gebhart/patrepeval huggingface dataset:
Intestinal absorption of elemental and standard enteral formulas in hypoproteinemic (volume expanded) rats (1988)

We examined the influence of a peptide-based enteral formula and a standard (intact protein) enteral formula on intestinal transcapillary and transmucosal water and protein fluxes during hypoproteinemia induced by plasma volume expansion. In 15 Sprague-Dawley rats, net transmucosal water flux and net transmucosal and capillary albumin clearances were monitored in jejunal loops before and during intravenous infusion (2.5 ml/min/kg) of Tyrodes solution. This procedure resulted in a 60% reduction in plasma protein concentration and net water secretion into the bowel lumen. Luminal perfusion with the peptide-based formula did not modify the magnitude of the reduction in plasma protein concentration, yet dramatically reduced transmucosal and transcapillary albumin clearances (p less than 0.05). In addition, a net absorptive water flux was maintained with the peptide-based formula during volume expansion despite hypoproteinemia. The response to luminal perfusion with the intact protein formula were not different from controls. The results of this study are consistent with previous observations that enteral feeding with a peptide-based formula significantly attenuates the diarrhea associated with acute hypoalbuminemia in the critically ill patient.
Small Interfering RNA–Directed Knockdown of Uracil DNA Glycosylase Induces Apoptosis and Sensitizes Human Prostate Cancer Cells to Genotoxic Stress (2009)

Uracil DNA glycosylase (UNG) is the primary enzyme responsible for removing uracil residues from DNA. Although a substantial body of evidence suggests that DNA damage plays a role in cancer cell apoptosis, the underlying mechanisms are poorly understood. In particular, very little is known about the role of base excision repair of misincorporated uracil in cell survival. To test the hypothesis that the repair of DNA damage associated with uracil misincorporation is critical for cancer cell survival, we used small interfering RNA (siRNA) to target the human UNG gene. In a dose-dependent and time-dependent manner, siRNA specifically inhibited UNG expression and modified the expression of several genes at both mRNA and protein levels. In LNCaP cells, p53, p21, and Bax protein levels increased, whereas Bcl2 levels decreased. In DU145 cells, p21 levels were elevated, although mutant p53 and Bax levels remained unchanged. In PC3 cells, UNG inhibition resulted in elevated p21 and Bax levels. In all three cell lines, UNG inhibition reduced cell proliferation, induced apoptosis, and increased cellular sensitivity to genotoxic stress. Furthermore, an in vitro cleavage experiment using uracil-containing double-stranded DNA as a template has shown that siRNA-mediated knockdown of UNG expression significantly reduced the uracil-excising activity of UNG in human prostate cancer cells, which was associated with DNA damage analyzed by comet assay. Taken together, these findings indicate that RNA interference-directed targeting of UNG is a convenient, novel tool for studying the biological role of UNG and raises the potential of its application for prostate cancer therapy.
Challenges of Large-Scale Biomedical Workflows on the Cloud -- A Case Study on the Need for Reproducibility of Results (2015)

Computational bioinformatics workflows are extensively used to analyse genomics data. With the unprecedented advancements in genomic sequence technology and opportunities for personalized medicines, it is essential that analysis results are repeatable by others, especially when moving into clinical environment. To cope with the complex computational demands of huge biological datasets, a shift to distributed compute resources is unavoidable. A case study was conducted in which three well established bioinformatics analysis groups across Australia were assigned to analyse exome sequence data from a range of patients with a rare condition: disorder of sex development. Initially these groups used their own in-house data processing pipelines, and subsequently used a common bioinformatics workbench based upon Galaxy and offered through the Australia-wide National eResearch Collaboration Tools and Resources (NeCTAR) Research Cloud. This paper describes the experiences in this work and the variability of results. We put forward principles that should be used to ensure reproducibility of scientific results moving forward.
The Construction of Chimeric T‐Cell Receptor with Spacer Base of Modeling Study of VHH and MUC1 Interaction (2011)

