Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular cloning of the protocatechuate 4,5-dioxygenase genes of Pseudomonas paucimobilis

We determined the nucleotide sequence of a 1.9-kilobase fragment of Pseudomonas paucimobilis SYK6 chromosomal DNA that included genes encoding protocatechuate 4,5-dioxygenase, the enzyme responsible for the aromatic ring fission of protocatechuate. Two open reading frames of 417 and 906 base pairs were found that had no homology with previously reported sequences, including those encoding protocatechuate 3,4-dioxygenase. Since both open reading frames were indispensable for the enzyme activity, they should encode the subunits of protocatechuate 4,5-dioxygenase. We named these genes ligA and ligB. Protocatechuate 4,5-dioxygenase was efficiently expressed in Escherichia coli with the aid of the lac promoter, and the polypeptides of the ligA and ligB gene products were identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and amino acid sequencing.
Randomized Soil Survey of the Distribution of Burkholderia pseudomallei in Rice Fields in Laos

ABSTRACT Melioidosis is a major cause of morbidity and mortality in Southeast Asia, where the causative organism (Burkholderia pseudomallei) is present in the soil. In the Lao People's Democratic Republic (Laos), B. pseudomallei is a significant cause of sepsis around the capital, Vientiane, and has been isolated in soil near the city, adjacent to the Mekong River. We explored whether B. pseudomallei occurs in Lao soil distant from the Mekong River, drawing three axes across northwest, northeast, and southern Laos to create nine sampling areas in six provinces. Within each sampling area, a random rice field site containing a grid of 100 sampling points each 5 m apart was selected. Soil was obtained from a depth of 30 cm and cultured for B. pseudomallei. Four of nine sites (44%) were positive for B. pseudomallei, including all three sites in Saravane Province, southern Laos. The highest isolation frequency was in east Saravane, where 94% of soil samples were B. pseudomallei positive with a geometric mean concentration of 464 CFU/g soil (95% confidence interval, 372 to 579 CFU/g soil; range, 25 to 10,850 CFU/g soil). At one site in northwest Laos (Luangnamtha), only one sample (1%) was positive for B. pseudomallei, at a concentration of 80 CFU/g soil. Therefore, B. pseudomallei occurs in Lao soils beyond the immediate vicinity of the Mekong River, alerting physicians to the likelihood of melioidosis in these areas. Further studies are needed to investigate potential climatic, soil, and biological determinants of this heterogeneity.
MNNG-induced Cell Death Is Controlled by Interactions between PARP-1, Poly(ADP-ribose) Glycohydrolase, and XRCC1*

PARP-1 (poly(ADP-ribose) polymerases) modifies proteins with poly(ADP-ribose), which is an important signal for genomic stability. ADP-ribose polymers also mediate cell death and are degraded by poly(ADP-ribose) glycohydrolase (PARG). Here we show that the catalytic domain of PARG interacts with the automodification domain of PARP-1. Furthermore, PARG can directly down-regulate PARP-1 activity. PARG also interacts with XRCC1, a DNA repair factor that is recruited by DNA damage-activated PARP-1. We investigated the role of XRCC1 in cell death after treatment with supralethal doses of the alkylating agent MNNG. Only in XRCC1-proficient cells MNNG induced a considerable accumulation of poly(ADP-ribose). Similarly, extracts of XRCC1-deficient cells produced large ADP-ribose polymers if supplemented with XRCC1. Consequently, MNNG triggered in XRCC1-proficient cells the translocation of the apoptosis inducing factor from mitochondria to the nucleus followed by caspase-independent cell death. In XRCC1-deficient cells, the same MNNG treatment caused non-apoptotic cell death without accumulation of poly(ADP-ribose). Thus, XRCC1 seems to be involved in regulating a poly(ADP-ribose)-mediated apoptotic cell death.
The changing demographics of traumatic spinal cord injury: An 11-year study of 831 patients

