gebhart/patrepeval huggingface dataset:
Anaerobic Biotransformation of 2,4-Dinitrotoluene and 2,6-Dinitrotoluene by<i>Clostridium acetobutylicum:</i>A Pathway through Dihydroxylamino Intermediates (1999)

Experiments were conducted to isolate and identify the intermediates and products of 2,4-dinitrotoluene and 2,6-dinitrotoluene metabolism by Clostridium acetobutylicum. Transformation of both dinitrotoluenes initially resulted in the formation of hydroxylaminonitrotoluenes. Subsequent transformation favored the formation of dihydroxylaminotoluenes, with a limited reduction to aminonitrotoluene isomers. In cell cultures, metabolism beyond the level of dihyroxylaminotoluene was not observed. In cell extracts, where activity could be maintained for periods in excess of those in cell cultures, further transformation yielded aminohydroxylaminotoluenes and eventually diaminotoluenes. These findings further demonstrate the potential for hydroxylamines to be significant intermediates of nitroaromatic transformation under anaerobic fermentative conditions. Interestingly, the rearrangement of dihydroxylaminotoluenes was not observed, as was the case in previous studies of 2,4-dihydroxylamino-6-nitrotoluene metabolism (e.g., the dihydroxylamino metabolite of 2,4,6-trinitrotoluene transformation by C. acetobutylicum). Dihydroxylaminotoluenes were found to be quite unstable, decomposing rapidly upon exposure to oxygen, complicating the assessment of their fate in remediation processes.
Scaling clustering algorithms for massive data sets using data streams (2004)

Computing clustering techniques on massive data sets is still not feasible nor efficient today. For instance, raw satellite imagery data can be replaced with compressed counterparts for many scientific applications. However, to facilitate scientific data analysis the high order correlation between the attributes in the data set as well as their nonparametric distribution must be preserved in the reduced data set. Therefore, practical data reduction can be achieved by partitioning the overall data set via a coarse regular spatial grid, and compressing each grid cell individually by computing multivariate histograms or k-means clustering. Clustering spatial data in high dimensional spaces using k-means is expensive both with regard to computational costs and memory requirements. In a traditional k-means implementation all N data points belonging to a grid cell must be kept in memory to be clustered at a time, which often establishes a bottleneck for scientific data sets. Our objective is to define a clustering algorithm that scales automatically to any number of data points in a single grid cell, and provides high quality clustering results.
CXCL1 induced by prostaglandin E2 promotes angiogenesis in colorectal cancer (2006)

Chronic inflammation is a well-known risk factor for cancer. Proinflammatory mediators such as prostaglandin E2 (PGE2) promote colorectal tumor growth by stimulating angiogenesis, cell invasion, and cell growth, and inhibiting apoptosis. Molecules that regulate tumor-associated angiogenesis provide promising therapeutic targets for treatment of colorectal cancer (CRC) as indicated by the recent development of the novel anti-angiogenic agent bevacizumab (Avastin). However, use of this drug only prolongs survival by several months, highlighting the importance of finding more effective treatment regimens. We report here that PGE2 induces expression of CXCL1 (growth-regulated oncogene alpha), a pro-angiogenic chemokine, in human CRC cells. More importantly, CXCL1 released from carcinoma cells induces microvascular endothelial cell migration and tube formation in vitro. Furthermore, PGE2 promotes tumor growth in vivo by induction of CXCL1 expression, which results in increased tumor microvessel formation. These results have potential clinical significance because we found that CXCL1 expression correlates with PGE2 levels in human CRCs. Collectively, our findings show for the first time that CXCL1 is regulated by PGE2 and indicate that CXCL1 inhibitors should be evaluated further as potential anti-angiogenic agents for treatment of CRC.
Heme and the Vasculature: an Oxidative Hazard that Induces Antioxidant Defenses in the Endothelium (1994)

