gebhart/patrepeval huggingface dataset:
Endocrine Changes Associated with a Dietary-Induced Increase in Ovulation Rate (Flushing) in Gilts (1989)

Effects of an increased level of dietary energy (flushing) on plasma concentrations of FSH, LH, insulin, progesterone and estradiol-17 beta and ovulation rate were studied in 16 gilts. Gilts received 5,400 kcal ME/d for one estrous cycle and the first 7 d of a second. On d 8 of the second estrous cycle, gilts received either 5,400 kcal ME/d (control [C], n = 8) or 11,000 kcal ME/d (flushed [F], n = 8) for the remainder of the estrous cycle. Blood was collected daily at 15-min intervals for 6 h from d 8 through estrus. Gilts were examined by laparotomy 6 d after estrus. Ovulation rate was greater (P less than .05) in F than C gilts (16.0 vs 9.4). Mean daily concentrations of FSH were greater (P less than .05) in F gilts at 5 d, 4 d and 3 d prior to estrus compared with C females. In both C and F gilts, FSH decreased (P less than .05) prior to estrus. Mean daily concentrations of LH and LH pulse amplitude were not different (P greater than .05) between treatments. Mean number of LH pulses/6 h at 4 d, 3 d and 2 d prior to estrus were greater (P less than .05) in F than in C gilts. In both treatments, LH pulse amplitude decreased (P less than .05) and pulse frequency increased (P less than .07) prior to estrus. Mean plasma concentrations of insulin tended to be higher (P less than .07) in F than in C females during the 7-d period before estrus.(ABSTRACT TRUNCATED AT 250 WORDS)
CAFASP-1: Critical assessment of fully automated structure prediction methods (1999)

The results of the first Critical Assessment of Fully Automated Structure Prediction (CAFASP-1) are presented. The objective was to evaluate the success rates of fully automatic web servers for fold recognition which are available to the community. This study was based on the targets used in the third meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP-3). However, unlike CASP-3, the study was not a blind trial, as it was held after the structures of the targets were known. The aim was to assess the performance of methods without the user intervention that several groups used in their CASP-3 submissions. Although it is clear that “human plus machine” predictions are superior to automated ones, this CAFASP-1 experiment is extremely valuable for users of our methods; it provides an indication of the performance of the methods alone, and not of the “human plus machine” performance assessed in CASP. This information may aid users in choosing which programs they wish to use and in evaluating the reliability of the programs when applied to their specific prediction targets. In addition, evaluation of fully automated methods is particularly important to assess their applicability at genomic scales. For each target, groups submitted the top-ranking folds generated from their servers. In CAFASP-1 we concentrated on fold-recognition web servers only and evaluated only recognition of the correct fold, and not, as in CASP-3, alignment accuracy. Although some performance differences appeared within each of the four target categories used here, overall, no single server has proved markedly superior to the others. The results showed that current fully automated fold recognition servers can often identify remote similarities when pairwise sequence search methods fail. Nevertheless, in only a few cases outside the family-level targets has the score of the top-ranking fold been significant enough to allow for a confident fully automated prediction.Because the goals, rules, and procedures of CAFASP-1 were different from those used at CASP-3, the results reported here are not comparable with those reported in CASP-3. Nevertheless, it is clear that current automated fold recognition methods can not yet compete with “human-expert plus machine” predictions. Finally, CAFASP-1 has been useful in identifying the requirements for a future blind trial of automated served-based protein structure prediction. Proteins Suppl 1999;3:209–217. © 1999 Wiley-Liss, Inc.
Real-Time Clinical Monitoring of Biomolecules (2013)

Continuous monitoring of clinical biomarkers offers the exciting possibility of new therapies that use biomarker levels to guide treatment in real time. This review explores recent progress toward this goal. We initially consider measurements in body fluids by a range of analytical methods. We then discuss direct tissue measurements performed by implanted sensors; sampling techniques, including microdialysis and ultrafiltration; and noninvasive methods. A future directions section considers analytical methods at the cusp of clinical use.
Beagle pup model of perinatal asphyxia: nimodipine studies. (1987)

