bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening the human exome: a comparison of whole genome and whole transcriptome sequencing
Authors: Cirulli Elizabeth T , Singh Abanish , Shianna Kevin V , Ge Dongliang , Smith Jason P , Maia Jessica M , Heinzen Erin L , Goedert James J , Goldstein David B ,   the Center for HIV/AIDS Vaccine Immunology (CHAVI)
Published: May 2012

Abstract
Background
There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, whole-exome sequencing using exon capture methods, and RNA-Seq. While whole-genome sequencing is the most complete, it remains sufficiently expensive that cost effective alternatives are important.

Results
Here we provide a systematic exploration of how well RNA-Seq can identify human coding variants by comparing variants identified through high coverage whole-genome sequencing to those identified by high coverage RNA-Seq in the same individual. This comparison allowed us to directly evaluate the sensitivity and specificity of RNA-Seq in identifying coding variants, and to evaluate how key parameters such as the degree of coverage and the expression levels of genes interact to influence performance. We find that although only 40% of exonic variants identified by whole genome sequencing were captured using RNA-Seq; this number rose to 81% when concentrating on genes known to be well-expressed in the source tissue. We also find that a high false positive rate can be problematic when working with RNA-Seq data, especially at higher levels of coverage.

Conclusions
We conclude that as long as a tissue relevant to the trait under study is available and suitable quality control screens are implemented, RNA-Seq is a fast and inexpensive alternative approach for finding coding variants in genes with sufficiently high expression levels.
Targeting acute myeloid leukemia cells with cytokines
Authors: Ferretti Elisa , Cocco Claudia , Airoldi Irma , Pistoia Vito 
Published: May 2012

Abstract
Review of data identifying IL-12 and IL-27 as potential therapeutic agents for pediatric AML by targeting leukemia initiating cells and/or blasts.
AML is a hematologic malignancy that represents 15–20% of all childhood acute leukemias and is responsible for more than one-half of pediatric leukemic deaths. The bulk tumor is continuously regenerated and sustained by rare leukemic ICs that proliferate slowly, thus resulting refractory to chemotherapeutic agents targeting highly proliferating cells within the tumor. Therefore, a complete eradication of the bulk tumor may depend on efficacy of therapies that target IC. In spite of the improvements in the treatment of AML, the difficulty to eradicate completely the disease incites research for innovative therapeutic approaches. In this regard, the role of cytokines in the treatment of AML has been investigated for many years, and some of them have been tested in clinical trials as a result of their immunomodulatory properties. Furthermore, recent preclinical studies highlighted the ability of the IL-12 superfamily cytokines as potent antileukemic agents that act directly on tumor cells and on leukemic IC, thus opening new perspectives for leukemic patient treatment. Here, we review the current knowledge about the antileukemic effects of cytokines, documented in preclinical and clinical studies, discussing their potential clinical application.
Combination Treatment with T4 and T3: Toward Personalized Replacement Therapy in Hypothyroidism?
Authors: Biondi Bernadette , Wartofsky Leonard 
Published: May 2012

Abstract

Context:
Levothyroxine therapy is the traditional lifelong replacement therapy for hypothyroid patients. Over the last several years, new evidence has led clinicians to evaluate the option of combined T3 and T4 treatment to improve the quality of life, cognition, and peripheral parameters of thyroid hormone action in hypothyroidism. The aim of this review is to assess the physiological basis and the results of current studies on this topic.

Evidence Acquisition:
We searched Medline for reports published with the following search terms: hypothyroidism, levothyroxine, triiodothyronine, thyroid, guidelines, treatment, deiodinases, clinical symptoms, quality of life, cognition, mood, depression, body weight, heart rate, cholesterol, bone markers, SHBG, and patient preference for combined therapy. The search was restricted to reports published in English since 1970, but some reports published before 1970 were also incorporated. We supplemented the search with records from personal files and references of relevant articles and textbooks. Parameters analyzed included the rationale for combination treatment, the type of patients to be selected, the optimal T4/T3 ratio, and the potential benefits of this therapy on symptoms of hypothyroidism, quality of life, mood, cognition, and peripheral parameters of thyroid hormone action.

