bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Models, Expression Repertoire, and Immune Response of Plasmodium vivax Reticulocyte Binding Proteins
Authors: Hietanen Jenni , Chim-ong Anongruk , Chiramanewong Thanprakorn , Gruszczyk Jakub , Roobsoong Wanlapa , Tham Wai-Hong , Sattabongkot Jetsumon , Nguitragool Wang 
Published: December 2015

ABSTRACT

Members of the
Plasmodium vivax
reticulocyte binding protein (PvRBP) family are believed to mediate specific invasion of reticulocytes by
P. vivax
. In this study, we performed molecular characterization of genes encoding members of this protein family. Through cDNA sequencing, we constructed full-length gene models and verified genes that are protein coding and those that are pseudogenes. We also used quantitative PCR to measure their
in vivo
transcript abundances in clinical
P. vivax
isolates. Like genes encoding related invasion ligands of
P. falciparum
,
Pvrbp
expression levels vary broadly across different parasite isolates. Through antibody measurements, we found that host immune pressure may be the driving force behind the distinctly high diversity of one of the family members, PvRBP2c. Mild yet significant negative correlation was found between parasitemia and the PvRBP2b antibody level, suggesting that antibodies to the protein may interfere with invasion.
Regulation of the
rhaEWRBMA
Operon Involved in
l
-Rhamnose Catabolism through Two Transcriptional Factors, RhaR and CcpA, in Bacillus subtilis
Authors: Hirooka Kazutake , Kodoi Yusuke , Satomura Takenori , Fujita Yasutaro 
Published: December 2015

ABSTRACT

The
Bacillus subtilis
rhaEWRBMA
(formerly
yuxG-yulBCDE
) operon consists of four genes encoding enzymes for
l
-rhamnose catabolism and the
rhaR
gene encoding a DeoR-type transcriptional regulator. DNase I footprinting analysis showed that the RhaR protein specifically binds to the regulatory region upstream of the
rhaEW
gene, in which two imperfect direct repeats are included. Gel retardation analysis revealed that the direct repeat farther upstream is essential for the high-affinity binding of RhaR and that the DNA binding of RhaR was effectively inhibited by
l
-rhamnulose-1-phosphate, an intermediate of
l
-rhamnose catabolism. Moreover, it was demonstrated that the CcpA/P-Ser-HPr complex, primarily governing the carbon catabolite control in
B. subtilis
, binds to the catabolite-responsive element, which overlaps the RhaR binding site.
In vivo
analysis of the
rhaEW
promoter-
lacZ
fusion in the background of
ccpA
deletion showed that the
l
-rhamnose-responsive induction of the
rhaEW
promoter was negated by the disruption of
rhaA
or
rhaB
but not
rhaEW
or
rhaM
, whereas
rhaR
disruption resulted in constitutive
rhaEW
promoter activity. These
in vitro
and
in vivo
results clearly indicate that RhaR represses the operon by binding to the operator site, which is detached by
l
-rhamnulose-1-phosphate formed from
l
-rhamnose through a sequence of isomerization by RhaA and phosphorylation by RhaB, leading to the derepression of the operon. In addition, the
lacZ
reporter analysis using the strains with or without the
ccpA
deletion under the background of
rhaR
disruption supported the involvement of CcpA in the carbon catabolite repression of the operon.

IMPORTANCE
Since
l
-rhamnose is a component of various plant-derived compounds, it is a potential carbon source for plant-associating bacteria. Moreover, it is suggested that
l
-rhamnose catabolism plays a significant role in some bacteria-plant interactions, e.g., invasion of plant pathogens and nodulation of rhizobia. Despite the physiological importance of
l
-rhamnose catabolism for various bacterial species, the transcriptional regulation of the relevant genes has been poorly understood, except for the regulatory system of
Escherichia coli
. In this study, we show that, in
Bacillus subtilis
, one of the plant growth-promoting rhizobacteria, the
rhaEWRBMA
operon for
l
-rhamnose catabolism is controlled by RhaR and CcpA. This regulatory system can be another standard model for better understanding the regulatory mechanisms of
l
-rhamnose catabolism in other bacterial species.
Model for the Controlled Synthesis of O-Antigen Repeat Units Involving the WaaL Ligase
Authors: Hong Yaoqin , Reeves Peter R. 
Published: December 2015

