gebhart/patrepeval huggingface dataset:
Thrombopoietin induces rapid resolution of thrombocytopenia after orthotopic liver transplantation through increased platelet production (2000)

Thrombopoietin (TPO) deficiency has been proposed as an important etiologic factor for thrombocytopenia in advanced-stage liver disease. To clarify the contributions of platelet production, platelet consumption, coagulation activation, and splenic sequestration to thrombocytopenia in liver disease, we studied TPO serum levels and markers of platelet production, platelet activation, and coagulation activation before and 14 days after orthotopic liver transplantation (OLT) in 18 patients with advanced liver cirrhosis. Thrombocytopenia before transplantation occurred with low-normal serum levels of TPO, normal levels of platelet and coagulation activation markers, and no increase in bone marrow production of platelets. TPO serum levels increased significantly on the first day after OLT, preceding the increase of reticulated platelets by 3 days and peripheral platelets by 5 days. Normalization of the peripheral platelet count occurred in most patients within 14 days of OLT, irrespective of the change in spleen size assessed by computed tomography volumetry. Normalization of platelet counts was not hampered by a certain degree of platelet activation observed during the steepest increase in the peripheral platelet count. Bone marrow production of platelets increased significantly within 2 weeks of transplantation. Low TPO serum levels with low platelet counts and without platelet consumption suggests low TPO production in end-stage liver disease. The rapid increase in TPO serum levels after transplantation induces an increase in the bone marrow production of platelets. Decreased TPO production in the cirrhotic liver is an important etiologic factor for thrombocytopenia in liver disease that is rapidly reversed by transplantation.
Deconstructing the Critical Theory Archive at UCI: An Experiment with EAC-CPF and Linked Open Data (2020)

The University of California, Irvine (UCI) Libraries has begun a pilot project exploring the use of Encoded Archival Context-Corporate Bodies, Persons, and Families (EAC-CPF) and linked open data to expose contextual information about holdings in UCI's Critical Theory Archive (CTA). The project team has identified a number of goals emphasizing public service, sustainability, and scalable experimentation. This work-in-progress article reports the pilot's background, scope, status through July 2014, and future plans.
Selenium flat-panel detector-based volume tomographic angiography imaging: phantom studies (1998)

A Selenium thin film transistor (STFT) array-based rotational volume tomographic digital angiography (VTDA) imaging system has been constructed. The system consists of an x-ray tube and a STFT detector that are separately mounted on a gantry. This system uses the STFT array as a two-dimensional (2D) detector so that a set of 2D projections can be acquired for a direct three-dimensional (3D) reconstruction. This paper presents the results of the preliminary phantom studies using the STFT- based volume tomographic angiography imaging system. This research work demonstrates through phantom studies that the STFT array introduces no distortion and the STFT-based VTDA imaging system has a higher spatial resolution and better contrast resolution than an image intensifier(II)-based system.
Distinguishing Between Mouse and Human Pluripotent Stem Cell Regulation: The Best Laid Plans of Mice and Men (2010)

Pluripotent stem cells (PSCs) have been derived from the embryos of mice and humans, representing the two major sources of PSCs. These cells are universally defined by their developmental properties, specifically their self-renewal capacity and differentiation potential which are regulated in mice and humans by complex transcriptional networks orchestrated by conserved transcription factors. However, significant differences exist in the transcriptional networks and signaling pathways that control mouse and human PSC self-renewal and lineage development. To distinguish between universally applicable and species-specific features, we collated and compared the molecular and cellular descriptions of mouse and human PSCs. Here we compare and contrast the response to signals dictated by the transcriptome and epigenome of mouse and human PSCs that will hopefully act as a critical resource to the field. These analyses underscore the importance of accounting for species differences when designing strategies to capitalize on the clinical potential of human PSCs.
Very fast containment of scanning worms (2004)

