bluuebunny/crossref_metadata_2025_split huggingface dataset:
Histologic grade as prognostic indicator for mucoepidermoid carcinoma: A population‐level analysis of 2400 patients
Authors: Chen Michelle M. , Roman Sanziana A. , Sosa Julie A. , Judson Benjamin L. 
Published: June 2013

BackgroundMucoepidermoid carcinoma (MEC) is an uncommon malignancy. To the best of our knowledge, this is the largest study investigating disease‐specific survival (DSS) of parotid MEC and the first population‐level study of the distribution of nodal metastases.MethodsPatients with MEC of the parotid gland were identified in the Surveillance, Epidemiology, and End Results (SEER) database (1988–2009).ResultsWe identified 2400 patients with MEC: 522 low grade, 1137 intermediate grade, and 741 high grade. Five‐year DSS rates for low‐grade, intermediate‐grade, and high‐grade MEC were 98.8%, 97.4%, and 67.0%, respectively (p < .001). Negative prognostic factors included high grade, increasing patient age, and tumor size, extraparenchymal extension, nodal metastases, and distant metastases. High‐grade MEC was more likely to have lymph node metastases in levels I to III (34.0%) than low‐grade (3.3%) and intermediate‐grade MEC (8.1%; p < .001).ConclusionGrade influences the prognosis and distribution of nodal metastases. Results indicate that management guidelines should vary based on grade. © 2013 Wiley Periodicals, Inc. Head Neck 36: 158–163, 2014
Circulating CD4‐positive lymphocyte levels as predictor of response to induction chemotherapy in patients with advanced laryngeal cancer
Authors: Dewyer Nicholas A. , Wolf Gregory T. , Light Emily , Worden Francis , Urba Susan , Eisbruch Avraham , Bradford Carol R. , Chepeha Douglas B. , Prince Mark E. , Moyer Jeffrey , Taylor Jeremy 
Published: June 2013

Background. Tumor regression after induction chemotherapy (ICT) identifies laryngeal cancers that are responsive to chemoradiation. Patient immune parameters have recently been associated with response to chemotherapy and may identify responding patients. A retrospective analysis was performed to determine if pretreatment, circulating T lymphocyte levels predicted ICT response in patients with advanced laryngeal cancer.Methods. Pretreatment, circulating T lymphocyte subpopulations were correlated with response to therapy and survival. Results were compared with similar data from an identical phase II trial involving patients with oropharyngeal cancer.Results. An increased percentage of CD4+ cells predicted response to ICT and suggested improved survival in patients with laryngeal, but not oropharyngeal, cancer. In the combined group of patients, increased CD4 levels predicted response to ICT.Conclusion. These findings demonstrate the potential importance of the immune system in chemotherapy response and clinical outcome. Differences in findings between patients with advanced laryngeal and oropharyngeal cancer may reflect different cellular immunity function in the patients with human papillomavirus (HPV)‐16+ oropharyngeal cancer. © 2013 Wiley Periodicals, Inc. Head Neck 36: 9–14, 2014
Preservation of greater auricular nerve during parotidectomy: Sensation, quality of life, and morbidity issues. A Systematic Review
Authors: George Michael , Karkos Petros D. , Dwivedi Raghav C. , Leong Samuel C. , Kim Dae , Repanos Costa 
Published: June 2013

BackgroundOur objectives were to assess the evidence of preservation of the greater auricular nerve in parotidectomy with regard to morbidity and quality of life.MethodsThis was a systematic review. Inclusion criteria were: English literature, prospective and retrospective studies. Exclusion criteria were: single case reports, “teaching” reviews. Outcome measures were: tactile sensation, pain, thermal sensitivity, and quality of life.ResultsAlthough quality of life does not seem to be adversely affected when the greater auricular nerve is sacrificed, preservation of the posterior branch was recommended in 8 studies. When preserving the nerve, the incremental operative time increase is no more than 10 to 5 minutes after a rapid learning curve.ConclusionsThere is level Ib evidence that preservation of the greater auricular nerve minimizes the postoperative sensory disturbance and should be considered whenever tumor clearance is not compromised. There is no evidence that overall quality of life is affected when the greater auricular nerve is sacrificed. © 2013 Wiley Periodicals, Inc. Head Neck 36: 603–608, 2014
Lymph node density—Prognostic value in head and neck cancer
Authors: Rudra Sonali , Spiotto Michael T. , Witt Mary Ellyn , Blair Elizabeth A. , Stenson Kerstin , Haraf Daniel J. 
Published: June 2013

