bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Molecular Methods To Improve the Detection of Burkholderia pseudomallei in Soil and Water Samples from Laos
Authors: Knappik Michael , Dance David A. B. , Rattanavong Sayaphet , Pierret Alain , Ribolzi Olivier , Davong Viengmon , Silisouk Joy , Vongsouvath Manivanh , Newton Paul N. , Dittrich Sabine 
Published: March 2015

ABSTRACT

Burkholderia pseudomallei
is the cause of melioidosis, a severe and potentially fatal disease of humans and animals. It is endemic in northern Australia and Southeast Asia and is found in soil and surface water. The environmental distribution of
B. pseudomallei
worldwide and within countries where it is endemic, such as the Lao People's Democratic Republic (Laos), remains unclear. However, this knowledge is important to our understanding of the ecology and epidemiology of
B. pseudomallei
and to facilitate public health interventions. Sensitive and specific methods to detect
B. pseudomallei
in environmental samples are therefore needed. The aim of this study was to compare molecular and culture-based methods for the detection of
B. pseudomallei
in soil and surface water in order to identify the optimal approach for future environmental studies in Laos. Molecular detection by quantitative real-time PCR (qPCR) was attempted after DNA extraction directly from soil or water samples or after an overnight enrichment step. The positivity rates obtained by qPCR were compared to those obtained by different culture techniques. The rate of detection from soil samples by qPCR following culture enrichment was significantly higher (84/100) than that by individual culture methods and all culture methods combined (44/100;
P
< 0.001). Similarly, qPCR following enrichment was the most sensitive method for filtered river water compared with the sensitivity of the individual methods and all individual methods combined. In conclusion, molecular detection following an enrichment step has proven to be a sensitive and reliable approach for
B. pseudomallei
detection in Lao environmental samples and is recommended as the preferred method for future surveys.
Lincomycin at Subinhibitory Concentrations Potentiates Secondary Metabolite Production by Streptomyces spp
Authors: Imai Yu , Sato Seizo , Tanaka Yukinori , Ochi Kozo , Hosaka Takeshi 
Published: March 2015

ABSTRACT

Antibiotics have either bactericidal or bacteriostatic activity. However, they also induce considerable gene expression in bacteria when used at subinhibitory concentrations (below the MIC). We found that lincomycin, which inhibits protein synthesis by binding to the ribosomes of Gram-positive bacteria, was effective for inducing the expression of genes involved in secondary metabolism in
Streptomyces
strains when added to medium at subinhibitory concentrations. In
Streptomyces coelicolor
A3(2), lincomycin at 1/10 of its MIC markedly increased the expression of the pathway-specific regulatory gene
act
II-ORF4 in the blue-pigmented antibiotic actinorhodin (ACT) biosynthetic gene cluster, which resulted in ACT overproduction. Intriguingly,
S. lividans
1326 grown in the presence of lincomycin at a subinhibitory concentration (1/12 or 1/3 of its MIC) produced abundant antibacterial compounds that were not detected in cells grown in lincomycin-free medium. Bioassay and mass spectrometry analysis revealed that some antibacterial compounds were novel congeners of calcium-dependent antibiotics. Our results indicate that lincomycin at subinhibitory concentrations potentiates the production of secondary metabolites in
Streptomyces
strains and suggest that activating these strains by utilizing the dose-response effects of lincomycin could be used to effectively induce the production of cryptic secondary metabolites. In addition to these findings, we also report that lincomycin used at concentrations for markedly increased ACT production resulted in alteration of the cytoplasmic protein (F
o
F
1
ATP synthase α and β subunits, etc.) profile and increased intracellular ATP levels. A fundamental mechanism for these unique phenomena is also discussed.
Role of Pex11p in Lipid Homeostasis in Yarrowia lipolytica
Authors: Dulermo Rémi , Dulermo Thierry , Gamboa-Meléndez Heber , Thevenieau France , Nicaud Jean-Marc 
Published: March 2015

