gebhart/patrepeval huggingface dataset:
Reservoir Modeling With Global Scaleup (2007)

Abstract We present a new global scale-up technology for calculating effective permeability and/or transmissibility. Using this innovative technology, we apply global flow solutions to improve scale-up accuracy. Global scale-up was proposed in the 1980s, and its benefits are well-described in the literature. However, global scale-up has not been adopted by the industry due to significant technical challenges in its application to real reservoir models. These models are often characterized by complex features like faults, pinch-outs, and isolated geobodies. Here, we overview several novel technologies that we have developed to overcome these difficulties. Numerical examples applying global scale-up to several reservoir models are presented. Comparisons with local scale-up methods currently used in the industry are made. The examples demonstrate that our new global scale-up technology leads to significant improvements in scale-up accuracy. In particular, when applied to challenging models with complicated fine-scale connectivity, the global scale-up method preserves the fine-scale connectivity more accurately than local scale-up methods. Sometimes, dramatic differences are seen. Moreover, we note that global scale-up can be especially effective when used in conjunction with unstructured grids. Accurate scale-up is a critical link between fine-scale geologic descriptions and coarse-scale reservoir simulation models used for development planning and reservoir management. Predictive reservoir models that are consistent with geologic and production data gathered at different scales are critical for these tasks. Global scale-up is a promising technique for building more accurate reservoir models.
Neuroprotective effect of epigallocatechin-3-gallate on retinal ganglion cells in optic nerve crush rat model (2011)

Objective To investigate the neuroprotective effect of epigallocatechin-gallate (EGCG),the major catechin found in green tea, in an optic nerve crush (ONC) rat model. Methods Seventy-two Wistar rats were divided randomly into four groups: normal control, sham-operation+ EGCG, ONC+vehicle, and ONC+ EGCG groups. Animals were treated intraperitoneally and orally with either vehicle (normal saline) or EGCG (25 mg/kg, injected daily for up to five days, and orally 2 mg/kg daily afterwards). Two days after the first injection, an ONC injury using a micro optic nerve clipper was performed at approximately 2 mm from the optic nerve head for 60 seconds. Fluorogold was injected into bilateral superior colliculi five days before sacrifice and fluorescent gold labeled retinal ganglion cells (RGC)were counted under fluorescence microscopy on days seven, 14 and 28 after optic nerve crush. Meanwhile,the expression of neurofilament triplet L (NF-L) was measured by immunohistochemistry and Western blotting. Results In the ONC + vehicle group, a progressive loss of RGC was observed;however,compared with the ONC+vehicle group, RGC density was significantly higher on day seven (t=3. 216, P=0. 009), day 14 (t=2. 609, P=0. 026) and day 28 (t=2. 792, P=0. 019) , and a significant increase of theNF-L protein expression has been observed on days seven, 14 and 28 after optic nerve crush in the ONC+EGCG group. Conclusions EGCG has a protective effect to the bodies and axons of the RGC after optic nerve crush.

Key words: 
Optic nerve injuries; Callic acid /therapeutic use; Retinal ganglion cells; Animal experimentation
Editing livestock genomes with site-specific nucleases (2013)

Over the past 5 years there has been a major transformation in our ability to precisely manipulate the genomes of animals. Efficiencies of introducing precise genetic alterations in large animal genomes have improved 100000-fold due to a succession of site-specific nucleases that introduce double-strand DNA breaks with a specificity of 10(-9). Herein we describe our applications of site-specific nucleases, especially transcription activator-like effector nucleases, to engineer specific alterations in the genomes of pigs and cows. We can introduce variable changes mediated by non-homologous end joining of DNA breaks to inactive genes. Alternatively, using homology-directed repair, we have introduced specific changes that support either precise alterations in a gene's encoded polypeptide, elimination of the gene or replacement by another unrelated DNA sequence. Depending on the gene and the mutation, we can achieve 10%-50% effective rates of precise mutations. Applications of the new precision genetics are extensive. Livestock now can be engineered with selected phenotypes that will augment their value and adaption to variable ecosystems. In addition, animals can be engineered to specifically mimic human diseases and disorders, which will accelerate the production of reliable drugs and devices. Moreover, animals can be engineered to become better providers of biomaterials used in the medical treatment of diseases and disorders.
Borrowing, resource transfers, and external shocks to developing countries : historical and counterfactual (1989)

