bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative and Comparative Genomic Analysis of HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas
Authors: Seiwert Tanguy Y. , Zuo Zhixiang , Keck Michaela K. , Khattri Arun , Pedamallu Chandra S. , Stricker Thomas , Brown Christopher , Pugh Trevor J. , Stojanov Petar , Cho Juok , Lawrence Michael S. , Getz Gad , Brägelmann Johannes , DeBoer Rebecca , Weichselbaum Ralph R. , Langerman Alexander , Portugal Louis , Blair Elizabeth , Stenson Kerstin , Lingen Mark W. , Cohen Ezra E.W. , Vokes Everett E. , White Kevin P. , Hammerman Peter S. 
Published: July 2014

Abstract
Purpose: The genetic differences between human papilloma virus (HPV)–positive and –negative head and neck squamous cell carcinomas (HNSCC) remain largely unknown. To identify differential biology and novel therapeutic targets for both entities, we determined mutations and copy-number aberrations in a large cohort of locoregionally advanced HNSCC.
Experimental Design: We performed massively parallel sequencing of 617 cancer-associated genes in 120 matched tumor/normal samples (42.5% HPV-positive). Mutations and copy-number aberrations were determined and results validated with a secondary method.
Results: The overall mutational burden in HPV-negative and HPV-positive HNSCC was similar with an average of 15.2 versus 14.4 somatic exonic mutations in the targeted cancer-associated genes. HPV-negative tumors showed a mutational spectrum concordant with published lung squamous cell carcinoma analyses with enrichment for mutations in TP53, CDKN2A, MLL2, CUL3, NSD1, PIK3CA, and NOTCH genes. HPV-positive tumors showed unique mutations in DDX3X, FGFR2/3 and aberrations in PIK3CA, KRAS, MLL2/3, and NOTCH1 were enriched in HPV-positive tumors. Currently targetable genomic alterations were identified in FGFR1, DDR2, EGFR, FGFR2/3, EPHA2, and PIK3CA. EGFR, CCND1, and FGFR1 amplifications occurred in HPV-negative tumors, whereas 17.6% of HPV-positive tumors harbored mutations in fibroblast growth factor receptor genes (FGFR2/3), including six recurrent FGFR3 S249C mutations. HPV-positive tumors showed a 5.8% incidence of KRAS mutations, and DNA-repair gene aberrations, including 7.8% BRCA1/2 mutations, were identified.
Conclusions: The mutational makeup of HPV-positive and HPV-negative HNSCC differs significantly, including targetable genes. HNSCC harbors multiple therapeutically important genetic aberrations, including frequent aberrations in the FGFR and PI3K pathway genes. Clin Cancer Res; 21(3); 632–41. ©2014 AACR.
See related commentary by Krigsfeld and Chung, p. 495
Female sex as a risk factor for thromboembolism and death in patients with incident atrial fibrillation
Authors: Rasmussen Lars Hvilsted , Skjøth Flemming , Overvad Kim , Albertsen Ida Ehlers , Lane Deirdre , Overvad Thure Filskov , Lip Gregory , Larsen Torben Bjerregaard 
Published: July 2014

SummarySeveral studies have demonstrated sex differences in risk of thromboembolism and death among patients with atrial fibrillation, but it is unclear to what extent these associations relate to actual physiological differences. To date, no study has investigated sex differences with concomitant control for lifestyle related factors known to influence stroke risk. We used data from the Danish Diet, Cancer and Health study, including 57,053 participants (52% female) aged 50–64 years. The study population for this study included the 2,895 patients (36% female) with incident atrial fibrillation after inclusion. Data were linked to outcomes identified using nationwide registries. Risk of thromboembolism and death according to female sex were analysed using Cox proportional hazards models. After a median follow-up of 5.0 years, 137 men and 62 women suffered a thromboembolic event, and 349 men and 151 women died. In a crude analysis, female sex was associated with a non-significant lower risk of thromboembolism (hazard ratio [HR] 0.82, 95% confidence interval [CI] 0.61–1.11). Adjustment for differences in antithrombotic therapy, relevant comorbidities and lifestyle did not change this association (HR 0.77, 95% CI 0.55–1.13). In the final model, female sex was associated with a lower risk of death (HR 0.65, 95% CI 0.51–0.84). The associations were similar in a sensitivity analysis of women not taking hormone replacement therapy, and the effect of hormone replacement therapy use within females was non-significant for both endpoints of thromboembolism and death. In conclusion, in a relatively young population of patients with atrial fibrillation, female sex was associated with a lower risk of thromboembolism and death.
Practice Patterns and Clinical Outcomes After Hybrid Coronary Revascularization in the United States
Authors: Harskamp Ralf E. , Brennan J. Matthew , Xian Ying , Halkos Michael E. , Puskas John D. , Thourani Vinod H. , Gammie James S. , Taylor Bradley S. , de Winter Robbert J. , Kim Sunghee , O’Brien Sean , Peterson Eric D. , Gaca Jeffrey G. 
Published: July 2014

Background—
Hybrid coronary revascularization (HCR) involves a combination of surgical and percutaneous techniques, which in selected patients may present an alternative to conventional coronary artery bypass grafting (CABG).

