bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediagnostic Calcium Intake and Lung Cancer Survival: A Pooled Analysis of 12 Cohort Studies
Authors: Yu Danxia , Takata Yumie , Smith-Warner Stephanie A. , Blot William , Sawada Norie , White Emily , Freedman Neal , Robien Kim , Giovannucci Edward , Zhang Xuehong , Park Yikyung , Gao Yu-Tang , Chlebowski Rowan T. , Langhammer Arnulf , Yang Gong , Severi Gianluca , Manjer Jonas , Khaw Kay-Tee , Weiderpass Elisabete , Liao Linda M. , Caporaso Neil , Krokstad Steinar , Hveem Kristian , Sinha Rashmi , Ziegler Regina , Tsugane Shoichiro , Xiang Yong-Bing , Johansson Mattias , Zheng Wei , Shu Xiao-Ou 
Published: March 2017

Abstract
Background: Lung cancer is the leading cause of cancer death. Little is known about whether prediagnostic nutritional factors may affect survival. We examined the associations of prediagnostic calcium intake from foods and/or supplements with lung cancer survival.
Methods: The present analysis included 23,882 incident, primary lung cancer patients from 12 prospective cohort studies. Dietary calcium intake was assessed using food-frequency questionnaires at baseline in each cohort and standardized to caloric intake of 2,000 kcal/d for women and 2,500 kcal/d for men. Stratified, multivariable-adjusted Cox regression was applied to compute hazard ratios (HR) and 95% confidence intervals (CI).
Results: The 5-year survival rates were 56%, 21%, and 5.7% for localized, regional, and distant stage lung cancer, respectively. Low prediagnostic dietary calcium intake (&lt;500–600 mg/d, less than half of the recommendation) was associated with a small increase in risk of death compared with recommended calcium intakes (800–1,200 mg/d); HR (95% CI) was 1.07 (1.01–1.13) after adjusting for age, stage, histology, grade, smoking status, pack-years, and other potential prognostic factors. The association between low calcium intake and higher lung cancer mortality was evident primarily among localized/regional stage patients, with HR (95% CI) of 1.15 (1.04–1.27). No association was found for supplemental calcium with survival in the multivariable-adjusted model.
Conclusions: This large pooled analysis is the first, to our knowledge, to indicate that low prediagnostic dietary calcium intake may be associated with poorer survival among early-stage lung cancer patients.
Impact: This multinational prospective study linked low calcium intake to lung cancer prognosis. Cancer Epidemiol Biomarkers Prev; 26(7); 1060–70. ©2017 AACR.
Low Cotinine Glucuronidation Results in Higher Serum and Saliva Cotinine in African American Compared to White Smokers
Authors: Murphy Sharon E. , Sipe Christopher J. , Choi Kwangsoo , Raddatz Leah M. , Koopmeiners Joseph S. , Donny Eric C. , Hatsukami Dorothy K. 
Published: March 2017

Abstract
Background: Tobacco exposure is often quantified by serum or saliva concentrations of the primary nicotine metabolite, cotinine. However, average cotinine concentrations are higher in African Americans (AA) compared with Whites with similar smoking levels. Cotinine is metabolized by UGT2B10 and CYP2A6, and low UGT2B10 activity is common in AA, due to the prevalence of a UGT2B10 splice variant.
Methods: UGT2B10 activity was phenotyped in 1,446 smokers (34% AA) by measuring the percentage of cotinine excreted as a glucuronide. Urinary total nicotine equivalents (TNE), the sum of nicotine and 6 metabolites, were determined to quantify smoking dose, and cotinine and 3′-hydroxycotinine were quantified in saliva (study 1) or serum (study 2).
Results: Ninety-seven smokers (78% AA) were null for UGT2B10 activity, and the saliva and serum cotinine levels, after adjustment for TNE and cigarettes per day (CPD), were 68% and 48% higher in these smokers compared with nonnull smokers (P &lt; 0.001). After adjustment for TNE and CPD, salivary cotinine was 35% higher, and serum cotinine 24% higher in AA versus White smokers, but with additional adjustment for UGT2B10 activity, there were no significant differences in saliva and serum cotinine concentrations between these two groups.
Conclusions: UGT2B10 activity significantly influences plasma cotinine levels, and higher cotinine concentrations in AA versus White smokers (after adjustment for smoking dose) result from lower levels of UGT2B10-catalyzed cotinine glucuronidation by AA.
Impact: UGT2B10 activity or genotype should be considered when using cotinine as a tobacco exposure biomarker, particularly in populations such as AA with high frequencies of UGT2B10 nonfunctional variants. Cancer Epidemiol Biomarkers Prev; 26(7); 1093–9. ©2017 AACR.
Immune Microenvironment in Microsatellite-Instable Endometrial Cancers: Hereditary or Sporadic Origin Matters
Authors: Pakish Janelle B. , Zhang Qian , Chen Zhongyuan , Liang Han , Chisholm Gary B. , Yuan Ying , Mok Samuel C. , Broaddus Russell R. , Lu Karen H. , Yates Melinda S. 
Published: March 2017

