gebhart/patrepeval huggingface dataset:
Small Molecule Antagonists of the CXCR2 and CXCR1 Chemokine Receptors as Therapeutic Agents for the Treatment of Inflammatory Diseases (2006)

In the past eight years, numerous series of small molecule CXCR2 and CXCR1 antagonists have been disclosed. These compounds have proved to be effective inhibitors of ELR+ chemokine-induced chemotaxis of neutrophils and other immune cells in vitro and have also been efficacious in several animal models of inflammatory disease. Although some of these compounds have been reported to be in clinical development, no data on clinical studies in patients with inflammatory disease has been revealed to date. This review details the medicinal chemistry and pharmacology of the aforementioned antagonist series.
The intriguing role of polymorphonuclear neutrophils in antitumor reactions (2001)

Polymorphonuclear neutrophils (PMNs) are the most abundant circulating blood leukocytes. They provide the first-line defense against infection and are potent effectors of inflammation. In addition, their release of soluble chemotactic factors guides the recruitment of both nonspecific and specific
The factor V B-domain provides two functions to facilitate thrombin cleavage and release of the light chain (1995)

Blood coagulation factors V and VIII are homologous proteins that have the domain organization A1-A2-B-A3-C1-C2. Upon thrombin activation, the B-domains of both molecules are released. Previous studies on factor VIII showed that the B-domain was not required for thrombin cleavage or activity. In contrast, deletion of the factor V B-domain (residues 709 to 1545) yielded a molecule with sevenfold reduced procoagulant activity that was not cleaved by thrombin. However, this factor V B-domain deletion molecule was activated by factor Xa, although the fold-activation was 85% that of wild-type factor V. Thrombin cleavage of factor V occurs initially after residue 709 and subsequently after residues 1018 and 1545. The requirement for thrombin cleavage within the B-domain at residue 1018 was evaluated by mutagenesis of Arg1018 to Ile. In the resultant R1018I mutant, the rate of thrombin activation and appearance of maximal cofactor activity was delayed and was consistent with delayed cleavage of the light chain at residue 1545. In contrast, the rate of factor Xa activation in the R1018I mutant was not altered. This finding suggests that thrombin cleavage at 1018 facilitates subsequent thrombin cleavage at 1545. Further mutagenesis was used to study the requirement for sequences within the factor V B-domain for thrombin cleavage at residue 1545. Whereas the factor V deletion molecule removing residues 709 to 1545 was not cleaved by thrombin, a smaller B-domain deletion molecule (residues 709 to 1476) containing an acidic amino acid-rich region (residues 1490 to 1520) was effectively cleaved by thrombin. These results show that residues 1476 to 1545, which contain an acidic amino acid-rich region, were required for thrombin cleavage of the light chain. Introduction of an acidic amino acid-rich region from factor VIII (residues 337 to 372) into the factor V 709 to 1545 deletion also restored thrombin cleavage of the light chain. In contrast, similar replacement with the acidic region from the factor VIII light chain (residues 1649 to 1689) was significantly less effective in promoting thrombin cleavage of the light chain. This finding suggests that the different acidic regions in factors V and VIII are not functionally equivalent in their interaction with thrombin.(ABSTRACT TRUNCATED AT 400 WORDS)
"Plugging into Enzymes": Nanowiring of Redox Enzymes by a Gold Nanoparticle (2003)

The reconstitution of an apo-flavoenzyme, apo-glucose oxidase, on a 1.4-nanometer gold nanocrystal functionalized with the cofactor flavin adenine dinucleotide and integrated into a conductive film yields a bioelectrocatalytic system with exceptional electrical contact with the electrode support. The electron transfer turnover rate of the reconstituted bioelectrocatalyst is approximately 5000 per second, compared with the rate at which molecular oxygen, the natural cosubstrate of the enzyme, accepts electrons (approximately 700 per second). The gold nanoparticle acts as an electron relay or "electrical nanoplug" for the alignment of the enzyme on the conductive support and for the electrical wiring of its redox-active center.
A Comprehensive Guyton Model Analysis of Physiologic Responses to Preadapting the Blood Volume as a Countermeasure to Fluid Shifts (1994)

