gebhart/patrepeval huggingface dataset:
Effects of Reservoir Heterogeneities on the Steam-Assisted Gravity-Drainage Process (2008)

Summary The success of steam-assisted gravity drainage (SAGD) has been demonstrated by both field and laboratory studies mostly on the basis of homogeneous reservoirs and reservoir models. A comprehensive understanding of the effects of reservoir heterogeneities on SAGD performance is required, however, for wider and more-successful implementation. This work presents a numerical investigation of the effects of reservoir heterogeneities on SAGD using a stochastic model of shale distribution. Two flow regions, the near-well region (NWR) and the above-well region (AWR), are identified to decouple the complex effects of reservoir heterogeneities on the SAGD process. Numerical simulations are conducted with various realizations of shale distribution to compare SAGD performance in terms of the effects of NWR and AWR. Hydraulic fracturing is proposed to enhance steam-chamber development for reservoirs with poor vertical communication, and the feasibility of hydraulic fracturing is discussed in terms of in-situ stress and well orientation. Fracturing both injectors and producers is found to improve steam distribution, oil production rate, and the oil-steam ratio.
Structure of a Bimodular Botulinum Neurotoxin Complex Provides Insights into Its Oral Toxicity (2013)

Botulinum neurotoxins (BoNTs) are produced by Clostridium botulinum and cause the fatal disease botulism, a flaccid paralysis of the muscle. BoNTs are released together with several auxiliary proteins as progenitor toxin complexes (PTCs) to become highly potent oral poisons. Here, we report the structure of a ∼760 kDa 14-subunit large PTC of serotype A (L-PTC/A) and reveal insight into its absorption mechanism. Using a combination of X-ray crystallography, electron microscopy, and functional studies, we found that L-PTC/A consists of two structurally and functionally independent sub-complexes. A hetero-dimeric 290 kDa complex protects BoNT, while a hetero-dodecameric 470 kDa complex facilitates its absorption in the harsh environment of the gastrointestinal tract. BoNT absorption is mediated by nine glycan-binding sites on the dodecameric sub-complex that forms multivalent interactions with carbohydrate receptors on intestinal epithelial cells. We identified monosaccharides that blocked oral BoNT intoxication in mice, which suggests a new strategy for the development of preventive countermeasures for BoNTs based on carbohydrate receptor mimicry.
Surface versus Molecular Siloxy Ligands in Well‐Defined Olefin Metathesis Catalysts: [{(RO)3SiO}Mo(NAr)(CHtBu)(CH2tBu)] (2006)

Surface organometallic chemistry: Similar electronic properties of molecular and surface siloxy ligands in 1 m and 1 were revealed by a structural investigation with solid-state NMR spectroscopy and a reactivity study in olefin metathesis. Despite similar initial turnover frequencies, the silica-supported catalyst 1 is more stable than 1 m and allows it to achieve higher turnovers, thus showing the advantage of site isolation on surfaces.
RENAL HYPERTENSION IN RATS IMMUNIZED AGAINST ANGIOTENSIN I AND ANGIOTENSIN II (1974)

Rats, actively immunized against angiotensin I (AI) and angiotensin II (AII), were subjected to unilateral renal artery constriction to determine whether the resulting hypertension, which may still ensue in the animal immunized against AII, could be prevented by such combined immunity. Sustained immunity to both AI and AII neither changed preoperative blood pressures of the rats from those of control mock-immunized rats nor altered the incidence or severity of renal dip hypertension. Vascular hyperresponsiveness to small quantities of free angiotensin could not be invoked to explain the hypertension, for there was no significant difference between mock-immunized hypertensive animals, and those remaining normotensive, regarding pressor sensitivity to intravenous AI, AII, renin, and norepinephrine. (AI + AII)-immunized hypertensive rats required AI doses averaging 260 times greater than nonimmune hypertensives to elicit equipressor responses, and were refractory to renin, but not to norepinephrine. Thus, while previous studies have not excluded direct participation of endogenous AI in renal clip hypertension in rats, evidence from our experiments makes it extremely difficult to sustain any pressor function therein for circulating AI or AII. Our results also preclude involvement of AII produced from circulating AI by conversion within arteriolar walls, close to receptor sites, since AI immunity would block this mechanism of action.
Time- and space-resolved dynamics of melting, ablation, and solidification phenomena induced by femtosecond laser pulses in germanium (2006)