Abstract
Purpose: Recent studies show that colorectal tumors with high microsatellite instability (MSI-H) have increased immunogenicity and response to immunotherapy compared with microsatellite-stable (MSS) tumors. It is not yet clear whether MSI-H endometrial cancer may also benefit from these therapies. It is also unknown whether immune response is equivalent in MSI-H endometrial cancer with sporadic or inherited Lynch syndrome origins.
Experimental Design: Multiplexed fluorescent IHC was used to compare matched MSI-H (n = 60) and MSS (n = 96) endometrial cancer specimens by evaluating immune cell populations in tumor and stroma compartments. Sporadic MSI-H and Lynch syndrome–associated (LS) MSI-H endometrial cancers were also directly compared.
Results: Increased immune cells were present in stroma of MSI-H endometrial cancer compared with MSS, including granzyme B+ cells, activated CTLs (CD8+granzyme B+), and PD-L1+ cells. Granzyme B+ cells and activated CTLs were also increased in the tumor compartment of MSI-H endometrial cancers. Comparing sporadic and LS MSI-H endometrial cancer showed distinct differences in immune cell populations, indicating that mechanisms underlying microsatellite instability alter immune response. Specifically, LS MSI-H endometrial cancer showed increased CD8+ cells and activated CTLs in stroma, with reduced macrophages in stroma and tumor compared with sporadic MSI-H. Sporadic MSI-H had increased PD-L1+ macrophages in stroma and tumor compared with LS MSI-H endometrial cancer.
Conclusions: MSI-H endometrial cancer has increased immune cell infiltration compared with MSS endometrial cancer and the hereditary or sporadic origin of microsatellite instability impacts immune response. Clinical trials to determine the role of immunotherapy in patients with MSI-H endometrial cancer must evaluate Lynch syndrome–related and sporadic MSI-H tumors separately. Clin Cancer Res; 23(15); 4473–81. ©2017 AACR.
Histone Methyltransferase G9a Drives Chemotherapy Resistance by Regulating the Glutamate–Cysteine Ligase Catalytic Subunit in Head and Neck Squamous Cell Carcinoma
Authors: Liu Chia-Wen , Hua Kuo-Tai , Li Kai-Chun , Kao Hsiang-Fong , Hong Ruey-Long , Ko Jenq-Yuh , Hsiao Michael , Kuo Min-Liang , Tan Ching-Ting 
Published: March 2017

Abstract
Transient chemotherapeutic response is a major obstacle to treating head and neck squamous cell carcinomas (HNSCC). Histone methyltransferase G9a has recently been shown to be abundantly expressed in HNSCC, and is required to maintain the malignant phenotype. In this study, we found that high G9a expression is significantly associated with poor chemotherapeutic response and disease-free survival in HNSCC patients. Similarly, G9a expression and enzymatic activity were elevated in cisplatin-resistant HNSCC cells. Genetic or pharmacologic inhibition of G9a sensitized the resistant cells to cisplatin, increasing cellular apoptosis. Mechanistic investigations indicated that G9a contributes to transcriptional activation of the glutamate-cysteine ligase catalytic subunit (GCLC), which results in upregulation of cellular glutathione (GSH) and drug resistance. In addition, we observed a significant positive correlation between G9a and GCLC expression in tumors of HNSCC patients. Taken together, our findings provide evidence that G9a protects HNSCC cells against chemotherapy by increasing the synthesis of GSH, and imply G9a as a promising target for overcoming cisplatin resistance in HNSCC. Mol Cancer Ther; 16(7); 1421–34. ©2017 AACR.
Sensitivity of Convection-Allowing Forecasts to Land Surface Model Perturbations and Implications for Ensemble Design
Authors: Duda Jeffrey D. , Wang Xuguang , Xue Ming 
Published: March 2017

