gebhart/patrepeval huggingface dataset:
Artificial Intelligent Logs for Formation Evaluation Using Case Studies in Gulf of Mexico and Trinidad & Tobago (2019)

Abstract Borehole-log data acquisition accounts for a significant proportion of exploration, appraisal and field development costs. As part of Shell technical competitive scoping, there is an ambition to increase formation evaluation value of information by leveraging drilling and mudlogging data, which traditionally often used in petrophysical or reservoir modelling workflow. Often data acquisition and formation evaluation for the shallow hole sections (or overburden) are incomplete. Logging-while-drilling (LWD) and/or wireline log data coverage is restricted to mostly GR, RES and mud log information and the quality of the logs varied depending on the vendor companies or year of the acquisition. In addition, reservoir characterization logs typically covered only the final few thousand feet of the wellbore thus preventing a full quantitative petrophysical, geomechanical, geological correlation and geophysical modelling, which caused limited understanding of overburden sections in the drilled locations and geohazards risls assessment. Use of neural networks (NN) to predict logs is a well-known in Petrophysic discipline and has often used technology since more than last 10 years. However, the NN model seldon utilized the drilling and mudlogging data (due to lack of calibration and inconsistency) and up until now the industry usually used to predict a synthetic log or fill gaps in a log. With the collaboration between Shell and Quantico, the project team develops a plug-in based on a novel artificial intelligence (AI) logs workflow using neural-network to generate synthetic/AI logs from offset wells logs data, drilling and mudlogging data. The AI logs workflow is trialled in Shell Trinidad &amp; Tobago and Gulf of Mexicooffshore fields. The results of this study indicate the neural network model provides data comparable to that from conventional logging tools over the study area. When comparing the resulting synthetic logs with measured logs, the range of variance is within the expected variance of repeat runs of a conventional logging tool. Cross plots of synthetic versus measured logs indicate a high density of points centralized about the one-to-one line, indicating a robust model with no systematic biases. The QLog approach provides several potential benefits. These include a common framework for producing DTC, DTS, NEU and RHOB logs in one pass from a standard set of drilling, LWD and survey parameters. Since this framework ties together drilling, formation evaluation and geophysical data, the artificial intelligence enhances and possibly enables other petrophysical/QI/rock property analysis that including seismic inversion, high resolution logs, log QC/editing, real-time LWD, drilling optimization and others.
Immunologic self-tolerance maintained by CD25+CD4+ naturally anergic and suppressive T cells: induction of autoimmune disease by breaking their anergic/suppressive state. (1998)

Elimination of CD25+ T cells, which constitute 5-10% of peripheral CD4+ T cells in normal naive mice, leads to spontaneous development of various autoimmune diseases. These immunoregulatory CD25+CD4+ T cells are naturally unresponsive (anergic) in vitro to TCR stimulation, and, upon stimulation, suppress proliferation of CD25-CD4+ T cells and CD8+ T cells. The antigen concentration required for stimulating CD25+CD4+ T cells to exert suppression is much lower than that required for stimulating CD25-CD4+ T cells to proliferate. The suppression, which results in reduced IL-2 production by CD25-CD4+ T cells, is dependent on cellular interactions on antigen-presenting cells (and not mediated by far-reaching or long-lasting humoral factors or apoptosis-inducing signals) and antigen non-specific in its effector phase. Addition of high doses of IL-2 or anti-CD28 antibody to the in vitro T cell stimulation culture not only breaks the anergic state of CD25+CD4+ T cells, but also abrogates their suppressive activity simultaneously. Importantly, the anergic/suppressive state of CD25+CD4+ T cells appeared to be their basal default condition, since removal of IL-2 or anti-CD28 antibody from the culture milieu allows them to revert to the original anergic/suppressive state. Furthermore, transfer of such anergy/suppression-broken T cells from normal mice produces various autoimmune diseases in syngeneic athymic nude mice. These results taken together indicate that one aspect of immunologic self-tolerance is maintained by this unique CD25+CD4+ naturally anergic/suppressive T cell population and its functional abnormality directly leads to the development of autoimmune disease.
Dendritic cells and immunity against cancer (2010)

