gebhart/patrepeval huggingface dataset:
Improved Assessment Of In-Situ Fluid Saturation With Multi-Dimensional Nmr Measurements And Conventional Well Logs (2012)

ABSTRACT Nuclear magnetic resonance (NMR) is widely used to assess petrophysical and fluid properties of porous rocks. In the case of fluid typing, two-dimensional (2D) NMR interpretation techniques have advantages over conventional one-dimensional (1D) interpretation as they provide additional discriminatory information about saturating fluids. However, often there is ambiguity as to whether fluids appraised with NMR measurements are mobile or residual. In some instances, high vertical heterogeneity of rock properties (e.g. across thinlybedded formations) can make it difficult to separate NMR fluid signatures from those due to pore-size distributions and fluids. There are also cases where conventional fluid identification methods based on resistivity and nuclear logs indicate dominant presence of water while NMR measurements indicate presence of water, hydrocarbon, and mud filtrate.
Drug Screening for ALS Using Patient-Specific Induced Pluripotent Stem Cells (2012)

Amyotrophic lateral sclerosis (ALS) is a late-onset, fatal disorder in which the motor neurons degenerate. The discovery of new drugs for treating ALS has been hampered by a lack of access to motor neurons from ALS patients and appropriate disease models. We generate motor neurons from induced pluripotent stem cells (iPSCs) from familial ALS patients, who carry mutations in Tar DNA binding protein-43 (TDP-43). ALS patient-specific iPSC-derived motor neurons formed cytosolic aggregates similar to those seen in postmortem tissue from ALS patients and exhibited shorter neurites as seen in a zebrafish model of ALS. The ALS motor neurons were characterized by increased mutant TDP-43 protein in a detergent-insoluble form bound to a spliceosomal factor SNRPB2. Expression array analyses detected small increases in the expression of genes involved in RNA metabolism and decreases in the expression of genes encoding cytoskeletal proteins. We examined four chemical compounds and found that a histone acetyltransferase inhibitor called anacardic acid rescued the abnormal ALS motor neuron phenotype. These findings suggest that motor neurons generated from ALS patient-derived iPSCs may provide a useful tool for elucidating ALS disease pathogenesis and for screening drug candidates.
Screening for cancer of the aerodigestive tract (1993)

In the United States, cancer of the oral cavity is the only region of the aerodigestive tract that lends itself to routine screening of the asymptomatic population older than 50 years. Although the incidence and mortality rate for oral cancer is nearly double that of cancer of the cervix (30,300 versus 13,500 and 7950 versus 4400, respectively), conducting a pelvic examination and Pap smear appears more acceptable than looking in the mouth. The inspection of the oral cavity should be part of every physical examination in the dentist's or the physician's office, particularly in patients older than 50 years who are heavy users of tobacco and alcohol. Ninety percent of all squamous cell cancers arise from the floor of the mouth, the ventrolateral aspect of the tongue, and the soft palate complex. The detection rate is increased from approximately 1 per 1000 in asymptomatic individuals older than 50 years to 1 per 200 in high-risk smokers and drinkers and to 1 in 7 for individuals once treated for oral cancer. Screening detects earlier stage cancers, for which treatment results in higher survival rates. While no randomized screening trials with a mortality end-point have been conducted (or are likely), there is evidence that population-based case-fatality rates are lower in races treated with earlier stages of oral cancer. This evidence is of little solace when the majority of patients are diagnosed with advanced disease when symptoms appear, rather than through screening at an earlier stage when asymptomatic. In one study, 94% of patients with oral cancer were seen by a doctor within the previous year. The average oral cancer patient had 10.7 physician encounters within 3 years of the diagnosis. In the United States, the early detection of cancers of the larynx and esophagus should be based upon early symptoms rather than on screening. A routine oral screening examination should be a part of every physical examination by a doctor or a dentist. It will detect earlier cancers and save lives.
Hepatocyte Nuclear Factor 4 Provokes Expression of Epithelial Marker Genes, Acting As a Morphogen in Dedifferentiated Hepatoma Cells (1998)

