bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concurrent chemoradiotherapy with or without surgery for patients with resectable esophageal cancer: An analysis of the National Cancer Data Base
Authors: Naik Kushal B. , Liu Yuan , Goodman Michael , Gillespie Theresa W. , Pickens Allan , Force Seth D. , Steuer Conor E. , Owonikoko Taofeek K. , Ramalingam Suresh S. , Higgins Kristin , Beitler Jonathan J. , Shin Dong M. , Willingham Field F. , El‐Rayes Bassel , Landry Jerome C. , Fernandez Felix G. , Saba Nabil F. 
Published: May 2017

BACKGROUNDPatients with resectable esophageal cancer (rEC) are managed with either concurrent chemoradiotherapy followed by surgery (CRSx) or concurrent chemoradiotherapy alone (cCR). To the authors' knowledge, there is insufficient evidence comparing the overall survival of patients treated with these 2 options.METHODSThe National Cancer Data Base was queried for rEC cases diagnosed from 2003 through 2011. Patients with previous cancers, cervical rEC, clinical stage T1N0 disease, or metastasis were excluded. cCR was defined as radiotherapy administered within 30 days of chemotherapy. CRSx was defined as cCR followed by esophagectomy within 90 days. Overall survival was compared using Kaplan‐Meier methods, propensity score matching, and extended Cox proportional hazards models.RESULTSOf the 11,122 eligible patients, 8091 (72.7%) received cCR and 3031 (27.3%) received CRSx. The odds of receiving CRSx were higher among patients with American Joint Committee on Cancer stage II disease (vs stage III), adenocarcinoma (vs squamous cell carcinoma), lesions of the lower one‐third of the esophagus, private insurance, and those living >25 miles from the treating facility or in areas with a higher median income or a greater percentage of high school‐educated residents. Patients aged >70 years, female patients, African‐American patients, those with ≥2 comorbidities, or those treated at community programs were more likely to receive cCR. After propensity score matching, the median and 10‐year survival rates were found to be significantly better with CRSx (32.5 months [95% confidence interval (95% CI), 29.6‐34.8 months] and 23.8% months [95% CI, 20.0‐27.9 months], respectively) compared with cCR (14.2 months [95% CI, 13.4‐15.5 months] and 6.1% months [95% CI, 3.9‐9.0 months], respectively).CONCLUSIONSData from the National Cancer Data Base support the inclusion of surgery after concurrent chemoradiotherapy for patients with locally advanced rEC. Cancer 2017;123:3476‐85. © 2017 American Cancer Society.
Statistical Analyses
Authors: Hardin Johanna , Kloke John 
Published: May 2017

AbstractIn this appendix, we provide an outline of methods used in analyzing biological data. We give a summary of types of data encountered and the appropriate methods to apply for the questions of interest. Statistical techniques described include the t test, the Wilcoxon rank sum test, the Mann‐Whitney‐Wilcoxon test, ANOVA, regression, and the chi‐square test. For each method, we give the appropriate assumptions, the details of the test, and a complete concrete example to follow. We also discuss related ideas such as multiple comparisons, why correlation does not imply causation, and ideas of sampling from a population. © 2017 by John Wiley & Sons, Inc.
Quantification of Lactate Dehydrogenase for Cell Viability Testing Using Cell Lines and Primary Cultured Astrocytes
Authors: Kaja Simon , Payne Andrew J. , Naumchuk Yuliya , Koulen Peter 
Published: May 2017

AbstractDrug discovery heavily relies on cell viability studies to assess the potential toxicity of drug candidates. L‐Lactate dehydrogenase (LDH) is a cytoplasmic enzyme that catalyzes the concomitant interconversions of pyruvate to L‐lactate and NADH to NAD+ during glycolysis, and the reverse reactions during the Cori cycle. In response to cellular damage, induced by endogenous cellular mechanisms or as a result of exogenously applied insults, LDH is released from the cytoplasm into the extracellular environment. Its stability in cell culture medium makes it a well‐suited correlate for the presence of damage and toxicity in tissues and cells. We herein present protocols for a reproducible and validated LDH assay optimized for several cell types. In contrast to commercially available LDH assays, often associated with proprietary formulations and high cost, our protocols provide ample opportunities for experiment‐specific optimization with low variability and cost. © 2017 by John Wiley & Sons, Inc.
Using Chromatin Immunoprecipitation in Toxicology: A Step‐by‐Step Guide to Increasing Efficiency, Reducing Variability, and Expanding Applications
Authors: McCullough Shaun D. , On Doan M. , Bowers Emma C. 
Published: May 2017

