gebhart/patrepeval huggingface dataset:
The BvgAS Regulon of <i>Bordetella pertussis</i> (2017)

Nearly all virulence factors in <i>Bordetella pertussis</i> are activated by a master two-component system, BvgAS, composed of the sensor kinase BvgS and the response regulator BvgA. When BvgS is active, BvgA is phosphorylated (BvgA~P), and virulence-activated genes (<i>vag</i>s) are expressed [Bvg(+) mode]. When BvgS is inactive and BvgA is not phosphorylated, virulence-repressed genes (<i>vrg</i>s) are induced [Bvg(-) mode]. Here, we have used transcriptome sequencing (RNA-seq) and reverse transcription-quantitative PCR (RT-qPCR) to define the BvgAS-dependent regulon of <i>B. pertussis</i> Tohama I. Our analyses reveal more than 550 BvgA-regulated genes, of which 353 are newly identified. BvgA-activated genes include those encoding two-component systems (such as <i>kdpED</i>), multiple other transcriptional regulators, and the extracytoplasmic function (ECF) sigma factor <i>brpL</i>, which is needed for type 3 secretion system (T3SS) expression, further establishing the importance of BvgA~P as an apex regulator of transcriptional networks promoting virulence. Using <i>in vitro</i> transcription, we demonstrate that the promoter for <i>brpL</i> is directly activated by BvgA~P. BvgA-FeBABE cleavage reactions identify BvgA~P binding sites centered at positions -41.5 and -63.5 in <i>bprL</i> Most importantly, we show for the first time that genes for multiple and varied metabolic pathways are significantly upregulated in the <i>B. pertussis</i> Bvg(-) mode. These include genes for fatty acid and lipid metabolism, sugar and amino acid transporters, pyruvate dehydrogenase, phenylacetic acid degradation, and the glycolate/glyoxylate utilization pathway. Our results suggest that metabolic changes in the Bvg(-) mode may be participating in bacterial survival, transmission, and/or persistence and identify over 200 new <i>vrg</i>s that can be tested for function.<b>IMPORTANCE</b> Within the past 20 years, outbreaks of whooping cough, caused by <i>Bordetella pertussis</i>, have led to respiratory disease and infant mortalities, despite good vaccination coverage. This is due, at least in part, to the introduction of a less effective acellular vaccine in the 1990s. It is crucial, then, to understand the molecular basis of <i>B. pertussis</i> growth and infection. The two-component system BvgA (response regulator)/BvgS (histidine kinase) is the master regulator of <i>B. pertussis</i> virulence genes. We report here the first RNA-seq analysis of the BvgAS regulon in <i>B. pertussis</i>, revealing that more than 550 genes are regulated by BvgAS. We show that genes for multiple and varied metabolic pathways are highly regulated in the Bvg(-) mode (absence of BvgA phosphorylation). Our results suggest that metabolic changes in the Bvg(-) mode may be participating in bacterial survival, transmission, and/or persistence.
Effect of Nickel Foam Current Collector on the Supercapacitive Properties of Cobalt Oxide Electrode (2008)

An electrode for supercapacitor using 3-dimensional porous nickel foam as a current collector and cobalt oxide as an active material was prepared and characterized in terms of morphology observation, crystalline property analysis, and the investigation of electrochemical property. The electrode surface showed that the cobalt oxide was homogeneously coated as the crystalline phase of Co₃O₄. Cyclic voltammetry for the Co₃O₄/nickel foam electrode exhibited higher specific capacitance values (445 F/g at 10 ㎷/s and 350 F/g at 200 ㎷/s) and excellent capacitance retention ratio (99% after 10⁴ cycles). It was proved that the nickel foam substrate played the roles in reducing the interfacial resistance with cobalt oxide and in improving the electrode density by embedding greater amount of cobalt oxide within it.
Hel-N1, an RNA-binding protein, is a ligand for an A + U rich region of the GLUT1 3' UTR. (1995)

