bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Urine with Nested PCR Targeting the Flagellin Gene (
fliC
) for Diagnosis of Typhoid Fever
Authors: Kumar Gopal , Pratap Chandra Bhan , Mishra Om Prakash , Kumar Kailash , Nath Gopal 
Published: April 2012

ABSTRACT

This study was planned to evaluate the efficacy of the use of nested PCR with a large volume of easily available urine as an effort to devise a test that can meet the levels necessary to be considered a gold standard for the diagnosis of typhoid fever. A total of 60 subjects with suspected cases of typhoid fever and 20 apparently healthy control subjects were included in the study. The study period extended from March 2010 to June 2011. Blood, urine, and stool specimens were collected from the participating individuals. Nested PCR was done targeting the flagellin gene (
fliC
) of
Salmonella enterica
subspecies
enterica
serotype Typhi. Specimens in all three categories could be collected from 22 of the subjects with suspected cases of typhoid fever; 21 of the 22 urine samples (95.4%) yielded a desired amplicon of 343 bp, whereas none of the urine samples collected from the 20 control subjects (0%) yielded the amplicon. The analyses of blood and stool samples were found to be inferior to urine sample analysis in sensitivity, with detection rates of 90.9% and 68.1%, respectively. Culture isolation was observed to display very poor sensitivity (31.8%). A large volume of urine may be the ideal specimen for PCR-based detection of typhoid fever.
Quantification by Real-Time PCR Assay of Staphylococcus aureus Load: a Useful Tool for Rapidly Identifying Persistent Nasal Carriers
Authors: Verhoeven Paul O. , Grattard Florence , Carricajo Anne , Lucht Frédéric , Cazorla Céline , Garraud Olivier , Pozzetto Bruno , Berthelot Philippe 
Published: April 2012

ABSTRACT

The Cepheid Xpert MRSA/SA nasal PCR assay was compared to culture for quantifying
Staphylococcus aureus
load from 104 nasal samples (
r
= 0.91,
P
< 0.0001). Using a bacterial load-based algorithm, the test was found able to predict the carrier state in 32 of 35 healthy volunteers (22 persistent and 13 nonpersistent carriers).
Analysis of the Excretion Dynamics and Genotypic Characteristics of Rotavirus A during the Lives of Pigs Raised on Farms for Meat Production
Authors: Miyazaki Ayako , Kuga Kazufumi , Suzuki Tohru , Tsunemitsu Hiroshi 
Published: April 2012

ABSTRACT
To determine the excretion dynamics and genotypic characteristics of rotavirus A (RVA), a longitudinal observational study was performed in 10 pigs from 3 litters at a farrow-to-finish farm. A total of 400 fecal samples were directly collected from the rectums of individual pigs (aged 7 to 217 days) at 3- to 14-day intervals. Seventy-one samples (17.5%) were positive for RVA by reverse transcription-PCR designed to detect the VP7 and VP4 genes. At least 13 combinations of 5 G (G2, G4, G5, G9, and G11) and 6 P (P[6], P[7], P[13], P[23], P[27], and P[34]) genotypes were identified by direct sequencing of the PCR products. We were able to detect RVA VP7 sequences from each pig 4 to 6 times with intervals of 7 to 52 days (from 7 to 119 days of age). Each pig harbored RVAs with at least 3 to 6 different combinations of G and P genotypes, while repeated excretions of RVAs carrying the same combinations of G and P genotypes were also observed. Virus shedding and changes in G and P genotypes appeared to be associated with movement of the pigs into weaning, growing, and finishing barns. These results indicated that, over their lifetimes, pigs raised for meat frequently and intermittently excrete genetically diverse RVAs.
Human Papillomavirus Type 16 Genetic Variants: Phylogeny and Classification Based on E6 and LCR
Authors: Cornet Iris , Gheit Tarik , Franceschi Silvia , Vignat Jerome , Burk Robert D. , Sylla Bakary S. , Tommasino Massimo , Clifford Gary M. ,   the IARC HPV Variant Study Group
Published: April 2012