Computer worms — malicious, self-propagating programs — represent a significant threat to large networks. One possible defense, containment, seeks to limit a worm’s spread by isolating it in a small subsection of the network. In this work we develop containment algorithms suitable for deployment in high-speed, low-cost network hardware. We show that these techniques can stop a scanning host after fewer than 10 scans with a very low false-positive rate. We also augment this approach by devising mechanisms for cooperation that enable multiple containment devices to more effectively detect and respond to an emerging infection. Finally, we discuss ways that a worm can attempt to bypass containment techniques in general, and ours in particular. 1
Rendering fur with three dimensional textures (1989)

We present a method for rendering scenes with fine detail via an object called a texel , a rendering primitive inspired by volume densities mixed with anisotropic lighting models. This technique solves a long outstanding problem in image synthesis: the rendering of furry surfaces.
Congenital Hypoglycemia Disorders: New Aspects of Etiology, Diagnosis, Treatment and Outcomes (2016)

Hypoglycemia continues to be an important cause of morbidity in neonates and children. Prompt diagnosis and management of the underlying hypoglycemia disorder is critical for preventing brain damage and improving outcomes. Congenital hyperinsulinism (HI) is the most common and severe cause of persistent hypoglycemia in neonates and children. Recent discoveries of the genetic causes of HI have improved our understanding of the pathophysiology, but its management is complex and requires the integration of clinical, biochemical, molecular, and imaging findings to establish the appropriate treatment according to the subtype. Here we present a summary of a recent international symposium on congenital hypoglycemia disorders with emphasis on novel molecular mechanisms resulting in HI, genetic diagnosis, overall approach to management, novel therapies under development, and current outcomes.
Evidence for an acute phase response in human intestinal epithelial cells (1993)

During the host response to inflammation/tissue injury there are many changes in intermediary metabolism including a dramatic change in the concentrations of many "acute phase" plasma proteins. Although many of these acute phase proteins are predominantly derived from the liver and the response can be elicited from liver cells incubated in tissue culture with cytokines such as interleukin-6 (IL-6), interleukin-1 (IL-1), tumor necrosis factor-alpha, interferon-gamma, leukemia inhibitory factor, interleukin-11 (IL-11), and oncostatin M, there is now evidence that the response can also be elicited in extrahepatic tissues and cell types. In this study, we show that many of the acute phase plasma proteins are expressed in human intestinal epithelial cell lines Caco2 and T84 and that their expression is induced or regulated by cytokines IL-6, IL-1, interferon, and tumor necrosis factor in a manner characteristic of the acute phase response. In fact, effects of IL-1 and IL-6 which are additive, synergistic, and antagonistic in liver cell lines are also observed in these intestinal epithelial cell lines. Responses to IL-6 and IL-1 are seen at all stages of differentiation of Caco2 cells from crypt-like enterocytes to villus-like enterocytes. Caco2 cells express binding sites for IL-6 at both poles, for IL-1 at the basolateral pole and, to a lesser extent, at the apical pole. T84 cells have IL-1 and IL-6 receptor binding sites only at the basolateral pole. IL-6 and IL-1 also regulate the expression of enterocyte-specific integral membrane proteins as exemplified by down-regulation of sucrase-isomaltase gene expression in response to IL-6. These data raise the possibility that enterocytes are involved in a local response to injury/inflammation at the epithelial surface and establish a model system for examining coordination of the acute phase response in a bipolar cell.
Rapid and Selective Nitroxyl (HNO) Trapping by Phosphines: Kinetics and New Aqueous Ligations for HNO Detection and Quantitation (2011)

Recent studies distinguish the biological and pharmacological effects of nitroxyl (HNO) from its oxidized/deprotonated product nitric oxide (·NO), but the lack of HNO detection methods limits the understanding its in vivo mechanisms and the identification of endogenous sources. We previously demonstrated that reaction of HNO with triarylphosphines provides aza-ylides and HNO-derived amides, which may serve as stable HNO biomarkers. We now report a kinetic analysis for the trapping of HNO by phosphines, ligations of enzyme-generated HNO, and compatibility studies illustrating the selectivity of phosphines for HNO over other physiologically relevant nitrogen oxides. Quantification of HNO using phosphines is demonstrated using an HPLC-based assay and ligations of phosphine carbamates generate HNO-derived ureas. These results further demonstrate the potential of phosphine probes for reliable biological detection and quantification of HNO.
CNS Delivery Via Adsorptive Transcytosis (2008)

