gebhart/patrepeval huggingface dataset:
Design and Synthesis of Isoxazoline Derivatives as Factor Xa Inhibitors. 1 (1999)

Intravascular clot formation is an important factor in a number of cardiovascular diseases. Therefore, the prevention of blood coagulation has become a major target for new therapeutic agents. One attractive approach is the inhibition of factor Xa (FXa), the enzyme directly responsible for thrombin activation. Herein we report a series of isoxazoline derivatives which are potent FXa inhibitors. Optimization of the side chain at the quaternary position of the isoxazoline ring led to SK549 which showed subnanomolar FXa potency (K(i) 0.52 nM). SK549 shows good selectivity for FXa compared to thrombin and trypsin, potent antithrombotic effect in the rabbit arterio-venous thrombosis model, and improved pharmacokinetics relative to other compounds evaluated from this series.
Neuropathic pain and the electrophysiology and pharmacology of nerve injury (2001)

Abstract Nociceptive pain serves the useful purpose of alerting the body to potential or actual tissue damage. By contrast, neuropathic pain that results from injury or damage to the nervous system persists long after all signs of the original injury have disappeared. Neuropathic pain presents a significant clinical problem as it responds poorly to classical analgesics such as non‐steroidal anti‐inflammatory drugs (NSAIDs) and to opioids; there is also no single, uniformly well‐tolerated drug that is reliably helpful. Treatment currently involves the use of anticonvulsant and/or antidepressant drugs. Electrophysiological experiments on dorsal root ganglion and spinal cord neurons of nerve‐injured experimental animals are yielding new information on the pathophysiology of neuropathic pain. Analysis of actions of various neuropeptides and neurotransmitters in these models has helped to explain the poor efficacy of opioids and suggests new therapeutic approaches to the management of neuropathic pain. Drugs that stimulate α2‐c‐adrenoceptors or that mimic the actions of neuropeptide Y, galanin, or the opioid‐like peptide, nociceptin, may be of use in this regard. Drug Dev. Res. 54:140–153, 2002. © 2002 Wiley‐Liss, Inc.
The Physiological Role of the Ribulose Monophosphate Pathway in Bacteria and Archaea (2006)

3-Hexulose-6-phosphate synthase (HPS) and 6-phospho-3-hexuloisomerase (PHI) are the key enzymes of the ribulose monophosphate pathway. This pathway, which was originally found in methylotrophic bacteria, is now recognized as a widespread prokaryotic pathway involved in formaldehyde fixation and detoxification. Recent progress, involving biochemical and genetic approaches in elucidating the physiological functions of HPS and PHI in methylotrophic as well as non-methylotrophic bacteria are described in this review. HPS and PHI orthologs are also found in a variety of archaeal strains. Some archaeal HPS orthologs are fused with other genes to form single ORF (e.g., the hps-phi gene of Pyrococcus spp. and the faeB-hpsB gene of Methanosarcina spp). These fused gene products exhibit functions corresponding to the individual enzyme activities, and are more efficient than equivalent systems made up of discrete enzymes. Recently, a novel metabolic function for HPS and PHI has been proposed in which these enzymes catalyze the reverse reaction for the biosynthesis of pentose phosphate in some archaeal strains. Thus the enzyme system plays a different role in bacteria and archaea by catalyzing the forward and reverse reactions respectively.
Configuration knowledge representations for Semantic Web applications (2003)

Today's economy exhibits a growing trend toward highly specialized solution providers cooperatively offering configurable products and services to their customers. This paradigm shift requires the extension of current standalone configuration technology with capabilities of knowledge sharing and distributed problem solving. In this context a standardized configuration knowledge representation language with formal semantics is needed in order to support knowledge interchange between different configuration environments. Languages such as Ontology Inference Layer (OIL) and DARPA Agent Markup Language (DAML+OIL) are based on such formal semantics (description logic) and are very popular for knowledge representation in the Semantic Web. In this paper we analyze the applicability of those languages with respect to configuration knowledge representation and discuss additional demands on expressivity. For joint configuration problem solving it is necessary to agree on a common problem definition. Therefore, we give a description logic based definition of a configuration problem and show its equivalence with existing consistency-based definitions, thus joining the two major streams in knowledge-based configuration (description logics and predicate logic/constraint based configuration).
Anti-Monocyte Chemoattractant Protein-1 Gene Therapy Attenuates Renal Injury Induced by Protein-Overload Proteinuria (2003)

