gebhart/patrepeval huggingface dataset:
Evolution of a Hybrid Roller Cone/PDC core bit (1980)

The development of the hot dry rock (HDR) geothermal resource, as presently being accomplished by the Los Alamos Scientific Laboratory (LASL), requires that sufficient quantities of good quality core be obtained at a reasonable cost. The use of roller cone core bits, with tungsten carbide inserts, was initiated by the Deep Sea Drilling Program. These bits were modified for continental drilling in deep, hot, granitic rock for the LASL HDR Geothermal Site at Fenton Hill, New Mexico in 1974. After the advent of monocrystalline diamond Stratapax pads, a prototype hybrid roller cone/Stratapax core bit was fabricated by Smith Tool, and tested at Fenton Hill in 1978. During the drilling for a deeper HDR reservoir system in 1979 and 1980, six of the latest generation of these bits, now called Hybrid Roller Cone/Polycrystalline Diamond Cutter (PDC) core bits, were successfully used in granitic rock at depths below 11,000 ft.
Steroid diabetes: from mechanism to treatment? (2014)

Glucocorticoids (GCs) are frequently prescribed anti-inflammatory and immunosuppressive drugs. In addition to their beneficial effects on disease activity, GCs have an extensive side effect profile, including adverse effects on metabolism resulting in the development of glucose intolerance and overt diabetes. Recent developments have led to renewed interest in the mechanisms underlying these diabetogenic effects of GCs. First, dissociated glucocorticoid receptor (GR) agonists were developed which are designed to segregate the anti-inflammatory and metabolic actions of GCs, potentially rendering compounds with a higher therapeutic index. Second, at present, 11-beta hydroxysteroid dehydrogenase type-1 inhibitors are under development. These compounds may lower tissue GC concentrations by inhibiting cortisone to cortisol conversion and are being evaluated in clinical trials as a novel treatment modality for the metabolic syndrome. Here, we provide an up-to-date overview of the current insights regarding the mechanisms responsible for the adverse metabolic effects of GCs that may lead to steroid diabetes. Particularly, we will focus on GC-related induction of insulin resistance and pancreatic islet-cell dysfunction. Finally, we will discuss how increased knowledge concerning the pathophysiology of steroid diabetes may result in improved treatment strategies.
Chondrogenic differentiation of mesenchymal stem cells is inhibited after magnetic labeling with ferumoxides (2004)

Magnetic resonance (MR) tracking of magnetically labeled cells is a relatively new technique to noninvasively determine the biodistribution and migration of transplanted or transfused stem cells in vivo.[1][1] The recent paper by Arbab et al[2][2] represents a significant step forward in bringing
Macrophage-tropic human immunodeficiency virus isolates from different patients exhibit unusual V3 envelope sequence homogeneity in comparison with T-cell-tropic isolates: definition of critical amino acids involved in cell tropism (1992)

Previous experiments indicate that the V3 hypervariable region of the human immunodeficiency virus (HIV) envelope protein influences cell tropism of infection; however, so far no consistent V3 sequence can account for macrophage or T-cell tropism. In these experiments, we studied infectious recombinant HIV clones constructed by using V3 region sequences of HIV isolates from 16 patients to search for sequences associated with cell tropism. Remarkable homology was seen among V3 sequences from macrophage-tropic clones from different patients, and a consensus V3 region sequence for patient-derived macrophage-tropic viruses was identified. In contrast, V3 sequences of T-cell-tropic clones from different patients were highly heterogeneous, and the results suggested that sequence diversity leading to T-cell tropism might be generated independently in each patient. Site-specific mutations identified amino acids at several positions on each side of the GPGR motif at the tip of the V3 loop as important determinants of tropism for T cells and macrophages. However, a wide variety of mutant V3 sequences induced macrophage tropism, as detected in vitro. Therefore, the homogeneity of macrophage-tropic patient isolates appeared to be the result of selection based on a biological advantage in vivo.
Cyanoacetamide Multicomponent Reaction (I): Parallel Synthesis Of Cyanoacetamides (2009)