Methods and Results—

Patients were included who underwent HCR (staged/concurrent) or isolated CABG in the Society of Thoracic Surgeons Adult Cardiac Surgery Database (July 2011 to March 2013). HCR represented 0.48% (n=950; staged=809, concurrent=141) of the total CABG volume (n=198 622) during the study period, and was performed in one-third of participating centers (n=361). Patients who underwent HCR had higher cardiovascular risk profiles in comparison with patients undergoing CABG. In comparison with CABG, median sternotomy (98.5% for CABG, 61.1% for staged HCR, and 52.5% for concurrent HCR), direct vision harvesting (98.9%, 66.0%, and 68.1%) and cardiopulmonary bypass (83.4%, 45%, and 36.9%) were less frequently used for staged and concurrent HCR, whereas robotic assistance (0.7%, 33.0%, and 30.5%) was more common. After adjustment, no differences were observed for the composite of in-hospital mortality and major morbidity (odds ratio, 0.93; 95% confidence interval, 0.75–1.16;
P
=0.53 for staged HCR, and odds ratio, 0.94; 95% confidence interval, 0.56–1.56;
P
=0.80 for concurrent HCR in comparison with CABG). There was no statistically significant association between operative mortality and either treatment group (odds ratio, 0.74; 95% confidence interval, 0.42–1.30;
P
=0.29 for staged HCR, and odds ratio, 2.26; 95% confidence interval, 0.99–5.17;
P
=0.053 for concurrent HCR in comparison with CABG).

Conclusion—
HCR, either as a staged or concurrent procedure, is performed in one-third of US hospitals and is reserved for a highly selected patient population. Although HCR may appear to be an equally safe alternative for CABG surgery, further randomized study is warranted.
A Note on the Early Sino-Vietnamese Loanword for ‘Rake/Harrow’
Authors: Alves Mark J. 
Published: July 2014

The Vietnamese word for ‘rake/harrow’ has been determined to be from the colloquial layer of pre-Tang Dynasty Early Sino-Vietnamese loanwords. Phonological, comparative, and historical data is provided to support this claim. The discussion addresses Vietnamese, Chinese, and Tai historical phonology and the language contact among these three groups.
Dans cet article, nous montrons que le mot vietnamien pour ‘râteau/herse’ appartient à la couche parlée des emprunts sino-vietnamiens anciens datant d’avant la dynastie des Tang. Des données phonologiques, comparatives et historiques corroborent cette hypothèse. La discussion aborde la phonogie historique du vietnamien, du chinois et du kradai, ainsi que le contact entre ces trois groupes de langues.
Studies on European species of the water mite family Aturidae Thor (Acari: Hydrachnidia)
Authors: GERECKE REINHARD 
Published: July 2014

Selected water mite species of the family Aturidae are revised. The following synonyms are established: Aturus intermedius serrata K. Viets, 1922 = A. asserculatus Walter, 1906; A. lelgioensis Rensburg, 1971 = A. natangensis Protz, 1900; A. oudemansi Besseling, 1932 = A. intermedius Protz, 1900. The proposal of E. Angelier (1965), to synonymize A. paucisetus Motaş & Tanasachi, 1946 with A. brachypus K. Viets, 1934 is rejected. Aturus elongatus Walter, 1927 (described after females, type material heavily damaged) and Ljania bipapillata subterranea Schwoerbel, 1964 (no type material available, no type locality defined) are considered as species incertae. Ljania macilenta longissima Schwoerbel, 1962 is redescribed and elevated to species rank. Two species of the genus Kongsbergia are described as new to science from interstitial habitats in the Central Mediterranean: K. albanorum sp. nov. from Western Sicily and K. jaentschi sp. nov. from Sicily and Sardinia. Woolastookia basilicalabrica sp. nov. is described from mountain streams in Southern Italy. Numerous new records are given, extending noteworthy the known distribution area of several species in Southern Europe. Aturus rotundus Romijn, 1921, Kongsbergia dentata Walter, 1947 and K. simillima K. Viets, 1949 are recorded for the first time from Italy, K. pectinigera Motaş & Tanasachi, 1946 from France and Italy; first records from Corsica are given for Aturus intermedius and A. spatulifer Piersig, 1904. Lectotypes are designated for Aturus asserculatus Walter, 1906; A. asserculatus serratus K. Viets, 1922; A. oudemansi Besseling, 1932.
The Influence of Stratification on the Instabilities in an Idealized Two-Layer Ocean Model
Authors: Irwin R. L. , Poulin F. J. 
Published: July 2014

