bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Perception of Lexical Stress in German: Effects of Segmental Duration and Vowel Quality in Different Prosodic Patterns
Authors: Kohler Klaus J. 
Published: November 2012

Abstract
Several decades of research, focusing on English, Dutch and German, have set up a hierarchy of acoustic properties for cueing lexical stress. It attributes the strongest cue to criterial-level f0 change, followed by duration, but low weight to energy and to stressed-vowel spectra. This paper re-examines the established view with new data from German. In the natural productions of the German word pair Kaffee ‘coffee’ – Café ‘locality’ (with initial vs. final stress in a North German pronunciation), vowel duration was manipulated in a complementary fashion across the two syllables in five steps, spanning the continuum from initial to final stress on each word. The two base words provided different vowel qualities as the second variable, the intervocalic fricative was varied in two values, long and short, taken from Café and Kaffee, and the generated test words were inserted in a low f0 tail and in a high f0 hat-pattern plateau, which both eliminated f0 change as a cue to lexical stress. The sentence stimuli were judged in two listening experiments by 16 listeners in each as to whether the first or the second syllable of the test word was stressed. The results show highly significant effects of vowel duration, vowel quality and fricative duration. The combined vowel-quality and fricative variable can outweigh vowel duration as a cue to lexical stress. The effect of the prosodic frame is only marginal, especially related to a rhythmic factor. The paper concludes that there is no general hierarchy with a fixed ranking of the variables traditionally adduced to signal lexical stress. Every prosodic embedding of segmental sequences defines the hierarchy afresh.
The Effect of Diurnal Sea Surface Temperature Warming on Climatological Air–Sea Fluxes
Authors: Clayson Carol Anne , Bogdanoff Alec S. 
Published: November 2012

Abstract
Diurnal sea surface warming affects the fluxes of latent heat, sensible heat, and upwelling longwave radiation. Diurnal warming most typically reaches maximum values of 3°C, although very localized events may reach 7°–8°C. An analysis of multiple years of diurnal warming over the global ice-free oceans indicates that heat fluxes determined by using the predawn sea surface temperature can differ by more than 100% in localized regions over those in which the sea surface temperature is allowed to fluctuate on a diurnal basis. A comparison of flux climatologies produced by these two analyses demonstrates that significant portions of the tropical oceans experience differences on a yearly average of up to 10 W m−2. Regions with the highest climatological differences include the Arabian Sea and the Bay of Bengal, as well as the equatorial western and eastern Pacific Ocean, the Gulf of Mexico, and the western coasts of Central America and North Africa. Globally the difference is on average 4.45 W m−2. The difference in the evaporation rate globally is on the order of 4% of the total ocean–atmosphere evaporation. Although the instantaneous, year-to-year, and seasonal fluctuations in various locations can be substantial, the global average differs by less than 0.1 W m−2 throughout the entire 10-yr time period. A global heat budget that uses atmospheric datasets containing diurnal variability but a sea surface temperature that has removed this signal may be underestimating the flux to the atmosphere by a fairly constant value.
Stratospheric Ozone and Temperature Simulated from the Preindustrial Era to the Present Day
Authors: Austin John , Horowitz Larry W. , Schwarzkopf M. Daniel , Wilson R. John , Levy Hiram 
Published: November 2012