ABSTRACT

Peroxisomes are essential organelles in the cells of most eukaryotes, from yeasts to mammals. Their role in β-oxidation is particularly essential in yeasts; for example, in
Saccharomyces cerevisiae
, fatty acid oxidation takes place solely in peroxisomes. In this species, peroxisome biogenesis occurs when lipids are present in the culture medium, and it involves the Pex11p protein family: ScPex11p, ScPex25p, ScPex27p, and ScPex34p.
Yarrowia lipolytica
has three Pex11p homologues, which are YALI0C04092p (YlPex11p), YALI0C04565p (YlPex11C), and YALI0D25498p (Pex11/25p). We found that these genes are regulated by oleic acid, and as has been observed in other organisms,
YlPEX11
deletion generated giant peroxisomes when mutant yeast were grown in oleic acid medium. Moreover, Δ
Ylpex11
was unable to grow on fatty acid medium and showed extreme dose-dependent sensitivity to oleic acid. Indeed, when the strain was grown in minimum medium with 0.5% glucose and 3% oleic acid, lipid body lysis and cell death were observed. Cell death and lipid body lysis may be partially explained by an imbalance in the expression of the genes involved in lipid storage, namely,
DGA1
,
DGA2
, and
LRO1
, as well as that of
TGL4
, which is involved in lipid remobilization.
TGL4
deletion and
DGA2
overexpression resulted in decreased oleic acid sensitivity and delayed cell death of Δ
Ylpex11
, which probably stemmed from the release of free fatty acids into the cytoplasm. All these results show that YlPex11p plays an important role in lipid homeostasis in
Y. lipolytica
.
In Vivo
Function of PTEX88 in Malaria Parasite Sequestration and Virulence
Authors: Matz Joachim M. , Ingmundson Alyssa , Costa Nunes Jean , Stenzel Werner , Matuschewski Kai , Kooij Taco W. A. 
Published: March 2015

ABSTRACT

Malaria pathology is linked to remodeling of red blood cells by eukaryotic
Plasmodium
parasites. Central to host cell refurbishment is the trafficking of parasite-encoded virulence factors through the
Plasmodium
translocon of exported proteins (PTEX). Much of our understanding of its function is based on experimental work with cultured
Plasmodium falciparum
, yet direct consequences of PTEX impairment during an infection remain poorly defined. Using the murine malaria model parasite
Plasmodium berghei
, it is shown here that efficient sequestration to the pulmonary, adipose, and brain tissue vasculature is dependent on the PTEX components thioredoxin 2 (TRX2) and PTEX88. While
TRX2
-deficient parasites remain virulent,
PTEX88
-deficient parasites no longer sequester in the brain, correlating with abolishment of cerebral complications in infected mice. However, an apparent trade-off for virulence attenuation was spleen enlargement, which correlates with a strongly reduced schizont-to-ring-stage transition. Strikingly, general protein export is unaffected in
PTEX88
-deficient mutants that mature normally
in vitro
. Thus, PTEX88 is pivotal for tissue sequestration
in vivo
, parasite virulence, and preventing exacerbation of spleen pathology, but these functions do not correlate with general protein export to the host erythrocyte. The presented data suggest that the protein export machinery of
Plasmodium
parasites and their underlying mechanistic features are considerably more complex than previously anticipated and indicate challenges for targeted intervention strategies.
The SrkA Kinase Is Part of the SakA Mitogen-Activated Protein Kinase Interactome and Regulates Stress Responses and Development in Aspergillus nidulans
Authors: Jaimes-Arroyo Rafael , Lara-Rojas Fernando , Bayram Özgür , Valerius Oliver , Braus Gerhard H. , Aguirre Jesús 
Published: March 2015

ABSTRACT

Fungi and many other eukaryotes use specialized mitogen-activated protein kinases (MAPK) of the Hog1/p38 family to transduce environmental stress signals. In
Aspergillus nidulans
, the MAPK SakA and the transcription factor AtfA are components of a central multiple stress-signaling pathway that also regulates development. Here we characterize SrkA, a putative MAPK-activated protein kinase, as a novel component of this pathway. Δ
srkA
and Δ
sakA
mutants share a derepressed sexual development phenotype. However, Δ
srkA
mutants are not sensitive to oxidative stress, and in fact,
srkA
inactivation partially suppresses the sensitivity of Δ
sakA
mutant conidia to H
2
O
2
, tert-butyl-hydroperoxide (
t
-BOOH), and menadione. In the absence of stress, SrkA shows physical interaction with nonphosphorylated SakA in the cytosol. We show that H
2
O
2
induces a drastic change in mitochondrial morphology consistent with a fission process and the relocalization of SrkA to nuclei and mitochondria, depending on the presence of SakA. SakA-SrkA nuclear interaction is also observed during normal asexual development in dormant spores. Using SakA and SrkA S-tag pulldown and purification studies coupled to mass spectrometry, we found that SakA interacts with SrkA, the stress MAPK MpkC, the PPT1-type phosphatase AN6892, and other proteins involved in cell cycle regulation, DNA damage response, mRNA stability and protein synthesis, mitochondrial function, and other stress-related responses. We propose that oxidative stress induces DNA damage and mitochondrial fission and that SakA and SrkA mediate cell cycle arrest and regulate mitochondrial function during stress. Our results provide new insights into the mechanisms by which SakA and SrkA regulate the remodelling of cell physiology during oxidative stress and development.
Systematic Knowledge Engineering: Building Bodies of Knowledge from Published Research
Authors: Biffl Stefan , Kalinowski Marcos , Rabiser Rick , Ekaputra Fajar , Winkler Dietmar 
Published: March 2015