Heme proteins transport oxygen and facilitate redox reactions. Heme, however, may be dangerous, especially when free in biologic systems. For example, iron released from hemoglobin-derived heme can catalyze oxidative injury to neuronal cell membranes and may be a factor in post-traumatic damage to the central nervous system. We have shown that heme catalyzes the oxidation of low density lipoproteins which can damage vascular endothelial cells. The endothelium is susceptible to damage by oxidants generated by activated phagocytes, and this has been invoked as an important mechanism in a number of pathologies including the Adulte Respiratory Distress Syndrome (ARDS), acute tubular necrosis, reperfusion injury and atherosclerosis. Because of its highly hydrophobic nature, heme readily intercalates into endothelial membranes and potentiates oxidant-mediated damage. This injury is dependent on the iron content of heme and is completely blocked when concomitant hemopexin is added. Ferrohemoglobin, when added to cultured endothelial cells, is without deleterious effects, but if oxidized to ferrihemoglobin (methemoglobin), it greatly amplifies oxidant damage. Methemoglobin, but not ferrohemoglobin, releases its hemes which can then be incorporated into endothelial cells. Cultured endothelial cells, when exposed to methemoglobin but not ferrohemoglobin, cytochrome c or metmyoglobin, potentiate this oxidant injury. Stabilization of the methemoglobin by cyanide, haptoglobin or capture of the heme by hemopexin abrogates this effect. Paradoxically, more prolonged exposure of endothelium to heme or methemoglobin renders them remarkably resistant to oxidant challenge. Endothelium defends itself from heme by induction of the heme degrading enzyme heme oxygenase and the concomitant production of large amounts of the iron binding protein ferritin.(ABSTRACT TRUNCATED AT 250 WORDS)
Self-Regulated Learning in Learning Environments With Pedagogical Agents That Interact in Natural Language (2010)

This article discusses the occurrence and measurement of self-regulated learning (SRL) both in human tutoring and in computer tutors with agents that hold conversations with students in natural language and help them learn at deeper levels. One challenge in building these computer tutors is to accommodate, encourage, and scaffold SRL because these skills are not adequately developed for most students. Automated measures of SRL are needed to track progress in meeting this challenge. A direct approach is to train students on fundamentals of metacognition and SRL, which is the approach taken by iSTART, MetaTutor, and other agent environments. An indirect approach to promoting SRL, taken by AutoTutor, is to track the student's knowledge and SRL based on the student's language and to respond intelligently with discourse moves to promote SRL. This fine-grained adaptivity considers the student's cognitive states, the discourse interaction, and the student's emotional states in a recent AutoTutor version.
Effects of Dosing Condition on the Oral Bioavailability of Green Tea Catechins after Single-Dose Administration of Polyphenon E in Healthy Individuals (2005)

We conclude that greater oral bioavailability of free catechins can be achieved by taking the Polyphenon E capsules on an empty stomach after an overnight fast. Polyphenon E up to a dose that contains 800 mg epigallocatechin gallate is well-tolerated when taken under the fasting condition. This dosing condition is also expected to optimize the biological effects of tea catechins.
Analysis and Economic Implication of X-Ray Film Reject in Diagnostic Radiology Department of Jimma University Specialized Hospital, Southwest Ethiopia (2017)

The findings from this study show that both the overall reject rate and individual reject rate were higher than the accepted range which could be due to machine fault, operator's technical limitations, or absence of quality control program in the department. We recommend that regular quality assurance and quality control procedure which are well documented should be established in the department.
Upregulation of the Hsp104 chaperone at physiological temperature during recovery from thermal insult (2004)

Thermal insult at 50 degrees C causes protein denaturation in yeast, but the cells survive if preconditioned at 37 degrees C. Survival depends on refolding of heat-denatured proteins. Refolding of cytoplasmic proteins requires Hsp104, the expression of which increases several-fold upon shift of the cells from physiological temperature 24 degrees C to 37 degrees C. We describe here a novel type of regulation of Hsp104, designated delayed upregulation (DUR). When Saccharomyces cerevisiae cells grown at 24 degrees C, preconditioned at 37 degrees C and treated briefly at 50 degrees C were shifted back to 24 degrees C, Hsp104 expression was negligible for 1 h, but increased then to a three to nine times higher level than that detected after growth at 24 degrees C, returning to normal after 5 h. A heat shock element (HSE) of the upstream sequence of HSP104 was necessary and sufficient for DUR, whereas stress response elements (STRE) were dispensable. Destruction of HSE plus all three STREs abolished Hsp104 expression, resulting in cell death after thermal insult. Deletion of MSN2/4, encoding transcription factors driving STRE-dependent gene expression, decreased DUR. Deletion of HOG1, encoding a heat-responsive and osmosensitive mitogen-activated protein kinase implicated to be functionally connected to Msn2/4p, abolished DUR. We suggest that DUR was regulated via HSE, required Hog1p and involved Msn2/4p-regulated gene products.
BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing (2017)

