gebhart/patrepeval huggingface dataset:
Physicochemical, molecular and immunological characterization of camel calf rennet: a comparison with buffalo rennet (2000)

Camel calf rennet (CCR) and buffalo calf rennet (BCR) were prepared from dried abomasa to study their physicochemical properties and electrophoretic behaviour and to carry out an immunological characterization of the rennet proteins. CCR was more thermostable than BCR. The milk clotting activity of both rennets increased as pH decreased. The optimum temperatures for CCR and BCR were 50 and 45 degrees C respectively. CCR was more sensitive to increased CaCl2 in milk than BCR. Addition of NaCl to milk in the range 0-100 g/l resulted in a marked decrease in the clotting activity of both rennets. When the rennets were treated with acetone, the activity of BCR was completely destroyed, but that of CCR was unaffected. The proteolytic activity of CCR was higher than that of BCR and pepsin towards both camel and cows' milk caseins at pH 6.0. SDS-PAGE electrophoretic patterns of CCR and BCR proteins gave two major bands with molecular masses estimated as 52 and 39 kDa for CCR and 50 and 35 kDa for BCR. Immunodiffusion and immunoelectrophoresis using anti-CCR serum demonstrated immunological cross reactivity between CCR and BCR.
Multiple health needs and homeless people (2004)

In the first of two articles looking at the health care needs of vulnerable groups, Brenda Roche outlines the health needs of homeless people
Cisplatin Biochemical Mechanism of Action: From Cytotoxicity to Induction of Cell Death Through Interconnections Between Apoptotic and Necrotic Pathways (2003)

Although cisplatin, cis-diamminedichloroplatinum(II), has been successfully used in the chemotherapy of cancer for more than 25 years, its biochemical mechanism of action is still unclear. The current accepted paradigm about cisplatin mechanism of action is that the drug induces its cytotoxic properties through binding to nuclear DNA and subsequent interference with normal transcription, and/or DNA replication mechanisms. If cisplatin-DNA adducts are not efficiently processed by cell machinery, cytotoxic processes eventually end up in cell death. However, before cisplatin enters the cell it may bind to phospholipids and phosphatidylserine in the cell membrane. In addition, in the cytoplasm many potential platinum-binding sites are also available, including RNA and sulfur-containing biomolecules. Moreover, there is much evidence suggesting that the cytotoxic effects induced by binding of cisplatin to non-DNA targets (especially proteins) may contribute to its biochemical mechanism of action. On the other hand, it has been found that several factors such as the dose of drug as well as the metabolic condition of the cell subjected to cisplatin aggression, may determine that cancer cells die through apoptosis or necrosis. In fact, it has recently been reported that both mechanisms of cell demise work in concert so that within a population of tumour cells there is a continuum of possible modes of cell death.
The DNA (cytosine-5) methyltransferases (1994)

The m5C-MTases form a closely-knit family of enzymes in which common amino acid sequence motifs almost certainly translate into common structural and functional elements. These common elements are located predominantly in a single structural domain that performs the chemistry of the reaction. Sequence-specific DNA recognition is accomplished by a separate domain that contains recognition elements not seen in other structures. This, combined with the novel and unexpected mechanistic feature of trapping a base out of the DNA helix, makes the m5C-MTases an intriguing class of enzymes for further study. The reaction pathway has suddenly become more complicated because of the base-flipping and much remains to be learned about the DNA recognition elements in the family members for which structural information is not yet available.
Characterization of the Intracellular Domain of Receptor Activator of NF-κB (RANK) (1998)

Various members of the tumor necrosis factor (TNF) receptor superfamily interact directly with signaling molecules of the TNF receptor-associated factor (TRAF) family to activate nuclear factor kappaB (NF-kappaB) and the c-Jun N-terminal kinase (JNK) pathway. The receptor activator of NF-kappaB (RANK), a recently described TNF receptor family member, and its ligand, RANKL, promote survival of dendritic cells and differentiation of osteoclasts. RANK contains 383 amino acids in its intracellular domain (residues 234-616), which contain three putative TRAF-binding domains (termed I, II, and III). In this study, we set out to identify the region of RANK needed for interaction with TRAF molecules and for stimulation of NF-kappaB and JNK activity. We constructed epitope-tagged RANK (F-RANK616) and three C-terminal truncations, F-RANK330, F-RANK427, and F-RANK530, lacking 85, 188, and 285 amino acids, respectively. From this deletion analysis, we determined that TRAF2, TRAF5, and TRAF6 interact with RANK at its C-terminal 85-amino acid tail; the binding affinity appeared to be in the order of TRAF2 > TRAF5 > TRAF6. Furthermore, overexpression of RANK stimulated JNK and NF-kappaB activation. When the C-terminal tail, which is necessary for TRAF binding, was deleted, the truncated RANK receptor was still capable of stimulating JNK activity but not NF-kappaB, suggesting that interaction with TRAFs is necessary for NF-kappaB activation but not necessary for activation of the JNK pathway.
Design of polyzinc finger peptides with structured linkers (2001)

