gebhart/patrepeval huggingface dataset:
Sensitivity of monomeric and dimeric forms of bovine seminal ribonuclease to human placental ribonuclease inhibitor (1992)

We have studied the inhibition of bovine pancreatic RNAase (RNAase A) and bovine seminal RNAase in its native dimeric form (RNAase BS-1) and in monomeric carboxymethylated form (MCM RNAase BS-1) by human placental RNAase inhibitor (RNAase inhibitor) in order to understand the effect of enzyme structure on its response to the inhibitor. Study of the inhibition as a function of inhibitor concentration revealed that RNAase A and MCM RNAase BS-1 were inhibited fully and the inhibitor-sensitivities of the two were comparable. But under identical inhibitor concentrations RNAase BS-1 was found to be virtually insensitive to the inhibitor; at higher (3-10-fold) inhibitor concentrations marginal inhibition of the native enzyme could be observed. When RNAase BS-1 was pretreated with 5 mM-dithiothreitol (DTT) and assayed, it exhibited greater inhibitor-sensitivity, presumably as a result of its partial monomerization on exposure to DTT. This DTT-mediated change in the response of RNAase BS-1 to the inhibitor did not, however, seem to occur either in the assay conditions (which included DTT) or even when the enzyme was pretreated with DTT in the presence of the substrate, suggesting an effect of the substrate on the enzyme behaviour towards the inhibitor. Independently, gel-filtration runs revealed that, although DTT treatment caused monomerization of RNase BS-1, this change did not take place when DTT treatment was carried out in the presence of the substrate. From our observations, we infer that differential inhibitor-sensitivity of the dimeric and monomeric forms of RNAase BS-1, the relative contents of the two forms and the influence of the substrate on them may be important determinants of the net enzyme activity in the presence of the inhibitor.
Laboratory diagnosis and interpretation of tests for syphilis (1995)

The lack of a method for demonstrating the presence of Treponema pallidum by growth necessitates the use of alternative methods. Traditionally, these methods are divided into direct detection methods (animal inoculation, dark-field microscopy, etc.) and serologic tests for the presence of patient antibody against T. pallidum. Serologic methods are further divided into two classes. One class, the nontreponemal tests, detects antibodies to lipoidal antigens present in either the host or T. pallidum; examples are the Venereal Disease Research Laboratory and rapid plasma reagin and tests. Reactivity in these tests generally indicates host tissue damage that may not be specific for syphilis. Because these tests are easy and inexpensive to perform, they are commonly used for screening, and with proper clinical signs they are suggestive of syphilis. The other class of test, the treponemal tests, uses specific treponemal antigens. Confirmation of infection requires a reactive treponemal test. Examples of the treponemal tests are the microhemagglutination assay for antibodies to T. pallidum and the fluorescent treponemal antibody absorption test. These tests are more expensive and complicated to perform than the nontreponemal tests. On the horizon are a number of direct antigen, enzyme-linked immunosorbent assay, and PCR techniques. Several of these techniques have shown promise in clinical trials for the diagnosis of congenital syphilis and neurosyphilis that are presently difficult to diagnose.
Robust automated shimming technique using arbitrary mapping acquisition parameters (RASTAMAP) (2004)

Quantitative MRI techniques as well as methods such as blood oxygen level-dependent (BOLD) imaging and in vivo spectroscopy require stringent optimization of magnetic field homogeneity, particularly when using high main magnetic fields. Automated shimming approaches require a method of measuring the main magnetic field, B(0), followed by adjusting the currents in resistive shim coils to maximize homogeneity. A robust automated shimming technique using arbitrary mapping acquisition parameters (RASTAMAP) using a 3D multiecho gradient echo sequence that measures B(0) with high precision was developed. Inherent compensation and postprocessing methods enable removal of artifacts due to hardware timing errors, gradient propagation delays, gradient amplifier asymmetry, and eddy currents. This allows field maps to be generated for any field of view, bandwidth, resolution, or acquisition orientation without custom tuning of sequence parameters. Field maps of an aqueous phantom show +/- 1 Hz variation with altered acquisition orientations and bandwidths. Subsequent fitting of measured shim coil field maps allows calculation of shim currents to produce optimum field homogeneity.
Therapeutic effect of anti-OX40L and anti-TNF-α MAbs in a murine model of chronic colitis (2003)