The Guyton model of fluid, electrolyte, and circulatory regulation is an extensive mathematical model capable of simulating a variety of experimental conditions. It has been modified for use at NASA to simulate head-down tilt, a frequently used analog of weightlessness. Weightlessness causes a headward shift of body fluids that is believed to expand central blood volume, triggering a series of physiologic responses resulting in large losses of body fluids. We used the modified Guyton model to test the hypothesis that preadaptation of the blood volume before weightless exposure could counteract the central volume expansion caused by fluid shifts, and thereby attenuate the circulatory and renal responses that result in body fluid losses. Simulation results show that circulatory preadaptation, by a procedure resembling blood donation immediately before head-down bedrest, is effective in damping the physiologic responses to fluid shifts and reducing body fluid losses. After 10 hours of head-down tilt, preadaptation also produces higher blood volume, extracellular volume, and total body water for 20 to 30 days of bedrest, compared with non-preadapted control. These results indicate that circulatory preadaptation before current Space Shuttle missions may be beneficial for the maintenance of reentry and postflight orthostatic tolerance in astronauts. This paper presents a comprehensive examination of the simulation results pertaining to changes in relevant physiologic variables produced by blood volume reduction before a prolonged head-down tilt. The objectives were to study and develop the countermeasure theoretically, to aid in planning experimental studies of the countermeasure, and to identify potentially disadvantageous physiologic responses that may be caused by the countermeasure.
Improving Metal Ion Specificity During In Vitro Selection of Catalytic DNA (2002)

Metal ions play important roles in both the structure and function of catalytic DNA and RNA. While most natural catalytic RNA molecules (ribozymes) are active in solutions containing Mg(2+), in vitro selection makes it possible to search for new catalytic DNA/RNA that are specific for other metal ions. However, previous studies have indicated that the in vitro selection protocols often resulted in catalytic DNA/RNA that were equally active or sometimes even more active with metal ions other than the metal ion of choice. To improve the metal ion specificity during the in vitro selection process, we implemented a negative selection strategy where the nucleic acid pool was subjected to a solution containing competing metal ions. As a result, those nucleic acids that were active with those metal ions are discarded. To demonstrate the effectiveness of the negative selection strategy, we carried out two parallel in vitro selections of Co(2+)-dependent catalytic DNA. When no negative selection was used in the selection process, the resulting catalytic DNA molecules were more active in solutions of Zn(2+) and Pb(2+) than in Co(2+). On the other hand, when the negative selection steps were inserted between the normal positive selection steps, the resulting catalytic DNA molecules were much more active with Co(2+) than in other metal ions including Zn(2+) and Pb(2+). These results suggest strongly that in vitro selection can be used to obtain highly active and specific transition metal ion-dependent catalytic DNA/RNA, which hold great promise as versatile and efficient endonucleases as well as sensitive and selective metal ion sensors.
Assessment of foetal risk associated with 93 non-US-FDA approved medications during pregnancy (2012)

Health care practitioners utilize the United States-Food and Drug Administration (US-FDA) pregnancy categorization (A, B, C, D, X) for making decision on the appropriateness of certain medications during pregnancy. Many non US-FDA approved medications are registered and marketed in Saudi Arabia. However, these medications do not have an assigned pregnancy risk categorization like those approved in the US. The objective of this review is to evaluate, report, and categorize the foetal risk associated with non-US-FDA approved medications registered by the Saudi Food and Drug Authority (S-FDA) according to the US-FDA pregnancy risk categorization system. We identified 109 non-US-FDA approved medications in the Saudi National Formulary (SNF) as of October 2007. We searched for data on functional or anatomical birth defects or embryocidal-associated risk using different databases and references. An algorithm for risk assessment was used to determine a pregnancy risk category for each medication. Out of 93 eligible medications, 73% were assigned category risk C, 10 medications (11%) were assigned category risk D, and 12 medications (13%) were assigned category risk B. Only three medications were judged to be safe during pregnancy based on the available evidence and were assigned category risk A. Inconsistencies in defining and reporting the foetal risk category among different drug regulatory authorities could create confusion and affect prescribing. We believe that standardization and inclusion of this information in the medication package insert is extremely important to all health care practitioners.
Expression of biological effector functions by immunoglobulin G molecules lacking the hinge region. (1981)