Abstract
Results from the simulation of a coupled chemistry–climate model are presented for the period 1860 to 2005 using the observed greenhouse gas (GHG) and halocarbon concentrations. The model is coupled to a simulated ocean and uniquely includes both detailed tropospheric chemistry and detailed middle atmosphere chemistry, seamlessly from the surface to the model top layer centered at 0.02 hPa. It is found that there are only minor changes in simulated stratospheric temperature and ozone prior to the year 1960. As the halocarbon amounts increase after 1970, the model stratospheric ozone decreases approximately continuously until about 2000. The steadily increasing GHG concentrations cool the stratosphere from the beginning of the twentieth century at a rate that increases with height. During the early period the cooling leads to increased stratospheric ozone. The model results show a strong, albeit temporary, response to volcanic eruptions. While chlorofluorocarbon (CFC) concentrations remain low, the effect of eruptions is shown to increase the amount of HNO3, reducing ozone destruction by the NOx catalytic cycle. In the presence of anthropogenic chlorine, after the eruption of El Chichón and Mt. Pinatubo, chlorine radicals increased and the chlorine reservoirs decreased. The net volcanic effect on nitrogen and chlorine chemistry depends on altitude and, for these two volcanoes, leads to an ozone increase in the middle stratosphere and a decrease in the lower stratosphere. Model lower-stratospheric temperatures are also shown to increase during the last three major volcanic eruptions, by about 0.6 K in the global and annual average, consistent with observations.
Reducing Biases in XBT Measurements by Including Discrete Information from Pressure Switches
Authors: Goes Marlos , Goni Gustavo , Keller Klaus 
Published: November 2012

Abstract
Biases in the depth estimation of expendable bathythermograph (XBT) measurements cause considerable errors in oceanic estimates of climate variables. Efforts are currently underway to improve XBT probes by including pressure switches. Information from these pressure measurements can be used to minimize errors in the XBT depth estimation. This paper presents a simple method to correct the XBT depth biases using a number of discrete pressure measurements. A blend of controlled simulations of XBT measurements and collocated XBT/CTD data is used along with statistical methods to estimate error parameters, and to optimize the use of pressure switches in terms of number of switches, optimal depth detection, and errors in the pressure switch measurements to most efficiently correct XBT profiles. The results show that given the typical XBT depth biases, using just two pressure switches is a reliable strategy for reducing depth errors, as it uses the least number of switches for an improved accuracy and reduces the variance of the resulting correction. Using only one pressure switch efficiently corrects XBT depth errors when the surface depth offset is small, its optimal location is at middepth (around or below 300 m), and the pressure switch measurement errors are insignificant. If two pressure switches are used, then results indicate that the measurements should be taken in the lower thermocline and deeper in the profile, at approximately 80 and 600 m, respectively, with an RMSE of approximately 1.6 m for pressure errors of 1 m.
Assimilation of High-Resolution Tropical Cyclone Observations with an Ensemble Kalman Filter Using NOAA/AOML/HRD’s HEDAS: Evaluation of the 2008–11 Vortex-Scale Analyses
Authors: Aksoy Altuğ , Aberson Sim D. , Vukicevic Tomislava , Sellwood Kathryn J. , Lorsolo Sylvie , Zhang Xuejin 
Published: November 2012

AbstractThe Hurricane Weather Research and Forecasting (HWRF) Ensemble Data Assimilation System (HEDAS) is developed to assimilate tropical cyclone inner-core observations for high-resolution vortex initialization. It is based on a serial implementation of the square root ensemble Kalman filter (EnKF). In this study, HWRF is used in an experimental configuration with horizontal grid spacing of 9 (3) km on the outer (inner) domain. HEDAS is applied to 83 cases from years 2008 to 2011. With the exception of two Hurricane Hilary (2011) cases in the eastern North Pacific basin, all cases are observed in the Atlantic basin. Observed storm intensity for these cases ranges from tropical depression to category-4 hurricane.Overall, it is found that high-resolution tropical cyclone observations, when assimilated with an advanced data assimilation technique such as the EnKF, result in analyses of the primary circulation that are realistic in terms of intensity, wavenumber-0 radial structure, as well as wavenumber-1 azimuthal structure. Representing the secondary circulation in the analyses is found to be more challenging with systematic errors in the magnitude and depth of the low-level radial inflow. This is believed to result from a model bias in the experimental HWRF caused by the overdiffusive nature of the planetary boundary layer parameterization utilized. Thermodynamic deviations from the observed structure are believed to be caused by both an imbalance between the number of the kinematic and thermodynamic observations in general and the suboptimal ensemble covariances between kinematic and thermodynamic fields. Future plans are discussed to address these challenges.
Toxin-antitoxin loci vapBC-1 and vapXD contribute to survival and virulence in nontypeable Haemophilus influenzae
Authors: Ren Dabin , Walker Anna N , Daines Dayle A 
Published: November 2012

Abstract

Background
Nontypeable Haemophilus influenzae (NTHi) is a significant human pathogen responsible for respiratory tract infections and the most common cause of recurrent otitis media. Type II toxin-antitoxin (TA) systems are genetic elements that code for a stable protein toxin and a labile antitoxin that are thought to be involved in metabolic regulation of bacteria by enabling a switch to a dormant state under stress conditions. The contribution to infection persistence of the NTHi TA loci vapBC-1 and vapXD was examined in this study.