Hel-N1, is an RRM protein which is a mammalian homologue of the Drosophila melanogaster RNA binding protein, ELAV (embryonic lethal abnormal vision). Hel-N1 binds to RNA containing short stretches of uridylates similar to those found in the 3' untranslated regions (3'-UTRs) of oncoprotein and cytokine mRNAs. The GLUT1 glucose transporter has an extensive 3' UTR that is AU-rich reminiscent of the 3'UTR of an oncogene mRNA. An in vitro RNA binding assay using Hel-N1 demonstrated binding to a specific portion of the GLUT1 3'UTR. Analysis of the folding pattern of this region depicted the retention of a stem loop structure, wherein the loop is composed of a stretch of uridylates. To further analyze the potential function of Hel-N1, stable transfectants were made in the 3T3-L1 cell line. The transfectants have been characterized, and the presence of the Hel-N1 DNA and protein verified. Data indicate Hel-N1 is a ligand for GLUT1 and its binding affects the stability and translatability of the GLUT1 message.
Leptin Levels in Preterm Human Breast Milk and Infant Formula (2001)

PBM leptin levels were highly variable and similar to levels reported for term breast milk. There was no effect of postnatal age on PBM leptin concentrations. Sterilization decreased detectable leptin levels, whereas feeding practices had no adverse effect on the quantity of leptin delivered. Although no infant formula contained leptin, leptin could be added to formula and delivered through various feeding methods without loss.
Neuropilin 1 is an entry factor that promotes EBV infection of nasopharyngeal epithelial cells (2015)

Epstein-Barr virus (EBV) is implicated as an aetiological factor in B lymphomas and nasopharyngeal carcinoma. The mechanisms of cell-free EBV infection of nasopharyngeal epithelial cells remain elusive. EBV glycoprotein B (gB) is the critical fusion protein for infection of both B and epithelial cells, and determines EBV susceptibility of non-B cells. Here we show that neuropilin 1 (NRP1) directly interacts with EBV gB(23-431). Either knockdown of NRP1 or pretreatment of EBV with soluble NRP1 suppresses EBV infection. Upregulation of NRP1 by overexpression or EGF treatment enhances EBV infection. However, NRP2, the homologue of NRP1, impairs EBV infection. EBV enters nasopharyngeal epithelial cells through NRP1-facilitated internalization and fusion, and through macropinocytosis and lipid raft-dependent endocytosis. NRP1 partially mediates EBV-activated EGFR/RAS/ERK signalling, and NRP1-dependent receptor tyrosine kinase (RTK) signalling promotes EBV infection. Taken together, NRP1 is identified as an EBV entry factor that cooperatively activates RTK signalling, which subsequently promotes EBV infection in nasopharyngeal epithelial cells.
Influence of insonification angle on echogenicity of B-mode images of atherosclerotic plaque in vitro (2002)

A newly developed (off-line) spatial compound scanner was used to scan formalin-fixed atherosclerotic carotid plaques. Forty-eight B-mode images were recorded using 7 insonification angles. All calculations were done on the envelope-detected image data. The mean amplitude level (MAL) in (relative) volts was calculated for the plaque region in each image. The standard deviation over the 48 MAL values were for each of the 7 angles between 0.12 V and 0.18 V. For each scan plane, the standard deviation was also calculated over the 7 images. The mean and standard deviation of these 48 numbers were 0.07 V and 0.04 V, respectively. Thus based on these data, the variation from scan plane to scan plane is normally larger than the variation over angle for a single scan plane.
Single-Trial Classification of Event-Related Potentials in Rapid Serial Visual Presentation Tasks Using Supervised Spatial Filtering (2014)

