gebhart/patrepeval huggingface dataset:
Collision-Induced Dissociative Chemical Cross-Linking Reagents and Methodology:  Applications to Protein Structural Characterization Using Tandem Mass Spectrometry Analysis (2006)

Chemical cross-linking combined with mass spectrometry is a viable approach to study the low-resolution structure of protein and protein complexes. However, unambiguous identification of the residues involved in a cross-link remains analytically challenging. To enable a more effective analysis across various MS platforms, we have developed a novel set of collision-induced dissociative cross-linking reagents and methodology for chemical cross-linking experiments using tandem mass spectrometry (CID-CXL-MS/MS). These reagents incorporate a single gas-phase cleavable bond within their linker region that can be selectively fragmented within the in-source region of the mass spectrometer, enabling independent MS/MS analysis for each peptide. Initial design concepts were characterized using a synthesized cross-linked peptide complex. Following verification and subsequent optimization of cross-linked peptide complex dissociation, our reagents were applied to homodimeric glutathione S-transferase and monomeric bovine serum albumin. Cross-linked residues identified by our CID-CXL-MS/MS method were in agreement with published crystal structures and previous cross-linking studies using conventional approaches. Common LC/MS/MS acquisition approaches such as data-dependent acquisition experiments using ion trap mass spectrometers and product ion spectral analysis using SEQUEST were shown to be compatible with our CID-CXL-MS/MS reagents, obviating the requirement for high resolution and high mass accuracy measurements to identify both intra- and interpeptide cross-links.
From Virchow to red cells (the unended quest). (1983)

For Virchow vessel wall, coagulability and flow were the three eventual culprits of thrombogenesis. Pharmacological progress in the three fields has not been parallel. Strangely enough they have found possible therapy in the order of their description: first the vessel wall with vasodilators. Then 'coagulability' with anticoagulants, thrombolytics, antiaggregants. It is only more recently that new methods of investigation have allowed assessment and pharmacology of the main determinant of flow in microvessels: red cell deformability.
Sensitivity and selectivity of the DNA damage sensor responsible for activating p53-dependent G1 arrest. (1996)

The tumor suppressor p53 contributes to maintaining genome stability by inducing a cell cycle arrest or apoptosis in response to conditions that generate DNA damage. Nuclear injection of linearized plasmid DNA, circular DNA with a large gap, or single-stranded circular phagemid is sufficient to induce a p53-dependent arrest. Supercoiled and nicked plasmid DNA, and circular DNA with a small gap were ineffective. Titration experiments indicate that the arrest mechanism in normal human fibroblasts can be activated by very few double strand breaks, and only one may be sufficient. Polymerase chain reaction assays showed that end-joining activity is low in serum-arrested human fibroblasts, and that higher joining activity occurs as cells proceed through G1 or into S phase. We propose that the exquisite sensitivity of the p53-dependent G1 arrest is partly due to inefficient repair of certain types of DNA damage in early G1.
r84, a Novel Therapeutic Antibody against Mouse and Human VEGF with Potent Anti-Tumor Activity and Limited Toxicity Induction (2010)

Vascular endothelial growth factor (VEGF) is critical for physiological and pathological angiogenesis. Within the tumor microenvironment, VEGF functions as an endothelial cell survival factor, permeability factor, mitogen, and chemotactic agent. The majority of these functions are mediated by VEGF-induced activation of VEGF receptor 2 (VEGFR2), a high affinity receptor tyrosine kinase expressed by endothelial cells and other cell types in the tumor microenvironment. VEGF can also ligate other cell surface receptors including VEGFR1 and neuropilin-1 and -2. However, the importance of VEGF-induced activation of these receptors in tumorigenesis is still unclear. We report the development and characterization of r84, a fully human monoclonal antibody that binds human and mouse VEGF and selectively blocks VEGF from interacting with VEGFR2 but does not interfere with VEGF:VEGFR1 interaction. Selective blockade of VEGF binding to VEGFR2 by r84 is shown through ELISA, receptor binding assays, receptor activation assays, and cell-based functional assays. Furthermore, we show that r84 has potent anti-tumor activity and does not alter tissue histology or blood and urine chemistry after chronic high dose therapy in mice. In addition, chronic r84 therapy does not induce elevated blood pressure levels in some models. The ability of r84 to specifically block VEGF:VEGFR2 binding provides a valuable tool for the characterization of VEGF receptor pathway activation during tumor progression and highlights the utility and safety of selective blockade of VEGF-induced VEGFR2 signaling in tumors.
H2O2 alters rat cardiac sarcomere function and protein phosphorylation through redox signaling (2010)