It has been postulated that protein filtered through glomeruli activates tubular epithelial cells, which secrete vasoactive and inflammatory substances including chemokines, leading to tubulointerstitial renal injury. The present study was designed to investigate the role of monocyte chemoattractant protein-1 (MCP-1) in this process and to evaluate the effectiveness of a kidney-targeted gene transfer technique using hydrodynamic pressure. Naked plasmid encoding 7ND (an MCP-1 antagonist) or a control plasmid was introduced into the left kidney of rats. Three days after gene transfer (day 0), intraperitoneal administration of bovine serum albumin (10 mg/g body wt per day) was started and continued for 14 or 21 d. RT-PCR showed that 7ND mRNA was expressed only in the gene-transfected kidney. Immunostaining showed that 7ND protein was localized in the interstitial cells. Macrophage infiltration was significantly reduced in the left kidney of rats treated with 7ND on days 14 and 21. In the right kidney, such effects were not observed. 7ND also attenuated tubular damage and decreased the number of apoptotic cells. Computer-assisted analysis revealed that the areas positively stained for alpha-smooth muscle actin (alpha SMA), fibronectin-EDA, type I collagen, and collagen fibrils were significantly reduced in the 7ND-treated kidney on day 21. Furthermore, 7ND gene therapy significantly reduced MCP-1 and TGF-beta 1 mRNA expression. These results demonstrate that MCP-1 plays an important role in the development of tubulointerstitial inflammation, tubular damage, and fibrosis induced by proteinuria. The fact that 7ND gene therapy had little effect on the contralateral kidney indicates that 7ND acted locally. This strategy may have a potential usefulness as a gene therapy against tubulointerstitial renal injury.
Interaction of Ammonia Monooxygenase from Nitrosomonas europaea with Alkanes, Alkenes, and Alkynes (1988)

Ammonia monooxygenase of Nitrosomonas europaea catalyzes the oxidation of alkanes (up to C(8)) to alcohols and alkenes (up to C(5)) to epoxides and alcohols in the presence of ammonium ions. Straight-chain, N-terminal alkynes (up to C(10)) all exhibited a time-dependent inhibition of ammonia oxidation without effects on hydrazine oxidation.
Human parvovirus B19 infections: Routine diagnosis by a new nested polymerase chain reaction assay (1993)

A nested primer PCR assay was developed to detect human parvovirus B19 in various clinical specimens in a routine diagnostic laboratory. Under optimized conditions the highly specific assay had a sensitivity of less than 10 genome units. For practical reasons, however, this sensitivity was adjusted to 10-100 virus genomes in diagnostic applications. Using clinical specimens from 200 patients with suspected B19 infection, nested PCR was shown to have important diagnostic advantages over the detection of B19 specific antibodies. The data suggest that on the basis of serological data as obtained with currently available test systems a considerable proportion of B19 infections would be misdiagnosed. Examples for the usefulness of the PCR assay in routine diagnosis are given.
Unusual regioversatility of acetyltransferase Eis, a cause of drug resistance in XDR-TB (2011)

The emergence of multidrug-resistant and extensively drug-resistant (XDR) tuberculosis (TB) is a serious global threat. Aminoglycoside antibiotics are used as a last resort to treat XDR-TB. Resistance to the aminoglycoside kanamycin is a hallmark of XDR-TB. Here, we reveal the function and structure of the mycobacterial protein Eis responsible for resistance to kanamycin in a significant fraction of kanamycin-resistant Mycobacterium tuberculosis clinical isolates. We demonstrate that Eis has an unprecedented ability to acetylate multiple amines of many aminoglycosides. Structural and mutagenesis studies of Eis indicate that its acetylation mechanism is enabled by a complex tripartite fold that includes two general control non-derepressible 5 (GCN5)-related N-acetyltransferase regions. An intricate negatively charged substrate-binding pocket of Eis is a potential target of new antitubercular drugs expected to overcome aminoglycoside resistance.
Perindopril Ameliorates Glomerular and Renal Tubulointerstitial Injury in the SHR/N-Corpulent Rat (1997)

