Miracle-dz/UniFAR-FTUs huggingface dataset:
MESNA (sodium 2-mercaptoethanesulfonate) for prevention of contrast medium-induced nephrotoxicity - controlled trial.

BACKGROUND The purpose of this study was to examine the efficacy of sodium 2-mercaptoethanesulfonate (MESNA), a reactive oxygen scavenger, in at-risk patients given radiographic contrast agents. Contrast-induced nephropathy (CIN) is a common complication of radiographic procedures; reactive oxygen species (ROS) could play a key role. METHODS We conducted a randomized, double-blinded, placebo-controlled trial in 100 patients with stable serum creatinine levels ≥ 150 µmol/l. They received an infusion of either 1,600 mg of MESNA (n = 51) or placebo (n = 49) plus 0.9% saline prior to and after contrast administration. CIN was defined as a ≥ 25% increase in serum creatinine after 48 h compared to baseline. RESULTS CIN occurred in 7 patients in the placebo group and none in the MESNA group (p = 0.005). The adjusted odds ratio for CIN was 0.17 (95% confidence interval 0.03 - 0.80, p = 0.026) in the MESNA group compared to the placebo group. Cystatin C concentrations decreased slightly in the MESNA group but increased in the control group (p < 0.05). CONCLUSION MESNA plus volume expansion before and during contrast exposure was effective in this single-center study for preventing CIN compared to volume expansion alone.
Mesenchymal Stem Cells Differentiate into an Endothelial Phenotype, Enhance Vascular Density, and Improve Heart Function in a Canine Chronic Ischemia Model

Background—Bone marrow–derived stem cells are under investigation as a treatment for ischemic heart disease. Mesenchymal stem cells (MSCs) have been used preferentially in the acute ischemia model; data in the chronic ischemia model are lacking. Methods and Results—Twelve dogs underwent ameroid constrictor placement. Thirty days later, they received intramyocardial injections of either MSCs (100×106 MSCs/10 mL saline) (n=6) or saline only (10 mL) (controls) (n=6). All were euthanized at 60 days. Resting and stress 2D echocardiography was performed at 30 and 60 days after ameroid placement. White blood cell count (WBC), C-reactive protein (CRP), creatine kinase MB (CK-MB), and troponin I levels were measured. Histopathological and immunohistochemical analyses were performed. Mean left ventricular ejection fraction was similar in both groups at baseline but significantly higher in treated dogs at 60 days. WBC and CRP levels were similar over time in both groups. CK-MB and troponin I increased from baseline to 48 hours, eventually returning to baseline. There was a trend toward reduced fibrosis and greater vascular density in the treated group. MSCs colocalized with endothelial and smooth muscle cells but not with myocytes. Conclusions—In a canine chronic ischemia model, MSCs differentiated into smooth muscle cells and endothelial cells, resulting in increased vascularity and improved cardiac function.
Methodbook: Recommending Move Method Refactorings via Relational Topic Models

During software maintenance and evolution the internal structure of the software system undergoes continuous changes. These modifications drift the source code away from its original design, thus deteriorating its quality, including cohesion and coupling of classes. Several refactoring methods have been proposed to overcome this problem. In this paper we propose a novel technique to identify Move Method refactoring opportunities and remove the Feature Envy bad smell from source code. Our approach, coined as Methodbook, is based on relational topic models (RTM), a probabilistic technique for representing and modeling topics, documents (in our case methods) and known relationships among these. Methodbook uses RTM to analyze both structural and textual information gleaned from software to better support move method refactoring. We evaluated Methodbook in two case studies. The first study has been executed on six software systems to analyze if the move method operations suggested by Methodbook help to improve the design quality of the systems as captured by quality metrics. The second study has been conducted with eighty developers that evaluated the refactoring recommendations produced by Methodbook. The achieved results indicate that Methodbook provides accurate and meaningful recommendations for move method refactoring operations.
Satellite and Station Observations Demonstrate Water Availability's Effect on Continental‐Scale Evaporative and Photosynthetic Land Surface Dynamics