ROS, such as H(2)O(2), are a component of pathological conditions in many organ systems and have been reported to be elevated in cardiac pathophysiology. The experiments presented here test the hypothesis that H(2)O(2) induces alterations in cardiac myofilament function by the posttranslational modification of sarcomeric proteins indirectly through PKC signaling. In vitro assessment of actomyosin Mg(2+)-ATPase activity of myofibrillar fractions showed blunted relative ATP consumption in the relaxed state (pCa 8.0) in response to treatment with 0.5 mM H(2)O(2) before myofilament isolation. The effect was attributable to downstream "redox signaling," inasmuch as the direct application of H(2)O(2) to isolated myofibrils did not alter Mg(2+)-ATPase activity. Ca(2+)-ATPase activity, which was used as a measure of myofibrillar myosin function, was unaffected by H(2)O(2). Functional experiments using rat cardiac trabeculae treated with 0.5 or 5 mM H(2)O(2) followed by detergent extraction of membranes demonstrated increased Ca(2+) sensitivity of force production, a faster rate of force redevelopment, and (for 5 mM) decreased maximum tension. Biochemical analysis of myocardial samples treated with 0.5 mM H(2)O(2) demonstrated increased phosphorylation of two sarcomeric proteins: cardiac troponin I and myosin-binding protein-C. These changes were eliminated by a general PKC inhibitor. However, H(2)O(2) and the general PKC activator PMA induced different phosphorylation patterns in cardiomyocytes in which PKC-delta was elevated by viral infection. These data provide evidence that PKC-dependent redox signaling affects the function of cardiac myofilaments and indicate modification of specific proteins through this signaling mechanism.
Herpes simplex virus infection of human fibroblasts and keratinocytes inhibits recognition by cloned CD8+ cytotoxic T lymphocytes. (1993)

CD8+ cytotoxic T lymphocytes (CTL) clones with specificity for herpes simplex virus (HSV) were derived from two donors with genital HSV-2 infection. These CTL clones specifically lysed HSV-infected autologous B lymphoblastoid cells, but not HSV-infected fibroblasts. Exogenous peptide loading sensitized both cell types to lysis by an HSV-specific CTL clone of known specificity. HSV infection rendered fibroblasts refractory to peptide sensitization. HSV infection also rendered fibroblasts and keratinocytes insensitive to lysis by allospecific CD8+ CTL clones. Lysis of B lymphoblastoid cells in this system was only slightly reduced by HSV infection. Reduction of fibroblast allospecific lysis was dose and time dependent and was blocked by acyclovir, indicating the involvement of a late HSV gene product. HSV caused a reduction of fibroblast cell surface HLA class I antigen, at least in part due to reduction of synthesis of heavy chain-beta 2 microglobulin heterodimers. These results suggest that HSV-induced blockade of antigen presentation by cutaneous cells to CD8+ CTL may be a mechanism by which HSV limits or evades the immune response of the host.
The chemokine network in systemic lupus erythematous nephritis (2007)

In response to renal immune complex accumulation in systemic lupus erythematosus (SLE), monocytes, T lymphocytes, and neutrophils infiltrate the kidney and mediate tissue injury and renal dysfunction. Chemotactic factors induced by immune complexes are responsible for recruiting these inflammatory cells to the kidney. Considerable attention has focused on the role of the chemokine network in regulating renal leukocyte recruitment in autoimmune glomerular diseases. In animal models of SLE nephritis, intervention studies directed at chemokines or chemokine receptors have provided definitive proof that specific chemokines are involved in the pathogenesis of renal inflammation. These same chemokines and chemokine receptors are expressed in the kidney during human SLE nephritis, and correlate with markers of renal injury and inflammation. This review will describe and integrate the animal and human data to build a case for targeting the chemokine network as a novel approach to the treatment of SLE nephritis. Anti-chemokine therapies hold the promise of efficacy with fewer adverse side-effects than the non-specific immunosuppression regimens currently in use.
A versatile plasmid vector system for the regulated expression of genes in Escherichia coli. (1994)