Interaction of OX40 (CD134) on T cells with its ligand (OX40L) on antigen-presenting cells has been implicated in pathogenic T cell activation. This study was performed to explore the involvement of OX40/OX40L in the development of T cell-mediated chronic colitis. We evaluated both the preventive and therapeutic effects of neutralizing anti-OX40L MAb on the development of chronic colitis in SCID mice induced by adoptive transfer of CD4(+)CD45RB(high) T cells as an animal model of Crohn's disease. We also assessed the combination of anti-OX40L and anti-TNF-alpha MAbs to improve the therapeutic effect. Administration of anti-OX40L MAb markedly ameliorated the clinical and histopathological disease in preventive and therapeutic protocols. In vivo treatment with anti-OX40L MAb decreased CD4(+) T cell infiltration in the colon and suppressed IFN-gamma, IL-2, and TNF-alpha production by lamina propria CD4(+) T cells. The combination with anti-TNF-alpha MAb further improved the therapeutic effect by abolishing IFN-gamma, IL-2, and TNF-alpha production by lamina propria CD4(+) T cells. Our present results suggested a pivotal role of OX40/OX40L in the pathogenesis of T cell-mediated chronic colitis. The OX40L blockade, especially in combination with the TNF-alpha blockade, may be a promising strategy for therapeutic intervention of Crohn's disease.
The effect of herbal supplementation on the severity of exercise-induced pulmonary haemorrhage (2005)

Abstract Exercise-induced pulmonary haemorrhage (EIPH) is a serious condition that affects the health and possibly the performance of all racehorses. However, only two treatments, furosemide and the Flair™ equine nasal strip, both of which reduce capillary transmural pressure, have been successful in reducing EIPH. Alternatively, transient impairment of platelet function and coagulation during exercise has been considered an additional contributor to EIPH. Consequently, herbal formulations designed to enhance platelet function, and hence coagulation, are hypothesized to reduce EIPH. To investigate the validity of this hypothesis, five Thoroughbred horses completed three maximal incremental exercise tests on a 10% inclined treadmill in a randomized cross-over design experiment. Treatments included twice daily oral administration (for 3 days) of a placebo (PL; cornstarch) and two herbal formulas, Yunnan Paiyao (YP) or Single Immortal (SI). Blood samples for coagulation profiles, complete blood counts and biochemistry profiles were collected before each exercise test. During each test, pulmonary arterial pressure, oxygen uptake, arterial blood gases, plasma lactate and time-to-fatigue were measured. Severity of EIPH was quantified via bronchoalveolar lavage (BAL) at 30–60 min post-exercise. The herbal formulations were not effective in decreasing EIPH (×10 6 red blood cells ml −1 BAL fluid: PL, 27.1±11.6; YP, 33.2±23.4; SI, 35.3±15.4, P &gt;0.05) or in changing any of the other variables measured with the exception of time-to-fatigue, which was slightly but significantly prolonged by Single Immortal compared with placebo and Yunnan Paiyao (PL, 670±9.6 s; YP, 665±5.5 s; SI, 685±7.9 s, P &lt;0.05). Thus, these results do not support the use of these herbal formulations in the prevention of EIPH.
Controlled physical random functions (2003)

A physical random function (PUF) is a random function that can only be evaluated with the help of a complex physical system. We introduce controlled physical random functions (CPUFs) which are PUFs that can only be accessed via an algorithm that is physically bound to the PUF in an inseparable way. CPUFs can be used to establish a shared secret between a physical device and a remote user. We present protocols that make this possible in a secure and flexible way, even in the case of multiple mutually mistrusting parties. Once established, the shared secret can be used to enable a wide range of applications. We describe certified execution, where a certificate is produced that proves that a specific computation was carried out on a specific processor. Certified execution has many benefits, including protection against malicious nodes in distributed computation networks. We also briefly discuss a software licensing application.
Robustness beyond shallowness: incremental deep parsing (2002)

