gebhart/patrepeval huggingface dataset:
Efficient Epoxidation of Olefins with ≥99% Selectivity and Use of Hydrogen Peroxide (2003)

Epoxides are an important class of industrial chemicals that have been used as chemical intermediates. Catalytic epoxidation of olefins affords an interesting production technology. We found a widely usable green route to the production of epoxides: A silicotungstate compound, [gamma-SiW10O34(H2O)2]4-, is synthesized by protonation of a divacant, lacunary, Keggin-type polyoxometalate of [gamma-SiW10O36]8- and exhibits high catalytic performance for the epoxidation of various olefins, including propylene, with a hydrogen peroxide (H2O2) oxidant at 305 kelvin. The effectiveness of this catalyst is evidenced by >/=99% selectivity to epoxide, >/=99% efficiency of H2O2 utilization, high stereospecificity, and easy recovery of the catalyst from the homogeneous reaction mixture.
The reverse Warburg effect: Aerobic glycolysis in cancer associated fibroblasts and the tumor stroma (2009)

Here, we propose a new model for understanding the Warburg effect in tumor metabolism. Our hypothesis is that epithelial cancer cells induce the Warburg effect (aerobic glycolysis) in neighboring stromal fibroblasts. These cancer-associated fibroblasts, then undergo myo-fibroblastic differentiation, and secrete lactate and pyruvate (energy metabolites resulting from aerobic glycolysis). Epithelial cancer cells could then take up these energy-rich metabolites and use them in the mitochondrial TCA cycle, thereby promoting efficient energy production (ATP generation via oxidative phosphorylation), resulting in a higher proliferative capacity. In this alternative model of tumorigenesis, the epithelial cancer cells instruct the normal stroma to transform into a wound-healing stroma, providing the necessary energy-rich micro-environment for facilitating tumor growth and angiogenesis. In essence, the fibroblastic tumor stroma would directly feed the epithelial cancer cells, in a type of host-parasite relationship. We have termed this new idea the "Reverse Warburg Effect." In this scenario, the epithelial tumor cells "corrupt" the normal stroma, turning it into a factory for the production of energy-rich metabolites. This alternative model is still consistent with Warburg's original observation that tumors show a metabolic shift towards aerobic glycolysis. In support of this idea, unbiased proteomic analysis and transcriptional profiling of a new model of cancer-associated fibroblasts (caveolin-1 (Cav-1) deficient stromal cells), shows the upregulation of both (1) myo-fibroblast markers and (2) glycolytic enzymes, under normoxic conditions. We validated the expression of these proteins in the fibroblastic stroma of human breast cancer tissues that lack stromal Cav-1. Importantly, a loss of stromal Cav-1 in human breast cancers is associated with tumor recurrence, metastasis, and poor clinical outcome. Thus, an absence of stromal Cav-1 may be a biomarker for the "Reverse Warburg Effect," explaining its powerful predictive value.
Medical Robotics and Computer-Integrated Surgery: Information-driven Systems for 21st Century Operating Rooms (2000)

The impact of Computer Integrated Surgery (CIS) on medicine in the next 20 years will be as great as that of Computer-Integrated Manufacturing on industrial production over the past 20 years. Development of advanced CIS systems isbest pursued within the context of systems-oriented multidisciplinary research providing close collaboration between engineering faculty, students, surgeons, and industry. This paper introduces basic themes of CIS systems and describes theoverall research strategy pursued within our NSF Engineering Research Center for Computer-Integrated Surgery. Weillustrate key concepts with examples drawn from our research.
Internetwork infrastructure requirements for virtual environments (1995)

Virtual environments (VEs) are a broad multidisciplinary research area that includes all aspects of computer science, virtual reality. virtual worlds, teleoperation and telepresence. A variety of network elements are required to scale up virtual environments to arbitrarily large sizes. simultaneously connecting thousands of interacting players and all kinds of information objects.
Real-time in vitro observation of cavitation in a prosthetic heart valve. (1992)

