bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface Potential Temperature as an Analysis and Forecasting Tool
Authors: Hoffman Eric G. 
Published: August 2010

Abstract
In the last decade, Fred Sanders was often critical of current surface analysis techniques. This led to his promoting the use of surface potential temperatures to distinguish between fronts, baroclinic troughs, and non-frontal baroclinic zones, and to the development of a climatology of surface baroclinic zones. In this paper, criticisms of current surface analysis techniques and the usefulness of surface potential temperature analyses are discussed. Case examples are used to compare potential temperature analyses and current National Centers for Environmental Prediction analyses.
The 1-yr climatology of Sanders and Hoffman is reconstructed using a composite technique. Annual and seasonal mean potential temperature analyses over the continental United States, southern Canada, northern Mexico, and adjacent coastal waters are presented. In addition, gridpoint frequencies of moderate and strong potential temperature gradients are calculated. The results of the mean potential temperature analyses show that moderate and strong surface baroclinic zones are favored along the coastlines and the slopes of the North American cordillera. Additional subsynoptic details, not found in Sanders and Hoffman, are identified. The availability of the composite results allows for the calculation of potential temperature gradient anomalies. It is shown that these anomalies can be used to identify significant frontal baroclinic zones that are associated with weak potential temperature gradients. Together the results and reviews in this paper show that surface potential temperature analyses are a valuable forecasting and analysis tool allowing analysts to distinguish and identify fronts, baroclinic troughs, and nonfrontal baroclinic zones.
Must Surprise Snowstorms be a Surprise?
Authors: Tracton M. Steven 
Published: August 2010

Abstract
Today, even with state-of-the-art observational, data assimilation, and modeling systems run routinely on supercomputers, there are often surprises in the prediction of snowstorms, especially the “big ones,” affecting coastal regions of the mid-Atlantic and northeastern United States. Little did the author know that lessons from Fred Sanders' synoptic meteorology class at the Massachusetts Institute of Technology (1967) would later (late 1980s) inspire him to pursue practical issues of predictability in the context of the development of ensemble prediction systems, strategies, and applications for providing information on the inevitable case-dependent uncertainties in forecasts. This paper is a brief qualitative and somewhat colloquial overview, based upon this author's personal involvement and experiences, intended to highlight some basic aspects of the source and nature of uncertainties in forecasts and to illustrate the sort of value added information ensembles can provide in dealing with uncertainties in predictions of East Coast snowstorms.
Strong Surface Fronts over Sloping Terrain and Coastal Plains
Authors: Bosart Lance F. , Wasula Alicia C. , Drag Walter H. , Meier Keith W. 
Published: August 2010

Abstract
This paper begins with a review of basic surface frontogenesis concepts with an emphasis on fronts located over sloping terrain adjacent to mountain barriers and fronts located in large-scale baroclinic zones close to coastlines. The impact of cold-air damming and differential diabatic heating and cooling on frontogenesis is considered through two detailed case studies of intense surface fronts. The first case, from 17 to 18 April 2002, featured the westward passage of a cold (side-door) front across coastal eastern New England in which 15°–20°C temperature decreases were observed in less than one hour. The second case, from 28 February to 4 March 1972, featured a long-lived front that affected most of the United States from the Rockies to the Atlantic coast and was noteworthy for a 50°C temperature contrast between Kansas and southern Manitoba, Canada.
In the April 2002 case most of New England was initially covered by an unusually warm, dry air mass. Dynamical anticyclogenesis over eastern Canada set the stage for a favorable pressure gradient to allow chilly marine air to approach coastal New England from the east. Diabatic cooling over the chilly (5°–8°C) waters of the Gulf of Maine allowed surface pressures to remain relatively high offshore while diabatic heating over the land (31°–33°C temperatures) enabled surface pressures to fall relative to over the ocean. The resulting higher pressures offshore resulted in an onshore cold push. Frontal intensity was likely enhanced prior to leaf out and grass green-up as virtually all of the available insolation went into sensible heating.
The large-scale environment in the February–March 1972 case favored the accumulation of bitterly cold arctic air in Canada. Frontal formation occurred over northern Montana and North Dakota as the arctic air moved slowly southward in conjunction with surface pressure rises east of the Canadian Rockies. The arctic air accelerated southward subsequent to lee cyclogenesis–induced pressure falls ahead of an upstream trough that crossed the Rockies. The southward acceleration of the arctic air was also facilitated by dynamic anticyclogenesis in southern Canada beneath a poleward jet-entrance region. Frontal intensity varied diurnally in response to differential diabatic heating. Three types of cyclogenesis events were observed over the lifetime of the event: 1) low-amplitude frontal waves with no upper-level support, 2) low-amplitude frontal waves that formed in a jet-entrance region, and 3) cyclones that formed ahead of advancing upper-level troughs. All cyclones were either nondeveloping or weak developments despite extreme baroclinicity, likely the result of large atmospheric static stability in the arctic frontal zone and unfavorable alongfront stretching deformation. Significant frontal–mountain interactions were observed over the Rockies and the Appalachians.
von Willebrand factor self-association on platelet GpIbα under hydrodynamic shear: effect on shear-induced platelet activation
Authors: Dayananda Kannayakanahalli M. , Singh Indrajeet , Mondal Nandini , Neelamegham Sriram 
Published: August 2010