AbstractHistone modifications work in concert with DNA methylation to regulate cellular structure, function, and response to environmental stimuli. More than 130 unique histone modifications have been described to date, and chromatin immunoprecipitation (ChIP) allows for the exploration of their associations with the regulatory regions of target genes and other DNA/chromatin‐associated proteins across the genome. Many variations of ChIP have been developed in the 30 years since its earliest version came into use, which makes it challenging for users to integrate the procedure into their research programs. Furthermore, the differences in ChIP protocols can confound efforts to increase reproducibility across studies. The streamlined ChIP procedure presented here can be readily applied to samples from a wide range of in vitro studies (cell lines and primary cells) and clinical samples (peripheral leukocytes) in toxicology. We also provide detailed guidance on the optimization of critical protocol parameters, such as chromatin fixation, fragmentation, and immunoprecipitation, to increase efficiency and improve reproducibility. Expanding toxicoepigenetic studies to more readily include histone modifications will facilitate a more comprehensive understanding of the role of the epigenome in environmental exposure effects and the integration of epigenetic data in mechanistic toxicology, adverse outcome pathways, and risk assessment. © 2017 by John Wiley & Sons, Inc.
Use of Primary Rat Hepatocytes for Prediction of Drug‐Induced Mitochondrial Dysfunction
Authors: Liu Cong , Sekine Shuichi , Song Binbin , Ito Kousei 
Published: May 2017

AbstractMitochondrial dysfunction plays a central role in drug‐induced liver injury. To evaluate drug‐induced mitochondrial impairment, several isolated mitochondria‐ or cell line‐based assays have been reported. Among them, culturing HepG2 cells in galactose provides a remarkable method to assess mitochondrial toxicity by activating mitochondrial aerobic respiration. We applied this assay to primary rat hepatocytes by culturing cells in galactose and hyperoxia to enhance the evaluation of metabolism‐related drug‐induced mitochondrial toxicity. Conventional culture of primary hepatocytes under high‐glucose and hypoxic conditions could force cells to switch energy generation to glycolysis. By contrast, cells cultured in galactose and hyperoxia could maintain energy generation from mitochondrial aerobic respiration, which is consistent with physiological conditions, and consequently improve the susceptibility of cells to mitochondrial toxicants. Measuring the toxicities of test compounds in primary rat hepatocytes cultured in modified conditions provides a useful model to identify mitochondrial dysfunction‐mediated drug‐induced hepatotoxicity. © 2017 by John Wiley & Sons, Inc.
Short hairpin RNA is more effective than long hairpin RNA in eliciting pointed loss‐of‐function phenotypes in Drosophila
Authors: Bartoletti Rosa , Capozzoli Benjamin , Moore Joneisha , Moran Jaynie , Shrawder Brandy , Vivekanand Pavithra 
Published: May 2017

AbstractPointed (Pnt) is a transcriptional activator that functions downstream of the highly conserved Receptor Tyrosine Kinase (RTK) signaling pathway. Pnt is an ETS family transcription factor and encodes for two proteins, PntP1 and PntP2. However, while PntP1 is constitutively active, PntP2 is only active after being phosphorylated by MAPK in the RTK pathway. As mutations in pnt perturb the development of several tissues, we wanted to examine the effect and efficacy of using RNAi to target Pnt. We have expressed pnt RNAi in the eyes, oocyte, and heart cells using three different RNAi lines: Valium20, Valium10, and VDRC. Valium20 is distinct since it generates a short hairpin RNA (shRNA), while Valium10 and VDRC produce long hairpin dsRNA. We found that for each tissue examined Valium20 exhibited the strongest phenotype while the Valium10 and VDRC lines produced varying levels of severity and that the long hairpin RNA produced by the Valium10 and VDRC lines are unable to effectively knockdown pnt in embryonic tissues.
Restoring fire to grasslands is critical for migrating shorebird populations
Authors: Hovick Torre J. , Carroll J. Matthew , Elmore R. Dwayne , Davis Craig A. , Fuhlendorf Samuel D. 
Published: May 2017