Several biological effector functions mediated by sites on the Fc region of human IgG1 have been studied in two variant IgG1 kappa monoclonal proteins (Dob and Lec) which contain deletions corresponding to the entire hinge region of the heavy chains. Neither Dob nor Lec protein in aggregated form was able to activate the classical complement pathway, and this was shown to be due to an inability to bind the first component of complement (C1). By rosette inhibition assays, Dob and Lec proteins were shown to have no measurable affinity for Fc receptors on human B cells or neutrophils. Dob and Lec proteins had a much reduced affinity for Fc receptors on the murine macrophage-like cell line P388D1 when compared to normal human IgG1. Furthermore, the hinge-deleted proteins were able to compete with murine IgG2b for P388D1 receptors but not with murine IgG2a. In contrast, the binding of Dob and Lec proteins to protein A from Staphylococcus aureus was entirely normal. The functional consequences of the hinge deletion were parallel to those seen when normal IgG1 was reduced and alkylated. It was concluded that the functional impotency of Dob and Lec proteins was related to the close association between the Fab and Fc regions in these molecules and the limited degree of segmental flexibility permitted in the absence of the hinge region. The data also suggest a major role for the C gamma 2 domain (C is the constant region) in mediating effector functions in normal IgG1.
Colliding beam fusion reactor (2002)

In this paper aspects of conceptual reactor designs are investigated that are based on the FRC configuration for D-T, D-He/sup 3/, and p-B/sup 11/ reactions. The fuel ions are of sufficient energy that the orbit size is large enough so that classical transport should prevail in the absence of long wavelength instabilities. We begin by reviewing briefly some evidence for classical confinement in such a system. Next we address the key issue of current maintenance by injecting beams of neutral atoms into an FRC. Although there are many theoretical papers on this subject, there are no experiments. Our investigation of this issue starts with a discussion of FRC experiments, the current carried by ions and the decay of current due to Coulomb interactions of electrons and ions. We then consider periodic pulses of injected neutrals in order to maintain a steady state ion current in the FRC. The injected neutrals constitute a source of ions and electrons and for a steady state there must be a sink. For a burning plasma the dominant sink is the fusion reactions.
OMG overview (1998)

article Free Access Share on OMG overview: CORBA and the OMA in enterprise computing Author: Jon Siegel Object Management Group, Framingham, MA Object Management Group, Framingham, MAView Profile Authors Info & Claims Communications of the ACMVolume 41Issue 10Oct. 1998 pp 37–43https://doi.org/10.1145/286238.286246Published:01 October 1998Publication History 61citation1,691DownloadsMetricsTotal Citations61Total Downloads1,691Last 12 Months52Last 6 weeks10 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Growth hormone treatment for sustained pain reduction and improvement in quality of life in severe fibromyalgia (2012)

Functional defects in growth hormone (GH) secretion and its efficacy as a complementary treatment have been suggested for fibromyalgia. This study investigated the efficacy and safety of low-dose GH as an add-on therapy in patients with both severe FM and low insulin-like growth factor 1 levels. A total of 120 patients were enrolled in a multicenter, placebo-controlled study for 18 months. They were randomly assigned to receive either 0.006 mg/kg/day of GH subcutaneously (group A, n=60) or placebo (group B, n=60) for 6 months (blind phase). The placebo arm was switched to GH treatment from month 6 to month 12 (open phase), and a follow-up period after GH discontinuation was performed until month 18. Standard treatment for fibromyalgia (selective serotonin re-uptake inhibitors, opioids, and amitriptyline) was maintained throughout the study. Number and intensity of tender points, Fibromyalgia Impact Questionnaire (FIQ) with its subscales, and EuroQol 5 dimensions test (EQ5D) with visual analogue scale (VAS) were assessed at different time points. At the end of the study, 53% of group A patients obtained fewer than 11 positive tender points, vs 33% of group B patients (P<.05). 39.1% vs 22.4% reached more than 50% improvement in VAS (P<.05). Group A patients showed significantly improved FIQ scores (P=.01) compared with group B. Although GH discontinuation worsened all scores in both groups during follow-up, impairment in pain perception was less pronounced in the GH-treated group (P=.05). In this largest and longest placebo-controlled trial performed in FM (NCT00933686), addition of GH to the standard treatment is effective in reducing pain, showing sustained action over time.
A DNA-Based Vaccine for the Prevention of Human Cytomegalovirus-Associated Diseases (2005)