Accurate detection of single-trial event-related potentials (ERPs) in the electroencephalogram (EEG) is a difficult problem that requires efficient signal processing and machine learning techniques. Supervised spatial filtering methods that enhance the discriminative information in EEG data are commonly used to improve single-trial ERP detection. We propose a convolutional neural network (CNN) with a layer dedicated to spatial filtering for the detection of ERPs and with training based on the maximization of the area under the receiver operating characteristic curve (AUC). The CNN is compared with three common classifiers: 1) Bayesian linear discriminant analysis; 2) multilayer perceptron (MLP); and 3) support vector machines. Prior to classification, the data were spatially filtered with xDAWN (for the maximization of the signal-to-signal-plus-noise ratio), common spatial pattern, or not spatially filtered. The 12 analytical techniques were tested on EEG data recorded in three rapid serial visual presentation experiments that required the observer to discriminate rare target stimuli from frequent nontarget stimuli. Classification performance discriminating targets from nontargets depended on both the spatial filtering method and the classifier. In addition, the nonlinear classifier MLP outperformed the linear methods. Finally, training based AUC maximization provided better performance than training based on the minimization of the mean square error. The results support the conclusion that the choice of the systems architecture is critical and both spatial filtering and classification must be considered together.
Oxidized Phospholipids Negatively Regulate Dendritic Cell Maturation Induced by TLRs and CD40 (2005)

Maturation of dendritic cells (DCs) induced by pathogen-derived signals via TLRs is a crucial step in the initiation of an adaptive immune response and therefore has to be well controlled. In this study, we demonstrate that oxidized phospholipids (ox-PLs), which are generated during infections, apoptosis, and tissue damage, interfere with DC activation, preventing their maturation. ox-PLs blocked TLR-3- and TLR-4-mediated induction of the costimulatory molecules CD40, CD80, CD83, and CD86, the cytokines IL-12 and TNF, as well as lymphocyte stimulatory capacity. CD40 and TLR-2-mediated cytokine production was also inhibited, whereas up-regulation of costimulatory molecules via these receptors was not affected by ox-PLs. Thus, formation of ox-PLs during the course of an inflammatory response may represent a negative-feedback loop preventing excessive and sustained immune reactions through regulating DC maturation.
User-Input Dependence Analysis via Graph Reachability (2008)

Bug-checking tools have been used with some success in recent years to find bugs in software. For finding bugs that can cause security vulnerabilities, bug checking tools require a program analysis which determines whether a software bug can be controlled by user-input. In this paper we introduce a static program analysis for computing user-input dependencies. This analysis can be used as a pre-processing filter to a static bug checking tool for identifying bugs that can potentially be exploited as security vulnerabilities. In order for the analysis to be applicable to large commercial software in the millions of lines of code, runtime speed and scalability of the user-input dependence analysis is of key importance. Our user-input dependence analysis takes both data and control dependencies into account. We extend static single assignment (SSA) form by augmenting phi-nodes with control dependencies. A formal definition of user-input dependence is expressed in a dataflow analysis framework as a meet-over-all-paths (MOP) solution. We reduce the equation system to a sparse equation system exploiting the properties of SSA. The sparse equation system is solved as a reachability problem that results in a fast algorithm for computing user-input dependencies. We have implemented a call-insensitive and a call-sensitive analysis. The paper gives preliminary results on the comparison of their efficiency for various benchmarks.
Ectopic expression of IGF‐I and Shh by skeletal muscle inhibits disuse‐mediated skeletal muscle atrophy and bone osteopenia in vivo (2003)

The loss of normal weight-bearing activity, which occurs during bed rest, limb immobilization, and spaceflight, stimulates a catabolic response within the musculoskeletal system, which results in a loss of skeletal muscle mass and bone mineral. The mechanism by which loading of muscle and bone is sensed and translated into signals controlling tissue formation remains a major question in the field of musculoskeletal research. In this investigation, we have examined the ability of two potentially anti-atrophic proteins, IGF-I and Shh, to inhibit disuse atrophy within muscle and bone, when electroporated into skeletal muscle. We have found that electroporation and ectopic expression of IGF-I and/or Shh within the gastrocnemius/soleus muscle significantly stimulated muscle fiber hypertrophy and increases in muscle size. In addition, we report that electroporation and ectopic expression of IGF-I and/or Shh within the gastrocnemius/soleus muscle attenuated the lost of muscle fiber area, muscle mass, and muscle mass density that normally occurs during disuse muscle atrophy. Finally, we found that ectopic expression of IGF-I and Shh within the gastrocnemius/soleus muscle inhibits parameters of osteopenia within the tibia and fibula associated with hindlimb unloading. These results support the theory that skeletal muscle can regulate bone maintenance and could offer potentially novel and efficient therapeutic options for attenuating muscle and bone atrophy during aging, illness and spaceflight.
Summarizing Blog Entries versus News Texts (2009)