Zinc finger domains are perhaps the most versatile of all known DNA binding domains. By fusing up to six zinc finger modules, which normally recognize up to 18 bp of DNA, designer transcription factors can be produced to target unique sequences within large genomes. However, not all continuous DNA sequences make good zinc finger binding sites. To avoid having to target unfavorable DNA sequences, we designed multizinc finger peptides with linkers capable of spanning long stretches of nonbound DNA. Two three-finger domains were fused by using either transcription factor IIIA for the Xenopus 5S RNA gene (TFIIIA) finger 4 or a non-sequence-specific zinc finger as a "structured" linker. Our gel-shift results demonstrate that these peptides are able to bind with picomolar affinities to target sequences containing 0--10 bp of nonbound DNA. Furthermore, these peptides display greater sequence selectivity and bind with higher affinity than similar six-finger peptides containing long, flexible linkers. These peptides are likely to be of use in understanding the behavior of polydactyl proteins in nature and in the targeting of human, animal, or plant genomes for numerous applications. We also suggest that in certain polydactyl peptides an individual finger can "flip" out of the major groove to allow its neighbors to bind shorter, nontarget DNA sequences.
Effect of an Aromatase Inhibitor on BMD and Bone Turnover Markers: 2-Year Results of the Anastrozole, Tamoxifen, Alone or in Combination (ATAC) Trial (18233230) (2006)

Anastrozole is associated with significant BMD loss and a small increase in bone turnover, whereas tamoxifen (and the combination) is associated with increased BMD and decreased remodeling. These data may explain the increased fracture risk observed with anastrozole treatment in the ATAC trial. The impact of anastrozole on bone should be weighed against its overall superior efficacy and tolerability as observed in the main ATAC trial.
Dimensional Control of Cobalt-hydroxide-carbonate Nanorods and Their Thermal Conversion to One-Dimensional Arrays of Co3O4 Nanoparticles (2003)

We report a detailed investigation on the formation of cobalt-basic-carbonate compounds [Co(OH)x(CO3)0.5(2-x)·nH2O] with dimensional and morphological controls. Two complementary precipitation methods developed in this work produce cobalt-basic-carbonate in the form of nanorods across a wide diameter span from 2 to 200 nm and a length up to 5 μm. Various controlling parameters were examined, such as anions in starting reagents, reaction temperature, aging time, and chemical compositions between the solid products and starting reagents. The resultant solids were characterized using XRD, FTIR, CHN, and TGA/DrTGA methods with respect to their formation process and thermal decomposition. More importantly, morphological aspects of the Co(OH)x(CO3)0.5(2-x)·nH2O and their heat-treated product Co3O4 were investigated with TEM/ED methods. It has been found that the Co(OH)x(CO3)0.5(2-x)·nH2O nanorods are grown along the [010] direction (orthorhombic). Upon thermal decomposition at ≥300 °C, the above nanorods self-assemble into one-dimensional arrays of Co3O4 nanoparticles along the [111] axis (cubic) of the spinel. Co3O4 nanorods can be prepared with this method in a small diameter regime of 20−40 nm.
Market-Based Coordination of Thermostatically Controlled Loads—Part II: Unknown Parameters and Case Studies (2015)

This two-part paper considers the coordination of a population of thermostatically controlled loads (TCLs) with unknown parameters to achieve group objectives. The problem involves designing the bidding and market clearing strategy to motivate self-interested users to realize efficient energy allocation subject to a peak energy constraint. The companion paper (Part I) formulates the problem and proposes a load coordination framework using the mechanism design approach. To address the unknown parameters, Part II of this paper presents a joint state and parameter estimation framework based on the expectation maximization algorithm. The overall framework is then validated using real-world weather data and price data, and is compared with other approaches in terms of aggregated load response. Simulation results indicate that our coordination framework can effectively improve the operational efficiency of the distribution system and reduce power congestion at key times.
Prognostic Value of Plasma von Willebrand Factor and Soluble P-Selectin as Indices of Endothelial Damage and Platelet Activation in 994 Patients With Nonvalvular Atrial Fibrillation (2003)

