gebhart/patrepeval huggingface dataset:
Quantifying the Effect of Kerogen on Electrical Resistivity Measurements in Organic-Rich Source Rocks (2013)

Interpretation of electrical resistivity logs in organic-rich source rocks has been challenging for petrophysicists. Conventional resistivity-porosity-saturation models (e.g., Archie’s, Dual-Water, and Waxman-Smits equations) assume that saline water is the only conductive part of the formation. However, this assumption is not reliable in organic-rich source rocks in the presence of highly mature organic matter, clay, and pyrite. Previous experimental studies indicate that aromaticity of kerogen increases with an increase in thermal maturity, which might lead to conductive behavior of kerogen. In this thesis, I investigated and quantified the effect of conductive kerogen on electrical resistivity of organic-rich source rocks. \n\nFirst, I investigated the reliability of conventional resistivity-porosity-saturation models in the assessment of fluid saturations in organic-rich source rocks using well logs and core measurements in the Haynesville shale-gas formation. Next, I numerically simulated electric field, electric currents, and electrical resistivity of pore-scale images of organic-rich source rocks. I quantified the effect of (a) volumetric concentration of kerogen, (b) kerogen conductivity, and (c) spatial connectivity of kerogen-water network on electrical resistivity of rocks using pore-scale numerical simulations. \n\nWell-log interpretation of the Haynesville shale-gas formation showed conventional resistivity-porosity-saturation models underestimate hydrocarbon saturation by 20% - 40% in the zones with high volumetric concentration of kerogen. In this thesis, I showed that the error in estimates of hydrocarbon saturation could be due to the impact of kerogen on electrical resistivity measurements. Pore-scale numerical simulations confirmed that conventional resistivity-porosity-saturation models could lead to 10% - 23% improvement in estimates of hydrocarbon saturation if the impact of conductive kerogen is taken into account. Results of this thesis act as the first step towards improving conventional resistivity-porosity-saturation models for estimation of fluid saturations in organic-rich source rocks.
Allosteric Effects of Mg2+ on the Gating of Ca2+-Activated K+ Channels From Mammalian Skeletal Muscle (1986)

Ca2+-activated K+ channels from rat muscle transverse tubule membranes were inserted into planar phospholipid bilayers, and the activation of these channels by Ca2+ was studied. On the cytoplasmic side of the channel, calcium ions (in the range 10-100 mumol l-1) increase the opening probability of the channel in a graded way. This 'activation curve' is sigmoid, with an average Hill coefficient of about 2. Magnesium ions, in the range 1-10 mmol l-1, increase the apparent affinity of the channel for Ca2+ and greatly enhance the sigmoidicity of the Ca2+ activation curve. In the presence of 10 mmol l-1 Mg2+, the Hill coefficient for Ca2+ activation is about 4.5. This effect depends upon Mg2+ concentration but not upon applied voltage. Mg2+ is effective only when added to the cytoplasmic side of the channel. The results argue that this high-conductance, Ca2+-activated K+ channel contains at least six Ca2+-binding sites involved in the activation process.
Fundamentals of neurogastroenterology (1999)

Current concepts and basic principles of neurogastroenterology in relation to functional gastrointestinal disorders are reviewed. Neurogastroenterology is emphasized as a new and advancing subspecialty of clinical gastroenterology and digestive science. As such, it embraces the investigative sciences dealing with functions, malfunctions, and malformations in the brain and spinal cord, and the sympathetic, parasympathetic and enteric divisions of the autonomic innervation of the digestive tract. Somatomotor systems are included insofar as pharyngeal phases of swallowing and pelvic floor involvement in defecation, continence, and pelvic pain are concerned. Inclusion of basic physiology of smooth muscle, mucosal epithelium, and the enteric immune system in the neurogastroenterologic domain relates to requirements for compatibility with neural control mechanisms. Psychologic and psychiatric relations to functional gastrointestinal disorders are included because they are significant components of neurogastroenterology, especially in relation to projections of discomfort and pain to the digestive tract.
Outer membrane of gram-negative bacteria. XII. Molecular-sieving function of cell wall (1976)