Adaptive cell immunotherapy with the use of chimeric receptors leads to the best and most specific response against tumors. Chimeric receptors consist of a signaling fragment, extracellular spacer, costimulating domain, and an antibody. Antibodies cause immunogenicity; therefore, VHH is a good replacement for ScFv in chimeric receptors. Since peptide sequences have an influence on chimeric receptors, the effect of peptide domains on each other's conformation were investigated. CD3Zeta, CD28, VHH and CD8α, and FcgIIα are used as signaling moieties, costimulating domain, antibody, and spacers, respectively. To investigate the influence of the ligation of spacers on the conformational structure of VHH, models of VHH were constructed. Molecular dynamics simulation was run to study the influence of the presence of spacers on the conformational changes in the binding sites of VHH. Root mean square deviation and root mean square fluctuation of critical segments in the binding site showed no noticeable differences with those in the native VHH. Results from molecular docking revealed that the presence of spacer FcgIIα causes an increasing effect on VHH with MUC1 interaction. Each of the constructs was transformed into the Jurkat E6.1. Expression analysis and evaluation of their functions were examined. The results showed good expression and function.
Acquired Chromosome 11q Deletion Involving the Ataxia Teleangiectasia Locus in B-Cell Non-Hodgkin’s Lymphoma: Correlation With Clinicobiologic Features (2000)

Though possibly not representing a primary genetic lesion in the majority of cases, the acquired ATM+/- status has clinicobiologic importance in NHL, possibly representing a major cytogenetic determinant of outcome.
Longhorn Ties Platform Apps to Core Operating System (2004)

Call it all-tools-for-all-things-Microsoft. That’s the way I’m beginning to think about Longhorn, Microsoft’s next-generation operating system, expected in 2006. The operating system will herald more than just the transition of mainstream computing to 64 bits. It will mark the emergence of a new, multifaceted programming model. Breaking away from traditional computer science taxonomy, where operating systems stood barely removed from the hardware abstraction layer, Longhorn will be more like a multi-tentacled container for a wide range of administration and application tools.
Multilingual Federated Searching Across Heterogeneous Collections (1998)

This article describes a scalable system for searching heterogeneous multilingual collections on the World Wide Web. It details a markup language for describing the characteristics of a search engine and its interface, and a protocol for requesting word translations between languages.
Ethical Regulation and Visual Methods: Making Visual Research Impossible or Developing Good Practice? (2012)

The ethical regulation of social research in the UK has been steadily increasing over the last decade or so and comprises a form of audit to which all researchers in Higher Education are subject. Concerns have been raised by social researchers using visual methods that such ethical scrutiny and regulation will place severe limitations on visual research developments and practice. This paper draws on a qualitative study of social researchers using visual methods in the UK. The study explored their views, the challenges they face and the practices they adopt in relation to processes of ethical review. Researchers reflected on the variety of strategies they adopted for managing the ethical approval process in relation to visual research. For some this meant explicitly ‘making the case’ for undertaking visual research, notwithstanding the ethical challenges, while for others it involved ‘normalising’ visual methods in ways which delimited the possible ethical dilemmas of visual approaches. Researchers only rarely identified significant barriers to conducting visual research from ethical approval processes, though skilful negotiation and actively managing the system was often required. Nevertheless, the climate of increasing ethical regulation is identified as having a potential detrimental effect on visual research practice and development, in some instances leading to subtle but significant self-censorship in the dissemination of findings.
Inhibition of Human Immunodeficiency Virus Type-1 by Retroviral Vectors Expressing Antisense-TAR (1994)

The human immunodeficiency virus type-1 (HIV-1) Tat activation response (TAR) region is essential for Tat-mediated trans-activation of the HIV-1 long terminal repeat (LTR). The TAR element is present on the 5' and 3' ends of all HIV-1 transcripts and is relatively conserved among different HIV-1 isolates. These properties make it an attractive target for anti-HIV-1 gene therapy strategies. We have constructed a Moloney murine leukemia-based retroviral vector that expresses a chimeric tRNA(iMet)-antisense TAR fusion transcript complementary to the HIV-1 TAR region. The potential of this anti-TAR retroviral vector to inhibit HIV-1 was initially tested by transient transfections with an HIV-1-LTR-Tat expression plasmid into HeLa-CAT cells. Anti-TAR inhibited Tat-mediated HIV-1 LTR-driven CAT reporter gene expression in a dose-dependent fashion. The antisense-TAR vector was then used to transduce the human SupT1 T cell line. Cotransfection of these SupT1 cells with a Tat expression plasmid plus an HIV-1 LTR-CAT reporter plasmid resulted in decreased CAT gene expression in comparison to control transduced SupT1 cells. The antisense-TAR engineered SupT1 cell line was then challenged with HIV-1MN.HIV-1 viral production was inhibited in SupT1 cells transduced with the antisense-TAR retroviral vector. Greater inhibition of HIV-1 was observed with antisense-TAR as compared to antisense-Tat expressing retroviral vector. These observations suggest that antisense-TAR retroviral vectors are potentially useful for clinical anti-HIV-1 gene therapy.
Controlling the anisotropy of holographic polymer-dispersed liquid-crystal gratings (2002)