Cyanoacetic acid derivatives are the starting materials for a plethora of multicomponent reaction (MCR) scaffolds. However the diversity of these scaffolds is hampered by the low variability of the cyanoacetic acid derivatives in the past. Here we describe valuable protocols for the parallel synthesis of arrays of cyanoacetamides on a multigram scale and involving very convenient work up by simple filtration and washing. Fifty-two products are described, and several applications are indicated. We foresee our protocol and the resulting derivatives to become very valuable to greatly expanding the large MCR scaffold space of cyanoacetic acid derivatives.
Recombinant human factor VIII‐specific affinity ligands selected from phage‐displayed combinatorial libraries of protein A (2001)

Factor VIII-specific affibodies were selected from phage displayed libraries constructed by combinatorial mutagenesis of an alpha helical bacterial receptor domain derived from staphylococcal protein A. Bead-immobilized recombinant human factor VIII (rVIII) (80 and 90 kDa chains) protein was used during competitive biopannings in the presence of free 80-kDa chain protein, resulting in the selection of several binders that showed dissociation constants (Kd) in the range 100-200 nM as determined by biosensor analyses. One variant (Z[rVIII:3], 90-kDa chain specific) was further characterized in small-scale affinity chromatography experiments, and showed efficient and selective recovery of biologically active rVIII from Chinese hamster ovary cell supernatant-derived feed stocks. The purity of the enriched rVIII was comparable with rVIII material purified by immunoaffinity chromatography using a 90-kDa chain-specific monoclonal antibody. Interestingly, epitope mapping showed that the monoclonal antibody and the affibody ligand competed for the same or at least overlapping epitopes on rVIII. In addition, the Z[rVIII:3] variant was produced by peptide synthesis with a C-terminal cysteine to enable directed coupling to solid supports. This 59-residue protein was analyzed by circular dichroism and showed a secondary structure content similar to that of the parental Z domain used as scaffold. In biosensor studies, the synthetic affibody was immobilized recruiting the C-terminal cysteine residue, and demonstrated to bind both recombinantly produced and plasma-derived factor VIII. From a secondary library, constructed by re-randomization of relevant positions identified after alignment of the first-generation variants, a panel of affinity-improved second-generation affibodies were selected of which one clone showed a dissociation constant (Kd) for rVIII of 5 nM. Several of these variants also showed higher apparent binding efficiencies towards rVIII when analyzed as immobilized ligands in biosensor experiments. Taken together, the results suggest that affibody ligands produced by bacterial or synthetic routes could be of interest as an alternative to monoclonal antibodies in purification processes or as diagnostic or monitoring tools.
Biological disposition and imaging of a radioiodinated alkylphosphocholine in two rodent models of breast cancer. (1996)

The ability of radioiodinated phospholipid analogs to accumulate in breast tumors reinforces the need for further investigation of this type of radiopharmaceutical as tumor imaging agents.
Discovery and characterization of sialic acid O-acetylation in group BStreptococcus (2004)

Group B Streptococcus (GBS) is the leading cause of human neonatal sepsis and meningitis. The GBS capsular polysaccharide is a major virulence factor and the active principle of vaccines in phase II trials. All GBS capsules have a terminal alpha 2-3-linked sialic acid [N-acetylneuraminic acid (Neu5Ac)], which interferes with complement-mediated killing. We show here that some of the Neu5Ac residues of the GBS type III capsule are O-acetylated at carbon position 7, 8, or 9, a major modification evidently missed in previous studies. Data are consistent with initial O-acetylation at position 7, and subsequent migration of the O-acetyl ester at positions 8 and 9. O-acetylation was also present on several other GBS serotypes (Ia, Ib, II, V, and VI). Deletion of the CMP-Neu5Ac synthase gene neuA by precise, in-frame allelic replacement gave intracellular accumulation of O-acetylated Neu5Ac, whereas overexpression markedly decreased O-acetylation. Given the known GBS Neu5Ac biosynthesis pathway, these data indicate that O-acetylation occurs on free Neu5Ac, competing with the CMP-Neu5Ac synthase. O-acetylation often generates immunogenic epitopes on bacterial capsular polysaccharides and can modulate human alternate pathway complement activation. Thus, our discovery has important implications for GBS pathogenicity, immunogenicity, and vaccine design.
High birefringence liquid crystalline materials (2008)

In this paper, nematic liquid crystalline materials and its mesogenic and physicochemical properties (mainly birefringence, dielectric anisotropy, and viscosity) will be discussed. The influence of number and position of fluorosubstitution on the ability of nematic phase formation in broad temperature range and on the value and sign of dielectric anisotropy will also be demonstrated.
Effects of Three Different Posting Methods on Controlling Abnormal Subtalar Pronation (1994)