Results
Deletions in vapBC-1, vapXD and vapBC-1 vapXD significantly decreased the survival of NTHi co-cultured with primary human respiratory tissue at the air-liquid interface and in the chinchilla model of otitis media. The TA deletions did not affect the growth dynamics of the mutants in rich media, their ultra-structural morphology, or display appreciable synergy during NTHi infections. The toxin and antitoxin proteins of both pairs heterodimerized in vivo. Consistent with our previous findings regarding the VapC-1 toxin, the NTHi VapD toxin also displayed ribonuclease activity.

Conclusions
We conclude that the vapBC-1 and vapXD TA loci enhance NTHi survival and virulence during infection in vitro and in vivo using a mechanism of mRNA cleavage, and that these conserved TA pairs represent new targets for the prophylaxis and therapy of otitis media and other NTHi-caused mucosal diseases.
DNAGear- a free software for spa type identification in Staphylococcus aureus
Authors: AL-Tam Faroq , Brunel Anne-Sophie , Bouzinbi Nicolas , Corne Philippe , Bañuls Anne-Laure , Shahbazkia Hamid Reza 
Published: November 2012

Abstract

Background

Staphylococcus aureus is both human commensal and an important human pathogen, responsible for community-acquired and nosocomial infections ranging from superficial wound infections to invasive infections, such as osteomyelitis, bacteremia and endocarditis, pneumonia or toxin shock syndrome with a mortality rate up to 40%. S. aureus reveals a high genetic polymorphism and detecting the genotypes is extremely useful to manage and prevent possible outbreaks and to understand the route of infection. One of current and expanded typing method is based on the X region of the spa gene composed of a succession of repeats of 21 to 27 bp. More than 10000 types are known. Extracting the repeats is impossible by hand and needs a dedicated software. Unfortunately the only software on the market is a commercial program from Ridom.

Findings
This article presents DNAGear, a free and open source software with a user friendly interface written all in Java on top of NetBeans Platform to perform spa typing, detecting new repeats and new spa types and synchronizing automatically the files with the open access database. The installation is easy and the application is platform independent. In fact, the SPA identification is a formal regular expression matching problem and the results are 100% exact. As the program is using Java embedded modules written over string manipulation of well established algorithms, the exactitude of the solution is perfectly established.

Conclusions
DNAGear is able to identify the types of the S. aureus sequences and detect both new types and repeats. Comparing to manual processing, which is time consuming and error prone, this application saves a lot of time and effort and gives very reliable results. Additionally, the users do not need to prepare the forward-reverse sequences manually, or even by using additional tools. They can simply create them in DNAGear and perform the typing task. In short, researchers who do not have commercial software will benefit a lot from this application.
Insect predators in northeast China and their impacts on Aphis glycines
Authors: Liu Jian , Xu Weijun , Wang Qiuyu , Zhao Kuijun 
Published: November 2012