Evapotranspiration and photosynthetic carbon uptake are both constrained by water availability, with presumed water‐limited and water‐independent but energy‐limited regimes. We investigate water availability's relationships with evaporative fluxes and photosynthetic measures at continental scale using surface and satellite‐based observations. The observation‐driven approach is independent of prior model‐based estimates. We find water‐limited and water‐independent regimes for both energy and carbon cycle processes in spatial and temporal aggregate, differences in water‐limitation relationships across ecohydrological regions, and more consistent signs of water limitation in photosynthetic than evaporative processes. Ecosystem water use efficiency's response to water availability changes in sign with aridity state across time and space generally but shows negative correlations in temporal anomalies.
Automatic Crater Recognition on Digital Terrain Model

This study is a topic of automatic detection of craters on DTM (Digital Terrain Model) of SELENE/LISM(TC). Automatic crater recognition has been studied as a kind of pattern-matching, which includes template matching, hereditary algorithm for making templates automatically, and application of general Hough transformation. Because general Hough transformation is able to detect ellipsoids as craters with lack of edge lines of (crater rim), we adopt this. First step is extracting edges from DTM, second is extracting candidates of craters as ellipsoids, and third is removal of miss-selecting through overlapped craters. In case of plural ellipsoids (overlapped ones, and concentric ones) verifications with ideal ellipsoids are succeeded. Order of emplacement was also confirmed. In case of verification with real data, the following types were succeeded; ellipsoids with lack of edge lines, ellipsoids with rough edge lines, and ellipsoids that departed from ellipsoid shapes. Each crater requires a set of parameters in the general Hough transformation; distance, cut-off, resolution, and threshold. In this study the set of parameters are swept for finding a crater. Smaller craters are detected, and each outline of the detected crater is deleted in order. Additional function is to record following parameters for crater statistics; diameter, coordinates, depth, and direction of incidence. We introduce preliminary results and verification of this tool in poster session.
Missing value imputation methods for gene-sample-time microarray data analysis

With the recent advances in microarray technology, the expression levels of genes with respect to the samples can be monitored synchronically over a series of time points. Such three-dimensional microarray data, termed gene-sample-time microarray data or GST data for short, may contain missing values. Current microarray analysis methods require complete data sets, and thus, either each row, column or tube containing missing values must be removed from the original GST data, or these missing values must be estimated before analysis. Imputation of missing values is, however, more recommended than removal of data in order to increase the effectiveness of analysis algorithms. In this paper, we extend automated imputation methods, devised for two-dimensional microarray data, to GST data. We implemented imputation methods for GST data based on Singular Value Decomposition (3SVDimpute), K-Nearest Neighbor (3KNNimpute), and gene and sample average methods (3Aimpute), and show that methods based on KNN yield the best results with the lowest normalized root mean squared error.
Robot Herds: Group Behaviors for Systems with Significant Dynamics

Birds, sh, and many other animals are able to move gracefully and e ciently as a herd, ock, or school. We would like to reproduce this behavior for herds of articial creatures with signi cant dynamics. This paper develops an algorithm for grouping behaviors and evaluates the performance of the algorithm on two types of systems: a full dynamic simulation of a legged robot that must balance as well as move with the herd and a point mass with minimal dynamics. Robust control algorithms for group behaviors of dynamic systems will allow us to generate realistic motion for animation using high-level controls, to develop synthetic actors for use in virtual environments, mobile robotics, and perhaps to improve our understanding of the behavior of biological systems.
Growth Phase-Dependent Activation of the DccRS Regulon of Campylobacter jejuni

ABSTRACT Two-component systems are widespread prokaryotic signal transduction devices which allow the regulation of cellular functions in response to changing environmental conditions. The two-component system DccRS (Cj1223c-Cj1222c) of Campylobacter jejuni is important for the colonization of chickens. Here, we dissect the DccRS system in more detail and provide evidence that the sensor DccS selectively phosphorylates the cognate effector, DccR. Microarray expression profiling, real-time reverse transcription-PCR (RT-PCR), electrophoretic mobility shift assay, and primer extension analyses revealed that the DccRS regulon of strain 81116 consists of five promoter elements, all containing the consensus direct repeat sequence WTTCAC-N6-TTCACW covering the putative −35 promoter regions. One of these promoters is located in front of an operon encoding a putative macrolide efflux pump while the others are in front of genes coding for putative periplasmic or membrane proteins. The DccRS-regulated genes in C. jejuni strain 81116 are needed to enhance early in vivo growth of C. jejuni in 7-day-old chickens. The DccRS system is activated in the late stationary bacterial growth phase, probably by released metabolic products. Whole-genome mRNA profiling and real-time RT-PCR analysis under these conditions demonstrated that the system has no influence on the transcription of genes outside the DccRS regulon.
A middleware architecture supporting seamless and secure multimedia services across an intertechnology radio access network

