gebhart/patrepeval huggingface dataset:
Data clouds (2009)

Keyword searches are attractive because they facilitate users searching structured databases. On the other hand, tag clouds are popular for navigation and visualization purposes over unstructured data because they can highlight the most significant concepts and hidden relationships in the underlying content dynamically. In this paper, we propose coupling the flexibility of keyword searches over structured data with the summarization and navigation capabilities of tag clouds to help users access a database. We propose using clouds over structured data (data clouds) to summarize the results of keyword searches over structured data and to guide users to refine their searches. The cloud presents the most significant words associated with the search results. Our keyword search model allows searching for entities than can span multiple tables in the database rather than just tuples, as existing keyword searches over databases do. We present several methods to compute the scores both for the entities and for the terms in the search results. We describe algorithms for keyword searches with data clouds and we present our system, CourseCloud, that offers a unified search and browse interface to a course database. We present experimental results showing (a) the appropriateness of the methods used for scoring terms, (b) the performance of the proposed algorithms, and (c) the effectiveness of CourseCloud compared to typical search and browse interfaces to a course database.
The Limitations of Antiepileptic Drug Monotherapy (1997)

Summary The success rate for antiepileptic drug (AED) monotherapy varies among seizure types and epilepsy syndromes, although monotherapy has been shown to be suitable for the majority of patients. Certain groups of patients, e.g., patients with partial seizures, with or without secondarily generalizing, are less satisfactorily controlled with monotherapy. Prospective studies have shown that 33–50% of patients with refractory partial epilepsies and symptomatic generalized epilepsies whose seizures are not satisfactorily controlled by monotherapy respond well to a combination of AEDs. Current consensus is that all patients should initially receive monotherapy [e.g., valproate (VPA) or carbamazepine (CBZ)] and, if unsuccessful, an alternative AED should be administered as monotherapy. Only if seizures are still not satisfactorily controlled should combination therapy be instituted. Studies have shown that combination therapy with VPA and CBZ brings seizures of many previously nonresponsive patients with refractory complex partial and secondary generalized epilepsies under control. However, to establish the limitations of monotherapy in an individual, the maximal tolerated dosage must have been administered. Full seizure control may occur in some patients only when the plasma concentration exceeds the therapeutic range.
Epitaxial Lateral Overgrowth of GaAs on a Si Substrate (1989)

Epitaxial lateral overgrowth (ELO) of GaAs on a Si substrate was successfully achieved by a combination of LPE and MBE. To prevent meltback of the Si substrate by Ga solution, a thin GaAs layer (2.4 µm) was grown by MBE prior to the deposition of SiO 2 by P-CVD. Uniform GaAs ELO layers with mirror surface were grown through a line-shaped window cut in SiO 2 film on a Si substrate with a GaAs layer. Chemical etching with an RC-1 etchant showed that there were no etch pits observed in ELO layers except in the region just over the line seed. Although cracks are observed in ELO layers due to the difference in thermal expansion coefficients between GaAs and Si, it is concluded that this technique is promising for obtaining dislocation- free GaAs on a Si substrate.
The Plasma Membrane Lactate Transporter MCT4, but Not MCT1, Is Up-regulated by Hypoxia through a HIF-1α-dependent Mechanism (2006)

The monocarboxylate transporter MCT4 mediates lactic acid efflux from most tissues that are dependent on glycolysis for their ATP production. Here we demonstrate that expression of MCT4 mRNA and protein was increased >3-fold by a 48-h exposure to 1% O(2), whereas MCT1 expression was not increased. The effect was mimicked by CoCl(2) (50 microm), suggesting transcriptional regulation by hypoxia-inducible factor 1alpha (HIF-1alpha). The predicted promoters for human MCT1, MCT2, and MCT4 were cloned into the pGL3 vector and shown to be active (luciferase luminescence) under basal conditions. Only the MCT4 promoter was activated (>2-fold) by hypoxia. No response was found in cells lacking HIF-1alpha. Four potential hypoxia-response elements were identified, but deletion analysis implicated only two in the hypoxia response. These were just upstream from the transcription start site and also found in the mouse MCT4 promoter. Mutation of site 2 totally abolished the hypoxic response, whereas mutation of site 1 only reduced the response. Gel-shift analysis demonstrated that nuclear extracts of hypoxic but not normoxic HeLa cells contained two transcription factors that bound to DNA probes containing these hypoxia-response elements. The major shifted band was abolished by mutation of site 2, and supershift analysis confirmed that HIF-1alpha bound to this site. Binding of the second factor was abolished by mutation of site 1. We conclude that MCT4, like other glycolytic enzymes, is up-regulated by hypoxia through a HIF-1alpha-mediated mechanism. This adaptive response allows the increased lactic acid produced during hypoxia to be rapidly lost from the cell.
Interaction of hepatocyte growth factor with heparan sulfate. Elucidation of the major heparan sulfate structural determinants (1994)