Evidence Synthesis:
The outcome of our analysis suggests that it may be time to consider a personalized regimen of thyroid hormone replacement therapy in hypothyroid patients.

Conclusions:
Further prospective randomized controlled studies are needed to clarify this important issue. Innovative formulations of the thyroid hormones will be required to mimic a more perfect thyroid hormone replacement therapy than is currently available.
A Local Paracrine and Endocrine Network Involving TGFβ, Cox-2, ROS, and Estrogen Receptor β Influences Reactive Stromal Cell Regulation of Prostate Cancer Cell Motility
Authors: Grubisha Melanie J. , Cifuentes M. E. , Hammes Stephen R. , DeFranco Donald B. 
Published: May 2012

Abstract
The tumor microenvironment plays a critical role in supporting cancer cells particularly as they disengage from limitations on their growth and motility imposed by surrounding nonreactive stromal cells. We show here that stromal-derived androgenic precursors are metabolized by DU145 human prostate cancer (PCa) cells to generate ligands for estrogen receptor-β, which act to limit their motility through transcriptional regulation of E-cadherin. Although primary human PCa-associated fibroblasts and the human WPMY-1-reactive prostate stromal cell line maintain this inherent estrogen receptor (ER)β-dependent motility inhibitor activity, they are subverted by TGF-β1 pro-oxidant signals derived from cocultured DU145 PCa cells. Specifically, stromal-produced H2O2, which requires Cox-2, acts as a second paracrine factor to inhibit ERβ activity in adjacent DU145 cells. Chromatin immunoprecipitation analysis reveals that ERβ recruitment to the E-cadherin promoter is inhibited when H2O2 is present. Both neutralization of H2O2 with catalase and prevention of its production by silencing Cox-2 expression in stromal cells restore the motility-suppression activity of stromal-derived ERβ ligand precursors. These data suggest that reactive stromal cells may still have a capacity to limit cancer cell motility through a local endocrine network but must be protected from pro-oxidant signals triggered by cancer cell-derived TGF-β1 to exhibit this cancer-suppressive function.
Characterization of Follistatin-Type Domains and Their Contribution to Myostatin and Activin A Antagonism
Authors: Cash Jennifer N. , Angerman Elizabeth B. , Keutmann Henry T. , Thompson Thomas B. 
Published: May 2012

Abstract
Follistatin (FST)-type proteins are important antagonists of some members of the large TGF-β family of cytokines. These include myostatin, an important negative regulator of muscle growth, and the closely related activin A, which is involved in many physiological functions, including maintenance of a normal reproductive axis. FST-type proteins, including FST and FST-like 3 (FSTL3), differentially inhibit various TGF-β family ligands by binding each ligand with two FST-type molecules. In this study, we sought to examine features that are important for ligand antagonism by FST-type proteins. Previous work has shown that a modified construct consisting of the FST N-terminal domain (ND) followed by two repeating follistatin domains (FSD), herein called FST ND-FSD1-FSD1, exhibits strong specificity for myostatin over activin A. Using cell-based assays, we show that FST ND-FSD1-FSD1 is unique in its specificity for myostatin as compared with similar constructs containing domains from FSTL3 and that the ND is critical to its activity. Furthermore, we demonstrate that FSD3 of FST provides affinity to ligand inhibition and confers resistance to perturbations in the ND and FSD2, likely through the interaction of FSD3 of one FST molecule with the ND of the other FST molecule. Additionally, our data suggest that this contact provides cooperativity to ligand antagonism. Cross-linking studies show that this interaction also potentiates formation of 1:2 ligand-FST complexes, whereas lack of FSD3 allows formation of 1:1 complexes. Altogether, these studies support that domain differences generate FST-type molecules that are each uniquely suited ligand antagonists.
Comparison between visual assessment of MTA and hippocampal volumes in an elderly, non-demented population
Authors: Cavallin Lena , Bronge Lena , Zhang Yi , Øksengård Anne-Rita , Wahlund Lars-Olof , Fratiglioni Laura , Axelsson Rimma 
Published: May 2012

