gebhart/patrepeval huggingface dataset:
Biochemical characterization of the chondroitinase ABC I active site (2005)

cABC I (chondroitinase ABC I) from Proteus vulgaris is a GalAG (galactosaminoglycan) depolymerizing lyase that cleaves its substrates at the glycosidic bond via beta-elimination. cABC I cleaves a particularly broad range of GalAG substrates, including CS (chondroitin sulphate), DS (dermatan sulphate) and hyaluronic acid. We recently cloned and recombinantly expressed cABC I in Escherichia coli, and completed a preliminary biochemical characterization of the enzyme. In the present study, we have coupled site-directed mutagenesis of the recombinant cABC I with a structural model of the enzyme-substrate complex in order to investigate in detail the roles of active site amino acids in the catalytic action of the enzyme. The putative catalytic residues His-501, Tyr-508, Arg-560 and Glu-653 were probed systematically via mutagenesis. Assessment of these mutants in kinetic and end-point assays provided direct evidence on the catalytic roles of these active-site residues. The crystal structure of the native enzyme provided a framework for molecular docking of representative CS and DS substrates. This enabled us to construct recombinant enzyme-substrate structural complexes. These studies together provided structural insights into the effects of the mutations on the catalytic mechanism of cABC I and the differences in its processing of CS and DS substrates. All His-501 mutants were essentially inactive and thereby implicating this amino acid to play the critical role of proton abstraction during catalysis. The kinetic data for Glu-653 mutants indicated that it is involved in a hydrogen bonding network in the active site. The proximity of Tyr-508 to the glycosidic oxygen of the substrate at the site of cleavage suggested its potential role in protonating the leaving group. Arg-560 was proximal to the uronic acid C-5 proton, suggesting its possible role in the stabilization of the carbanion intermediate formed during catalysis.
Absence of an Apolipoprotein E ϵ4 Allele Is Associated With Increased Parietal Regional Cerebral Blood Flow Asymmetry in Alzheimer Disease (1998)

Greater parietal rCBF asymmetry is involved in epsilon4- AD than in epsilon4+ AD. Lack of the epsilon4 allele may be associated with other (as yet undiscovered) genetic or environmental risk factors, which confer greater neuropathological asymmetry.
Requirement of pp60c-src expression for osteoclasts to form ruffled borders and resorb bone in mice. (1992)

Targeted disruption of the c-src proto-oncogene in mice has shown that src expression is required for normal bone resorption, since the src-deficient mutants develop osteopetrosis. To evaluate the mechanisms by which src-deficiency affects osteoclast function, we treated src-deficient mice with the stimulants of bone resorption, IL-1, parathyroid hormone, and parathyroid hormone-related protein, and analyzed the effects by quantitative bone histomorphometry and electron microscopy. Increased numbers of multinucleated cells with the morphological characteristics of osteoclasts appeared on bone surfaces, but these cells did not form ruffled borders or normal resorption lacunae. To confirm these in vivo findings, we cultured src-mutant bone marrow cells on dentine slices in the presence of 1,25 dihydroxyvitamin D3. Increased numbers of multinucleated cells were formed, but unlike normal murine bone marrow cells, they did not form resorption pits. These results indicate that osteoclasts appear in the absence of pp60c-src, but that pp60c-src expression is required for mature osteoclasts to form ruffled borders and resorb bone.
Immunoproteasomes Largely Replace Constitutive Proteasomes During an Antiviral and Antibacterial Immune Response in the Liver (2001)

