bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding how visual attention locks on to a location: Toward a computational model of the N2pc component
Authors: Tan Mingxuan , Wyble Brad 
Published: September 2014

AbstractCompeting theories regarding the neural mechanism underlying the N2pc suggest that it reflects target enhancement or distractor suppression, but we suggest a different theory. In our study, participants viewed a bilateral dual‐stream rapid serial visual presentation (RSVP). Each trial had either one or two targets (T1, T2) presented either in the same or different streams. We found that the N2pc elicited by T1 was not affected by an immediately following T2 at the same location. However, if T2 was on the opposite hemifield, a second N2pc was elicited. These results suggest that the N2pc reflects neural processes involved in localizing a target to initiate the deployment of attention, rather than the sustained enhancement of processing at that location or distractor inhibition. We have created a computational model of a convergent gradient‐filter model of attention that reproduces the observed event‐related potential traces and makes five testable predictions to be addressed in future work.
The Evaluation of Evidence for Auto-Correlated Data in Relation to Traces of Cocaine on Banknotes
Authors: Wilson Amy , Aitken Colin , Sleeman Richard , Carter James 
Published: September 2014

SummaryMuch research in recent years for evidence evaluation in forensic science has focused on methods for determining the likelihood ratio in various scenarios. When the issue in question is whether evidence is associated with a person who is or is not associated with criminal activity then the problem is one of discrimination. A procedure for the determination of the likelihood ratio is developed when the evidential data are believed to be driven by an underlying latent Markov chain. Three other models that assume auto-correlated data without the underlying Markov chain are also described. The performances of these four models and a model assuming independence are compared by using data concerning traces of cocaine on banknotes.
Group Sequential Method for Observational Data by Using Generalized Estimating Equations: Application to Vaccine Safety Datalink
Authors: Cook Andrea J. , Wellman Robert D. , Nelson Jennifer C. , Jackson Lisa A. , Tiwari Ram C. 
Published: September 2014

SummaryPost-market medical product surveillance is important for detecting rare adverse events that are not identified during preapproval. The goal of surveillance is to assess over time for elevated rates of adverse events for new medical products. These studies utilize administrative databases from multiple large health plans. We propose a group sequential method using a permutation approach with generalized estimating equations to account for confounding. A simulation study is conducted to evaluate the performance of the group sequential generalized estimating equation method compared with two other approaches. The methods are then applied to a vaccine safety application from the Vaccine Safety Datalink.
VGI and Reference Data Correspondence Based on Location‐Orientation Rotary Descriptor and Segment Matching
Authors: Mohammadi Nazila , Malek Mohammadreza 
Published: September 2014

AbstractVolunteered geographic information (VGI) is spatial data that has been contributed by numerous volunteers in the form of user‐generated content. VGI provides the ability for non‐experts to collect and share geographic information. Comparison of a VGI dataset with a reference dataset in order to find data correspondence is a common process in some analyses of VGI data, such as quantitative analysis of its quality. This study addresses this case and presents an automated feature matching method for VGI linear data. The proposed method consists of two main steps. In the first step, a feature point matching method based on a novel descriptor, named Location‐Orientation Rotary Descriptor (LORD), is performed. The proposed LORD descriptor uses the location and orientation information of the linear data in a log polar structure and in a rotary manner. In the second step, a new segment matching strategy based on the buffered linear features is performed to reject the outliers of the previous step. The usefulness of the proposed method was demonstrated by applying it to the OpenStreetMap (OSM) dataset, as a VGI dataset, using an official reference dataset.
Numerical calculation of three-point branched covers of the projective line
Authors: Klug Michael , Musty Michael , Schiavone Sam , Voight John 
Published: September 2014

AbstractWe exhibit a numerical method to compute three-point branched covers of the complex projective line. We develop algorithms for working explicitly with Fuchsian triangle groups and their finite-index subgroups, and we use these algorithms to compute power series expansions of modular forms on these groups.
Characterization ofblaTEM-52-Carrying Plasmids of Extended-Spectrum-β-Lactamase-Producing Salmonella enterica Isolates from Chicken Meat with a Common Supplier in Japan
Authors: Matsumoto Yuko , Izumiya Hidemasa , Sekizuka Tsuyoshi , Kuroda Makoto , Ohnishi Makoto 
Published: September 2014

