bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infrared composition of the Large Magellanic Cloud
Authors: Siudek M. , Pollo A. , Takeuchi T. T. , Ita Y. , Kato D. , Onaka T. 
Published: March 2013

AbstractThe evolution of galaxies and the history of star formation in the Universe are among the most important topics in today’s astrophysics. Especially, the role of small, irregular galaxies in the star-formation history of the Universe is not yet clear. Using the data from the AKARI IRC survey of the Large Magellanic Cloud at 3.2, 7, 11, 15, and 24 μm wavelengths, i.e., at the mid- and near-infrared, we have constructed a multiwavelength catalog containing data from a cross-correlation with a number of other databases at different wavelengths. We present the separation of different classes of stars in the LMC in color-color, and color-magnitude, diagrams, and analyze their contribution to the total LMC flux, related to point sources at different infrared wavelengths.
Prognosis and Predictors of Surgical Complications in Hepatocellular Carcinoma Patients With or Without Cirrhosis after Hepatectomy
Authors: Mizuguchi Toru , Kawamoto Masaki , Meguro Makoto , Nakamura Yukio , Ota Shigenori , Hui Thomas T. , Hirata Koichi 
Published: March 2013

AbstractBackgroundAlthough poor liver function is associated with a high morbidity rate and poor prognosis in hepatocellular carcinoma (HCC) patients, the exact effects of liver pathology on the surgical outcomes of HCC patients are poorly understood. The purpose of this study was to assess how the liver pathology of HCC patients affects their prognosis and complications rate after liver resection.MethodsBetween January 2006 and November 2010, 149 consecutive hepatocellular carcinoma patients, including 79 noncirrhosis patients and 70 cirrhosis patients, were enrolled in this study.ResultsAmong the noncirrhotic patients, operative time, fresh frozen plasma (FFP) transfusion requirement, tumor size, and serum retinol binding protein (RBP) levels were significantly higher in the complications group than in the complications‐free groups. On the other hand, in the cirrhotic patients the prothrombin time (PT) and indocyanine green retention value at 15 min (ICGR15) of the complications group were significantly lower and higher, respectively, than those of the complications‐free group. In the noncirrhotic patients, recurrence‐free survival and overall survival did not differ between the complications and complications‐free groups. On the other hand, in the cirrhotic patients, the recurrence‐free survival and overall survival of the complications‐free group were significantly longer than those of the complications group.ConclusionsIn the noncirrhotic patients, surgical complications had no prognostic effect, whereas they had a significant survival impact in the cirrhotic patients. The surgical strategy for HCC should be based on the patient’s pathological background.
Polysaccharide hydrolysis with engineeredEscherichia colifor the production of biocommodities
Authors: Muñoz-Gutiérrez Iván , Martinez Alfredo 
Published: March 2013

AbstractEscherichia coli can ferment a broad range of sugars, including pentoses, hexoses, uronic acids, and polyols. These features make E. coli a suitable microorganism for the development of biocatalysts to be used in the production of biocommodities and biofuels by metabolic engineering. E. coli cannot directly ferment polysaccharides because it does not produce and secrete the necessary saccharolytic enzymes; however, there are many genetic tools that can be used to confer this ability on this prokaryote. The construction of saccharolytic E. coli strains will reduce costs and simplify the production process because the saccharification and fermentation can be conducted in a single reactor with a reduced concentration or absence of additional external saccharolytic enzymes. Recent advances in metabolic engineering, surface display, and excretion of hydrolytic enzymes provide a framework for developing E. coli strains for the so-called consolidated bioprocessing. This review presents the different strategies toward the development of E. coli strains that have the ability to display and secrete saccharolytic enzymes to hydrolyze different sugar-polymeric substrates and reduce the loading of saccharolytic enzymes.
New strategy to improve efficiency for gene replacement in Klebsiella pneumoniae
Authors: Wei Dong , Sun Junsong , Shi Jiping , Liu Pengfu , Hao Jian 
Published: March 2013