As more and more people are expressing their opinions on the web in the form of weblogs (or blogs), research on the blogosphere is gaining popularity. As the outcome of this research, different natural language tools such as querybased opinion summarizers have been developed to mine and organize opinions on a particular event or entity in blog entries. However, the variety of blog posts and the informal style and structure of blog entries pose many difficulties for these natural language tools. In this paper, we identify and categorize errors which typically occur in opinion summarization from blog entries and compare blog entry summaries with traditional news text summaries based on these error types to quantify the differences between these two genres of texts for the purpose of summarization. For evaluation, we used summaries from participating systems of the TAC 2008 opinion summarization track and updated summarization track. Our results show that some errors are much more frequent to blog entries (e.g. topic irrelevant information) compared to news texts; while other error types, such as content overlap, seem to be comparable. These findings can be used to prioritize these error types and give clear indications as to where we should put effort to improve blog summarization.
Towards an architecture for artificial animated creatures (2002)

We present a methodology used to implement artificial animated creatures. Our control architecture considers using local sensory information to provide the creatures with perception, deals with dynamics and kinematics issues and provides a well structured way to control the creature resources. Three artificial creatures with different sensors/actuators/dynamics characteristics show the versatility of the architecture. As a practical result, by using the same control structure, the artificial animated creatures are able to perform different tasks, like visual monitoring of their environments and progression on a rough terrain.
NVP-AEW541: A Selective Small Molecule IGF-1R Tyrosine Kinase Inhibitor Is Active Against Multiple Myeloma and Other Hematologic Neoplasias and Solid Tumors. (2004)

Abstract We have shown that insulin-like growth factors (IGFs) and their receptor IGF-1R play critical roles in proliferation, survival and drug-resistance of a broad spectrum of hematologic malignancies and solid tumors and that selective inhibitors of IGF-1R kinase activity have in vivo anti-tumor activity in clinically relevant orthotopic tumor models (Cancer Cell2004;5:221–30). We now describe the in vitro and in vivo activity of NVP-AEW541, a novel pyrrolo[2,3-d] pyrimidine selective IGF-1R tyrosine kinase inhibitor with 27-fold selectivity for IGF-1R vs. its highly homologous insulin receptor. NVP-AEW541 is active (at sub-uM levels) against diverse tumor types, including >30 MM cell lines and >10 primary tumor cells from MM patients (including cells resistant to Dex, alkylating agents, anthracyclines, thalidomide, or its immunomodulatory derivatives, IMiDs, bortezomib, and/or Apo2L/TRAIL); and cell lines from diverse hematologic malignancies (including B- and T-ALL, AML, CML, and lymphoma subtypes) and solid tumors (e.g. breast, prostate, lung, thyroid, ovarian, renal Ca, retinoblastoma and sarcomas). All studied tumor cells expressed IGF-1R, without any correlation between mean fluorescence intensity of expression of IGF-1R (or its decoy non-signaling counterpart IGF-2R/CD222) and the degree of tumor cell sensitivity to NVP-AEW541. The in vitro anti-tumor effects of NVP-AEW541 were highly consistent with those of other selective anti-IGF-1R neutralizing agents, including another IGF-IR inhibitor of the pyrrolo[2,3-d] pyrimidine structural class (NVP-ADW742) or anti-human IGF-1R-specific neutralizing mAb’s (aIR3). NVP-AEW541 counteracts the proliferative/anti-apoptotic effect of serum on tumor cells from the entire spectrum of diseases that were studied, but more prominently against MM cells. Importantly, NVP-AEW541 had in vivo anti-tumor activity in a SCID/NOD mice model of diffuse MM. Mechanistically, IGF-1R inhibition by NVP-AEW541 blocks key growth/survival pathways (e.g. PI-3K/Akt, Ras/Raf/MAPK, IKK-a/NF-kB); blocks expression of inhibitors of apoptosis (e.g. FLIP, cIAP-2, survivin); and suppresses both constitutive and serum- or IGF-1-induced upregulation of proteasome activity. These molecular sequelae can explain why NVP-AEW541 sensitized tumor cells (e.g. MM, PrCa, BrCa or sarcomas) to other anti-cancer drugs (e.g. Dex, cytotoxic chemotherapeutics and PS-341); blunted tumor cell responses to other growth factors (e.g. MM or PrCa cell response to IL-6); overcame the drug-resistance phenotype conferred by bone marrow stromal cells; and abrogated VEGF production in co-cultures of MM cells with BMSCs. These studies further confirm that IGF-1R plays major role in growth/survival of neoplastic cells, indicate that IGF-1R pathway can be targeted with multiple clinically applicable approaches; and provide proof-of-principle for clinical trials of NVP-AEW541, e.g. in MM, a disease particularly dependent upon IGF-1R function.
Facial expressive robotic head system for human-robot communication and its application in home environment (2004)