Adsorptive-mediated transcytosis (AMT) provides a means for brain delivery of medicines across the blood-brain barrier (BBB). The BBB is readily equipped for the AMT process: it provides both the potential for binding and uptake of cationic molecules to the luminal surface of endothelial cells, and then for exocytosis at the abluminal surface. The transcytotic pathways present at the BBB and its morphological and enzymatic properties provide the means for movement of the molecules through the endothelial cytoplasm. AMT-based drug delivery to the brain was performed using cationic proteins and cell-penetrating peptides (CPPs). Protein cationization using either synthetic or natural polyamines is discussed and some examples of diamine/polyamine modified proteins that cross BBB are described. Two main families of CPPs belonging to the Tat-derived peptides and Syn-B vectors have been extensively used in CPP vector-mediated strategies allowing delivery of a large variety of small molecules as well as proteins across cell membranes in vitro and the BBB in vivo. CPP strategy suffers from several limitations such as toxicity and immunogenicity--like the cationization strategy--as well as the instability of peptide vectors in biological media. The review concludes by stressing the need to improve the understanding of AMT mechanisms at BBB and the effectiveness of cationized proteins and CPP-vectorized proteins as neurotherapeutics.
Lagrangian formulation of underwater vehicles' dynamics (2002)

Key properties of the equations of motion for underwater vehicles are derived both theoretically and experimentally. The equations of motion for underwater vehicles are derived in a Lagrangian framework. The Lagrangian approach has several distinctive advantages compared to the Newtonian approach. This is especially true in the context of underwater vehicles. The derivation of the hydrodynamic added inertia and the vehicle's rigid body equations of motion can be done in a common framework. The added inertia is given a clear and physical interpretation when the vehicle-ambient water system is considered from an energy point of view instead of a force-moment approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Filtercake Integrity and Reservoir Damage (1998)

Abstract Filtercake performance is of particular importance in openhole completions where formation impairment cannot be bypassed by perforation. Emphasis is placed on producing a thin, tough and highly impermeable cake to seal the wellbore during drilling. Once completed and the well is brought onstream, the filtercake is required to break down without the need for expensive clean up treatments. Filtercake integrity can then play an important role in the cleanup of a reservoir. Back production is assumed to cause the cake either to detach from the formation or rupture. Cake-rock adhesion and inherent filtercake strength are therefore important in determining how the cake breaks down to allow oil flow. If the cake-rock adhesion is strong compared to the internal strength of the cake, the cake may pinhole, or blister to allow flow. If it is relatively weak the entire cake may lift off cleanly. This latter case may cause further production problems if the cake subsequently seals the completion hardware. This paper presents laboratory data on filtercake strength and its relation to cleanup by back-production for typical reservoir drilling fluids. Critical components are identified. The role of bridging solids particle size in determining the balance between adhesion and rupture strength will be demonstrated. Filtercake design to optimize removal through the exploitation of functional weak links will be discussed. P. 111
Transformation Resistance in a Premature Aging Disorder Identifies a Tumor-Protective Function of BRD4 (2014)

Advanced age and DNA damage accumulation are prominent risk factors for cancer. The premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS) provides a unique opportunity for studying the interplay between DNA damage and aging-associated tumor mechanisms, given that HGPS patients do not develop tumors despite elevated levels of DNA damage. Here, we have used HGPS patient cells to identify a protective mechanism to oncogenesis. We find that HGPS cells are resistant to neoplastic transformation. Resistance is mediated by the bromodomain protein BRD4, which exhibits altered genome-wide binding patterns in transformation-resistant cells, leading to inhibition of oncogenic dedifferentiation. BRD4 also inhibits, albeit to a lower extent, the tumorigenic potential of transformed cells from healthy individuals. BRD4-mediated tumor protection is clinically relevant given that a BRD4 gene signature predicts positive clinical outcome in breast and lung cancer. Our results demonstrate a protective function for BRD4 and suggest tissue-specific roles for BRD4 in tumorigenesis.
A Concentrated and Stable Aerosol Formulation of Cationic Lipid:DNA Complexes Giving High-Level Gene Expression in Mouse Lung (1997)