We have demonstrated by affinity chromatography that hepatocyte growth factor (HGF) binds strongly to heparan sulfate (HS). This substantiates previous suggestions that cell-surface heparan sulfate proteoglycans constitute the so-called low affinity cellular binding sites for HGF. Using a recombinant human HGF affinity column, we have analyzed the effects of various specific chemical and enzymatic modifications/depolymerizations of HS on its affinity in order to elucidate the polysaccharide structural determinants. Interaction is shown to be only slightly affected by digestion with heparinase I or III or by replacement of N-sulfates with N-acetyl groups. This suggests a specific role for sulfated domains containing nonsulfated IdceA residues, with only a small contribution from N-sulfates and IdceA(2-OSO3) residues. In addition, disaccharide analyses of various HGF-binding oligosaccharides indicate that affinity is more closely associated with 6-O-sulfation of GlcNSO3 residues than with sulfation at any other position. Although interaction can be demonstrated with heparinase III-resistant oligosaccharides as small as hexasaccharides, the highest affinity was found with oligosaccharides containing a minimum of 10-12 monosaccharides. The structural specificity of the HGF-HS interaction is thus shown to be radically different from that previously described for the basic fibroblast growth factor-HS interaction.
Aeromicrobium ponti sp. nov., isolated from seawater (2008)

A novel actinomycete strain, designated HSW-1T, was isolated from seawater collected from Hwasun Beach on the coast of Jeju Island, Republic of Korea. The cells were aerobic, Gram-positive, oxidase-negative, catalase-positive, non-motile rods. The colonies were circular, smooth, convex and yellow in colour. The cell-wall peptidoglycan of this organism contained ll-diaminopimelic acid as the diagnostic diamino acid. The polar lipids included phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol and three unknown phospholipids. The predominant menaquinone was MK-9(H4). The major fatty acids were C18 : 1 omega 9c, C16 : 0, C16 : 0 2-OH and 10-methyl C18 : 0. The DNA G+C content was 74.0 mol%. A neighbour-joining tree based on 16S rRNA gene sequences showed that this organism falls within the radiation of the genus Aeromicrobium. The closest phylogenetic neighbours were the type strains of Aeromicrobium erythreum (98.2 % 16S rRNA gene sequence similarity), Aeromicrobium alkaliterrae (97.9 %), Aeromicrobium marinum (97.3 %) and Aeromicrobium fastidiosum (97.0 %). The DNA-DNA relatedness values between the novel isolate and its closest relative, A. erythreum DSM 8599T, ranged between 32 and 36 %. On the basis of the phenotypic and DNA-DNA hybridization data, strain HSW-1T represents a novel species of the genus Aeromicrobium, for which the name Aeromicrobium ponti sp. nov. is proposed. The type strain is HSW-1T (=DSM 19178T=KACC 20565T).
A review of Parkinson's disease (2008)

Although there is no cure, there are several management options for the early treatment of PD. As the disease progresses, further treatment options are available; however, the management of late-stage motor complications and non-motor symptoms remains particularly challenging and will benefit from further clinical research.
Cytochrome b5 modulation of 17α hydroxylase and 17–20 lyase (CYP17) activities in steroidogenesis (2005)