A series of plasmid expression vectors, which support the regulated and efficient expression of genes in Escherichia coli, have been constructed. The vectors consist of a DNA replication origin cassette, a promoter cassette, an efficient ribosome binding site together with a polylinker region and a lacZ gene. Several types of replication origins and promoter sequences are each available on cassettes. Fusion of the 5' TG dinucleotide of the gene under consideration to the A nucleotide, present on the vector, results in an ATG start codon and allows, in combination with the plasmid-borne ribosome binding site, the efficient expression of the cloned gene. Additionally, a second fusion of the gene at its 3' end with the lacZ gene, which is available in all three reading frames relative to the polylinker region, allows rapid selection of the correctly fused genes. As an example of the cloning of a regulatory gene, this vector system was used for the expression of the dnaA gene, of Escherichia coli, the initiator protein for DNA replication.
Design, Synthesis, and Biological Evaluation of 16-Substituted 4-Azasteroids as Tissue-Selective Androgen Receptor Modulators (SARMs) (2009)

A novel series of 16-substituted-4-azasteroids has been identified as potential tissue-selective androgen receptor modulators. These ligands display potent hAR binding and agonist activity, low virilizing potential, and good pharmacokinetic profiles in dogs. On the basis of its in vitro profile, 21 was evaluated in the OVX and ORX rat models and exhibited an osteoanabolic, tissue-selective profile.
Traditional knowledge systems in large cardamom farming: biophysical and management diversity in Indian mountainous regions (2009)

Large cardamom ( Amomum subulatum ) is a perennial cash crop grown under the Himalayan alder ( Alnus nepalensis ) or mix forest tree species in the hills of Nepal, Darjeeling hills, Sikkim and Bhutan. The cardamom based agroforestry system in the Himalayas has proved to be a sustainable land use practice at the landscape level supporting multiple functions and ecosystem services. Large cardamom agroforestry is a mountain adaptive slope land management and production system that helps conserving soil and water, maintain soil fertility and high rate of carbon sequestration than any other land use systems in the region. The system is a major contributor of sustainable development in the mountain region by providing socio-ecological sustainability, watershed functions, and cultural, educational and recreational values in additional to the employment opportunities in ecotourism. Some of the ecological functions of the system are habitat and corridor for wild animals, conduit of water, energy, gene flow, seeds, etc. barrier for wind, nutrients and animals, etc. while the system also help augmenting sustainability and well being of the upstream and downstream communities.
The structure of the lipid anchor ofCampylobacter jejunipolysaccharide (2006)

Campylobacter jejuni is a leading cause of gastroenteritis in humans. Campylobacter jejuni produces extracellular polysaccharides that have been characterized structurally and shown to be independent of lipopolysaccharides. Furthermore, it has been suggested that these C. jejuni polysaccharides are capsular in nature, although their lipid anchor has not been identified. In this report, the occurrence of a lipid-linked capsular-like polysaccharide in C. jejuni is conclusively shown, and the lipid anchor identified as dipalmitoyl-glycerophosphate.
Debonding monitoring of composite repair patches using embedded small-diameter FBG sensors (2007)

Small-diameter fiber Bragg grating (FBG) sensors were applied to the debonding monitoring of composite repair patches. The target of the monitoring consists of carbon fiber reinforced plastic (CFRP) patches and an aluminum substrate. The specimens were prepared through simple means: the tabular patches adhered to both sides of the aluminum substrate using epoxy adhesive films. Under cyclic loading conditions, the debonding progressed between the aluminum substrate and the adhesive layers. Before the embedding of the FBG sensors, the embedding location was determined using the calculation of the sensor signals, also called the reflection spectra. When the cyclic loading was stopped at a pre-determined numbers of cycles, the reflection spectra were measured at stress conditions of both 0 and 200 MPa. The newly appearing peak in the reflection spectrum indicated the arrival of debonding at the FBG sensors. As the debonding length increased, the intensity of the peak was found to increase. The relationship between the spectral change and the debonding length was verified by the simulated spectra and the strain distributions calculated by finite element (FE) analysis. As a result, the debonding length could be evaluated quantitatively by the spectral changes in the FBG sensors.
The ligand-binding domain of the cell surface receptor for urokinase-type plasminogen activator. (1991)