In this work we investigate the optical properties of electrically switched transmission gratings fabricated holographically using polymer-dispersed liquid-crystal (PDLC) materials. We have found that the PDLC mixture can be used to control the diffractive properties of the liquid-crystal composite gratings. In one limit the gratings are highly isotropic and in the other limit the gratings are highly anisotropic with a large birefringence. The experimental results are compared to theories that include the birefringence of the grating. From theoretical fits to the experimental data, measurements of the liquid-crystal distribution and alignment are obtained.
Immune Function in Transgenic Mice Overexpressing Growth Hormone (GH) Releasing Hormone, GH or GH Antagonist (1999)

Effects of life-long exposure to high levels of homologous or heterologous growth hormone (GH) and effects of GH resistance on selected parameters of immune function were studied in adult male transgenic mice overexpressing GH releasing hormone (GHRH), bovine (b) GH or an antagonistic bGH analog. In metallothionein I (MT)-bGH transgenic mice with high peripheral levels of bovine GH, there were significant increases in the absolute weight of the thymus and the spleen and in the mitogenic responses of splenocytes to concanavalin A (ConA), lipopolysaccharide (LPS) and phytohemagglutinin (PHA), as compared to age-matched normal animals. There were no significant differences between MT-bGH transgenic and normal mice in splenocyte viability or in delayed-type hypersensitivity measured by the allergic contact dermatitis response to oxazolone. Similar results, including significant stimulation of splenocyte responses to ConA, LPS, and PHA, were obtained in MT-hGHRH transgenic mice in which overexpression of GHRH leads to striking pituitary enlargement and massive elevation of peripheral levels of homologous (mouse) GH. In MT-bGH-antagonist transgenic mice in which overexpression of an antagonistic bGH analog interferes with the actions of endogenous GH, spleen weight was reduced but proliferative responses of splenocytes to ConA, LPS, and PHA were not affected. It is concluded that overexpression of heterologous or homologous GH in transgenic mice can lead to significant stimulation of some parameters of immune function, whereas antagonism of GH action by expression of an antagonistic GH analog does not affect splenocyte responses to mitogens.
Hydrogen passivation and activation of oxygen complexes in silicon (2001)

We report first-principles calculations in terms of which we describe the role of hydrogen in passivating or activating oxygen complexes in Si. In particular we find that attaching H to a pre-existing oxygen cluster can change the electric activity of the cluster. Furthermore, the addition of a hydrogen atom in the core structure of thermal donors can account for the NL10 electron-paramagnetic-resonance signal. The interaction of H with the thermal-donor-like defects at the Si–SiO2 is also discussed.
Identity-Based Encryption from the Weil Pairing (2003)

We propose a fully functional identity-based encryption (IBE) scheme. The scheme has chosen ciphertext security in the random oracle model assuming a variant of the computational Diffie--Hellman problem. Our system is based on bilinear maps between groups. The Weil pairing on elliptic curves is an example of such a map. We give precise definitions for secure IBE schemes and give several applications for such systems.
Di- and tri-methoxystyryl derivatives of heterocyclic nitrogen compounds. (1981)