Abstract Context/objective Traumatic spinal cord injuries (T-SCI) have a devastating impact and place a significant financial burden on the healthcare system. The incidence of T-SCI ranges from 10.4 to 83 cases per million and varies with age, sex, or geographical region. This study describes the epidemiology and demographic characteristics of patients treated for T-SCI in our region over 11 years. Design Retrospective cohort study. Setting Single Level-I trauma center in Québec, Canada. Participants Patients who sustained T-SCI between 1 April 2000 and 31 March 2011. Interventions None. Outcome measures Data concerning T-SCI patients was retrieved from the Québec Trauma Registry. Information on age, sex, trauma, level of injury, type and severity of neurological deficit (ASIA scale), and treatment was extracted. Annual, age-standardized rates of T-SCI were calculated and trends over time were examined. Results Eight hundred and thirty-one patients with T-SCI were identified. The incidence of T-SCI did not change over time but there was a 13-year increase in age between 2002 and 2010. More than 60% of patients aged 55 years or more were injured following a fall and 80% became tetraplegic. These patients were more likely to have central cord syndrome (CCS) and incomplete neurological injury, compared to younger patients. The incidence of CCS increased from 25 to 37% over 11 years. Conclusions The T-SCI population is aging and is more frequently sustaining injuries associated with CCS, incomplete neurological deficits and tetraplegia.
Prostaglandin E2 Protects the Heart From Ischemia-Reperfusion Injury via Its Receptor Subtype EP4

Background—In the heart with acute myocardial infarction, production of prostaglandin (PG) E2 increases significantly. In addition, several subtypes of PGE2 receptors (EPs) have been reported to be expressed in the heart. The role of PGE2 in cardiac ischemia-reperfusion (I/R) injury, however, remains unknown. We intended to clarify the role of PGE2 via EP4, an EP subtype, in I/R injury using mice lacking EP4 (EP4−/− mice). Methods and Results—In murine cardiac ventricle, competitive reverse transcription–polymerase chain reaction revealed the highest expression level of EP4 mRNA among EP mRNAs. EP4−/− mice had larger infarct size than wild-type mice in a model of I/R; the left anterior descending coronary artery was occluded for 1 hour, followed by 24 hours of reperfusion. In addition, isolated EP4−/− hearts perfused according to the Langendorff technique had greater functional and biochemical derangements in response to I/R than wild-type hearts. In vitro, AE1-329, an EP4 agonist, raised cAMP concentration remarkably in noncardiomyocytes, whereas the action was weak in cardiomyocytes. When 4819-CD, another EP4 agonist, was administered 1 hour before coronary occlusion, it reduced infarct size significantly in wild-type mice. Notably, a similar cardioprotective effect was observed even when it was administered 50 minutes after coronary occlusion. Conclusions—Both endogenous PGE2 and an exogenous EP4 agonist protect the heart from I/R injury via EP4. The potent cardioprotective effects of 4819-CD suggest that the compound would be useful for treatment of acute myocardial infarction.
18F-Fluromisonidazole PET Imaging as a Biomarker for the Response to 5,6-Dimethylxanthenone-4-Acetic Acid in Colorectal Xenograft Tumors

The aim of this study was to evaluate 18F-fluromisonidazole (18F-FMISO) PET for monitoring the tumor response to the antivascular compound 5,6-dimethylxanthenone-4-acetic acid (DMXAA; vadimezan). Methods: 18F-FMISO PET was performed 3 h before and 24 h after treatment with DMXAA (20 mg/kg) in mice bearing HT29 xenograft tumors. Pimonidazole was coadministered with the first 18F-FMISO injection, and 2-(2-nitro-1H-imidazol-1-yl)-N-(2,2,3,3,3-pentafluoropropyl)acetamide (EF5) was coadministered with the second one. Hoechst 33342 was administered 5 min before sacrifice. Digital autoradiograms of tumor sections were acquired; this acquisition was followed by immunofluorescence microscopic visualization of pimonidazole, EF5, the Hoechst 33342, CD31, and α-smooth muscle actin. Results: DMXAA treatment resulted in a marked reduction in the 18F-FMISO mean standardized uptake value (SUVmean) in approximately half of the treated tumors. The reduction in SUVmean correlated with a decrease in the fraction of tumor area staining positive for both EF5 and pimonidazole. Compared with untreated controls, tumors with decreasing SUVmean had significantly fewer perfused microvessels. Conclusion: 18F-FMISO PET could distinguish between different tumor responses to DMXAA treatment. However, a reduction in 18F-FMISO SUVmean after DMXAA treatment was indicative of reduced perfusion and therefore delivery of 18F-FMISO, rather than a reduction in tumor hypoxia.
Assessment of the Stereo-Radargrammetric Mapping Potential of TerraSAR-X Multibeam Spotlight Data