We compared the effects of long-term treatment with the angiotensin-converting enzyme inhibitor perindopril and triple therapy (hydrochlorothiazide, reserpine, and hydralazine) on the metabolic and renal features in the SHR/N-corpulent (cp) rat, a genetic model of non-insulin-dependent diabetes mellitus and hypertension. Obese male SHR/N-cp rats (4 to 6 weeks old) were fed a 54% carbohydrate diet containing 18% sucrose and 36% starch. After 2 months on the diet, rats were assigned to one of three groups: one group (n=8) received perindopril (PE); the second group (n=8) received triple therapy (TT); and the third group (n=8) did not receive therapy. Treatment was maintained for 3 to 4 months. Body weight, food intake, and fasting levels of serum glucose and insulin did not differ among the three groups. Control rats exhibited progressive proteinuria in parallel with the rise in systolic blood pressure (SBP). Both PE and TT equally lowered SBP to normal levels and reduced proteinuria in treated rats. However, the reduction of proteinuria was greater and more sustained with PE than with TT (P<.05), whereas the effect of TT on proteinuria was delayed. Plasma renin activity was increased in PE and TT rats compared with control rats (P<.02). Semiquantitative analysis of renal lesions showed that the percentage of glomeruli with mesangial expansion and sclerosis and the tubulointerstitial score (an index of severity of tubulointerstitial lesions, namely tubular atrophy, inflammatory cellular infiltrates, and interstitial fibrosis) was reduced in both PE and TT rats. However, the reduction of glomerulosclerosis and tubulointerstitial lesions was greater in PE than in TT rats (P<.01). The percentage of glomerular sclerosis was positively correlated with the severity score of tubulointerstitial lesions (r=.60, P<.01). We conclude that PE is more effective than TT in halting the progression of proteinuria in the SHR/N-cp rat with non-insulin-dependent diabetes mellitus and hypertension. The antiproteinuric effect of PE is associated with significant reduction in glomerulosclerosis and tubulointerstitial lesions, independent of the effect of treating hypertension.
Multiple-Mutation Reaction: a Method for Simultaneous Introduction of Multiple Mutations into theglpKGene ofMycoplasma pneumoniae (2005)

In Mycoplasma pneumoniae, the UGA opal codon specifies tryptophan rather than a translation stop site. This often makes it difficult to express Mycoplasma proteins in E. coli isolates. In this work, we developed a strategy for the one-step introduction of several mutations. This method, the multiple-mutation reaction, is used to simultaneously replace nine opal codons in the M. pneumoniae glpK gene.
Microglial α7 nicotinic acetylcholine receptors drive a phospholipase C/IP3pathway and modulate the cell activation toward a neuroprotective role (2006)

Microglia perform both neuroprotective and neurotoxic functions in the brain, with this depending on their state of activation and their release of mediators. Upon P2X(7) receptor stimulation, for example, microglia release small amounts of TNF, which protect neurons, whereas LPS causes massive TNF release leading to neuroinflammation. Here we report that, in rat primary cultured microglia, nicotine enhances P2X(7) receptor-mediated TNF release, whilst suppressing LPS-induced TNF release but without affecting TNF mRNA expression via activation of alpha7 nicotinic acetylcholine receptors (alpha7 nAChRs). In microglia, nicotine elicited a transient increase in intracellular Ca(2+) levels, which was abolished by specific blockers of alpha7 nAChRs. However, this response was independent of extracellular Ca(2+) and blocked by U73122, an inhibitor of phospholipase C (PLC), and xestospongin C, a blocker of the IP(3) receptor. Repeated experiments showed that currents were not detected in nicotine-stimulated microglia. Moreover, nicotine modulation of LPS-induced TNF release was also blocked by xestospongin C. Upon LPS stimulation, inhibition of TNF release by nicotine was associated with the suppression of JNK and p38 MAP kinase activation, which regulate the post-transcriptional steps of TNF synthesis. In contrast, nicotine did not alter any MAP kinase activation, but enhanced Ca(2+) response in P2X(7) receptor-activated microglia. In conclusion, microglial alpha7 nAChRs might drive a signaling process involving the activation of PLC and Ca(2+) release from intracellular Ca(2+) stores, rather than function as conventional ion channels. This novel alpha7 nAChR signal may be involved in the nicotine modification of microglia activation towards a neuroprotective role by suppressing the inflammatory state and strengthening the protective function.
Ureaplasma Urealyticum Cultured from Brain Tissue of Preterm Twins who Died of Intraventricular Hemorrhage (1993)