We have recently shown that stable expression of an epitope-tagged cDNA of the hepatocyte- enriched transcription factor, hepatocyte nuclear factor (HNF)4, in dedifferentiated rat hepatoma H5 cells is sufficient to provoke reexpression of a set of hepatocyte marker genes. Here, we demonstrate that the effects of HNF4 expression extend to the reestablishment of differentiated epithelial cell morphology and simple epithelial polarity. The acquisition of epithelial morphology occurs in two steps. First, expression of HNF4 results in reexpression of cytokeratin proteins and partial reestablishment of E-cadherin production. Only the transfectants are competent to respond to the synthetic glucocorticoid dexamethasone, which induces the second step of morphogenesis, including formation of the junctional complex and expression of a polarized cell phenotype. Cell fusion experiments revealed that the transfectant cells, which show only partial restoration of E-cadherin expression, produce an extinguisher that is capable of acting in trans to downregulate the E-cadherin gene of well-differentiated hepatoma cells. Bypass of this repression by stable expression of E-cadherin in H5 cells is sufficient to establish some epithelial cell characteristics, implying that the morphogenic potential of HNF4 in hepatic cells acts via activation of the E-cadherin gene. Thus, HNF4 seems to integrate the genetic programs of liver-specific gene expression and epithelial morphogenesis.
Pancreas cancer and the role of soluble immunoglobulin-like transcript 3 (ILT3). (2007)

Attempts to ameliorate the poor prognosis of pancreatic cancer have been largely unsuccessful. Interventions to enhance patients' immune responses to malignancies have been also largely unsuccessful. We now describe an immune-escape mechanism mediated by the inhibitory receptor immunoglobulin-like transcript 3 (ILT3) which may be responsible for such failures. Using a humanized severe combined immunodeficiency (SCID) mouse model, we demonstrate that soluble and membrane ILT3 induce CD8+ T suppressor cells and prevent rejection of allogeneic tumor transplants. Furthermore, we found that patients with carcinoma of the pancreas produce the soluble ILT3 protein, which induces the differentiation of CD8+ T suppressor cells and impairs T cell responses in mixed lymphocyte culture. These responses are restored by anti-ILT3 mAb or by depletion of sILT3 from the serum. Immunohistochemical staining of biopsies from the tumors and metastatic lymph nodes suggest that CD68+ tumor associated macrophages represent the major source of soluble ILT3. Alternative splicing, resulting in the loss of the ILT3 transmembrane domain may contribute to the release of ILT3 in the circulation. These data suggest that ILT3 depletion or blockade is crucial to the success of immunobiotherapy, particularly in pancreatic cancer.
Infections withCryptococcus neoformansin the Acquired Immunodeficiency Syndrome (1989)

We reviewed the records of 106 patients with cryptococcal infections and the acquired immunodeficiency syndrome (AIDS) treated at San Francisco General Hospital. We examined four issues: the efficacy of treatment with amphotericin plus flucytosine as compared with amphotericin alone, the efficacy of suppressive therapy, the prognostic clinical characteristics, and the course of nonmeningeal cryptococcosis. In 48 of the 106 patients (45 percent), cryptococcosis was the first manifestation of AIDS. Among the 89 patients with cryptococcal meningitis confirmed by culture, survival did not differ significantly between those treated with amphotericin plus flucytosine (n = 49) and those treated with amphotericin alone (n = 40). Flucytosine had to be discontinued in over half the patients because of cytopenia. Long-term suppressive therapy with either ketoconazole or amphotericin was associated with improved survival, as compared with survival in the absence of suppressive therapy (median survival, greater than or equal to 238 vs. 141 days; P less than 0.004). The only clinical features independently associated with a shorter cumulative survival were hyponatremia and a positive culture for cryptococcus from an extrameningeal source. The 14 patients with nonmeningeal cryptococcosis had a median survival (187 days) and rate of relapse (20 percent) similar to those in the patients with meningitis (165 days and 17 percent, respectively). From this retrospective study of cryptococcal infections in patients with AIDS we conclude that the addition of flucytosine to amphotericin neither enhances survival nor prevents relapse, but long-term suppressive therapy appears to benefit these patients.
Changing the substrate specificity of a chitooligosaccharide oxidase from Fusarium graminearum by model‐inspired site‐directed mutagenesis (2007)