Abstract
This work investigates the instability of a two-layer Bickley jet in the context of the rotating shallow water (RSW) model. This provides a general context in which the instability of oceanographic jets with simple stratification can be investigated. The three objectives of this work are as follows: First, the study investigates the morphology of unstable modes that can occur in this two-layer model. This is done by performing a linear stability analysis to investigate different types of flows both with and without vertical shear. Second, the authors study how the growth rates of the unstable modes are affected by changes in the stratification. Third, this study looks at the nonlinear evolution of some of these instabilities to determine how easy it is for nonprimary instabilities to develop. This is motivated by the fact that in the literature there have been many investigations that have found a multitude of unstable modes in this model, and it is not evident as to how easily they can be generated in oceanographic flows.
Storm-Scale Ensemble Kalman Filter Assimilation of Total Lightning Flash-Extent Data
Authors: Mansell Edward R. 
Published: July 2014

Abstract
A set of observing system simulation experiments (OSSEs) demonstrates the potential benefit from ensemble Kalman filter (EnKF) assimilation of total lightning flash mapping data. Synthetic lightning data were generated to mimic the Geostationary Lightning Mapper (GLM) instrument that is planned for the Geostationary Operational Environmental Satellite-R series (GOES-R) platform. The truth simulation was conducted using multimoment bulk microphysics, explicit electrification mechanisms, and a branched lightning parameterization to produce 2-min-averaged synthetic pseudo-GLM observations at 8-km GLM resolution and at a hypothetical 1-km resolution.
The OSSEs use either perfect (two-moment bulk) or imperfect (single-moment, graupel only) microphysics. One OSSE with perfect microphysics included the same electrification physics as the truth simulation to generate lightning flash rates and flash-extent densities (FED). The other OSSEs used linear relationships between flash rate and graupel echo volume as the observation operator. The assimilation of FED at 8-km horizontal resolution can effectively modulate the convection simulated at 1-km horizontal resolution by sharpening the location of reflectivity echoes and the spatial location probability of convective updrafts. Tests with zero flash rates show that the lightning assimilation can help to limit spurious deep convection, as well. Pseudo-GLM observations at 1 km further sharpen the analyses of location (updraft and reflectivity) of the relatively simple storm structure.
The Effect of Platelet-Rich Plasma on Muscle Contusion Healing in a Rat Model
Authors: Delos Demetris , Leineweber Matthew J. , Chaudhury Salma , Alzoobaee Saif , Gao Yingxin , Rodeo Scott Alan 
Published: July 2014

Background: Current therapy for muscle contusions is usually limited to nonsteroidal anti-inflammatory drugs and/or use of the RICE principle (rest, ice, compression, elevation); thus, other forms of treatment that can potentially accelerate the rate of healing are desirable. Hypotheses: A local injection of platelet-rich plasma (PRP) would lead to accelerated healing rates compared with controls; also, delayed administration of PRP would lead to a blunted response compared with immediate treatment. Study Design: Controlled laboratory study. Methods: Forty-six male Lewis rats each underwent a single blunt, nonpenetrating impact to the gastrocnemius muscle via a drop-mass technique and subsequently received either a single injection of saline into the area of injury immediately after injury (controls, n = 11) or rat PRP (either immediately after injury [PRP day 0, n = 12], the first day after injury [PRP day 1, n = 12], or the third day after injury [PRP day 3, n = 11]). The primary outcome was maximal isometric torque strength of the injured muscle, which was assessed before injury as well as on postinjury days 1, 4, 7, 10, and 14. All animals were sacrificed on postinjury day 15. Histological and immunohistochemical analyses were performed on 6 specimens from each group after sacrifice. Results: The mean platelet concentration in the PRP was 2.19 × 106 (±2.69 × 105)/μL. The mean white blood cell count in the PRP was 22.54 × 103/μL. Each group demonstrated statistically significant decreases in maximal isometric torque strength after injury when compared with preinjury levels, followed by significant increases back toward baseline values by postinjury day 14 (controls, 90.6% ± 7.90%; PRP day 0, 105.0% ± 7.60%; PRP day 1, 92.4% ± 7.60%; PRP day 3, 77.8% ± 7.90%) ( P = .121). There were no statistically significant differences between the treatment and control groups at any of the time points. There were also no statistically significant differences between any of the groups in the percentage of centronucleated fibers (controls, 3.31% ± 5.10%; PRP day 0, 0.62% ± 1.59%; PRP day 1, 3.24% ± 5.77%; PRP day 3, 2.13% ± 3.26%) ( P = .211) or the presence of inflammatory cells and macrophages. Conclusion: In this rat contusion model, a local injection of PRP into the injured gastrocnemius muscle resulted in no significant differences in functional or histological outcomes, indicating no likely benefit to healing. Additionally, there was no significant difference between immediate or delayed administration of PRP. Clinical Relevance: Before PRP can be recommended for the treatment of muscle contusion injuries, further translational and clinical investigations need to be performed.
APRIL levels strongly correlate with IL-17 in systemic lupus erythematosus
Authors: Eilertsen GØ , Nossent J C 
Published: July 2014