ABSTRACTThe acquisition of resistance to cephalosporins amongSalmonellaspp. is a major public health concern. This study identified clonal plasmids carryingblaTEM-52from 10Salmonella entericaserovar Infantis and Manhattan isolates from retail chicken meats that originated from a common supplier in Japan. Whole-genome analyses of the representative plasmids, including pYM4, revealed that they are 38 kb in size and that pYM4 is identical to pDKX1 from beef in Denmark, suggesting a global dissemination of resistance mediated by the plasmids.
Genotypic and Phenotypic Profiles of Escherichia coli Isolates Belonging to Clinical Sequence Type 131 (ST131), Clinical Non-ST131, and Fecal Non-ST131 Lineages from India
Authors: Hussain Arif , Ranjan Amit , Nandanwar Nishant , Babbar Anshu , Jadhav Savita , Ahmed Niyaz 
Published: September 2014

ABSTRACT

In view of the epidemiological success of CTX-M-15-producing lineages of
Escherichia coli
and particularly of sequence type 131 (ST131), it is of significant interest to explore its prevalence in countries such as India and to determine if antibiotic resistance, virulence, metabolic potential, and/or the genetic architecture of the ST131 isolates differ from those of non-ST131 isolates. A collection of 126
E. coli
isolates comprising 43 ST131
E. coli
, 40 non-ST131
E. coli
, and 43 fecal
E. coli
isolates collected from a tertiary care hospital in India was analyzed. These isolates were subjected to enterobacterial repetitive intergenic consensus (ERIC)-based fingerprinting, O typing, phylogenetic grouping, antibiotic sensitivity testing, and virulence and antimicrobial resistance gene (VAG) detection. Representative isolates from this collection were also analyzed by multilocus sequence typing (MLST), conjugation, metabolic profiling, biofilm production assay, and zebra fish lethality assay. All of the 43 ST131
E. coli
isolates were exclusively associated with phylogenetic group B2 (100%), while most of the clinical non-ST131 and stool non-ST131
E. coli
isolates were affiliated with the B2 (38%) and A (58%) phylogenetic groups, respectively. Significantly greater proportions of ST131 isolates (58%) than non-ST131 isolates (clinical and stool
E. coli
isolates, 5% each) were technically identified to be extraintestinal pathogenic
E. coli
(ExPEC). The clinical ST131, clinical non-ST131, and stool non-ST131
E. coli
isolates exhibited high rates of multidrug resistance (95%, 91%, and 91%, respectively), extended-spectrum-β-lactamase (ESBL) production (86%, 83%, and 91%, respectively), and metallo-β-lactamase (MBL) production (28%, 33%, and 0%, respectively). CTX-M-15 was strongly linked with ESBL production in ST131 isolates (93%), whereas CTX-M-15 plus TEM were present in clinical and stool non-ST131
E. coli
isolates. Using MLST, we confirmed the presence of two NDM-1-positive ST131
E. coli
isolates. The aggregate bioscores (metabolite utilization) for ST131, clinical non-ST131, and stool non-ST131
E. coli
isolates were 53%, 52%, and 49%, respectively. The ST131 isolates were moderate biofilm producers and were more highly virulent in zebra fish than non-ST131 isolates. According to ERIC-based fingerprinting, the ST131 strains were more genetically similar, and this was subsequently followed by the genetic similarity of clinical non-ST131 and stool non-ST131
E. coli
strains. In conclusion, our data provide novel insights into aspects of the fitness advantage of
E. coli
lineage ST131 and suggest that a number of factors are likely involved in the worldwide dissemination of and infections due to ST131
E. coli
isolates.
Pharmacokinetics and Safety of Intravitreal Caspofungin
Authors: Shen Ying-Cheng , Liang Chiao-Ying , Wang Chun-Yuan , Lin Keng-Hung , Hsu Min-Yen , Yuen Hon-Leung , Wei Li-Chen 
Published: September 2014

