gebhart/patrepeval huggingface dataset:
Environmental scenario search and visualization (2007)

We have developed Environmental Scenario Search Engine (ESSE) for parallel data mining of a set of conditions inside distributed, very large databases from multiple environmental domains. The prime goal for ESSE design is to allow a user to query the environmental data archives in human linguistic terms. The mapping between the human language and the computer system involves fuzzy logic. Imagine for example that the end user doesn't need all of the weather data covering the Moscow region for the last 50 years, but rather needs an example of an atmospheric front near Moscow. Further imagine that this user needs satellite images of the front and he wants to know how often such fronts occur or if they have been increasing in the last 10 years. ESSE data mining and visualization portal combines metadata search, interactive fuzzy scenario query editor and event visualization system. Visualization system is implemented as MS Windows application based on NASA World Wind 3D globe and as a web application built upon OGC WMS and Microsoft Virtual Earth control.
XToll, a recombinant chaperonin 10 as an anti-inflammatory immunomodulator. (2008)

CBio Ltd, under license from the University of Queensland, is developing a recombinant form of chaperonin 10, known as XToll, for the potential anti-inflammatory treatment of rheumatoid arthritis, psoriasis and multiple sclerosis. All three indications have been evaluated in phase IIa clinical trials. By May 2005, a phase IIa trial for Crohn's disease had been terminated due to slow recruitment. The company has not disclosed plans for future development for this indication.
On Active Resonance and Flutter Suppression Techniques (1989)

This paper deals first with robust controller design via LQG and H[sigma] techniques. Such controllers then form a basis for augmentations with adaptive control loops to achieve resonance suppression. This work has been motivated by earlier adaptive flutter suppression schemes and is expected to lead to more effective adaptive flutter suppression schemes.
Adipose Tissue Dysfunction and Altered Systemic Amino Acid Metabolism Are Associated with Non-Alcoholic Fatty Liver Disease (2015)

Fatty liver is a major cause of obesity-related morbidity and mortality. The aim of this study was to identify early metabolic alterations associated with liver fat accumulation in 50-to 55year-old men (n = 49) and women (n = 52) with and without NAFLD.
Simultaneous Wavelength-Swept Generation in NIR and SWIR Bands Over Combined 329-nm Band Using Swept-Pump Fiber Optical Parametric Oscillator (2010)

We report the demonstration of a new wavelength-swept source. Utilizing narrowband, widely tunable fiber optical parametric process as the gain and the wavelength selection mechanism in a ring laser topology, simultaneous access to two distinct bands (NIR and SWIR) over 329 nm was achieved. A nonmechanical cavity-tuning mechanism allowed for ultrafast sweep rate, limited primarily by the speed of the tunable pump source confined to a conventional 1550-nm band. With the experimentally verified order-of-magnitude enhancement in sweep range and speed, the source opens a path for spectral scanning at an unprecedented speed and range while relying on existing tuning technologies.
Osteoclast Numbers in Lewis Rats with Adjuvant-induced Arthritis: Identification of Preferred Sites and Parameters for Rapid Quantitative Analysis (2004)

This study defined the best site for quantifying osteoclasts in male Lewis rats with mycobacteria-induced adjuvant arthritis. Hind paw sections of normal and arthritic rats (n = 6 per group) taken 7 days after disease onset were stained for osteoclasts using an anti-human cathepsin K primary antibody. Erosions and osteoclasts were assessed using semiquantitative scores (entire section) and quantitative measures (in calcaneus, navicular tarsal, and tibia). Bone area in arthritic rats was significantly reduced (P </= 0.05) by 39-55%, with the greatest decrease in the tarsal. Osteoclasts in arthritic rats were significantly increased (P </= 0.05) relative to normal in calcaneus (sevenfold), tarsal (194-fold), and tibia (threefold). The most useful quantitative indices were bone area and total osteoclasts, both defined as a percentage of total area measured. Semiquantitative scores for bone erosion and osteoclasts paralleled the quantitative indices. These data show that the navicular tarsal is the most sensitive site at which to assess arthritis in rats with this variant of adjuvant-induced arthritis.
PRECLINICAL AND CLINICAL EVALUATION OF A CDR-GRAFTED (HUMANIZED) ANTI-CARCINOEMBRYONIC ANTIGEN (CEA) MONOCLONAL ANTIBODY (MAb) (1994)