A technique for real-time in vitro observation of cavitation on a prosthetic heart valve operating in a ventricular assist device under normal physiologic conditions has been developed. Considering the documented observation of cavitation erosion in heart valve components from human explants, and the potential risk of blood damage that cavitation presents, the technique developed in this study may prove useful in the design of prosthetic heart valves and ventricular assist devices. Cavitation of a glycerol blood analog fluid has been documented for a Medtronic/Hall prosthetic heart valve operating in a Penn State Electric Ventricular Assist Device. The ventricular assist device was operated in a mock circulatory system under normal physiologic conditions. The valve was located in the mitral position, with the cavitation occurring on the inlet side after valve closure. Bubble cavitation was seen on the valve occluder face, and vortex cavitation was observed at two locations in the vicinity of the valve occluder and housing. The cavity growth and collapse cycle for these forms of vaporous cavitation was less than 1 msec. Stroboscopic photography and stroboscopic videography with frame grabbing were used to document the cavity life cycle. With beat rate held constant, the cavity duration time was found to decrease with increasing mean venous return pressure.
The collagen substrate specificity of human neutrophil collagenase. (1987)

The substrate specificity of human neutrophil collagenase was examined using both monomeric and fibrillar collagens. The neutrophil enzyme cleaved types I, II, and III collagens, but failed to attack types IV or V. Against monomeric collagen substrates at 25 degrees C, the neutrophil enzyme displayed values for the Michaelis constant (Km) of 0.6-1.8 X 10(-6) M, essentially indistinguishable from the substrate affinities that characterize human fibroblast collagenase. Catalytic rates, however, varied considerably; type I collagen was cleaved with a specificity (kappa cat/Km) some 20-fold greater than type III. Type II collagen was degraded with intermediate selectivity, approximately equal to 25% of the type I rate, but 450% that of type III. This specificity contrasted markedly with that of human fibroblast collagenase, which cleaved human type III collagen 15-fold faster than type I and greater than 500-fold more rapidly than type II. Interestingly, the 20-fold selectivity for type I over type III exhibited by neutrophil collagenase against monomeric collagens was largely abolished following the reconstitution of these substrates into insoluble fibrils, falling to a value of just 1.5-fold. The distinctive and opposite preference by the human fibroblast enzyme for monomeric type III collagen over type I (15-fold) was similarly reduced to less than 2-fold upon substrate aggregation. The transition from native soluble collagen monomers into insoluble fibrils appeared to be handled by both the human neutrophil and fibroblast collagenases with similar facility on type I substrates. By comparison, however, the neutrophil enzyme degraded type III collagen fibrils faster than would have been predicted from solution rates, while the fibroblast enzyme cleaved such fibrils much slower than expected from solution values. In exploring this phenomenon further, solvent deuterium isotope effects were measured. The deuterium studies suggest that neutrophil collagenase, acting on type III fibrils (kappa H2O/kappa D2O = 5.0), is less sensitive to factors which govern the availability of water at the relatively hydrophobic site of peptide bond hydrolysis in the collagen molecule than is fibroblast collagenase (kappa H2O/kappa D2O = 15.0).
Dynamic maintenance of multidimensional range data partitioning for parallel data processing (1998)

Star schema has been a typical model for both online transaction processing in traditional databases and online analytical processing in large data warehouses. In the star schema, the dominant VO~UIIXS of data are stored in the relationship table in terms of databases or the fact table in terms of data warehouses. Sometimes this relationship or fact table is called multidimensional table, cube, or data set. In this paper, we present a parallel method to partition the fact table in terms of multidimensional space for parallel star query processing. Also a dynamic approach to maintain load balance among all the processors is given in terms of a set of heuristics for the cases when the fact table undergoes frequent updates such as insertions/deletions. The multidimensionally partitioned data sets in the fact table are stored as leaf nodes in a multidimensional range tree, and each data set stored in the leaf node is mapped into each processor for parallel data partitioning and star query processing. As far as load balance is concerned in each of processors, we try to maintain the distribution of data volumes m uniform as possible by the set of heuristics for the star query processing in OLAP. literature, and their variations can be utilized to fulfill the needs in the implementation of OLAP systems [l] [2] [6
Segmented filamentous bacteria in a defined bacterial cocktail induce intestinal inflammation in SCID mice reconstituted with CD45RBhigh CD4+ T cells (2007)

