bluuebunny/crossref_metadata_2025_split huggingface dataset:
Communicating with Biobank Participants: Preferences for Receiving and Providing Updates to Researchers
Authors: Mester Jessica L. , Mercer MaryBeth , Goldenberg Aaron , Moore Rebekah A. , Eng Charis , Sharp Richard R. 
Published: January 2015

Abstract
Background: Research biobanks collect biologic samples and health information. Previous work shows that biobank participants desire general study updates, but preferences about the method or frequency of these communications have not been explored. Thus, we surveyed participants in a long-standing research biobank.
Methods: Eligible participants were drawn from a study of patients with personal/family history suggestive of Cowden syndrome, a poorly recognized inherited cancer syndrome. Participants gave blood samples and access to medical records and received individual results but had no other study interactions. The biobank had 3,618 participants at sampling. Survey eligibility included age ≥18 years, enrollment within the biobank's first 5 years, normal PTEN analysis, and contiguous U.S. address. Multivariate logistic regression analyses identified predictors of participant interest in Internet-based versus offline methods and methods allowing participant–researcher interaction versus one-way communication. Independent variables were narrowed by independent Pearson correlations by cutoff P &lt; 0.2, with P &lt; 0.02 considered significant.
Results: Surveys were returned from 840 of 1,267 (66%) eligible subjects. Most (97%) wanted study updates, with 92% wanting updates at least once a year. Participants preferred paper (66%) or emailed (62%) newsletter methods, with 95% selecting one of these. Older, less-educated, and lower-income respondents strongly preferred offline approaches (P &lt; 0.001). Most (93%) had no concerns about receiving updates and 97% were willing to provide health updates to researchers.
Conclusion: Most participants were comfortable receiving and providing updated information. Demographic factors predicted communication preferences.
Impact: Researchers should make plans for ongoing communication early in study development and funders should support the necessary infrastructure for these efforts. Cancer Epidemiol Biomarkers Prev; 24(4); 708–12. ©2015 AACR.
Resolution and Dynamical Core Dependence of Atmospheric River Frequency in Global Model Simulations
Authors: Hagos Samson , Leung L. Ruby , Yang Qing , Zhao Chun , Lu Jian 
Published: January 2015

Abstract
This study examines the sensitivity of atmospheric river (AR) frequency simulated by a global model with different grid resolutions and dynamical cores. Analysis is performed on aquaplanet simulations using version 4 of the Community Atmosphere Model (CAM4) at 240-, 120-, 60-, and 30-km model resolutions, each with the Model for Prediction Across Scales (MPAS) and High-Order Methods Modeling Environment (HOMME) dynamical cores. The frequency of AR events decreases with model resolution and the HOMME dynamical core produces more AR events than MPAS. Comparing the frequencies determined using absolute and percentile thresholds of large-scale conditions used to define an AR, model sensitivity is found to be related to the overall sensitivity of subtropical westerlies, atmospheric precipitable water content and profile, and to a lesser extent extratropical Rossby wave activity to model resolution and dynamical core. Real-world simulations using MPAS at 120- and 30-km grid resolutions also exhibit a decrease of AR frequency with increasing resolution over the southern east Pacific, but the difference is smaller over the northern east Pacific. This interhemispheric difference is related to the enhancement of convection in the tropics with increased resolution. This anomalous convection sets off Rossby wave patterns that weaken the subtropical westerlies over the southern east Pacific but has relatively little effect on those over the northern east Pacific. In comparison to the NCEP-2 reanalysis, MPAS real-world simulations are found to underestimate AR frequencies at both resolutions likely because of their climatologically drier subtropics and poleward-shifted jets. This study highlights the important links between model climatology of large-scale conditions and extremes.
Initial Conditions for Convective-Scale Ensemble Forecasting Provided by Ensemble Data Assimilation
Authors: Harnisch Florian , Keil Christian 
Published: January 2015