ABSTRACT

The Wzx/Wzy O-antigen pathway involves synthesis of a repeat unit (O unit) consisting of 3 to 8 sugars on an inner-membrane-embedded lipid carrier. These O units are translocated across the membrane to its periplasmic face by Wzx, while retaining linkage to the carrier, and then polymerized by Wzy to O-antigen polymer, which WaaL ligase transfers to a lipopolysaccharide precursor to complete lipopolysaccharide synthesis, concomitantly releasing the lipid carrier. This lipid carrier is also used for peptidoglycan assembly, and sequestration is known to be toxic. Thus, O-unit synthesis must involve precise regulation to meet demand but avoid overproduction. Here we show that loss of WaaL reverses a known growth defect in a
Salmonella
mutant that otherwise accumulates O-unit intermediates and propose that WaaL is also involved in a novel feedback mechanism to regulate O-unit synthesis, based on the availability of O units on the periplasmic face of the membrane.
Probing WWγ coupling through e−γ → νeW− at ILC
Authors: Kumar Satendra , Poulose P. 
Published: December 2015

The anomalous [Formula: see text] coupling is probed through [Formula: see text] at the ILC. With a spectacular single lepton final state, this process is well suited to study the above coupling. Cross-section measurements can probe [Formula: see text] to about [Formula: see text] for a luminosity of 100 fb[Formula: see text] at 500 GeV center-of-mass energy with unpolarized electron beam. The limits derivable on [Formula: see text] from the total cross-section are comparatively more relaxed. Exploiting the energy-angle double distribution of the secondary muons, kinematic regions sensitive to these couplings are identified. The derivable limit on [Formula: see text] could be improved to a few per-mil, focusing on such regions. More importantly, the angular distributions at fixed energy values, and energy distribution at fixed angles present very interesting possibility of distinguishing the case of [Formula: see text] and [Formula: see text].
Potential for measurement of the distribution of DNA folds in complex environments using Correlated X-ray Scattering
Authors: Schenk Gundolf , Krajina Brad , Spakowitz Andrew , Doniach Sebastian 
Published: December 2015

In vivo chromosomal behavior is dictated by the organization of genomic DNA at length scales ranging from nanometers to microns. At these disparate scales, the DNA conformation is influenced by a range of proteins that package, twist and disentangle the DNA double helix, leading to a complex hierarchical structure that remains undetermined. Thus, there is a critical need for methods of structural characterization of DNA that can accommodate complex environmental conditions over biologically relevant length scales. Based on multiscale molecular simulations, we report on the possibility of measuring supercoiling in complex environments using angular correlations of scattered X-rays resulting from X-ray free electron laser (xFEL) experiments. We recently demonstrated the observation of structural detail for solutions of randomly oriented metallic nanoparticles [D. Mendez et al., Philos. Trans. R. Soc. B 360 (2014) 20130315]. Here, we argue, based on simulations, that correlated X-ray scattering (CXS) has the potential for measuring the distribution of DNA folds in complex environments, on the scale of a few persistence lengths.
Blocking HSP90 Addiction Inhibits Tumor Cell Proliferation, Metastasis Development, and Synergistically Acts with Zoledronic Acid to Delay Osteosarcoma Progression
Authors: Ory Benjamin , Baud'huin Marc , Verrecchia Franck , Royer Bénédicte Brounais-Le , Quillard Thibaut , Amiaud Jérôme , Battaglia Séverine , Heymann Dominique , Redini Francoise , Lamoureux Francois 
Published: December 2015