Amplicon-based next-generation sequencing (NGS) has been widely adopted for genetic variation detection in human and other organisms. Conventional data analysis paradigm includes primer trimming before read mapping. Here we introduce BAMClipper that removes primer sequences after mapping original sequencing reads by soft-clipping SAM/BAM alignments. Mutation detection accuracy was affected by the choice of primer handling approach based on real NGS datasets of 7 human peripheral blood or breast cancer tissue samples with known BRCA1/BRCA2 mutations and >130000 simulated NGS datasets with unique mutations. BAMClipper approach detected a BRCA1 deletion (c.1620_1636del) that was otherwise missed due to edge effect. Simulation showed high false-negative rate when primers were perfectly trimmed as in conventional practice. Among the other 6 samples, variant allele frequencies of 5 BRCA1/BRCA2 mutations (indel or single-nucleotide variants) were diluted by apparently wild-type primer sequences from an overlapping amplicon (17 to 82% under-estimation). BAMClipper was robust in both situations and all 7 mutations were detected. When compared with Cutadapt, BAMClipper was faster and maintained equally high primer removal effectiveness. BAMClipper is implemented in Perl and is available under an open source MIT license at https://github.com/tommyau/bamclipper.
Pressureless Sintering of Zirconium Diboride Using Boron Carbide and Carbon Additions (2007)

The synergistic roles of boron carbide and carbon additions in the enhanced densification of zirconium diboride (ZrB 2 ) by pressureless sintering have been studied. ZrB 2 was sintered to >99% relative density at 1900°C. The combination of 2 wt% boron carbide and 1 wt% carbon promoted densification by removing surface oxide impurities (ZrO 2 and B 2 O 3 ) and inhibiting grain growth. Four‐point bending strength (473±43 MPa), Vickers' microhardness (19.6±0.4 GPa), fracture toughness (3.5±0.6 MPa·m 1/2 ), and Young's modulus (507 GPa) were measured. Thermal gravimetry showed that the combination of additives did not have an adverse effect on the oxidation behavior.
Mobile robot for power substation inspection: a survey (2017)

This paper presents the most important achievements in the field of electric power substation equipment's inspection by mobile robot. To accelerate the realization of unattended substation, which would improve the reliability, safety and intelligence of power substation, the field of automated power substation equipment's inspection has been greatly developed over the last decade. The paper addresses the power substation inspection robot, which is considered as one of the most active fields of research on mobile robot, from its history to design requirements, the robot system architecture analysis and modeling, reliability technology of the robot, autonomy and universality of substation equipment inspection. Besides, summaries and suggestions on the development and research trend of inspection robot, which should be addressed in the future, are given. The present work may serve as reference for initial design of robots for some complex and dangerous working environments. And some unique insights for the inspection robot provided in this paper may be of help to further research and application of power facilities inspection.
Comparing tightly and loosely coupled mesochronous synchronizers in a NoC switch architecture (2009)

With the advent of networks-on-chip (NoCs), the interest for mesochronous synchronizers is again on the rise due to the intricacies of skew-controlled chip-wide clock tree distribution. Recently proposed schemes agree on a source synchronous design style with some form of ping-pong buffering to counter timing and metastability concerns. However, the integration issues of such synchronizers in a NoC setting are still largely uncovered. Most schemes are in fact placed between communicating switches, thus neglecting the abrupt increase of buffering resources needed at switch input stages. This paper goes a step forward and aims at deep integration of the synchronizer in the switch architecture, thus merging key tasks such as synchronization, buffering and flow control into a unique architecture block. This paper compares the integrated and the loosely coupled solutions from a performance and area viewpoint, while devoting special attention to their robustness with respect to physical design parameters.
Effect of biosynthetic manipulation of heme on insolubility of Vitreoscilla hemoglobin in Escherichia coli (1994)