Abstract
A kilometer-scale ensemble data assimilation system (KENDA) based on a local ensemble transform Kalman filter (LETKF) has been developed for the Consortium for Small-Scale Modeling (COSMO) limited-area model. The data assimilation system provides an analysis ensemble that can be used to initialize ensemble forecasts at a horizontal grid resolution of 2.8 km. Convective-scale ensemble forecasts over Germany using ensemble initial conditions derived by the KENDA system are evaluated and compared to operational forecasts with downscaled initial conditions for a short summer period during June 2012.
The choice of the inflation method applied in the LETKF significantly affects the ensemble analysis and forecast. Using a multiplicative background covariance inflation does not produce enough spread in the analysis ensemble leading to a degradation of the ensemble forecasts. Inflating the analysis ensemble instead by either multiplicative analysis covariance inflation or relaxation inflation methods enhances the analysis spread and is able to provide initial conditions that produce more consistent ensemble forecasts. The forecast quality for short forecast lead times up to 3 h is improved, and 21-h forecasts also benefit from the increased spread.
Doubling the ensemble size has not only a clear positive impact on the analysis but also on the short-term ensemble forecasts, while a simple representation of model error perturbing parameters of the model physics has only a small impact. Precipitation and surface wind speed ensemble forecasts using the high-resolution KENDA-derived initial conditions are competitive compared to the operationally used downscaled initial conditions.
Forward screening for seedling tolerance to Fe toxicity reveals a polymorphic mutation in ferric chelate reductase in rice
Authors: Ruengphayak Siriphat , Ruanjaichon Vinitchan , Saensuk Chatree , Phromphan Supaporn , Tragoonrung Somvong , Kongkachuichai Ratchanee , Vanavichit Apichart 
Published: January 2015

Abstract

Background
Rice contains the lowest grain Fe content among cereals. One biological limiting factor is the tolerance of rice to Fe toxicity. Reverse and forward genetic screenings were used to identify tolerance to Fe toxicity in 4,500 M4 lines irradiated by fast neutrons (FN).

Findings
Fe-tolerant mutants were successfully isolated. In the forward screen, we selected five highly tolerant and four highly intolerant mutants based on the response of seedlings to 300 ppm Fe. Reverse screening based on the polymorphic coding sequence of seven Fe homeostatic genes detected by denaturing high performance liquid chromatography (dHPLC) revealed MuFRO1, a mutant for OsFRO1 (LOC_Os04g36720). The MuFRO1 mutant tolerated Fe toxicity in the vegetative stage and had 21-30% more grain Fe content than its wild type. All five highly Fe-tolerant mutants have the same haplotype as the MuFRO1, confirming the important role of OsFRO1 in Fe homeostasis in rice.

Conclusions
FN radiation generated extreme Fe-tolerant mutants capable of tolerating different levels of Fe toxicity in the lowland rice environment. Mutants from both reverse and forward screens suggested a role for OsFRO1 in seedling tolerance to Fe toxicity. The MuFRO1 mutant could facilitate rice production in the high-Fe soil found in Southeast Asia.
Comparison of DNA methylation profiles in human fetal and adult red blood cell progenitors
Authors: Lessard Samuel , Beaudoin Mélissa , Benkirane Karim , Lettre Guillaume 
Published: January 2015

Abstract
Background
DNA methylation is an epigenetic modification that plays an important role during mammalian development. Around birth in humans, the main site of red blood cell production moves from the fetal liver to the bone marrow. DNA methylation changes at the β-globin locus and a switch from fetal to adult hemoglobin production characterize this transition. Understanding this globin switch may improve the treatment of patients with sickle cell disease and β-thalassemia, two of the most common Mendelian diseases in the world. The goal of our study was to describe and compare the genome-wide patterns of DNA methylation in fetal and adult human erythroblasts.

Methods
We used the Illumina HumanMethylation 450 k BeadChip to measure DNA methylation at 402,819 CpGs in ex vivo-differentiated erythroblasts from 12 fetal liver and 12 bone marrow CD34+ donors.

Results
We identified 5,937 differentially methylated CpGs that overlap with erythroid enhancers and binding sites for erythropoiesis-related transcription factors. Combining this information with genome-wide association study results, we show that erythroid enhancers define particularly promising genomic regions to identify new genetic variants associated with fetal hemoglobin (HbF) levels in humans. Many differentially methylated CpGs are located near genes with unanticipated roles in red blood cell differentiation and proliferation. For some of these new candidate genes, we confirm the correlation between DNA methylation and gene expression levels in red blood cell progenitors. We also provide evidence that DNA methylation and genetic variation at the β-globin locus independently control globin gene expression in adult erythroblasts.