Abstract
In this exploratory study, a series of perturbations to the land surface model (LSM) component of the Weather Research and Forecasting (WRF) Model was developed to investigate the sensitivity of forecasts of severe thunderstorms and heavy precipitation at 4-km grid spacing and whether such perturbations could improve ensemble forecasts at this scale. The perturbations (generated using a combination of perturbing fixed parameters and using separate schemes, one of which—Noah-MP—is new among the WRF modeling community) were applied to a 10-member ensemble including other mixed physics parameterizations and compared against an identically configured ensemble that did not include the LSM perturbations to determine their impact on probabilistic forecasts. A third ensemble using only the LSM perturbations was also configured.
The results from 14 (in total) 36-h ensemble forecasts suggested the LSM perturbations resulted in systematic improvement in ensemble dispersion and error characteristics. Lower-tropospheric temperature, moisture, and wind fields were all improved, as were probabilistic precipitation forecasts. Biases were not systematically altered, although some outlier members are present. Examination of near-surface temperature and mixing ratio fields, surface energy fluxes, and soil fields revealed tendencies caused by certain perturbations. A case study featuring tornadic supercells illustrated the physical causes of some of these tendencies. The results of this study suggest LSM perturbations can sample a dimension of model error not yet sampled systematically in most ensembles and should be included in convection-allowing ensembles.
Multimodality Treatment of Early‐Stage Tonsil Cancer
Authors: Roden Dylan F. , Schreiber David , Givi Babak 
Published: March 2017

ObjectiveCompare survival outcomes between unimodality and multimodality treatments for early‐stage tonsil squamous cell carcinoma (SCC).Study Design and SettingReview of the National Cancer Database.Subjects and MethodsPatients were selected if they were <70 years old with clinical stage I‐II SCC of the tonsil, as documented in the National Cancer Database from 1998 to 2011. Palliative and nonstandard treatments were excluded. Propensity score matching was performed, controlling for tumor stage, age, race, comorbidity, insurance status, and year of diagnosis. Overall survival (OS) was compared with the Kaplan‐Meier method and log‐rank test.ResultsWe identified 3247 patients. Radiotherapy (RT) was delivered in 1295 patients (39.9%), surgery in 824 (25.4%), and surgery + RT in 1128 (34.7%). Patients treated with surgery + RT had the highest 5‐year OS (81.1%), followed by surgery (67.4%) and RT (63.4%; P <. 001). In a propensity score–matched subpopulation of 2378 patients, the 5‐year OS was 78.8% for surgery + RT, 66.7% for surgery, and 64.5% for RT (P <. 001). Among patients who underwent surgical tonsillectomy plus elective neck dissection and/or adjuvant RT, the 5‐year OS was equal (P =. 29), and all were superior to RT alone (P <. 001).ConclusionMultimodality treatment is associated with the greatest survival in early‐stage tonsil cancer. The addition of tonsillectomy to RT confers a 20% increase in survival. The current guidelines might not offer the most effective treatment. An up‐front surgical approach, followed by appropriately selected adjuvant therapy, may result in improved survival for early‐stage tonsil SCC. These findings merit investigation in a prospective clinical trial.
Weak-form Efficiency After Global Financial Crisis: Emerging Stock Market Evidence
Authors: Emenike Kalu O.  
Published: March 2017

This article investigates weak-form efficiency of the Nigerian Stock Exchange (NSE) and its sectors for the post-global financial crisis period using autocorrelation test, Ljung–Box Q test, McLeod-Li portmanteau test and ARCH-LM test. The descriptive statistics show that the returns of NSE and its sectors are positive. The results show that (i) investors can only predict banking sector return using superior fundamental analysis of their intrinsic values; (ii) prediction of the NSE 30 and Shari’ah equities sector returns require nonlinear model and fundamental analysis and (iii) consumer goods sector and oil and gas sector may be predicted using both technical and fundamental analyses. JEL Classification: G11, 14
Histologic Chorioamnionitis, Amniotic Fluid Interleukin 6, Krebs von den Lungen 6, and Transforming Growth Factor β1 for the Development of Neonatal Bronchopulmonary Dysplasia
Authors: Matsumura Hisako , Ichiba Hiroyuki , Ohnishi Satoshi , Saito Mika , Shintaku Haruo 
Published: March 2017