Only SFB bacteria together with a defined SPF mixture were effective in triggering intestinal inflammation in the model of IBD in reconstituted SCID mice, while no colitis was detected in GF mice or in mice colonized either with SPF microflora or monoassociated only with SFB or colonized by Bacteroides distasonis + SFB or Fusobacterium mortiferum + SFB.
Assessment of sperm function for IVF (1988)

Recent advances in our ability to understand and manipulate the fundamental mechanisms regulating human sperm function have led to the development of a new generation of diagnostic techniques, designed to give objective data on the functional competence of human spermatozoa. These techniques have proved to be of value in predicting the ability of patients' spermatozoa to fertilize the human ovum in vitro and in the evaluation of techniques and reagents of relevance to the therapeutic application of IVF, including sperm preparation protocols and reagents for the artificial enhancement of sperm function. Moreover the use of sperm function tests has shed light on the biochemical nature of the lesions present in the spermatozoa of subfertile males, with particular emphasis on the role played by reactive oxygen species. As a result of such studies we are now in a position to adopt a more rational approach to the development of modified IVF protocols for the treatment of male infertility.
Multisegmented Nanowires: a Step towards the Control of the Domain Wall Configuration (2017)

Cylindrical nanowires synthesized by controlled electrodeposition constitute excellent strategic candidates to engineer magnetic domain configurations. In this work, multisegmented CoNi/Ni nanowires are synthesized for tailoring a periodic magnetic structure determined by the balance between magnetocrystalline and magnetostatic energies. High-resolution Transmission Electron Microscopy confirms the segmented growth and the sharp transition between layers. Although both CoNi and Ni segments have similar fcc cubic crystal symmetry, their magnetic configuration is quite different as experimentally revealed by Magnetic Force Microscopy (MFM) imaging. While the Ni segments are single domain with axial magnetization direction, the CoNi segments present two main configurations: a single vortex state or a complex multivortex magnetic configuration, which is further interpreted with the help of micromagnetic simulations. This original outcome is ascribed to the tight competition between anisotropies. The almost monocrystalline fcc structure of the CoNi segments, as revealed by the electron diffraction patterns, which is atypical for its composition, contributes to balance the magnetocrystalline and shape anisotropies. The results of MFM measurements performed under in-plane magnetic field demonstrate that it is possible to switch from the multivortex configuration to a single vortex configuration with low magnetic fields.
STIM1, an essential and conserved component of store-operated Ca2 + channel function (2005)

Store-operated Ca2+ (SOC) channels regulate many cellular processes, but the underlying molecular components are not well defined. Using an RNA interference (RNAi)-based screen to identify genes that alter thapsigargin (TG)-dependent Ca2+ entry, we discovered a required and conserved role of Stim in SOC influx. RNAi-mediated knockdown of Stim in Drosophila S2 cells significantly reduced TG-dependent Ca2+ entry. Patch-clamp recording revealed nearly complete suppression of the Drosophila Ca2+ release-activated Ca2+ (CRAC) current that has biophysical characteristics similar to CRAC current in human T cells. Similarly, knockdown of the human homologue STIM1 significantly reduced CRAC channel activity in Jurkat T cells. RNAi-mediated knockdown of STIM1 inhibited TG- or agonist-dependent Ca2+ entry in HEK293 or SH-SY5Y cells. Conversely, overexpression of STIM1 in HEK293 cells modestly enhanced TG-induced Ca2+ entry. We propose that STIM1, a ubiquitously expressed protein that is conserved from Drosophila to mammalian cells, plays an essential role in SOC influx and may be a common component of SOC and CRAC channels.
Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family. (1989)

Phytochrome is a plant regulatory photoreceptor that mediates red light effects on a wide variety of physiological and molecular responses. DNA blot analysis indicates that the Arabidopsis thaliana genome contains four to five phytochrome-related gene sequences. We have isolated and sequenced cDNA clones corresponding to three of these genes and have deduced the amino acid sequence of the full-length polypeptide encoded in each case. One of these proteins (phyA) shows 65-80% amino acid sequence identity with the major, etiolated-tissue phytochrome apoproteins described previously in other plant species. The other two polypeptides (phyB and phyC) are unique in that they have low sequence identity (approximately 50%) with each other, with phyA, and with all previously described phytochromes. The phyA, phyB, and phyC proteins are of similar molecular mass, have related hydropathic profiles, and contain a conserved chromophore attachment region. However, the sequence comparison data indicate that the three phy genes diverged early in plant evolution, well before the divergence of the two major groups of angiosperms, the monocots and dicots. The steady-state level of the phyA transcript is high in dark-grown A. thaliana seedlings and is down-regulated by light. In contrast, the phyB and phyC transcripts are present at lower levels and are not strongly light-regulated. These findings indicate that the red/far light-responsive phytochrome photoreceptor system in A. thaliana, and perhaps in all higher plants, consists of a family of chromoproteins that are heterogeneous in structure and regulation.
Alternate gram staining technique using a fluorescent lectin (1990)