Background It is important to have a replicable easy method for monitoring atrophy progression in Alzheimer's disease. Volumetric methods for calculating hippocampal volume are time-consuming and commonly used in research. Visual assessments of medial temporal lobe atrophy (vaMTA) is a rapid method for clinical use. This method has not been tested in a large non-demented population in comparison with volumetry mesurements. Since hippocampal volume decreases with time even in normal aging there is also a need to study the normal age differences of medial temporal lobe atrophy. Purpose To compare visual assessment of medial temporal lobe atrophy (vaMTA) with hippocampal volume in a healthy, non-demented elderly population. To describe normal ageing using vaMTA. Material and Methods Non-demented individuals aged 60, 66, 72, 78, 81, 84, and ≥87 years old were recruited from the Swedish National study on Ageing and Care in Kungsholmen (SNAC-K), Sweden. Standard magnetic resonance imaging (MRI) scans, vaMTA, and calculations of hippocampal volumes were performed in 544 subjects. Results Significant correlation (rs = −0.32, P < 0.001, sin; and rs = −0.26, P < 0.001, dx) was found between hippocampal volume measurements and vaMTA. In normal ageing, almost 95% of ≤66-year-olds had a medial temporal lobe atrophy (MTA) score ≤1, with possible scores ranging from 0 to 4. Subjects aged 72, 78, and 81 years scored ≤2, while the two oldest age groups had scores ≤3. Conclusion There was a highly significant correlation between volumetric measurements of the hippocampus and MTA scoring. In normal ageing, there is increasing MTA score. For non-demented elderly individuals ≤70 years, an MTA score of 0–1 may be considered normal, compared with MTA ≤2 for 70–80-years and MTA 3 for >80-year-old individuals.
Testing and Use of Environmentally Acceptable Lubricants
Authors: Rhee In-Sik 
Published: May 2012

Description
Discover the latest research on biobased and other Environmentally Acceptable (EA) Lubricants. With the increased interest in EA Lubricants, this book is a must-have for those in the agricultural, construction, forestry, lumber, and mining industries where involuntary or accidental fluid leakage or spillage is detrimental to the environment.
Ten peer-reviewed papers cover
Performance Comparison and Design Issue on Different GaN Power Transistor Structures
Authors: Lee Chwan-Ying , Hung Chien-Chung , Kuo Wei-Hung , Chen Young-Shying , Lee Lurng-Shehng , Yen Cheng-Tyng , Lin Suh-Fang , Xuan Rong , Ku Tzu-Kun , Tsai Ming-Jinn 
Published: May 2012

ABSTRACTThree types of Ganium Nitride (GaN) transistors were studied in this work. The devices were fabricated and exhibited unique characteristics over on-state current and off-state blocking performances. We also compared the performance differences of devices fabricated by multiepitaxial GaN/AlGaN layers on different substrates (Sapphire and Si) and evaluated the correlations among starting substrate, device variation, and manufacturing uniformity. The first device is a normally-on device with Sapphire substrate which shows good drain saturation current (Idsat) and breakdown characteristics, but the gate leakage current is quite large. The second device is a normally-off GaN transistor named metal-insulate-semiconductor (MIS) heterojunction field-effect transistor (MIS-HFET) which exhibits good performance with threshold voltage (Vth) of 3V and breakdown voltage (Vbd) of over 1800V. However the third device is a normally-off GaN metal-oxide-semiconductor field-elect transistor (MOSFET) structure which is rather difficult to exhibit good blocking characteristic due to inadequate doping process control of the reduce-surface-field (RESURF) region.
Lift-off Methods for MEMS Devices
Authors: Chang Shih-Chia , Kempisty Jeffrey M. 
Published: May 2012