s: Fifth Conference on Radioimmunodetection and Radioimmunotherapy of Cancer: Session X: Reengineered Antibodies: PDF Only
Effect of IL‐2‐Bax, a novel interleukin‐2‐receptor‐targeted chimeric protein, on bleomycin lung injury1 (2005)

The role of lymphocytes in the pathogenesis of lung fibrosis is not clear, but the weight of the evidence supports a pro-fibrotic effect for lymphocytes. The high-affinity interleukin-2 receptor (haIL-2R) is expressed on activated, but not quiescent, T lymphocytes. This selective expression of haIL-2R provides the basis for therapeutic strategies that target IL-2R-expressing cells. We hypothesized that elimination of activated lymphocytes by IL-2R-targeted chimeric proteins might ameliorate lung fibrosis. We investigated the effects of IL-2-Bax, a novel apoptosis-inducing IL-2R-targeted chimeric protein, on bleomycin-induced lung injury in mice. Treatment groups included (i) a single intratracheal instillation of bleomycin and twice-daily intraperitoneal injections of IL-2-Bax; (ii) intratracheal bleomycin and intraperitoneal IL-2-PE66(4Glu), an older-generation chimeric protein; (iii) intratracheal bleomycin/intraperitoneal PBS; (iv) intratracheal saline/intraperitoneal PBS. Lung injury was evaluated 14 days after intratracheal instillation by cell count in bronchoalveolar lavage (BAL) fluid, semi-quantitative and quantitative histomorphological measurements and by biochemical analysis of lung hydroxyproline. Bleomycin induced a BAL lymphocytosis that was significantly attenuated by IL-2-Bax and IL-2-PE66(4Glu). However, morphometric parameters and lung hydroxyproline were unaffected by the chimeric proteins. These results show that IL-2-Bax reduces the lymphocytic infiltration of the lungs in response to bleomycin, but this effect is not accompanied by a decrease in lung fibrosis.
Cost Aggregation and Occlusion Handling With WLS in Stereo Matching (2008)

This paper presents a novel method for cost aggregation and occlusion handling for stereo matching. In order to estimate optimal cost, given a per-pixel difference image as observed data, we define an energy function and solve the minimization problem by solving the iterative equation with the numerical method. We improve performance and increase the convergence rate by using several acceleration techniques such as the Gauss-Seidel method, the multiscale approach, and adaptive interpolation. The proposed method is computationally efficient since it does not use color segmentation or any global optimization techniques. For occlusion handling, which has not been performed effectively by any conventional cost aggregation approaches, we combine the occlusion problem with the proposed minimization scheme. Asymmetric information is used so that few additional computational loads are necessary. Experimental results show that performance is comparable to that of many state-of-the-art methods. The proposed method is in fact the most successful among all cost aggregation methods based on standard stereo test beds.
Cortisol, Hypothermic, and Behavioral Responses to Ipsapirone in Patients with Bipolar Depression and Normal Controls (1998)

To examine if 5-HT1A receptor function is involved in the pathophysiology of bipolar depression, we measured the cortisol, hypothermic and behavioral responses to ipsapirone, a 5-HT1A receptor agonist, in 8 patients with bipolar depression and 26 normal controls. After obtaining blood samples for baseline cortisol levels and measuring baseline body temperature, a single dose of 0.3 mg/kg of ipsapirone was administered orally to all the subjects, and further blood and temperature readings were obtained every 30 min for 3 h. The results showed that the administration of ipsapirone led to a significant increase in cortisol release and a significant decrease in body temperature both in bipolar depressed patients and normal controls. There was no significant difference in the cortisol or hypothermic responses to ipsapirone between groups. However, there was a significant positive correlation between the Hamilton Depression Rating (HAMD) scores and the hypothermic response in the depressed patients, while the HAMD scores were not significantly correlated with the cortisol response. Comparing our findings with those of previous studies, we suggest that the alterations in 5-HT1A receptor sensitivity in depressed patients may be related to the severity of depression, and they may only occur in more severely depressed patients.
Dramatic rate acceleration in titanocene catalyzed epoxide openings: cofactors and Lewis acid cocatalysis (1998)