Advances in gene therapy vectors and techniques hold promise for treatment of many inherited and acquired diseases. For lung indications, especially those involving the epithelium, delivery of the gene therapy vehicle ideally will involve the use of an aerosol. Aerosol delivery of transgenes using cationic lipids is currently limited by the ability to generate highly concentrated formulations of lipid:DNA complexes that are stable and retain their activity following aerosolization. We have examined many of the variables inherent in aerosolizing cationic lipid gene delivery vehicles and have devised a new formulation that incorporates small amounts of a polyethylene glycol-containing lipid. This formulation has allowed the preparation of concentrated dispersions of cationic lipid:plasmid DNA (pDNA) complexes (> 20 mM pDNA) at approximately 10-fold higher concentrations than previously reported. Most of the pDNA in these formulations was bound to the lipid component and thereby protected from nebulizer-induced shearing; the pDNA also maintained full biological activity both in vitro and in vivo. This new formulation thus represents a significant improvement over current methods to prepare concentrated, active cationic lipid gene delivery vectors, and provides a new tool with which to test gene transfer to the lung.
Mir-302 reprograms human skin cancer cells into a pluripotent ES-cell-like state (2008)

Renewal of stem cells differs from cancer cell growth in self-controlled cell division. The mir-302 microRNA (miRNA) family (mir-302s) is expressed most abundantly in slow-growing human embryonic stem (ES) cells, and quickly decreases after cell differentiation and proliferation. Therefore, mir-302s was investigated as one of the key factors essential for maintenance of ES cell renewal and pluripotency in this study. The Pol-II-based intronic miRNA expression system was used to transgenically transfect the mir-302s into several human cancer cell lines. The mir-302-transfected cells, namely, miRNA-induced pluripotent stem (mirPS) cells, not only expressed many key ES cell markers, such as Oct3/4, SSEA-3, SSEA-4 ,Sox2, and Nanog, but also had a highly demethylated genome similar to a reprogrammed zygotic genome. Microarray analyses further revealed that genome-wide gene expression patterns between the mirPS and human ES H1 and H9 cells shared over 86% similarity. Using molecular guidance in vitro, these mirPS cells could differentiate into distinct tissue cell types, such as neuron-, chondrocyte-, fibroblast-, and spermatogonia-like primordial cells. Based on these findings, we conclude that mir-302s not only function to reprogram cancer cells into an ES-like pluripotent state but also to maintain this state under a feeder-free cultural condition, which may offer a great opportunity for therapeutic intervention.
The ClpP component of Clp protease is the sigma 32-dependent heat shock protein F21.5 (1990)

The genes that encode the subunits of the Clp protease of Escherichia coli, clpA and clpP, appear to be regulated differently from each other. The clpA gene does not seem to be under heat shock control (Y. S. Katayama, S. Gottesman, J. Pumphrey, S. Rudikoff, W. P. Clark, and M. R. Maurizi, J. Biol. Chem. 263:15226-15236, 1988). In contrast, the level of ClpP protein was increased in rpoH+ cells but not in null rpoH cells after an upshift in temperature from 17 to 43 degrees C. The level of ClpP protein in a null dnaK strain was also elevated relative to the level of ClpP protein in an otherwise isogenic dnaK+ strain. In two-dimensional gels, the ClpP protein was located in the position of the previously unidentified heat shock protein F21.5. No protein spot corresponding to F21.5 was present in two-dimensional gels of a null clpP strain. The clpP gene, therefore, appears to be a heat shock gene, expressed in a sigma 32-dependent manner and negatively regulated by DnaK; the product of clpP is the previously unidentified heat shock protein F21.5.
Highly Regio-Selective Synthesis of β-Amino Alcohol by Reaction with Aniline and Propylene Carbonate in Self Solvent System over Large Pore Zeolite Catalyst (2011)

The nucleophilic ring opening of epoxides with amines is a well known route for the synthesis of β-amino alcohols. The use of carbonates offers significant advantages over epoxides as they are far less hazardous materials, safe for handling, do not require high-pressure equipment and most notably the possibility of solvent less reactions. In this work, utilization of zeolite as host catalyst in the reaction media for synthesis of β-amino alcohols without using solvent is reported.
Lifespan, age changes and tumour incidence in an ageing C57BL mouse colony (1976)