Femtosecond time-resolved microscopy has been used to analyze the structural transformation dynamics (melting, ablation, and solidification phenomena) induced by intense $130\phantom{\rule{0.3em}{0ex}}\mathrm{fs}$ laser pulses in single-crystalline (100)-germanium wafers on a time scale from $\ensuremath{\sim}100\phantom{\rule{0.3em}{0ex}}\mathrm{fs}$ up to $10\phantom{\rule{0.3em}{0ex}}\mathrm{ns}$. Complementary information on longer time scales $(350\phantom{\rule{0.3em}{0ex}}\mathrm{ps}--1.4\phantom{\rule{0.3em}{0ex}}\ensuremath{\mu}\mathrm{s})$ has been obtained by means of simultaneous streak camera and photodiode measurements of the sample surface reflectivity. In the ablative regime, transient surface reflectivity patterns are observed by fs microscopy on a ps to ns time scale as a consequence of the complex spatial density structure of the ablating material. Complementing point-probing streak camera measurements allow one to characterize the temporal evolution in real time up to $40\phantom{\rule{0.3em}{0ex}}\mathrm{ns}$ after the fs-laser pulse excitation. Fs microscopy reveals additional reflectivity patterns for fluences below the ablation threshold of the germanium. It is shown that these patterns are originating from the selective removal of the native oxide layer at the wafer surface within a certain fluence range. After solidification, and in contrast to other semiconductors, surface amorphization has not been observed in (100)-germanium upon femtosecond laser pulse irradiation in the studied fluence range.
The 12S adenoviral E1A protein immortalizes avian cells and interacts with the avian RB product. (1993)

Quail cells were immortalized for the first time by using retroviruses expressing the 12S adenoviral E1A gene. In these cells, interaction between the 12S E1A product and the quail RB protein was shown, suggesting that the 12S adenoviral E1A product works in avian cells through similar biochemical pathways as in mammalian cells by interacting and inactivating host cellular proteins, including the RB product. These results confirm that the RB product exhibits a universal function among higher vertebrates in controlling cellular growth and tumor progression.
Reprogramming of Liver to Pancreas (2008)

Islet grafts have demonstrated that patients with diabetes would benefit greatly by beta-cell therapy. However, the paucity of available islets for transplantation as well as the immunological barriers faced in allogeneic transplantation represent a tremendous barrier to regenerative approaches to the treatment of diabetes. Here, we present a strategy and protocols to transdifferentiate developmentally related hepatocytes into beta-cells by the ectopic expression of critical beta-cell transcription factors.
Methylation Array Analysis of Preoperative and Postoperative Saliva DNA in Oral Cancer Patients (2008)

We report methylation array analysis of 807 cancer-associated genes in the saliva of oral cancer patients before and after oral cancer resection. Our methylation biomarker approach shows the proof of principle that methylation array analysis of saliva can produce a set of cancer-related genes that are specific and can be used as a composite biomarker for the early detection of oral cancer.
Down-regulation of copper/zinc superoxide dismutase causes apoptotic death in PC12 neuronal cells. (1994)

The discovery of missense mutations leading to reduced enzymatic activity in the copper/zinc superoxide dismutase (SOD1) in human familial amyotrophic lateral sclerosis has heightened interest in the role of free radicals in neurodegenerations but left the mechanisms by which they may cause neuronal death unexplained. We have approached this problem by specifically inhibiting the synthesis of SOD1 in cultured PC12 cells with antisense oligonucleotides. Cell survival in both untreated and nerve growth factor (NGF)-treated PC12 cells was inhibited by down-regulation of SOD1, with NGF-treated cells dying at lower levels of inhibition than untreated cells. Dying cells showed DNA degradation characteristic of apoptosis and could be rescued by the antioxidant vitamin E, with a combination of vitamin E and NGF being most efficacious. These results suggest that the induction of cell death by inhibition of SOD1 is due to free radical induction of apoptosis and that growth factor therapy for free-radical-mediated disease may require antioxidants in order to be effective.
PD-1 Expression in Acute Hepatitis C Virus (HCV) Infection Is Associated with HCV-Specific CD8 Exhaustion (2006)