Calcium antagonists may be of significant benefit in the pharmacotherapy of cerebral ischemia, possibly by improving postischemic cerebral blood flow (CBF). This study evaluated the effects of the calcium antagonist nimodipine on CBF in a newborn beagle pup model of perinatal asphyxia lasting 5 minutes. Immediately after the asphyxial episode, nimodipine (2 micrograms/kg/min) or saline was infused for 10 minutes, following which [14C]iodoantipyrine determinations of CBF were performed. In noninsulted pups, nimodipine caused both significant decreases in CBF to cortical and deep gray structures as well as a decrease in mean arterial blood pressure (MABP) (p less than 0.05). In insulted pups, nimodipine similarly decreased MABP (p less than 0.001) and CBF to cortical and deep gray matter regions. Nimodipine appeared to have no effect on arterial blood gases and EEG tracings in either insulted or noninsulted pups. Although nimodipine may be shown to improve neurologic outcome in asphyxiated newborn infants, the limits of this study do not show the mechanism to be that of improving CBF.
Heap profiling for space-efficient Java (2001)

We present a heap-profiling tool for exploring the potential for space savings in Java programs. The output of the tool is used to direct rewriting of application source code in a way that allows more timely garbage collection (GC) of objects, thus saving space. The rewriting can also avoid allocating some objects that are never used. The tool measures the difference between the actual collection time and the potential earliest collection time of objects for a Java application. This time difference indicates potential savings. Then the tool sorts the allocation sites in the application source code according to the accumulated potential space saving for the objects allocated at the sites. A programmer can investigate the source code surrounding the sites with the highest savings to find opportunities for code rewriting that could save space. Our experience shows that in many cases simple code rewriting leads to actual space savings and in some cases also to improvements in program runtime. Experimental results using the tool and manually rewriting code show average space savings of 18% for the SPECjvm98 benchmark suite. Results for other benchmarks are also promising. We have also classified the program transformations that we have used and argue that in many cases improvements can be achieved by an optimizing compiler.
Epstein-Barr virus enters B cells and epithelial cells by different routes (1992)

Epstein-Barr virus (EBV) infects two cell types, B lymphocytes and epithelial cells. Electron microscopic studies have shown that the virus fuses with the lymphoblastoid cell line Raji but is endocytosed into thin-walled non-clathrin-coated vesicles in normal B cells before fusion takes place. To compare early interactions of EBV with epithelial cells and B cells, a fluorescence dequenching assay of fusion was employed, using virus labeled either with the pH-insensitive probe octadecyl rhodamine B chloride (R18) or with 5(N-octadecanoyl) aminofluorescein (AF), which loses emission intensity at a pH below 7.4. Fusion of virus labeled with R18 could be monitored with B cells, Raji cells, and epithelial cells. Lowering the extracellular pH or pretreatment of cells with ammonium chloride or methylamine had no effect on these measurements. In contrast, fusion of virus labeled with AF could be measured with Raji cells and epithelial cells, but not with normal B cells unless cells were previously treated with ammonium chloride. Fusion of virus with normal B cells was inhibited with chlorpromazine, chloroquine, and sodium azide, but none of these reagents had any effect on fusion with Raji or epithelial cells. These results suggest that entry of EBV into nonpolarized suspensions of epithelial cells occurs by fusion at the cell surface, that EBV may be incapable of fusing with normal B cells unless it has first been endocytosed, and that pH appears to be irrelevant to either event. A combination of the two probes, R18 and AF, may have general use for determining the sites of entry of enveloped viruses that fuse in a pH-independent manner.
Safety consideration for storage allocation optimizations (1988)

article Free Access Share on Safety consideration for storage allocation optimizations Author: D. R. Chase Olvetti Research Center, Menlo Park, CA Olvetti Research Center, Menlo Park, CAView Profile Authors Info & Claims ACM SIGPLAN NoticesVolume 23Issue 7July 1988 pp 1–10https://doi.org/10.1145/960116.53991Published:01 June 1988Publication History 27citation666DownloadsMetricsTotal Citations27Total Downloads666Last 12 Months11Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Human CD4+ T lymphocytes recognize a highly conserved epitope of human T lymphotropic virus type 1 (HTLV-1)<i>env</i>gp21 restricted by HLA DRB1*0101 (1998)