This article presents a middleware architecture to support multimedia services across intertechnology radio access networks in a secure and seamless manner. The proposed architecture uses the media-independent handover framework, where the handover decision function is based on triggering/collecting statistics from the physical, network, and application layers so that an ongoing multimedia session (video) can be transferred seamlessly and securely (using context transfer) across intertechnology radio access networks. Simulation results show that when a vertical handover is based on the proposed MIH framework (including the context transfer of AAA information), handover latency is reduced by 38 percent during WiFi to UMTS handover and 20 percent during UMTS to WiFi handover compared to a non-MIH-based handover scheme.
Antibodies from dengue patient sera cross‐react with endothelial cells and induce damage

Dengue virus infection causes a wide range of diseases from the mild febrile illness dengue fever to the life‐threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Vascular leakage and hemorrhagic syndrome are the clinical features associated with dengue infection, yet the mechanisms remain unclear. In this study, the cross‐reactivity of dengue patient sera with endothelial cells was demonstrated. There were higher percentages of endothelial cells reactive with dengue hemorrhagic fever/dengue shock syndrome patient sera than those with dengue fever patient sera. The percentages of endothelial cells reactive with patient serum IgM were higher than those with IgG. Further studies showed that the endothelial cell binding activity was inhibited by pretreatment with dengue virus nonstructural protein 1 (NS1). The antibodies against NS1 produced after dengue virus infection may, at least in part, account for the cross‐reactivity of patient sera with endothelial cells. Furthermore, dengue patient sera induced endothelial cell apoptosis via a caspase‐dependent pathway that was also inhibited by NS1 pretreatment. In addition to apoptosis, patient sera caused cell lysis in the presence of complement, and DHF/DSS patient sera showed higher percentages of cytotoxicity than dengue fever patient sera. Thus, the generation of cross‐reactive autoantibodies against endothelial cells would lead to their dysfunction, which may play a role in the pathogenesis of dengue virus infection. J. Med. Virol. 69:82–90, 2003. © 2003 Wiley‐Liss, Inc.
A Framework for State and Trace Interpolation

We address the problem of reasoning about interleavings in safety verification of concurrent processes. Inthe literature, there are two prominent techniques for pruning the search space. First, there isstate-based interpolation where a collection of formulas can be generalized by taking into acc ount the property to be verified. Second, there aretrace-based methods, collectively known as “Partial Order Reduction”, which operate by weakening the concept of a trace by abstracting the total order in the trace into a partial order. We first contribute by further weakening the concept of Partial Order Reduction to Trace Interpolation, in order to adapt it for a symbolic execution framework with abstraction. The main contribution of this p aper, however, is a framework that synergistically combines stat e and trace interpolation so that the sum is more than its parts.
Synergistic plasticity of intrinsic conductance and electrical coupling restores synchrony in an intact motor network

Motor neurons of the crustacean cardiac ganglion generate virtually identical, synchronized output despite the fact that each neuron uses distinct conductance magnitudes. As a result of this variability, manipulations that target ionic conductances have distinct effects on neurons within the same ganglion, disrupting synchronized motor neuron output that is necessary for proper cardiac function. We hypothesized that robustness in network output is accomplished via plasticity that counters such destabilizing influences. By blocking high-threshold K+ conductances in motor neurons within the ongoing cardiac network, we discovered that compensation both resynchronized the network and helped restore excitability. Using model findings to guide experimentation, we determined that compensatory increases of both GA and electrical coupling restored function in the network. This is one of the first direct demonstrations of the physiological regulation of coupling conductance in a compensatory context, and of synergistic plasticity across cell- and network-level mechanisms in the restoration of output. DOI: http://dx.doi. org/10.7554/eLife.16879. 001
0 M ar 2 00 3 Topological dimension of singular-hyperbolic attractors