AbstractFire is a disturbance process that maintains the structure and function of grassland ecosystems while sustaining grassland biodiversity. Conversion of grasslands to other land uses coupled with altered disturbance regimes has greatly diminished the habitat available to many grassland‐dependent species. These changes have been linked to declines in breeding bird populations, but may also be critical for migrating bird populations such as those shorebird species that depend on mesic grasslands during migration. We examined migratory shorebird use of burned grasslands in the southern Great Plains of North America using DISTANCE sampling to estimate and compare bird densities across recently burned and not recently burned landscapes (1–5 yr post fire). We conducted two surveys per week for 8–10 weeks along a 54‐km route starting at the end of March and concluding in mid‐May during 2014–2015. We encountered 2,509 total shorebirds in recently burned areas compared to 130 individuals in areas that were unburned. Fire was a major attractant for our three focal species with American Golden‐plover (Pluvialis dominica), Upland Sandpiper (Bartramia longicauda), and Killdeer (Charadrius vociferus) densities of 20.48, 11.09, and 26.09 birds/km2in burned areas compared with 0.00, 1.27, and 0.92 birds/km2in unburned areas, respectively. This research illustrates the importance of burned grassland for migrating shorebirds, a phenomenon that has largely gone unreported previously. Generally, these findings add to a body of knowledge that demonstrates the value of managing grasslands with historic disturbances that vary over space and time. The application of these findings should improve decision‐making for shorebird conservation and provides evidence that prescribed fire planning should include consideration for breeding, transient, and non‐breeding populations that vary in their temporal use of the landscape.
Floral resource availability from groundcover promotes bee abundance in coffee agroecosystems
Authors: Fisher Kaleigh , Gonthier David J. , Ennis Katherine K. , Perfecto Ivette 
Published: May 2017

AbstractPatterns of bee abundance and diversity across different spatial scales have received thorough research consideration. However, the impact of short‐ and long‐term temporal resource availability on biodiversity has been less explored. This is highly relevant in tropical agricultural systems for pollinators, as many foraging periods of pollinators extend beyond flowering of any single crop species. In this study, we sought to understand how bee communities in tropical agroecosystems changed between seasons, and if short‐ and long‐term floral resource availability influenced their diversity and abundance. We used a threshold analysis approach in order to explore this relationship at two time scales. This study took place in a region dominated by coffee agroecosystems in Southern Mexico. This was an ideal system because the landscape offers a range of coffee management regimes that maintain heterogeneity in floral resource availability spatially and temporally. We found that the bee community varies significantly between seasons. There were higher abundances of native social, solitary and managed honey bees during the dry season when coffee flowers. Additionally, we found that floral resources from groundcover, but not trees, were associated with bee abundance. Further, the temporal scale of the availability of these resources is important, whereby short‐term floral resource availability appears particularly important in maintaining high bee abundance at sites with lower seasonal complementarity. We argue that in addition to spatial resource heterogeneity, temporal resource heterogeneity is critical in explaining bee community patterns, and should thus be considered to promote pollinator conservation.
Pulmonary hypertension due to left heart disease: analysis of survival according to the haemodynamic classification of the 2015 ESC/ERS guidelines and insights for future changes
Authors: Palazzini Massimiliano , Dardi Fabio , Manes Alessandra , Bacchi Reggiani Maria L. , Gotti Enrico , Rinaldi Andrea , Albini Alessandra , Monti Enrico , Galiè Nazzareno 
Published: May 2017