Clinicians should consider combined posting or rear-foot posting alone when maximal control of rear-foot frontal-plane pronation is desired, though forefoot posting alone and the orthotic shell also provide control of rear-foot frontal-plane pronation.
Structure-activity relationships for inhibition of papain by peptide Michael acceptors (1992)

Two series of peptidyl Michael acceptors, N-Ac-L-Phe-NHCH2CH = CH-E with different electron withdrawing groups (E = CO2CH3, 1a; SO2CH3, 1b; CO2H, 1c; CN, 1d; CONH2, 1e; and C6H4-p-NO2, 1f) and R-NHCH2CH = CHCOOCH3 with different recognition and binding groups (R = N-Ac-D-Phe, 2a; N-Ac-L-Leu, 3a; N-Ac-L-Met, 4a; PhCH2CH2CO, 5a; PhCO, 6a), were synthesized and evaluated as inactivators against papain. It was found that the inhibition of papain by peptidyl Michael acceptors is a general phenomenon and that the intrinsic chemical reactivity of the E group in the Michael acceptors has a direct effect on the kinetics of the inactivation process as reflected in k2/Ki. At pH 6.2, the reactivity of papain toward the Michael acceptors is about 283,000-fold higher than the reactivity of the model thiol 3-mercaptopropionate. This large increase in reactivity is attributable to at least 2 factors; one is the low apparent pKa of Cys-25 of papain, and the other is the recruitment of catalytic power by specific enzyme-substrate interactions. The unexpectedly high reactivity of 1c (E = COOH) was rationalized by proposing a direct interaction of the acid group with His-159 in the active site of papain. The unexpected inactivity of 1f (E = C6H4-p-NO2) as a Michael acceptor and its very powerful competitive inhibition of papain were rationalized by molecular graphics which showed the nitrophenyl moiety rotated out of conjugation with the olefin and interacting instead with the hydrophobic S1' region of papain. A plot of log (k2/Ki) for 1a-6a vs log (kcat/Km) for analogous R-Gly-p-NA substrates was linear (r = 0.98) with slope of 0.83, suggesting that binding energy from specific enzyme-ligand interactions can be used to drive the self-inactivation reaction to almost the same extent as it is used to drive catalysis.
Erb and c-Kit Receptors Have Distinctive Patterns of Expression in Adult and Developing Taste Papillae and Taste Buds (2000)

Twenty four different protein tyrosine kinases (PTKs) were amplified from a taste-enriched cDNA library using PCR. The expression of four protein tyrosine kinase receptors (EGFR, ErbB2, ErbB3, and c-kit) was examined in adult and developing rat taste papillae. All four of these receptors were expressed in overlapping populations of differentiated taste cells within adult taste buds. Taste bud basal cells were ErbB2(+) but did not express the other Erb receptors. During prenatal development, the Erb receptors were expressed extensively in the basal cells around developing papillae, and ErbB2 and c-kit immunoreactive neuronal fibers were seen in close association with taste papillae. In early postnatal stages, ErbB2(+) and c-kit(+) neuronal fibers were often seen entering the taste papillae epithelium, where new taste buds form, and by postnatal day 2 (P2), individual ErbB2(+) and c-kit(+) cells were seen in this region as well. Between P3 and P8, c-kit was highly expressed at the bottom of foliate papillae trenches. The extensive expression of the Erb and c-kit receptors in adult taste buds and in and around developing papillae suggests that these receptors may play a role in the prenatal and postnatal development of gustatory papillae and taste buds.
Impact of interferon beta-1a on neurologic disability in relapsing multiple sclerosis (1997)

The primary clinical outcome for the IFN beta-1a clinical trial underestimated clinical benefits of treatment. Results in this report demonstrate that IFN beta-1a treatment is associated with robust, clinically important beneficial effects on disability progression in relapsing MS patients.
Biology of cloned cytotoxic T lymphocytes specific for lymphocytic choriomeningitis virus: clearance of virus in vivo (1984)