Chitooligosaccharide oxidase (ChitO) catalyzes the oxidation of C1 hydroxyl moieties on chitooligosaccharides and in this way displays a different substrate preference as compared to other known oligosaccharide oxidases. ChitO was identified in the genome of Fusarium graminearum and a structural model revealed that one active site residue (Q268) was likely to be involved in the recognition of the N-acetyl moiety on the chitooligosaccharide substrates. The substrate specificity of wild type ChitO and the Q268R mutant were examined and confirmed that Q268 is indeed involved in N-acetyl recognition.
Characterization of serologic and cell-mediated reactivity of a 38-kDa antigen isolated from Mycobacterium tuberculosis. (1987)

An antigen of Mycobacterium tuberculosis with an m.w. of 38,000 has been isolated by affinity chromatography using a monoclonal antibody. This antibody bound only to an antigen found in M. tuberculosis and Mycobacterium bovis BCG. The specificity of the antigen was tested in a vertical study by immunodetection on western blots reacted with hyperimmune sera against M. tuberculosis, M. bovis, and 10 other Mycobacterium species. The antigen was detected only by antisera to M. tuberculosis and M. bovis. Specificity in cell-mediated immunity was tested by skin tests in guinea pigs sensitized with M. tuberculosis, Mycobacterium intracellulare, and Mycobacterium kansasii and by lymphocyte proliferation tests. The 38-kDa antigen induced positive skin test reactions regardless of the Mycobacterium species used to sensitize the animal. The ability of the 38-kDa antigen to sensitize for cell-mediated immunity was tested by injecting mice with the 38-kDa antigen and challenging their lymphocytes in vitro with various mycobacterial antigens. Lymphocyte proliferation was observed in the presence of 38-kDa antigen, M. tuberculosis sonicate antigen, and tuberculin purified protein derivative and to M. kansasii and M. intracellulare. The 38-kDa antigen may contain a specific epitope detected by serology, but also contains epitopes that are cross-reactive for cellular immunity.
Management Guidelines & Operational Requirements for the Address and Routing Parameter Area Domain ("arpa") (2001)

This memo describes the management and operational requirements for the address and routing parameter area ("arpa") domain.The "arpa" domain is used to support a class of infrastructural identifier spaces, providing a distributed database that translates elements of a structured name space derived from a protocol family to service names.The efficient and reliable operation of this DNS space is essential to the integrity of operation of various services within the Internet.The Internet Architecture Board (IAB) has the responsibility, in cooperation with the Internet Corporation for Assigned Names and Numbers (ICANN), to manage the "arpa" domain.This document describes the principles used by the IAB in undertaking this role.
Selective and Stable DNA Base Pairing without Hydrogen Bonds (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSelective and Stable DNA Base Pairing without Hydrogen BondsTracy J. Matray and Eric T. KoolView Author Information Department of Chemistry, University of Rochester Rochester, New York 14627 Cite this: J. Am. Chem. Soc. 1998, 120, 24, 6191–6192Publication Date (Web):June 5, 1998Publication History Received29 January 1998Published online5 June 1998Published inissue 1 June 1998https://pubs.acs.org/doi/10.1021/ja9803310https://doi.org/10.1021/ja9803310rapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views1529Altmetric-Citations172LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aromatic compounds,Genetics,Hydrocarbons,Nucleic acids,Stability Get e-Alerts
Validating a Custom Multiplex ELISA Against Individual Commercial Immunoassays Using Clinical Samples (2007)