Abstract
We previously reported the method for introducing gene replacement into Klebsiella pneumoniae through Red-assisted homologous recombination; and it demonstrated that a higher transformation efficiency required long flanking arms at both ends of the linear DNA. The assembly job of the linear DNA is usually time-consuming and laborious. We report here an innovative method for DNA exchange in K. pneumoniae based on PCR-mediated Red recombination. The novel procedure enables rapid gene replacement in K. pneumoniae without prior cloning of the gene of interest; the key modification is to perform PCR reaction to generate linear DNA with extra non-homologous fragments on both ends as mercenary sequences which come from a TA-cloning plasmid. We give a demonstration by deleting the gene dhak1 in K. pneumoniae with high efficiency of about 20 CFU/μg DNA using the new technique.
A Nondegenerate Penalized Likelihood Estimator for Variance Parameters in Multilevel Models
Authors: Chung Yeojin , Rabe-Hesketh Sophia , Dorie Vincent , Gelman Andrew , Liu Jingchen 
Published: March 2013

Group-level variance estimates of zero often arise when fitting multilevel or hierarchical linear models, especially when the number of groups is small. For situations where zero variances are implausible a priori, we propose a maximum penalized likelihood approach to avoid such boundary estimates. This approach is equivalent to estimating variance parameters by their posterior mode, given a weakly informative prior distribution. By choosing the penalty from the log-gamma family with shape parameter greater than 1, we ensure that the estimated variance will be positive. We suggest a default log-gamma(2,λ) penalty with λ→0, which ensures that the maximum penalized likelihood estimate is approximately one standard error from zero when the maximum likelihood estimate is zero, thus remaining consistent with the data while being nondegenerate. We also show that the maximum penalized likelihood estimator with this default penalty is a good approximation to the posterior median obtained under a noninformative prior.Our default method provides better estimates of model parameters and standard errors than the maximum likelihood or the restricted maximum likelihood estimators. The log-gamma family can also be used to convey substantive prior information. In either case—pure penalization or prior information—our recommended procedure gives nondegenerate estimates and in the limit coincides with maximum likelihood as the number of groups increases.
Hearing relative clauses boosts relative clause usage (and referential clarity) in young Turkish language learners
Authors: SARILAR AYŞE , MATTHEWS DANIELLE , KÜNTAY AYLIN C. 
Published: March 2013

ABSTRACTOn account of both their functional and their morphosyntactic characteristics, relative clauses are often viewed as indicators of complexity in child language. Morphosyntactic properties of Turkish make use of particularly arduous relative clauses in spontaneous early discourse. A matching sticker selection task was used to determine whether Turkish-learning 3- and 4-year-olds can be trained to use subject relative clauses and uniquely identifying constructions. Upon their selection of the accurate sticker, the children were exposed to relative clause constructions (relative clause condition), sentences with demonstrative pronouns (demonstrative noun phrase condition), or a general approval (positive feedback condition). The number of relative clauses increased from pretest to posttest only in the relative clause condition; the rate of using adequately discriminating forms increased in all the three conditions, albeit with a steeper increase in the relative clause condition. The results are discussed in the framework of both structural and pragmatic priming.
Uniform Total Internal Reflection Fluorescence Illumination Enables Live Cell Fluorescence Resonance Energy Transfer Microscopy
Authors: Lin Jia , Hoppe Adam D. 
Published: March 2013