Hepatitis C virus (HCV)-specific CD8 cell exhaustion may represent a mechanism of HCV persistence. The inhibitory receptor PD-1 has been reported to be up-regulated in exhausted CD8 cells. Therefore, we studied PD-1 expression longitudinally during acute HCV infection. Most HCV-specific CD8 cells expressed PD-1 at the time of acute illness, irrespective of the final outcome. PD-1 expression declined with the acquisition of a memory phenotype and recovery of an efficient CD8 cell function in resolving HCV infections, whereas high levels were maintained when HCV persisted and HCV-specific CD8 cells remained dysfunctional. Blocking PD-1/PDL-1 interaction with an anti-PDL-1 antibody improved the capacity of expansion of virus-specific CD8 cells.
On-Chip Titration of an Anticoagulant Argatroban and Determination of the Clotting Time within Whole Blood or Plasma Using a Plug-Based Microfluidic System (2006)

This paper describes extending plug-based microfluidics to handling complex biological fluids such as blood, solving the problem of injecting additional reagents into plugs, and applying this system to measuring of clotting time in small volumes of whole blood and plasma. Plugs are droplets transported through microchannels by fluorocarbon fluids. A plug-based microfluidic system was developed to titrate an anticoagulant (argatroban) into blood samples and to measure the clotting time using the activated partial thromboplastin time (APTT) test. To carry out these experiments, the following techniques were developed for a plug-based system: (i) using Teflon AF coating on the microchannel wall to enable formation of plugs containing blood and transport of the solid fibrin clots within plugs, (ii) using a hydrophilic glass capillary to enable reliable merging of a reagent from an aqueous stream into plugs, (iii) using bright-field microscopy to detect the formation of a fibrin clot within plugs and using fluorescent microscopy to detect the production of thrombin using a fluorogenic substrate, and (iv) titration of argatroban (0-1.5 microg/mL) into plugs and measurement of the resulting APTTs at room temperature (23 degrees C) and physiological temperature (37 degrees C). APTT measurements were conducted with normal pooled plasma (platelet-poor plasma) and with donor's blood samples (both whole blood and platelet-rich plasma). APTT values and APTT ratios measured by the plug-based microfluidic device were compared to the results from a clinical laboratory at 37 degrees C. APTT obtained from the on-chip assay were about double those from the clinical laboratory but the APTT ratios from these two methods agreed well with each other.
Inhibition of Urokinase Activity by the Antiangiogenic Factor 16K Prolactin: Activation of Plasminogen Activator Inhibitor 1 Expression (1998)

The N-terminal fragment of PRL (16K PRL) is an antiangiogenic factor that, in vitro, inhibits several components of angiogenesis including basic fibroblast growth factor (bFGF)-induced cell division, migration, and organization of capillary endothelial cells. An essential step in the regulation of angiogenesis is the activation of urokinase (urokinase type plasminogen activator, uPA), which in turn activates a cascade of proteases that play essential roles in endothelial cell migration and tissue remodeling. Treatment of bovine capillary endothelial cells (BBEC) with 16K PRL inhibited bFGF-stimulated urokinase activity in BBEC as detected by plasminogen substrate gel assay. 16K PRL did not appear to be acting via an effect on uPA expression because no change in messenger RNA levels were observed. However, protein levels of plasminogen activator inhibitor-1 (PAI-1), a specific inhibitor of urokinase, were increased by 16K PRL independent of the action of bFGF. The 16K PRL-induced increase in PAI-1 protein levels appear to be the result of increased expression of the PAI-1 gene. Increased production of PAI-1 induced by 16K PRL results in the formation of inactive PAI-1/uPA complexes, consistent with the observed decrease in uPA activity.
Advances in Photoacoustic Noninvasive Glucose Testing (1999)