Context. Software engineering researchers conduct systematic literature reviews (SLRs) to build bodies of knowledge (BoKs). Unfortunately, relevant knowledge collected in the SLR process is not publicly available, which considerably slows down building BoKs incrementally. Objective. We present and evaluate the Systematic Knowledge Engineering (SKE) process to support efficiently building BoKs from published research. Method. SKE is based on the SLR process and on Knowledge Engineering practices to build a Knowledge Base (KB) by reusing intermediate data extraction results from SLRs. We evaluated the feasibility of applying SKE by building a Software Inspection BoK KB from published experiments and a Software Product Line BoK KB from published experience reports. We compared the effort, benefits, and risks of building BoK KBs regarding the SKE and the traditional SLR processes. Results. The application of SKE for incrementally collecting and organizing knowledge in the context of a BoK was feasible for different domains and different types of evidence. While the efforts for conducting the SKE and traditional SLR processes are comparable, SKE provides significant benefits for building BoKs. Conclusions. SKE enables researchers in a scientific community to reuse and incrementally build knowledge in a BoK. SKE is ready to be evaluated in other software engineering domains.
Keratin 19, a Cancer Stem Cell Marker in Human Hepatocellular Carcinoma
Authors: Kawai Takayuki , Yasuchika Kentaro , Ishii Takamichi , Katayama Hokahiro , Yoshitoshi Elena Yukie , Ogiso Satoshi , Kita Sadahiko , Yasuda Katsutaro , Fukumitsu Ken , Mizumoto Masaki , Hatano Etsuro , Uemoto Shinji 
Published: March 2015

Abstract
Purpose: Keratin 19 (K19) is a known marker of poor prognosis and invasion in human hepatocellular carcinoma (HCC). However, the relationship between K19 and cancer stem cells (CSCs) is unclear. Here, we determined whether K19 can be used as a new CSC marker and therapeutic target in HCC.
Experimental Design: HCC cell lines were transfected with a K19 promoter–driven enhanced green fluorescence protein gene. CSC characteristics, epithelial–mesenchymal transition (EMT), and TGFb/Smad signaling were examined in FACS-isolated K19+/K19− cells. K19 and TGFb receptor 1 (TGFbR1) expression in 166 consecutive human HCC surgical specimens was examined immunohistochemically.
Results: FACS-isolated single K19+ cells showed self-renewal and differentiation into K19− cells, whereas single K19− cells did not produce K19+ cells. K19+ cells displayed high proliferation capacity and 5-fluorouracil resistance in vitro. Xenotransplantation into immunodeficient mice revealed that K19+ cells reproduced, differentiated into K19− cells, and generated large tumors at a high frequency in vivo. K19+ cells were found to be involved in EMT and the activation of TGFb/Smad signaling, and these properties were suppressed by K19 knockdown or treatment with a TGFbR1 inhibitor. The TGFbR1 inhibitor also showed high therapeutic effect against K19+ tumor in the mouse xenograft model. Immunohistochemistry of HCC specimens showed that compared with K19− patients, K19+ patients had significantly poorer recurrence-free survival and higher tumor TGFbR1 expression.
Conclusions: K19 is a new CSC marker associated with EMT and TGFb/Smad signaling, and it would thus be a good therapeutic target for TGFbR1 inhibition. Clin Cancer Res; 21(13); 3081–91. ©2015 AACR.
All-Arthroscopic Suprapectoral Versus Open Subpectoral Tenodesis of the Long Head of the Biceps Brachii
Authors: Gombera Mufaddal Mustafa , Kahlenberg Cynthia A. , Nair Rueben , Saltzman Matthew D. , Terry Michael A. 
Published: March 2015