BackgroundThe purpose of this study was to determine the prognostic value of lymph node density in head and neck cancer.MethodsWe utilized a prospective, multicenter database of 223 patients with head and neck cancer to identify patients who underwent lymph node dissection before chemoradiation to assess the prognostic significance of lymph node density.ResultsIn 38 patients who met study criteria, lymph node density ≤0.20 predicted for improved overall survival (OS; 79% vs 50%; p = .04). Lymph node density was also associated with a trend toward improved 3‐year locoregional control (96% vs 79%; p = .14) and distant metastasis–free survival (93% vs 78%; p = .13). In the patients with treatment failure distantly or locoregionally, that failure was earlier in patients with lymph node density >0.20 than in patients with lymph node density ≤0.20 (median, 12.7 months vs 5.2 months; p = .004).ConclusionOur data suggest that lymph node density predicts for OS in patients with head and neck cancer and that the difference in OS may be because of differences in time to failure. © 2013 Wiley Periodicals, Inc. Head Neck 36: 266–272, 2014
Regulation of bile acid metabolism: New insights from inside
Authors: Quintero Pablo , Arrese Marco 
Published: June 2013

Sayin SI, Wahlstrom A, Felin J, Jantti S, Marschall HU, Bamberg K, et al. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab 2013;17:225-235. (Reprinted with permission).

Abstract

Bile acids are synthesized from cholesterol in the liver and further metabolized by the gut microbiota into secondary bile acids. Bile acid synthesis is under negative feedback control through activation of the nuclear receptor farnesoid X receptor (FXR) in the ileum and liver. Here we profiled the bile acid composition throughout the enterohepatic system in germfree (GF) and conventionally raised (CONV-R) mice. We confirmed a dramatic reduction in muricholic acid, but not cholic acid, levels in CONV-R mice. Rederivation of Fxr-deficient mice as GF demonstrated that the gut microbiota regulated expression of fibroblast growth factor 15 in the ileum and cholesterol 7a-hydroxylase (CYP7A1) in the liver by FXR-dependent mechanisms. Importantly, we identified tauroconjugated beta- and alpha-muricholic acids as FXR antagonists. These studies suggest that the gut microbiota not only regulates secondary bile acid metabolism but also inhibits bile acid synthesis in the liver by alleviating FXR inhibition in the ileum.
Changes of soil surface roughness under water erosion process
Authors: Zheng Zi‐Cheng , He Shu‐Qin , Wu Fa‐Qi 
Published: June 2013

AbstractThe objective of this study was to determine the changing characteristics of soil surface roughness under different rainfall intensities and examine the interaction between soil surface roughness and different water erosion processes. Four artificial management practices (raking cropland, artificial hoeing, artificial digging, and contour tillage) were used according to the local agriculture customs of the Loess Plateau of China to simulate different types of soil surface roughness, using an additional smooth slope for comparison purposes. A total of 20 rainfall simulation experiments were conducted in five 1 m by 2 m boxes under two rainfall intensities (0.68 and 1.50 mm min−1) on a 15° slope. During splash erosion, soil surface roughness decreased in all treatments except raking cropland and smooth baseline under rainfall intensity of 0.68 mm min−1, while increasing for all treatments except smooth baseline under rainfall intensity of 1.50 mm min−1. During sheet erosion, soil surface roughness decreased for all treatments except hoeing cropland under rainfall intensity of 0.68 mm min−1. However, soil surface roughness increased for the artificial hoeing and raking cropland under rainfall intensity of 1.50 mm min−1. Soil surface roughness has a control effect on sheet erosion for different treatments under two rainfall intensities. For rill erosion, soil surface roughness increased for raking cropland and artificial hoeing treatments, and soil surface roughness decreased for artificial digging and the contour tillage treatments under two rainfall intensities. Under rainfall intensity of 0.68 mm min−1, the critical soil surface roughness was 0.706 cm for the resistance control of runoff and sediment yield. Under rainfall intensity of 1.50 mm min−1, the critical soil surface roughness was 1.633 cm for the resistance control of runoff, while the critical soil surface roughness was 0.706 cm for the resistance control of sediment yield. These findings have important implications for clarifying the erosive nature of soil surface roughness and harnessing sloped farmland. Copyright © 2013 John Wiley & Sons, Ltd.
Direct exposure at the air–liquid interface: evaluation of an in vitro approach for simulating inhalation of airborne substances
Authors: Rach Jessica , Budde Jessica , Möhle Niklas , Aufderheide Michaela 
Published: June 2013