Abstract
Purpose: Despite recent improvements in therapeutic management of osteosarcoma, ongoing challenges in improving the response to chemotherapy warrants the development of new strategies to improve overall patient survival. Among them, HSP90 is a molecular chaperone involved in the maturation and stability of various oncogenic proteins leading to tumor cells survival and disease progression. We assessed the antitumor properties of a synthetic HSP90 inhibitor, PF4942847, alone or in combination with zoledronic acid in osteosarcoma.
Experimental Design: The effects of PF4942847 were evaluated on human osteosarcoma cells growth and apoptosis. Signaling pathways were analyzed by Western blotting. The consequence of HSP90 therapy combined or not with zoledronic acid was evaluated in mice bearing HOS-MNNG xenografts on tumor growth, associated bone lesions, and pulmonary metastasis. The effect of PF4942847 on osteoclastogenesis was assessed on human CD14+ monocytes.
Results: In osteosarcoma cell lines, PF4942847 inhibited cell growth in a dose-dependent manner (IC50 ±50 nmol/L) and induced apoptosis with an increase of sub-G1 fraction and cleaved PARP. These biologic events were accompanied by decreased expression of Akt, p-ERK, c-Met, and c-RAF1. When administered orally to mice bearing osteosarcoma tumors, PF4942847 significantly inhibited tumor growth by 80%, prolonged survival compared with controls, and inhibited pulmonary metastases by blocking c-Met, FAK, and MMP9 signaling. In contrast to 17-allylamino-17-demethoxygeldanamycin (17-AAG), PF4942847 did not induce osteoclast differentiation, and synergistically acted with zoledronic acid to delay osteosarcoma progression and prevent bone lesions.
Conclusions: All these data provide a strong rationale for clinical evaluation of PF4942847 alone or in combination with zoledronic acid in osteosarcoma. Clin Cancer Res; 22(10); 2520–33. ©2015 AACR.
Surgical Guidance in Prostate Cancer: “From Molecule to Man” Translations
Authors: van Leeuwen Fijs W.B. , van der Poel Henk G. 
Published: December 2015

Abstract
Given the frequency of the disease and the difficulty of tumor resections, image-guided surgery technologies may aid the surgical management of prostate cancer patients. The “from molecule to man” translation of such approaches is, however, complex and depends on many different features, both from a technical and a practical perspective. Clin Cancer Res; 22(6); 1304–6. ©2015 AACR.
See related article by Sonn et al., p. 1403
The Doylestown Algorithm: A Test to Improve the Performance of AFP in the Detection of Hepatocellular Carcinoma
Authors: Wang Mengjun , Devarajan Karthik , Singal Amit G. , Marrero Jorge A. , Dai Jianliang , Feng Ziding , Rinaudo Jo Ann S. , Srivastava Sudhir , Evans Alison , Hann Hie-Won , Lai Yinzhi , Yang Hushan , Block Timothy M. , Mehta Anand 
Published: December 2015

Abstract
Biomarkers for the early diagnosis of hepatocellular carcinoma (HCC) are needed to decrease mortality from this cancer. However, as new biomarkers have been slow to be brought to clinical practice, we have developed a diagnostic algorithm that utilizes commonly used clinical measurements in those at risk of developing HCC. Briefly, as α-fetoprotein (AFP) is routinely used, an algorithm that incorporated AFP values along with four other clinical factors was developed. Discovery analysis was performed on electronic data from patients who had liver disease (cirrhosis) alone or HCC in the background of cirrhosis. The discovery set consisted of 360 patients from two independent locations. A logistic regression algorithm was developed that incorporated log-transformed AFP values with age, gender, alkaline phosphatase, and alanine aminotransferase levels. We define this as the Doylestown algorithm. In the discovery set, the Doylestown algorithm improved the overall performance of AFP by 10%. In subsequent external validation in over 2,700 patients from three independent sites, the Doylestown algorithm improved detection of HCC as compared with AFP alone by 4% to 20%. In addition, at a fixed specificity of 95%, the Doylestown algorithm improved the detection of HCC as compared with AFP alone by 2% to 20%. In conclusion, the Doylestown algorithm consolidates clinical laboratory values, with age and gender, which are each individually associated with HCC risk, into a single value that can be used for HCC risk assessment. As such, it should be applicable and useful to the medical community that manages those at risk for developing HCC. Cancer Prev Res; 9(2); 172–9. ©2015 AACR.
Patient-Specific Quantitation of Mitral Valve Strain by Computer Analysis of Three-Dimensional Echocardiography
Authors: Ben Zekry Sagit , Freeman Jeff , Jajoo Aarti , He Jiwen , Little Stephen H. , Lawrie Gerald M. , Azencott Robert , Zoghbi William A. 
Published: December 2015

Background—
A paucity of data exists on mitral valve (MV) deformation during the cardiac cycle in man. Real-time 3-dimensional (3D) echocardiography now allows dynamic volumetric imaging of the MV, thus enabling computerized modeling of MV function directly in health and disease.