Background: Pathologic changes of the long head of the biceps tendon are a recognized source of shoulder pain in adults that can be treated with tenotomy or tenodesis when nonoperative measures are not effective. It is not clear whether arthroscopic or open biceps tenodesis has a clinical advantage. Hypothesis: Pain relief and shoulder function after all-arthroscopic suprapectoral biceps tenodesis are similar to outcomes after an open subpectoral tenodesis. Study Design: Cohort study; Level of evidence, 3. Methods: A prospective database was reviewed for patients undergoing an all-arthroscopic suprapectoral or open subpectoral biceps tenodesis. Adult patients with a minimum 18-month follow-up were included. Patients undergoing a concomitant rotator cuff or labral repair were excluded. The groups were matched to age within 3 years, sex, and time to follow-up within 3 months. Pain improvement, development of a “Popeye” deformity, muscle cramping, postoperative American Shoulder and Elbow Surgeons scores, satisfaction scores, and complications were evaluated. Results: Forty-six patients (23 all-arthroscopic, 23 open) with an average age of 57.2 years (range, 45-70 years) were evaluated at a mean follow-up of 30.1 months (range, 21.1-44.9 months). No patients in either group developed a Popeye deformity or complained of arm cramping. There was no significant difference in mean American Shoulder and Elbow Surgeons scores between the open and all-arthroscopic groups (92.3 vs 88.9; P = .42); similarly, there was no significant difference in patient satisfaction scores between the groups (8.9 vs 9.1; P = .73). Eighteen patients (78.3%) in the arthroscopic cohort and 16 (69.6%) in the open cohort fully returned to athletic activity ( P = .50). Eight patients (34.8%) in the arthroscopic group and 10 (39.1%) in the open group reported pain at night or with heavy activities. There were no complications in the all-arthroscopic group. There were 2 complications in the open group that resolved by final follow-up. Conclusion: Biceps tenodesis remains a reliable treatment for pathologic abnormality of the long head of the biceps. Patients undergoing an all-arthroscopic suprapectoral tenodesis in the distal aspect or distal to the bicipital groove showed similar pain relief and clinical outcomes as compared with patients undergoing open subpectoral tenodesis. Open subpectoral biceps tenodesis may carry a higher complication risk secondary to a more invasive technique.
Gender differences in HIV risk behaviors in individuals recently released from prison: results of a pilot study
Authors: Zhu Gefei A , Birnbaum Nathan , Carroll-Scott Amy , Evans Linda , Fiellin Lynn E , Wang Emily A 
Published: March 2015

Abstract

Background
Individuals recently released from prison engage in risky behaviors that predispose them to contracting HIV. Women may be at increased risk in the immediate period post-release, given higher rates of poverty, food insecurity, and substance dependence and lower educational attainment compared with men.

Methods
We describe gender differences in HIV risk behaviors using validated measures and assess potential mediators of this relationship using data from a cross-sectional study of 109 individuals recently released from prison.

Results
Women had higher rates of HIV drug-related risk behaviors compared with men (mean score 2.72 vs. 0.068; p = .003) and HIV sex-related risk behaviors (mean score 4.32 vs. 2.31; p = .016). Women also had higher mean incomes and severity of drug and alcohol use compared with men, but equally high rates of food insecurity and low levels of AIDS knowledge. In multivariate analysis, the relationship between gender and HIV drug-related and sex-related risk behaviors was attenuated by a greater monthly income ([drug] adjusted β 0.82, 95% CI -1.02 – 2.66, p = 0.38; [sex] adjusted β 0.75, 95% CI -1.04 – 2.54, p = 0.41), as well as severity of drug use ([drug] adjusted β 0.79, 95% CI -0.55 – 2.13, p = 0.24; [sex] adjusted β 0.09, 95% CI -1.17 – 1.35, p = 0.89).

Conclusions
Women had higher rates of HIV risk behaviors compared with men post-release. Gender specific interventions may be useful in reducing risky drug-related and sex-related behaviors in the period immediately following release.
Development and application of a robust chronostratigraphic framework in Gulf of Mexico Mesozoic exploration
Authors: Olson Hilary Clement , Snedden John W. , Cunningham Robert 
Published: March 2015

Renewed interest in Mesozoic exploration, onshore and offshore, in the Gulf of Mexico (GOM) has precipitated a new look at Mesozoic biostratigraphy and how these age-diagnostic bioevents can help to establish a sequence-stratigraphic framework for the basin. We have developed a new chronostratigraphic framework, primarily founded on biostratigraphic age-diagnostic data, specifically developed for Mesozoic strata of the GOM basin. Our goal was to provide a systematic and consistent framework that serves as a reference for the order and timing of depositional sequences and key surfaces in the GOM Mesozoic stratigraphic section. The new chronostratigraphic framework was based on (1) our work delineating significant physical stratigraphic surfaces from seismic and well-log data in the GOM, (2) Mesozoic biostratigraphic data from 202 onshore and offshore wells in the GOM, and (3) published literature from the GOM and other studies. The chronostratigraphic framework was formalized in an online Mesozoic biostratigraphy table and summarized in a Mesozoic stratigraphy chart. The use of the framework was key to our ability to correlate within the GOM basin, and we evaluated several examples of seismic and well-log interpretation using the new chronostratigraphic framework, including onshore-offshore correlation, identification and correlation of source rocks, and interpretation of structural anomalies. These examples illustrated how the chronostratigraphic framework enabled us to reduce uncertainty in identifying and correlating Mesozoic units from land to the deepwater GOM basin. The framework also allowed us to better compare our work with other research groups, within academia and industry, and permitted a higher level of integration of work and comments from various applied industry workers.
The Ovary Is an Alternative Site of Origin for High-Grade Serous Ovarian Cancer in Mice
Authors: Kim Jaeyeon , Coffey Donna M. , Ma Lang , Matzuk Martin M. 
Published: March 2015