Vitreoscilla hemoglobin (VHb) is accumulated at high levels in both soluble and insoluble forms when expressed from its native promoter on a pUC19-derived plasmid in Escherichia coli. Examination by atomic absorption spectroscopy and electron paramagnetic resonance spectroscopy revealed that the insoluble form uniformly lacks the heme prosthetic group (apoVHb). The purified soluble form contains heme (holoVHb) and is spectroscopically indistinguishable from holoVHb produced by Vitreoscilla cells. This observation suggested that a relationship may exist between the insolubility of apoVHb and biosynthesis of heme. To examine this possibility, a series of experiments were conducted to chemically and genetically manipulate the formation and conversion of 5-aminolevulinic acid (ALA), a key intermediate in heme biosynthesis. Chemical perturbations involved supplementing the growth medium with the intermediate ALA and the competitive inhibitor levulinic acid which freely cross the cell barrier. Genetic manipulations involved amplifying the gene dosage for the enzymes ALA synthase and ALA dehydratase. Results from both levulinic acid and ALA supplementations indicate that the level of soluble holoVHb correlates with the heme level but that the level of insoluble apoVHb does not. The ratio of soluble to insoluble VHb also does not correlate with the level of total VHb accumulated. The effect of amplifying ALA synthase and ALA dehydratase gene dosage is complex and may involve secondary factors. Results indicate that the rate-limiting step of heme biosynthesis in cells overproducing VHb does not lie at ALA synthesis, as it reportedly does in wild-type E. coli (S. Hino and A. Ishida, Enzyme 16:42-49, 1973).
A New Class of Rotary Piston Machine Suitable for Compressors, Pumps and Internal Combustion Engines (1972)

The mechanisms and porting requirements of a new class of rotary piston machine are described. The machines can be regarded as a generalization to three dimensions of that class of planetary motion machine which includes the Wankel. Important features of the Wankel engine are retained, namely a compact arrangement, a sliding contact seal grid and multiple chambers on each rotor, but these new machines have twice as many chambers on each rotor, and they apply results of three-dimensional rigid body dynamics to select piston motions which involve very low inertial forces. An experimental engine is described with some results.
1321. Studies in the indole series. Part I. Indolylalkylamines (1965)

B. Heath-Brown and P. G. Philpott, J. Chem. Soc., 1965, 7165 DOI: 10.1039/JR9650007165
Activity and fluorescence changes of lactate dehydrogenase induced by guanidine hydrochloride in reverse micelles (1994)

Denaturants activate several multimeric enzymes in reverse micelles [Garza-Ramos, G., Darszon, A., Tuena de Gómez-Puyou, M. & Gómez-Puyou, A. (1992) Eur. J. Biochem. 205, 509-517]. Here, the effect on activity and intrinsic fluorescence of pig heart lactate dehydrogenase (LDH) in reverse micelles [formed with 0.2 M cetyltrimethylammonium bromide in octane/hexanol (8.6:1, by vol.)] was explored at various water and guanidine hydrochloride (Gdn/HCl) concentrations. Emission fluorescence spectra of LDH in aqueous media and in micelles were similar. As in all aqueous media, 1.0 M Gdn/HCl in the water phase of reverse micelles produced fluorescence quenching and a blue shift of the maximal emission. In 5.0 M Gdn/HCl, instead of the red shift and significant quenching seen in water, the maximum emission further shifted to the blue and was only slightly quenched. Gdn/HCl titrations of activity and fluorescence changes of LDH in micelles with different water contents showed that at Wo ([H2O]/[surfactant]) of 6.6, 8.3, or 12.5, increasing concentrations of Gdn/HCl up to 0.6 M produced small changes in fluorescence, whereas activity increased several-fold. At higher denaturant concentrations, activity decreased with significant fluorescence changes. In reverse micelles with 1 M Gdn/HCl, Vmax but not Km of LDH decreased with time. Under these conditions, there was progressive quenching of LDH fluorescence. The results show that in reverse micelles different Gdn/HCl concentrations induce variations in activity with or without alterations of the intrinsic fluorescence of LDH. The results also indicate that in reverse micelles, concentrations of Gdn/HCl below 1.0 M cause an enhancement of protein flexibility; this is accompanied by a marked increase in activity without important changes in intrinsic fluorescence. 1.0 M Gdn/HCl produces perturbations of inter-subunit contacts that lead to fluorescence quenching and loss of catalytic activity, probably as consequence of dimerization of tetrameric LDH.
MEL gene polymorphism in the genus Saccharomyces (1993)