We present a case of premature twins, born at 24 weeks of gestation. Both infants died of intraventricular hemorrhage, aged 1 and 3 days, respectively. Ureaplasma urealyticum was isolated from brain tissue obtained at the autopsy of both infants. Our observations lend additional evidence of the role of U. urealyticum as a central nervous system pathogen in premature infants.
IKKγ/NEMO Facilitates the Recruitment of the IκB Proteins into the IκB Kinase Complex (2001)

IKKgamma/NEMO is an essential regulatory component of the IkappaB kinase complex that is required for NF-kappaB activation in response to various stimuli including tumor necrosis factor-alpha and interleukin-1beta. To investigate the mechanism by which IKKgamma/NEMO regulates the IKK complex, we examined the ability of IKKgamma/NEMO to recruit the IkappaB proteins into this complex. IKKgamma/NEMO binding to wild-type, but not to a kinase-deficient IKKbeta protein, facilitated the association of IkappaBalpha and IkappaBbeta with the high molecular weight IKK complex. Following tumor necrosis factor-alpha treatment of HeLa cells, the majority of the phosphorylated form of endogenous IkappaBalpha was associated with the high molecular weight IKK complex in HeLa cells and parental mouse embryo fibroblasts but not in IKKgamma/NEMO-deficient cells. Finally, we demonstrate that IKKgamma/NEMO facilitates the association of the IkappaB proteins and IKKbeta and leads to increases in IKKbeta kinase activity. These results suggest that an important function of IKKgamma/NEMO is to facilitate the association of both IKKbeta and IkappaB in the high molecular weight IKK complex to increase IkappaB phosphorylation.
LASCA plant collections (1984)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Multifaceted link between cancer and inflammation (2011)

Increasing evidence from epidemiological, preclinical and clinical studies suggests that dysregulated inflammatory response plays a pivotal role in a multitude of chronic ailments including cancer. The molecular mechanism(s) by which chronic inflammation drives cancer initiation and promotion include increased production of pro-inflammatory mediators, such as cytokines, chemokines, reactive oxygen intermediates, increased expression of oncogenes, COX-2 (cyclo-oxygenase-2), 5-LOX (5-lipoxygenase) and MMPs (matrix metalloproteinases), and pro-inflammatory transcription factors such as NF-κB (nuclear factor κB), STAT3 (signal transducer and activator of transcription 3), AP-1 (activator protein 1) and HIF-1α (hypoxia-inducible factor 1α) that mediate tumour cell proliferation, transformation, metastasis, survival, invasion, angiogenesis, chemoresistance and radioresistance. These inflammation-associated molecules are activated by a number of environmental and lifestyle-related factors including infectious agents, tobacco, stress, diet, obesity and alcohol, which together are thought to drive as much as 90% of all cancers. The present review will focus primarily on the role of various inflammatory intermediates responsible for tumour initiation and progression, and discuss in detail the critical link between inflammation and cancer.
Stabilization of Exosome-targeting Peptides via Engineered Glycosylation (2015)

Exosomes are secreted extracellular vesicles that mediate intercellular transfer of cellular contents and are attractive vehicles for therapeutic delivery of bimolecular cargo such as nucleic acids, proteins, and even drugs. Efficient exosome-mediated delivery in vivo requires targeting vesicles for uptake by specific recipient cells. Although exosomes have been successfully targeted to several cellular receptors by displaying peptides on the surface of the exosomes, identifying effective exosome-targeting peptides for other receptors has proven challenging. Furthermore, the biophysical rules governing targeting peptide success remain poorly understood. To evaluate one factor potentially limiting exosome delivery, we investigated whether peptides displayed on the exosome surface are degraded during exosome biogenesis, for example by endosomal proteases. Indeed, peptides fused to the N terminus of exosome-associated transmembrane protein Lamp2b were cleaved in samples derived from both cells and exosomes. To suppress peptide loss, we engineered targeting peptide-Lamp2b fusion proteins to include a glycosylation motif at various positions. Introduction of this glycosylation motif both protected the peptide from degradation and led to an increase in overall Lamp2b fusion protein expression in both cells and exosomes. Moreover, glycosylation-stabilized peptides enhanced targeted delivery of exosomes to neuroblastoma cells, demonstrating that such glycosylation does not ablate peptide-target interactions. Thus, we have identified a strategy for achieving robust display of targeting peptides on the surface of exosomes, which should facilitate the evaluation and development of new exosome-based therapeutics.
Chemical and Genetic Wrappers for Improved Phage and RNA Display (2008)