Methods and Results—

MV imaging using 3D transesophageal echocardiography was performed in 10 normal subjects and 10 patients with moderate-to-severe or severe organic mitral regurgitation. Using proprietary 3D software, patient-specific models of the mitral annulus and leaflets were computed at mid- and end-systole. Strain analysis of leaflet deformation was derived from these models. In normals, mean strain intensity averaged 0.11±0.02 and was higher in the posterior leaflet than in the anterior leaflet (0.13±0.03 versus 0.10±0.02;
P
<0.05). Mean strain intensity was higher in patients with mitral regurgitation (0.15±0.03) than in normals (0.11±0.02;
P
=0.05). Higher mean strain intensity was noted for the posterior leaflet in both normal and organic valves. Regional valve analysis revealed that both anterior and posterior leaflets have the highest strain concentration in the commissural zone, and the boundary zone near the annulus and at the coaptation line, with reduced strain concentration in the central leaflet zone.

Conclusions—
In normals, MV strain is higher in the posterior leaflet, with the highest strain at the commissures, annulus, and coaptation zones. Patients with organic mitral regurgitation have higher strain than normals. Three-dimensional echocardiography allows noninvasive and patient-specific quantitation of strain intensities because of MV deformations and has the potential to improve noninvasive characterization and follow-up of MV disease.
Targeted Transthoracic Acoustic Activation of Systemically Administered Nanodroplets to Detect Myocardial Perfusion Abnormalities
Authors: Porter Thomas R. , Arena Christopher , Sayyed Samer , Lof John , High Robin R. , Xie Feng , Dayton Paul A. 
Published: December 2015

Background—
Liquid core nanodroplets containing condensed gaseous fluorocarbons can be vaporized at clinically relevant acoustic energies and have been hypothesized as an alternative ultrasound contrast agent instead of gas-core agents. The potential for targeted activation and imaging of these agents was tested with droplets formulated from liquid octafluoropropane (C3) and 1:1 mixtures of C3 with liquid decafluorobutane (C3C4).

Methods and Results—

In 8 pigs with recent myocardial infarction and variable degrees of reperfusion, transthoracic acoustic activation was attempted using 1.3 to 1.7 MHz low (0.2 mechanical index [MI]) or high MI (1.2 MI) imaging in real time (32–64 Hertz) or triggered 1:1 at end systole during a 20% C3 or C3C4 droplet infusion. Any perfusion defects observed were measured and correlated with delayed enhancement magnetic resonance imaging and postmortem staining. No myocardial contrast was produced with any imaging setting when using C3C4 droplets or C3 droplets during low MI real-time imaging. However, myocardial contrast was observed in all 8 pigs with C3 droplets when using triggered high MI imaging and in 5 of 6 pigs that had 1.7 MHz real time-high MI imaging. Although quantitative myocardial contrast was lower with real-time high MI imaging than 1:1 triggering, the correlation between real-time resting defect size and infarct size was good (
r
=0.97;
P
<0.001), as was the correlation with number of transmural infarcted segments by delayed enhancement imaging.

Conclusions—
Targeted transthoracic acoustic activation of infused intravenous C3 nanodroplets is effective, resulting in echogenic and persistent microbubbles which provide real-time high MI visualization of perfusion defects.
Validation of The Bureau of Meteorology’s Global, Diffuse, and Direct Solar Exposure Forecasts Using the ACCESS Numerical Weather Prediction Systems
Authors: Gregory Paul A. , Rikus Lawrie J. 
Published: December 2015

AbstractForecast solar exposure fields produced by the Australian Bureau of Meteorology’s updated numerical weather prediction systems were validated against multiple sites for the 2012 calendar year. The updated systems are denoted as the Australian Community Climate and Earth-System Simulator (ACCESS) model and became operational in August 2010. The systems are based on the Met Office’s Unified Model and feature improved assimilation methods and radiation parameterizations that were expected to greatly improve forecasts of solar exposure several days in advance. In this study forecasts of global, direct, and diffuse exposure from the mesoscale model ACCESS-A were validated. Statistics were generated for all-sky and clear-sky conditions. Additionally, evaluation of the model’s forecast exposure through single-layer low clouds was conducted. Results show an improvement in global forecasts relative to the older operational model; however, forecasts of diffuse and direct exposure still suffer from large biases. These can be attributed to the choices of the asymmetry factor used in the two-stream approximation for incoming radiation, which determines scattering of the direct beam through clouds.
Nonlinear Response of a Tropical Cyclone Vortex to Prescribed Eyewall Heating with and without Surface Friction in TCM4: Implications for Tropical Cyclone Intensification
Authors: Heng Junyao , Wang Yuqing 
Published: December 2015