Since the late 1970's the buildup and servicing of external debt has dominated the economic situation in many developing countries. This paper gathers some statistical evidence on the magnitude of lending and repayment and on the question of whether repayment reduces the resources available for development. The evidence largely confirms commonly held beliefs. Although most debtor countries have made net transfers of resources to creditors, middle-income countries that have not had to reschedule their debts have averaged smaller net transfers than those that did reschedule. Adverse changes in terms of trade since 1978 accounted for most of the debt buildup in many non-oil developing countries. The mostly favorable terms of trade for oil exporters, on the other hand, gave them large gains that could have more than covered the losses of the oil importing developing countries. Heavy borrowing by oil exporters during favorable times seems to have been a major factor in precipitating the debt crisis. Since the debt crisis, the highly indebted countries have greatly increased their official borrowing. Increased official lending might help the resource balance and domestic investment of lower-income countries more than those of middle-income countries with high commercial debts.
Dietary calcium, sex hormones, and bone mineral density in men. (1990)

Dietary calcium intake has a role in the determination or maintenance, or both, of the axial but not the appendicular skeleton in adult men.
Electronic dephasing, vibrational relaxation, and solvent friction in molecular nonlinear optical line shapes (1988)

The role of solvation dynamics in molecular nonlinear optical line shapes is analyzed using a reduced description based on the time evolution of the density matrix in Liouville space. Langevin equations are used to treat the coupling of the solvent to the molecular electronic and nuclear degrees of freedom. Electronic dephasing is calculated using a solvation coordinate which satisfies a generalized Fokker–Planck equation, and vibrational relaxation is related to the solvent viscosity and friction. The combined effect of both processes is incorporated into appropriate multitime correlation functions which are evaluated using a Liouville-space generating function. The present eigenstate-free approach is particularly suitable for calculating spectral line shapes as well as rate processes (isomerization, electron transfer) of large polyatomic molecules in condensed phases.
Prominent neurodegeneration and increased plaque formation in complement-inhibited Alzheimer's mice (2002)

Abnormal accumulation of beta-amyloid (Abeta) in Alzheimer's disease (AD) is associated with prominent brain inflammation. Whereas earlier studies concluded that this inflammation is detrimental, more recent animal data suggest that at least some inflammatory processes may be beneficial and promote Abeta clearance. Consistent with these observations, overproduction of transforming growth factor (TGF)-beta1 resulted in a vigorous microglial activation that was accompanied by at least a 50% reduction in Abeta accumulation in human amyloid precursor protein (hAPP) transgenic mice. In a search for inflammatory mediators associated with this reduced pathology, we found that brain levels of C3, the central component of complement and a key inflammatory protein activated in AD, were markedly higher in hAPP/TGF-beta1 mice than in hAPP mice. To assess the importance of complement in the pathogenesis of AD-like disease in mice, we inhibited C3 activation by expressing soluble complement receptor-related protein y (sCrry), a complement inhibitor, in the brains of hAPP mice. Abeta deposition was 2- to 3-fold higher in 1-year-old hAPP/sCrry mice than in age-matched hAPP mice and was accompanied by a prominent accumulation of degenerating neurons. These results indicate that complement activation products can protect against Abeta-induced neurotoxicity and may reduce the accumulation or promote the clearance of amyloid and degenerating neurons. These findings provide evidence for a role of complement and innate immune responses in AD-like disease in mice and support the concept that certain inflammatory defense mechanisms in the brain may be beneficial in neurodegenerative disease.
Noncoding RNA transcripts. (2003)

Recent analyses of the human genome and available data about the other higher eukaryotic genomes have revealed that, in contrast to Eubacteria and Archaea, only a small fraction of the genetic material (ca 1.5%) codes for proteins. Most of genomic DNA and its RNA transcripts are involved in regulation of gene expression, which can be exerted at either the transcriptional level, controlling whether a gene is transcribed and to what extent, or at the post-translational level, regulating the fate of the transcribed RNA molecules, including their stability, efficiency of their translation and subcellular localization. Noncoding RNA genes produce functional RNA molecules (ncRNAs) rather than encoding proteins. These stable RNAs act by multiple mechanisms such as RNA-RNA base pairing, RNA-protein interactions and intrinsic RNA activity, as well as regulate diverse cellular functions, including RNA processing, mRNA stability, translation, protein stability and secretion. Non-protein-coding RNAs are known to play significant roles. Along with transfer RNAs, ribosomal RNAs and mRNAs, ncRNAs contribute to gene splicing, nucleotide modification, protein transport and regulation of gene expression.
Preparing for Precision Medicine (2012)

Precision medicine uses clinicopathological indexes and molecular profiling to create diagnostic, prognostic, and therapeutic strategies tailored to the patient. Its success depends on establishing frameworks for regulating, compiling, and interpreting key information.
Sequence and localization of a partial cDNA encoding the human alpha 3 chain of type IV collagen. (1991)