ABSTRACTIn toxicology, the strategies for testing the hazardous potential of substances are changing as a result of the ongoing progress in the development of in vitro methods and the demand of the authorities to reduce animal testing. Even in the complex field of inhalation toxicology with its high requirements on the technical implementation and cell culture models, the preconditions for using such methods are fulfilled. We here introduce a sophisticated technique that enables the stable and reproducible exposure of cultivated cells to airborne substances at the air–liquid interface by means of the CULTEX® Radial Flow System (RFS) module. The feasibility and suitability of the experimental setup is demonstrated by dose‐response investigations of mainstream cigarette smoke and particulate matter of four substances in different lung epithelial cell lines. A dose‐dependent cytotoxcity of the test substances was verified by applying different exposure times. The high reproducibility of the results indicate the reliability of the presented method and recommend the integration of such in vitro approaches in the field of inhalation toxicology by advancing their regulatory validation. Copyright © 2013 John Wiley & Sons, Ltd.
Quantum Chemical Calculations of Intramolecular Vibrational Redistribution and Energy Transfer of Dipeptides (GlyTyr and LeuTyr) and Applications to the RRKM Theory
Authors: Yang Ling , Niu Yingli , Zhu Chaoyuan , Fujimura Yuichi , Shiu Yingjen , Yu Jian‐Guo , Lin Sheng‐Hsien 
Published: June 2013

AbstractRecently the quantum chemistry program can provide the anharmonic potentials for polyatomic molecules and clusters. It makes the quantum calculation of intramlecular vibrational redistribution (IVR) rates and intramolecular vibrational energy transfer possible. In the present paper, we apply the adiabatic approximation method to treat these two intramolecular energy redistribution processes. Using this method, we calculate the IVR rates of the dipeptides (glycyl tyrosine (GlyTyr) and leucyl tyrosine (LeuTyr)) and their cation radicals from the high frequency modes to the low frequency modes. Our theoretical results of the IVR lifetimes of the high frequency modes, like C‐H, N‐H, and O‐H stretching modes, for both GlyTyr and LeuTyr molecules and their cation radicals are about 1 ps, 10 ps, and 100 ps, respectively. It provides theoretical support for the claim that IVR takes place prior to dissociation and the IVR rates are determined by the functional group rather than the degrees of freedom of the system. Thus the Rice‐Ramsperger‐Kassel‐Marcus (RRKM) theory is suitable for investigating the photodissociation process of dipeptides. In addition, the calculated intramolecular energy transfer rate from O‐H stretching mode of the C‐termius of dipeptides to N‐H mode of N‐terminus is close to IVR rate.
Observational study of the cooling behavior of interstellar helium pickup ions in the inner heliosphere
Authors: Chen Jun Hong , Möbius Eberhard , Gloeckler George , Bochsler Peter , Bzowski Maciej , Isenberg Philip A. , Sokół Justyna M. 
Published: June 2013

AbstractThe velocity distribution of interstellar pickup ions (PUIs) has typically been described as evolving through fast pitch angle scattering followed by adiabatic cooling while being transported radially outward with the solar wind. In combination, the ionization rate, which controls the radial profile of the interstellar neutrals, and the cooling process determine the slope of the observed PUI distributions. Thus far, a cooling index of 3/2 for the PUI velocity distributions has been used in almost all studies. This value is based on the implicit assumptions of immediate PUI isotropization due to pitch angle scattering and solar wind expansion with the square of the distance from the Sun. Here we determine the observed cooling index in a comparison of He+ PUI distributions taken for 1 month in the upwind direction with ACE SWICS from 1999 through 2010 over the past solar cycle with such an isotropic PUI model, treating the cooling index as a free parameter. The ionization rate is obtained simultaneously from independent observations. To separate effects of slow pitch angle scattering of PUIs, the comparison is repeated for times restricted to perpendicular interplanetary magnetic field (IMF). When averaged over the entire data set, the cooling index is very close to 3/2. However, it varies substantially from 1.1 to 1.9 between samples, shows a distinct variation with solar activity, and has a significant correlation with sunspot number when data are restricted to nearly perpendicular IMF () excluding the slow pitch angle scattering in the radial IMF direction. The potential influence of slow pitch angle scattering, solar wind structures, and electron ionization on the cooling index and its variations is discussed.
Fungal High‐throughput Taxonomic Identification tool for use with Next‐Generation Sequencing (FHiTINGS)
Authors: Dannemiller Karen C. , Reeves Darryl , Bibby Kyle , Yamamoto Naomichi , Peccia Jordan 
Published: June 2013