Fluorescence-labeled wheat germ agglutinin binds specifically to N-acetylglucosamine in the outer peptidoglycan layer of gram-positive bacteria. The peptidoglycan layer of gram-negative bacteria is covered by a membrane and is not labeled by the lectin. By exploiting this phenomenon, an alternative Gram staining technique has been developed.
Laser-induced endothelial cell activation supports fibrin formation (2010)

Laser-induced vessel wall injury leads to rapid thrombus formation in an animal thrombosis model. The target of laser injury is the endothelium. We monitored calcium mobilization to assess activation of the laser-targeted cells. Infusion of Fluo-4 AM, a calcium-sensitive fluorochrome, into the mouse circulation resulted in dye uptake in the endothelium and circulating hematopoietic cells. Laser injury in mice treated with eptifibatide to inhibit platelet accumulation resulted in rapid calcium mobilization within the endothelium. Calcium mobilization correlated with the secretion of lysosomal-associated membrane protein 1, a marker of endothelium activation. In the absence of eptifibatide, endothelium activation preceded platelet accumulation. Laser activation of human umbilical vein endothelial cells loaded with Fluo-4 resulted in a rapid increase in calcium mobilization associated cell fluorescence similar to that induced by adenosine diphosphate (10 μM) or thrombin (1 U/mL). Laser activation of human umbilical vein endothelial cells in the presence of corn trypsin inhibitor treated human plasma devoid of platelets and cell microparticles led to fibrin formation that was inhibited by an inhibitory monoclonal anti-tissue factor antibody. Thus laser injury leads to rapid endothelial cell activation. The laser activated endothelial cells can support formation of tenase and prothrombinase and may be a source of activated tissue factor as well.
Enamel caries initiation and progression following low fluence (energy) argon laser and fluoride treatment. (1995)

The aim of this study was to evaluate the effect of low fluence argon laser (AL) and acidulated phosphate fluoride (APF) treatment on caries initiation (CI) and progression (CP) in human enamel. Twenty caries-free molars were divided into tooth quarters. Tooth quarters from each specimen were assigned to one of four groups: 1) Control; 2) AL Only; 3) AL before APF; 4) APF before AL. AL was at 0.25 watts for 10 seconds (12.0 +/- 0.5 J/cm2). APF treatment was with a 1.23% gel for 4 minutes. Lesions were created in two treated, sound enamel windows per tooth quarter with an acidified gel. After CI and CP, sections were obtained and imbibed with water for polarized light study. Mean body of the lesion (BL) depths were determined and compared among groups (ANOVA & DMR). After CI, BL depths were: 189 +/- 29 micrometers for Control, 133 +/- 23 micrometers for AL only; 91 +/- 17 micrometers for AL before APF; and 83 +/- 14 micrometers for APF before AL. After CP, BL depths were: 321 +/- 43 micrometers for Control, 206 +/- 35 micrometers for AL only; 118 +/- 21 micrometers for AL before APF; and 114 +/- 19 micrometers for APF before AL. After CI and CP, argon laser irradiation alone resulted in significant reductions in lesion depth when compared with controls (p<0.05). APF treatment before or after argon laser exposure resulted in a significant reduction in lesion depth when compared with AL alone or control groups (p<0.05). Caries initiation and progression in vitro are affected to a significant extent when low fluence (energy) argon laser irradiation of sound enamel alone or in conjunction with APF treatment is done. This caries-protective effect occurs at an argon laser fluence (energy) that is capable of polymerizing visible light-cured resins.
The compact electro-acupuncture system for multi-modal feedback electro-acupuncture treatment (2012)