A novel type IV collagen, alpha 3(IV), has recently been identified in human and bovine basement membranes. Here we describe the cloning and sequencing of a cDNA encoding 218 residues of the NC1 domain of the human alpha 3(IV) chain. Of interest is the possible role of abnormalities of the alpha 3(IV) chain in Alport syndrome, as suggested by the failure to detect the NC1 domain of alpha 3(IV) in the basement membranes of some Alport syndrome patients. To determine whether the alpha 3(IV) gene (COL4A3) may be mutated in Alport syndrome, we localized it, by somatic cell hybrid analysis and in situ hybridization of metaphase chromosomes, to chromosome 2q35-2q37. Mutations in alpha 3(IV) cannot therefore be responsible for the vast majority of cases of Alport syndrome, which have been shown to be X linked. One explanation for the immunochemical data implicating alpha 3(IV) in Alport syndrome pathogenesis is that mutations of the alpha 5(IV) chain, which has been localized to Xq22 and found to be mutated in at least three kindreds with Alport syndrome, lead to failure to incorporate the alpha 3(IV) chains into the multimeric structure of glomerular basement membrane in a stable fashion.
Miller-Fisher syndrome associated with Campylobacter jejuni bearing lipopolysaccharide molecules that mimic human ganglioside GD3 (1996)

A Campylobacter jejuni strain of serotype O:10 was isolated from a patient who had Miller-Fisher syndrome. In its biochemical reactions and cellular morphology, the isolate was characteristic of typical C. jejuni. Antibodies against extracted lipopolysaccharide (LPS) were detected by passive hemagglutination in the acute- and convalescent-phase patient sera. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting with the O:10 antiserum, it was demonstrated that the strain possessed both low- and high-molecular-weight molecules. Chemical analysis of the LPS revealed that the core oligosaccharide has a terminal trisaccharide epitope consisting of two molecules of sialic acid linked to galactose, a structure reflecting the terminal region of human ganglioside GD3. As this trisaccharide is also present in LPS cores of serotype O:19 strains from patients with Guillain-Barré syndrome but not in cores of nonneuropathic C. jejuni, a possible role for the trisaccharide in the etiology of neuropathies is indicated, and a difference for distinguishing neuropathic strains from nonneuropathic strains may be the presence of a sialyltransferase required for the synthesis of this trisaccharide.
Chiral Allylic and Allenic Stannanes as Reagents for Asymmetric Synthesis (1996)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChiral Allylic and Allenic Stannanes as Reagents for Asymmetric SynthesisJames A. MarshallView Author Information Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208 Cite this: Chem. Rev. 1996, 96, 1, 31–48Publication Date (Web):February 1, 1996Publication History Received2 June 1995Revised9 August 1995Published online1 February 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/cr950037fhttps://doi.org/10.1021/cr950037fresearch-articleACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views3141Altmetric-Citations388LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Adducts,Aldehydes,Group 14 compounds,Reagents,Transition states Get e-Alerts
Persistent Campylobacter jejuni Infections in Patients Infected with Human Immunodeficiency Virus (HIV) (1988)

We identified Campylobacter jejuni infections in four patients infected with the human immunodeficiency virus (HIV); three had persistent and severe C. jejuni infections. Multiple isolates obtained from each patient had the same biochemical and serotypic characteristics, indicating recurrent infection rather than reinfection with unrelated strains. Serum antibody responses to C. jejuni group antigens by enzyme-linked immunosorbent assay were markedly impaired in the three patients with persistent infection compared with forty-two immunocompetent C. jejuni-infected controls and with the HIV-infected patient who readily cleared the organism. One patient was bacteremic; his blood isolate was killed by normal serum but was resistant to his own serum, whereas a simultaneous stool isolate of a different serotype was sensitive. Failure of two patients to eradicate the organism and long-term administration of erythromycin therapy led to the in-vivo development of resistance to this antibiotic, which is most frequently used to treat C. jejuni infections.
The influence of nitrate on microbial processes in oil industry production waters (2001)

Sulfide accumulation due to bacterial sulfate reduction is responsible for a number of serious problems in the oil industry. Among the strategies to control the activity of sulfate-reducing bacteria (SRB) is the use of nitrate, which can exhibit a variety of effects. We investigated the relevance of this approach to souring oil fields in Oklahoma and Alberta in which water flooding is used to enhance oil recovery. SRB and nitrate-reducing bacteria (NRB) were enumerated in produced waters from both oil fields. In the Oklahoma field, the rates of sulfate reduction ranged from 0.05 to 0.16 microM S day(-1) at the wellheads, and an order of magnitude higher at the oil-water separator. Sulfide production was greatest in the water storage tanks in the Alberta field. Microbial counts alone did not accurately reflect the potential for microbial activities. The majority of the sulfide production appeared to occur after the oil was pumped aboveground, rather than in the reservoir. Laboratory experiments showed that adding 5 and 10 mM nitrate to produced waters from the Oklahoma and Alberta oil fields, respectively, decreased the sulfide content to negligible levels and increased the numbers of NRB. This work suggests that sulfate reduction control measures can be concentrated on aboveground facilities, which will decrease the amount of sulfide reinjected into reservoirs during the disposal of oil field production waters.
Two Distinct Isoforms of cDNA Encoding Rainbow Trout Androgen Receptors (1999)