The purified urokinase plasminogen activator receptor (u-PAR) was cleaved into two fragments by mild chymotrypsin treatment. The smaller fragment (apparent Mr 16,000) possessed the ligand-binding capability, as shown by chemical cross-linking analysis. This fragment constituted the NH2-terminal part of the intact receptor, probably including the whole sequence 1-87, and contained N-linked carbohydrate. After detergent phase separation in the Triton X-114 system, the fragment was present in the water phase where its binding activity could be demonstrated in the absence of the rest of the protein. An analysis of internal homology in the amino acid sequence of u-PAR revealed the presence of three repeats of approximately 90 residues each. The ligand-binding fragment corresponds to the first repeat, supporting that this unit is a structurally autonomous domain. Domains homologous with the internal repeats of u-PAR constitute the extracellular part of Ly-6 antigens and of the squid glycoprotein Sgp-2. Like u-PAR, these proteins are attached to the membrane by a glycosyl-phosphatidylinositol anchor. The hydrophilic, ligand-binding u-PAR domain identified in the present study has potential applications in interfering with cell-surface plasmin-mediated proteolysis.
Nonidentical Induction of the Guanylate Binding Protein and the 56K Protein by Type I and Type II Interferons (1986)

Upon the addition of interferon (IFN) to cultured human cells, the expression of genes encoding the 56K and the guanylate binding protein (GBP) is specifically induced. We have analyzed their expression at the protein and the mRNA levels and studied how their regulation differs in cells treated with different IFNs. In the type I IFN (alpha and beta)-treated cells, we detected the accumulation of the 56K protein primarily in the cytoplasm. The 56K protein was undetectable in untreated cells or in cells treated with type II IFN (IFN-gamma). In contrast, a greater amount of GBP was synthesized in cells treated with type II IFN than in cells treated with type I IFN. The differential induction of these two proteins correlates well with the relative amounts of their mRNAs in type I and type II IFN-treated cells. In addition, the IFN-induced synthesis of the 56K protein was found in certain cell lines in which the GBP synthesis was not detected. These results suggest that the regulation of these two genes requires dissimilar factors which are activated or induced to different extents by type I and type II IFNs.
Postmortem Analysis of Bone Growth into Porous-Coated Acetabular Components* (1997)

Microradiography, backscattered electron microscopy, and histological analysis were used to conduct a quantitative postmortem study of seven consecutively retrieved anatomical porous replacement acetabular components that had been inserted during total hip arthroplasties. Screws had been used for the initial fixation of six components. The microradiographic analysis of all seven components showed that an average (and standard deviation) of 84 +/- 9 per cent (range, 72 to 93 per cent) of the porous coating was in direct apposition to the periprosthetic bone. The backscattered electron images demonstrated that an average of 12 +/- 6 per cent (range, 4 to 21 per cent) of the space available in the porous coating was occupied by ingrown bone. The amount of bone ingrowth was not significantly different among the three zones delineated by DeLee and Charnley. Uniformity of bone growth into the porous coating suggests that the preferential loading that occurs in the superior region did not differentially affect the bone ingrowth. The present study showed that consistent bone growth into anatomical porous replacement acetabular components can be achieved.
Purification and characterization of the D-alanyl-D-alanine-adding enzyme from Escherichia coli (1990)