High synthetic efficiency concerning yield and catalytic turn-over in intermolecular C–C bond forming reactions of radicals derived from epoxides can be achieved by means of hydrogen bonding with cofactors or by Lewis acid cocatalysis.
Digital Transcript Profile Analysis with aRNA-LongSAGE Validates FERMT1 As a Potential Novel Prognostic Marker for Colon Cancer (2011)

FERMT1 is a novel prognostic factor for colon carcinoma.
Validating internal controls for quantitative plant gene expression studies (2004)

Our results support that quantitative comparisons of candidate reference genes are an important part of real-time RT-PCR studies that seek to precisely evaluate variation in gene expression. The method we demonstrated facilitates statistical and graphical evaluation of gene expression stability. Selection of the best reference gene for a given set of experimental conditions should enable detection of biologically significant changes in gene expression that are too small to be revealed by less precise methods, or when highly variable reference genes are unknowingly used in real-time RT-PCR experiments.
The Structure of Clostridium perfringens NanI Sialidase and Its Catalytic Intermediates (2008)

Clostridium perfringens is a Gram-positive bacterium responsible for bacteremia, gas gangrene, and occasionally food poisoning. Its genome encodes three sialidases, nanH, nanI, and nanJ, that are involved in the removal of sialic acids from a variety of glycoconjugates and that play a role in bacterial nutrition and pathogenesis. Recent studies on trypanosomal (trans-) sialidases have suggested that catalysis in all sialidases may proceed via a covalent intermediate similar to that of other retaining glycosidases. Here we provide further evidence to support this suggestion by reporting the 0.97A resolution atomic structure of the catalytic domain of the C. perfringens NanI sialidase, and complexes with its substrate sialic acid (N-acetylneuramic acid) also to 0.97A resolution, with a transition-state analogue (2-deoxy-2,3-dehydro-N-acetylneuraminic acid) to 1.5A resolution, and with a covalent intermediate formed using a fluorinated sialic acid analogue to 1.2A resolution. Together, these structures provide high resolution snapshots along the catalytic pathway. The crystal structures suggested that NanI is able to hydrate 2-deoxy-2,3-dehydro-N-acetylneuraminic acid to N-acetylneuramic acid. This was confirmed by NMR, and a mechanism for this activity is suggested.
Regulation of protein synthesis in Swiss 3T3 fibroblasts. Rapid activation of the guanine-nucleotide-exchange factor by insulin and growth factors (1992)

Insulin, whole serum, phorbol esters and epidermal growth factor each rapidly stimulate protein synthesis in serum-depleted Swiss 3T3 fibroblasts. The activation of protein synthesis by each of these agents is associated with stimulation of the activity of the guanine-nucleotide-exchange factor (GEF). This protein recycles the initiation factor eIF-2 by promoting exchange of GDP bound to eIF-2 for GTP. Activation of GEF is rapid, becoming maximal within 15 min. The degree of activation of GEF by these stimuli (to greater than 170% of control for insulin, serum or epidermal growth factor; 120% for phorbol dibutyrate) is more than enough to account for their effects on the overall rate of translation. Stimulation of protein synthesis and GEF activity occurs at low nanomolar insulin concentrations, indicating they are mediated through the insulin receptor. The best-characterized mechanism for regulating GEF activity is through changes in the phosphorylation of the smallest subunit of eIF-2 (eIF-2 alpha); however, none of the stimuli studied altered the level of phosphorylation of eIF-2 alpha in Swiss fibroblasts. It seems that direct regulation of GEF activity may be occurring here, and possible mechanisms for this are discussed.
A Synthetic Cell-Penetrating Dominant-Negative ATF5 Peptide Exerts Anticancer Activity against a Broad Spectrum of Treatment-Resistant Cancers (2016)