This paper describes a robotic-head system as a multimodal communication device for human-robot interaction, and the system's potential application in home environments. Most robotic systems for natural user interaction have facial expressions, since facial expressiveness is regarded as a key component to developing personal attachment along with prosodic expressiveness. In the first part of the paper is the description of our robotic head system Character Robot Face (CRF). A deformation approach and a parametric normalization scheme are proposed to produce facial expressions of nonhuman face models with high recognition rates. In the second half of the paper, CRF is endowed with artificial emotions and assigned tasks conceivable in home environments. A coordination mechanism between the robot's mood (an activated emotion) and its task is proposed so that the robot can, by referring to the emotion-task history, select a task depending on its current mood if there is no explicit task command from the user. When the robot performs a task, a particular emotion value gets boosted according to the same emotion-task history so that the emotion is more likely to be activated.
Predicting Treatment Responses and Disease Progression in Myeloma using Serum Vascular Endothelial Growth Factor and Hepatocyte Growth Factor Levels (2003)

Angiogenesis is a crucial process in the progression of multiple myeloma (MM). Vascular endothelial growth factor (VEGF) and hepatocyte growth factor (HGF) are multifunctional cytokines that potently stimulate angiogenesis during tumor neovascularization. VEGF is secreted by MM cells. It induces proliferation of MM cells and stimulates IL-6 expression by microvascular endothelial cells and bone marrow stroma cells, suggesting both autocrine and paracrine functions for VEGF in MM. HGF and the HGF receptor, c-Met, are expressed simultaneously in MM cell lines and in freshly isolated MM cells, suggesting a possible role for HGF in MM cell proliferation. This review focuses on the clinical significance of serum levels of VEGF and HGF in MM.
Study of Auroral VLF Hiss Observed at Syowa Station, Antarctica (1976)

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Decarbonylative Olefination of Aldehydes to Alkenes (2019)

New atom-economical alternatives to Wittig chemistry are needed to construct olefins from carbonyl compounds, but none have been developed to-date. Here we report an atom-economical olefination of carbonyls via aldol-decarbonylative coupling of aldehydes using robust and recyclable supported Pd catalysts, producing only CO and H<sub>2</sub>O as waste. The reaction affords homocoupling of aliphatic aldehydes, as well as heterocoupling of aliphatic and aromatic ones. Computations provide insight into the selectivity and thermodynamics of the reaction. The tandem aldol-decarbonylation reaction opens the door to exploration of new carbonyl reactivity to construct olefins.
Computer-integrated quality information system (2002)

The author describes the design and implementation of a quality information system in the computer-integrated manufacturing environment. Various data elements related to quality functions an be integrated through a closed-loop quality information system. It is suggested that an emerging generation of computer workstations, communication protocols, and database management systems will make the computer-integrated quality information system a reality at affordable prices. A systems development methodology for designing and implementing quality information systems is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
[Application of fluorescence in situ hybridization (FISH) in sputum cytologic diagnosis of lung cancer]. (2000)

FISH can detect aneuploid malignant cells in sputum and be used as a complementary technique to cytologic diagnosis of lung cancer.