An attractor is a transitive set of a flow to which all positive orbit close to it converges. An attractor is singular-hyperbolic if it has singularities (all hyperbolic) and is partially hyperbolic with volume expanding central direction [16]. The geometric Lorenz attractor [6] is an example of a singular-hyperbolic attractor with topological dimension ≥ 2. We shall prove that all singular-hyperbolic attractors on compact 3-manifolds have topological dimension ≥ 2. The proof uses the methods in [15].
Retrieval of Radiology Reports Citing Critical Findings with Disease-Specific Customization

Background: Communication of critical results from diagnostic procedures between caregivers is a Joint Commission national patient safety goal. Evaluating critical result communication often requires manual analysis of voluminous data, especially when reviewing unstructured textual results of radiologic findings. Information retrieval (IR) tools can facilitate this process by enabling automated retrieval of radiology reports that cite critical imaging findings. However, IR tools that have been developed for one disease or imaging modality often need substantial reconfiguration before they can be utilized for another disease entity. Purpose: This paper: 1) describes the process of customizing two Natural Language Processing (NLP) and Information Retrieval/Extraction applications – an open-source toolkit, A Nearly New Information Extraction system (ANNIE); and an application developed in-house, Information for Searching Content with an Ontology-Utilizing Toolkit (iSCOUT) – to illustrate the varying levels of customization required for different disease entities and; 2) evaluates each application’s performance in identifying and retrieving radiology reports citing critical imaging findings for three distinct diseases, pulmonary nodule, pneumothorax, and pulmonary embolus. Results: Both applications can be utilized for retrieval. iSCOUT and ANNIE had precision values between 0.90-0.98 and recall values between 0.79 and 0.94. ANNIE had consistently higher precision but required more customization. Conclusion: Understanding the customizations involved in utilizing NLP applications for various diseases will enable users to select the most suitable tool for specific tasks.
Association between cerebral infarction and increased serum bacterial antibody levels in young adults

Increased antibody levels against several bacteria were found in 15 of the 34 stroke patients (44%) under the age of 45 years, but in only six of the 68 controls (9%) (p < 0.001). Based on the serologic data, the most common preceding infections were streptococ‐cal, staphylococcal, and enterobacterial. There was no relationship between viral antibodies and cerebral infarction. When the clinical history of the patients was also taken into consideration, stroke was found to be associated with a recent infection in 68% of the patients, as compared with 26% for the second most common risk factor, ethanol intoxication. The results suggest an association between cerebral infarction and bacterial infections in young adults.
Frequency, sequence, and side of ovulation in women menstruating normally.

Sixteen women ovulating normally who were awaiting donor insemination participated in the study. Pelvic ultrasonography was performed with a real time sector scanner (Advanced Diagnostic Research 4000 S/L) at least once during each cycle as close as possible to the day when basal body temperature was lowest. Ovulation was confirmed by records of biphasic basal body temperature, mean duration ofluteal phase of 14 (SEM 2) days, and a mid-luteal plasma progesterone concentration -38-4 nmol/l (12 ngtml). Statistical analysis was based on the Bernolli distribution, assuming that in normal circumstances there is a 50% chance of ovulation occurring in either ovary. A total of 97 follicles was observed in 16 women during 90 cycles. In seven cycles (8%) two follicles were observed, always in the same ovary. Of the 97 follicles, 62 (64%) were detected in the right and 35 (36%) in the left ovary (p<0-01) (table). Alternation of side of ovulation in at least four consecutive
CS2164, a novel multi‐target inhibitor against tumor angiogenesis, mitosis and chronic inflammation with anti‐tumor potency