Abstract We report here on in vitro and in vivo experiments that are intended to explore the feasibility of photoacoustic spectroscopy as a tool for the noninvasive measurement of blood glucose. The in vivo results from oral glucose tests on eight subjects showed good correlation with clinical measurements but indicated that physiological factors and person-to-person variability are important. In vitro measurements showed that the sensitivity of the glucose measurement is unaffected by the presence of common blood analytes but that there can be substantial shifts in baseline values. The results indicate the need for spectroscopic data to develop algorithms for the detection of glucose in the presence of other analytes.
Indium Phosphide‐Based Semiconductor Nanocrystals and Their Applications (2012)

Semiconductor nanocrystals or quantum dots (QDs) are nanometer‐sized fluorescent materials with optical properties that can be fine‐tuned by varying the core size or growing a shell around the core. They have recently found wide use in the biological field which has further enhanced their importance. This review focuses on the synthesis of indium phosphide (InP) colloidal semiconductor nanocrystals. The two synthetic techniques, namely, the hot‐injection and heating‐up methods are discussed. Different types of the InP‐based QDs involving their use as core, core/shell, alloyed, and doped systems are reviewed. The use of inorganic shells for surface passivation is also highlighted. The paper is concluded by some highlights of the applications of these systems in biological studies.
A new class of fuzzy operators for image processing: design and implementation (2002)

The author presents a class of fuzzy operators which aim at extending the application range of fuzzy techniques to image processing applications not related to pattern recognition. Implementation aspects and specific design techniques based on genetic algorithms are discussed. An application concerning the design of a fuzzy operator for edge-preserving smoothing of an image is described in detail.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cardiosphere-derived cells do not improve cardiac function in rats with cardiac failure (2017)

Our study challenges the effectiveness of CDC in post-ischemic heart failure.
DNA amplification polymorphisms of the cultivated mushroom Agaricus bisporus (1992)

Single 10-bp primers were used to generate random amplified polymorphic DNA (RAPD) markers from commercial and wild strains of the cultivated mushroom Agaricus bisporus via the polymerase chain reaction. Of 20 primers tested, 19 amplified A. bisporus DNA, each producing 5 to 15 scorable markers ranging from 0.5 to 3.0 kbp. RAPD markers identified seven distinct genotypes among eight heterokaryotic strains; two of the commercial strains were shown to be related to each other through single-spore descent. Homokaryons recovered from protoplast regenerants of heterokaryotic strains carried a subset of the RAPD markers found in the heterokaryon, and both of the haploid nuclei from two heterokaryons were distinguishable. RAPD markers also served to verify the creation of a hybrid heterokaryon and to analyze meiotic progeny from this new strain: most of the basidiospores displayed RAPD fingerprints identical to that of the parental heterokaryon, although a few selected slow growers were homoallelic at a number of loci that were heteroallelic in the parent, suggesting that they represented rare homokaryotic basidiospores; crossover events between a RAPD marker locus and its respective centromere appeared to be infrequent. These results demonstrate that RAPD markers provide an efficient alternative for strain fingerprinting and a versatile tool for genetic studies and manipulations of A. bisporus.
Cell morphology and property relationships of microcellular foamed pvc/wood‐fiber composites (1998)

Abstract Wood‐fiber composites make use of cellulose fibers as a reinforcing filler in the polymer matrix and are known to have a lower material cost and a higher stiffness than neat polymers. However, the lower material cost and enhanced stiffness of wood‐fiber composites are achieved at the expense of other properties such as the ductility and impact strength. Since microcellular plastics exhibit a higher impact strength, higher toughness, and increased fatigue life compared to unfoamed plastics, microcellular foaming of wood‐fiber composites will improve the mechanical properties of the composites and therefore increase the usefulness of the materials. In this paper, microcellular foamed PVC/wood‐fiber composites with unique cell morphology and material composition are characterized. Microcellular structures are produced in PVC/wood‐fiber composites by first saturating the composite samples with CO 2 under high pressure followed by rapidly decreasing the solubility of gas in the samples. The void fraction of the microcellular foamed PVC/wood‐fiber composites is controlled by tailoring the composition of materials and the foaming process parameters. The results indicate that tensile and impact properties of microcellular foamed PVC/wood‐fiber composites are most sensitive to changes in the cell morphology and the surface modification of fibers.
Development and Characterization of Microsatellite Markers for the Cape Gooseberry Physalis peruviana (2011)