Introduction Activated self-reactive B cells play an important part in systemic lupus erythematosus (SLE). A proliferation-inducing ligand (APRIL) and B cell-activating factor (BAFF) are B-cell specific stimulators, but activate B cells through different receptors. We investigated the reciprocal association between serum APRIL (s-APRIL), serum BAFF (s-BAFF) and immunological and clinical findings in SLE patients. Methods A cross-sectional case-control study was performed in 100 SLE patients (87% female, age 49 years, disease duration 12 years). APRIL and BAFF levels were measured by sandwich ELISA, compared with healthy controls and correlated with autoantibody, cytokine (IL-6 and IL-17) and clinical findings through nonparametric and multivariate regression analyses. Results Both median s-APRIL (478 vs. 0 pg/ml, p = 0.01) and s-BAFF (1720 vs. 0.9 pg/ml, p < 0.001) were higher in SLE patients than controls. Increased s-BAFF was observed in 86% of patients, while s-APRIL was increased only in 17% ( p < 0.01). S-APRIL correlated with s-BAFF in controls ( p = 0.04), but not in SLE ( p = 0.8). Increased s-APRIL was strongly and independently associated with IL-17 activation ( p < 0.001), while increased s-BAFF levels were associated with anti-nucleosome antibody presence ( p = 0.001). Disease activity and organ damage were associated with s-BAFF but not s-APRIL. Conclusions While both s-BAFF and s-APRIL levels are elevated in SLE patients, they reflect different immunologic and clinical pathways. The strong association between s-APRIL and IL-17 activation supports a role for Th17 helper cells in B cell activation in SLE.
Nestolaite, CaSeO3·H2O, a new mineral from the Little Eva mine, Grand County, Utah, USA
Authors: Kasatkin A. V. , Plášil J. , Marty J. , Agakhanov A. A. , Belakovskiy D. I. , Lykova I. S. 
Published: July 2014

AbstractNestolaite (IMA 2013-074), CaSeO3·H2O, is a new mineral species from the Little Eva mine, Grand County, Utah, USA. It is named in honour of the prominent Italian mineralogist and crystallographer Fabrizio Nestola. The new mineral was found on sandstone matrix as rounded aggregates up to 2 mm across and up to 0.05 μm thick consisting of tightly intergrown oblique-angled, flattened to acicular crystals up to 30 μm long and up to 7 μm (very rarely up to 15 μm) thick. Nestolaite associates with cobaltomenite, gypsum, metarossite, orschallite and rossite. The new mineral is light violet and transparent with a white streak and vitreous lustre. The Mohs hardness is 2½. Nestolaite is brittle, has uneven fracture and perfect cleavage on {100}. The measured and calculated densities areDmeas. = 3.18(2) g/cm3andDcalc.= 3.163 g/cm3. Optically, nestolaite is biaxial positive. The refractive indices are α = 1.642(3), β = 1.656(3), γ = 1.722(6). The measured 2Vis 55(5)° and the calculated 2Vis 51°. In transmitted light nestolaite is colourless. It does not show pleochroism but has strong pseudoabsorption caused by high birefringence. The chemical composition of nestolaite (wt.%, electronmicroprobe data) is: CaO 28.97, SeO2 61.14, H2O (calc.) 9.75, total 99.86. The empirical formula calculated on the basis of 4 O a.p.f.u. (atoms per formula unit) is Ca0.96Se1.02O3·H2O. The Raman spectrum is dominated by the Se–O stretching and O–Se–O bending vibrations of the pyramidal SeO3groups and O–H stretching modes of the H2O molecules. The mineral is monoclinic, space groupP21/c, witha= 7.6502(9),b= 6.7473(10),c= 7.9358(13) Å, β = 108.542 (12)°,V= 388.37(10) Å3andZ= 4. The eight strongest powder X-ray diffraction lines are [dobsin Å(hkl) (Irel)]: 7.277 (100)(100), 4.949 (110)(37), 3.767 (002)(29), 3.630 (200)(58), 3.371 (020)(24), 3.163 (02)(74), 2.9783 (21)(74) and 2.7231 (112)(31). The crystal structure of nestolaite was determined by means of the Rietveld refinement from the powder data toRwp= 0.019. Nestolaite possesses a layered structure consisting of CaΦ–SeO3sheets, composed of edge-sharing polyhedra. Adjacent sheets are held by H bonds emanating from the single (H2O) group within the sheets. The nestolaite structure is topologically unique.
Preamble-based frequency-domain joint CFO and STO estimation for OQAM-based filter bank multicarrier
Authors: Caekenberghe Stijn Van , Bourdoux André , der Perre Liesbet Van , Louveaux Jérôme 
Published: July 2014

