gebhart/patrepeval huggingface dataset:
Immunoaffinity Ultrafiltration with Ion Spray HPLC/MS for Screening Small-Molecule Libraries (1997)

A solution-phase screening method for libraries of pharmaceutically relevant molecules is presented. The technique is applicable to screening combinatorial libraries of 20-30 closely related molecules. In this report, individual benzodiazepines are selected from a multicomponent library mixture by formation in solution of noncovalent immunoaffinity complexes with antibodies raised to therapeutically proven drugs such as nitrazepam, temazepam, or oxazepam. Captured compounds are separated from nonspecifically bound library components by centrifugal ultrafiltration. The specifically selected molecules retained on the filter are subsequently liberated from the antibodies by acidification and analyzed by HPLC coupled with pneumatically assisted electrospray (ion spray) ionization mass spectrometric detection. Competition by the benzodiazepines for limited antibody binding sites is controlled by varying the stoichiometry of the complexation mixture. This procedure selects library components with the greatest affinity for a particular antibody. Specific capture of benzodiazepines is demonstrated by screening both a pool of structurally similar benzodiazepines and a more complex mixture of benzodiazepines with an additional set of unrelated compounds. Affinity ultrafiltration and electrospray mass spectrometry complement each other to enhance screening and identification of pooled drug candidates and potentially can be extended to other small-molecule combinatorial libraries and macromolecular receptor preparations.
Upregulation of vascular endothelial growth factor in ischemic and non-ischemic human and experimental retinal disease. (1997)

Vascular endothelial growth factor (VEGF) is induced by hypoxia and it has been implicated in the development of iris and retinal neovascularization (NV) in ischemic retinopathies in which it has been suggested that Muller cells are responsible for increased VEGF production. VEGF, however, is also known to be a potent mediator of vascular permeability in other tissues and may perform this function in retina. Immunohistochemical staining for VEGF was performed on a variety of human and experimental ischemic and non-ischemic ocular disorders in which blood retinal barrier (BRB) breakdown is known to occur to determine if there is an upregulation of VEGF in these conditions. We found increased VEGF immunoreactivity in ganglion cells of rats with oxygen-induced ischemic retinopathy and in ganglion cells, the inner plexiform layer, and some cells in the inner nuclear layer of rats with experimental autoimmune uveoretinitis (EAU), in which there was no identifiable ischemia or NV. In rats with EAU, VEGF staining intensity increased from 8 to 11 days after immunization, coincident with BRB failure. These results were confirmed using two distinct anti-VEGF antibodies and by immunoblot and the immunohistochemical staining was eliminated by pre-incubating the antibodies with VEGF peptide. VEGF staining was also increased in the retina and iris of patients with ischemic retinopathies, such as diabetic retinopathy and retinal vascular occlusive disease, and in patients with disorders in which retinal ischemia does not play a major role, such as aphakic/ pseudophakic cystoid macular edema, retinoblastoma, ocular inflammatory disease or infection, and choroidal melanoma. VEGF was primarily localized within retinal neurons and retinal pigmented epithelial cells in these cases. In addition or in association with its role of inducing NV, VEGF may contribute to BRB breakdown in a variety of ocular disorders and blockage of VEGF signaling may help to reduce some types of macular edema.
Living Radical Polymerization Immobilized on Wang Resins:  Synthesis and Harvest of Narrow Polydispersity Poly(methacrylate)s (2001)