CYP17 is a steroidogenic enzyme located in the zona fasciculata and zona reticularis of the adrenal cortex and gonad tissues and which has dual functions - hydroxylation and as a lyase. The first activity gives hydroxylation of pregnenolone and progesterone at the C(17) position to generate 17alpha-hydroxypregnenolone and 17alpha-hydroxyprogesterone, while the second enzymic activity cleaves the C(17)-C(20) bond of 17alpha-hydroxypregnenolone and 17alpha-hydroxyprogesterone to form dehydroepiandro-sterone and androstenedione respectively. The modulation of these two activities occurs through cytochrome b(5). Association of cytochrome b(5) and CYP17 is thought to be based primarily on electrostatic interactions in which the negatively charged residues pair up with positively charged residues on the proximal surface of the CYP17 molecule. Non-specific interactions of the hydrophobic membrane regions of cytochrome b(5) and CYP17 are also thought to play a crucial role in the association of these two haemoproteins. Although cytochrome b(5) is known to stimulate CYP activity by contributing the second electron in the catalytic cycle, in the case of CYP17, the mechanism of cleavage stimulation proceeds via an allosteric mode. It is hypothesised that cytochrome b(5) promotes the cleavage by aligning the iron-oxygen complex attack onto the C(20) rather than the C(17) atom of the steroid substrate molecule. Thus, further understanding of the mechanism of modulation by cytochrome b(5) of the hydroxylase and lyase activities should shed new insights on developing therapeutic targets in CYP17-linked biochemical processes such as adrenarche, polycystic ovary syndrome and prostate cancer.
Building a more secure web browser (2008)

The modern web browser has envolved from a relatively simple client application designed to display static data into a complex networked operating system tasked with managing many facets of online experience. Support for dynamic content, multimedia data and third-party plung-ins greatly enriches the browsing experience at the cost of increased complexity of the browser itself, rersulting in a plague of security vulnerabilities that provide hackers with easy access to systems. To addrress the root of this problem, we designedand implemented the OPWeb browser into smaller subsystems, isolated each subsystem, and made all communications between subsystems and the ability to limit the effects of compromised subsystems.
Combining low-dose or metronomic chemotherapy with anticancer vaccines (2013)

Therapeutic vaccination is regarded as a promising strategy against multiple hematological malignancies including lymphoma. However, this approach alone possesses limited potential for the treatment of established tumors. As several anticancer regimens relies on the combination of multiple drugs, it is reasonable to predict that also cancer vaccination will be most effective in the context of multimodal approaches. In particular, low-dose or metronomic chemotherapy could be coupled to anticancer vaccines to improve the efficacy of this immunotherapeutic interventions. This review summarizes recent findings in support of the use of anticancer vaccines combined with low-dose or metronomic chemotherapy for the treatment and management of lymphoid malignancies.
Fluvastatin induces apoptosis of vascular endothelial cells: blockade by glucocorticoids (2003)

Statins block de novo synthesis of cholesterol by inhibiting the enzyme, HMG CoA reductase. The product of this reaction, mevalonic acid, is also a precursor of isoprenoids, molecules required for the activation of signaling G-proteins, such as Ras. Signal transduction pathways involving Ras are important for cell survival and this may be why statins induce apoptotic death of several cell types. Given that statins are used to treat vascular disease, surprisingly no studies have been conducted on vascular endothelial cells. Here we show that fluvastatin (FS), at concentrations from 1-2 microM, blocks growth and induces apoptosis of the endothelial cell line, EA.hy 926. Considerable redundancy is known to exist in cell signaling and in vivo toxicity of FS might be prevented by other signaling pathways, like those activated by adrenal or sex steroids. RT-PCR analysis revealed the expression of the androgen and glucocorticoid receptor in EA.hy 926 cells. Although the androgen, dihydrotestesterone (DHT) had no effect, the glucocorticoid, dexamethasone (Dex), blocked FS-induced apoptosis. Cell cycle analysis revealed that 24 h exposure to FS prevented cells from leaving G(1) and 24-48 h later a marked sub-G(1) peak was observed. Dex was able to reduce the sub-G(1) peak, but it failed to block accumulation of cells in G(1), indicating that it's effect was specific for blockade of apoptosis, and not specific to an effect on FS alone. This study strongly suggests that glucocorticoids have a role to play in preventing vascular injury and they may provide the reason why statins are not inherently toxic to vascular endothelial cells, in vivo.
Efficient Establishment of Mouse Embryonic Stem Cell Lines from Single Blastomeres and Polar Bodies (2006)