Background: Chorioamnionitis (CAM) is an important risk factor for the development of bronchopulmonary dysplasia (BPD) in preterm infants. Objectives: To evaluate the effects of CAM on the development of BPD using interleukin 6 (IL-6), Krebs von den Lungen 6 (KL-6), and transforming growth factor β1 (TGF-β1) in the amniotic fluid as markers for inflammation, lung injury, and fibrosis/remodeling, respectively. Methods: Amniotic fluid concentrations of IL-6, KL-6, and TGF-β1 were measured with enzyme-linked immunosorbent assay or electrochemiluminescence immunoassay. Results: Of the 36 preterm infants, 18 were exposed to histologically confirmed CAM. Of these, 12 were later diagnosed as having BPD. The IL-6, KL-6, and TGF-β1 levels in the amniotic fluid significantly increased with increasing histologic severity of CAM. Moreover, these markers were higher in the BPD group with histologic CAM than those without. Conclusions: Our study suggests that CAM is likely to induce inflammatory, injury, and remodeling processes in the fetal lung.
Physical Activity in Patients Treated With Peritoneal Dialysis
Authors: Thangarasa Tharshika , Imtiaz Rameez , Hiremath Swapnil , Zimmerman Deborah 
Published: March 2017

Background: Patients with chronic diseases are known to benefit from exercise. Despite a lack of compelling evidence, patients with end-stage kidney disease treated with peritoneal dialysis are often discouraged from participating in exercise programs that include resistance training due to concerns about the development of hernias and leaks. The actual effects of physical activity with or without structured exercise programs for these patients remain unclear. The purpose of this study is to more completely define the risks and benefits of physical activity in the end-stage kidney disease population treated with peritoneal dialysis. Methods/design: We will conduct a systematic review examining the effects of physical activity on end-stage kidney disease patients treated with peritoneal dialysis. For the purposes of this review, exercise will be considered a purposive subcategory of physical activity. The primary objective is to determine if physical activity in this patient population is associated with improvements in mental health, physical functioning, fatigue and quality of life and if there is an increase in adverse outcomes. With the help of a skilled librarian, we will search MEDLINE, EMBASE, CINAHL, and Cochrane Central Register of Controlled Trials for randomized trials and observational studies. We will include adult end-stage kidney disease patients treated with peritoneal dialysis that have participated in an exercise training program or had their level of physical activity assessed directly or by self-report. The study must include an assessment of the association between physical activity and one of our primary or secondary outcomes measures. We will report study quality using the Cochrane Risk of Bias Assessment Tool for randomized controlled trials and the Newcastle–Ottawa Scale for observational studies. Quality across studies will be assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. The results of this review may help to inform guideline development for exercise recommendations specific to this patient population. Systematic review registration: PROSPERO:CRD42016041695.
Subclinical psychotic experiences and subsequent contact with mental health services
Authors: Bhavsar Vishal , Maccabe James H. , Hatch Stephani L. , Hotopf Matthew , Boydell Jane , McGuire Philip 
Published: March 2017

BackgroundAlthough psychotic experiences in people without diagnosed mental health problems are associated with mental health service use, few studies have assessed this prospectively or measured service use by real-world clinical data.AimsTo describe and investigate the association between psychotic experiences and later mental health service use, and to assess the role of symptoms of common mental health disorders in this association.MethodWe linked a representative survey of south-east London (SELCoH-1, n=1698) with health records from the local mental healthcare provider. Cox regression estimated the association of PEs with rate of mental health service use.ResultsAfter adjustments, psychotic experiences were associated with a 1.75-fold increase in the rate of subsequent mental health service use (hazard ratio (HR) 1.75, 95% CI 1.03–2.97) compared with those without PEs. Participants with PEs experienced longer care episodes compared with those without.ConclusionsPsychotic experiences in the general population are important predictors of public mental health need, aside from their relevance for psychoses. We found psychotic experiences to be associated with later mental health service use, after accounting for sociodemographic confounders and concurrent psychopathology.
Bone Density Screening in Postmenopausal Women With Early-Stage Breast Cancer Treated With Aromatase Inhibitors
Authors: Stratton Jamie , Hu Xin , Soulos Pamela R. , Davidoff Amy J. , Pusztai Lajos , Gross Cary P. , Mougalian Sarah S. 
Published: March 2017