The measurement of multiple antigens in a single sample poses clinical and methodological challenges. Here we describe the validation of a multiplexed sandwich enzyme-linked immunosorbent assay (ELISA) array (microELISA) of nine antigens. The antigens tested simultaneously were: alpha-fetoprotein (AFP), prostate specific antigen (PSA), carcinoembryonic antigen (CEA), cancer antigen 125 (CA 125), CA 15-3, CA 19-9, beta-human chorionic gonadotropin (beta-hCG), luteinizing hormone (LH), and follicle stimulating hormone (FSH). At least 44 clinical samples were tested for each antigen. microELISA results for the nine antigens were then compared with clinical laboratory results obtained for the same antigens in individual chemiluminescent immunoassays. The microELISA had a coefficient of variation (cv) of 7.3% within an assay and 12.6% for assays run at different times. A statistical comparison of results from the microELISA with results from the clinical laboratory showed that the assays had correlation coefficients ranging from 0.99 to 0.76, and Deming regression demonstrated that four of the nine assays were high-quality assays and not statistically different to the individual assays. To determine if the differences in the assays were due to methodology, the microELISA was also compared with conventional ELISAs using identical antibodies and reagents. Deming regression demonstrated that five of the eight assays were high-quality, indicating that a poor correlation between a microELISA and an individual immunoassay are partly due to antibody differences.
Potential tumor or organ-imaging agents. 30. Radioiodinated phospholipid ethers (1989)

A radioiodinated analogue of a naturally occurring alkyl lysophospholipid (ALP) was synthesized for evaluation as a potential tumor-localizing imaging agent. rac-1-[12-(m-Iodophenyl)dodecyl]-2-methylglycero-3-phosphocholine (ET-12IP-OMe, 14) was radiolabeled with iodine-125 via an isotope-exchange procedure. Tissue distribution studies with [125I]ET-12IP-OMe in tumor-bearing rats revealed an immediate tumor uptake of radioactivity. Although radioactivity was also present in nontarget tissues at this time, clearance of tracer from the tumor was much slower and thus provided a suitable tumor to nontarget tissue ratio at 24 h. As a result of this selective accumulation, it was possible to clearly delineate the tumor with gamma-camera scintigraphy.
Staufen‐mediated mRNA decay (2013)

Staufen1 (STAU1)-mediated mRNA decay (SMD) is an mRNA degradation process in mammalian cells that is mediated by the binding of STAU1 to a STAU1-binding site (SBS) within the 3'-untranslated region (3'-UTR) of target mRNAs. During SMD, STAU1, a double-stranded (ds) RNA-binding protein, recognizes dsRNA structures formed either by intramolecular base pairing of 3'-UTR sequences or by intermolecular base pairing of 3'-UTR sequences with a long-noncoding RNA (lncRNA) via partially complementary Alu elements. Recently, STAU2, a paralog of STAU1, has also been reported to mediate SMD. Both STAU1 and STAU2 interact directly with the ATP-dependent RNA helicase UPF1, a key SMD factor, enhancing its helicase activity to promote effective SMD. Moreover, STAU1 and STAU2 form homodimeric and heterodimeric interactions via domain-swapping. Because both SMD and the mechanistically related nonsense-mediated mRNA decay (NMD) employ UPF1; SMD and NMD are competitive pathways. Competition contributes to cellular differentiation processes, such as myogenesis and adipogenesis, placing SMD at the heart of various physiologically important mechanisms.
Intradiscal Electrothermal Annuloplasty: The IDET Procedure (2001)

Intradiscal electrothermal annuloplasty is a minimally invasive procedure for the treatment of lumbar degenerative disc disease. This procedure has been used in the lumbar spine of patients who have failed conservative treatment regimens and who might otherwise be candidates for a spinal fusion procedure. As this is a new, recently developed procedure, there is only relatively short-term follow-up data available, and as such, the procedure has not been widely accepted.
3D printed microfluidic devices with integrated versatile and reusable electrodes (2014)