ABSTRACT

Caspofungin exhibits potent antifungal activities against
Candida
and
Aspergillus
species. The elimination rate and retinal toxicity of caspofungin were determined in this study to assess its pharmacokinetics and safety in the treatment of fungal endophthalmitis. Intravitreal injections of 50 μg/0.1 ml of caspofungin were administered to rabbits. Levels of caspofungin in the vitreous and aqueous humors were determined using high-performance liquid chromatography (HPLC) at selected time intervals (10 min and 1, 2, 4, 8, 16, 24, and 48 h), and the half-lives were calculated. Eyes were intravitreally injected with caspofungin to obtain concentrations of 10 μg/ml, 50 μg/ml, 100 μg/ml, and 200 μg/ml. Electroretinograms were recorded 4 weeks after injections, and the injected eyes were examined histologically. The concentrations of intravitreal caspofungin at various time points exhibited an exponential decay with a half-life of 6.28 h. The mean vitreous concentration was 6.06 ± 1.76 μg/ml 1 h after intravitreal injection, and this declined to 0.47 ± 0.15 μg/ml at 24 h. The mean aqueous concentration showed undetectable levels at all time points. There were no statistical differences in scotopic
a
-wave and
b
-wave responses between control eyes and caspofungin-injected eyes. No focal necrosis or other abnormality in retinal histology was observed. Intravitreal caspofungin injection may be considered to be an alternative treatment for fungal endophthalmitis based on its antifungal activity, lower retinal toxicity, and lower elimination rate in the vitreous. More clinical data are needed to determine its potential role as primary therapy for fungal endophthalmitis.
Platelet Profile in Patients with Acute Bacterial Skin and Skin Structure Infections Receiving Tedizolid or Linezolid: Findings from the Phase 3 ESTABLISH Clinical Trials
Authors: Lodise Thomas P. , Fang Edward , Minassian Sonia L. , Prokocimer Philippe G. 
Published: September 2014

ABSTRACT

Tedizolid, the active moiety of tedizolid phosphate, is a recently approved oxazolidinone antibacterial with activity against a wide range of Gram-positive pathogens, including resistant strains such as methicillin-resistant
Staphylococcus aureus
. To date, 6 days of 200 mg tedizolid once daily has been shown to be noninferior to 10 days of 600 mg linezolid twice daily in two randomized, double-blind phase 3 trials (ESTABLISH-1 and ESTABLISH-2) for the treatment of patients with acute bacterial skin and skin structure infections (ABSSSIs). The intent of this study was to characterize the platelet profiles of patients receiving tedizolid relative to linezolid over the course of treatment using pooled data from these two trials. The occurrences of clinically defined and statistical analysis plan–specified reduced platelet counts were assessed at the study days 7 to 9 visit, the study days 11 to 13 visit, and the posttherapy evaluation (PTE) visit. At the study days 7 to 9 visit, incidences of reduced platelet counts were low and largely similar between the groups. The only notable difference was a lower incidence of thrombocytopenia (platelet counts, <150,000 cells/mm
3
) among patients who received tedizolid (3.2%) relative to those who received linezolid (5.6%). At the study days 11 to 13 visit, patients who received tedizolid had lower incidences of platelet counts of <150,000 cells/mm
3
(−5.9%), <112,500 cells/mm
3
(−2.4%), and <100,000 cells/mm
3
(−1.9%) than patients in the linezolid group. Similar differences were noted at the PTE visit. Findings across the two phase 3 ABSSSI trials suggest that 6 days of 200 mg tedizolid daily confers a low potential for reduced platelet counts among patients with ABSSSIs. (The ESTABLISH-1 and ESTABLISH-2 trials have been registered at ClinicalTrials.gov under registration numbers NCT01170221 and NCT01421511, respectively.)
pncA
and
bptA
Are Not Sufficient To Complement Ixodes scapularis Colonization and Persistence by Borrelia burgdorferi in a Linear Plasmid lp25-Deficient Background
Authors: Gilmore Robert D. , Brandt Kevin S. , Hyde Jenny A. 
Published: September 2014

ABSTRACT

The complex segmented genome of
Borrelia burgdorferi
is comprised of a linear chromosome along with numerous linear and circular plasmids essential for tick and/or mammalian infectivity. The pathogenic necessity for specific borrelial plasmids has been identified; most notably, infections of the tick vector and mammalian host both require linear plasmid 25 (lp25). Genes carried on lp25, specifically
bptA
and
pncA
, are postulated to play a role for
B. burgdorferi
to infect and persist in
Ixodes
ticks. In this study, we complemented an lp25-deficient borrelial strain with
pncA
alone or
pncA
accompanied by
bptA
to evaluate the ability of the complemented strains to restore larval colonization and persistence through transstadial transmission relative to that of wild-type
B. burgdorferi
. The acquisition of the complemented strains by tick larvae from infected mice and/or the survival of these strains was significantly decreased when assayed by cultivation and quantitative PCR (qPCR). Only 10% of the
pncA
-complemented strain organisms were found by culture to survive 17 days following larval feeding, while 45% of the
pncA
- and
bptA
-complemented strain organisms survived, with similar results by PCR. However, neither of the complemented
B. burgdorferi
strains was capable of persisting through the molt to the nymphal stage as analyzed by culture. qPCR analyses of unfed nymphs detected
B. burgdorferi
genomes in several nymphs at low copy numbers, likely indicating the presence of DNA from dead or dying cells. Overall, the data indicate that
pncA
and
bptA
cannot independently support infection, suggesting that lp25 carries additional gene(s) or regulatory elements critical for
B. burgdorferi
survival and pathogenesis in the
Ixodes
vector.
Frequency, interobserver reproducibility and clinical significance of equivocal peaks in PCR clonality testing using Euroclonality/BIOMED-2 primers
Authors: Park Il Joong , Bena James , Cotta Claudiu V , Hsi Eric D , Jegalian Armin G , Rogers Heesun J , Tubbs Raymond R , Wang Lu , Cook James R 
Published: September 2014