Our data support the idea that CP-d/n-ATF5-S1, administered as a single reagent or in combination with other drugs, holds promise as an innovative, safe, and efficient antineoplastic agent against treatment-resistant cancers. Clin Cancer Res; 22(18); 4698-711. ©2016 AACR.
A Mutant of Arabidopsis Deficient in the Elongation of Palmitic Acid (1994)

The overall fatty acid composition of leaf lipids in a mutant of Arabidopsis thaliana was characterized by an increased level of 16:0 and a concomitant decrease of 18-carbon fatty acids as a consequence of a single recessive nuclear mutation at the fab1 locus. Quantitative analysis of the fatty acid composition of individual lipids established that lipids synthesized by both the prokaryotic and eukaryotic pathways were affected by the mutation. Direct enzyme assays demonstrated that the mutant plants were deficient in the activity of 3-ketoacyl-acyl carrier protein synthase II; therefore, it is inferred that fab1 may encode this enzyme. Labeling experiments with [14C]acetate and lipase positional analysis indicated that the mutation results in a small shift in the partitioning of lipid synthesis between the prokaryotic and eukaryotic pathways. Synthesis of chloroplast lipids by the prokaryotic pathway was increased with a corresponding reduction in the eukaryotic pathway.
Proteinase trapping: screening for viral proteinase mutants by alpha complementation. (1991)

Many virally encoded proteinases cleave themselves out of a polyprotein, with cleavage occurring usually at their own N terminus. This property was used to develop an in vivo screening system using the lacZ gene fragment of M13mp18. When a fusion protein of the alpha fragment of beta-galactosidase and an active 2A proteinase of human rhinovirus 2 was expressed, alpha complementation was not affected, as the 2A proteinase cleaved itself off the alpha fragment. However, fusion of an inactive 2A prevented alpha complementation, as the 2A polypeptide remained fused to the alpha fragment. After random mutation of the 2A gene by PCR amplification, mutants were screened; M13 phage defective in alpha complementation were obtained at an efficiency of 5% and were shown to contain mutated 2A genes. Intermolecular cleavage was then examined by expressing an alpha fragment-inactive proteinase fusion protein as substrate for an active 2A proteinase expressed from an M13 vector. alpha complementation indicated intermolecular processing of the 2A cleavage site on the alpha fragment-inactive proteinase fusion protein. This versatile system thus allows the high-density screening of both active and inactive proteinase mutants, cleaving either intramolecularly or intermolecularly, and should be applicable to other proteinases of high specificity.
Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis (1980)

We assess various approximate forms for the correlation energy per particle of the spin-polarized homogeneous electron gas that have frequently been used in applications of the local spin density approximation to the exchange-correlation energy functional. By accurately recalculating the RPA correlation energy as a function of electron density and spin polarization we demonstrate the inadequacies of the usual approximation for interpolating between the para- and ferro-magnetic states and present an accurate new interpolation formula. A Padé approximant technique is used to accurately interpolate the recent Monte Carlo results (para and ferro) of Ceperley and Alder into the important range of densities for atoms, molecules, and metals. These results can be combined with the RPA spin-dependence so as to produce a correlation energy for a spin-polarized homogeneous electron gas with an estimated maximum error of 1 mRy and thus should reliably determine the magnitude of non-local corrections to the local spin density approximation in real systems.
ChemInform Abstract: Syntheses and Antibacterial Activity of Novel 6‐Fluoro‐7‐(gem‐ disubstituted‐piperazin‐1‐yl)‐quinolines. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Characterization of the ethanol-inducible alc gene expression system in tomato (2005)