AbstractPredators of Aphis glycines Matsumura (Hemiptera: Aphididae) were surveyed and their ability to suppress A. glycines population growth was determined in Harbin, northeast China (45.4°N, 126.4°E). Field surveys were conducted on 21 fixed sampling sites in 2004 and 17 in 2005. Impacts of natural enemies of A. glycines were studied using exclosure experiments. Thirteen natural enemies were found, the most abundant of which was Propylaea japonica (Thunberg), Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae), Chrysopa sinica Tjeder, Chrysopa phyllochroma Wesmael, Chrysopa formosa Brauer (Neuroptera: Chrysopidae), Hemerobius humuli Linnaeus (Neuroptera: Hemerobiidae), Orius Wolff sp. (Heteroptera: Anthocoridae), Nabis stenoferus Hsiao (Heteroptera: Reduviidae), Deraeocoris punctulatus (Fallén) (Heteroptera: Miridae), and Episyrphus balteata (De Geer) (Diptera: Syrphidae). Three exclosure treatment types were established, large-mesh cages, small-mesh cages, and no cages. In exclosures, A. glycines density in small-mesh cages peaked at numbers 3.75-fold higher than in large-mesh cages and 17.44-fold higher than on plants with no cages in 2004. In 2005, these numbers were 4.59-fold and 60.98-fold. Temperature was not a factor in exclosures, but relative humidity had significant effects. These results indicated that existing predator communities could partially suppress soybean aphid population density in soybean fields in northeast China.
Pathogenic Long-Lived Plasma Cells and Their Survival Niches in Autoimmunity, Malignancy, and Allergy
Authors: Winter Oliver , Dame Christof , Jundt Franziska , Hiepe Falk 
Published: November 2012

Abstract
Long-lived plasma cells survive in a protected microenvironment for years or even a lifetime and provide humoral memory by establishing persistent Ab titers. Long-lived autoreactive, malignant, and allergen-specific plasma cells are likewise protected in their survival niche and are refractory to immunosuppression, B cell depletion, and irradiation. Their elimination remains an essential therapeutic challenge. Recent data indicate that long-lived plasma cells reside in a multicomponent plasma cell niche with a stable mesenchymal and a dynamic hematopoietic component, both providing essential soluble and membrane-bound survival factors. Alternative niches with different hematopoietic cell components compensate fluctuations of single cell types but may also harbor distinct plasma cell subsets. In this Brief Review, we discuss conventional therapies in autoimmunity and multiple myeloma in comparison with novel drugs that target plasma cells and their niches. In the future, such strategies may enable the specific depletion of pathogenic plasma cells while leaving the protective humoral memory intact.
Utility of Cardiac Magnetic Resonance in the Evaluation of Unselected Patients with Possible Arrhythmogenic Right Ventricular Cardiomyopathy
Authors: Looi Khang Li , Edwards Colin , Hart Hamish , Christiansen Jonathan P. 
Published: November 2012

Introduction Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a rare but important cause of sudden cardiac death. We investigated the role of cardiac magnetic resonance imaging (CMR) in the evaluation of patients with suspected ARVC referred by a general cardiology service. Methods Ninety-two patients (mean age 48 ± 15, 49% female), referred for CMR assessment of possible ARVC, were reviewed. CMR included both functional and tissue characteristic imaging. Results No patients had ARVC based on the 1994 Task Force Criteria (TFC) prior to CMR, but 4 met proposed Modified TFC; 15% met one major (±1 minor) TFC, 71% 1 or 2 minor TFC, and 14% no TFC. Reasons for CMR referral included symptomatic arrhythmia of likely RV origin (28%), Electrocardiogram/Holter abnormalities (28%), echocardiographic features suspicious of ARVC (19%), and family history of ARVC (8%). CMR findings strongly suggestive of ARVC were found in nine patients (10%), although only three were considered typical. Of these patients two met 1 major TFC and seven met 1 or 2 minor TFC. CMR findings included RV thinning, aneurysm, and diastolic out-pouching, but only 1 patient had definite fatty infiltration of the RV. Incidentally, CMR detected important, previously undiagnosed pathology, including anomalous pulmonary venous drainage (2 patients) and non-ischaemic cardiomyopathy (6%). CMR was normal in 63%, with minor abnormalities in 29%. Conclusions CMR may play an important diagnostic role in the evaluation of possible ARVC. Patients who do not meet TFC for diagnosis may have CMR features typical of ARVC. Additionally CMR may detect other hitherto undiagnosed structural or functional abnormalities that alter patient management. However the majority of patients referred have a low pretest probability of ARVC, and the rate of normal CMR scans is high.
The Pain Experience and Cooperation of Patients in Consecutive Cataract Surgery
Authors: Asian Lokman , Aslankurt Murat , Çekic Osman , Aksoy Adrian , Yildiz Hüseyin 
Published: November 2012