The proteasome is critically involved in the production of MHC class I-restricted T cell epitopes. Proteasome activity and epitope production are altered by IFN-gamma treatment, which leads to a gradual replacement of constitutive proteasomes by immunoproteasomes in vitro. However, a quantitative analysis of changes in the steady state subunit composition of proteasomes during an immune response against viruses or bacteria in vivo has not been reported. Here we show that the infection of mice with lymphocytic choriomeningitis virus or Listeria monocytogenes leads to an almost complete replacement of constitutive proteasomes by immunoproteasomes in the liver within 7 days. Proteasome replacements were markedly reduced in IFN-gamma(-/-) mice, but were only slightly affected in IFN-alphaR(-/-) and perforin(-/-) mice. The proteasome regulator PA28alpha/beta was up-regulated, whereas PA28gamma was reduced in the liver of lymphocytic choriomeningitis virus-infected mice. Proteasome replacements in the liver strongly altered proteasome activity and were unexpected to this extent, since an in vivo half-life of 12 days had been previously assigned to constitutive proteasomes in the liver. Our results suggest that during the peak phase of viral and bacterial elimination the antiviral cytotoxic T lymphocyte response is directed mainly to immunoproteasome-dependent T cell epitopes, which would be a novel parameter for the design of vaccines.
The frequency of apoptosis correlates with the prognosis of gleason grade 3 adenocarcinoma of the prostate (1995)

In carcinoma of the prostate, apoptosis can be recognized in standard H & E sections and quantitated by light microscopy. The apoptotic index may provide additional prognostic information in the predominant grade of early stage carcinoma. Cancer 1995; 75:522-9.
Induction of activation-driven death (apoptosis) in activated but not resting peripheral blood T cells (1993)

Signaling via the CD3/TCR complex induces programmed cell death (apoptosis) in immature thymocytes and transformed T lymphocytes (hybridomas or leukemic cells). Accumulating evidence indicates, however, that apoptosis can be triggered also in mature peripheral T cells. Here we show that a significant fraction of cells of a given IL-2-dependent TCR-alpha beta + clone or polyclonal short term line is killed when cultured for 20 h in the presence of PHA, anti-CD3 (OKT3), or anti-TCR (BMA031) mAb. Apoptosis can be triggered by these stimuli in CD4+, CD8+, and CD4-CD8- (double-negative) TCR-alpha beta+ clones. Activation-driven cell death (as quantified by propidium iodide staining and FACS analysis) is associated with fragmentation of DNA into oligonucleosomal bands of approximately 200 bp. Although freshly isolated peripheral blood T cells are largely resistant to apoptosis, the sensitivity to anti-CD3/TCR mAb or PHA-triggered cell death gradually increases upon activation and IL-2-dependent culture of T cells, and reaches a plateau level after 15 to 20 days. These data indicate that stimuli that activate resting T cells initiate death by apoptosis in activated T cells. The implications of these results for the regulation of cellular immune responses and the establishment of peripheral tolerance will be discussed.
Human Embryonic Stem Cell-Derived Cardiomyocytes Can Be Maintained in Defined Medium without Serum (2006)

Current procedures for the maintenance of cardiomyocytes from human embryonic stem (hES) cells rely on either co-culture with mouse cells or medium containing fetal bovine serum (FBS). Due to exposure to animal products, these methods carry the risk of potential pathogen contamination and increased immunogenicity. Additionally, FBS introduces inherent variability in the cultures due to the inevitable differences in serum lots. Here we investigated whether a defined serum-free medium containing creatine, carnitine, taurine, and insulin (CCTI) could maintain hES cell-derived cardiomyocytes. We show that hES cell-derived cardiomyocytes maintained in the CCTI medium in the absence of any feeders exhibit similar phenotypes to those maintained in serum, as indicated by the following observations: (1) comparable levels of cardiac gene transcription were found in cells grown in serum-containing medium versus those in the CCTI medium; (2) cardiomyocyte-associated proteins were expressed in cells cultured in the CCTI medium; (3) beating cells in the CCTI medium responded to pharmacological agents in a dose-dependent manner; and (4) the vast majority of the beating embryoid bodies displayed ventricular-like action potentials (APs), and the ventricular cells in serum-containing medium and the CCTI medium had indistinguishable AP properties. Therefore, culturing hES cell-derived cardiomyocytes in serum-free medium as described here should facilitate the use of the cells for in vitro and in vivo applications.
Comparative antimicrobial activities of antiseptic mouthrinses against isogenic planktonic and biofilm forms of Actinobacillus actinomycetemcomitans (2001)