AbstractImprovements in DNA sequencing technology provide unprecedented opportunities to explore fungal diversity, but also present challenges in data analysis due to the large number of sequences generated. Here, we describe an open source software program “FHiTINGS” that utilizes the output of a BLASTn (blastall) search to rapidly identify, classify, and parse internal transcribed spacer (ITS) DNA sequences produced in fungal ecology studies that utilize next‐generation DNA sequencing. This tool was designed for use with 454 pyrosequencing and is also appropriate for use with any sequencing platform that allows for BLAST searches against the indicated ITS database. For each sequence, FHiTINGS uses the lowest common ancestor method (LCA) to produce a single identification from BLAST output results, and then assigns taxonomic ranks from species through kingdom when possible for each sequence based on the Index Fungorum database. The program then sums and sorts this data into tabular form to enable rapid analysis of the sample, including α‐diversity measures or richness. In silico testing demonstrates the time required to analyze and classify 1000 sequences is reduced from over 2 h by manual sorting to <1 min of computational time when using FHiTINGS, and that the classification output from the software is consistent with that derived from manual sorting of the data.
Modelling wildfire activity in Iberia with different atmospheric circulation weather types
Authors: Trigo Ricardo M. , Sousa Pedro M. , Pereira Mário G. , Rasilla Domingo , Gouveia Célia M. 
Published: June 2013

AbstractThis work focuses on the spatial and temporal variability of burnt area (BA) in the entire Iberian Peninsula (IP) and on the construction of statistical models to reproduce the inter‐annual variability. A novel common dataset was assembled for the whole IP by merging the registered BA from 66 administrative regions of both Portugal and Spain. We applied a cluster analysis to identify larger regions with similar fire regimes and results point to the existence of four clusters (Northwestern, Northern, Southwestern and Eastern) whose spatial patterns and seasonal fire regimes are shown to be related with constraining factors such as topography, vegetation cover and climate conditions. The relationship between BA at monthly time scale with both long‐term climatic pre‐conditions and short‐term synoptic forcing was assessed using correlation and regression analysis based on: (1) temperature and precipitation from 2 to 7 months in advance to fire peak season, (2) synoptic weather patterns derived from 11 distinct Weather Types Classifications (WTC). Different relations were obtained for each IP region with a relevant link being identified between BA and short‐term synoptic forcing for all clusters, while the relation with long‐term climatic preconditioning was relevant for all but one cluster. Stepwise regression models based on the best climatic and synoptic circulation predictors were developed with cross‐validation to avoid over fitting. The performance of the models varies within IP regions, though models exclusively based on WTC tend to better reproduce the annual BA time series than those merely based on pre‐conditioning climatic information. Nevertheless, the use of both synoptic and climatic predictors provides the best results, particularly for the two western clusters, with Pearson correlation coefficient values higher than 0.7. Finally, it is shown that typical synoptic configurations that favour high values of BA correspond to dry and warm wind flows associated with anti‐cyclonic regimes.
Reconstructing Quaternary Rhine–Meuse dynamics in the southern North Sea: architecture, seismo‐lithofacies associations and malacological biozonation
Authors: RIJSDIJK K. F. , KROON I. C. , MEIJER T. , PASSCHIER S. , VAN DIJK T. A. G. P. , BUNNIK F. P. M. , JANSE A. C. 
Published: June 2013