The compact electro-acupuncture (EA) system is proposed for the multi-modal feedback EA treatment. It is composed of a needle, a smart patch, and an interconnecting conductive thread. The 3cm diameter compact EA patch is implemented with the EA controller integrated circuit (IC) and the small coin battery on the planar-fashionable circuit board (P-FCB) technology. It can achieve the user convenience and the low manufacturing cost at once by removing the wire connections. The EA controller IC programs the stimulation current and also monitors the electromyography (EMG) and the skin temperature during the EA stimulation. The measured data can be wirelessly transmitted to the external EA analyzer through the body channel communication with low power consumption. The external EA analyzer can check the patient's status, such as the muscle fatigue and the change of the skin temperature, and the practitioner can change the stimulation parameters for the optimal curative value. The proposed compact EA system is fully implemented and tested on the human body.
Genotypic Identification of Rickettsia tsutsugamushi by Restriction Fragment Length Polymorphism Analysis of DNA Amplified by the Polymerase Chain Reaction (1996)

We combined the nested polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) for genotypic identification of Rickettsia tsutsugamushi. Four primers were selected from the DNA sequence of the gene encoding a 56-kD serotype-specific antigen of the Karp strain. Nested PCR produced rickettsia-specific products of approximately 0.6 kb in the amplification of DNA prepared from three reference strains (Gilliam, Karp, and Kato) and two prototype strains (Irie and Hirano) prevalent in the Miyazaki Prefecture of Japan. When the nested PCR products obtained from these five strains were digested with Hha I, profiles specific to each strain were generated. Fourteen of 17 DNA samples of peripheral blood mononuclear cells from patients with scrub typhus tested positive in the nested-PCR, providing a rickettsia-specific band. The serotype of infected rickettsia of 10 patients were diagnosed as Irie and those of four patients were diagnosed as Hirano by indirect immunofluorescence methods. The fragment profiles of the PCR products of these 14 patients after digestion with Hha I corresponded closely with those serotypes. However, the PCR products from two of four samples, which were similar to Hirano strain by a serologic method and by the pattern of digestion with Hha I, produced different RFLP profiles upon further digestion with Hinf I and Alu I. These results may suggest that genetic variation exists within serotypes. Genotypic identification of R. tsutsugamushi by means of PCR-RFLP using three restriction enzymes is apparently useful.
Burst-Modulated Waveforms Optimize Electrical Stimuli for Charge Efficiency and Fiber Selectivity (2015)

We demonstrate an alternative method of designing electrical stimuli-termed burst modulation--for producing different patterns of nerve fiber recruitment. By delivering electrical charge in bursts of "pulsons"--miniature pulses-instead of as long continuous pulses, our method can optimize the waveform for stimulation efficiency and fiber selectivity. In our in vivo validation experiments, while maintaining C fibers of the rat vagus nerve at ∼ 50% activation with different waveforms, the burst-modulated waveform produced 11% less A fiber activation than the standard rectangular pulse waveform (rectangular: 50.8±1.5% of maximal A response, mean ± standard error of the mean; burst-modulated: 39.8 ±1.3%), which equates to a 20% reduction in A fiber response magnitude. In addition, the burst-modulated waveform required 45% less stimulus charge per phase to maintain 50% C fiber activation (rectangular: 20.7 ±0.86 μC; burst-modulated: 11.3 ±0.41 μC ). Burst-modulated waveforms produced consistent patterns of fiber recruitment within and across animals, which indicate that our methods of stimulus design and response analysis provide a reliable way to study neurostimulation and deliver therapy.
Characterization of smooth lipopolysaccharides and O polysaccharides of Brucella species by competition binding assays with monoclonal antibodies (1997)

Previously, four epitope specificities on the O chain of Brucella species were reported: M, A, C, and C/Y. In this work, according to monoclonal antibody binding to smooth lipopolysaccharides of Yersinia enterocolitica 0:9, Brucella abortus W99 (A-dominant strain), and B. melitensis Rev1 (M-dominant strain), seven O-chain epitope specificities were defined: M, A, C (M > A), C (M = A), C/Y (M > A), C/Y (M = A) and C/Y (A > M). Competitive binding assays between these monoclonal antibodies suggested that these different epitopes are probably overlapping structures.