AbstractThe function of the mechanosensitive, multimeric blood protein von Willebrand factor (VWF) is dependent on its size. We tested the hypothesis that VWF may self-associate on the platelet glycoprotein Ibα (GpIbα) receptor under hydrodynamic shear. Consistent with this proposition, whereas Alexa-488–conjugated VWF (VWF-488) bound platelets at modest levels, addition of unlabeled VWF enhanced the extent of VWF-488 binding. Recombinant VWF lacking the A1-domain was conjugated with Alexa-488 to produce ΔA1-488. Although ΔA1-488 alone did not bind platelets under shear, this protein bound GpIbα on addition of either purified plasma VWF or recombinant full-length VWF. The extent of self-association increased with applied shear stress more than ∼ 60 to 70 dyne/cm2. ΔA1-488 bound platelets in the milieu of plasma. On application of fluid shear to whole blood, half of the activated platelets had ΔA1-488 bound, suggesting that VWF self-association may be necessary for cell activation. Shearing platelets with 6-μm beads bearing either immobilized VWF or anti-GpIbα mAb resulted in cell activation at shear stress down to 2 to 5 dyne/cm2. Taken together, the data suggest that fluid shear in circulation can increase the effective size of VWF bound to platelet GpIbα via protein self-association. This can trigger mechanotransduction and cell activation by enhancing the drag force applied on the cell-surface receptor.
Expression patterns of NKG2A, KIR, and CD57 define a process of CD56dim NK-cell differentiation uncoupled from NK-cell education
Authors: Björkström Niklas K. , Riese Peggy , Heuts Frank , Andersson Sandra , Fauriat Cyril , Ivarsson Martin A. , Björklund Andreas T. , Flodström-Tullberg Malin , Michaëlsson Jakob , Rottenberg Martin E. , Guzmán Carlos A. , Ljunggren Hans-Gustaf , Malmberg Karl-Johan 
Published: August 2010

AbstractNatural killer (NK) cells are lymphocytes of the innate immune system that, following differentiation from CD56bright to CD56dim cells, have been thought to retain fixed functional and phenotypic properties throughout their lifespan. In contrast to this notion, we here show that CD56dim NK cells continue to differentiate. During this process, they lose expression of NKG2A, sequentially acquire inhibitory killer cell inhibitory immunoglobulin-like receptors and CD57, change their expression patterns of homing molecules, and display a gradual decline in proliferative capacity. All cellular intermediates of this process are represented in varying proportions at steady state and appear, over time, during the reconstitution of the immune system, as demonstrated in humanized mice and in patients undergoing hematopoietic stem cell transplantation. CD56dim NK-cell differentiation, and the associated functional imprint, occurs independently of NK-cell education by interactions with self–human leukocyte antigen class I ligands and is an essential part of the formation of human NK-cell repertoires.
An improved classification of G-protein-coupled receptors using sequence-derived features
Authors: Peng Zhen-Ling , Yang Jian-Yi , Chen Xin 
Published: August 2010

Abstract

Background
G-protein-coupled receptors (GPCRs) play a key role in diverse physiological processes and are the targets of almost two-thirds of the marketed drugs. The 3 D structures of GPCRs are largely unavailable; however, a large number of GPCR primary sequences are known. To facilitate the identification and characterization of novel receptors, it is therefore very valuable to develop a computational method to accurately predict GPCRs from the protein primary sequences.

Results
We propose a new method called PCA-GPCR, to predict GPCRs using a comprehensive set of 1497 sequence-derived features. The principal component analysis is first employed to reduce the dimension of the feature space to 32. Then, the resulting 32-dimensional feature vectors are fed into a simple yet powerful classification algorithm, called intimate sorting, to predict GPCRs at five levels. The prediction at the first level determines whether a protein is a GPCR or a non-GPCR. If it is predicted to be a GPCR, then it will be further predicted into certain family, subfamily, sub-subfamily and subtype by the classifiers at the second, third, fourth, and fifth levels, respectively. To train the classifiers applied at five levels, a non-redundant dataset is carefully constructed, which contains 3178, 1589, 4772, 4924, and 2741 protein sequences at the respective levels. Jackknife tests on this training dataset show that the overall accuracies of PCA-GPCR at five levels (from the first to the fifth) can achieve up to 99.5%, 88.8%, 80.47%, 80.3%, and 92.34%, respectively. We further perform predictions on a dataset of 1238 GPCRs at the second level, and on another two datasets of 167 and 566 GPCRs respectively at the fourth level. The overall prediction accuracies of our method are consistently higher than those of the existing methods to be compared.