HTLV-1 causes two distinct human diseases, HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and adult T cell leukaemia/lymphoma (ATL). Persistently infected individuals carry a risk of <1% of developing either disease. These basic epidemiological data imply that virus-host interactions, especially immunogenetic factors, influence the outcome of infection. Several studies showed that the HLA class II DR1 DQ5 haplotype is over-represented in HAM/TSP, but rare in ATL. Therefore, we selected four patients with HAM/TSP and one seronegative control who all carried the HLA DR1 DQ5 haplotype. We analysed the CD4+ T lymphocyte response against eight synthetic peptides of HTLV-1 envelope (env) glycoprotein gp21, a crucial target antigen in HAM/TSP. The first of two immunodominant epitopes corresponded to a domain of the HTLV-1 envelope protein which had previously been shown to be essential for HTLV-1 envelope function. The second immunodominant epitope overlapped a highly conserved sequence of the retroviral transmembrane envelope protein. DR1 (DRB1*0101)-restricted T lymphocytes were activated by the conserved peptide sequence in nanomolar concentrations. In contrast, this conserved sequence can also induce non-specific, cAMP-mediated immunosuppressive effects on T cells when added in micromolar concentrations to culture media, as shown by Haraguchi S, Good RA, James-Yarish M, Cianciolo GJ, Day NK, Proc Natl Acad Sci USA 1995; 92:5568-71. Hence, HTLV-1 env gp21 might exert either stimulating immunological or immunosuppressive effects in HTLV-1-infected individuals, depending on the level of its expression and the presence of HLA DRB1*0101.
Photohydrolysis of DNA by polyaminobenzenediazonium salts (1989)

J. P. Behr, J. Chem. Soc., Chem. Commun., 1989, 101 DOI: 10.1039/C39890000101
Direct Measurement of the Coherence Length of Edge States in the Integer Quantum Hall Regime (2008)

We have determined the finite temperature coherence length of edge states in the integer quantum Hall effect regime. This was realized by measuring the visibility of electronic Mach-Zehnder interferometers of different sizes, at filling factor 2. The visibility shows an exponential decay with the temperature. The characteristic temperature scale is found inversely proportional to the length of the interferometer arm, allowing one to define a coherence length l_(phi). The variations of l_(phi) with magnetic field are the same for all samples, with a maximum located at the upper end of the quantum Hall plateau. Our results provide the first accurate determination of l_(phi) in the quantum Hall regime.
Coding artifacts removal using biased anisotropic diffusion (2002)

Biased anisotropic diffusion is applied to the coding artifacts removal of the DCT based codec. It is formulated as a cost minimization problem. The weighting factors of the cost function are controlled such that the solution removes the blocking effect and conceals the block losses. It has an advantage over other postprocessing schemes because it handles the discontinuity of the image, smoothes the image selectively, and takes the visual masking in to account. Features needed for the weighting factors are extracted directly from the DCT coefficients to reduce the computational complexity.
Testing Delone and Mclean’s Model in Financial Institutions (2013)

Abstract. Information Systems (IS) success is critical in organizations, because of its direct and indirect impact on information flow inside and outside organizations, and therefore, it affects decision making process, that influence organizational success. The main objective of this study is to provide a further insight in to IS success, develop measurement tools for IS success, and then, test Delone and Mclean’s model to ensure its validity and explanations to IS success factors. In order to test the research hypotheses, data were collected from IS end users in Palestinian financial institutions using a questionnaire. 189 usable surveys were used in data analysis. After that , construct validity and the internal consistency reliability of the measures were tested, using Coronbach's Alpha test. The results show high reliability of all used measures, where Coronbach's Alpha exceeds 0.7. Hypothesis embedded in the research model were tested using correlation, regression, and stepwise multiple regression analysis. The main findings supports Delone and Mclean’s model, and shows that the model offers good explanation of IS success in Palestinian financial institutions, where most of the hypothesis were accepted.
The clinical and cost-effectiveness of left ventricular assist devices for end-stage heart failure: a systematic review and economic evaluation (2005)