AimsPCR studies for lymphoid clonality are now widely employed, especially using Euroclonality/BIOMED-2 primers. Criteria for interpretation as a clonal result, however, have proven controversial. This study examines the frequency and clinical significance of equivocal amplification patterns and measures the interobserver reproducibility of clonality interpretations.MethodsAt our institution, results of each primer set are first classified as clonal, non-clonal or abnormal (equivocal peak on polyclonal background). Final results for all primer sets are then collectively reported as positive (≥1 clonal result), negative (non-clonal results) or indeterminate (≥1 abnormal result) for a clonal population. Results of 274 consecutive clonality cases were reviewed, and the interobserver reproducibility of individual primer set reactions and final results was determined in a subset of 30 cases.Results44/161 (27%) B-cell and 50/163 (31%) T-cell cases contained at least one abnormal peak. Of these, 29 (64%) and 31 (62%), respectively, showed clonal results in another primer set. Interobserver reproducibility was excellent for most primer sets and for final interpretations, but only fair to good for IGK V-J and TCRB D-J1+2 primer sets. A definitive diagnosis of lymphoma was rendered in 93%, 20% and 6% of B-cell cases and 90%, 42%, and 14% of T-cell cases positive, indeterminate or negative for a clonal population, respectively.ConclusionsUsing a subjective approach, abnormal (equivocal) peaks are frequently observed in routine practice. However, most cases with abnormal peaks contain clonal rearrangements in other primer sets, facilitating overall interpretation of final results with excellent interobserver reproducibility.
BESiDE
Authors: McIntyre Lesley J. 
Published: September 2014

This article describes BESiDE, a multi-disciplinary research project that investigates themes of ageing, wellbeing, accessibility and digital technologies within the context of built environment design. Through the development of dialogue tools, indoor localization and physical activity tracking sensors, BESiDE is taking steps towards enhancing understanding of accessibility within the design of care home environments.
Focused on initial reflections from contemporary design practice, we have found that, design guidance; a lack of research 'tools' to engage with users; an absent research culture; and missing elements of design training, are factors preventing a designer's holistic engagement with the experiences of older people and technologies within the built environment. In addition to reviewing these findings, an overview of BESiDE'S continuing work and methods planned for assessing the accessibility within older peoples' care environments is discussed.
Telomere-Regulating Genes and the Telomere Interactome in Familial Cancers
Authors: Robles-Espinoza Carla Daniela , del Castillo Velasco-Herrera Martin , Hayward Nicholas K. , Adams David J. 
Published: September 2014

AbstractTelomeres are repetitive sequence structures at the ends of linear chromosomes that consist of double-stranded DNA repeats followed by a short single-stranded DNA protrusion. Telomeres need to be replicated in each cell cycle and protected from DNA-processing enzymes, tasks that cells execute using specialized protein complexes such as telomerase (that includes TERT), which aids in telomere maintenance and replication, and the shelterin complex, which protects chromosome ends. These complexes are also able to interact with a variety of other proteins, referred to as the telomere interactome, to fulfill their biological functions and control signaling cascades originating from telomeres. Given their essential role in genomic maintenance and cell-cycle control, germline mutations in telomere-regulating proteins and their interacting partners have been found to underlie a variety of diseases and cancer-predisposition syndromes. These syndromes can be characterized by progressively shortening telomeres, in which carriers can present with organ failure due to stem cell senescence among other characteristics, or can also present with long or unprotected telomeres, providing an alternative route for cancer formation. This review summarizes the critical roles that telomere-regulating proteins play in cell-cycle control and cell fate and explores the current knowledge on different cancer-predisposing conditions that have been linked to germline defects in these proteins and their interacting partners. Mol Cancer Res; 13(2); 211–22. ©2014 AACR.
Functional TCR Retrieval from Single Antigen-Specific Human T Cells Reveals Multiple Novel Epitopes
Authors: Simon Petra , Omokoko Tana A. , Breitkreuz Andrea , Hebich Lisa , Kreiter Sebastian , Attig Sebastian , Konur Abdo , Britten Cedrik M. , Paret Claudia , Dhaene Karl , Türeci Özlem , Sahin Ugur 
Published: September 2014