Multiple lines of evidence indicate that in the transplant population human cytomegalovirus (HCMV) infection and its associated diseases are controlled by humoral and cellular immune responses similar to those that arise in asymptomatic, healthy individuals during a naturally-acquired infection. The dominant antibody response to HCMV is to the major surface glycoprotein B (gB) and the dominant cellular immune response is to the tegument phosphoprotein (pp65). We propose that an immunotherapeutic plasmid DNA (pDNA) vaccination approach that induces the requisite responses to major immunological targets of HCMV may provide relief from HCMV-associated diseases in the transplant setting. We have developed gene-based immunotherapeutic products consisting of pDNAs encoding gB and pp65 of HCMV. When tested individually in mice, both pDNAs were highly immunogenic. Relative to vaccination with either gB or pp65 pDNA delivered alone, vaccination with gB and pp65 pDNAs delivered together in phosphate-buffered saline (PBS) elicited reduced antibody and T cell responses to each antigen. Formulating this bivalent vaccine with a poloxamer-based delivery system (VF-P1205-02A), however, significantly increased the antigen-specific immune responses relative to those induced with the bivalent vaccine in PBS, and completely abrogated the decrease in pp65-specific T cell responses observed in mice covaccinated with the pDNAs in PBS. Based on these data, and a favorable safety and toxicity profile in preclinical studies, the bivalent HCMV vaccine consisting of gB and pp65 pDNAs delivered with VF-P1205-02A has advanced to human clinical trials.
Antibody-based therapy in Alzheimer's disease (2011)

Antibodies against Aβ will not only broaden the therapeutic repertoire but also our knowledge about the pathology in AD. Further results of the clinical trials and new antibody-based approaches will shed light on the importance of Aβ and its removal in AD.
Function of the C-terminus of 29 DNA polymerase in DNA and terminal protein binding (2004)

The thumb subdomain, located in various family B DNA polymerases in the C-terminal region, has been shown in their crystal structures to move upon binding of DNA, changing its conformation to nearly completely wrap around the DNA. It has therefore been involved in DNA binding. In agreement with this, partial proteolysis studies of phi29 DNA polymerase have shown that the accessibility of the cleavage sites located in their C-terminal region is reduced in the presence of DNA or terminal protein (TP), indicating that a conformational change occurs in this region upon substrate binding and suggesting that this region might be involved in DNA and TP binding. Therefore, we have studied the role of the C-terminus of phi29 DNA polymerase by deletion of the last 13 residues of this enzyme. This fragment includes a previously defined region conserved in family B DNA polymerases. The resulting DNA polymerase Delta13 was strongly affected in DNA binding, resulting in a distributive replication activity. Additionally, the capacity of the truncated polymerase to interact with TP was strongly reduced and its initiation activity was very low. On the other hand, its nucleotide binding affinity and its fidelity were not affected. We propose that the C-terminal 13 amino acids of phi29 DNA polymerase are involved in DNA binding and in a stable interaction with the initiator protein TP, playing an important role in the intrinsic processivity of this enzyme during polymerization.
Identification of DPPA4 and other genes as putative Sox2:Oct‐3/4 target genes using a combination of in silico analysis and transcription‐based assays (2008)