ABSTRACT
Naturally occurring genetic variants of human papillomavirus type 16 (HPV16) are common and have previously been classified into 4 major lineages; European-Asian (EAS), including the sublineages European (EUR) and Asian (As), African 1 (AFR1), African 2 (AFR2), and North-American/Asian-American (NA/AA). We aimed to improve the classification of HPV16 variant lineages by using a large resource of HPV16-positive cervical samples collected from geographically diverse populations in studies on HPV and/or cervical cancer undertaken by the International Agency for Research on Cancer. In total, we sequenced the entire E6 genes and long control regions (LCRs) of 953 HPV16 isolates from 27 different countries worldwide. Phylogenetic analyses confirmed previously described variant lineages and subclassifications. We characterized two new sublineages within each of the lineages AFR1 and AFR2 that are robustly classified using E6 and/or the LCR. We could differentiate previously identified AA1, AA2, and NA sublineages, although they could not be distinguished by E6 alone, requiring the LCR for correct phylogenetic classification. We thus provide a classification system for HPV16 genomes based on 13 and 32 phylogenetically distinguishing positions in E6 and the LCR, respectively, that distinguish nine HPV16 variant sublineages (EUR, As, AFR1a, AFR1b, AFR2a, AFR2b, NA, AA1, and AA2). Ninety-seven percent of all 953 samples fitted this classification perfectly. Other positions were frequently polymorphic within one or more lineages but did not define phylogenetic subgroups. Such a standardized classification of HPV16 variants is important for future epidemiological and biological studies of the carcinogenic potential of HPV16 variant lineages.
Cerebrovascular geometry in the anterior circulation: an analysis of diameter, length and the vessel taper
Authors: Rai Ansaar T , Hogg Jeffery P , Cline Brendan , Hobbs Gerald 
Published: April 2012

BackgroundA study was undertaken to determine the typical length, diameter and taper of vessels in the anterior cerebral circulation.MethodsThe sample size was calculated at 100 patients based on similar measurements in the literature and divided into cohorts based on gender and side. These patients were consecutively collected from a population that had undergone CT angiography and did not have any vascular abnormality. The arterial diameter was measured at the proximal cavernous internal carotid artery (ICA), the ICA terminus, the middle cerebral artery (MCA) origin and an M2 origin. The length between these endpoints was calculated along the center line. The vessel taper was calculated for the ICA as the change in caliber per unit length.ResultsThe mean length of the ICA from the proximal cavernous segment to the ICA terminus was 33.1±6.1 mm. The mean diameter at the cavernous ICA and the ICA terminus was 5±0.6 mm and 3.6±0.4 mm, respectively. The mean ICA taper was 0.04±0.02 mm/1 mm. For the MCA, the diameter at the MCA and M2 origins measured 3.1±0.4 mm and 2.4±0.4 mm, respectively. The mean MCA length was 22.5±8.1 mm. There was no significant difference based on gender or between right and left sides. Patients aged >60 years had longer ICAs (p=0.02), larger cavernous ICA (p=0.003), ICA terminus (p<0.0001) and MCA origin (p=0.01) diameters than those aged 40–60 years. The ICA vessel taper did not change with age.ConclusionICA and MCA vessel size did not change based on gender or side. Older patients had more redundant vessels based on diameter and length. The ICA has a gentle taper from its proximal cavernous segment to the ICA terminus. This information can be important in planning interventions or designing endovascular devices.
ENHANCED CONTROL OF EXCIMER LASER PULSE TIMING USING TUNABLE ADDITIVE NOISE
Authors: MINGESZ ROBERT , BARNA ANGELA , GINGL ZOLTAN , MELLAR JANOS 
Published: April 2012

Recently we have shown a system developed to precisely control the laser pulse timing of excimer lasers [R. Mingesz, Z. Gingl, G. Almasi, A. Csengeri and P. Makra, Utilising jitter noise in the precise synchronisation of laser pulses, Fluct. Noise Lett. 8 (2008) L41–L49]. The electronic circuit based on an embedded microcontroller and utilized the natural jitter noise of the laser pulse generation to improve the long term regulation of the delay of the laser related to an external trigger pulse. Based on our results we have developed an improved system that uses additional, programmable time delay units to tune the noise source to further enhance performance and allows reduction of complexity in the same time. A mixed-signal microcontroller generates a randomly dithered delay of the pulse generation moment to enhance the resolution and also runs a dedicated algorithm to optimize regulation. The compact, flexible hardware supports further enhancements; the signal processing algorithm can be replaced even by in-system reprogramming. Optimized processing and the relaxed hardware requirements may also support low-power operation, wireless communication, therefore the application possibilities may be extended to many other disciplines.
Potential Vorticity Attribution and Causality
Authors: Spengler Thomas , Egger Joseph 
Published: April 2012