AbstractThe determination of the epitope specificity of disease-associated T-cell responses is relevant for the development of biomarkers and targeted immunotherapies against cancer, autoimmune, and infectious diseases. The lack of known T-cell epitopes and corresponding T-cell receptors (TCR) for novel antigens hinders the efficient development and monitoring of new therapies. We developed an integrated approach for the systematic retrieval and functional characterization of TCRs from single antigen-reactive T cells that includes the identification of epitope specificity. This is accomplished through the rapid cloning of full-length TCR-α and TCR-β chains directly from single antigen-specific CD8+ or CD4+ T lymphocytes. The functional validation of cloned TCRs is conducted using in vitro–transcribed RNA transfer for expression of TCRs in T cells and HLA molecules in antigen-presenting cells. This method avoids the work and bias associated with repetitive cycles of in vitro T-cell stimulation, and enables fast characterization of antigen-specific T-cell responses. We applied this strategy to viral and tumor-associated antigens (TAA), resulting in the retrieval of 56 unique functional antigen-specific TCRs from human CD8+ and CD4+ T cells (13 specific for CMV-pp65, 16 specific for the well-known TAA NY-ESO-1, and 27 for the novel TAA TPTE), which are directed against 39 different epitopes. The proof-of-concept studies with TAAs NY-ESO-1 and TPTE revealed multiple novel TCR specificities. Our approach enables the rational development of immunotherapy strategies by providing antigen-specific TCRs and immunogenic epitopes. Cancer Immunol Res; 2(12); 1230–44. ©2014 AACR.
Phylogenetic position and taxonomic assignment of Thlaspi aghricum P.H.Davis &amp; K.Tan (Brassicaceae)
Authors: Fırat Mehmet , Özüdoğru Barış , Tarıkahya Hacıoğlu Burcu , Bülbül Ali Savaş , Al-Shehbaz Ihsan Ali , Mummenhoff Klaus 
Published: September 2014

A general review of the taxonomic status of Thlaspi past and present is given, and a critical evaluations of its segregates based on both morphological and molecular data are presented. ITS molecular phylogenetic study of Thlaspi aghricum and related species, as well as seed-coat morphology and anatomy strongly support the placement of the species in Noccaea. The new combination N. aghrica is proposed, and detailed description and distribution of the species are given.
Community Support and Transition of Research to Operations for the Hurricane Weather Research and Forecasting Model
Authors: Bernardet L. , Tallapragada V. , Bao S. , Trahan S. , Kwon Y. , Liu Q. , Tong M. , Biswas M. , Brown T. , Stark D. , Carson L. , Yablonsky R. , Uhlhorn E. , Gopalakrishnan S. , Zhang X. , Marchok T. , Kuo B. , Gall R. 
Published: September 2014

Abstract
The Hurricane Weather Research and Forecasting Model (HWRF) is an operational model used to provide numerical guidance in support of tropical cyclone forecasting at the National Hurricane Center. HWRF is a complex multicomponent system, consisting of the Weather Research and Forecasting (WRF) atmospheric model coupled to the Princeton Ocean Model for Tropical Cyclones (POM-TC), a sophisticated initialization package including a data assimilation system and a set of postprocessing and vortex tracking tools. HWRF’s development is centralized at the Environmental Modeling Center of NOAA’s National Weather Service, but it incorporates contributions from a variety of scientists spread out over several governmental laboratories and academic institutions. This distributed development scenario poses significant challenges: a large number of scientists need to learn how to use the model, operational and research codes need to stay synchronized to avoid divergence, and promising new capabilities need to be tested for operational consideration. This article describes how the Developmental Testbed Center has engaged in the HWRF developmental cycle in the last three years and the services it provides to the community in using and developing HWRF.