Recently, ES cell lines were established from single blastomeres taken from eight-cell embryos in mice and humans with success rates of 4% and 2%, respectively, which suggests that the method could be used in regenerative medicine to reduce ethical concerns over harm to embryos. However, those studies used other ES cells as supporting cells. Here, we report a simple and highly efficient method of establishing mouse ES cell lines from single blastomeres, in which single blastomeres are simply plated onto a feeder layer of mouse embryonic fibroblasts with modified ES cell medium. A total of 112 ES cell lines were established from two-cell (establishment rate, 50%-69%), early four-cell (28%-40%), late four-cell (22%), and eight-cell (14%-16%) stage embryos. We also successfully established 18 parthenogenetic ES cell lines from first (36%-40%) and second polar bodies (33%), the nuclei of which were reconstructed to embryos by nuclear transfer. Most cell lines examined maintained normal karyotypes and expressed markers of pluripotency, including germline transmission in chimeric mice. Our results suggest that the single cells of all early-stage embryos or polar bodies have the potential to be converted into ES cells without any special treatment.
Auto-Calibration of a Compound-Type Omnidirectional Camera (2005)

We propose a method for auto-calibrating a compound-type omnidirectional camera (system). This camera produces spherical panoramic image through stitching some individual images captured by several modular cameras, each of which covers a different field of view of the full viewing sphere. By auto-calibration we mean that our algorithm works online in a self-calibration manner: it receives as input image point correspondences only, and outputs all the camera parameters. The calibration task consists of lens-distortion-removal, intrinsic-calibration, and relative-orientation. The focus of the paper is an algorithm for automatically removing lens distortion. By exploiting planar projective invariants, our algorithm is capable of estimating centre-of-distortion and distortion parameters efficiently without using any nonlinear iteration.
Dehydroepiandrosterone protects mice from endotoxin toxicity and reduces tumor necrosis factor production (1992)

Recent reports have demonstrated an immunomodulating activity of dehydroepiandrosterone (DHEA) different from that described for glucocorticoids. The present study was designed to test DHEA's activity in endotoxic shock and to investigate its effect on endotoxin-induced production of tumor necrosis factor (TNF). Mortality of CD-1 mice exposed to a lethal dose of lipopolysaccharide (LPS; 800 micrograms per mouse) was reduced from 95 to 24% by treatment with a single dose of DHEA, given 5 min before LPS. LPS administration resulted in high levels of TNF, a response that was significantly blocked by DHEA, both in vivo and in vitro. DHEA treatment also reduced LPS-induced increments in serum corticosterone levels, a parameter considered not to be mediated by TNF. In another experimental model, mice sensitized with D-galactosamine, followed by administration of recombinant human TNF, were subjected to 89% mortality rate, which was reduced to 55% in DHEA-treated mice. These data show that DHEA protects mice from endotoxin lethality. The protective effect is probably mediated by reduction of TNF production as well as by effecting both TNF-induced and non-TNF-induced phenomena.
HfO/sub 2/ and HfAlO for CMOS: thermal stability and current transport (2002)

This paper reports the thermal stability of HfO/sub 2/ with/without Al inclusion (based on XRD and leakage current data), and energy band diagrams for metal/HfO/sub 2//Si structures as well as associated current transport mechanisms (based on gate current characteristics at various temperatures).
A Double-Blind Crossover Study of Two Cyclobenzaprine Regimens in Primary Fibromyalgia Syndrome (1993)

In a double-blind crossover study, the efficacy and tolerability of oral cyclobenzaprine administered in two different regimens were compared in 40 patients affected by primary fibromyalgia syndrome. The patients were randomly divided into two groups. Each group of 20 patients was treated for 15 days with either a single dose of 10 mg/day cyclobenzaprine at bedtime or 30 mg/day cyclobenzaprine in three equal doses daily. Following treatment there was a 15-day washout period before the groups were crossed over to the other treatment. Both regimens resulted in a significant decline in the number of tender points; significant improvements were also reported in the quality of sleep, anxiety, fatigue, irritable bowel syndrome and stiffness. There was no significant difference in efficacy between the two therapeutic regimens at any stage during the trial. The frequency of reported side-effects was significantly greater (P < 0.001) when patients received 30 mg/day cyclobenzaprine (26 patients, 84%) than when they received 10 mg/day (10 patients, 27%). A dose of 10 mg cyclobenzaprine at bedtime significantly improved the symptomatology of patients affected by primary fibromyalgia syndrome. The higher dose did not further reduce these symptoms but did result in a higher incidence of side-effects.
Rapid Recruitment of Neutrophils Containing Prestored IL-12 During Microbial Infection (2000)

