Ink4a/Arf loss to induce the formation of astrocytomas through a mechanism mediated by activation of signal transducer and activator of transcription 3 (STAT3). TrkB activation positively correlated with Ccl2 expression. TrkB-induced astrocytomas remained dependent on TrkB signaling for survival, highlighting a role of NTRK2 as an addictive oncogene. Furthermore, the QKI-NTRK2 fusion associated with human astrocytoma transformed Ink4a−/−/Arf−/− astrocytes, and this process was also mediated via STAT3 signaling.

Conclusions.
Our findings provide evidence that constitutively activated NTRK2 alleles, notably the human tumor-associated QKI-NTRK2 fusion, can cooperate with Ink4a/Arf loss to drive astrocytoma formation. Therefore, we propose NTRK2 as a potential therapeutic target in the subset of astrocytoma patients defined by QKI-NTRK2 fusion.
Measuring Economic Policy Uncertainty*
Authors: Baker Scott R. , Bloom Nicholas , Davis Steven J. 
Published: July 2016

Abstract
We develop a new index of economic policy uncertainty (EPU) based on newspaper coverage frequency. Several types of evidence—including human readings of 12,000 newspaper articles—indicate that our index proxies for movements in policy-related economic uncertainty. Our U.S. index spikes near tight presidential elections, Gulf Wars I and II, the 9/11 attacks, the failure of Lehman Brothers, the 2011 debt ceiling dispute, and other major battles over fiscal policy. Using firm-level data, we find that policy uncertainty is associated with greater stock price volatility and reduced investment and employment in policy-sensitive sectors like defense, health care, finance, and infrastructure construction. At the macro level, innovations in policy uncertainty foreshadow declines in investment, output, and employment in the United States and, in a panel vector autoregressive setting, for 12 major economies. Extending our U.S. index back to 1900, EPU rose dramatically in the 1930s (from late 1931) and has drifted upward since the 1960s.
Evaluating Public Programs with Close Substitutes: The Case of Head
Start*
Authors: Kline Patrick , Walters Christopher R. 
Published: July 2016

Abstract
We use data from the Head Start Impact Study (HSIS) to evaluate the cost-effectiveness of Head Start, the largest early childhood education program in the United States. Head Start draws roughly a third of its participants from competing preschool programs, many of which receive public funds. We show that accounting for the fiscal impacts of such program substitution pushes estimates of Head Start’s benefit-cost ratio well above one under a wide range of assumptions on the structure of the market for preschool services and the dollar value of test score gains. To parse the program’s test score impacts relative to home care and competing preschools, we selection-correct test scores in each care environment using excluded interactions between experimental assignments and household characteristics. We find that Head Start generates larger test score gains for children who would not otherwise attend preschool and for children who are less likely to participate in the program.
Electrocaloric and elastocaloric effects in soft materials
Authors: Trček Maja , Lavrič Marta , Cordoyiannis George , Zalar Boštjan , Rožič Brigita , Kralj Samo , Tzitzios Vassilios , Nounesis George , Kutnjak Zdravko 
Published: July 2016

Materials with large caloric effect have the promise of realizing solid-state refrigeration which has potential to be more efficient and environmentally friendly compared with current cooling technologies. Recently, the focus of caloric effects investigations has shifted towards soft materials. An overview of recent direct measurements of the large electrocaloric effect (ECE) in a composite mixture of a liquid crystal and nanoparticles (NPs) and large elastocaloric (eC) effect in main-chain liquid crystal elastomers is given. In mixtures of 12CB liquid crystal with functionalized CdSSe NPs, an ECE exceeding 5 K was found in the vicinity of the isotropic to smectic A phase transition. It is shown that the NPs smear the isotropic to smectic coexistence range in which a large ECE is observed due to latent heat enhancement. NPs acting as traps for ions reduce the moving-ion density and consequently the Joule heating. Direct eC measurements indicate that the significant eC response can be found in main-chain liquid crystalline elastomers, but at a fraction of the stress field in contrast to other eC materials. Both soft materials could play a significant role as active cooling elements or parts of thermal diodes in development of new cooling devices.
This article is part of the themed issue ‘Taking the temperature of phase transitions in cool materials’.
Elastocaloric effect in CuAlZn and CuAlMn shape memory alloys under compression
Authors: Qian Suxin , Geng Yunlong , Wang Yi , Pillsbury Thomas E. , Hada Yoshiharu , Yamaguchi Yuki , Fujimoto Kenjiro , Hwang Yunho , Radermacher Reinhard , Cui Jun , Yuki Yoji , Toyotake Koutaro , Takeuchi Ichiro 
Published: July 2016