A series of mono-, di-, and trimethoxystyryl derivatives of heterocyclic nitrogen compounds were prepared to test the N-O-O triangulation hypothesis of Zee-Cheng and Cheng. Of 29 free bases submitted for KB cell culture test, only 2-(3,4-methylenedioxystyryl)benzoxazole and 4-(2,5-dimethoxystyryl)cinnoline were active (ED50 of 4 microgram/ml or less). Methiodide salts were more potent: 8 of 14 were active. 2-(2,4,6-Trimethoxystyryl)quinoline methiodide and 4-(2,4,5-trimethoxystyryl)quinoline methiodide had ED50 of 0.4 and 0.9 microgram/ml, respectively. The methiodides of 2-(2,3,4-, 4-(2,4,5-, 4-(2,4,6-, and 2,4-bis-(2,4,6-trimethoxystyryl)quinoline and 1-(2,4,6-trimethoxystyryl) isoquinoline and the propiodide of 4-(2,4,6-trimethoxystyryl)quinoline were active against P388 leukemia. Several of the active compounds do not conform to the dimensions of the Zee-Cheng and Cheng triangle.
Enhanced γ-Carboxylation of Recombinant Factor X Using a Chimeric Construct Containing the Prothrombin Propeptide (2000)

Factor Xa is the serine protease component of prothrombinase, the enzymatic complex responsible for thrombin generation. Production of recombinant factor X/Xa has proven to be difficult because of inefficient gamma-carboxylation, a critical post-translational modification. The affinities of the vitamin K-dependent propeptides for the gamma-carboxylase vary over 2 logs, with the propeptide of factor X having the highest affinity followed by the propeptides of factor VII, protein S, factor IX, protein C, and prothrombin [Stanley, T. B. (1999) J. Biol. Chem. 274, 16940-16944]. On the basis of this observation, it was hypothesized that exchanging the propeptide of factor X with one that binds the gamma-carboxylase with a reduced affinity would enhance gamma-carboxylation by allowing greater substrate turnover. A chimeric cDNA consisting of the human prothrombin signal sequence and propeptide followed by mature human factor X was generated and stably transfected into HEK 293 cells, and modified factor X was purified from conditioned medium. The results indicate that on average 85% of the total factor X produced with the prothrombin propeptide was fully gamma-carboxylated, representing a substantial improvement over a system that employs the native factor X propeptide, with which on average only 32% of the protein is fully gamma-carboxylated. These results indicate that the affinity of the gamma-carboxylase for the propeptide greatly influences the extent of gamma-carboxylation. It was also observed that regardless of which propeptide sequence is directing gamma-carboxylation (factor X or prothrombin), two pools of factor X are secreted; one is uncarboxylated and a second is fully gamma-carboxylated, supporting the notion that the gamma-carboxylase is a processive enzyme.
The fate of human platelets perfused through the pig liver: implications for xenotransplantation (2010)

Our observation of pig LSEC phagocytosis of human platelets describes a novel mechanism of large-particle uptake in the liver. The creation of a model system to study xenotransplantation-induced thrombocytopenia makes possible the investigation into mechanisms that mediate platelet loss.
Fundamental understanding of the biochemical conversion of Buddleja davidii to fermentable sugars (2011)

Lignocellulosic bioethanol is currently being explored as a substitution to fossil fuels. Many lignocellulosic materials are being examined but the importance is to find those with attractive agro-energy features. Producing lignocellulosic ethanol is challenging because lignocellulosic biomass is resistant to chemical and biological degradation. To reduce biomass recalcitrance, a pretreatment stage is required. Pretreatment is considered to be the most intensive operating/operating cost component of cellulosic ethanol production. Therefore, research is heavily focused on understanding the effect of pretreatment technologies on the fundamental characteristics of lignocellulosic biomass. &#13;\n\tThe first study in the thesis investigates Buddleja davidii as a potential biomass source for bioethanol production. The work focuses on the determination of ash, extractives, lignin, hemicellulose, and cellulose content in this plant, as well as detailed elucidation of the chemical structures of both lignin and cellulose by NMR spectroscopy. The study showed that B. davidii has several unique agro-energy features as well as some undesired characteristics. &#13;\n\tThe second study presents research on the ethanol organosolv pretreatment (EOP) of B. davidii and its ability to produce enzymatically hydrolysable substrates. It was concluded that the removal of hemicellulose, delignification, reduction in the degree of polymerization (DP) of cellulose, and the conversion of crystalline cellulose dimorphs (Iα/Iβ) to the easily degradable para-crystalline and amorphous celluloses were the characteristics accounted for efficient enzymatic deconstruction of B. davidii after EOP. &#13;\n\tThe third study provides a detailed elucidation of the chemical structure of ethanol organosolv lignin (EOL) of B. davidii by NMR spectroscopy. Such research was needed to understand the pretreatment mechanism in the context of delignification and alteration of the lignin structure. Future applications of the resulted EOL will be valuable for industrially viable bioethanol production process. EOP mainly cleaved β-O-4' interlinkages via homolysis, decreased the DP of lignin, and increased the degree of condensation of lignin. EOL had low oxygen content, molecular weight, and aliphatic OH as well as high phenolic OH, which are qualities that make it suitable for different co-product applications. &#13;\n\tThe last study provides information on the anatomical characteristics of pretreated B. davidii biomass after EOP. The importance of this research was to further understand the alterations that occur to the cellular structure of the biomass which can then be correlated with its enzymatic digestibility. The results concluded that the physical distribution of lignin within the biomass matrix and the partial removal of middle lamella lignin were key factors influencing enzymatic hydrolysis.
AT&T Network Architecture Evolution (1987)