T cells can reject established tumours when adoptively transferred into patients, thereby demonstrating the power of the immune system for cancer therapy. However, it has proven difficult to maintain adoptively transferred T cells in the long term. Vaccines have the potential to induce tumour-specific effector and memory T cells. However, clinical efficacy of current vaccines is limited, possibly because tumours skew the immune system by means of myeloid-derived suppressor cells, inflammatory type 2 T cells and regulatory T cells (Tregs), all of which prevent the generation of effector cells. To improve the clinical efficacy of cancer vaccines in patients with metastatic disease, we need to design novel and improved strategies that can boost adaptive immunity to cancer, help overcome Tregs and allow the breakdown of the immunosuppressive tumour microenvironment. This can be achieved by exploiting the fast increasing knowledge about the dendritic cell (DC) system, including the existence of distinct DC subsets that respond differentially to distinct activation signals, (functional plasticity), both contributing to the generation of unique adaptive immune responses. We foresee that these novel cancer vaccines will be used as monotherapy in patients with resected disease and in combination with drugs targeting regulatory/suppressor pathways in patients with metastatic disease.
Use of in vitro protein synthesis from polymerase chain reaction-generated templates to study interaction of Escherichia coli transcription factors with core RNA polymerase and for epitope mapping of monoclonal antibodies (1991)

The interaction of two Escherichia coli transcription factors (sigma 54 and sigma 32) with the core RNA polymerase was studied here. We examined the core binding ability of various fragments of these two transcription factors using a novel method for the in vitro synthesis of truncated proteins in a coupled transcription-translation (S-30) system. The method uses DNA templates generated by the polymerase chain reaction to direct synthesis of precisely truncated fragments of the encoded protein. Primers for the polymerase chain reaction contain transcription and translation signals so that the resulting product can be incubated in the S-30 directly. The synthesized proteins were used for mapping of both functional domains and epitopes of monoclonal antibodies to sigma 54 and sigma 32.
Rearrangements of chromosome 3 involving bands 3q21 and 3q26 are associated with normal or elevated platelet counts in acute nonlymphocytic leukemia (1985)

Fourteen patients with acute nonlymphocytic leukemia (ANLL) or dysmyelopoietic syndromes were found to have abnormalities involving the long arm of chromosome 3. In eight patients, the structural rearrangements involved both bands 3q21 and 3q26 and included t(3;3) (four patients), inv(3) (three patients), and ins(5;3) (one patient). Before treatment, seven of these eight patients had platelet counts above 100,000 per microliter, five had normal or elevated platelet counts, and four had significantly elevated platelet counts (600,000 to 1,731,000 per microliter). In each of the eight cases, normal or elevated platelet counts were associated with marked abnormalities of megakaryocytopoiesis, including increased numbers of megakaryocytes and numerous micromegakaryocytes. Classification within the French-American-British system was difficult in most of these cases; however, the leukemia in five of the eight patients with abnormalities of chromosome 3 that involved both bands 3q21 and 3q26 was classified as M4. The remaining six of the 14 patients had translocations between chromosome 3 and another chromosome. None involved both bands 3q21 and 3q26, and a break in either q21 or q26 was noted in only two patients. One of the six, who had ANLL (M4) with a normal platelet count, had a 3;5 translocation which involved band 3q25. These data suggest that in patients with ANLL, abnormalities of chromosome 3 which simultaneously involve bands 3q21 and 3q26 are associated with unusually high platelet counts.
Sustainable approaches in agriculture – A review (2005)

Adverse effect of indiscriminate use of agrochemicals in agriculture is now being increasingly realized. It is the need of the hour to meet the challenges of our current and future food demand without deteriorating the environmental quality. A sustainable rather than intensive and exploitive approach to crop production is imperative to meet the unified objective of both food as well as environmental security. The potential role of integrated nutrient management and integrated pest management are well recognized to be the important contributing factors to economical viability in short run and environmental sustainability in long run and therefore they need to be given utmost priority in the crop production strategy for reorientation towards ecofriendly agriculture.
Automating curation using a natural language processing pipeline (2008)

The technologies being developed were shown to be readily adapted to the BioCreative II tasks. Although high performance may be obtained on individual tasks such as gene mention recognition and normalization, and document classification, tasks in which a number of components must be combined, such as detection and normalization of interacting protein pairs, are still challenging for NLP systems.
Epitopes on the S1 subunit of pertussis toxin recognized by monoclonal antibodies (1989)