Abstract
Although named “ovarian cancer,” it has been unclear whether the cancer actually arises from the ovary, especially for high-grade serous carcinoma (HGSC), also known as high-grade serous ovarian cancer, the most common and deadliest ovarian cancer. In addition, the tumor suppressor p53 is the most frequently mutated gene in HGSC. However, whether mutated p53 can cause HGSC remains unknown. In this study, we bred a p53 mutation, p53R172H, into conditional Dicer-Pten double-knockout (DKO) mice, a mouse model duplicating human HGSC, to generate triple-mutant (TKO) mice. Like DKO mice, these TKO mice develop metastatic HGSCs originating from the fallopian tube. Unlike DKO mice, however, even after fallopian tubes are removed in TKO mice, ovaries alone can develop metastatic HGSCs, indicating that a p53 mutation can drive HGSC arising from the ovary. To confirm this, we generated p53R172H-Pten double-mutant mice, one of the genetic control lines for TKO mice. As anticipated, these double-mutant mice also develop metastatic HGSCs from the ovary, verifying the HGSC-forming ability of ovaries with a p53 mutation. Our study therefore shows that ovaries harboring a p53 mutation, as well as fallopian tubes, can be a distinct tissue source of high-grade serous ovarian cancer in mice.
Adiponectin-Mediated Antilipotoxic Effects in Regenerating Pancreatic Islets
Authors: Ye Risheng , Wang Miao , Wang Qiong A. , Scherer Philipp E. 
Published: March 2015

Abstract
Pathways that stimulate β-cell regeneration remain of great clinical interest, yet effective therapeutic avenues that promote survival or reconstitution of β-cell mass remain elusive. Using a mouse model with inducible β-cell apoptosis followed by adiponectin-mediated regeneration, we aimed to identify key molecules boosting β-cell viability. In the regenerating pancreatic islets, we examined changes within the transcriptome and observed an extensive up-regulation of genes encoding proteins involved in lipid transport and metabolism. The most prominent targets were further confirmed by quantitative PCR and immunofluorescence. Among the upstream regulators predicted by pathway analysis of the transcriptome, we detected enhanced levels of 2 key transcription factors, Hepatocyte Nuclear Factor 4α and Peroxisome Proliferator-Activated Receptorα. Our data suggest that improving pancreatic islet lipid metabolism as an important antilipotoxic phenomenon to boost β-cell regeneration. This is primarily mediated by the adipokine adiponectin that exerts its action on both the beta-cell directly as well as on the adipocyte. Adiponectin induces lipid metabolism gene expression in regenerating islets through Hepatocyte Nuclear Factor 4α and Peroxisome Proliferator-Activated Receptorα. Adiponectin also modulates leptin levels via preserving adipose tissue mass in the insulinopenic state.
An Origin of Complicated Infrared Spectra of Perfluoroalkyl Compounds Involving a Normal Alkyl Group
Authors: Hasegawa Takeshi , Shimoaka Takafumi , Tanaka Yuki , Shioya Nobutaka , Morita Kohei , Sonoyama Masashi , Amii Hideki , Takagi Toshiyuki , Kanamori Toshiyuki 
Published: March 2015

Abstract
Perfluoroalkyl (Rf) compounds containing a normal alkyl group often yield highly complicated infrared (IR) spectra especially in the C–F stretching vibration (νC–F) region. To reveal the reason behind this, the IR p-polarized multiple-angle incidence resolution spectrometry (pMAIRS) is employed to measure a monolayer of CF3(CF2)9(CH2)3COOH deposited on a silicon substrate. The compound is known to spontaneously aggregate to form a molecular assembly with the closest packing, in which the molecules are oriented perpendicular to the substrate. The IR pMAIRS spectra apparently prove that the complexity of the νC–F region is due to the normal alkyl part directly connected to the Rf group because the carbons in the Rf group are vibrated as a coupled oscillator, and the oscillation of the alkyl part propagates to the Rf part along the molecular axis.