Wang resin has been transformed into an initiator for copper(I)-mediated living radical polymerization of methacrylates at initiator loading of 0.9 and 3.5 mmol g-1. The immobilized initiator was characterized by ATR FTIR, gel phase 13C NMR, and solid-state CP/MAS 13C NMR using two different spinning frequencies as well as a TOSS pulse sequence. The immobilized initiator has been used to prepare poly(methyl methacrylate), PMMA, homopolymer, and poly(methyl methacrylate)-block-poly(benzyl methacrylate-co-methyl methacrylate), P(MMA)-block-P(BzMA-co-MMA), block copolymers. The poly(methacrylate)s have been harvested from the insoluble resin by a simple trifluoroacetic acid, TFA, wash which selectively cleaved the activated benzyl ester linkage, so as to facilitate analysis. At an initiator loading of 0.9 mmol g-1 the Mn increases linearly with conversion with kinetics following first-order behavior in monomer as would be expected for living polymerization. After 3 h a 61.9% conversion of MMA is reached, with the isolated polymer chains having an average number molar mass, Mn, of 8200 and a polydispersity, PDI, of 1.18. High conversions, >90%, lead to considerable increases in Mn and PDI. Moreover, small amounts of “free” chains present in the supernatant, ca. 5−8% after 4 h of reaction time, were found. The morphology of the beads was monitored by SEM with the integrity being maintained throughout the transformations. Attempts to prepare true block copolymers via a two-stage process involving isolation of the Wang resins with the first block and subsequent reuse to attach the second block were not satisfactory. However, a one-shot addition of BzMA at high conversion of MMA allowed the synthesis of P(MMA)-block-P(BzMA-co-MMA) with a narrow molar mass distribution, as confirmed with SEC, DSC, and NMR. The paper demonstrates that Wang immobilized chemistry can be used to prepare excellent polymers maintaining the characteristics of analogous homogeneous living radical polymerizations while allowing for catalyst removal by simple washing procedures. The potential for automation of this chemistry for high throughput synthesis has been demonstrated.
Asymmetric quantum wells with enhanced QCSE: modulation behaviour and application for integrated laser/modulator (1997)

We have optimized asymmetric InGaAsP QWs with respect to the quantum confined Stark effect (QCSE). We have found structures with a red shift of 40 meV at a field of 70 kV/cm. Moreover, it was our aim to find structures with a strong blue shift. A new principle for the integration of a laser and a modulator is presented, which is based on the application of blue shift asymmetric QW's in the active layer for laser and modulator simultaneously. A calculation of the laser and modulation properties for a QW-structure with 27 meV blue shift at a field variation of 70 kV/cm is presented.
Prospective Study of Placental Angiogenic Factors and Maternal Vascular Function Before and After Preeclampsia and Gestational Hypertension (2010)

These observations support a role for placenta-derived angiogenic biomarkers in the control of maternal vascular resistance of preeclampsia. Gestational hypertension develops differently, with a hyperdynamic circulation and angiogenic biomarker profile similar to normotensive pregnancy. Larger studies of unselected women are needed to ascertain whether measures of these angiogenic biomarkers assist with the prediction and prognosis of preeclampsia and whether postpartum measures of serum PlGF have a role in predicting future cardiovascular disease.
Therapeutic Use of Calcimimetics (2006)

It has long been recognized that the secretion of PTH by chief cells in the parathyroid gland is regulated by extracellular ionized calcium. The molecular mechanism by which extracellular Ca2+ performs this feat was deduced by the cloning of the extracellular calcium-sensing receptor (CaSR) in 1993 in the laboratories of Brown and Hebert. The CaSR is a G protein-coupled cell surface receptor that belongs to family 3 of the GPCR superfamily. The CaSR senses the extracellular ionic activity of the divalent minerals Ca2+ and Mg2+ and translates this information, via a complex array of cellular signaling pathways, to modify cell and tissue function. Genetic studies have demonstrated that the activity of this receptor determines the steady-state plasma calcium concentration in humans by regulating key elements in the calcium homeostatic system. CaSR agonists (calcimimetics) and antagonists (calcilytics) have been identified and have provided both current and potential therapies for a variety of disorders. Calcimimetics can effectively reduce PTH secretion in all forms of hyperparathyroidism. They are likely to become a major therapy for secondary hyperparathyroidism associated with renal failure and for treatment of certain patients with primary hyperparathyroidism. On the therapeutic horizon are calcilytics that can transiently increase PTH and may prove useful in the treatment of osteoporosis.
Site-directed mutagenesis of the human DNA repair enzyme HAP1: identification of residues important for AP endonuclease and RNase H activity (1995)