The permeability function the cell wall of gram-negative bacteria such as Salmoenlla was investigated by producing cells with an expanded periplasmic volume, and incubating them with radioactive non-utilizable oligo- and polysaccharides or polyethylene glycols. To quantitative the extent of penetration of these hydrophilic compounds into the periplasm, the radioactivity of the cell pellet was determined after centrifugation. We found that only di- and trisaccharides could fully diffuse into the periplasm, whereas higher-molecular-weight saccharides were nonpenetrable. In addition, low-molecular-weight polyethylene glycols rapidly diffused across the cell wall. Kinetics experiments also showed that both sucrose and raffinose in the periplasm exchanged rapidly with sugars in the medium, even at 0 degrees C. These results suggest that the cell wall acts as a molecular sieve, with an exclusion limit near 550 to 650 daltons for saccharides. We also suggest that the diffusion of these hydrophilic compounds most likely occurs through water-filled pores present in the cell wall of gram-negative bacteria.
Taura syndrome in Penaeus vannamei:demonstration of a viral etiology (1995)

Taura syndrome (TS) was hypothesized to be caused by a virus and proven experimentally by meeting the criteria of Rivers' postulates. This was accomplished through 3 serial infectivity studies utilizing specific-pathogen-free Penaeus vannamei as the host for the TS virus (TSV). Test animals were infected via intramuscular injection with either a crude or cell-free suspension of the virus. The source of the crude homogenate was TSV-infected Ecuadorian P. vannarnel, which were collected during August 1993. Both types of viral inocula caused cumulative mortalities of 73 to 87'.';, among treatment groups. Diagnosis of TS was based on histological analysis of moribund shrimp collected during each experiment. All moribund shrimp, collected between 1 to 3 d post-injection, demonstrated moderate to severe pathognomonic TS les~ons. Both gross external and histological lesions, characteristic of chronic phase TS, were observed In 25 to 100"t, of all survivors. Virions with a buoyant density of approximately 1.337 g m1 ', lcosahedral morphology, and a diameter of 31 to 32 nm, characteristics which suggest that TSV is a member of either the Picornaviridae or Nodaviridae, were recovered from the dead shrimp collected during each of the 3 infectivity studies. Comparisons of TSV samples isolated from naturally infected P. vannamei from Hawaii (USA) and Ecuador indicate that the same virus was responsible for the TS epizootics in both of these shrimp growing regions.
Assessment of Her-1, Her-2, and Her-3 Expression and Her-2 Amplification in Advanced Stage Ovarian Carcinoma (2005)

The human epidermal growth factor receptor (Her) family of receptor tyrosine kinases includes Her-1, Her-2, and Her-3. The overexpression of Her-1 and Her-2 have been reported previously in surface epithelial ovarian cancer. Although up to one-third of ovarian carcinomas have been found to have amplification or overexpression of Her-2, responses to trastuzumab therapy in these patients have been disappointing. In this study, we examined Her-1, Her-2, and Her- 3 protein expression as well as the frequency of Her-2 amplification in a series of 103 high-grade, advanced-stage (FIGO stage III or IV) ovarian surface epithelial carcinomas. Immunohistochemical staining using commercially available antibodies against Her-1-3 and fluorescence in situ hybridization (FISH) using probes against Her-2 and chromosome 17 centromere (CEP) were performed on a tissue microarray containing cores of tumor from 103 surface epithelial carcinomas (85 serous, 6 mixed surface epithelial, 5 clear cell, 3 endometrioid, 3 undifferentiated, 1 mucinous). Nine of 99 (9.1%) tumors were positive for Her-1 expression and 5 of 102 (4.9%) tumors were positive for Her-2 expression, with 1 showing strong immunoreactivity. None of the Her-1 positive tumors exhibited Her-2 immunoreactivity. There was no correlation between Her-1 or Her-2 expression and survival. Using Her-2:centromere fluorescence ratios of 2.0 or 1.5 as cutoffs in assessment of Her-2 amplification, 8 of 75 (10.7%) and 25 of 75 (33.3%) tumors, respectively, showed Her-2 amplification. Two of eight tumors that showed higher level (>2) Her-2 amplification by FISH also were positive for Her-2 by immunohistochemistry. Only 3 of 103 tumors expressed Her-3. Immunoreactivity for Her-1 and Her-2 was less frequently observed in this series than has been previously reported. The strong correlation between Her-2 immunostaining and amplification characteristic of breast carcinoma is not seen in ovarian carcinoma. These results indicated that few patients with ovarian carcinoma have tumors that would benefit from therapy targeted specifically against Her-1, Her-2, or Her-3.
Dynamic DNA methylation change in the CpG island region of p15 during human myeloid development (2001)