Conclusions
The comprehensive set of 1497 features is believed to be capable of capturing information about amino acid composition, sequence order as well as various physicochemical properties of proteins. Therefore, high accuracies are achieved when predicting GPCRs at all the five levels with our proposed method.
Lamellipodium extension and membrane ruffling require different SNARE-mediated trafficking pathways
Authors: Skalski Michael , Yi Qing , Kean Michelle J , Myers Dennis W , Williams Karla C , Burtnik Angela , Coppolino Marc G 
Published: August 2010

Abstract

Background
Intracellular membrane traffic is an essential component of the membrane remodeling that supports lamellipodium extension during cell adhesion. The membrane trafficking pathways that contribute to cell adhesion have not been fully elucidated, but recent studies have implicated SNARE proteins. Here, the functions of several SNAREs (SNAP23, VAMP3, VAMP4 and syntaxin13) are characterized during the processes of cell spreading and membrane ruffling.

Results
We report the first description of a SNARE complex, containing SNAP23, syntaxin13 and cellubrevin/VAMP3, that is induced by cell adhesion to an extracellular matrix. Impairing the function of the SNAREs in the complex using inhibitory SNARE domains disrupted the recycling endosome, impeded delivery of integrins to the cell surface, and reduced haptotactic cell migration and spreading. Blocking SNAP23 also inhibited the formation of PMA-stimulated, F-actin-rich membrane ruffles; however, membrane ruffle formation was not significantly altered by inhibition of VAMP3 or syntaxin13. In contrast, membrane ruffling, and not cell spreading, was sensitive to inhibition of two SNAREs within the biosynthetic secretory pathway, GS15 and VAMP4. Consistent with this, formation of a complex containing VAMP4 and SNAP23 was enhanced by treatment of cells with PMA. The results reveal a requirement for the function of a SNAP23-syntaxin13-VAMP3 complex in the formation of lamellipodia during cell adhesion and of a VAMP4-SNAP23-containing complex during PMA-induced membrane ruffling.

Conclusions
Our findings suggest that different SNARE-mediated trafficking pathways support membrane remodeling during ECM-induced lamellipodium extension and PMA-induced ruffle formation, pointing to important mechanistic differences between these processes.
Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia
Authors: Tapio Miika , Ozerov Mikhail , Tapio Ilma , Toro Miguel A , Marzanov Nurbiy , Ćinkulov Mirjana , Goncharenko Galina , Kiselyova Tatyana , Murawski Maziek , Kantanen Juha 
Published: August 2010

Abstract

Background
Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation.

Results
Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity.

Conclusions
During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.
Multi-locus analysis of human infective Cryptosporidium species and subtypes using ten novel genetic loci
Authors: Bouzid Maha , Tyler Kevin M , Christen Richard , Chalmers Rachel M , Elwin Kristin , Hunter Paul R 
Published: August 2010

Abstract

Background

Cryptosporidium is a protozoan parasite that causes diarrheal illness in a wide range of hosts including humans. Two species, C. parvum and C. hominis are of primary public health relevance. Genome sequences of these two species are available and show only 3-5% sequence divergence. We investigated this sequence variability, which could correspond either to sequence gaps in the published genome sequences or to the presence of species-specific genes. Comparative genomic tools were used to identify putative species-specific genes and a subset of these genes was tested by PCR in a collection of Cryptosporidium clinical isolates and reference strains.

Results
The majority of the putative species-specific genes examined were in fact common to C. parvum and C. hominis. PCR product sequence analysis revealed interesting SNPs, the majority of which were species-specific. These genetic loci allowed us to construct a robust and multi-locus analysis. The Neighbour-Joining phylogenetic tree constructed clearly discriminated the previously described lineages of Cryptosporidium species and subtypes.

Conclusions
Most of the genes identified as being species specific during bioinformatics in Cryptosporidium sp. are in fact present in multiple species and only appear species specific because of gaps in published genome sequences. Nevertheless SNPs may offer a promising approach to studying the taxonomy of closely related species of Cryptosporidia.
Automated quantitative gait analysis in animal models of movement disorders
Authors: Vandeputte Caroline , Taymans Jean-Marc , Casteels Cindy , Coun Frea , Ni Yicheng , Van Laere Koen , Baekelandt Veerle 
Published: August 2010

Abstract

Background
Accurate and reproducible behavioral tests in animal models are of major importance in the development and evaluation of new therapies for central nervous system disease. In this study we investigated for the first time gait parameters of rat models for Parkinson's disease (PD), Huntington's disease (HD) and stroke using the Catwalk method, a novel automated gait analysis test. Static and dynamic gait parameters were measured in all animal models, and these data were compared to readouts of established behavioral tests, such as the cylinder test in the PD and stroke rats and the rotarod tests for the HD group.