To identify the neutralizing epitopes on the S1 subunit (A promoter) of pertussis toxin, we characterized anti-S1 monoclonal antibodies (MAbs) X2X5, 3CX4, and 6FX1. We confirmed by immunoblot analysis that these MAbs bind to the S1 subunit and not to the B oligomer of pertussis toxin and that they recognize different epitopes by a competitive binding enzyme-linked immunosorbent assay. These MAbs had differential abilities to neutralize the lymphocytosis-promoting factor activity of pertussis toxin in mice: 3CX4 and 6FX1 had partial neutralizing abilities, while MAb X2X5 had none. With these MAbs, the epitopes on the S1 subunit were examined by using trypsinized S1 peptides, recombinant truncated S1 molecules, and synthetic peptides. The non-neutralizing MAb X2X5 bound in immunoblots to tryptic peptides of various sizes as small as 1.5 kilodaltons; the neutralizing MAbs 3CX4 and 6FX1 bound only to a 24-kilodalton tryptic peptide band. Immunoblot studies with recombinant truncated S1 molecules demonstrated that amino acid residues 7 to 14 and 15 to 26 play an important role in the binding of neutralizing MAbs and the non-neutralizing MAb, respectively. The binding of these MAbs was not dependent upon the presence of C-terminal amino acid residues 188 to 234. To further define B-cell epitopes, the binding of the MAbs we tested to synthetic peptides representing the entire S1 subunit were examined. Neutralizing MAbs 3CX4 and 6FX1 bound to none of these peptides, further suggesting that these MAbs recognize conformational epitopes. The non-neutralizing MAb X2X5 bound to peptides 11 to 26 and 16 to 30, demonstrating that the major antigenic determinant recognized by this MAb is a linear epitope located within residues 16 to 26.
Evaluation of the autoSCAN-W/A rapid system for identification and susceptibility testing of gram-negative fermentative bacilli (1992)

The autoSCAN-Walk-Away (W/A) system for identification and susceptibility testing was evaluated for 400 gram-negative fermentative bacteria by using the API 20E (366 isolates) and/or tube biochemical tests as the reference identification system and a frozen microdilution MIC tray system for susceptibility testing. The W/A system performed well for identification of this group of organisms representing 14 genera and 30 species, showing a sensitivity of 96% and results available in 2 h. Of the 16 misidentifications, 6 were with Serratia liquefaciens. A total of 63 isolates (17%) required further tests to complete the identification, compared with 106 (29%) of the isolates which required additional tests for the API 20E identification. Approximately half (32) of the additional tests with the W/A system were required in order to separate Citrobacter diversus from C. amalonaticus. For susceptibility determinations, the W/A system demonstrated an overall agreement of 93% (4,102 determinations) with 40 major errors (0.98%). However, of the 906 resistant organism-drug combinations in the study, there were 115 very major errors, for a false-susceptibility rate of 12.7% of the resistance determinations. Among these very major errors, 80% occurred with piperacillin and the cephalosporins. The W/A system completed the MIC determinations in 7 h; however, the difficulty in detecting resistance with some antimicrobial agents limited the advantages of the rapid susceptibility testing.
The design and engineering of nucleic acid nanoscale assemblies (1996)

It is possible to design DNA molecules that can form unusual structures and topologies. Stable DNA-branched junctions have been used to construct polyhedral catenated molecules with the connectivities of a cube and of a truncated octahedron. The truncated octahedron has been constructed following a solid-support-based methodology. Branched-DNA molecules are flexible, suggesting that triangular and deltahedral DNA objects should be favored as the components of two- and three-dimensional nucleic acid arrays. DNA polyhedra are complex catenanes. The engineering of single-stranded DNA knots and catenanes exploits the fact that a node can be equated with a half-turn of DNA.
Behavioral Studies of Hallucinogenic Drugs in Animals: Implications for Schizophrenia Research (1998)