Abstract
The recent debate on whether surface friction contributes positively or negatively to tropical cyclone (TC) intensification has been clarified based on two idealized numerical experiments, one without and the other with surface friction, using the fully compressible, nonhydrostatic TC model, version 4 (TCM4), with prescribed eyewall heating. The results show that with surface friction included, the intensification rate of the TC vortex is largely reduced, indicating that surface friction contributes negatively to TC intensification. Results from tangential wind budgets demonstrate that although surface friction largely enhances the boundary layer inflow and the contraction of the radius of maximum wind (RMW), the positive tangential wind tendency resulting from the frictionally induced inward absolute angular momentum (AAM) transport in the boundary layer is not large enough to offset the negative tendency due to the direct frictional loss of AAM to the surface. Results from the Sawyer–Eliassen equation suggest that the balanced response to eyewall heating is the major mechanism for TC intensification and the unbalanced dynamics due to the presence of surface friction seem to spin up tangential wind in the surface layer near the RMW where the flow is strongly subgradient and spin down tangential wind immediately above where the flow is strongly supergradient. Although surface friction shows an overall net negative effect on TC intensification, it plays a critical role in producing the realistic boundary layer structure with enhanced inflow, a low-level jet in tangential wind with supergradient nature, and a shallow outflow layer at the top of the inflow boundary layer.
Initial teacher training to promote health and well-being in schools – A systematic review of effectiveness, barriers and facilitators
Authors: Shepherd Jonathan , Pickett Karen , Dewhirst Sue , Byrne Jenny , Speller Viv , Grace Marcus , Almond Palo , Roderick Paul 
Published: December 2015

Objectives: To conduct a systematic review of effectiveness, and barriers and facilitators, of initial teacher training to promote health and well-being in schools. Design: Systematic review of the literature. Method: A total of 20 bibliographic databases were searched, including MEDLINE, EMBASE and the Social Science Citation Index. Studies were included if they reported research into the processes and/or outcomes of initial (pre-service) teacher training to promote health. Results: A total of 20 studies met the inclusion criteria, mainly from the UK and Australia. Twelve studies assessed outcomes, commonly using uncontrolled before and after assessment designs. Sixteen studies evaluated the processes of training. Training was diverse in terms of content, format and health topics. The studies demonstrated short-term increases in trainee teachers’ factual knowledge of health issues, a general increase in teachers’ confidence to teach about health and to identify and help children with specific health issues. There was an increase in teachers’ positive beliefs about their role in promoting children’s health. None of the studies assessed changes in pupil outcomes. The training was generally considered acceptable and adequate by trainee teachers. However, some of the trainees felt that they still lacked knowledge and confidence to address sensitive health issues on entering teaching practice. Conclusion: This systematic review identified some evidence for the effectiveness of teacher training for health and highlighted factors which facilitate and inhibit effective training. Further evaluation, using controlled trial designs with long-term follow-up of teacher and pupil outcomes, may enable teachers to effectively address the health and education needs of school pupils.
Cataloguing government documents using the MARC 21: A case study of materials from the AP Vojvodina government sessions
Authors: Rudić Gordana , Dimić Surla Bojana , Ivanović Dragan 
Published: December 2015

The paper provides suggestions for cataloguing session materials (especially minutes of sessions) using the MARC 21 Format for Bibliographic Data and MARC 21 Format for Authority Data. The suggested solution is shown on the example of materials from the government of the Autonomous Province of Vojvodina in Serbia (APV) sessions. Two business applications were developed on the basis of this MARC 21 cataloguing of the materials: a web application for searching government materials and a web application for generating various reports for the APV government. The web application supports searching metadata as well as the full text of the material and search criteria may include all of the given words or exact phrase. The examples of the reports supported by the application are: total number of sessions; total number of agenda items and sub-items; session attendance by the government members.