HAP1 protein, the major apurinic/apyrimidinic (AP) endonuclease in human cells, is a member of a homologous family of multifunctional DNA repair enzymes including the Escherichia coli exonuclease III and Drosophila Rrp1 proteins. The most extensively characterised member of this family, exonuclease III, exhibits both DNA- and RNA-specific nuclease activities. Here, we show that the RNase H activity characteristic of exonuclease III has been conserved in the human homologue, although the products resulting from RNA cleavage are dissimilar. To identify residues important for enzymatic activity, five mutant HAP1 proteins containing single amino acid substitutions were purified and analysed in vitro. The substitutions were made at sites of conserved amino acids and targeted either acidic or histidine residues because of their known participation in the active sites of hydrolytic nucleases. One of the mutant proteins (replacement of Asp-219 by alanine) showed a markedly reduced enzymatic activity, consistent with a greatly diminished capacity to bind DNA and RNA. In contrast, replacement of Asp-90, Asp-308 or Glu-96 by alanine led to a reduction in enzymatic activity without significantly compromising nucleic acid binding. Replacement of His-255 by alanine led to only a very small reduction in enzymatic activity. Our data are consistent with the presence of a single catalytic active site for the DNA- and RNA-specific nuclease activities of the HAP1 protein.
Neutrophil elastase and acute lung injury: Prospects for sivelestat and other neutrophil elastase inhibitors as therapeutics (2002)

Further study of the role of NE inhibition as a treatment for ALI is warranted. Additional clinical and preclinical studies with sivelestat and various other NE inhibitors should not only clarify the clinical potential of this intervention strategy, but also better define the activities of NE in inflammatory disorders such as ALI and multiple organ failure.
The embryonal carcinoma stem cell Ela-like activity involves a differentiation-regulated transcription factor (1990)

Murine F9 embryonal carcinoma (EC) stem cells have an Ela-like transcription activity that is undetectable in F9 cells differentiated to parietal endoderm-like cells (F9-PE). The Ela-inducible adenovirus E2A promoter has been used to further define this activity and we show that in vitro the transcription of this promoter in F9 EC and F9-PE cell extracts reflects the regulation in vivo. In EC cell extracts several trans-acting protein factors bind to E2A promoter sequences. A distal domain containing a CRE binds proteins present in F9 EC, F9-PE and Hela cell extracts. Sequences between -71 and -50 define a multiplicity of binding activities, termed DRTF1, all of which are down regulated as EC stem cells differentiate. DRTF2, a low abundance, regulated binding activity requires DNA sequences that overlap those required by DRTF1. The CRE and the DRTF1 binding site compete for transcription in vitro, indicating that in EC cell extracts the respective proteins function as positively acting, binding site dependent transcription factors. Comparison of DRTF1 with the previously defined HeLa cell factor E2F, induced during adenovirus infection, indicates that although both factors recognise the same region of the promoter there are clear differences between them. These data indicate that multiple factors are necessary for efficient transcription of the E2A promoter in F9 EC cell extracts and suggest that DRTF1 is responsible, at least in part, for the developmental regulation of the cellular Ela-like activity.
Intracellular Stability of Anti-caspase-3 Intrabodies Determines Efficacy in Retargeting the Antigen (2001)

Although intracellular antibodies (intrabodies) are being explored as putative therapeutic and research reagents, little is known about the principles that dictate the efficacy of these molecules. In our efforts to address this issue, we generated a panel of five intrabodies, directed against catalytically inactive murine caspase-3, by screening single-chain antibody (Fv) phage display libraries. Here we determined criteria that single-chain Fv fragments must fulfill to act as efficient intrabodies. The affinities of these intrabodies, as measured by surface plasmon resonance, varied approximately 5-fold (50-250 nm). Despite their substantial sequence similarity, only two of the five intrabodies were able to significantly accumulate intracellularly. These disparities in intracellular expression levels were reflected by differences in the stability of the purified protein species when analyzed by urea denaturation studies. We observed varied efficiencies in retargeting the antigen murine caspase-3, from the cytosol to the nucleus, mediated by intrabodies tagged with an SV40 nuclear localization signal. Our results demonstrate that the intrinsic stability of the intrabody, rather than its affinity for the antigen, dictates its intracellular efficacy.
A Model Vaccine Exploiting Fungal Mannosylation to Increase Antigen Immunogenicity (2005)