Although the review showed that LVADs are clinically effective as a BTT with ESHF, the economic evaluation indicated that they are not cost-effective. With the limited and declining availability of donor hearts for transplantation, it appears that the future of the technology is in its use as an LTCS. Further research is needed to examine the clinical effectiveness of LVADs for people with ESHF, assessing patient survival, functional ability, quality of life and adverse events. Evaluations of the clinical effectiveness of LVADs should include economic evaluations, as well as data on quality of life, utilities, resources and costs. A systematic review of the epidemiology of ESHF should be undertaken to assess its potential impact.
Relationship between the individual collagenases of Clostridium histolyticum: evidence for evolution by gene duplication (1984)

The relationship between the six collagenases (alpha, beta, gamma, delta, epsilon, and zeta) isolated and characterized in the preceding papers [Bond, M.D., & Van Wart, H.E. (1984) Biochemistry (preceding two papers in this issue)] has been investigated. Chemical modification reactions establish that all six enzymes contain essential carboxyl, tyrosine, and lysine residues. Circular dichroism spectra of the peptide bond region show that the secondary structures of the collagenases are very similar. Ouchterlony double-immunodiffusion experiments carried out with antiserum prepared against beta-collagenase indicate that all six collagenases are cross-reactive. Reverse-phase high-pressure liquid chromatography elution profiles of tryptic digests of these collagenases and sodium dodecyl sulfate electrophoresis gels of the peptides formed on reaction with cyanogen bromide have been obtained. The results indicate that the class I collagenases have extensive sequence homology with each other and that the class II collagenases have extensive sequence homology with each other but that the enzymes in the two classes have substantially different sequences. In addition, the data show that beta-collagenase probably consists of domains that have homologous amino acid sequences, which may have arisen by full or partial intragenic gene duplication. This may account for the unusually high molecular weight of this and the other collagenases. Finally, on the basis of the similarities between the collagenases in the two classes, it is suggested that one class evolved from the other by gene duplication followed by independent evolution by point mutations to yield enzymes with different substrate specificities.
Application of Digital Image Correlation (DIC) in resonance machines for measuring fatigue crack growth (2014)

This paper presents a simple experimental procedure that greatly facilitates the use of digital image correlation (DIC) techniques in fatigue test conducted in resonant testing machines, without the need of test interruptions. This is possible due to the implementation of USB interface optical microscopes of very small dimensions, so that they can be mounted on the specimen as a contact extensometer. Thus, the microscopesample assembly oscillates at the resonance frequency of the test. This is how, although the resonant testing machine is in motion, and although the specimen is subjected to fatigue, changing its dimensions according to the applied load, the acquired image is completely static. This allows the evaluation of the plastic deformations generated by the crack growth, avoiding the elastic ones. Preliminary results on monitoring cracks with this technique on flat specimens with cylindrical notches of 1050 aluminium alloy are also presented.
Reconfigurable silicon thermo-optical device based on spectral tuning of ring resonators (2011)

A novel tunable and reconfigurable thermo-optical device is theoretically proposed and analyzed in this paper. The device is designed to be entirely compatible with CMOS process and to work as a thermo-optical filter or modulator. Numerical results, made by means of analytical and Finite-Difference Time-Domain (FDTD) methods, show that a compact device enables a broad bandwidth operation, of up to 830 GHz, which allows the device to work under a large temperature variation, of up to 96 K.
Direct Identification of<i>Vibrio vulnificus</i>in Clinical Specimens by Nested PCR (1998)