Among patients with AF who received aspirin, raised levels of vWf (endothelial damage/dysfunction) were predictive of stroke and vascular events, but raised sP-sel levels (platelet activation) were not associated with increased cardiovascular risk. Endothelial damage/dysfunction (or vWf itself) may play an important role in the mechanisms behind stroke and cardiovascular outcome among aspirin-treated AF patients and might represent a target for novel therapies or an adjunctive aid to risk stratification in AF.
A Fluorine Scan of Thrombin Inhibitors to Map the Fluorophilicity/Fluorophobicity of an Enzyme Active Site: Evidence for CF⋅⋅⋅CO Interactions (2003)

Die hohe Fluorophilie der HCαCO-Einheit von Asn 98 im aktiven Zentrum von Thrombin zeigt sich bei der röntgenstrukturanalytischen Charakterisierung eines Komplexes mit einem künstlichen Inhibitor (siehe Bild, Abstände in Å). Auch in den Röntgenstrukturanalysen zahlreicher kleiner Moleküle werden an HCαCO-Carbonyleinheiten kleine CF⋅⋅⋅HCα- und CF⋅⋅⋅CO-Abstände gefunden.
CCR9+ and CD103+ tolerogenic dendritic cell populations in food allergy patients undergoing oral immunotherapy (2011)

Rationale CD103+ DCs (dendritic cells) and CCR9+ pDCs (plasmacytoid DCs) have been implicated in promoting tolerance to antigens through regulatory-T cell induction. We have conducted food oral immunotherapy (OIT) clinical studies for the last 3 years at Stanford University. We hypothesized that subjects with food allergies have low CD103+ and CCR9+ expression on their DCs but that these DC populations change over time while on therapy.
Conservation and Diversity of Eukaryotic Translation Initiation Factor eIF3 (1997)

The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA. We report the cloning and characterization of human cDNAs encoding two of its subunits, p110 and p36. It was found that the second slowest band during polyacrylamide gel electrophresis of eIF3 subunits in sodium dodecyl sulfate contains two proteins: p110 and p116. Analysis of the cloned cDNA encoding p110 indicates that its amino acid sequence is 31% identical to that of the yeast protein, Nip1. The p116 cDNA was cloned and characterized as a human homolog of yeast Prt1, as described elsewhere (Methot, N., Rom, E., Olsen, H., and Sonenberg, N. (1997) J. Biol. Chem. 272, 1110-1116). p36 is a WD40 repeat protein, which is 46% identical to the p39 subunit of yeast eIF3 and is identical to TRIP-1, a phosphorylation substrate of the TGF-beta type II receptor. The p116, p110, and p36 subunits localize on 40 S ribosomes in cells active in translation and co-immunoprecipitate with affinity-purified antibodies against the p170 subunit, showing that these proteins are integral components of eIF3. Although p36 and p116 have homologous protein subunits in yeast eIF3, the p110 homolog, Nip1, is not detected in yeast eIF3 preparations. The results indicate both conservation and diversity in eIF3 between yeast and humans.
Primary sequence of the Escherichia coli fadBA operon, encoding the fatty acid-oxidizing multienzyme complex, indicates a high degree of homology to eucaryotic enzymes (1990)

In Escherichia coli at least five enzyme activities required for the beta-oxidation of fatty acids are associated with a multienzyme complex composed of two subunits in alpha 2 beta 2 conformation (A. Pramanik et al., J. Bacteriol. 137:469-473, 1979). In the present work, the DNA sequence of the genes encoding these two subunits, fadB and fadA, has been determined. The direction of transcription was from fadB to fadA rather than from fadA to fadB, as suggested previously (S. K. Spratt et al., J. Bacteriol. 158:535-542, 1984). Only 10 nucleotides separated the coding sequences for the two peptides, confirming the suggestion that these genes form an operon. The peptides encoded by fadB and fadA were 729 amino acids and 387 amino acids, respectively, in length. The larger and smaller peptides had predicted molecular masses of 79,678 and 40,876 Da, respectively. Recently, the sequence of the fadA gene was published in a separate report (Yang et al., J. Biol. Chem. 265:10424-10429, 1990). In this work, most of the DNA sequence for fadA was confirmed, and 10 errors were corrected. Three of these nucleotide changes resulted in five amino acid residue changes predicted in the carboxy terminus of the fadA-encoded peptide. By comparison to other peptide sequences, the alpha subunit encoded within fadB had 31% perfect identity with the rat peroxisomal enoyl-coenzyme A:hydratase-3-hydroxyacyl-coenzyme A dehydrogenase trifunctional enzyme over the entire length of the two peptides. In agreement with the work of Yang et al., the beta subunit encoded within fadA had 35 to 45% perfect identity with five thiolase genes from different eucaryotic sources over the entire length of the peptide.
Regulation of fibronectin and type I collagen mRNA levels by transforming growth factor-beta. (1987)