ABSTRACTMapping the Middle to Upper Pleistocene Rhine–Meuse sequence in the southern North Sea based on new core and seismic data has allowed a detailed palaeoenvironmental re‐assessment. An integrated seismo‐lithostratigraphic and malacological biostratigraphic framework is correlated with the optically stimulated luminescence‐dated Rhine–Meuse sequence onshore. The data point to a dynamic interplay of fluvial and marine systems in the southern part of the North Sea driven by longer‐term (>100 ka) tectonic and epeirogenic processes and shorter‐term (<10 ka) climatic processes. The final permanent breaching of the Cretaceous chalk at the Strait of Dover during the Saalian (Marine Isotope Stage 6, MIS 6) ice age led to the formation of the ‘Eurogeul’ belt, a gravelly sand belt that represents the largest concentration of gravelly fluvial sediments in the southern North Sea. The formation and preservation of the Rhine–Meuse sequence is related to long‐term (>100 ka) uplift of the Wealden–Artois synclinorium and compaction‐driven subsidence of Tertiary shales within the Voorne Trough. The dominant erosive sedimentary signatures within the Rhine–Meuse sequence resulted through shorter‐term (<10 ka) interplay of Pleistocene transgressions, glaciations and the permanent breaching of the Cretaceous chalk at the Strait of Dover by the Palaeo‐Channel river during the Saalian (MIS 6).
Lipid characterization and properties of protein hydrolysates obtained from discarded Mediterranean fish species
Authors: García‐Moreno Pedro J , Pérez‐Gálvez Raúl , Espejo‐Carpio F Javier , Muñío María M , Guadix Antonio , Guadix Emilia M 
Published: June 2013

AbstractBACKGROUNDDiscards are an important fraction of the by‐products produced by the fishing industry. As a consequence of their low commercial acceptance, it is necessary to provide added value to these underutilized materials. In this study the lipid fraction of three discarded fish species in the western Mediterranean Sea, namely sardine (Sardina pilchardus), mackerel (Scomber colias) and horse mackerel (Trachurus trachurus), was characterized and the angiotensin I‐converting enzyme (ACE)‐inhibitory and antioxidative activities of their protein hydrolysates were evaluated.RESULTSProcessing of these biomaterials led to oils with a high content of omega‐3 polyunsaturated fatty acids (PUFAs), ranging from 220.5 g kg−1 for horse mackerel to 306.0 g kg−1 for sardine. Regarding the protein fraction, most of the hydrolysates presented ACE inhibition values higher than 60%, corresponding to IC50 values varying from 345 µg protein mL−1 for mackerel to 400 µg protein mL−1 for sardine. Moreover, most of the hydrolysates exhibited acceptable antioxidative activity, namely 35–45% inhibition of 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH).CONCLUSIONThis study suggests that the three discarded species evaluated are valuable raw materials for the production of bioactive ingredients such as omega‐3 PUFAs and protein hydrolysates exhibiting antihypertensive and antioxidative activities. © 2013 Society of Chemical Industry
Analysis of a conserved cellulase transcriptional regulator reveals inducer‐independent production of cellulolytic enzymes in Neurospora crassa
Authors: Coradetti Samuel T. , Xiong Yi , Glass N. Louise 
Published: June 2013

AbstractCellulose is recalcitrant to deconstruction to glucose for use in fermentation strategies for biofuels and chemicals derived from lignocellulose. In Neurospora crassa, the transcriptional regulator, CLR‐2, is required for cellulolytic gene expression and cellulose deconstruction. To assess conservation and divergence of cellulase gene regulation between fungi from different ecological niches, we compared clr‐2 function with its ortholog (clrB) in the distantly related species, Aspergillus nidulans. Transcriptional profiles induced by exposure to crystalline cellulose were similar in both species. Approximately 50% of the cellulose‐responsive genes showed strict dependence on functional clr‐2/clrB, with a subset of 28 genes encoding plant biomass degrading enzymes that were conserved between N. crassa and A. nidulans. Importantly, misexpression of clr‐2 under noninducing conditions was sufficient to drive cellulase gene expression, secretion, and activity in N. crassa, to a level comparable to wild type exposed to Avicel. However, misexpression of clrB in A. nidulans was not sufficient to drive cellulase gene expression under noninducing conditions, although an increase in cellulase activity was observed under crystalline cellulose conditions. Manipulation of clr‐2 orthologs among filamentous fungi may enable regulated cellulosic enzyme production in a wide array of culture conditions and host strains, potentially reducing costs associated with enzyme production for plant cell wall deconstruction. However, this functionality may require additional engineering in some species.