In Saccharomyces spp. the ability to use melibiose depends on the presence of a MEL gene encoding alpha-galactosidase. We used two cloned MEL genes as probes to characterize the physical structure and chromosomal location of the MEL genes in several industrial and natural Mel+ strains of Saccharomyces cerevisiae, Saccharomyces pastorianus, and Saccharomyces bayanus. Electrokaryotyping showed that all of the S. pastorianus strains and most of the S. bayanus strains studied had one MEL locus. The MEL gene in S. bayanus strains was similar but not identical to the S. pastorianus MEL gene. Mel+ S. cerevisiae strains had one to seven loci containing MEL sequences. The MEL genes of these strains could be divided into two categories on the basis of hybridization to MEL1, one group exhibiting strong hybridization to MEL1 and the other group exhibiting weak hybridization to MEL1. In S. pastorianus and S. bayanus strains, the MEL gene was expressed as a single 1.5-kb transcript, and the expression was galactose inducible. In some S. cerevisiae strains, the MEL genes were expressed even without induction at fairly high levels. Expression was usually further induced by galactose. In two strains, CBS 5378 and CBS 4903, expression of the MEL genes was at the same level without induction as it was in most other strains with induction. In all S. cerevisiae strains, irrespective of the number of MEL genes, mRNA of only one size (1.6 kb) was observed.
Observation of lymphatic vessels in orbital fat of patients with inflammatory conditions: a form fruste of lymphangiogenesis? (2004)

In the absence of antibodies specific for lymphatic vessels, analysis of lymphatic vessels within different tissues has been widely performed with light microscopic and, most importantly, electron microscopic techniques. In regard to lymphatic vessels in the ocular globe and the periocular structures, controversy remains about the specific distribution of lymphatic channels. It is postulated that bulbar and retrobulbar tissues are devoid of lymphatic vessels, but lymphatic vessels have been demonstrated in lacrimal gland and epibulbar conjunctiva. In this study, we analyzed orbital fat for the presence of lymphatic tissue using D2-40, a monoclonal antibody, specific for lymphatic vessels. We found lymphatic vessels present within bulbar conjunctiva extending to the level of the ciliary apparatus. No lymphatics were identified in healthy anterior orbital adipose tissue. In two cases of orbital mucor-mycosis and one case of panendophthalmitis, significant lymphovascular proliferation was present within granulation tissue associated with the acute inflammation. We conclude that lymph vessel proliferation may be induced in inflammatory conditions in tissues which are normally devoid of lymph channels.
The metal interlayer in the charge generation layer of tandem organic light-emitting diodes (2013)

This work studies the interface in the charge generation layer (CGL), consisting of aluminum (Al) doped in poly(ethylene glycol) dimethyl ether as an n-type layer and 2, 3, 5, 6-tetrafluoro-7, 7, 8, 8-tetracyanoquinodimethane (F4-TCNQ) doped in N,N′-bis-(1-naphthyl)-N,N′-diphenyl-1,1′-biphenyl-4-4′-diamine as an p-type layer, in tandem organic light-emitting diodes (OLEDs). Introducing a thin high work function metal interlayer (e.g., Ag or Au) effectively improves the transport and inhibits the accumulation of charges in the CGL, which markedly reduces the operating voltage and enhances the efficiency of tandem OLEDs. We attribute that the high density of surface states on metal clusters (interlayer) reduce the junction barrier to facilitate the transport of carriers through CGL. Experimental results show enhancements of tandem OLEDs by an additional metal interlayer as follows: luminous efficiency increases from 37.2 to 51.4 cd A−1, the light turn-on voltage decreases from 9.2 to 6.6 V, and luminescence at 10 mA cm−2 increases from 3712 to 5211 cd m−2.