Abstract
The electrostatic analogy provides a well-known paradigm for the concept of potential vorticity (PV) attribution. Just as electric fields can be attributed to electric charges, so are localized PV anomalies thought to induce far fields of flow and temperature, at least after geostrophic adjustment. Piecewise PV inversion (PPVI) exploits this concept. Idealized examples of PPVI are discussed by selecting isolated anomalies that are inverted to yield the far field “caused” by the PV anomaly. The causality of attribution is tested in this study by seeking an unbalanced initial state containing the same PV anomaly but without a far field from which the balanced state can be attained by geostrophic adjustment. It is shown that the far field of a balanced axisymmetric PV anomaly in shallow water, without mean PV gradients, may evolve from a localized anomaly without a far field. For the more general example of the electrostatics analogy, namely a three-dimensional spherical PV anomaly, the initial state has to be nonhydrostatic and needs to exhibit a mass deficit. As this mass deficit cannot be removed during hydrostatic and geostrophic adjustment, it follows that PV attribution does not imply a causal relationship between the far field of a PV anomaly and the anomaly itself.
Bidimensional Diagnostics, Variability, and Trends of Northern Hemisphere Blocking
Authors: Davini Paolo , Cagnazzo Chiara , Gualdi Silvio , Navarra Antonio 
Published: April 2012

AbstractIn this paper, Northern Hemisphere winter blocking is analyzed through the introduction of a set of new bidimensional diagnostics based on geopotential height that provide information about the occurrence, the duration, the intensity, and the wave breaking associated with the blocking. This analysis is performed with different reanalysis datasets in order to evaluate the sensitivity of the index and the diagnostics adopted. In this way, the authors are able to define a new category of blocking placed at low latitudes that is similar to midlatitude blocking in terms of the introduced diagnostics but is unable to divert or block the flow. Furthermore, over the Euro-Atlantic sector it is shown that it is possible to phenomenologically distinguish between high-latitude blocking occurring over Greenland, north of the jet stream and dominated by cyclonic wave breaking, and the traditional midlatitude blocking localized over Europe and driven by anticyclonic wave breaking. These latter events are uniformly present in a band ranging from the Azores up to Scandinavia. Interestingly, a similar distinction cannot be pointed out over the Pacific basin where the blocking activity is dominated by high-latitude blocking occurring over eastern Siberia. Finally, considering the large impact that blocking may have on the Northern Hemisphere, an analysis of the variability and the trend is carried out. This shows a significant increase of Atlantic low-latitude blocking frequency and an eastward displacement of the strongest blocking events over both the Atlantic and Pacific Oceans.
Empirical Correction of XBT Data
Authors: Hamon M. , Reverdin G. , Le Traon P.-Y. 
Published: April 2012

Abstract
The authors use a collocation method between XBT and CTD/Ocean Station Data (OSD; including bottle cast and low-resolution CTD) from World Ocean Database 2005 (WOD2005) to statistically correct the XBT fall rate. An analysis of the annual median bias on depth shows that it is necessary to apply a thermal correction, a second-order correction on the depth, as well as a depth offset representing measurement errors during XBT deployment. Data were separated into several categories: shallow and deep XBTs and below or above 10°C of vertically averaged ocean temperatures (in the top 400 m). Also, XBT measurements in the western Pacific between 1968 and 1985 were processed separately because of large regional biases. The estimated corrections deviate from other published estimates with some large variations in time of both linear and curvature terms in the depth corrections, and less time variation of the temperature correction for the deep XBTs. This analysis of heat content derived from corrected XBTs provides at first order a similar variability to other estimates from corrected XBTs and mechanical bathythermographs (MBTs). It shows a fairly prominent trend in 0–700-m ocean heat content of 0.39 × 1022 J yr−1 between 1970 and 2008.
Effects of Functional Fascial Taping on pain and function in patients with non-specific low back pain: a pilot randomized controlled trial
Authors: Chen Shu-Mei , Alexander Ron , Lo Sing Kai , Cook Jill 
Published: April 2012