Schizophrenic and schizotypal patients exhibit deficits in the habituation and prepulse inhibition (PPI) of startle responses, providing operational measures of the sensorimotor gating or filtering deficits suggested to contribute to cognitive disorganization in these patients. In rats, hallucinogens, entactogens, and NMDA antagonists share the ability to both retard startle habituation and disrupt PPI. Extensive pharmacological studies in rats have indicated that the effects of hallucinogens on habituation are mediated by direct agonist actions at 5-HT2 receptors. The effects of the entactogens on both habituation and PPI reflect indirect agonist actions due to the stimulation of presynaptic serotonin release. These observations in rats have supported the development of 5-HT2A antagonists for the treatment of schizophrenia. Animal studies have shown that PPI is modulated by multiple interacting neurotransmitters, including dopaminergic, serotonergic, cholinergic, GABAergic, and glutamatergic systems within cortical, limbic, striatal, and brainstem structures. The effects of PCP and other NMDA antagonists on PPI are insensitive to either dopaminergic or serotonergic antagonists, but are reduced by atypical antipsychotics such as clozapine, olanzapine, and Seroquel. Thus, the PCP model of schizophrenia-like deficits in sensorimotor gating offers promise for the identification and neurobiological investigation of atypical antipsychotics. The cross-species study of homologous gating functions, such as habituation and PPI, in animal models and psychiatric patients provides novel opportunities for the exploration of neurobiological substrates relevant to the group of schizophrenias.
Interaction of dietary fat saturation and cholesterol level on cholesterol synthesis measured using deuterium incorporation. (1994)

To examine interactive effects of dietary fat saturation and cholesterol level on serum lipids and de novo cholesterogenesis, moderately hypercholesterolemic subjects were fed solid-foods diets containing 30% fat (80 mg C.1000 Kcal-1) in which 2/3 fat was either corn oil or beef tallow, with and without 120 mg C.1000 Kcal-1, for 5 wk. At the end of each diet period, subjects were given deuterium (D) oxide orally and de novo cholesterol synthesis was measured over 24 h from D incorporation into cholesterol as fractional synthesis rates (FSR) and absolute synthetic rate (ASR) into the rapid exchangeable cholesterol pool. Plasma total and low density lipoprotein levels were elevated (P < 0.01) with both beef tallow and cholesterol feeding. High density lipoprotein (HDL) levels were not influenced by fat saturation or cholesterol level; however, HDL was higher with addition of cholesterol to corn oil versus beef tallow (P < 0.02). Plasma triglycerides were higher (P < 0.02) with beef tallow feeding but were not influenced by cholesterol level. FSR was increased (P < 0.02) by feeding corn oil, versus beef fat, but not by dietary cholesterol level. Calculated cholesterol pools sizes did not differ across groups; however, ASR was also elevated with corn oil versus beef tallow feeding (P < 0.02). Results indicate that corn oil feeding lowers circulating cholesterol by mechanisms other than reduced synthesis, and that cholesterol at the level of supplementation used is not associated with feedback inhibition of cholesterogenesis. However, with the exception of HDL levels, dietary fat saturation and cholesterol levels do not interactively influence circulating lipoprotein cholesterol levels and cholesterol synthesis.
Transition States of Strain-Promoted Metal-Free Click Chemistry:  1,3-Dipolar Cycloadditions of Phenyl Azide and Cyclooctynes (2008)

Density functional theory (B3LYP) calculations on the transition states for the Huisgen 1,3-dipolar cycloadditions of phenyl azide with acetylene, cyclooctyne, and difluorocyclooctyne are reported. The low activation energy of the cyclooctyne "strain-promoted" cycloaddition (DeltaE = 8.0) compared to the strain-free acetylene cycloaddition (DeltaE = 16.2) is due to decreased distortion energy (DeltaEd) of cyclooctyne (DeltaDeltaEd = 4.6) and phenyl azide (DeltaDeltaEd = 4.5) to achieve that cycloaddition transition state. Electronegative fluorine substituents on cyclooctyne further increase the rate of cycloaddition by increasing interaction energies.
Taxonomic Study of Bacteria Isolated from Plants: Proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov. (1995)