The network of the future will use technologies and architectures that meet the telecommunications needs of our customers. These customer needs are embodied in three AT&T corporate goals: maintain and strengthen the core businesses, expand the focus on data networking, and establish a major position in international markets. To address these goals, AT&T will provide a network that is lowest in cost and rich in features and functionality. Key elements in the network evolution are an aggressive plan for digitalization, implementation of distributed network intelligence, and deployment of advanced technologies. These key elements allow AT&T to expand its existing services and introduce new services including: data capabilities oriented toward customer network management; modernized private networks such as EPSCS; domestic services offered globally; ISDN; and enhanced services. The plans for the AT&T network extend to the year 2000 and beyond to ensure AT&T's leadership position.
Active human immunodeficiency virus protease is required for viral infectivity. (1988)

Retroviral proteins are synthesized as polyprotein precursors that undergo proteolytic cleavages to yield the mature viral proteins. The role of the human immunodeficiency virus (HIV) protease in the viral replication cycle was examined by use of a site-directed mutation in the protease gene. The HIV protease gene product was expressed in Escherichia coli and observed to cleave HIV gag p55 to gag p24 and gag p17 in vitro. Substitution of aspartic acid residue 25 (Asp-25) of this protein with an asparagine residue did not affect the expression of the protein, but it eliminated detectable in vitro proteolytic activity against HIV gag p55. A mutant HIV provirus was constructed that contained the Asn-25 mutation within the protease gene. SW480 human colon carcinoma cells transfected with the Asn-25 mutant proviral DNA produced virions that contained gag p55 but not gag p24, whereas virions from cells transfected with the wild-type DNA contained both gag p55 and gag p24. The mutant virions were not able to infect MT-4 lymphoid cells. In contrast, these cells were highly sensitive to infection by the wild-type virions. These results demonstrate that the HIV protease is an essential viral enzyme and, consequently, an attractive target for anti-HIV drugs.
Morphometry of nuclei of the normal and malignant prostate in relation to DNA ploidy. (1992)

Fine needle biopsies from 70 patients with prostate carcinoma and 10 patients with benign hyperplasia were used to study area, variation in size and form factors of the nuclei by image analysis. The results were related to DNA ploidy of the cell populations as measured by flow cytometry, cytologic grade and patients' survival. Nuclear area differed significantly between benign lesions and tumors. It increased in diploid low-grade tumors from a normal value of 54.2 +/- 3.1 microns2 to 75.6 +/- 5.3 microns2. In aneuploid tumors with an increase in the chromosome number, the nuclear size further increased to about twice that of benign nuclei. Variation in size also differed between benign and malignant epithelium, with a further increase between diploid and gross aneuploid tumors. While nuclear size and variation in nuclear size made it possible to discriminate malignant from benign lesions, form factor did not differ between benign and malignant lesions. In follow-up, however, none of these factors reached significance for predicting survival.
Hemophagocytic lymphohistiocytosis (2011)

Recent scientific and clinical insights are expanding understanding and recognition of HLH, driving an evolution in how it is defined, and suggesting future directions for improving therapy of this disorder.