We report two 3D printed devices that can be used for electrochemical detection. In both cases, the electrode is housed in commercially available, polymer-based fittings so that the various electrode materials (platinum, platinum black, carbon, gold, silver) can be easily added to a threaded receiving port printed on the device; this enables a module-like approach to the experimental design, where the electrodes are removable and can be easily repolished for reuse after exposure to biological samples. The first printed device represents a microfluidic platform with a 500 × 500 μm channel and a threaded receiving port to allow integration of either polyetheretherketone (PEEK) nut-encased glassy carbon or platinum black (Pt-black) electrodes for dopamine and nitric oxide (NO) detection, respectively. The embedded 1 mm glassy carbon electrode had a limit of detection (LOD) of 500 nM for dopamine and a linear response (R(2) = 0.99) for concentrations between 25-500 μM. When the glassy carbon electrode was coated with 0.05% Nafion, significant exclusion of nitrite was observed when compared to signal obtained from equimolar injections of dopamine. When using flow injection analysis with a Pt/Pt-black electrode and standards derived from NO gas, a linear correlation (R(2) = 0.99) over a wide range of concentrations (7.6-190 μM) was obtained, with the LOD for NO being 1 μM. The second application showcases a 3D printed fluidic device that allows collection of the biologically relevant analyte adenosine triphosphate (ATP) while simultaneously measuring the release stimulus (reduced oxygen concentration). The hypoxic sample (4.8 ± 0.5 ppm oxygen) released 2.4 ± 0.4 times more ATP than the normoxic sample (8.4 ± 0.6 ppm oxygen). Importantly, the results reported here verify the reproducible and transferable nature of using 3D printing as a fabrication technique, as devices and electrodes were moved between labs multiple times during completion of the study.
Shoulder arthroscopy: surgical technique. (1993)

Arthroscopic techniques for shoulder arthroscopy have evolved and been refined constantly over the last decade. Significant advances have been made, compared to the first arthroscopic intraarticular examinations on cadavers by Takagi in 1918. Advances in fiberoptics, computer technology, and surgical instrumentation, coupled with innovative ideas and improved operative skills, have opened a new era in the orthopedic evaluation of intraarticular structures and treatment of pathology by the orthopedic surgeon. Arthroscopic examination of the glen humeral joint and sub acromial bursa permits the surgeon to visually assess, document, and treat shoulder pathology in an injury specific manner. Critical to effective use of this technology and skill is a comprehensive and reproducible system for thorough examination and documentation, so that no abnormality is inadvertently overlooked and treatments are effectively performed. In this fashion, standardization is developed for evaluating surgical treatments and providing a common base for professional communication and continued education within the orthopedic community. At the Southern California Orthopedic Institute, a comprehensive 15-point glenohumeral and 8-point subacromial examination from both posterior and anterior portals has been developed and is widely accepted in most arthroscopic forums. The operating room set-up, instrumentation, patient positioning, and the authors' preference for systematic glenohumeral arthroscopy and bursoscopy will be described. Specific methods for-arthroscopic subacromial decompression, distal clavicle resection, and evaluation of the rotator cuff will be outlined. It is imperative that the surgeon have a complete knowledge of normal shoulder anatomy and common variants.
The generalized tree quorum protocol (1992)

In this paper, we present a low-cost fault-tolerant protocol for managing replicated data. We impose a logical tree structure on the set of copies of an object and develop a protocol that uses the information available in the logical structure to reduce the communication requirements for read and write operations. The tree quorum protocol is a generalization of the static voting protocol with two degrees of freedom for choosing quorums. In general, this results in significantly lower communication costs for comparable data availability. The protocol exhibits the property of graceful degradation, i.e., communication costs for executing operations are minimal in a failure-free environment but may increase as failures occur. This approach in designing distributed systems is desirable since it provides fault-tolerance without imposing unnecessary costs on the failure-free mode of operations.
Manipulation of Individual Carbon Nanotubes and Their Interaction with Surfaces (1998)

We demonstrate that the tip of an atomic force microscope (AFM) can be used to control the shape and position of individual multiwalled carbon nanotubes dispersed on a surface. Specifically we can bend, straighten, translate, rotate, andunder certain conditionscut nanotubes. Such manipulations are feasible due to the interaction between nanotubes and the substrate, which can stabilize highly strained nanotube configurations. Direct evidence for this interaction is provided by the study of elastic distortions of tubes interacting with other tubes and the substrate. From the observed deformations of nanotubes with 100 Å diameter, for example, we obtain a binding energy of 0.8 ± 0.3 eV/Å. This interaction forces nanotubes to conform to the structure of the substrate, and the resulting distortions should induce corresponding changes in their electronic structure and electrical transport properties.