Our data show that 1 X 10(7) to 1.5 X 10(7) lymphocytic choriomeningitis virus-specific, H-2-restricted cloned cytotoxic T lymphocytes (CTL) administered intravenously into acutely infected mice totally cleared virus from the spleens (10(4) to 10(5) PFU per spleen reduced to less than 50 PFU per spleen) by 24 h. This activity was genetically restricted in that cloned CTL could reduce titers of infectious virus in syngeneic C57BL/6 mice but not allogeneic BALB/c mice. Dose-response analysis indicated that at least 3 X 10(6) to 5 X 10(6) cloned CTL injected intravenously were needed to reduce significant amounts of infectious virus in the spleens. No infectious virus could be recovered from the spleens for at least 4 days after injection of cloned CTL. Hence, CTL play a major role in elimination of infectious virus from spleens during lymphocytic choriomeningitis virus infection. Our results also indicate that cloned CTL propagated in vitro for long periods of time can mediate a biologically relevant effect in vivo. These cells should be of considerable value in defining the precise manner in which CTL bring about control of viral infection, analyzing lymphocyte trafficking, and the potential use of cloned CTL in immunotherapy against viral disease.
Low Fidelity DNA Synthesis by a Y Family DNA Polymerase Due to Misalignment in the Active Site (2002)

Sulfolobus solfataricus DNA polymerase IV (Dpo4) is a member of the Y family of DNA polymerases whose crystal structure has recently been solved. As a model for other evolutionarily conserved Y family members that perform translesion DNA synthesis and have low fidelity, we describe here the base substitution and frameshift fidelity of DNA synthesis by Dpo4. Dpo4 generates all 12 base-base mismatches at high rates, 11 of which are similar to those of its human homolog, DNA polymerase kappa. This result is consistent with the Dpo4 structure, implying lower geometric selection for correct base pairs. Surprisingly, Dpo4 generates C.dCMP mismatches at an unusually high average rate and preferentially at cytosine flanked by 5'-template guanine. Dpo4 also has very low frameshift fidelity and frequently generates deletions of even noniterated nucleotides, especially cytosine flanked by a 5'-template guanine. Both unusual features of error specificity suggest that Dpo4 can incorporate dNTP precursors when two template nucleotides are present in the active site binding pocket. These results have implications for mutagenesis resulting from DNA synthesis by Y family polymerases.
Urodynamic Effect of Acute Transcutaneous Posterior Tibial Nerve Stimulation in Overactive Bladder (2003)

These results suggest an objective acute effect of posterior tibial nerve stimulation on urodynamic parameters. Improved bladder overactivity is an encouraging argument to propose posterior tibial nerve stimulation as a noninvasive treatment modality in clinical practice.
Expression of TGF-β Superfamily Receptors in Dental Pulp (1997)

Transforming growth factor-beta (TGF-beta) superfamily members and their cell-surface receptors may play inductive and/or regulatory roles in tooth development and repair. It will be important to identify the complete set of TGF-beta superfamily receptors, to examine their temporal and spatial localization during tooth development, and to elucidate the cascade of molecular events of tooth formation induced by the TGF-beta superfamily. In this report, we have cloned the cDNAs encoding potential receptors for TGF-beta superfamily members in rat incisor pulp and bovine adult pulp which are regarded as embryonic and adult pulp, respectively. We analyzed poly (A)+ RNA from rat incisor pulp and bovine adult pulp by reverse-transcriptase/polymerase chain-reaction (RT-PCR), using a degenerate primers corresponding to the most conserved amino acid sequences in the intracellular serine/threonine kinase of type I or type II like kinase-1 (ALK-1), ALK-2, ALK-3 (bone morphogenetic protein receptor type IA, BMPR-IA), ALK-4 (B1), ALK-5, ALK-6 (BMPR-IB), and BMPR-II (BMP type II receptor) was found to be in dental pulp. Northern blot analysis further detected TGF-beta type II receptor (T beta R-II) mRNA transcript in addition to the above-identified receptors. These results provide the first evidence of multiple type I and type II receptors for TGF-beta s, activins, and BMPs expressed in embryonic and adult pulp, implicating diverse function in tooth development and pulp tissue repair.
Properties, Potentials, and Prospects of Antifreeze Proteins (2008)