AbstractFluorescence resonance energy transfer (FRET) microscopy is a powerful technique to quantify dynamic protein-protein interactions in live cells. Total internal reflection fluorescence (TIRF) microscopy can selectively excite molecules within about 150 nm of the glass-cell interface. Recently, these two approaches were combined to enable high-resolution FRET imaging on the adherent surface of living cells. Here, we show that interference fringing of the coherent laser excitation used in TIRF creates lateral heterogeneities that impair quantitative TIRF-FRET measurements. We overcome this limitation by using a two-dimensional scan head to rotate laser beams for donor and acceptor excitation around the back focal plane of a high numerical aperture objective. By setting different radii for the circles traced out by each laser in the back focal plane, the penetration depth was corrected for different wavelengths. These modifications quell spatial variations in illumination and permit calibration for quantitative TIRF-FRET microscopy. The capability of TIRF-FRET was demonstrated by imaging assembled cyan and yellow fluorescent protein–tagged HIV-Gag molecules in single virions on the surfaces of living cells. These interactions are shown to be distinct from crowding of HIV-Gag in lipid rafts.
An Efficient Resource to Accelerate Research into the Cause and Prevention of Breast Cancer: The Love/Avon Army of Women
Authors: S Love 
Published: March 2013

Abstract
Background: It is well established that more research into the cause and prevention of breast cancer is needed. While studies are done in cell lines and lab animals, translation of findings to women is often delayed due to difficulty in recruitment. The Dr. Susan Love Research Foundation received a grant from the Avon Foundation for Women to form the Love/Avon Army of Women (AOW); an on-line recruitment resource designed to partner women with researchers in order to accelerate breast cancer research. Methods: Researchers submit a proposal to the AOW Scientific Advisory Committee. If a study is accepted, a mass e-mail describing the study procedures and inclusion/exclusion criteria is sent to the entire AOW database. Women sign up at www.armyofwomen.org to join and receive AOW e-mails about breast cancer research studies. Women self-select based on interest and study criteria, and undergo a secondary on-line screening before contact information is passed on to the researcher for the enrollment process. Results: Over 371,000 women have signed up, including survivors and women without a history of breast cancer, ranging from ages 18 to 100, representing all 50 US states and 49 countries. To date, the AOW has recruited for 70 studies. The diversity of the AOW members has proved beneficial for many studies, such as those needing to enroll racial/ethnic minorities, women of varying sexual orientations, or young survivors. A secondary goal of the AOW is to assist researchers new to research with human subjects. The AOW has successfully helped researchers cross the chasm, coaching them on what it takes to transition their research from animal models to human subjects. Conclusions: The AOW has proved to be a successful resource for scientists to accelerate accrual, expand the number and diversity of their subject population and to obtain exactly the type of specimens they need when they need it. This partnership between women and scientists has revolutionized research and accelerated efforts to eradicate breast cancer. The public is ready and willing to partner with the research community to find the answer to urgent clinical problems.
Smoking and Colorectal Cancer Risk by Tumor Genetic and Epigenetic Subtypes: A Molecular Pathological Epidemiology (MPE) Study
Authors: R Nishihara , AT Chan , S Ogino 
Published: March 2013

Abstract
Purpose: It remains to be investigated whether smoking is associated with colorectal carcinogenesis through specific epigenetic or genetic alterations, or abnormal protein expression. We comprehensively examined the influence of smoking on colorectal cancer risk by specific tumor molecular features, including epigenetic status (CpG island methylator phenotype [CIMP]), genomic instability (microsatellite instability [MSI]), oncogenic mutations (BRAF, KRAS, and PIK3CA), and tumor protein expressions (DNA methyltransferase-3B [DNMT3B], TP53, PTGS2 [cyclooxygenase-2], FASN, and CTNNB1 [b-catenin]). Methods: Follow-up of 134,204 individuals in two U.S. nationwide prospective cohorts (Nurses' Health Study [1980–2008] and Health Professionals Follow-up Study [1986–2008]) resulted in 1,292 incident rectal and colon cancers with available molecular data. Duplication method Cox proportional hazards model was used to calculate multivariate hazard ratio (HR) for developing a specific subtype of tumor according to smoking status. Results: Compared with never smokers, smoking of ≥40 cumulative pack-years was associated with increased risks for specific molecular types of colorectal cancer. Multivariate HRs are 2.12 for CIMP-high cancer (95% confidence interval [CI], 1.48- 3.03), 2.27 for MSI-high cancer (95% CI, 1.56–3.31), 2.00 for BRAF-mutated cancer (95% CI, 1.37–2.92), 1.37 for KRAS-wild-type cancer (95% CI, 1.12–1.68), 1.30 for PIK3CA-wild-type cancer (95% CI, 1.07–1.58), 1.33 for TP53-negative cancer (95% CI, 1.05–1.69), 1.37 for PTGS2-positive cancer (95% CI, 1.09–1.73), 1.36 for FASN-positive cancer (95% CI, 1.07–1.73), and 1.35 for CTNNB1-negative cancer (95% CI, 1.04–1.74). The influence of smoking significantly differed according to status of CIMP (P = 0.001 for heterogeneity test of CIMP-low vs. CIMP-high) and MSI (P = 0.0003 for heterogeneity test of MSS vs. MSI-high). There was no statistically significant differential association of smoking with other molecular subtypes. Conclusion: This molecular pathological epidemiology (MPE) study suggests that smoking might primarily cause epigenetic alterations, which lead to oncogenic mutations in colonic cells.
Cross-Sectional & Longitudinal Associations between Light-Intensity Physical Activity & Physical Function Among Cancer Survivors
Authors: C Blair , M Morey , R Desmond , R Sloane , D Snyder , H Cohen , W Demark-Wahnefried 
Published: March 2013