We examined the kenetics of p15 methylation and expression during myeloid development. We treated human cord blood CD34+ cells with either GM-CSF alone or in combination with stem cell factor and followed methylation at this locus using bisulfite genomic sequencing. CD34+ cells were found to be either fully methylated or completely unmethylated at 27 CpG dinucleotide sites in exon 1 and at 18 CpG sites in the promoter region of the p15 gene. A time-course study showed that the percentage of the allelic methylation of p15 CpG island increased to approximately 50% to 60% until 7 days after cytokine stimulation, then decreased to less than 10% after 21 days. The methylation was also observed in bone marrow CD34+ cells exposed to GM-CSF. p15 expression varied inversely with methylation. Expression was negligible or at low levels until 14 days, after which it increased substantially. The frequency of myeloid colony-forming cells in the progeny decreased and myeloid-specific markers increased in the later stages. Based on our observations on cells grown with GM-CSF and 5-aza-2′-deoxycytidine, DNA methylation of the p15 promoter region CpG island appears to be associated with proliferation rather than differentiation of normal human myeloid progenitors.
Human Papillomavirus Type 16 L1 Capsomeres Induce L1-Specific Cytotoxic T Lymphocytes and Tumor Regression in C57BL/6 Mice (2003)

We analyzed capsomeres of human papillomavirus type 16 (HPV16) consisting of the L1 major structural protein for their ability to trigger a cytotoxic T-cell (CTL) response. To this end, we immunized C57BL/6 mice and used the L1(165-173) peptide for ex vivo restimulation of splenocytes prior to analysis ((51)Cr release assay and enzyme-linked immunospot assay [ELISPOT]). This peptide was identified in this study as a D(b)-restricted naturally processed CTL epitope by HPV16 L1 sequence analysis, major histocompatibility complex class I binding, and (51)Cr release assays following immunization of C57BL/6 mice with HPV16 L1 virus-like particles (VLPs). HPV16 L1 capsomeres were obtained by purification of HPV16 L1 lacking 10 N-terminal amino acids after expression in Escherichia coli as a glutathione S-transferase fusion protein (GST-HPV16 L1 Delta N10). Sedimentation analysis revealed that the majority of the purified protein consisted of pentameric capsomeres, and assembled particles were not observed in minor contaminating higher-molecular-weight material. Subcutaneous (s.c.) as well as intranasal immunization of C57BL/6 mice with HPV16 L1 capsomeres triggered an L1-specific CTL response in a dose-dependent manner as measured by ELISPOT and (51)Cr release assay. Significant reduction of contaminating bacterial endotoxin (lipopolysaccharide) from the capsomere preparation did not diminish the immunogenicity. Antibody responses (serum and vaginal) were less robust under the experimental conditions employed. In addition, s.c. vaccination with HPV16 L1 capsomeres induced regression of established tumors expressing L1 determinants (C3 tumor cells). Our data demonstrate that capsomeres are potent inducers of CTL responses similar to completely assembled T=7 VLPs. This result is of potential relevance for the development of (combined prophylactic and therapeutic) HPV-specific vaccines, since capsomeres can be produced easily and also can be modified to incorporate heterologous sequences such as early HPV proteins.
Therapy for Recurrent Respiratory Papillomatosis (2002)

Human papillomaviruses types 6 or 11 are aetiological agents of recurrent respiratory papillomatosis, a disease characterized by benign exophytic tumours usually on the vocal cords. Surgery debulks the tumours, but these growths generally recur at regular intervals. Adjunct medical treatments, aimed at containing the virus and growth of tumours, include indole-3-carbinol or its dimer diindolylmethane, interferon, photodynamic therapy and others. Preventive and therapeutic vaccines hold promise for eliminating the virus.
Development and function of bombesin-like peptides and their receptors (2005)