The results of this study, in which antimicrobial mouthrinses were tested against biofilm-forming and planktonic strains of the same organism, provide a clear demonstration of the resistance to antimicrobial agents conferred by biofilm formation and provide additional support for employing tests using biofilms to more accurately assess the relative activities of antiplaque agents in vitro.
Evolutionary Computation in Financial Engineering: A Roadmap of GAs and GP (1998)

this article, wewould liketo#rst summarize a few major insights revealed in those two articles and then provide a roadmap for readers to initialize their own trails.
Chlorination of endogenous amines by isolated neutrophils. Ammonia-dependent bactericidal, cytotoxic, and cytolytic activities of the chloramines. (1984)

Isolated human neutrophilic leukocytes were stimulated to produce hydrogen peroxide (H2O2) and to secrete cytoplasmic granule components including myeloperoxidase into the medium. Myeloperoxidase catalyzed the oxidation of chloride (Cl-) by H2O2 to yield hypochlorous acid (HOCl), which reacted with endogenous nitrogen compounds to yield derivatives containing nitrogen-chlorine (N-Cl) bonds. Compounds available for reaction with HOCl were ammonia (NH+4), taurine, alpha-amino acids, and granule proteins and peptides that were released into the medium. A portion of the N-Cl derivatives formed under these conditions accumulated in the extracellular medium. These long lived oxidizing agents were characterized as hydrophilic, low molecular weight, mono-N-chloramine (RNHCl) derivatives based on their absorption spectrum, ability to oxidize 5-thio-2-nitrobenzoic acid and to chlorinate ammonia (NH+4), and behavior upon ultrafiltration, gel chromatography, and extraction with organic solvents. The RNHCl derivatives were of low toxicity, but reacted with NH+4 to yield the lipophilic oxidizing agent monochloramine (NH2Cl). Therefore, the addition of NH+4 conferred bactericidal, cytotoxic, and cytolytic activities on the RNHCl derivatives. The results indicate that taurine and other neutrophil amines protect neutrophils and other cells against oxidative attack by acting as a trap for HOCl and by competing with endogenous NH+4 for reaction with HOCl. However, the RNHCl derivatives act as a reserve of oxidizing equivalents that is converted to a toxic form when an increase in NH+4 concentration favors formation of NH2Cl.
Decreased Atherosclerotic Lesion Formation in Human Serum Paraoxonase Transgenic Mice (2002)

Our results indicate that PON1 protects against atherosclerosis in a dose-dependent manner and suggest that it may be a potential target for developing therapeutic agents for the treatment of cardiovascular disease.
Translational Efficiency of Transfer RNA's: Uses of an Extended Anticodon (1982)

Transfer RNA's are probably very strongly selected for translational efficiency. In this article, the argument is presented that the coding performance of the triplet anticodon is enhanced by selection of a matching anticodon loop and stem sequence. the anticodon plus these nearby sequence features (the extended anticodon) therefore contains more coding information than the anticodon alone and can perform more efficiently and accurately at the ribosome. This idea successfully accounts for the relative efficiencies of many transfer RNA's.
Prevalence of Botanical Extract Allergy in Patients with Contact Dermatitis (2004)

Contact allergy to botanicals was common in this highly selected group of patients. Contact dermatitis patients who use botanical products and whose reactions are not fully explained by standard patch testing may benefit from more extensive patch testing to botanical extracts.
Conventional and biventricular pacing in patients with first-degree atrioventricular block (2012)

Recent reports suggest that first-degree atrioventricular block is not benign. However, there is no evidence that shortening of the PR interval can improve outcome except for symptomatic patients with a very long PR interval ≥0.3 s. Because these patients require continual forced pacing, biventricular pacing should be used according to accepted guidelines for third-degree AV block. Functional atrial undersensing may occur in patients with conventional dual-chamber pacing and first-degree AV block because the sinus P-wave tends to be displaced into the post-ventricular atrial refractory period (PVARP) an arrangement that may cause a pacemaker syndrome. Prevention requires programming a shorter AV and PVARP that is feasible because retrograde conduction is rare in first-degree AV block patients. A relatively new pacing mode to minimize right ventricular stimulation has been designed by eliminating the traditional AV interval but with dual-chamber backup. This pacing mode permits the establishment of very long AV intervals that may cause pacemaker syndrome. About 50% of patients undergoing cardiac resynchronization therapy (CRT) have a PR interval ≥200 ms. The CRT patients with first-degree AV block are prone to develop electrical desynchronization more easily than those with a normal PR interval. The duration of desynchronization after exceeding the upper rate on exercise is also more pronounced. AV junctional ablation is rarely necessary in patients with first-degree AV block but should be considered for symptomatic functional atrial undersensing or when the disturbances caused by first-degree AV block during CRT cannot be managed by programming.
SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity (2012)