Abstract
Purpose: While moderate-vigorous intensity physical activities (MVPA) confer the greatest health benefits, evidence suggests that light-intensity activities are also beneficial, particularly for older adults and individuals with moderate-severe comorbidities. Cross-sectional and longitudinal associations between light-intensity physical activity and physical function were examined in elderly cancer survivors, who are at increased risk for age- and treatment related comorbidities, including accelerated functional decline. Methods: The analysis included 641 breast, prostate, and colorectal cancer survivors (54% female) aged 65 and older who participated in a 1-year, home-based diet and exercise intervention designed to reduce the rate of physical function decline. Pre- and post-intervention physical activity and function were assessed via the CHAMPS questionnaire, the SF-36 physical function subscale (PFS) and the Late Life Function and Disability Index basic and advanced lower-extremity function (LEF) subscales. ANCOVA was used to compare means of physical function across levels of PA intensity (low-light (LLPA): 1.0-2.0 METs; high-light (HLPA): 2.1-2.9 METs; MVPA: ≥3.0 METs). Results: After adjustment for age, sex, BMI, comorbidities, symptoms, and MVPA, increasing tertiles of baseline light-intensity activity were associated with higher scores for all 3 measures of baseline physical function (all p-values &lt;0.005). Associations were stronger for HLPA than for LLPA. Compared with survivors who decreased or remained stable in MVPA and HLPA at the post-intervention follow-up, those who increased in HLPA, but not MVPA, reported higher physical function scores (LSMeans (95% CI): SF-36 PFS: −5.58 (−7.96, −3.20) vs. −2.54 (−5.83, 0.75), p = 0.14; basic LEF: -2.00 (−3.45, −0.55) vs. 0.28 (−1.72, 2.28), p = 0.07; advanced LEF: −2.58 (−4.00, −1.15) vs. 0.44 (-1.52, 2.40), p = 0.01). Conclusions: Our findings suggest that increasing light-intensity activities, especially HLPA, may be a viable approach to reducing the rate of physical function decline in individuals who are unable or reluctant to initiate or maintain adequate levels of moderate-intensity activities.
The Role of Geography in Low Mammography Screening Rates and Late-Stage Breast Cancer Diagnosis in Utah
Authors: KA Henry , NM Stroup , AY Kinney 
Published: March 2013