TerraSAR-X can acquire image data in various resolutions down to a range of about 1 m. Moreover, the sensor can operate at various imaging beams and thus acquire image data at different off-nadir viewing angles. These circumstances led to a stimulation of the traditional stereo-mapping approach, as TerraSAR-X image pairs became available in high resolution and in various geometric dispositions. With respect to 3-D surface mapping, TerraSAR-X stereo data processing, therefore, is a serious alternative to synthetic aperture radar interferometry, which can be addressed as the evolving mapping technique of the last decade. Within the TerraSAR-X science program of the German Aerospace Center (DLR), high-resolution multibeam data sets in Spotlight mode were acquired for several Austrian test sites. In general, three images were obtained from either ascending or descending orbits. In order to exploit the 3-D mapping accuracy of TerraSAR-X, stereo-radargrammetric mapping techniques were applied to the data sets, thereby utilizing stereo pairs as well as multi-image data sets in various dispositions. This paper focuses on one of the selected test sites and refers to the issues of 2-D and 3-D mapping-accuracy assessment as well as to surface model and vegetation-height-model generation. Validation of these products was widely restricted to visual analysis due to the lack of adequate high-quality reference products.
A PMMA-based micro pressure sensor chip using carbon nanotubes as sensing elements

A polymer-based MEMS pressure sensor was fabricated using bulk multi-walled carbon nanotube (MWNT) as piezoresistive sensing elements. The development of the pressure sensor includes fabrication of 300/spl mu/m thick polymethylmethacrylate (PMMA) diaphragms using SU8 molding/hot-embossing technique and AC electrophoretic manipulation of MWNT bundles on the diaphragms. We have measured the pressure-resistance dependency of these MWNT-based micro sensors and preliminary results indicated that the MWNT sensors were capable of sensing input pressure variations. Moreover, the I-V measurements of the resulting devices revealed that the nominal resistance of the sensing elements can be adjusted by annealing the MWNTs through electrical current heating, which offers a potential method for resistance-off set calibration. Based on these experimental evidences, we propose that carbon nanotubes (CNTs) is a novel material for fabricating micro pressure sensors on polymer substrates - which may serve as alternative sensors for silicon based pressure sensors when bio-compatibility and low-cost applications are required.
A Power Supply of Self-Powered Online Monitoring Systems for Power Cords

This paper presents a power supply of self-powered online monitoring systems for power cords. The proposed power supply obtains energy from the magnetic field induced by wire-carrying currents using a specially designed coil-based magnetic energy harvester (CMEH). The CMEH reduces the influence of the magnetic flux leakage and can harvest enough energy, especially when the wire-carrying current is small. The magnetic core of the CMEH contains two special C-cores and all end faces are tooth profile. The relationship between the magnetic flux leakage and the number of teeth has been analyzed. The design details of the power supply circuit including the unit for power management and overvoltage protection are given in this paper. Test results show that the overvoltage protective unit can protect the supercapacitor from over its max operating voltage. With the low dropout regulator unit function, the power supply is capable of providing a stable output voltage.
Towards Scalable Cluster Auditing through Grammatical Inference over Provenance Graphs

Investigating the nature of system intrusions in large distributed systems remains a notoriously difficult challenge. While monitoring tools (e.g., Firewalls, IDS) provide preliminary alerts through easy-to-use administrative interfaces, attack reconstruction still requires that administrators sift through gigabytes of system audit logs stored locally on hundreds of machines. At present, two fundamental obstacles prevent synergy between system-layer auditing and modern cluster monitoring tools: 1) the sheer volume of audit data generated in a data center is prohibitively costly to transmit to a central node, and 2) systemlayer auditing poses a “needle-in-a-haystack” problem, such that hundreds of employee hours may be required to diagnose a single intrusion. This paper presents Winnower, a scalable system for auditbased cluster monitoring that addresses these challenges. Our key insight is that, for tasks that are replicated across nodes in a distributed application, a model can be defined over audit logs to succinctly summarize the behavior of many nodes, thus eliminating the need to transmit redundant audit records to a central monitoring node. Specifically, Winnower parses audit records into provenance graphs that describe the actions of individual nodes, then performs grammatical inference over individual graphs using a novel adaptation of Deterministic Finite Automata (DFA) Learning to produce a behavioral model of many nodes at once. This provenance model can be efficiently transmitted to a central node and used to identify anomalous events in the cluster. We implement Winnower for Docker Swarm container clusters and evaluate our system against real-world applications and attacks. We show that Winnower dramatically reduces storage and network overhead associated with aggregating system audit logs, by as much as 98%, without sacrificing the important information needed for attack investigation. Winnower thus represents a significant step forward for security monitoring in distributed systems.
Repeat-pass SAR interferometry over forested terrain