Sox2 and Oct-3/4 function as master regulators during mammalian embryogenesis, where they are believed to regulate a critical gene regulatory network by cooperatively binding to DNA regulatory regions composed of adjacent HMG and POU motifs (HMG/POU cassettes). Previous studies have identified seven genes that contain highly active HMG/POU cassettes (referred to as Sox2:Oct-3/4 target genes). Importantly, nearly all known Sox2:Oct-3/4 target genes appear to be essential for embryogenesis. Recent genome-wide ChIP-chip studies identified over 300 genes that are co-occupied by Sox2 and Oct-3/4, which suggests that most Sox2:Oct-3/4 target genes remain to be identified. The work described here used a 3-step strategy for identifying additional Sox2:Oct-3/4 target genes. First, we employed in silico analysis to search for putative HMG/POU cassettes in 50 genes reported to be co-occupied by Sox2 and Oct-3/4 in embryonic stem cells. We identified 39 genes that contain putative HMG/POU cassettes. Next, we tested the activity of seven of the putative HMG/POU cassettes in a transcription-based assay and determined that nearly all are functional. Finally, as a proof-of-principle, we tested one of the seven cassettes (DPPA4) in the context of its endogenous promoter using a promoter/reporter gene construct. DPPA4 was tested in part because it was shown recently to play an important role in ES cell self-renewal. We determined that the 5' flanking region of the DPPA4 gene contains a functional HMG/POU cassette and behaves as a Sox2:Oct-3/4 target gene. Finally, we used a transcription-based assay to help develop a refined consensus sequence for HMG/POU cassettes.
Generalized Anxiety Disorder and Psychiatric Comorbidities Such as Depression, Bipolar Disorder, and Substance Abuse (2009)

Generalized anxiety disorder (GAD) has a high rate of comorbidity with other psychiatric disorders, including major depressive disorder (MDD), bipolar disorder, other anxiety disorders, and substance use disorders. The similarities between GAD and MDD have led some to suggest that GAD should be reclassified as a mood disorder. The concurrence of GAD with another disorder heightens a patient's risk for impairment, disability, and suicidality. Clinical trials for GAD and disorders that are most likely to occur with GAD have generally not taken comorbidity into account, and there is a paucity of data guiding how comorbidity should inform treatment selection. Research into the biology and psychopathology underlying the high rate of comorbidity of GAD and into efficacious interventions for GAD with comorbidity is needed.
Low molecular weight hyaluronic acid effects on murine macrophage nitric oxide production (2010)

Hyaluronic acid (HA) is increasingly used for a number of medical device applications. Since the chemical structure of HA is identical no matter its bacterial or animal origin, it should be the ideal biomaterial. However, short term transient inflammatory reactions are common, while rare long-term adverse events may correlate with subclinical chronic inflammation. Concern has been raised that low molecular weight components or degradation fragments from implanted HA may directly stimulate inflammatory reactions. This study examined a panel of HA molecular weights from the unitary disaccharide up to 1.7 x 10(6) Dalton lengths, in which endotoxin was assayed at a very low level (less than 0.03 EU/mg). The murine cell line RAW 264.7, rat splenocytes, and rat adherent differentiated primary macrophages were assayed for nitric oxide production under a variety of inflammatory conditions plus or minus HA. Under the highest inflammatory states, nitric oxide production was mildly suppressed by HMW-HA while slightly augmented by LMW-HA at mg/mL concentrations. However, at micromolar concentrations fragments below 5000 Daltons, thought to have drug-like qualities, were without effect. These data support the hypothesis that if endotoxin is reduced to an extremely low level, LMW-HA may not directly provoke normal tissue macrophage-mediated inflammatory reactions.
Capacity of cognitive radio networks (2012)

This chapter develops the fundamental capacity limits and associated transmission techniques for different cognitive radio network paradigms. These limits are based on the premise that the cognitive radios of secondary users are intelligent wireless communication devices that exploit side information about their environment to improve spectrum utilization. This side information typically consists of knowledge about the activity, channels, encoding strategies, and/or transmitted data sequences of the primary users with which the secondary users share the spectrum. Based on the nature of the available side information as well as regulatory constraints on spectrum usage, cognitive radio systems seek to underlay, overlay, or interweave the secondary users' signals with the transmissions of primary users. This chapter develops the fundamental capacity limits for all three cognitive radio paradigms. These capacity limits provide guidelines for the spectral efficiency possible in cognitive radio networks, as well as practical design ideas to optimize performance of such networks.