Androgens play an important role in male sexual differentiation and development. The activity of androgens is mediated by an androgen receptor (AR), which binds to specific DNA recognition sites and regulates transcription. We describe here the isolation of two distinct rainbow trout cDNA clones, designated rtAR-alpha and rtAR-beta, which contain the entire androgen receptor coding region. Comparison of the predicted amino acid sequence of rtAR-alpha to that of rtAR-beta revealed 85% identity. Interestingly, despite this high homology, rtAR-alpha activated transcription of an androgen-responsive reporter gene in co-transfection assays, but rtAR-beta did not. These results suggest that rainbow trout contains two distinct isoforms of androgen receptors whose functions differ. The region of rtAR-beta responsible for its inactivity was mapped to its ligand binding domain by analyzing chimeras of the rtAR-alpha, rtAR-beta, and rtGR-I (glucocorticoid) receptors. Alteration of any one of three out of four segments within this domain restored activity. Extracts made from COS-1 cells transfected with an rtAR-alpha expression plasmid produced a high level of [3H]mibolerone binding, whereas no binding was observed by extracts of cells transfected with an rtAR-beta expression plasmid. These data demonstrate that the lack of transactivation activity of rtAR-beta is due to its inability to bind hormone.
HIV Treatment Failure: Testing for HIV Resistance in Clinical Practice (1998)

Perrin and Talenti discuss how to evaluate antiretroviral therapy for AIDS. Their examination of data from the Swiss HIV cohort study suggest that failure or success is more complicated than analysis of virus replication. These observations have an impact on discussions of the relevance of HIV resistance testing to clinical practice.
ScFv construct and functional mapping, using site-directed mutagenesis of the monoclonal antibody TS1 (2003)

ScFv construct and functional mapping, using site-directed mutagenesis of the monoclonal antibody TS1
Using Azobenzene‐Embedded Self‐Assembled Monolayers To Photochemically Control Cell Adhesion Reversibly (2009)

A celling point: A mixed self-assembled monolayer comprising two types of alkanethiols--one containing an azobenzene unit terminated with a peptide, the other containing a hexa(ethylene glycol) group that resists nonspecific cell adhesion--enables cell adhesion to be modulated photochemically. The reversible conversion of the azobenzene moiety between E and Z configurations allows the surface to either support or resist cell adhesion.
Review article: modulation of the brain–gut axis as a therapeutic approach in gastrointestinal disease (2006)

This review discusses the rationale for modulation of the brain-gut axis in the treatment of functional gastrointestinal disorders and highlights the most promising current and future therapeutic strategies.
Serotonin transporter genotype, morning cortisol and subsequent depression in adolescents (2009)

The short allele of 5-HTTLPR may moderate the association between morning cortisol and the subsequent onset of a depressive episode.
Effect of folic acid and B vitamins on risk of cardiovascular events and total mortality among women at high risk for cardiovascular disease: a randomized trial. (2008)

clinicaltrials.gov Identifier: NCT00000541.
An lmproved method for directly sequencing PCR-amplified material using dimethyl sulphoxide (1989)

Journal Article An lmproved method for directly sequencing PCR-amplified material using dimethyl sulphoxide Get access Peter R. Winship Peter R. Winship Sir William Dunn School of Pathology, University of OxfordSouth Parks Road, Oxford OX1 3R-E, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 3, 11 February 1989, Page 1266, https://doi.org/10.1093/nar/17.3.1266 Published: 11 February 1989 Article history Received: 06 January 1989 Published: 11 February 1989
Developing a 3D-agent for the august dialogue system. (1999)

In our continuing work with multimodal text-to-speech synthesis with high quality for speechreading, a new talking head has been developed with the purpose of acting as an interactive agent in a dialogue system, set up in a public exhibition area in downtown Stockholm. The new agent conforms to the same set of basic control parameters as our earlier faces, allowing us to control it using existing rules for visual speech synthesis. To add to the realism and believability of the dialogue system, the agent has been given a rich repertoire of extra-linguistic gestures and expressions, including emotional cues, turn-taking signals and prosodic cues such as punctuators and emphasizers. Studies of user reactions indicated that people have a positive attitude towards our new agent.