The efficacy of the ethanol-inducible alc transgene expression system, derived from the filamentous fungus Aspergillus nidulans, has been demonstrated in transgenic tomato. Two direct comparisons have been made. First, this study has utilized two transgenic lines carrying distinct reporter genes (chloramphenicol acetyltransferase and beta-glucuronidase) to distinguish aspects of induction determined by the nature of the gene/gene product rather than that of the plant. Second, comparisons have been made to data generated in other species in order to identify any species-specific effects. The induction profiles for different genes in different species have shown remarkable similarity indicating the broad applicability of this gene switch. While there are minor differences observed between species, these probably arise from diversity in their metabolism. A series of potential alternative inducers have also been tested, revealing that ethanol (through metabolism to acetaldehyde) is better than other alcohols and ketones included in this study. Expression driven by alc was demonstrated to vary spatially, the upper younger leaves having higher activity than the lower older leaves; this will be important for some applications, and for experimental design. The highest levels of activity from ethanol-inducible transgene expression were determined to be the equivalent of those from the constitutive Cauliflower Mosaic Virus 35S promoter. This suggests that the alc system could be an important tool for plant functional genomics.
Modified RNA sequence pools forin vitroselection (1994)

We report the use of modified RNA, in which the 2'-OH group of pyrimidines is replaced by a 2'-amino (2'-NH2) group to identify high affinity ligands specific for human neutrophil elastase (HNE) by in vitro selection. Compared to unmodified RNA the 2'-NH2-modified RNA ligands show enhanced stability in human serum and urine. Use of RNase T1 cleavage data in the presence of K+ and Li+ ions suggests that the modified RNA ligands selected for HNE form an intermolecular G-quartet structure.
Bombesin antagonists inhibit proangiogenic factors in human experimental breast cancers (2004)

The overexpression of angiogenic factors such as vascular endothelial growth factor (VEGF), fibroblast growth factor (FGF) and insulin-like growth factors (IGFs) plays a role in the migration and proliferation of endothelial cells in many cancers. Consequently, we investigated the effects of bombesin/gastrin-releasing peptide (GRP) antagonists on the expression of these angiogenic factors, the activities of matrix metalloproteinases (MMPs)-2 and -9, as well as the vascular density in MDA-MB-435 human oestrogen-independent breast cancers. Nude mice bearing orthotopic xenografts of MDA-MB-435 breast cancers were treated with bombesin/GRP antagonists for 6 weeks. Daily administration of 20 microg of RC-3095 or 10 microg of RC-3940-II significantly decreased the weight of MDA-MB-435 cancers by 44 and 53%, respectively. The inhibition of tumour growth was associated with a substantial reduction in the expression of mRNA and protein levels of basic fibroblast growth factor (bFGF), IGF-II and VEGF-A in the tumours. Both bombesin/GRP antagonists significantly decreased the vessel density of the tumours by about 37%, as shown by immunohistochemical detection of vessels on tumour slides. Gelatinolytic activities, detected by zymography, revealed a 33-46% reduction in MMP-9 activity after the treatment with either antagonist. In vitro studies revealed that MDA-MB-435 cells secrete bFGF, IGF-II and VEGF-A, and the secretion of these factors is inhibited by RC-3095 and RC-3940-II. This study demonstrates the antiangiogenic effect of bombesin/GRP antagonists RC-3095 and RC-3940-II, and underscores their possible therapeutic application for treatment of breast cancers.
A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity (2001)

The recent completion of the deletion of essentially all of the ORFs in yeast is an important new resource for identifying the phenotypes of unknown genes. Each ORF is replaced with a cassette containing unique tag sequences that allow rapid parallel analysis of strains in a pool by using hybridization to a high-density oligonucleotide array. We examined the utility of this system to identify genes conferring resistance to UV irradiation by using a pool of 4,627 individual homozygous deletion strains (representing deletions of all nonessential genes). We identified most of the nonessential genes previously shown to be involved in nucleotide excision repair, in cell cycle checkpoints, in homologous recombination, and in postreplication repair after UV damage. We also identified and individually confirmed, by replacing the genes, three new genes, to our knowledge not previously reported to confer UV sensitivity when deleted. Two of these newly identified genes have human orthologs associated with cancer, demonstrating the potential of this system to uncover human genes affecting sensitivity to DNA-damaging agents and genes potentially involved in cancer formation.