The Escherichia coli D-alanyl-D-alanine-adding enzyme, which catalyzes the final cytoplasmic step in the biosynthesis of the bacterial peptidoglycan precursor UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-meso-diaminopimelyl-D-Ala-D- Ala, has been purified to homogeneity from an E. coli strain that harbors a recombinant plasmid bearing the structural gene for this enzyme, murF. The enzyme is a monomer of molecular weight 49,000, and it has a turnover number of 784 min-1 for ATP-driven amide bond formation. Experiments monitoring the fate of radiolabeled UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-meso-2,6-diaminopimelate and D-trifluoroalanine proved that the preceding enzyme in the D-alanine branch pathway, D-alanine:D-alanine ligase (ADP), is capable of synthesizing fluorinated dipeptides, which the D-Ala-D-Ala-adding enzyme can then incorporate to form UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-meso-2,6-diaminopimelyl-D-++ +trifluoroAla-D- trifluoroAla.
Allogeneic bone marrow transplantation for relapsed and refractory lymphoma using genotypically HLA-identical and alternative donors. (1991)

Twenty-two patients, ages 16.6 to 43.9 years (median age, 30 years), with relapsed or refractory lymphoma were treated by allogeneic bone marrow transplantation after high-dose chemotherapy with or without total body irradiation (TBI). Seven patients had Hodgkin's disease, four had low-grade histology non-Hodgkin's lymphoma (NHL), seven had intermediate-grade NHL, and four had high-grade NHL. Of the 22 patients, 17 received T-cell (CD-3)-depleted marrow after intensive pretransplant chemoradiotherapy, and five received T-cell-replete grafts after chemotherapy-based preparative regimens. Five patients were transplanted from donors other than genotypically HLA-identical siblings: four from partially HLA-matched relatives, and one from a phenotypically HLA-identical unrelated donor. Acute graft-versus-host disease (GVHD) was less than or equal to grade II in all patients, and chronic GVHD was limited or absent in all but one patient. Of the 21 assessable patients, 17 (80.9%) achieved complete remissions. Death due to transplant-associated complications occurred in five patients, and five patients have relapsed. Thirteen patients are alive, and 12 are continuously relapse-free at a median follow-up of longer than 28 months (range, greater than 10 to greater than 58 months) from transplant. The cumulative probability of treatment failure from relapse or progression of lymphoma was 29% (95% confidence interval [CI], 12% to 51%), while the actuarial lymphoma-free (ie, event-free) survival plateau is 54.6% (95% CI, 34% to 76%). For young patients with advanced malignant lymphoma, allogeneic bone marrow transplantation appears superior to salvage chemotherapy for achievement of long-term, lymphoma-free survival and may be preferable to autologous bone marrow transplantation for selected patients.
Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586 (2002)

We present a complete DNA sequence and metabolic analysis of the dominant oral bacterium Fusobacterium nucleatum. Although not considered a major dental pathogen on its own, this anaerobe facilitates the aggregation and establishment of several other species including the dental pathogens Porphyromonas gingivalis and Bacteroides forsythus. The F. nucleatum strain ATCC 25586 genome was assembled from shotgun sequences and analyzed using the ERGO bioinformatics suite (http://www.integratedgenomics.com). The genome contains 2.17 Mb encoding 2,067 open reading frames, organized on a single circular chromosome with 27% GC content. Despite its taxonomic position among the gram-negative bacteria, several features of its core metabolism are similar to that of gram-positive Clostridium spp., Enterococcus spp., and Lactococcus spp. The genome analysis has revealed several key aspects of the pathways of organic acid, amino acid, carbohydrate, and lipid metabolism. Nine very-high-molecular-weight outer membrane proteins are predicted from the sequence, none of which has been reported in the literature. More than 137 transporters for the uptake of a variety of substrates such as peptides, sugars, metal ions, and cofactors have been identified. Biosynthetic pathways exist for only three amino acids: glutamate, aspartate, and asparagine. The remaining amino acids are imported as such or as di- or oligopeptides that are subsequently degraded in the cytoplasm. A principal source of energy appears to be the fermentation of glutamate to butyrate. Additionally, desulfuration of cysteine and methionine yields ammonia, H(2)S, methyl mercaptan, and butyrate, which are capable of arresting fibroblast growth, thus preventing wound healing and aiding penetration of the gingival epithelium. The metabolic capabilities of F. nucleatum revealed by its genome are therefore consistent with its specialized niche in the mouth.