Abstract
Filter bank multicarrier systems, similarly to orthogonal frequency division multiplexing (OFDM), are very sensitive to carrier frequency offset (CFO) and symbol timing offset (STO). In this paper, a low-complexity preamble-based joint CFO and STO technique is presented. It is based on a relatively long preamble in order to improve the CFO estimation performance as well as avoid interference coming from the data following this preamble. After CFO and STO correction, the preamble can be reused to estimate the channel. Unlike most current techniques, the CFO and STO estimation occurs in the frequency domain. This allows for a low-complexity estimation with respect to time-domain techniques and, as will be shown by simulations, provide even better performance in a reasonable range. The drawback however is that the estimation range is shorter. Specifically, for large STOs (and to a smaller extent large CFOs), the performance decreases below time-domain estimations. Two versions of the STO estimation technique will be presented, the second one being an approximation of the first one, making it less complex yet also less precise. The performance is assessed by means of computer simulations, testing for both large and small STOs, and compared with existing techniques.
Exploring Pharmacological Activities and Signaling of Morphinans Substituted in Position 6 as Potent Agonists Interacting with the μ Opioid Receptor
Authors: Haddou Tanila Ben , Malfacini Davide , Calo Girolamo , Aceto Mario D , Harris Louis S , Traynor John R , Coop Andrew , Schmidhammer Helmut , Spetea Mariana 
Published: July 2014

Background: Opioid analgesics are the most effective drugs for the treatment of moderate to severe pain. However, they also produce several adverse effects that can complicate pain management. The μ opioid (MOP) receptor, a G protein-coupled receptor, is recognized as the opioid receptor type which primarily mediates the pharmacological actions of clinically used opioid agonists. The morphinan class of analgesics including morphine and oxycodone are of main importance as therapeutically valuable drugs. Though the natural alkaloid morphine contains a C-6-hydroxyl group and the semisynthetic derivative oxycodone has a 6-carbonyl function, chemical approaches have uncovered that functionalizing position 6 gives rise to a range of diverse activities. Hence, position 6 of N-methylmorphinans is one of the most manipulated sites, and is established to play a key role in ligand binding at the MOP receptor, efficacy, signaling, and analgesic potency. We have earlier reported on a chemically innovative modification in oxycodone resulting in novel morphinans with 6-acrylonitrile incorporated substructures. Results: This study describes in vitro and in vivo pharmacological activities and signaling of new morphinans substituted in position 6 with acrylonitrile and amido functions as potent agonists and antinociceptive agents interacting with MOP receptors. We show that the presence of a 6-cyano group in N-methylmorphinans has a strong influence on the binding to the opioid receptors and post-receptor signaling. One 6-cyano- N-methylmorphinan of the series was identified as the highest affinity and most selective MOP agonist, and very potent in stimulating G protein coupling and intracellular calcium release through the MOP receptor. In vivo, this MOP agonist showed to be greatly effective against thermal and chemical nociception in mice with marked increased antinociceptive potency than the lead molecule oxycodone. Conclusion: Development of such novel chemotypes by targeting position 6 provides valuable insights on ligand-receptor interaction and molecular mode of action, and may aid in identification of opioid therapeutics with enhanced analgesic properties and fewer undesirable effects.