Detailed data from a colony of C57BL mice kept for research into ageing processes are given on weights of 13 organs between the ages of 6 and 30 months; pathological findings and x-ray results from animals aged 6, 24 and 30 months; age-specific tumour incidences in 24 organs in 3-month period up to 36 months of age. Results of previously published age-related studies of reproductive capacity, dental abnormalities and brain changes are summarised.
A Decline in C 6 Antibody Titer Occurs in Successfully Treated Patients with Culture-Confirmed Early Localized or Early Disseminated Lyme Borreliosis (2005)

C(6), a Borrelia burgdorferi-derived peptide, is used as the antigen in the C(6)-Lyme disease diagnostic test. We assessed retrospectively whether a fourfold decrease or a decrease to a negative value in anti-C(6) antibody titer is positively correlated with a positive response to treatment in a sample of culture-confirmed patients with either early localized (single erythema migrans [EM]; n=93) or early disseminated (multiple EM; n=27) disease. All of these patients had been treated with antibiotics and were free of disease within 6 to 12 months of follow-up. Results show that a serum specimen taken at this time was either C(6) negative or had a >or=4-fold decrease in C(6) antibody titer with respect to a specimen taken at baseline (or during the early convalescent period if the baseline specimen was C(6) negative) for all of the multiple-EM patients (P<0.0001) and in 89% of the single-EM patients (P<0.0001). These results indicate that a decline in anti-C(6) antibody titer coincides with effective antimicrobial therapy in patients with early localized or early disseminated Lyme borreliosis.
The Global Circulation of Seasonal Influenza A (H3N2) Viruses (2008)

Antigenic and genetic analysis of the hemagglutinin of approximately 13,000 human influenza A (H3N2) viruses from six continents during 2002-2007 revealed that there was continuous circulation in east and Southeast Asia (E-SE Asia) via a region-wide network of temporally overlapping epidemics and that epidemics in the temperate regions were seeded from this network each year. Seed strains generally first reached Oceania, North America, and Europe, and later South America. This evidence suggests that once A (H3N2) viruses leave E-SE Asia, they are unlikely to contribute to long-term viral evolution. If the trends observed during this period are an accurate representation of overall patterns of spread, then the antigenic characteristics of A (H3N2) viruses outside E-SE Asia may be forecast each year based on surveillance within E-SE Asia, with consequent improvements to vaccine strain selection.
Maternal embryonic leucine zipper kinase transcript abundance correlates with malignancy grade in human astrocytomas (2007)

We have performed cDNA microarray analyses to identify gene expression differences between highly invasive glioblastoma multiforme (GBM) and typically benign pilocytic astrocytomas (PA). Despite the significant clinical and pathological differences between the 2 tumor types, only 63 genes were found to exhibit 2-fold or greater overexpression in GBM as compared to PA. Forty percent of these genes are related to the regulation of the cell cycle and mitosis. QT-PCR validation of 6 overexpressed genes: MELK, AUKB, ASPM, PRC1, IL13RA2 and KIAA0101 confirmed at least a 5-fold increase in the average expression levels in GBM. Maternal embryonic leucine zipper kinase (MELK) exhibited the most statistically significant difference. A more detailed investigation of MELK expression was undertaken to study its oncogenic relevance. In the examination of more than 100 tumors of the central nervous system, we found progressively higher expression of MELK with astrocytoma grade and a noteworthy uniformity of high level expression in GBM. Similar level of overexpression was also observed in medulloblastoma. We found neither gene promoter hypomethylation nor amplification to be a factor in MELK expression, but were able to demonstrate that MELK knockdown in malignant astrocytoma cell lines caused a reduction in proliferation and anchorage-independent growth in in vitro assays. Our results indicate that GBM and PA differ by the expression of surprisingly few genes. Among them, MELK correlated with malignancy grade in astrocytomas and represents a therapeutic target for the management of the most frequent brain tumors in adult and children.