This paper reports the elastocaloric effect of two Cu-based shape memory alloys: Cu68Al16Zn16(CuAlZn) and Cu73Al15Mn12(CuAlMn), under compression at ambient temperature. The compression tests were conducted at two different rates to approach isothermal and adiabatic conditions. Upon unloading at a strain rate of 0.1 s−1(adiabatic condition) from 4% strain, the highest adiabatic temperature changes (ΔTad) of 4.0 K for CuAlZn and 3.9 K for CuAlMn were obtained. The maximum stress and hysteresis at each strain were compared. The stress at the maximum recoverable strain of 4.0% for CuAlMn was 120 MPa, which is 70% smaller than that of CuAlZn. A smaller hysteresis for the CuAlMn alloy was also obtained, about 70% less compared with the CuAlZn alloy. The latent heat, determined by differential scanning calorimetry, was 4.3 J g−1for the CuAlZn alloy and 5.0 J g−1for the CuAlMn alloy. Potential coefficients of performance (COPmat) for these two alloys were calculated based on their physical properties of measured latent heat and hysteresis, and a COPmatof approximately 13.3 for CuAlMn was obtained.This article is part of the themed issue ‘Taking the temperature of phase transitions in cool materials’.
Estimates of local biodiversity change over time stand up to scrutiny
Authors: Vellend Mark , Dornelas Maria , Baeten Lander , Beauséjour Robin , Brown Carissa D. , De Frenne Pieter , Elmendorf Sarah C. , Gotelli Nicholas J. , Moyes Faye , Myers-Smith Isla H. , Magurran Anne E. , McGill Brian J. , Shimadzu Hideyasu , Sievers Caya 
Published: July 2016

AbstractTwo recent meta-analyses of local-scale biodiversity change over time, by the authors of the present paper, have been subject to a harsh critique. Here we use new data and analyses to respond to the main points of this critique. First, a central argument of the critique was that short-term time series lead to biased estimates of long-term biodiversity change. However, we show here that this conclusion was based entirely on two fundamental mistakes in the simulations used to support it. Second, we show that the critic's conclusion that there are negative relationships between temporal biodiversity change and study duration is entirely dependent on: (i) the unrealistic assumption that biodiversity change can be positive when study duration = 0; (ii) the use of only a subset of the available data; (iii) inclusion of a single outlier data point in a single study (out of 100 in this case); and/or (iv) a choice to use log ratios rather than slopes (when available) as the metric of temporal biodiversity change. In short, the evidence does not support the conclusion that studies of longer duration tend to find local diversity decline. Finally, the critique highlighted the obviously true fact that studies in the ecological literature represent a geographically biased sample of locations on Earth; this issue was noted in both original papers, and is relevant for all ecological data syntheses. This fact was used by the critics to cast doubt on our conclusion that, outside of areas converted to croplands or asphalt, the distribution of temporal biodiversity trends is centered on zero. As a scientific rule, future studies based on more or different data may cause us to modify our conclusion, but at present, alternative conclusions based on the geographic-bias argument rely entirely on speculation. In sum, the critique raises points of uncertainty typical of all ecological studies, but it falls far short of providing an evidence-based alternative interpretation for our results, which are now supported by syntheses of hundreds of individual data sets of temporal biodiversity change.
Whole genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver
Authors: Li Xin , Liu Yun , Salz Tal , Hansen Kasper D. , Feinberg Andrew 
Published: July 2016

AbstractDNA methylation at the 5-postion of cytosine (5mC) is a well-established epigenetic modification which regulates gene expression and cellular plasticity in development and disease. The ten-eleven translocation (TET) gene family is able to oxidize 5mC to 5-hydroxymethyl-cytosine (5hmC), providing an active mechanism for DNA demethylation, and may also provide its own regulatory function. Here we applied oxidative bisulfite sequencing to generate whole-genome DNA methylation and hydroxymethylation maps at single-base resolution in paired human liver and lung normal and cancer. We found that 5hmC is significantly enriched in CpG island (CGI) shores while depleted in CGIs themselves, in particular at active genes, resulting in a 5hmC but not 5mC bimodal distribution around CGI corresponding to H3K4me1 marks. Hydroxymethylation on promoters, gene bodies, and transcription termination regions showed strong positive correlation with gene expression within and across tissues, suggesting that 5hmC is a mark of active genes and could play a role gene expression mediated by DNA demethylation. Comparative analysis of methylomes and hydroxymethylomes revealed that 5hmC is significantly enriched in both tissue specific DMRs (t-DMRs) and cancer specific DMRs (c-DMRs), and 5hmC is negatively correlated with methylation changes, particularly in non-CGI associated DMRs. Together these findings indicate that changes in 5mC as well as in 5hmC and coupled to H3K4me1 correspond to differential gene expression in tissues and matching tumors, revealing an intricate gene expression regulation through interplay of methylome, hydroxyl-methylome, and histone modifications.