Purpose: In postmenopausal women with breast cancer treated with aromatase inhibitors (AIs), most expert panels advise baseline bone mineral density testing with a dual-energy x-ray absorptiometry (DXA) scan repeated every 1 to 2 years. How often this recommendation is followed is unclear. Methods: We performed a retrospective analysis of women with stage I to III breast cancer who started AI therapy from January 1, 2008, to December 31, 2010, with follow-up through December 31, 2012, by using the SEER-Medicare database. Selection criteria included AI use for ≥ 6 months and no recent osteoporosis diagnosis or bisphosphonate use. We used multivariable logistic regression to investigate associations between patient characteristics and receipt of a baseline DXA scan. In patients who continued AI treatment, we assessed rates of follow-up scans. Results: In the sample of 2,409 patients (median age, 74 years), 51.0% received a baseline DXA scan. Demographic characteristics associated with the absence of a baseline DXA scan were older age (85 to 94 years v 67 to 69 years; odds ratio [OR], 0.62; 95% CI, 0.42 to 0.92) and black v white race (OR, 0.68; 95% CI, 0.47 to 0.97). Among patients who underwent a baseline DXA scan and continued AI for 3 years, 28.0% had a repeat DXA scan within 2 years and 65.9% within 3 years. In aggregate, of the 1,164 patients who continued with AI treatment for 3 years, only 34.5% had both a baseline and at least one DXA scan during the 3-year follow-up period. Conclusion: The majority of older Medicare beneficiaries with breast cancer treated with AIs do not undergo appropriate bone mineral density evaluation.
Picopore: A tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality
Authors: Gigante Scott 
Published: March 2017

Oxford Nanopore Technologies' (ONT) MinION and PromethION long-read sequencing technologies are emerging as genuine alternatives to established Next-Generation Sequencing technologies. A combination of the highly redundant file format and a rapid increase in data generation have created a significant problem both for immediate data storage on MinION-capable laptops, and for long-term storage on lab data servers. We developed Picopore, a software suite offering three methods of compression. Picopore's lossless and deep lossless methods provide a 25% and 44% average reduction in size, respectively, without removing any data from the files. Picopore's raw method provides an 88% average reduction in size, while retaining biologically relevant data for the end-user. All methods have the capacity to run in real-time in parallel to a sequencing run, reducing demand for both immediate and long-term storage space.
Adsorption of Pyrene from Aqueous Solutions onto Sepiolite
Authors: Sabah Eyüp , Ouki Sabeha 
Published: March 2017

AbstractPolycyclic aromatic hydrocarbons (PAHs) are a large class of organic compounds which are commonly mentioned and have been shown to be highly carcinogenic and to persist in the environment for many years. An inexpensive remediation method has yet to be found, so the current study was undertaken to test the use of sepiolite, a fibrous clay mineral, as a potentially inexpensive and effective solid-phase adsorbent for sequestering PAHs. Pyrene was chosen as a model PAH due to the specific volatility, miscibility, and relatively soluble properties of the compound. A sepiolite of Turkish origin was then investigated to explore its potential to adsorb hydrophobic organic compounds from aqueous solution. The microstructure and morphology of the sepiolite were characterized using elemental analysis, X-ray diffractometry (XRD), Fourier-transform infrared (FTIR) spectroscopy, field emission scanning electron microscopy (FE-SEM), and specific surface area from N2 adsorption isotherms. The pyrene adsorption isotherms were closely fitted to the Langmuir model and the coefficients of determination (RP2) were higher than 0.999. The results indicated that the high affinity of pyrene for sepiolite surfaces was dominated by the structural channels and the large number of Si-OH groups located on the basal surfaces. The intracrystalline interactions of pyrene with the sepiolite were, however, more favorable than pyrene interactions with sepiolite surface Si-OH groups, which can react directly with pyrene to form true covalent bonds (chemical interactions). Finally, the FE-SEM images initially revealed that, after sepiolite was loaded with adsorbed pyrene, a fairly straight and rigid arrangement of fibers occurred due to the aggregation of laths to form rods and the increased amounts of adsorbed pyrene.