This study was performed to establish optimal nested PCR conditions and a high-yield DNA extraction method for the direct identification of Vibrio vulnificus in clinical specimens. We designed two sets of primers targeting the V. vulnificus hemolysin/cytolysin gene. The target of the first primer set (P1-P2; sense, 5'-GAC-TAT-CGC-ATC-AAC-AAC-CG-3', and antisense, 5'-AGG-TAG-CGA-GTA-TTA-CTG-CC-3', respectively) is a 704-bp DNA fragment. The second set (P3-P4; sense, 5'-GCT-ATT-TCA-CCG-CCG-CTC-AC-3', and antisense, 5'-CCG-CAG-AGC-CGT-AAA-CCG-AA-3', respectively) amplifies an internal 222-bp DNA fragment. We developed a direct DNA extraction method that involved boiling the specimen pellet in a 1 mM EDTA-0.5% Triton X-100 solution. The new DNA extraction method was more sensitive and reproducible than other conventional methods. The DNA extraction method guaranteed sensitivity as well, even when V. vulnificus cells were mixed with other bacteria such as Escherichia coli or Staphylococcus aureus. The nested PCR method could detect as little as 1 fg of chromosomal DNA and single CFU of V. vulnificus. We applied the nested PCR protocol to a total of 39 serum specimens and bulla aspirates from septicemic patients. Seventeen (94.4%) of the 18 V. vulnificus culture-positive specimens were positive by the nested PCR. Eight (42.1%) of the 19 culture-negative samples gave positive nested PCR results.
Ferromagnetism (1993)

Described as THE classic text on magnetism, FERROMAGNETISM covers the basics of magnetics, as well as in-depth coverage of magnetic materials. IEEE Press has now brought this important cornerstone of magnetics research back into print. Recognized for its breadth of coverage, this book includes information on magnetic phenomenon and theories, magnetic materials, basic magnetization and domain theory, as well as many fundamental expressions, and useful technical data on many materials
Probing Cucurbituril Assemblies in Water with TEMPO-like Nitroxides: A Trinitroxide Supraradical with Spin−Spin Interactions (2009)

Nitroxide free radicals are demonstrated to be useful guests for probing cucurbit[n]uril (CB[n]) assemblies in water by EPR spectroscopy. CB[7] and CB[8] significantly aggregate either in solution or in the solid state (as evidenced by a single-crystal X-ray structure in which CB[8] forms supramolecular triangles with 4-methoxy-TEMPO). The included nitroxides show a striking resistance to biologically relevant reduction, benefiting from the carcerand effect of CB[7] and CB[8] solutions.
Image-based rendering of complex scenes from a multi-camera rig (2005)

Image-based rendering is a method to synthesise novel views from a set of given real images. Two methods to extrapolate novel views of complex scenes with occlusions and large depth discontinuities from images of a moving uncalibrated multi-camera rig are discribed. The real camera viewpoints are calibrated from the image data and dense depth maps are estimated for each real view. Novel views are synthesised from this representation with view-dependent image-based rendering techniques at interactive rates. Since the 3-D scene geometry is available in this approach, it is well suited for mixed reality applications where synthetic 3-D objects are seamlessly embedded in the novel view.
Pyruvate Orthophosphate Dikinase of C<sub>3</sub> Seeds and Leaves as Compared to the Enzyme from Maize (1984)

Pyruvate orthophosphate dikinase (PPDK) was found in various immature seeds of C(3) plants (wheat, pea, green bean, plum, and castor bean), in some C(3) leaves (tobacco, spinach, sunflower, and wheat), and in C(4) (maize) kernels. The enzyme in the C(3) plants cross-reacts with rabbit antiserum against maize PPDK. Based on protein blot analysis, the apparent subunit size of PPDK from wheat seeds and leaves and from sunflower leaves is about 94 kdaltons, the same as that of the enzyme from maize, but is slightly less (about 90 kdaltons) for the enzyme from spinach and tobacco leaves. The amount of this enzyme per mg of soluble protein in C(3) seeds and leaves is much less than in C(4) leaves. PPDK is present in kernels of the C(4) plant, Zea mays in amounts comparable to those in C(4) leaves.Regulatory properties of the enzyme from C(3) tissues (wheat) are similar to those of the enzyme from C(4) leaves with respect to in vivo light activation and dark inactivation (in leaves) and in vivo cold lability (seeds and leaves).Following incorporation of (14)CO(2) by illuminated wheat pericarp and adjoining tissue for a few seconds, the labeled metabolites were predominantly products resulting from carboxylation of phosphoenolpyruvate, with lesser labeling of compounds formed by carboxylation of ribulose 1,5-bisphosphate and operation of the reductive pentose phosphate cycle of photosynthesis. PPDK may be involved in mechanisms of amino acid interconversions during seed development.