An Achilles heel inherent to all molecular display formats, background binding between target and display system introduces false positives into screens and selections. For example, the negatively charged surfaces of phage, mRNA, and ribosome display systems bind with unacceptably high nonspecificity to positively charged target molecules, which represent an estimated 35% of proteins in the human proteome. Here we report the first systematic attempt to understand why a broad class of molecular display selections fail, and then solve the underlying problem for both phage and RNA display. Firstly, a genetic strategy was used to introduce a short, charge-neutralizing peptide into the solvent-exposed, negatively charged phage coat. The modified phage (KO7(+)) reduced or eliminated nonspecific binding to the problematic high-pI proteins. In the second, chemical approach, nonspecific interactions were blocked by oligolysine wrappers in the cases of phage and total RNA. For phage display applications, the peptides Lys(n) (where n=16 to 24) emerged as optimal for wrapping the phage. Lys(8), however, provided effective wrappers for RNA binding in assays against the RNA binding protein HIV-1 Vif. The oligolysine peptides blocked nonspecific binding to allow successful selections, screens, and assays with five previously unworkable protein targets.
Tumor necrosis factor alpha/cachectin is a growth factor for thymocytes. Synergistic interactions with other cytokines. (1988)

Recombinant murine (rm) TNF-alpha but not recombinant human (rh) TNF-alpha induces the proliferation of murine thymocytes in the presence of a comitogenic stimulus. This effect does not appear to be due to the production of significant levels of IL-1, IL-2, or IL-4. although not directly mitogenic (i.e., in the absence of PHA-P) for thymocytes, rmTNF-alpha amplifies the direct mitogenic signals from hIL-1 and rhIL-2 but not rmIL-4. In the presence of PHA-P, thymocytes stimulated with hIL-1, rhIL-2, and rmIL-4 produced significant amounts of TNF-alpha. Although rhTNF-alpha does not induce a proliferative response, it will competitively inhibit the proliferative response of thymocytes to rmTNF-alpha. These data suggest a critical role for TNF-alpha in the intrathymic proliferation of developing T cells.
The crystal structure of an N-terminal two-domain fragment of vascular cell adhesion molecule 1 (VCAM-1): a cyclic peptide based on the domain 1 C-D loop can inhibit VCAM-1-alpha 4 integrin interaction. (1995)

Vascular cell adhesion molecule 1 (VCAM-1) represents a structurally and functionally distinct class of immunoglobulin superfamily molecules that bind leukocyte integrins and are involved in inflammatory and immune functions. X-ray crystallography defines the three-dimensional structure of the N-terminal two-domain fragment that participates in ligand binding. Residues in domain 1 important for ligand binding reside in the C-D loop, which projects markedly from one face of the molecule near the contact between domains 1 and 2. A cyclic peptide that mimics this loop inhibits binding of alpha 4 beta 1 integrin-bearing cells to VCAM-1. These data demonstrate how crystallographic structural information can be used to design a small molecule inhibitor of biological function.
The human genome project. (1993)

The Human Genome Project in the United States is now well underway. Its programmatic direction was largely set by a National Research Council report issued in 1988. The broad framework supplied by this report has survived almost unchanged despite an upheaval in the technology of genome analysis. This upheaval has primarily affected physical and genetic mapping, the two dominant activities in the present phase of the project. Advances in mapping techniques have allowed good progress toward the specific goals of the project and are also providing strong corollary benefits throughout biomedical research. Actual DNA sequencing of the genomes of the human and model organisms is still at an early stage. There has been little progress in the intrinsic efficiency of DNA-sequence determination. However, refinements in experimental protocols, instrumentation, and project management have made it practical to acquire sequence data on an enlarged scale. It is also increasingly apparent that DNA-sequence data provide a potent means of relating knowledge gained from the study of model organisms to human biology. There is as yet little indication that the infusion of technology from outside biology into the Human Genome Project has been effectively stimulated. Opportunities in this area remain large, posing substantial technical and policy challenges.
Potential clinical applications of siRNA technique: benefits and limitations (2010)

RNAi technique will become an important and potent weapon for fighting against various diseases. RNAi technique has benefits and limitations in its potential clinical applications. Overcoming the obstacles is still a formidable task.