Robustness is a key issue for natural language processing in general and parsing in particular, and many approaches have been explored in the last decade for the design of robust parsing systems. Among those approaches is shallow or partial parsing, which produces minimal and incomplete syntactic structures, often in an incremental way. We argue that with a systematic incremental methodology one can go beyond shallow parsing to deeper language analysis, while preserving robustness. We describe a generic system based on such a methodology and designed for building robust analyzers that tackle deeper linguistic phenomena than those traditionally handled by the now widespread shallow parsers. The rule formalism allows the recognition of n-ary linguistic relations between words or constituents on the basis of global or local structural, topological and/or lexical conditions. It offers the advantage of accepting various types of inputs, ranging from raw to chunked or constituent-marked texts, so for instance it can be used to process existing annotated corpora, or to perform a deeper analysis on the output of an existing shallow parser. It has been successfully used to build a deep functional dependency parser, as well as for the task of co-reference resolution, in a modular way.
Identification and expression of G protein-coupled receptors (1998)

Cloning of G Protein--Coupled Receptor Genes: The Use of Homology Screening and the Polymerase Chain Reaction (A. Marchese, et al.). Practical Approaches for Cloning G Protein--Coupled Receptors Using Mammalian Cell Expression (T. Murphy). G Protein--Coupled Receptor Informatics and the Orphan Problem (K. Lynch). The Use of Xenopus laevis Oocytes for the Study of G Protein--Coupled Receptors (A. Lee & M. Durieux). Stable Expression of G Protein--Coupled Receptors in Mammalian Cells (K. Neve & R. Neve). Heterologous Expression in Primary Cell Cultures (R. Leonard). Expression of G Protein--Coupled Receptors in Escherichia coli (R. Grisshammer). Large--Scale Expression/Purification of G Protein--Coupled Receptors Mammalian Cells (A. Robeva & J. Linden). High--Level Expression of G Protein--Coupled Receptors in the Baculovirus/SF9 Cell Expression System (N. Rondeau, et al.). Expression of G Protein--Coupled Receptors in Drosophila Schneider 2 Cells (M. Graziano, et al.). Heterologous G Protein--Coupled Receptors Expressed in Saccharomyces cerevisiae: Methods for Genetic Analysis and Ligand Identification (M. Pausch, et al.). Index.
Delineating Functional Competencies: A Component Model (1987)

This article describes a model for representing functional competencies in students with disabilities. Although strategies exist to identify skills and activities that are functional for students with severe handicaps, these strategies provide relatively little information on how to separate the functional skills into meaningful component parts that represent the range of behaviors needed in the natural environment. Data are presented to illustrate the narrow range of behaviors included in task analyses in current literature on skill acquisition. The Component Model of Functional Life Routines provides a systematic alternate approach to delineating the behaviors required in natural environments.
Dehydration of 4‐oximinocarboxylic acids with dicyclohexylcarbodiimide (1965)

Abstract Treatment of 4‐oximino‐4‐phenylbutyric acid with dicyclohexylcarbodiimide gave 6 H ‐3‐phenyl‐4, 5‐dihydro‐6‐oxo‐1, 2‐oxazine (IId), which was characterized by its infrared spectrum and some reactions. Ring cleavage of IId was easily accomplished by acid or base such as hydrochloric acid, alcohol or amines. The treatment of 4‐oximino‐valeric acid with dicyclohexylcarbodiimide was also studied.
Microelectromechanical systems based Stewart platform with sub-nano resolution (2012)

There have been difficulties in the fabrication of microelectromechanical systems (MEMS) based Stewart platforms [D. Stewart, Proc. Inst. Mech. Eng. 180(15), 371 (1965)]. The macroscale positioning technology, such as universal joints, ball and roller bearings, and commercial actuators, used for building the macro Stewart platforms could not be fit into MEMS version machines. In this paper, we report that these difficulties were overcome at the National Institute of Standards and Technology (NIST). A prototype of NIST’s MEMS-based Stewart platform showed six degree-of-freedom kinematic capability with sub-nano-scale resolution. This MEMS Stewart platform can be adopted as a precision stage for sub nano-scale applications, such as the atomic force microscope and manipulation of molecules.
Using reliability information to annotate RNA secondary structures (1998)