Neutrophils are well known to rapidly migrate to foci of infection, where they exert microbicidal functions. We sought to determine whether neutrophils responding to in vivo infection with the protozoan pathogen Toxoplasma gondii were capable of IL-12 production as suggested by recent in vitro studies. Intraperitoneal infection induced a neutrophil influx by 4 h, accompanied by ex vivo IL-12 p40 and p70 release. Approximately 85% of the neutrophils displayed intracellular stores of IL-12, as determined by flow cytometry and confocal fluorescence microscopy. Neutrophils from IFN-gamma knockout mice also expressed IL-12, ruling out an IFN-gamma-priming requirement. Neither infected nor uninfected peritoneal macrophages displayed intracellular IL-12, but these cells were strongly IL-10(+). Infection per se was unnecessary for IL-12 production because peritoneal and peripheral blood neutrophils from uninfected animals contained IL-12(+) populations. Expression of the granulocyte maturation marker Gr-1 (Ly-6G) was correlated with IL-12 production. Mice depleted of their granulocytes by mAb administration at the time of infection had decreased serum levels of IL-12 p40. These results suggest a model in which neutrophils with prestored IL-12 are rapidly mobilized to an infection site where they are triggered by the parasite to release cytokine. Our findings place neutrophils prominently in the cascade of early events leading to IL-12-dependent immunity to T. gondii.
Vacuum encapsulation of resonant devices using permeable polysilicon (1999)

This paper reports on a novel manufacturable, in situ vacuum micropackaging technology. Permeable polysilicon etch-access windows enable rapid removal of sacrificial material from beneath the shell (e.g., 1 mm wide shells cleared of PSG within 2 minutes) and practically eliminate internal deposition of the sealing film. Inside the vacuum encapsulation shells were lateral microresonators. These devices were selected for packaging because they are well characterized vacuum probes. Measured mechanical quality factors four months after sealing have been shown to be above 3000. These quality factors indicate a cavity pressure near 600 mTorr four months after vacuum encapsulation.
Insulin resistance and pancreatic cell failure (2006)

It is now well accepted that diabetes mellitus is one of the main threats to human health in the twenty-first century. The total number of people with diabetes worldwide was estimated at between 151 million and 171 million in 2000 and is projected to increase to 221 million in 2010 and to 366 million in 2030. Needless to say, the increase in the number of people with diabetes will be accompanied by an increase in the number of those with diabetic complications such as nephropathy, retinopathy, neuropathy, and atherosclerosis. The global mortality attributable to diabetes in the year 2000 was estimated at 2.9 million deaths, a number that will also increase. Given that type 2 diabetes accounts for more than 90% of cases of diabetes worldwide, it is important that we understand the pathogenesis of this condition and develop new approaches to its prevention and treatment.
Leukemia Inhibitory Factor Promotes Neural Stem Cell Self-Renewal in the Adult Brain (2006)

Although neural stem cells (NSCs) persist in various areas of the adult brain, their contribution to brain repair after injury is very limited. Treatment with exogenous growth factors can mitigate this limitation, suggesting that the brain environment is normally deficient in permissive cues and that it may be possible to stimulate the latent regenerative potential of endogenous progenitors with appropriate signals. We analyzed the effects of overexpressing the cytokine leukemia inhibitory factor (LIF) on adult neurogenesis in the normal brain. We found that LIF reduces neurogenesis in the olfactory bulb and subventricular zone by acting directly on NSCs. LIF appears to promote NSC self-renewal, preventing the emergence of more differentiated cell types. This ultimately leads to an expansion of the NSC pool. Our results have implications for the development of therapeutic strategies for brain repair and suggest that LIF may be useful, in combination with other factors, in promoting regeneration in the adult brain.