Although inhibitors targeting tumor angiogenic pathway have provided improvement for clinical treatment in patients with various solid tumors, the still very limited anti‐cancer efficacy and acquired drug resistance demand new agents that may offer better clinical benefits. In the effort to find a small molecule potentially targeting several key pathways for tumor development, we designed, discovered and evaluated a novel multi‐kinase inhibitor, CS2164. CS2164 inhibited the angiogenesis‐related kinases (VEGFR2, VEGFR1, VEGFR3, PDGFRα and c‐Kit), mitosis‐related kinase Aurora B and chronic inflammation‐related kinase CSF‐1R in a high potency manner with the IC50 at a single‐digit nanomolar range. Consequently, CS2164 displayed anti‐angiogenic activities through suppression of VEGFR/PDGFR phosphorylation, inhibition of ligand‐dependent cell proliferation and capillary tube formation, and prevention of vasculature formation in tumor tissues. CS2164 also showed induction of G2/M cell cycle arrest and suppression of cell proliferation in tumor tissues through the inhibition of Aurora B‐mediated H3 phosphorylation. Furthermore, CS2164 demonstrated the inhibitory effect on CSF‐1R phosphorylation that led to the suppression of ligand‐stimulated monocyte‐to‐macrophage differentiation and reduced CSF‐1R+ cells in tumor tissues. The in vivo animal efficacy studies revealed that CS2164 induced remarkable regression or complete inhibition of tumor growth at well‐tolerated oral doses in several human tumor xenograft models. Collectively, these results indicate that CS2164 is a highly selective multi‐kinase inhibitor with potent anti‐tumor activities against tumor angiogenesis, mitosis and chronic inflammation, which may provide the rationale for further clinical assessment of CS2164 as a therapeutic agent in the treatment of cancer.
Polymorphisms in gyrA and gyrB Genes among Mycobacterium avium subsp. paratuberculosis Type I, II, and III Isolates

ABSTRACT The analysis of the gyrA and gyrB genes of a panel of Mycobacterium avium subsp. paratuberculosis isolates from types I, II, and III detected type-specific single nucleotide polymorphisms. Based on these results, we developed a PCR and restriction enzyme analysis to discriminate type I and III isolates. The application of this technique would be the unique strategy to characterize these strains when there is not enough bacterial growth to perform pulsed-field gel electrophoresis and IS900 restriction fragment length polymorphism.
Modelling patterns and drivers of post-fire forest effects through a remote sensing approach

ii ACKNOWLEDGEMENTS . iv TABLE OF CONTENTS . v LIST OF TABLES . ix LIST OF FIGURES . x LIST OF ABBREVIATIONS . xiv Chapter 1: GENERAL INTRODUCTION . 1 1.1 Preface . 1 1.2 Background . 1 1.3 Forest fire and forest pattern terminology . 3 1.4 Modeling post-fire effects and forest recovery patterns using remote sensing . 5 1.4. 1 Mapping burned area . 5 1.4. 2 Mapping burn severity . 7 1.4. 3 Trajectory of post-fire forest regrowth patterns . 10 1.4. 4 Assessment of environmental factors affecting post-fire forest patterns . 13 1.4. 5 Summary and research gaps . 15 1.5 Research hypothesis and objectives . 18 1.6 Organization of this dissertation . 19 Chapter 2: COMPOSITING MODIS TIME SERIES FOR RECONSTRUCTING BURNED AREAS IN THE TAIGA-STEPPE TRANSITION ZONE OF BOREAL LARCH FOREST . 20 2.1 Preface . 20 2.2 Abstract . 20 2.3 Introduction . 21 2.4 Materials and methods . 23 2.4. 1 Study area. 23 2.4. 2 Satellite data . 25 2.4. 3 Analyzing fire occurrence patterns and reconstructing MODIS time-series composites . 26 2.4. 4 Sampling method for model calibration on clear-land MODIS composite . 28 2.4. 5 Statistic analysis and mapping time series of burned areas . 31
Simultaneous communication and processor voltage scaling for dynamic and leakage energy reduction in time-constrained systems

We propose a new technique for the combined voltage scaling of processors and communication links, taking into account dynamic as well as leakage power consumption. The voltage scaling technique achieves energy efficiency by simultaneously scaling the supply and body bias voltages in the case of processors and buses with repeaters, while energy efficiency on fat wires is achieved through dynamic voltage swing scaling. We also introduce a set of accurate communication models for the energy estimation of voltage scalable embedded systems. In particular, we demonstrate that voltage scaling of bus repeaters and dynamic adaption of the voltage swing on fat wires can significantly influence the system's energy consumption. Experimental results, conducted on numerous generated benchmarks and a real-life example, demonstrate that substantial energy savings can be achieved with the proposed techniques.