Identifying protein surface regions preferentially recognizable by antibodies (antigenic epitopes) is at the heart of new immuno-diagnostic reagent discovery and vaccine design, and computational methods for antigenic epitope prediction provide crucial means to serve this purpose. Many linear B-cell epitope prediction methods were developed, such as BepiPred, ABCPred, AAP, BCPred, BayesB, BEOracle/BROracle, and BEST, towards this goal. However, effective immunological research demands more robust performance of the prediction method than what the current algorithms could provide. In this work, a new method to predict linear antigenic epitopes is developed; Support Vector Machine has been utilized by combining the Tri-peptide similarity and Propensity scores (SVMTriP). Applied to non-redundant B-cell linear epitopes extracted from IEDB, SVMTriP achieves a sensitivity of 80.1% and a precision of 55.2% with a five-fold cross-validation. The AUC value is 0.702. The combination of similarity and propensity of tri-peptide subsequences can improve the prediction performance for linear B-cell epitopes. Moreover, SVMTriP is capable of recognizing viral peptides from a human protein sequence background. A web server based on our method is constructed for public use. The server and all datasets used in the current study are available at http://sysbio.unl.edu/SVMTriP.
Structural properties of `naked' gold nanoparticles formed by synchrotron X-ray irradiation (2007)

The formation of colloidal unmodified (naked) gold nanoparticles is investigated by irradiation of a precursor solution with X-rays from a synchrotron source. An interesting morphological evolution as a function of exposure time, from cross-linked network-like structure to individual particles, has been discovered. The particle size decreased with the exposure time and was influenced by the ionic strength of the precursor solution. Contrary to gamma-ray exposure, an OH radical scavenger was not required for cluster formation.
Covalent binding of methotrexate to immunoglobulins and the effect of antibody-linked drug on tumor growth in vivo. (1981)

In an attempt to design cancer chemotherapeutic agents of improved specificity by linking them to antibodies against tumor-associated antigens, we studied the binding of methotrexate (MTX) to immunoglobulins by three different methods, initially using a model system that consisted of bovine serum albumin and rabbit anti-bovine serum albumin immunoglobulin G (IgG). One method used coupling via water-soluble 1-ethyl-3-(3′-dimethylaminopropyl)carbodiimide (ECDI), whereas two others used reactive intermediate derivatives of MTX, i.e. , an active ester formed by reaction with N -hydroxysuccinimide or a mixed anhydride formed by reaction with acetic anhydride. The ECDI and active ester methods yielded covalent conjugates as established by: ( a ) lack of binding of MTX to IgG in the absence of ECDI or when MTX was added without prior activation; and ( b ) the presence of a constant amount of MTX in the IgG fraction after gel filtration. The active ester method was the most effective. Ten mol of MTX per mol of IgG could be incorporated with retention of 90% of the anti-bovine serum albumin activity of an equimolar amount of unconjugated IgG and with recovery of 70% of the original protein. In the ECDI procedure, there was 50% loss of protein, and the recovered protein retained only 50% antibody activity at an incorporation level of 8 mol of MTX per mol of IgG. Conjugates containing 12 mol of drug per mol of IgG lost all antibody activity. MTX conjugated by both the active ester and ECDI methods partially retained the ability to inhibit dihydrofolate reductase. The mixed anhydride procedure failed to incorporate more than 2 to 3 mol of MTX per mol of IgG even when there was a 200-fold molar excess of anhydride in the reaction mixture. The conjugate retained full antibody activity, but neither it nor the product resulting from the reaction of MTX with acetic anhydride inhibited dihydrofolate reductase.