Amphibian bombesin and its related peptides consist a family of neuropeptides in many vertebrate species. Bombesin and two major bombesin-like peptide in mammals, gastrin-releasing peptide (GRP) and neuromedin B (NMB), have been shown to elicit various physiological effects. These include inhibition of feeding, smooth muscle contraction, exocrine and endocrine secretions, thermoregulation, blood pressure and sucrose regulations and cell growth. Receptors for GRP and NMB (GRP-R and NMB-R), as well as third subtype of bombesin-like peptide receptor (BRS-3) have been cloned. These receptors are G-protein-coupled receptors and are expressed in various brain regions and in the digestive tract. In this paper, we will summarize studies on these peptides and their receptors, with special reference to research using gene-knockout mice. These studies clearly demonstrated the role of three receptors in vivo and in vitro. We will also discuss the phylogeny of these receptors.
Marker antibody expression stratifies Crohn's disease into immunologically homogeneous subgroups with distinct clinical characteristics (2000)

The findings suggest that by taking into account the magnitude of the host immune response, Crohn's disease can now be stratified on an immunological basis into more homogeneous clinically distinct subgroups, characterised by greater uniformity among anatomical distribution of disease and disease behaviour.
Biologic properties of molecularly cloned and expressed murine interleukin-3 (1985)

Interleukin-3 (IL-3) (multipotential colony-stimulating factor [multi-CSF] ) is an important regulator of hemopoiesis. We recently isolated a cDNA clone of this gene and describe in this manuscript the biologic properties of the expressed gene product. An SV40 expression vector carrying cDNA encoding murine interleukin-3 was constructed so that expression of the IL-3 gene was placed under the control of the SV40 early promoter. When the expression vector was transfected to COS-1 monkey cells, IL-3 activity was secreted into the medium, reaching maximal levels 72 hours after transfection. The IL-3 produced by the COS-1 cells was partially purified using diethylaminoethyl Sephacel and phenyl-Sepharose, and its chromatographic properties were the same as IL-3 produced by the WEHI-3 cell line. The biologic activities of the "expressed" IL-3 include the "induction" of 20-alpha-hydroxysteroid dehydrogenase (20-alpha-SDH) in splenic lymphocytes from nu/nu mice, proliferative activity for 32D cl-23 and FDC-P1 cell lines, and colony-stimulating activity for granulocyte-macrophage, eosinophil, megakaryocyte, natural killer-like, erythroid, and multipotential colony-forming cells from murine fetal liver and adult bone marrow.
Investigation of cellulose convertibility and ethanolic fermentation of sugarcane bagasse pretreated by wet oxidation and steam explosion (2006)

Abstract Sugarcane bagasse was pretreated by wet oxidation (WO) at 195 °C for 15 min under either alkaline, neutral or acidic conditions, and by steam explosion (STEX) at 205 °C for 10 min. Alkaline WO was more favourable than neutral and acidic WO for the following enzymatic hydrolysis of cellulose, giving 792 g kg −1 glucose yield after 48 h. The enzymatic hydrolysis of the fibres in the whole slurry was inhibited by inhibitory compounds contained in the prehydrolysate in comparison with the hydrolysis of the washed solid fibres in buffer. The inhibition increased proportionally with formic acid concentration in the pretreated liquid fraction. Cellulose conversion was higher for simultaneous saccharification and fermentation (SSF) than for separate hydrolysis. The highest SSF conversion (829 g kg −1 ) was obtained for the material treated by alkaline WO. The fermentability of the prehydrolysates by Saccharomyces cerevisiae was evaluated. Stronger inhibition of ethanolic fermentation was observed in the prehydrolysate obtained by steam explosion. The inhibition was more noticeable for the volumetric productivity than for the ethanol yield. The volumetric productivity was reduced by 94.5 and 91.2% for STEX and WO, respectively, whereas the ethanol yield was reduced only by 45.2 and 31.0%, correspondingly, for STEX and WO. Furan aldehydes seemed to be mainly responsible for the inhibition of the fermentation. Copyright © 2006 Society of Chemical Industry
Mechanism of deuterium addition and exchange of propene over silica-supported gold and silver catalysts (1988)