AbstractFive different methods were explored for the formation of the lift-off mold. In the first method, a tri-level resist scheme was used to generate a lift-off mold. The lift-off mold has a vertical wall slope. In the second method, an aluminum/photoresist double layer was used as the mold material. An overhang structure is obtained by undercutting the underlying aluminum layer. In the third method, a composite layer of two different photoresists (AZ 1811 and LOR 10A) was used to form the lift-off mold. With the fast dissolution rate of the underlying LOR 10A photoresist an overhanging mask structure was obtained. Since regular photoresists were used as part of the mold material in these three lift-off methods, they are suitable for thin film materials with thickness of ≤2 μm and processing temperatures ≤100°C. For thicker device film materials and higher processing temperature (∼200°C), methods 4 and 5 using negative resists, Futurrex NR7-3000PY (∼3 μm) and SU-8 (∼50 μm), respectively, were experimented with to form the lift-off mask. The fabrication processes used in these two methods were relatively simple and a negative wall slope was readily obtained. While Futurrex photoresist is easily stripped by the resist remover provided by the manufacturer, there is no effective chemical solution available for the removal of SU-8. We found that plasma etching with a mixture of O2 and C2F6 can be used for the removal of SU-8.
Micro-Molded High Q Polymer Resonators for Optical Loss Determination
Authors: Martin Andrea L. , Srinivasan Akil , Armani Deniz K. , Min Bumki , Vahala Kerry J. 
Published: May 2012

AbstractReplica molding of ultra-high-Q toroidal microresonators can produce polymer microresonators with material-limited quality factors (Q). This was demonstrated previously using polymers which cure thermally. In this work, high Q polymer microresonators were fabricated using the replica molding technique from previously uncharacterized polymers which require either a thermal or UV cure. The quality factor and effective refractive index of whispering gallery modes was measured at wavelengths ranging from the visible (680nm) through the near-IR (1550nm). The optical absorption coefficient (material absorption) of these previously uncharacterized polymers was determined from the quality factor and effective refractive index of the polymer.
Slums and Malnourishment: Evidence From Women in India
Authors: Swaminathan Hema , Mukherji Arnab 
Published: May 2012

Objectives. We examined the association between slum residence and nutritional status in women in India by using competing classifications of slum type. Methods. We used nationally representative data from the 2005–2006 National Family Health Survey (NFHS-3) to create our citywide analysis sample. The data provided us with individual, household, and community information. We used the body mass index data to identify nutritional status, whereas the residential status variable provided slum details. We used a multinomial regression framework to model the 3 nutrition states—undernutrition, normal, and overnutrition. Results. After we controlled for a range of attributes, we found that living in a census slum did not affect nutritional status. By contrast, living in NFHS slums decreased the odds of being overweight by 14% (95% confidence interval [CI] = 0.79, 0.95) and increased the odds of being underweight by 10% (95% CI = 1.00, 1.22). Conclusions. The association between slum residence and nutritional outcomes is nuanced and depends on how one defines a slum. This suggests that interventions targeted at slums should look beyond official definitions and include current living conditions to effectively reach the most vulnerable.
Changes in Smoking Prevalence in 8 Countries of the Former Soviet Union Between 2001 and 2010
Authors: Roberts Bayard , Gilmore Anna , Stickley Andrew , Rotman David , Prohoda Vladimir , Haerpfer Christian , McKee Martin 
Published: May 2012

Objectives. We sought to present new data on smoking prevalence in 8 countries, analyze prevalence changes between 2001 and 2010, and examine trend variance by age, location, education level, and household economic status. Methods. We conducted cross-sectional household surveys in 2010 in Armenia, Belarus, Georgia, Kazakhstan, Kyrgyzstan, Moldova, Russia, and Ukraine. We compared smoking prevalence with a related 2001 study for the different countries and population subgroups, and also calculated the adjusted prevalence rate ratios of smoking. Results. All-age 2010 smoking prevalence among men ranged from 39% (Moldova) to 59% (Armenia), and among women from 2% (Armenia) to 16% (Russia). There was a significantly lower smoking prevalence among men in 2010 compared with 2001 in Belarus, Kazakhstan, Kyrgyzstan, and Russia, but not for women in any country. For all countries combined, there was a significantly lower smoking prevalence in 2010 than in 2001 for men aged 18 to 39 years and men with a good or average economic situation. Conclusions. Smoking prevalence appears to have stabilized and may be declining in younger groups, but remains extremely high among men, especially those in lower socioeconomic groups.
Global Health—A Circumpolar Perspective
Authors: Chatwood Susan , Bjerregaard Peter , Young T. Kue 
Published: May 2012