Ag mannosylation represents a promising strategy to augment vaccine immunogenicity by targeting Ag to mannose receptors (MRs) on dendritic cells. Because fungi naturally mannosylate proteins, we hypothesized that Ags engineered in fungi would have an enhanced capacity to stimulate T cell responses. Using the model Ag OVA, we generated proteins that differentially expressed N- and O-linked mannosylation in the yeast Pichia pastoris and compared them to their unglycosylated counterparts produced in Escherichia coli. We found that yeast-derived OVA proteins containing N-linkages, extensive O-linkages, or both were more potent than the unmannosylated Ags at inducing OVA-specific CD4+ T cell proliferation. This elevated response to fungal Ags was inhibited by mannan, suggesting involvement of MRs. However, the macrophage MR (CD206) was not essential, because macrophage MR-deficient dendritic cells were fully competent in presenting yeast-derived OVA Ags. Thus, the use of fungal glycosylation to provide N-linked and/or extensive O-linked mannosylation increased the capacity of the model Ag OVA to stimulate Ag-specific T cell responses in an MR-dependent manner. These data have implications for vaccine design by providing proof of principle that yeast-derived mannosylation can enhance immunogenicity.
Calcium-Sensing Receptor (CaSR) in Human Brains Pathophysiology: Roles in Late-Onset Alzheimers Disease (LOAD) (2009)

Although the calcium-sensing receptor (CaSR) is expressed by all types of nerve cells in widespread areas of the human central nervous system (CNS), so far its roles in brain pathophysiology remain largely unknown. Here, we review the available evidence concerning the stages of development of sporadic late-onset Alzheimer's disease (LOAD) and the roles therein played by CaSR signaling. As the brain ages, its ability to dispose of dangerous synapse-targeting soluble amyloid beta-(1-42) (sAbeta42) oligomers released from normal neuronal activity declines. As their levels slowly rise, these oligomers increasingly target and eliminate synapses and prevent synapse formation, thereby eroding the foundations of memory formation and cognitive functions. In this initial stage, neurons, even though synaptically impaired, remain alive. Concurrently, sAbeta42 oligomers by binding to CaSR on human astrocytes induce via mitogen activated protein kinase (MAPK) activity the release of huge amounts nitric oxide (NO), which by itself and after conversion to peroxynitrite (ONOO(-)) damages neighboring neurons. When the sAbeta42 oligomers increasingly aggregate into fibrillar plaques, they attract and activate microglial macrophages that, while trying to clear the plaques, produce via Abeta-activated CaSR signaling several proinflammatory cytokines and reactive oxygen species (ROS). Notably, the microglial cytokines, like sAbeta42 oligomers, induce human astrocytes to make large amounts of NO and hence ONOO(-) via CaSR signal-dependent MAPK activity. The microglial cytokines-activated astrocytes might also produce their own sAbeta42, which would combine with neuron- and microglia-released sAbeta42 to increase the fibrillar burden and promote the further production of reactive oxygen species (ROS), NO/ONOO(-), and proinflammatory cytokines to efficiently kill both normal and functionally impaired (undead) neurons. But, on a somewhat positive note, we speculate that the astrocytes' CaSR-stimulated MAPK activities might also induce vascular endothelial growth factor (VEGF) expression and production. This might in turn enhance neuronal stem cells neurogenesis at least in the subgranular zone (SGZ) of the hippocampal dentate gyrus.
Studies on Pneumococcus vaccine alone or mixed with DTP and on Pneumococcus type 6B and Haemophilis influenzae type b capsular polysaccharide-tetanus toxoid conjugates in two-to five-year-old children with sickle cell anemia (1990)

Pneumococcus vaccine, injected alone or mixed with diphtheria-tetanus toxoid-pertussis, did not elicit significant concentrations of pneumococcus type 6 antibodies in 2- to 5-year-old sickle cell anemia patients (n = 22). Reinjection 5 months later failed to elicit a booster response to pneumococcus type 6. We then injected conjugates of pneumococcus type 6B and of Haemophilus influenzae type b (Hib), each bound to tetanus toxoid (TT), alternatively at monthly intervals into sickle cell anemia patients of the same age group (n = 25); most received 3 injections of each vaccine. Pneumococcus vaccine was administered to 19 patients and Hib to 1 at approximately 1 year of age. Blood samples were taken before each and approximately 6 months after the last injection. Infrequent and minimal local reactions and only 6 episodes of fever (3%) occurred after injection of the conjugates. Pneumococcus type 6B-TT elicited a rise in the geometric mean concentration of pneumococcus type 6 antibodies (Ab) from 104 ng of antibody nitrogen (AbN)/ml in preimmunization sera to 385 ng of AbN/ml after the first injection (P less than 0.01). There were further increases after the 2 subsequent injections; 6 months after the third injection, the mean concentration was 940 ng of AbN/ml and 15 of 16 (94%) had greater than 300 ng of AbN/ml. Hib-TT elicited a 160-fold increase of Hib antibodies to a geometric mean concentration of 39.0 micrograms of Ab/ml after the first injection. These levels rose approximately 2-fold following 2 additional injections to 71.7 micrograms/ml and declined to 10.7 micrograms/ml at the 6-month sampling.(ABSTRACT TRUNCATED AT 250 WORDS)
Disk arrays: high-performance, high-reliability storage subsystems (1994)