Human platelet-derived transforming growth factor-beta (TGF-beta 1) increases the accumulation of the extracellular matrix proteins, fibronectin and type I collagen, in mesenchymal and epithelial cells. To determine the basis for this effect, we have examined the levels of mRNAs corresponding to fibronectin and alpha 2(I) procollagen in NRK-49 rat fibroblasts and L6E9 rat myoblasts treated with TGF-beta 1. TGF-beta 1 increased severalfold the levels of mRNAs for both proteins. The kinetics of this effect were similar for both mRNA species. The increase in fibronectin and alpha 2(I) procollagen mRNAs was detectable 2 h after addition of TGF-beta 1 to the cells and their maximal levels remained constant for several days. Actinomycin D, but not cycloheximide, inhibited the increase in fibronectin and alpha 2(I) procollagen mRNA levels induced by TGF-beta 1. The results indicate that TGF-beta 1 controls the composition and abundance of extracellular matrices at least in part by inducing a coordinate increase in the levels of fibronectin and type I collagen mRNAs.
The ovalbumin gene - sequence of putative control regions (1980)

We present the sequence of regions of the chicken ovalbumin gene believed to be important in the control of initiation of transcription, splicing, and transcription termination or polyadenylation. Comparison with corresponding areas of other genes reveals some homologous regions which might play a role in these processes.
Shape Selective Growth of CdS One-Dimensional Nanostructures by a Thermal Evaporation Process (2006)

CdS one-dimensional nanoforms such as nanowires, nanoribbons, network-like nanowires, pearl necklace type nanowires, helical-like nanowires, and nanowire arrays were formed on Si substrates by a simple thermal evaporation route. The shapes of the one-dimensional CdS nanoforms were controlled by varying the experimental parameters such as temperature and position of the substrates. Formation of the CdS one-dimensional nanoforms was initiated by the Au catalyzed vapor-liquid-solid technique, whereas the vapor-solid process played a crucial role in defining the shapes of the nanoforms. Different optical characterizations such as optical absorbance, photoluminescence, and Raman spectroscopy were adopted to explore the physical and structural quality of these CdS nanoforms.
Cystatin A expression reduces bile salt-induced apoptosis in a rat hepatoma cell line (1998)

We have previously demonstrated abrogation of bile salt-induced apoptosis by cathepsin B inhibitors. However, caspases have been strongly implicated in apoptosis, and the mechanistic interface between caspase and cathepsin B activation is unclear. Thus our aims were to determine the mechanistic relationship between caspases and cathepsin B in bile salt-induced apoptosis in a rat hepatoma cell line. Expression of cystatin A was used to inhibit cathepsin B, whereas Z-Val-Ala-Asp-fluoromethyl ketone (Z-VAD-FMK) was used to inhibit caspases. Cystatin A expression prevented cathepsin B activation and apoptosis during treatment with glycochenodeoxycholate (GCDC), a toxic bile salt. Caspase N-acetyl-Asp-Glu-Val-Asp-7-amino-4-methylcoumarin (DEVD-AMC) hydrolytic activity increased in both wild-type and cystatin A-transfected cells treated with GCDC, demonstrating caspase activation despite inhibition of cathepsin B. In contrast, Z-VAD-FMK blocked both DEVD-AMC hydrolytic activity and cathepsin B activity during GCDC treatment. Our data demonstrate that 1) bile salt-induced apoptosis can be inhibited by the cystatin A transgene and 2) caspase and cathepsin B activation are linked mechanistically with cathepsin B downstream of caspases.
Photoinitiated Nitric Oxide-Releasing Tertiary S-Nitrosothiol-Modified Xerogels (2012)