Abstract
Purpose: Mammography screening rates in Utah have been lower than other states for nearly 20 years. We examine the role of geographic factors on mammography screening rates and late-stage breast cancer diagnosis in Utah. Methods: Mammography screening data from the 2008 and 2010 Utah Behavioral Risk Factor Surveillance System included Utah women aged 40–74 (weighted N = 417,064). Utah Cancer Registry data included women 40+ years, who were diagnosed with breast cancer from 2004–2008 (N = 6,500). Multilevel logistic regression was used to examine the association between measures of geographic access to mammography (travel time, geo access scores, rural/urban residence) and individual factors (age, race/ethnicity, insurance) and the odds of (a) not having a mammogram within the last two years and (b) being diagnosed with late stage breast cancer. Geo access scores are composite values based on the number of mammography facilities and the distribution of drive times. Results: Overall 32.7% (95%CI 31.1%–34.5%) of Utah women 40–74 reported not having a mammogram within the last 2 years and 31.3% of women aged 40+ were diagnosed with late-stage breast cancer. A disproportionate number 43.1% (95%CI 39.9%–46.3%) of women 40–49 did not have a mammogram within the last 2 years compared to women 50–74 (26.8% 95%CI 24.9%–28.7%). Geographic access measures were not associated with mammography screening and late-stage breast cancer diagnosis among women 40–74. Travel time was moderately significant for women living &gt;20 minutes from a mammography facility compared to women living &lt;5 min (OR = 1.23 95%CI 1.01–1.50), even after controlling for age, race/ethnicity, and insurance status. Women aged 50+ with low geo access scores had higher odds (OR = 1.20 95%CI 1.04 1.37) of late-stage breast cancer diagnosis compared to women with high geo access scores. Conclusion: Geographic access may be a risk factor for late-stage breast cancer for specific segments of the population, who may benefit from targeted interventions to improve early detection. Future work should consider alternate geographic access measures and other potential sociodemographic or cultural barriers to screening in Utah.
Predictors of Colorectal Cancer Surveillance among Radiation-treated Survivors of Childhood Cancer
Authors: C Daniel , P Nathan , K Oeffinger , K Stratton , W Leisenring , K Whelan , J Waterbor , T Henderson , G Armstrong , K Krull , L Robison , C Kohler 
Published: March 2013

Abstract
Purpose: To identify predictors of adherence to colorectal cancer (CRC) surveillance guidelines among survivors of childhood cancer who received ≥30 Gy radiotherapy to the abdomen, pelvis, or spine, and were 36 years or older at the time of last contact. Methods: We sought to identify predictors of self-reported CRC surveillance participation among 5-year survivors who completed the Childhood Cancer Survivor Study (CCSS) 2007 Follow-Up Questionnaire and met the criteria above. Univariate and multivariable generalized linear models with a log link and Poisson distribution were used to calculate relative risks (RR) with 95% confidence intervals (95% CI) for adherence to CRC surveillance guidelines (i.e., home stool blood testing and/or colonoscopy/sigmoidoscopy). Results: The mean age of 711 childhood cancer survivors eligible for the study was 44 years (SD = 5.2 years). Among them, 231 (32.5%) reported ever performing home stool blood testing and 276 (38.8%) reported ever having colonoscopy or sigmoidoscopy. Of the 711 participants, 60 (8.4%) reported home stool blood testing in the past year (meeting screening guidelines for the general adult population) and 207 (29.1%) reported having a colonoscopy or sigmoidoscopy in the past 5 years (meeting surveillance recommendations for survivors of childhood cancer treated with radiation). In the multivariable analyses, factors associated with CRC surveillance were age 50 years or older (RR = 2.4, 95% CI = 1.9–2.9); having routine cancer follow-up visit within one year prior to questionnaire completion (RR = 1.7, 95% CI = 1.2–2.5); having a physical impairment requiring the assistance of others for routine activities of daily living (RR = 1.7, 95% CI = 1.2–2.2); and having discussed future cancer risk with a physician at their most recent follow-up visit (RR = 1.3, 95% CI = 1.1–1.6). Conclusions: More than 70% of survivors at risk for CRC were not screened as recommended. Indeed, unless a physician discussed their future cancer risk, most survivors were not screened until they reached age 50, the time at which CRC screening is recommended for individuals at average CRC risk. These findings underscore the need for education of survivors and their physicians regarding the heightened CRC risk following radiation.