Repeat-pass synthetic aperture radar (SAR) interferometry provides the possibility of producing topographic maps and geocoded as well as radiometrically calibrated radar images. However, the usefulness of such maps and images depends on our understanding of how different types of terrain affect the radar measurements. It is essential that the scene coherence between passes is sdcient. In this paper, we derive a general system model including both radar system and scene scattering properties. The model is used to interpret measurements over a forested area where the scene coherence varies between 0.2 and 0.5. The coherence is found to be sensitive to temperature changes around 0°C but surprisingly insensitive to wind speed. The interferometric height discontinuity at the forest to openfield boundary shows good agreement with in situ tree height measurements for a dense boreal forest, but is observed to decrease for a less dense forest. This suggests the possibility of estimating bole volume from the interferometric tree height and a ground DEM. The decrease of scene coherence over a dense forest with increasing baseline is also used to estimate the effective scattering layer thickness.
Electronic Commerce: Factors Involved in its Adoption from a Bibliometric Analysis

This article presents findings of a study that aimed to identify key factors in the adoption of e-commerce. The study involved a bibliometric analysis of statistical information from 408 scientific publications related to the theme, registered in the Scopus database, through a structured search equation. The collected records were used to calculate bibliometric indicators of quantity, quality and structure. Additionally, an analysis of increasing, decreasing, and emerging thematics was carried out to identify the topics of greatest interest on this subject. Findings indicate that this is a prolific research field, in which the fastest growing topic is the study of e-commerce adoption in small and medium sized enterprises in emerging economies. The analysis also revealed the current use of new models to evaluate adoption factors. That is the case of the Technology Organization Environment Framework used as an alternative to the Technology Acceptance Model--which remains the most widely used. Likewise, Structural Equation Analysis was found to be one of the most frequently used options for statistical analysis in the publications studied. A research agenda intending to contribute with directions for further research in the area is presented at the end of the article.
A Multistep High-Content Screening Approach to Identify Novel Functionally Relevant Target Genes in Pancreatic Cancer

In order to foster the systematic identification of novel genes with important functional roles in pancreatic cancer, we have devised a multi-stage screening strategy to provide a rational basis for the selection of highly relevant novel candidate genes based on the results of functional high-content analyses. The workflow comprised three consecutive stages: 1) serial gene expression profiling analyses of primary human pancreatic tissues as well as a number of in vivo and in vitro models of tumor-relevant characteristics in order to identify genes with conspicuous expression patterns; 2) use of ‘reverse transfection array’ technology for large-scale parallelized functional analyses of potential candidate genes in cell-based assays; and 3) selection of individual candidate genes for further in-depth examination of their cellular roles. A total of 14 genes, among them 8 from “druggable” gene families, were classified as high priority candidates for individual functional characterization. As an example to demonstrate the validity of the approach, comprehensive functional data on candidate gene ADRBK1/GRK2, which has previously not been implicated in pancreatic cancer, is presented.
A measurement procedure for viscous and coulomb friction

This paper presents a viscous and coulomb friction measurement procedure for mechanical systems equipped with high-precision velocity sensors. The proposed method exploits the structure of the velocity response predicted by several standard friction models when a force or torque is applied in a ramp fashion. Experimental results show the high accuracy of the proposed measurement procedure.
NF-kappaB activation and Fas ligand overexpression in blood and plaques of patients with carotid atherosclerosis: potential implication in plaque instability.