The demonstrated superiority of the active ester method in producing active conjugates prompted us to use this technique for linking MTX to a rabbit IgG antibody against the mouse EL4 lymphoma. Conjugates containing 13 mol of MTX per mol of IgG retained their reactivity with EL4 cells on membrane immunofluorescence assay. When tumor-inoculated mice (104 EL4 cells/animal) were given injections of this conjugate on Days 1, 4, and 7 after inoculation (MTX dose, 4 mg/kg/injection), they survived significantly longer than did mice treated with equivalent amounts of drug alone, antitumor IgG alone, drug followed by antibody, or drug linked to non-tumor-specific IgG. Eight of 11 mice treated with this MTX-anti-EL4 IgG conjugate survived tumor free for an observation period of 90 days, whereas control mice died at 17.3 ± 2.47 (S.D.) days after tumor inoculation.
Role of Reactive Oxygen Species in the Radiation Response of Human Hematopoietic Stem/Progenitor Cells (2013)

Hematopoietic stem/progenitor cells (HSPCs), which are present in small numbers in hematopoietic tissues, can differentiate into all hematopoietic lineages and self-renew to maintain their undifferentiated phenotype. HSPCs are extremely sensitive to oxidative stressors such as anti-cancer agents, radiation, and the extensive accumulation of reactive oxygen species (ROS). The quiescence and stemness of HSPCs are maintained by the regulation of mitochondrial biogenesis, ROS, and energy homeostasis in a special microenvironment called the stem cell niche. The present study evaluated the relationship between the production of intracellular ROS and mitochondrial function during the proliferation and differentiation of X-irradiated CD34(+) cells prepared from human placental/umbilical cord blood HSPCs. Highly purified CD34(+) HSPCs exposed to X-rays were cultured in liquid and semi-solid medium supplemented with hematopoietic cytokines. X-irradiated CD34(+) HSPCs treated with hematopoietic cytokines, which promote their proliferation and differentiation, exhibited dramatically suppressed cell growth and clonogenic potential. The amount of intracellular ROS in X-irradiated CD34(+) HSPCs was significantly higher than that in non-irradiated cells during the culture period. However, neither the intracellular mitochondrial content nor the mitochondrial superoxide production was elevated in X-irradiated CD34(+) HSPCs compared with non-irradiated cells. Radiation-induced gamma-H2AX expression was observed immediately following exposure to 4 Gy of X-rays and gradually decreased during the culture period. This study reveals that X-irradiation can increase persistent intracellular ROS in human CD34(+) HSPCs, which may not result from mitochondrial ROS due to mitochondrial dysfunction, and indicates that substantial DNA double-strand breakage can critically reduce the stem cell function.
Molecular cloning, characterization, and expression of human ADP-ribosylation factors: two guanine nucleotide-dependent activators of cholera toxin. (1989)

ADP-ribosylation factors (ARFs) are small guanine nucleotide-binding proteins that enhance the enzymatic activities of cholera toxin. Two ARF cDNAs, ARF1 and ARF3, were cloned from a human cerebellum library. Based on deduced amino acid sequences and patterns of hybridization of cDNA and oligonucleotide probes with mammalian brain poly(A)+ RNA, human ARF1 is the homologue of bovine ARF1. Human ARF3, which differs from bovine ARF1 and bovine ARF2, appears to represent a newly identified third type of ARF. Hybridization patterns of human ARF cDNA and clone-specific oligonucleotides with poly(A)+ RNA are consistent with the presence of at least two, and perhaps four, separate ARF messages in human brain. In vitro translation of ARF1, ARF2, and ARF3 produced proteins that behaved, by SDS/PAGE, similar to a purified soluble brain ARF. Deduced amino acid sequences of human ARF1 and ARF3 contain regions, similar to those in other G proteins, that are believed to be involved in GTP binding and hydrolysis. ARFs also exhibit a modest degree of homology with a bovine phospholipase C. The observations reported here support the conclusion that the ARFs are members of a multigene family of small guanine nucleotide-binding proteins. Definition of the regulation of ARF mRNAs and of function(s) of recombinant ARF proteins will aid in the elucidation of the physiologic role(s) of ARFs.