A number of heuristic descriptors have been developed previously in conjunction with the mfold package that describe the propensity of individual bases to participate in base pairs and whether or not a predicted helix is "well-determined." They were developed for the "energy dot plot" output of mfold. Two descriptors, P-num and H-num, are used to measure the level of promiscuity in the association of any given nucleotide or helix with alternative complementary pairs. The third descriptor, S-num, measures the propensity of bases to be single-stranded. In the current work, we describe a series of programs that were developed in order to annotate individual structures with "well-definedness" information. We use color annotation to present the information. The programs can annotate PostScript files that are created by the mfold package or the PostScript secondary structure plots produced by the Weiser and Noller program XRNA (Weiser B, Noller HF, 1995, XRNA: Auto-interactive program for modeling RNA, The Center for Molecular Biology of RNA, Santa Cruz, California: University of California; Internet: ftp://fangio.ucsc.edu/pub/XRNA). In addition, these programs can annotate ss files that serve as input to XRNA. The annotation package can also handle structure comparison with a reference structure. This feature can be used to compare predicted structure with a phylogenetically deduced model, to compare two different predicted foldings, and to identify conformational changes that are predicted between wild-type and mutant RNAs. We provide several examples of application. Predicted structures of two RNase P RNAs were colored with P-num information and further annotated with comparative information. The comparative model of a 16S rRNA was annotated with P-num information from mfold and with base pair probabilities obtained from the Vienna RNA folding package. Further annotation adds comparisons with the optimal foldings obtained from mfold and the Vienna package, respectively. The results of all of these analyses are discussed in the context of the reliability of structure prediction.
Chemopreventive effects of calcium but not aspirin supplementation in cholic acid-promoted colon carcinogenesis: correlation with intermediate endpoints (1995)

Epidemiological studies have suggested that increased intake of calcium (Ca) or aspirin (ASA) is associated with a reduced risk for colon cancer. To delineate a possible mechanism of action, the present study used male F344 rats in an azoxymethane (AOM)-induced colon tumor model to study the single and interactive effects of Ca and ASA on cholic acid-promoted experimental colon carcinogenesis. Following initiation with AOM, a promotion diet containing 0.5% cholic acid was fed for 34 weeks until the adenoma development stage. Cholic acid was used as a surrogate for high-fat diets and to promote carcinogenesis. Diets were supplemented with CaCO3 (2% Ca by weight), 250 p.p.m. ASA, or both. After 34 weeks, the diets were switched during the progression stage and rats were killed at week 51. Several intermediate endpoints were examined during the course of AOM carcinogenesis to determine their reliability as predictors of colon cancer risk. Intermediate endpoints included colon crypt height measurement, colon mucosal ornithine decarboxylase (ODC) and colon mucosal protein kinase C (PKC) activities. The biomarkers were examined at the beginning of the study at 2 weeks, and thereafter at 5, 15, 30 and 40 weeks of dietary treatment. Animals were necropsied at week 51 and tumor incidence and numbers were analyzed for correlation with biomarkers. Survival was highest in the group fed CaCO3 during the promotion stage and tumor burden was lowest in groups fed CaCO3 during this stage. Supplementation during the progression stage was ineffective. The cholic acid promotion model resulted in increased ODC which was inhibited by intervention during the promotion stage with Ca, but not ASA. PKC was also activated by cholic acid feeding, and this effect was modulated by intervention in the promotional stage with Ca or ASA. Colon tumor incidence and burden was increased by cholic acid promotion and decreased by Ca, but not affected by ASA. In summary, Ca is a more effective chemopreventive agent in cholic acid-promoted colon carcinogenesis than ASA, impacting both incidence and tumor number. Colonic ODC, but not PKC may be a suitable predictor of risk and response in chemoprevention trials for colon cancer.
Quenched Auto-Ligating DNAs:  Multicolor Identification of Nucleic Acids at Single Nucleotide Resolution (2004)