Conclusions
Our DNA methylome maps confirm the widespread dynamic changes in DNA methylation that occur during human erythropoiesis. These changes tend to happen near erythroid enhancers, further highlighting their importance in erythroid regulation and HbF production. Finally, DNA methylation may act independently of the transcription factor BCL11A to repress fetal hemoglobin production. This provides cues on strategies to more efficiently re-activate HbF production in sickle cell disease and β-thalassemia patients.
A cross-sectional study of pain sensitivity, disease-activity assessment, mental health, and fibromyalgia status in rheumatoid arthritis
Authors: Joharatnam Nalinie , McWilliams Daniel F , Wilson Deborah , Wheeler Maggie , Pande Ira , Walsh David A 
Published: January 2015

Abstract
Introduction
Pain remains the most important problem for people with rheumatoid arthritis (RA). Active inflammatory disease contributes to pain, but pain due to non-inflammatory mechanisms can confound the assessment of disease activity. We hypothesize that augmented pain processing, fibromyalgic features, poorer mental health, and patient-reported 28-joint disease activity score (DAS28) components are associated in RA.

Methods
In total, 50 people with stable, long-standing RA recruited from a rheumatology outpatient clinic were assessed for pain-pressure thresholds (PPTs) at three separate sites (knee, tibia, and sternum), DAS28, fibromyalgia, and mental health status. Multivariable analysis was performed to assess the association between PPT and DAS28 components, DAS28-P (the proportion of DAS28 derived from the patient-reported components of visual analogue score and tender joint count), or fibromyalgia status.

Results
More-sensitive PPTs at sites over or distant from joints were each associated with greater reported pain, higher patient-reported DAS28 components, and poorer mental health. A high proportion of participants (48%) satisfied classification criteria for fibromyalgia, and fibromyalgia classification or characteristics were each associated with more sensitive PPTs, higher patient-reported DAS28 components, and poorer mental health.

Conclusions
Widespread sensitivity to pressure-induced pain, a high prevalence of fibromyalgic features, higher patient-reported DAS28 components, and poorer mental health are all linked in established RA. The increased sensitivity at nonjoint sites (sternum and anterior tibia), as well as over joints, indicates that central mechanisms may contribute to pain sensitivity in RA. The contribution of patient-reported components to high DAS28 should inform decisions on disease-modifying or pain-management approaches in the treatment of RA when inflammation may be well controlled.
Peripheral blood CD4+CD25+CD127low regulatory T cells are significantly increased by tocilizumab treatment in patients with rheumatoid arthritis: increase in regulatory T cells correlates with clinical response
Authors: Kikuchi Jun , Hashizume Misato , Kaneko Yuko , Yoshimoto Keiko , Nishina Naoshi , Takeuchi Tsutomu 
Published: January 2015

Abstract
Introduction
Tocilizumab (TCZ), an anti-interleukin-6 receptor antibody, is clinically effective against rheumatoid arthritis (RA), and several reports have indicated how TCZ influences a number of mechanisms underlying RA pathogenesis. However, it is still unclear whether TCZ affects inflammatory cells in peripheral blood and whether any such changes are associated with clinical response. We evaluated associations between proportions of subsets of peripheral immune cells and clinical response in patients with RA treated with TCZ.

Methods
Thirty-nine consecutive patients with RA who started to receive TCZ as their first biologic between March 2010 and April 2012 were enrolled. The proportions of several subsets of peripheral cells with their levels of expression of differentiation markers, activation markers and costimulatory molecules were measured sequentially from baseline to week 52 by flow cytometry analysis.

Results
Clinical Disease Activity Index (CDAI) remission was achieved in 53.8% of patients at week 52 of TCZ therapy. The proportions of CD4+CD25+CD127low regulatory T cells (Treg) and HLA-DR+ activated Treg cells significantly increased with TCZ therapy (P < 0.001 and P < 0.001, respectively), whereas proportions of CD3+CD4+CXCR3−CCR6+CD161+ T helper 17 cells did not change over the 52 weeks. The proportions of CD20+CD27+ memory B cells, HLA-DR+CD14+ and CD69+CD14+ activated monocytes, and CD16+CD14+ monocytes significantly decreased (P < 0.001, P < 0.001, P < 0.001 and P < 0.001, respectively). Among them, only the change in Treg cells was inversely correlated with the change in CDAI score (ρ = −0.40, P = 0.011). The most dynamic increase in Treg cells was observed in the CDAI remission group (P < 0.001).