Physalis peruviana, commonly known as Cape gooseberry, is an Andean Solanaceae fruit with high nutritional value and interesting medicinal properties. In the present study we report the development and characterization of microsatellite loci from a P. peruviana commercial Colombian genotype. We identified 932 imperfect and 201 perfect Simple Sequence Repeats (SSR) loci in untranslated regions (UTRs) and 304 imperfect and 83 perfect SSR loci in coding regions from the assembled Physalis peruviana leaf transcriptome. The UTR SSR loci were used for the development of 162 primers for amplification. The efficiency of these primers was tested via PCR in a panel of seven P. peruviana accessions including Colombia, Kenya and Ecuador ecotypes and one closely related species Physalis floridana. We obtained an amplification rate of 83% and a polymorphic rate of 22%. Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species.
Antiangiogenic therapy targeting the tyrosine kinase receptor for vascular endothelial growth factor receptor inhibits the growth of colon cancer liver metastasis and induces tumor and endothelial cell apoptosis. (1999)

Increased vascular endothelial growth factor (VEGF) expression is associated with colon cancer metastases. We hypothesized that inhibition of VEGF receptor activity could inhibit colon cancer liver metastases. BALB/c mice underwent splenic injection with CT-26 colon cancer cells to generate metastases. Mice received daily i.p. injections of vehicle, tyrosine kinase inhibitor for Flk-1/KDR (SU5416) or tyrosine kinase inhibitor for VEGF, basic fibroblast growth factor, and platelet-derived growth factor receptors (SU6668). SU5416 and SU6668 respectively inhibited metastases (48.1% and 55.3%), microvessel formation (42.0% and 36.2%), and cell proliferation (24.4% and 27.3%) and increased tumor cell (by 2.6- and 4.3-fold) and endothelial cell (by 18.6- and 81.4-fold) apoptosis (P<0.001). VEGF receptor inhibitors increased endothelial cell apoptosis, suggesting that VEGF may serve as an endothelial survival factor.
Perturbed dentate gyrus function in serotonin 5-HT 2C receptor mutant mice (1998)

Serotonin systems have been implicated in the regulation of hippocampal function. Serotonin 5-HT2C receptors are widely expressed throughout the hippocampal formation, and these receptors have been proposed to modulate synaptic plasticity in the visual cortex. To assess the contribution of 5-HT2C receptors to the serotonergic regulation of hippocampal function, mice with a targeted 5-HT2C-receptor gene mutation were examined. An examination of long-term potentiation at each of four principal regions of the hippocampal formation revealed a selective impairment restricted to medial perforant path-dentate gyrus synapses of mutant mice. This deficit was accompanied by abnormal performance in behavioral assays associated with dentate gyrus function. 5-HT2C receptor mutants exhibited abnormal performance in the Morris water maze assay of spatial learning and reduced aversion to a novel environment. These deficits were selective and were not associated with a generalized learning deficit or with an impairment in the discrimination of spatial context. These results indicate that a genetic perturbation of serotonin receptor function can modulate dentate gyrus plasticity and that plasticity in this structure may contribute to neural mechanisms underlying hippocampus-dependent behaviors.
American College of Rheumatology provisional criteria for defining clinical inactive disease in select categories of juvenile idiopathic arthritis (2011)

The modified criteria, termed the "criteria for CID in select categories of JIA," have excellent feasibility and face, content, criterion, and discriminant validity to detect CID in select categories of JIA. The small changes made to the preliminary criteria set did not alter the area under the receiver operating characteristic curve (0.954) or accuracy (91%), but have increased face and content validity.
3′‐Modified Oligonucleotides and their Conjugates (2000)

Solid-phase synthesis of 3'-aminoalkyl, 3'-thioalkyl, and 3'-polyethyleneglycol are described. The first two are important as specific points of attachment for a large variety of reporter groups; the latter is important because of its increased cell membrane permeability, which aids in the development of antisense drugs. These protocols cover details of the synthetic organic chemistry needed to make each solid support, as well as DNA synthesis, workup, characterization, and conjugation.