Global health should encompass circumpolar health if it is to transcend the traditional approach of the “rich North” assisting the “poor South.” Although the eight Arctic states are among the world’s most highly developed countries, considerable health disparities exist among regions across the Arctic, as well as between northern and southern regions and between indigenous and nonindigenous populations within some of these states. While sharing commonalities such as a sparse population, geographical remoteness, harsh physical environment, and underdeveloped human resources, circumpolar regions in the northern hemisphere have developed different health systems, strategies, and practices, some of which are relevant to middle and lower income countries. As the Arctic gains prominence as a sentinel of global issues such as climate change, the health of circumpolar populations should be part of the global health discourse and policy development.
Improving Adult Immunization Practices Using a Team Approach in the Primary Care Setting
Authors: Gannon Meghan , Qaseem Amir , Snooks Qianna , Snow Vincenza 
Published: May 2012

Objectives. The objective of this study was to improve the immunization rates of primary care practices using a team approach. Methods. Practices performed 35 random chart abstractions at 2 time points and completed a survey about immunizations at baseline and 12 months after intervention. Data were collected for the following immunizations: influenza, pneumococcal, tetanus diphtheria (Td)/tetanus diphtheria pertussis (Tdap), hepatitis A, hepatitis B, meningococcal, varicella, herpes zoster, and human papilloma virus. Between baseline and after intervention, practice teams were given feedback reports and access to an online educational tool, and attended quality improvement coaching conference calls. Results. Statistically significant improvements were seen for Td/Tdap (45.6% pre-intervention, 55.0% post-intervention; P ≤ .01), herpes zoster (12.3% pre-intervention, 19.3% post-intervention; P ≤ .01), and pneumococcal (52.2% pre-intervention, 74.5% post-intervention; P ≤ .01) immunizations. Data also revealed an increase in the number of physicians who discussed herpes zoster and pneumococcal vaccinations with their patients (23.2% pre-intervention, 43.3% post-intervention; P ≤ .01 and 19.9% pre-intervention, 43.0% post-intervention; P ≤ .01, respectively) as well as an increase in physicians using the Centers for Disease Control and Prevention immunization schedule (52.9% pre-intervention, 88.2% post-intervention; P ≤ .02). Conclusions. The immunization rates of the primary care practices involved in this study improved.
Training Primary Care Physicians for Local Health Authority Duties in Texas
Authors: Mobley James , Zuniga Miguel A. 
Published: May 2012

Only one fourth of Texas counties have a local health authority (LHA) or health district. Primary care physicians in the remaining counties could be trained in public health basics by providing an online LHA training course and courses at annual meetings of the Texas Medical Association and the Texas Academy of Family Physicians. The Texas Department of State Health Services should develop a web portal for LHAs. The Texas Association of Local Health Officials should also provide automatic limited membership for LHAs. These initiatives would provide public health training to primary care physicians and would greatly improve availability of public health services for the citizens of Texas.
Implementation of Workplace-Based Smoking Cessation Support Activities and Smoking Cessation Among Employees: The Finnish Public Sector Study
Authors: Kouvonen Anne , Kivimäki Mika , Oksanen Tuula , Pentti Jaana , Heponiemi Tarja , Väänänen Ari , Virtanen Marianna , Vahtera Jussi 
Published: May 2012

Objectives. We investigated the relationship between implementation of workplace smoking cessation support activities and employee smoking cessation. Methods. In 2 cohort studies, participants were 6179 Finnish public-sector employees who self-reported as smokers at baseline in 2004 (study 1) or 2008 (study 2) and responded to follow-up surveys in 2008 (study 1; n = 3298; response rate = 71%) or 2010 (study 2; n = 2881; response rate = 83%). Supervisors’ reports were used to assess workplace smoking cessation support activities. We conducted multilevel logistic regression analyses to examine changes in smoking status. Results. After adjustment for sociodemographic characteristics, number of cigarettes smoked per day, work unit size, shift work, type of job contract, health status, and health behaviors, baseline smokers whose supervisors reported that the employing agency had offered pharmacological treatments or financial incentives were more likely than those in workplaces that did not offer such support to have quit smoking. In general, associations were stronger among moderate or heavy smokers (≥ 10 cigarettes/day) than among light smokers (< 10 cigarettes/day). Conclusions. Cessation activities offered by employers may encourage smokers, particularly moderate or heavy smokers, to quit smoking.