AbstractAimsPulmonary hypertension (PH) is a relevant complication of left heart disease (LHD). The 2015 ESC/ERS PH guidelines report two different haemodynamic subsets of PH due to LHD (PH‐LHD) based on levels of pulmonary vascular resistance (PVR) and diastolic pressure gradient (DPG): isolated post‐capillary PH (Ipc‐PH) and combined post‐ and pre‐capillary PH (Cpc‐PH). The objective of this study is to evaluate the prognostic value of Ipc‐PH and Cpc‐PH.Methods and resultsData from 276 consecutive incident patients with PH‐LHD were included. According to the guidelines, Ipc‐PH is defined by DPG <7 mmHg and/or PVR ≤3 Wood units (WU) and Cpc‐PH by DPG ≥7 mmHg and/or PVR >3 WU. Using this definition, we identified three patient groups: Ipc‐PH with both normal PVR and DPG (108 patients); Cpc‐PH with both increased PVR and DPG (66 patients); and an intermediate group with either increased PVR or DPG (102 patients). Survival was estimated using the Kaplan–Meier method and compared between groups using the log‐rank test. Patients with Ipc‐PH had better survival compared with the group of patients with Cpc‐PH (P = 0.026) and the intermediate group (P = 0.025). No survival difference was detected between patients with Cpc‐PH and the intermediate group (P = 0.891). Patients with normal PVR had a better survival compared with those with elevated PVR (P = 0.012); while no difference was observed according to the level of DPG (P = 0.253).ConclusionPatients with Ipc‐PH have a better prognosis compared with patients with Cpc‐PH and with patients with isolated increase of PVR or DPG. Pulmonary vascular resistance has a better predictive value than DPG in patients with PH‐LHD.
Clinical phenotypes and outcome of patients hospitalized for acute heart failure: the ESC Heart Failure Long‐Term Registry
Authors: Chioncel Ovidiu , Mebazaa Alexandre , Harjola Veli‐Pekka , Coats Andrew J. , Piepoli Massimo Francesco , Crespo‐Leiro Maria G. , Laroche Cecile , Seferovic Petar M. , Anker Stefan D. , Ferrari Roberto , Ruschitzka Frank , Lopez‐Fernandez Silvia , Miani Daniela , Filippatos Gerasimos , Maggioni Aldo P. ,   on behalf of the ESC Heart Failure Long‐Term Registry Investigators
Published: May 2017

AimsTo identify differences in clinical epidemiology, in‐hospital management and 1‐year outcomes among patients hospitalized for acute heart failure (AHF) and enrolled in the European Society of Cardiology Heart Failure Long‐Term (ESC‐HF‐LT) Registry, stratified by clinical profile at admission.Methods and resultsThe ESC‐HF‐LT Registry is a prospective, observational study collecting hospitalization and 1‐year follow‐up data from 6629 AHF patients. Among AHF patients enrolled in the registry, 13.2% presented with pulmonary oedema (PO), 2.9% with cardiogenic shock (CS), 61.1% with decompensated heart failure (DHF), 4.8% with hypertensive heart failure (HT‐HF), 3.5% with right heart failure (RHF) and 14.4% with AHF and associated acute coronary syndromes (ACS‐HF). The 1‐year mortality rate was 28.1% in PO, 54.0% in CS, 27.2% in DHF, 12.8% in HT‐HF, 34.0% in RHF and 20.6% in ACS‐HF patients. When patients were classified by systolic blood pressure (SBP) at initial presentation, 1‐year mortality was 34.8% in patients with SBP <85 mmHg, 29.0% in those with SBP 85–110 mmHg, 21.2% in patients with SBP 110–140 mmHg and 17.4% in those with SBP >140 mmHg. These differences tended to diminish in the months post‐discharge, and 1‐year mortality for the patients who survived at least 6 months post‐discharge did not vary significantly by either clinical profile or SBP classification.ConclusionRates of adverse outcomes in AHF remain high, and substantial differences have been found when patients were stratified by clinical profile or SBP. However, patients who survived at least 6 months post‐discharge represent a more homogeneous group and their 1‐year outcome is less influenced by clinical profile or SBP at admission.
Simulation to Enhance Shale Gas Recovery Using Carbon Dioxide in Silica Nanopores with Different Sizes
Authors: Sun Haoyang , Zhao Hui , Qi Na , Li Ying 
Published: May 2017

AbstractAn understanding of molecular behavior on a microscopic level is always important not only to find out the natural principles but also to decide how to solve problems in applications. In this study, the grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulation methods were employed to investigate the adsorption and diffusion properties of CH4 and CO2 in silica nanopores with different sizes, and the displacement of residual CH4 in silica nanopores by CO2 at a constant temperature of 323 K and various pressures was studied. The microscopic molecular states of the adsorbed CH4 and CO2 in nanopores of various sizes are different. The competitive adsorption of CO2 over CH4 occurs broadly because of the different intensity of interactions between the gases molecules and the pore surface, of which the degree decreases with the increase of the pore size. An effective displacement process of residual adsorbed CH4 by CO2 was performed, and it is found that the displacement is enhanced with the increase of the CO2 bulk pressure and that the pore size has a significant influence on the displacement. According to the results, CO2 capture and storage (CCS) and the enhancement of CH4 recovery could be achieved at the same time in silica nanopores. This work provides microscopic information on the molecular behavior of CH4 and CO2 in silica nanopores and testifies to the efficiency of the displacement of CH4 by CO2 in silica nanopores with various sizes to provide useful guidance for applications in the enhancement of shale gas recovery by CO2.
Nanostructured phenolic matrices: Effect of different nanofillers on the thermal degradation properties and reaction to fire of a resol
Authors: Rallini M. , Wu H. , Natali M. , Koo J. , Torre L. 
Published: May 2017