Purpose The aim of this study was to investigate the pain experience and the cooperation of patients during consecutive cataract surgery. Methods In this prospective, randomized study, 60 consecutive adult patients with bilateral senile cataracts were recruited. All operations were performed with clear corneal phacoemulsification (phaco) technique under topical and intracameral anesthesia without sedation. The first surgery was performed in the eye with high-grade cataract. The other eye was operated within 3 months. Every patient was graded using a visual analogue scale (VAS) from 0 (no pain) to 10 (unbearable pain) after the surgery. The cooperation of the patient was graded from 0 (no event) to 3 (marked eye and head movement and lid squeezing) by the surgeon. The VAS scores and cooperation of patients were the main outcome measurements. Results The mean VAS score was 1.50± 0.81 in the first surgery and 2.15±0.79 in the other eye surgery (p<0.001). The patient cooperation score was 1.50±0.81 in the first surgery and 2.18±0.77 in the other eye surgery (p<0.001). The VAS and patient cooperation scores were positively correlated (r=0.633, p<0.001) in the study group. The VAS and patient cooperation scores were similar based on sex and laterality. Conclusions Patients who previously underwent phaco surgery in one eye experience more pain and have worse cooperation during the other eye phaco surgery.
Safety and Efficacy of 0.1% Clobetasone Butyrate Eyedrops in the Treatment of Dry Eye in Sjögren Syndrome
Authors: Aragona Pasquale , Spinella Rosaria , Rania Laura , Postorino Elisa , Sommario Margherita S. , Roszkowska Anna M. , Puzzolo Domenico 
Published: November 2012

Purpose To study the effects of a low administration rate and low concentration (0.1%) of clobetasone butyrate eyedrops in patients with Sjögren syndrome (SS). Methods This prospective, double-masked, randomized, placebo-controlled study included 40 subjects divided into 2 treatment groups: group 1 (2% polyvinylpyrrolidone eyedrops and placebo) and group 2 (2% polyvinylpyrrolidone and 0.1% clobetasone butyrate, 1 drop BID). The treatment lasted for 30 days, with visits at enrollment, baseline, day 15, day 30, and after 15 days of treatment discontinuation. At each visit, symptoms questionnaire, tear film break-up time, corneal fluorescein stain, lissamine green stain, conjunctival impression cytology for human leukocyte antigen–DR (HLA-DR) expression, intraocular pressure (IOP) measurement, and fundus examination were performed. Results No changes in IOP or fundus examination were observed in either group at each time point. Group 1 patients showed at day 30 a statistically significant amelioration of symptoms and reduction of HLA-DR expression. No changes in other parameters were detected. Group 2 patients showed at day 15 a statistically significant improvement of corneal and conjunctival stain versus baseline values and group 1 at the same time; after 30 days the symptoms score was statistically significantly better than baseline values and group 1 at the same time. The HLA-DR expression and the epithelial cells area were statistically significantly reduced versus baseline and group 1 at the same time. Conclusions Anti-inflammatory therapy is critical for the treatment of SS dry eye. Clobetasone butyrate, at low dosage, proved to be safe and effective in treating this condition.
Isolation of intact and pure chloroplasts from leaves of Arabidopsis thaliana plants acclimated to low irradiance for studies on Rubisco regulation
Authors: Grabsztunowicz Magda , Jackowski Grzegorz 
Published: November 2012

<p>A protocol is presented for low-cost and fast isolation of intact and pure chloroplasts from leaves of plants acclimated to low irradiance. The protocol is based on a differential centrifugation of cleared leaf homogenate and omits a centrifugation on Percoll gradient step. The intactness and purity of the chloroplasts isolated from leaves of low irradiance-acclimated plants by using this protocol (confirmed by phase contrast microscopy as well as enzymatic and immunological approaches) allows plausible studies on low irradiance-dependent Rubisco regulation.</p>