The synthesis of a tertiary thiol-bearing silane precursor (i.e., N-acetyl penicillamine propyltrimethoxysilane or NAPTMS) to enable enhanced NO storage stability at physiological temperature is described. The novel silane was co-condensed with alkoxy- or alkylalkoxysilanes under varied synthetic parameters (e.g., water to silane ratio, catalyst and solvent concentrations, and reaction time) to evaluate systematically the formation of stable xerogel films. The resulting xerogels were subsequently nitrosated to yield tertiary RSNO-modified coatings. Total NO storage ranged from 0.87 to 1.78 μmol cm(-2) depending on the NAPTMS concentration and xerogel coating thickness. Steric hindrance near the nitroso functionality necessitated the use of photolysis to liberate NO. The average NO flux for irradiated xerogels (20% NAPTMS balance TEOS xerogel film cast using 30 μL) in physiological buffer at 37 °C was ∼23 pmol cm(-2) s(-1). The biomedical utility of the photoinitiated NO-releasing films was illustrated by their ability to both reduce Pseudomonas aeruginosa adhesion by ∼90% relative to control interfaces and eradicate the adhered bacteria.
The Predominant Cultivable Flora of Sound and Carious Human Root Surfaces (1994)

Little detailed knowledge exists about the composition of the human root flora. Therefore, the predominant cultivable flora (PCF) was determined for samples of: (1) plaque from sound root surfaces (SRS) in eight subjects without root caries, (2) plaque from incipient root lesions (IRL) in eight subjects with root caries, and (3) carious material from advanced root lesions (ARL) in nine other subjects with root caries. Generally, one root surface was sampled per subject, and organisms-358, 512, and 389 for SRS, IRL, and ARL, respectively-were identified by standard methods. It was found that: (1) streptococci, actinomyces, and veillonellae constituted 84.2, 57.8, and 65.7% of the PCF of SRS, IRL, and ARL samples, respectively; (2) a wide variety of other Gram-positive cocci and Gram-positive and -negative rods was also present; (3) the PCF of many samples was often dominated by few organisms, the identity of which differed from sample to sample; (4) a negative and no association with root caries existed for the PCF levels of the non-mutans streptococci (non-MS) and the actinomyces; and (5) mutans streptococci (MS) and lactobacilli (L) were not always present among the PCF of IRL and ARL, respectively, and non-MS were isolated from the PCF of most lesions and actinomyces from all lesions. Our findings illustrate the complexity of the root surface flora and suggest that root caries development involves organisms other than MS and L.
Diet and Exercise in the Treatment of NIDDM: The need for early emphasis (1994)

Lifestyle modification consisting of diet combined with aerobic exercise can be effective for controlling NIDDM and reducing risk factors associated with macrovascular complications in both men and women. The program was far more effective in controlling the disease in patients taking no medication or oral agents compared with patients taking insulin. These results stress the need for early emphasis on lifestyle modification in the treatment of NIDDM.
Identification of the Glucosyltransferase That Converts Hydroxymethyluracil to Base J in the Trypanosomatid Genome (2014)

O-linked glucosylation of thymine in DNA (base J) is an important regulatory epigenetic mark in trypanosomatids. β-d-glucopyranosyloxymethyluracil (base J) synthesis is initiated by the JBP1/2 enzymes that hydroxylate thymine, forming 5-hydroxymethyluracil (hmU). hmU is then glucosylated by a previously unknown glucosyltransferase. A recent computational screen identified a possible candidate for the base J-associated glucosyltransferase (JGT) in trypanosomatid genomes. We demonstrate that recombinant JGT utilizes uridine diphosphoglucose to transfer glucose to hmU in the context of dsDNA. Mutation of conserved residues typically involved in glucosyltransferase catalysis impairs DNA glucosylation in vitro. The deletion of both alleles of JGT from the genome of Trypanosoma brucei generates a cell line that completely lacks base J. Reintroduction of JGT in the JGT KO restores J synthesis. Ablation of JGT mRNA levels by RNAi leads to the sequential reduction in base J and increased levels of hmU that dissipate rapidly. The analysis of JGT function confirms the two-step J synthesis model and demonstrates that JGT is the only glucosyltransferase enzyme required for the second step of the pathway. Similar to the activity of the related Ten-Eleven Translocation (TET) family of dioxygenases on 5mC, our studies also suggest the ability of the base J-binding protein enzymes to catalyze iterative oxidation of thymine in trypanosome DNA. Here we discuss the regulation of hmU and base J formation in the trypanosome genome by JGT and base J-binding protein.