Conclusion
This study demonstrates that TCZ affected proportions of circulating immune cells in patients with RA. The proportion of Treg cells among CD4+ cells correlated well with clinical response.
Noisy training for deep neural networks in speech recognition
Authors: Yin Shi , Liu Chao , Zhang Zhiyong , Lin Yiye , Wang Dong , Tejedor Javier , Zheng Thomas Fang , Li Yinguo 
Published: January 2015

Abstract
Deep neural networks (DNNs) have gained remarkable success in speech recognition, partially attributed to the flexibility of DNN models in learning complex patterns of speech signals. This flexibility, however, may lead to serious over-fitting and hence miserable performance degradation in adverse acoustic conditions such as those with high ambient noises. We propose a noisy training approach to tackle this problem: by injecting moderate noises into the training data intentionally and randomly, more generalizable DNN models can be learned. This ‘noise injection’ technique, although known to the neural computation community already, has not been studied with DNNs which involve a highly complex objective function. The experiments presented in this paper confirm that the noisy training approach works well for the DNN model and can provide substantial performance improvement for DNN-based speech recognition.
Combined Training Enhances Skeletal Muscle Mitochondrial Oxidative Capacity Independent of Age
Authors: Irving Brian A. , Lanza Ian R. , Henderson Gregory C. , Rao Rajesh R. , Spiegelman Bruce M. , Nair K. Sreekumaran 
Published: January 2015

Context:
Skeletal muscle from sedentary older adults exhibits reduced mitochondrial abundance and oxidative capacity.

Objective:
The primary objective was to determine whether 8 weeks of combined training (CT) has a more robust effect than endurance training (ET) or resistance training (RT) on mitochondrial physiology in healthy young (18–30 years) and older (≥65 years) adults.

Intervention:
Thirty-four young and 31 older adults were randomly assigned to 8 weeks of ET, RT, and control/CT. Control subjects completed 8 weeks of no exercise (control) followed by 8 weeks of CT. Body composition, skeletal muscle strength, and peak oxygen uptake were measured before and after the intervention. Vastus lateralis muscle biopsy samples were obtained before and 48 hours after the intervention. Mitochondrial physiology was evaluated by high-resolution respirometry and expression of mitochondrial proteins and transcription factors by quantitative PCR and immunoblotting.

Results:
ET and CT significantly increased oxidative capacity and expression of mitochondrial proteins and transcription factors. All training modalities improved body composition, cardiorespiratory fitness, and skeletal muscle strength. CT induced the most robust improvements in mitochondria-related outcomes and physical characteristics despite lower training volumes for the ET and RT components. Importantly, most of the adaptations to training occurred independent of age.

Conclusion:
Collectively, these results demonstrate that both ET and CT increase muscle mitochondrial abundance and capacity although CT induced the most robust improvements in the outcomes measured. In conclusion, CT provides a robust exercise regimen to improve muscle mitochondrial outcomes and physical characteristics independent of age.
Iron Deficiency, An Independent Risk Factor for Isolated Hypothyroxinemia in Pregnant and Nonpregnant Women of Childbearing Age in China
Authors: Yu Xiaohui , Shan Zhongyan , Li Chenyan , Mao Jinyuan , Wang Weiwei , Xie Xiaochen , Liu Aihua , Teng Xiaochun , Zhou Weiwei , Li Chenyang , Xu Bin , Bi Lihua , Meng Tao , Du Jianling , Zhang Shaowei , Gao Zhengnan , Zhang Xiaomei , Yang Liu , Fan Chenling , Teng Weiping 
Published: January 2015

Context:
Isolated hypothyroxinemia during early pregnancy may irreversibly damage the neurodevelopment of offspring. However, the causes are not well clarified.

Objective:
To explore the association of iron deficiency (ID) with hypothyroid function of women in early pregnancy and nonpregnant women.

Design:
A total of 7953 pregnant women of ≤ 12 weeks gestation and 2000 childbearing-aged women were recruited. A subpopulation including 3340 pregnant women and 1052 nonpregnant women with sufficient iodine intake and negative thyroid peroxidase antibody were studied. Mild and severe cases of hypothyroxinemia were defined as free T4 levels below the 10th percentile and the 5th percentile, respectively, with normal TSH. Total body iron, serum ferritin, and serum transferrin receptor were used as indicators for iron nutrition.