Antifreeze proteins (AFPs) are a group of proteins that protect organisms from deep freezing temperatures and are expressed in vertebrates, invertebrates, plants, bacteria, and fungi. The nuclear magnetic resonance, x-ray structure, and many spectroscopic studies with AFPs have been instrumental in determining the structure-function relationship. Mutational studies have indicated the importance of hydrophobic residues in ice binding. Various studies have pointed out that the mechanism of AFP action is through its adsorption on the ice surface, which leads to a curved surface, preventing further growth of ice by the "Kelvin effect." The AFPs have potential industrial, medical, and agricultural application in different fields, such as food technology, preservation of cell lines, organs, cryosurgery, and cold hardy transgenic plants and animals. However, the applications of AFPs are marred by high cost due to low yield. This review deals with the source and properties of AFPs from an angle of their application and their potential. The possibility of production using different molecular biological techniques, which will help increase the yield, is also dealt with.
Characterization of In Vitro Resistance Development to the Novel Echinocandin CD101 in Candida Species (2016)

ABSTRACT CD101 is a novel echinocandin with a long half-life undergoing clinical development for treatment of candidemia/invasive candidiasis and vulvovaginal candidiasis. The potential for and mechanisms underlying the development of resistance to CD101 in Candida species were investigated by using spontaneous resistance and serial passage selection methodologies. Four Candida spp. ( C. albicans , C. glabrata , C. parapsilosis , and C. krusei ) were chosen for resistance characterization with CD101, anidulafungin, and caspofungin. The frequency of spontaneous, single-step mutations conferring reduced susceptibility to CD101 at 1× the agar growth inhibition concentration was low across all species, with median frequencies ranging from 1.35 × 10 −8 to 3.86 × 10 −9 , similar to ranges generated for anidulafungin and caspofungin. Serial passage of Candida spp. on agar plates containing drug gradients demonstrated a low potential for resistance development, with passage 20 CD101-selected strains possessing increases in MICs equivalent to or lower than those for the majority of strains generated under selection with anidulafungin and caspofungin. A total of 12 fks “hot spot” mutations were identified, typically in strains with the highest MIC shifts. Cross-resistance was broadly observed among the 3 echinocandins evaluated, with no CD101-selected mutants (with or without fks hot spot mutations) exhibiting reduced susceptibility to CD101 but not also to anidulafungin and/or caspofungin. Consistent with currently approved echinocandins, CD101 demonstrates a low potential for resistance development, which could be further enhanced in vivo by the high maximum concentration of drug in serum ( C max )/area under the concentration-time curve (AUC) plasma drug exposure achieved with once-weekly dosing of CD101.
A Computer Model of Normal Conduction in the Human Atria (2000)

Although considerable progress has been made in understanding the process of wavefront propagation and arrhythmogenesis in human atria, technical concerns and issues of patient safety have limited experimental investigations. The present work describes a finite volume-based computer model of human atrial activation and current flow to complement these studies. Unlike previous representations, the model is three-dimensional, incorporating both the left and right atria and the major muscle bundles of the atria, including the crista terminalis, pectinate muscles, limbus of the fossa ovalis, and Bachmann's bundle. The bundles are represented as anisotropic structures with fiber directions aligned with the bundle axes. Conductivities are assigned to the model to give realistic local conduction velocities within the bundles and bulk tissue. Results from simulations demonstrate the role of the bundles in a normal sinus rhythm and also reveal the patterns of activation in the septum, where experimental mapping has been extremely challenging. To validate the model, the simulated normal activation sequence and conduction velocities at various locations are compared with experimental observations and data. The model is also used to investigate paced activation, and a mechanism of the relative lengthening of left versus right stimulation is presented. Owing to both the realistic geometry and the bundle structures, the model can be used for further analysis of the normal activation sequence and to examine abnormal conduction, including flutter. The full text of this article is available at http://www.circresaha.org.
Computational Methods for Gene Expression-Based Tumor Classification (2000)

Gene expression profiles may offer more or additional information than classic morphologic- and histologic-based tumor classification systems. Because the number of tissue samples examined is usually much smaller than the number of genes examined, efficient data reduction and analysis methods are critical. In this report, we propose a principal component and discriminant analysis method of tumor classification using gene expression profile data. Expression of 2000 genes in 40 tumor and 22 normal colon tissue samples is used to examine the feasibility of gene expression-based tumor classification systems. Using this method, the percentage of correctly classified normal and tumor tissue was 87.0%. The combined approach using principal components and discriminant analysis provided superior sensitivity and specificity compared to an approach using simple differences in the expression levels of individual genes.