As the performance of other system components continues to improve rapidly, storage subsystem performance becomes increasingly important. Storage subsystem performance and reliability can be enhanced by logically grouping multiple disk drives into disk arrays. Array data organizations are defined by their data distribution schemes and redundancy mechanisms. The various combinations of these two components make disk arrays suitable for a wide range of environments. Many array implementation decisions also result in trade-offs between performance and reliability. Disk arrays are thus an essential tool for satisfying storage performance and reliability requirements, while proper selection of a data organization can tailor an array to a particular environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Correlations of In Vivo β-Cell Function Tests With β-Cell Mass and Pancreatic Insulin Content in Streptozocin-Administered Baboons (1991)

In vivo beta-cell function tests are used increasingly in humans during the preclinical phase of insulin-dependent diabetes mellitus (IDDM), but the severity of the beta-cell loss responsible for the abnormalities seen in these tests is unknown. We have measured several physiological beta-cell function tests--fasting plasma glucose, glucose disappearance constant, fasting insulin, acute insulin responses to arginine (AIRarginine) and glucose (AIRglucose), and glucose potentiation of AIRarginine (delta AIRarginine/delta G) and two direct objective measurements (pancreatic insulin content [PIC] and quantitative beta-cell mass)--in adolescent male baboons (Papio anubis/cyanocephalus). We have correlated in vivo measurements obtained within 3 days after the animals were killed with in vitro estimates of PIC and beta-cell mass in 15 animals, (2 nondiabetic requiring insulin treatment and 13 after varying doses of streptozocin to induce degrees of beta-cell damage ranging from normoglycemia to severe hyperglycemia). There was a strong linear correlation between beta-cell mass and PIC (r = 0.79, P less than 0.001). Physiological measures of beta-cell function were significantly correlated with both PIC and beta-cell mass. The correlations between physiological measures and beta-cell mass were linear and intercepted the beta-cell mass axis at 0.15-0.2 g, suggesting that in vivo measures of beta-cell function approach 0 when there is still approximately 40-50% of the beta-cell mass detectable histologically. With PIC, the linear correlations intercepted the axes close to 0. These findings provide considerable validity to the measurements of beta-cell function used in preclinical IDDM in humans.(ABSTRACT TRUNCATED AT 250 WORDS)
Experience in Continuous analytics as a Service (CaaaS) (2011)

Mobile applications, such as those on WebOS, increasingly depend on continuous analytics results of real-time events, for monitoring oil & gas production, watching traffic status and detecting accident, etc, which has given rise to the need of providing Continuous analytics as a Service (CaaaS). While representing a paradigm shift in cloud computing, CaaaS poses several challenges in scalability, latency, time-window semantics, transaction control and result-set staging.A data stream is infinite thus can only be analyzed in granules. We propose a continuous query model over both static relations and dynamic streaming data, which allows a long-standing SQL query instance to run cycle by cycle, each cycle for a chunk of data from the data stream, using a cut-and-rewind mechanism. We further support the cycle-based transaction model with cycle-based isolation and visibility, for delivering analytics results to the clients continuously while the query is running. To have the continuously generated analytics results staged efficiently, we developed the table-ring and label switching mechanism characterized by staging data through metadata manipulation without physical data moving and copying. To scale-out analytics computation, we support both parallel database based and network distributed Map-Reduce based infrastructure with multiple cooperating engines.We have built the proposed infrastructure by extending the PostgreSQL engine. We tested the throughput and latency of this service based on a well-known stream processing benchmark; the results show that the proposed approach is highly competitive. Our experiments indicate that the database technology can be extended and applied to real-time continuous analytics service provisioning.