SummaryIn this work, the effect of 6 different fillers as a nanomodifier of phenolic matrix was evaluated in thermal stability and reaction to fire. The chosen nanoparticles were montmorillonite, silica, carbon black, and 3 carbides—boron, silicon, and zirconium carbides. The nanofillers were mechanically dispersed in the matrix, and the dispersion and distribution of the nanosized particles in the matrix was evaluated by transmission electron microscopy. The thermal stability of nanocomposites was investigated by thermogravimetric analysis both in nitrogen and in air while the thermal combustion properties were measured using a microscale combustion calorimeter. The experimental data highlighted the remarkable effects of nanoboron carbide on the thermal properties it can confer to the phenolic matrix. Rheological behavior of the blends was also investigated to evaluate the effect of the different fillers on the viscosity of the nanostructured matrices.
Changing trends in the management of the neck in oropharyngeal squamous cell carcinoma
Authors: Jouhi Lauri , Atula Timo , Saarilahti Kauko , Hagström Jaana , Haglund Caj , Mohamed Hesham , Mäkitie Antti , Keski‐Säntti Harri 
Published: May 2017

AbstractBackgroundTreatment for oropharyngeal squamous cell carcinoma (SCC) has changed toward a more oncologic approach. We evaluated treatment of the neck, the incidence of regional recurrences, and factors associated with regional recurrence during the treatment approach transition period in patients with regional lymph node metastasis.MethodsAll patients with oropharyngeal SCC diagnosed at the Helsinki University Hospital during 2000‐2009 were analyzed for clinicopathological factors, treatment, p16 expression, and regional recurrence.ResultsAltogether, 169 patients had a complete response, and among them regional recurrence occurred in 5 patients (4.7%) treated with surgery ± radiotherapy (RT) or chemoradiotherapy (CRT) and in 2 patients (3.2%) treated with RT or CRT ± surgery. All these 7 patients had N2b disease or higher, and 5 of them had regional recurrence in the contralateral side of the neck.ConclusionThe incidence of regional recurrence was low, and remained unchanged despite the increased use of RT or CRT ± surgery. Treatment and follow‐up of the contralateral neck warrants special attention in patients with advanced neck disease (≥N2b).
Photobiomodulation therapy on wound treatment subsequent to Q‐switched Nd: YAG laser tattoo removal in rat model
Authors: Imrigha Nada Abusalah Almabrouk , Bidin Noriah , Lau Pik Suan , Musa Nurfatin , Zakaria Nurlaily , Krishnan Ganesan 
Published: May 2017

AbstractQ‐switched Nd: YAG laser is the most effective laser for tattoo removal. Photobiomodulation (PBM) therapy is an alternative method applied to accelerate the wound healing. This paper investigated the effects of PBM therapy using 808 nm diode laser on tattooed skin after laser tattoo removal. Forty‐five rats were selected and tattooed with black ink on their dorsal, and then distributed into three groups. G0 was received non‐laser irradiation. G1 was treated by laser tattoo removal using 1064 nm with energy density of 3.4 J/cm2 without PBM therapy, while G2 was treated daily with PBM therapy using 808 nm diode laser of 5 J/cm2 after a single session of laser tattoo removal. The effects of tattoo removal and healing progress of the wound were analyzed using histological studies. Findings showed 808 nm laser promotes the healing process through enhancing epithelialization and collagen deposition. Moreover, PBM therapy stimulated immune cells to improve phagocytosis process for removing the tattoo ink fragments effectively. The PBM therapy treated group was capable of improving the healing process and increasing the quality of skin following the laser tattoo removal. It was also found that stimulation of cellular function by PBM therapy increased tattoo clearance efficiency.