Objectives: To compare the short-term and medium-term effect of Functional Fascial Taping to placebo taping on pain and function in people with non-specific low back pain. Design: A pilot randomized controlled trial with a 2-week intervention, and 2-, 6- and 12-week follow-up. Setting: Individuals with non-specific low back pain recruited from local communities. Participants: Forty-three participants with non-specific low back pain for more than 6 weeks were randomized into either Functional Fascial Taping group ( n = 21) or placebo group ( n = 22). Interventions: The intervention group was treated with Functional Fascial Taping while the control group was treated with placebo taping. Both groups received four treatments over 2 weeks. Main outcome measures: Worst and average pain and function were assessed at baseline, after the 2-week intervention, and at 6 and 12 weeks follow-up. Results: The Functional Fascial Taping group demonstrated significantly greater reduction in worst pain compared to placebo group after the 2-week intervention ( P = 0.02, effect size = 0.74; 95% confidence interval 0.11–1.34). A higher proportion of participants in Functional Fascial Taping group attained the minimal clinically important difference in worst pain ( P = 0.007) and function ( P = 0.007) than those in placebo group after the 2-week intervention. There were no significant differences in either group’s disability rating or clinically important difference in average pain at any time. Conclusions: Functional Fascial Taping reduced worst pain in patients with non-acute non-specific low back pain during the treatment phase. No medium-term differences in pain or function were observed.
Phenotype diversity in type 1 Gaucher disease: discovering the genetic basis of Gaucher disease/hematologic malignancy phenotype by individual genome analysis
Authors: Lo Sarah M. , Choi Murim , Liu Jun , Jain Dhanpat , Boot Rolf G. , Kallemeijn Wouter W. , Aerts Johannes M. F. G. , Pashankar Farzana , Kupfer Gary M. , Mane Shrikant , Lifton Richard P. , Mistry Pramod K. 
Published: April 2012

AbstractGaucher disease (GD), an inherited macrophage glycosphingolipidosis, manifests with an extraordinary variety of phenotypes that show imperfect correlation with mutations in the GBA gene. In addition to the classic manifestations, patients suffer from increased susceptibility to hematologic and nonhematologic malignancies. The mechanism(s) underlying malignancy in GD is not known, but is postulated to be secondary to macrophage dysfunction and immune dysregulation arising from lysosomal accumulation of glucocerebroside. However, there is weak correlation between GD/cancer phenotype and the systemic burden of glucocerebroside-laden macrophages. Therefore, we hypothesized that genetic modifier(s) may underlie the GD/cancer phenotype. In the present study, the genetic basis of GD/T-cell acute lymphoblastic lymphoma in 2 affected siblings was deciphered through genomic analysis. GBA gene sequencing revealed homozygosity for a novel mutation, D137N. Whole-exome capture and massively parallel sequencing combined with homozygosity mapping identified a homozygous novel mutation in the MSH6 gene that leads to constitutional mismatch repair deficiency syndrome and increased cancer risk. Enzyme studies demonstrated that the D137N mutation in GBA is a pathogenic mutation, and immunohistochemistry confirmed the absence of the MSH6 protein. Therefore, precise phenotype annotation followed by individual genome analysis has the potential to identify genetic modifiers of GD, facilitate personalized management, and provide novel insights into disease pathophysiology.
Runx1 regulates embryonic myeloid fate choice in zebrafish through a negative feedback loop inhibiting Pu.1 expression
Authors: Jin Hao , Li Li , Xu Jin , Zhen Fenghua , Zhu Lu , Liu P. Paul , Zhang Mingjie , Zhang Wenqing , Wen Zilong 
Published: April 2012

AbstractProper cell fate choice in myelopoiesis is essential for generating correct numbers of distinct myeloid subsets manifesting a wide spectrum of subset-specific activities during development and adulthood. Studies have suggested that myeloid fate choice is primarily regulated by transcription factors; however, new intrinsic regulators and their underlying mechanisms remain to be elucidated. Zebrafish embryonic myelopoiesis gives rise to neutrophils and macrophages and represents a promising system to derive new regulatory mechanisms for myeloid fate decision in vertebrates. Here we present an in vivo study of cell fate specification during zebrafish embryonic myelopoiesis through characterization of the embryos with altered Pu.1, Runx1 activity alone, or their combinations. Genetic analysis shows that low and high Pu.1 activities determine embryonic neutrophilic granulocyte and macrophage fate, respectively. Inactivation and overexpression of Runx1 in zebrafish uncover Runx1 as a key embryonic myeloid fate determinant that favors neutrophil over macrophage fate. Runx1 is induced by high Pu.1 level and in turn transrepresses pu.1 expression, thus constituting a negative feedback loop that fashions a favorable Pu.1 level required for balanced fate commitment to neutrophils versus macrophages. Our findings define a Pu.1-Runx1 regulatory loop that governs the equilibrium between distinct myeloid fates by assuring an appropriate Pu.1 dosage.
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data
Authors: Peterson Elena S , McCue Lee Ann , Schrimpe-Rutledge Alexandra C , Jensen Jeffrey L , Walker Hyunjoo , Kobold Markus A , Webb Samantha R , Payne Samuel H , Ansong Charles , Adkins Joshua N , Cannon William R , Webb-Robertson Bobbie-Jo M 
Published: April 2012

Abstract

Background
The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates.

Results
VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data.

Conclusions
VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php.