Results
Hemiparkinsonian rats were generated by unilateral injection of the neurotoxin 6-hydroxydopamine in the striatum or in the medial forebrain bundle. For Huntington's disease, a transgenic rat model expressing a truncated huntingtin fragment with multiple CAG repeats was used. Thirdly, a stroke model was generated by a photothrombotic induced infarct in the right sensorimotor cortex. We found that multiple gait parameters were significantly altered in all three disease models compared to their respective controls. Behavioural deficits could be efficiently measured using the cylinder test in the PD and stroke animals, and in the case of the PD model, the deficits in gait essentially confirmed results obtained by the cylinder test. However, in the HD model and the stroke model the Catwalk analysis proved more sensitive than the rotarod test and also added new and more detailed information on specific gait parameters.

Conclusion
The automated quantitative gait analysis test may be a useful tool to study both motor impairment and recovery associated with various neurological motor disorders.
Self-medication with antibiotics in rural population in Greece: a cross-sectional multicenter study
Authors: Skliros Eystathios , Merkouris Panagiotis , Papazafiropoulou Athanasia , Gikas Aristofanis , Matzouranis George , Papafragos Christos , Tsakanikas Ioannis , Zarbala Irene , Vasibosis Alexios , Stamataki Petroula , Sotiropoulos Alexios 
Published: August 2010

Abstract

Background
Self-medication is an important driver of antimicrobial overuse as well as a worldwide problem. The aim of the present study was to estimate the use of antibiotics, without medical prescription, in a sample of rural population presenting in primary care in southern Greece.

Methods
The study included data from 1,139 randomly selected adults (545 men/594 women, mean age ± SD: 56.2 ± 19.8 years), who visited the 6 rural Health Centres of southern Greece, between November 2009 and January 2010. The eligible participants were sought out on a one-to-one basis and asked to answer an anonymous questionnaire.

Results
Use of antibiotics within the past 12 months was reported by 888 participants (77.9%). 508 individuals (44.6%) reported that they had received antibiotics without medical prescription at least one time. The major source of self-medication was the pharmacy without prescription (76.2%). The antibiotics most frequently used for self-medication were amoxicillin (18.3%), amoxicillin/clavulanic acid (15.4%), cefaclor (9.7%), cefuroxim (7.9%), cefprozil (4.7%) and ciprofloxacin (2.3%). Fever (41.2%), common cold (32.0%) and sore throat (20.6%) were the most frequent indications for the use of self-medicated antibiotics.

Conclusion
In Greece, despite the open and rapid access to primary care services, it appears that a high proportion of rural adult population use antibiotics without medical prescription preferably for fever and common cold.
Irradiation of the potential cancer stem cell niches in the adult brain improves progression-free survival of patients with malignant glioma
Authors: Evers Patrick , Lee Percy P , DeMarco John , Agazaryan Nzhde , Sayre James W , Selch Michael , Pajonk Frank 
Published: August 2010

AbstractBackgroundGlioblastoma is the most common brain tumor in adults. The mechanisms leading to glioblastoma are not well understood but animal studies support that inactivation of tumor suppressor genes in neural stem cells (NSC) is required and sufficient to induce glial cancers. This suggests that the NSC niches in the brain may harbor cancer stem cells (CSCs), Thus providing novel therapy targets. We hypothesize that higher radiation doses to these NSC niches improve patient survival by eradicating CSCs.Methods55 adult patients with Grade 3 or Grade 4 glial cancer treated with radiotherapy at UCLA between February of 2003 and May of 2009 were included in this retrospective study. Using radiation planning software and patient radiological records, the SVZ and SGL were reconstructed for each of these patients and dosimetry data for these structures was calculated.ResultsUsing Kaplan-Meier analysis we show that patients whose bilateral subventricular zone (SVZ) received greater than the median SVZ dose (= 43 Gy) had a significant improvement in progression-free survival if compared to patients who received less than the median dose (15.0 vs 7.2 months PFS; P = 0.028). Furthermore, a mean dose >43 Gy to the bilateral SVZ yielded a hazard ratio of 0.73 (P = 0.019). Importantly, similarly analyzing total prescription dose failed to illustrate a statistically significant impact.ConclusionsOur study leads us to hypothesize that in glioma targeted radiotherapy of the stem cell niches in the adult brain could yield significant benefits over radiotherapy of the primary tumor mass alone and that damage caused by smaller fractions of radiation maybe less efficiently detected by the DNA repair mechanisms in CSCs.