We describe the synthesis and study of multicolor quenched autoligating (QUAL) probes for identification and discrimination of closely related RNA and DNA sequences in solution and in bacteria. In these probes, a dabsyl quencher doubles as an activator in the oligonucleotide-joining reaction. The oligonucleotides remain dark until they bind at adjacent sites, and "light up" on nucleophilic displacement of the dabsyl probe by the phosphorothioate probe. Four fluorescent dye conjugates were prepared and tested with probes and targets that differ by one nucleotide. Experiments on polymer beads show clear color-based discrimination of DNAs added in solution. Two-color quenched probe pairs were then tested in the discrimination of 16S rRNA sequences in Escherichia coli. Single nucleotide resolution was achieved in the cells with green/red QUAL probes, allowing identification of a one-base sequencing error in the 16S rRNA database. Finally, QUAL probes were successfully applied in live bacterial cells. The method requires only incubation followed by fluorescence imaging, and requires no enzymes, added reagents, cross-linking, fixing, or washes. Because probes must bind side-by-side to generate signal, there is little or no interference from unintended protein binding, which can occur with other probe types. The results suggest that QUAL probes may be of general use in the detection and identification of sequences in solution, on microarrays, and in microorganisms.
Analysis of the inflammatory network in benign prostate hyperplasia and prostate cancer (2003)

Our data clearly demonstrate that various inflammatory and cell biological cascades are involved which either lead to BPH or can be linked to the development of PCA. The exact cell biological mechanisms may provide novel therapeutic options in the treatment of both diseases.
n‐3 PUFA Esterified to Glycerol or as Ethyl Esters Reduce Non‐Fasting Plasma Triacylglycerol in Subjects with Hypertriglyceridemia: A Randomized Trial (2014)

To date, treatment of hypertriglyceridemia with long-chain n-3 polyunsaturated fatty acids (n-3 PUFA) has been investigated solely in fasting and postprandial subjects. However, non-fasting triacylglycerols are more strongly associated with risk of cardiovascular disease. The objective of this study was to investigate the effect of long-chain n-3 PUFA on non-fasting triacylglycerol levels and to compare the effects of n-3 PUFA formulated as acylglycerol (AG-PUFA) or ethyl esters (EE-PUFA). The study was a double-blinded randomized placebo-controlled interventional trial, and included 120 subjects with non-fasting plasma triacylglycerol levels of 1.7-5.65 mmol/L (150-500 mg/dL). The participants received approximately 3 g/day of AG-PUFA, EE-PUFA, or placebo for a period of eight weeks. The levels of non-fasting plasma triacylglycerols decreased 28% in the AG-PUFA group and 22% in the EE-PUFA group (P < 0.001 vs. placebo), with no significant difference between the two groups. The triacylglycerol lowering effect was evident after four weeks, and was inversely correlated with the omega-3 index (EPA + DHA content in erythrocyte membranes). The omega-3 index increased 63.2% in the AG-PUFA group and 58.5% in the EE-PUFA group (P < 0.001). Overall, the heart rate in the AG-PUFA group decreased by three beats per minute (P = 0.045). High-density lipoprotein (HDL) cholesterol increased in the AG-PUFA group (P < 0.001). Neither total nor non-HDL cholesterol changed in any group. Lipoprotein-associated phospholipase A2 (LpPLA2) decreased in the EE-PUFA group (P = 0.001). No serious adverse events were observed. Supplementation with long-chain n-3 PUFA lowered non-fasting triacylglycerol levels, suggestive of a reduction in cardiovascular risk. Regardless of the different effects on heart rate, HDL, and LpPLA2 that were observed, compared to placebo, AG-PUFA, and EE-PUFA are equally effective in reducing non-fasting triacylglycerol levels.
Endotoxin in Septic Shock (1993)

Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland and Department of Anesthesiology, University of Maryland, Baltimore, Maryland Address correspondence and reprint requests to William D. Hoffman, M.D., Senior Investigator, Department of Critical Care Medicine, National Institutes of Health, Building 10, Room 7D43, 9000 Rockville Pike, Bethesda, MD 20892. The authors thank Robert L. Danner, MD, for careful review of the manuscript and Lee Hoffman for editorial assistance. Accepted for publication April 20, 1993
Biochemical changes of plasma in paratroops after parachuting: a preliminary investigation. (1999)

Whether these changes can potentially serve as useful biomarkers to assess possible abnormal stress in parachutists and to evaluate the health condition and to select parachutists remains to be further studied.