Results:
Serum free T4 levels were significantly lower in both pregnant and nonpregnant women with ID compared with the corresponding groups without ID (both P &lt; .05). The prevalence of mild and severe hypothyroxinemia was markedly higher in women with ID than those without, in both pregnant and nonpregnant women (all P &lt; .01). Logistic regression indicated that ID was an independent risk factor for both mild and severe hypothyroxinemia in pregnancy (odds ratio [OR] = 2.440, 95% confidence interval [CI]: 1.324–4.496, P = .004; and OR = 3.278, 95% CI: 1.443–7.446, P = .005, respectively) and nonpregnancy (OR = 2.662, 95% CI: 1.330–5.329, P = .006; and OR = 3.254, 95% CI: 1.375–7.700, P = .007, respectively).

Conclusions:
An association between ID and isolated hypothyroxinemia was found in both pregnant and nonpregnant childbearing-aged women, independent of the effects of iodine and thyroid autoimmunity. We speculate that ID may be a pathogenic factor for hypothyroxinemia, even in pregnant women during the first trimester.
Photochemical Chlorination and Oxygenation Reaction of Cyclohexene Sensitized by Ga(III) Porphyrin–Clay Minerals System with High Durability and Usability
Authors: Tsukamoto Takamasa , Shimada Tetsuya , Shiragami Tsutomu , Takagi Shinsuke 
Published: January 2015

Abstract
Photochemical chlorination and oxygenation reaction of cyclohexene sensitized by gallium(III) porphyrin–clay hybrid compound was investigated. Gallium(III) porphyrin did not aggregate on the clay surface, and thus, maintained photoactivity for the photochemical reaction. Gallium(III) porphyrin without clay decomposed immediately in the photochemical reaction. On the other hand, gallium(III) porphyrin adsorbed on clay was more stable than that without clay during the photochemical reaction and the altered porphyrin on clay still had photocatalytic ability along with original porphyrin. It was suggested that gallium(III) porphyrin was protected by clay surface during the photochemical reaction. In addition, the efficiency for the photochemical chlorination and oxygenation reaction was kept even at high porphyrin adsorption densities on clay. These findings are beneficial to construct efficient and durable photochemical reaction systems.
Synthesis of Pyrroles from β-Enamines and Nitroolefins Catalyzed by I2 under High-speed Vibration Milling (HSVM)
Authors: Xu Hui , Li Yujin , Xing Mengming , Jia Jianhong , Han Liang , Ye Qing , Gao Jianrong 
Published: January 2015

Abstract
A solvent-free reaction, using a high-speed vibration milling (HSVM) technique, has been developed for the synthesis of polysubstituted pyrroles from β-enamines and nitroolefins as the raw materials, by using iodine as the catalyst. The influences of the vibration frequency and the reaction time were investigated and a series of 2,3,4-polysubstituted pyrroles were obtained in good yields at short reaction times (20 min) under the HSVM condition. It is an efficient, simple, and moderate approach for synthesizing polysubstituted pyrroles under the HSVM conditions.
Development of a Simultaneous SANS/FTIR Measuring System
Authors: Kaneko Fumitoshi , Seto Naoki , Sato Shuma , Radulescu Aurel , Schiavone Maria Maddalena , Allgaier Jürgen , Ute Koichi 
Published: January 2015

Abstract
A novel method for the simultaneous measurement of small-angle neutron scattering and Fourier transform infrared spectroscopy (SANS/FTIR) has been developed. The method was realized by building a device consisting of a portable FTIR spectrometer and an optical system that allows both a neutron beam and an infrared beam to pass through a sample coaxially. The device was installed on a small-angle neutron diffractometer, KWS2 of the Jülich Centre for Neutron Science (JCNS) outstation at Heinz Maier-Leibnitz Center (MLZ) in Garching, Germany. In order to check the performance of this measuring system, the structural changes in a cocrystal of syndiotactic polystyrene with triethylene glycol dimethyl ether, were followed during the course of heating.
Radical Addition to Corannulene Mediated by Visible-light-photoredox Catalysts
Authors: Nakajima Kazunari , Ashida Yuya , Nojima Sunao , Nishibayashi Yoshiaki 
Published: January 2015

Abstract
Functionalization of corannulene has been extensively studied, however, radical addition reactions toward corannulene have been unexplored to date. Herein, we report the photochemical addition reaction of amines to corannulene via radical intermediates using photoredox catalysts.