BACKGROUND AND PURPOSE Apoptosis is present in human atherosclerotic lesions. Nuclear factor-kappaB (NF-kappaB) is involved in the transcriptional regulation of the proapoptotic protein Fas ligand (FasL). We have analyzed NF-kappaB activation and FasL expression in atherosclerotic plaques and peripheral blood mononuclear cells (PBMCs) of patients with carotid stenosis. METHODS NF-kappaB activation and FasL and active caspase-3 expression were analyzed in 32 human carotid plaques. NF-kappaB activation and FasL mRNA were tested in PBMCs of patients and healthy volunteers. We analyzed whether the NF-kappaB inhibitor parthenolide regulates FasL expression and cytotoxicity in human T cells. RESULTS The inflammatory region of plaques showed an increase in NF-kappaB activation (3393+/-281 versus 1029+/-100 positive nuclei per mm(2), P<0.001) and FasL (16+/-1.4% versus 13+/-1.8%, P<0.05) and active caspase-3 (3.3+/-0.6 versus 1.5+/-0.3%, P<0.05) expression compared with the fibrous area. Activated NF-kappaB and FasL protein were colocalized in plaque cells. In PBMCs obtained from those patients the day of endarterectomy, NF-kappaB activation and FasL expression were significantly increased compared with healthy controls (1.5+/-0.1 versus 0.5+/-0.1 and 2.1+/-0.1 versus 1.2+/-0.1 arbitrary units, respectively; P<0.001). There was a significant correlation between NF-kappaB activation and FasL expression. In activated T cells, parthenolide decreased NF-kappaB activation, FasL promoter activity, and mRNA expression. Parthenolide also decreased cytotoxicity of activated Jurkat cells on FasL-sensitive cells. CONCLUSIONS NF-kappaB activation and FasL overexpression occur in PBMCs and atherosclerotic lesions of patients with carotid stenosis. The NF-kappaB-FasL pathway could be involved in the mechanisms underlying plaque instability in humans.
Design and Analysis of W-Band Injection-Locked Frequency Divider Using Split Transformer-Coupled Oscillator Technique

A W-band injection-locked frequency divider (ILFD) with low-power and wide locking range is presented in this paper. The operation frequency and locking range are enhanced by using split transformer-coupled oscillator. The optimum bias and the size of the injection transistor are chosen to achieve wider locking range without increasing chip area and dc power consumption. The proposed ILFD is implemented in 90-nm CMOS and exhibits 25.4% locking range from 75.1 to 99 GHz at an input power of 0 dBm without any tuning mechanism. The core dc power consumption is 2.45 mW with a supply voltage of 0.7 V and the core chip size is <inline-formula> <tex-math notation="LaTeX">$0.13 \times 0.2$ </tex-math></inline-formula> mm<sup>2</sup>.
Effectiveness of Six Improved Cookstoves in Reducing Household Air Pollution and Their Acceptability in Rural Western Kenya

Background Household air pollution (HAP) from biomass fuel burning is linked to poor health outcomes. Improved biomass cookstoves (ICS) have the potential to improve HAP. Objectives A pre-/post- intervention study assessed the impact of six ICS on indoor air quality and acceptability of ICS to local users in rural Western Kenya. Methods We measured mean personal and kitchen level concentrations of particulate matter <2. 5μm in diameter (PM2.5, μg/m3) and carbon monoxide (CO, ppm) during the 48-hour period of each ICS use in 45 households. We compared these levels to those observed with traditional 3-stone fire (TSF) use. We assessed ICS acceptability through interviews and focus groups. We evaluated association of stove type, fuel use, and factors related to cooking practices with mean kitchen PM2.5 and CO using multivariable regression. Results Stove type, exclusive ICS use (vs. concurrent TSF use), and the amount of fuel used were independently associated with kitchen PM2.5 and CO levels. Reductions (95%CI) in mean PM2.5 compared to TSF, ranged by ICS from 11.9% (-2.8–24.5) to 42.3% (32.3–50.8). Reductions in kitchen CO compared to TSF, ranged by ICS from -5.8% (-21.9–8.2) to 34.5% (23.2–44.1). Mean kitchen PM2.5 ranged from 319μg/m3 to 518μg/m3 by ICS. Women thought ICS were easy to use, more efficient, produced less smoke, and cooked faster, compared to TSF. Women also reported limitations for each ICS. Conclusions We documented reductions in HAP from ICS compared to TSF. The PM2.5 levels with ICS use were still considerably higher than WHO indoor air quality guidelines. Achieving maximal potential of ICS requires adherence to more exclusive use and addressing user reported ICS limitations.