The taxonomic positions of 10 strains of 3-ketolactose-forming bacteria which were isolated from the roots of plants (Rosa sp., Psychotria nairobiensis, Ardisia crispa, Prunus persica, and apple trees) were investigated. The DNA base compositions of these strains ranged from 64.0 to 65.7 mol%, the isoprenoid quinone of each strain was ubiquinone 10, 3-hydroxy fatty acids were lacking in the cellular fatty acids of these organisms, and all of the strains contained a sphingolipid with the long-chain base dihydrosphingosin. These are characteristics of the genus Sphingomonas. On the basis of morphological, physiological, and chemotaxonomic characteristics, together with DNA-DNA hybridization and 16S ribosomal DNA sequence comparison data, we propose the following four new species of the genus Sphingomonas: Sphingomonas rosa (type strain, IFO 15208) for the strains isolated from rose plants and formerly named [Agrobacterium rhizogenes]; Sphingomonas pruni (type strain, IFO 15498) for the strains isolated from Prunus persica; and Sphingomonas asaccharolytica (type strain, IFO 15499) and Sphingomonas mali (type strain, IFO 15500) for the strains isolated from apple trees. Two strains which were isolated from Psychotria nairobiensis and formerly named [Chromobacterium lividum] were identified as Sphingomonas yanoikuyae strains.
The Incidence and Management of Infusion Reactions To Infliximab: A Large Center Experience (2003)

Infliximab infusions were accompanied by acute reactions in approximately 5% of infusions. These reactions did not seem to be true IgE-mediated type I hypersensitivity events. Using appropriate treatment protocols, these reactions were effectively treated and prevented upon retreatment in nearly all patients. Delayed reactions were rare, occurring in <1% of infusions.
Das Mülheimer Normaldruck‐Polyäthylen‐Verfahren (1955)

Abstract Es wird dargelegt, wie man überhaupt im Mülheimer Institut zur Entdeckung des „Normaldruck‐Polyäthylen‐Verfahrens”︁ gekommen ist, denn diese Entdeckungsgeschichte ist für sich schon interessant und verdient es, festgehalten zu werden. Es werden weiter eine Reihe grundsätzlicher Angaben über das neue Verfahren und das neue Polyäthylen gemacht. Doch müssen eine Reihe wichtiger Probleme, die bei der technischen Herstellung des Mülheimer Polyäthylens eine Rolle spielen, unbehandelt bleiben. Dazu gehören u. a. die Fragen nach dem Wesen der Katalysatoren und ihrer Wirkungsweise. Auch entwicklungstechnische Einzelheiten zur Verarbeitung des neuen Kunststoffes werden nicht gebracht, weil diese Entwicklung in der Hand der Lizenznehmerfirmen liegt.
A hierarchical multiple classifier learning algorithm (2002)

We describe a hierarchical multiple classifier learning algorithm that was developed to provide a tool for classifier construction in medical applications. The mechanism uses data clustering and sub-class labeling to reduce the overhead of training and enhance the classification accuracy. The results of using this method are compared to a hand-built classifier and to other multiple classifier algorithms.
Megakaryocyte-targeted synthesis of the integrin β3-subunit results in the phenotypic correction of Glanzmann thrombasthenia (2000)

Glanzmann thrombasthenia is an inherited bleeding disorder characterized by qualitative or quantitative defects of the platelet-specific integrin, IIbβ3. As a result, IIbβ3 cannot be activated and cannot bind to fibrinogen, leading to a loss of platelet aggregation. Thrombasthenia is clinically characterized by mucocutaneous hemorrhage with episodes of intracranial and gastrointestinal bleeding. To develop methods for gene therapy of Glanzmann thrombasthenia, a murine leukemia virus (MuLV)-derived vector, −889PlA2β3, was transduced into peripheral blood CD34+ cells from 2 patients with thrombasthenia with defects in the β3 gene. The human IIb promoter was used in this vector to drive megakaryocyte-targeted expression of the wild-type β3 subunit. Proviral DNA and IIbβ3 biosynthesis were detected after in vitro differentiation of transduced thrombasthenic CD34+ cells with megakaryocyte growth and development factor. Flow cytometric analysis of transduced patient samples indicated that 19% of megakaryocyte progeny expressed IIbβ3 on the surface at 34% of normal receptor levels. Treatment of transduced megakaryocytes with a combination of agonists including epinephrine and the thrombin receptor-activating peptide induced the IIbβ3 complex to form an activated conformation capable of binding fibrinogen as measured by PAC-1 antibody binding. Transduced cells retracted a fibrin clot in vitro similar to megakaryocytes derived from a normal nonthrombasthenic individual. These results demonstrate ex vivo phenotypic correction of Glanzmann thrombasthenia and support the potential use of hematopoietic CD34+ cells as targets for IIb promoter-driven MuLV vectors for gene therapy of platelet disorders.