The mechanism of the C3H6–D2 reaction over silica-supported Au and Ag catalysts has been studied by applying microwave spectroscopy as well as kinetic measurements. A large kinetic isotope effect was observed for the rate of propane formation between the C3H6–H2 and C3H6–D2 reactions, indicating that hydrogen dissociation is the rate-determining step. Both deuterium addition and exchange processes proceeded via an associative mechanism involving n-propyl as well as s-propyl species, although the methyl hydrogen of propene was less active for exchange through this process. In addition, intramolecular 1,3- and 2,3-hydrogen-shift processes were observed for the first time; they proceeded only in the presence of gaseous hydrogen and caused the exchange of the methyl hydrogen of propene. The characteristic features of supported Group IB metals in this reaction are compared with those of Group VIII metals, and the possible structures of reaction intermediates are discussed in detail.
Is Your Cloud-Hosted Database Truly Elastic? (2013)

Elasticity has been recognized as one of the most appealing features for users of cloud services. It represents the ability to dynamically and rapidly scale up or down the allocated computing resources on demand. In practice, it is difficult to understand the elasticity requirements of a given application and workload, and to assess if the elasticity provided by a cloud service will meet these requirements. In this experience paper, we take the position that a deep understanding of the capabilities of cloud-hosted database services is a crucial requirement for cloud users in order to bring forward the vision of deploying data-intensive applications on cloud platforms. We argue that it is important that cloud users become able to paint a comprehensive picture of the relationship between the capabilities of the different type of cloud database services, the application characteristics and workloads, and the geographical distribution of the application clients and the underlying database replicas. We discuss the current elasticity capabilities of the different categories of cloud database services and identify some of the main challenges for deploying a truly elastic database tier on cloud environments. Finally, we propose a benchmarking mechanism that can evaluate the elasticity capabilities of cloud database services in different application scenarios and workloads.
Visualization of elongation factor G on the Escherichia coli 70S ribosome: The mechanism of translocation (1998)

During protein synthesis, elongation factor G (EF-G) binds to the ribosome and promotes the step of translocation, a process in which tRNA moves from the A to the P site of the ribosome and the mRNA is advanced by one codon. By using three-dimensional cryo-electron microscopy, we have visualized EF-G in a ribosome-EF-G-GDP-fusidic acid complex. Fitting the crystal structure of EF-G-GDP into the cryo density map reveals a large conformational change mainly associated with domain IV, the domain that mimics the shape of the anticodon arm of the tRNA in the structurally homologous ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, whose position in the ribosome is known from a study of the pretranslocational complex, implying that EF-G displaces the A-site tRNA to the P site by physical interaction with the anticodon arm.
Interaction of trans-diamminedichloroplatinum(II) with DNA: formation of monofunctional adducts and their reaction with glutathione (1987)

Bifunctional reactions with DNA are responsible for the toxic action of the cancer chemotherapeutic drug cis-diamminedichloroplatinum(II) (cis-DDP). Thiourea has previously been used to trap transient monofunctional adducts in DNA before they rearrange to the toxic lesions. In these studies, thiourea was used to quantify the monofunctional adducts produced by the ineffective isomer trans-DDP. Rather than trapping monofunctional adducts, thiourea labilized them from DNA. At short time periods, 85% of trans-DDP bound to double-stranded DNA as monofunctional adducts of deoxyguanosine. Rearrangement to bifunctional adducts in double-stranded DNA was 50% complete in 24 h but was much more rapid in single-stranded DNA with 100% complete rearrangement in 24 h. The ineffectiveness of trans-DDP therefore results from a high proportion of monofunctional adducts in DNA that rearrange very slowly to toxic bifunctional adducts. The persistent monofunctional adducts react rapidly with glutathione, which would further reduce their potential toxicity by preventing them from rearranging to more toxic bifunctional adducts.
Abstract: Energy dissipation in catalysis (1974)

The dissipation of the reaction energy and its possible consequences in catalysis on supported metal crystallites are considered. The modes and times required for energy dissipation can influence reaction rates by processes involving excited intermediate molecules at the surface and by producing locally high catalyst temperatures. The boundary resistance at the metal-crystallite-insulator-support interface is shown to play a significant role in determining the temperature-time behavior of a catalyst crystallite. Calculations indicate that crystallite temperatures may be several hundred degrees higher than that of the substrate. A distinct size effect is also predicted with small crystallites attaining much higher temperatures than large ones. The latter may be important in determining the stability of catalysts toward sintering.