gebhart/patrepeval huggingface dataset:
Efficient program analysis using DJ graphs (1996)

Program analysis is a process of estimating properties of a program statically. Program analyses have many applications, including compiler optimizations, software maintenance and testing, and program verification. In this dissertation we present a new framework for efficient program analysis. At the heart of our approach is a new program representation called the DJ Graph. Using DJ graphs we present several new algorithms for solving problems encountered in program analysis. The problems that we have solved range from a simple loop identification problem to sophisticated exhaustive and incremental data flow analysis, including the construction of Sparse Evaluation Graphs. The algorithms presented here are simple, more general, and/or more efficient than existing methods for solving similar problems. To study the effectiveness of our algorithms on real programs we implemented many of them, and experimented on a number of FORTRAN procedures taken from standard benchmark suites. Our results indicate that the algorithms presented here perform well in practice.
Estimating Menstrual Blood Loss in Women With Normal and Excessive Menstrual Fluid Volume (2001)

In Brief OBJECTIVE To examine the relationship between total fluid volume at menstruation and the volume of blood loss, and to assess the feasibility of using total fluid volume to estimate menstrual blood loss. METHODS Fifty-three women were studied over two menstrual periods each. Hemoglobin in menstrual pads and tampons was measured using the alkaline hematin technique; total menstrual fluid volume was simultaneously measured using a weighing technique and meticulous care to avoid evaporation. RESULTS Despite period-to-period change in measured total menstrual fluid and menstrual blood loss volumes, there was a significant correlation between total fluid volume and blood loss (r = .93, P < .001). Blood comprised 48% of total menstrual flow for women with moderately heavy blood loss (>60 mL) and 50% for women with excessive blood loss (>100 mL). Regression estimation of blood loss from total fluid volume was reasonably accurate. For clinical purposes, estimated blood volumes correctly classified 98% of periods in terms of actual blood loss as normal (<60 mL blood), moderately heavy (60–100 mL), or excessive (>100 mL). CONCLUSION If total fluid volume is measured carefully, the estimate of actual blood loss is sufficiently accurate for clinical purposes. This simple technique has considerable clinical potential, and inexpensive commercial packs for this purpose could easily be developed. Total menstrual fluid volume is easy to measure and provides an accurate estimate of actual blood loss.
Signal Transmission from Individual Mammalian Nerve Cell to Field‐Effect Transistor (2004)

Direct electrical interfacing of a semiconductor device to an individual mammalian nerve cell is reported. The firing neuron directly controls the source–drain current of a buried channel electrolyte–oxide–silicon (EOS) field-effect transistor. The experiment demonstrates the feasibility of noninvasive monitoring of neuronal systems by semiconductor chips at the level of individual cells and lays the foundation for applications of very-large-scale integration technology in neuroscience and pharmacology.
Suppression of Protein Adsorption at Glassy Carbon Electrodes Covalently Modified with Tetraethylene Glycol Diamine (1999)

Adsorption of high molecular weight species on electrode surfaces can complicate the application of voltammetric techniques to clinical and environmental samples. The performance of tetraethylene glycol diamine as a protective electrode coating has been examined. Glassy carbon electrodes were covalently modified with the diamine via an electrochemically assisted reaction. The voltammetric response of ferrocenemonocarboxylic acid (FCA) at unmodified and modified electrodes in the presence and absence of bovine serum albumin (BSA), lysozyme and ribonuclease (RNase) was used to monitor surface fouling by protein adsorption. Modified electrodes which retained very high sensitivity for FCA oxidation also exhibited excellent resistance to adsorption of all three proteins.
Classification of gene microarrays by penalized logistic regression (2004)

Classification of patient samples is an important aspect of cancer diagnosis and treatment. The support vector machine (SVM) has been successfully applied to microarray cancer diagnosis problems. However, one weakness of the SVM is that given a tumor sample, it only predicts a cancer class label but does not provide any estimate of the underlying probability. We propose penalized logistic regression (PLR) as an alternative to the SVM for the microarray cancer diagnosis problem. We show that when using the same set of genes, PLR and the SVM perform similarly in cancer classification, but PLR has the advantage of additionally providing an estimate of the underlying probability. Often a primary goal in microarray cancer diagnosis is to identify the genes responsible for the classification, rather than class prediction. We consider two gene selection methods in this paper, univariate ranking (UR) and recursive feature elimination (RFE). Empirical results indicate that PLR combined with RFE tends to select fewer genes than other methods and also performs well in both cross-validation and test samples. A fast algorithm for solving PLR is also described.
Dynamic Human Surface Reconstruction Using a Single Kinect (2013)

This paper presents a system for robust dynamic human surface reconstruction using a single Kinect. The single Kinect provides a self-occluded and noisy RGBD data. Thus it is challenging to track the whole human surface robustly. To overcome both incompleteness and data noise, we adopt a template to confine the shape in the un-seen part, and propose a two-stage tracking pipeline. The first stage tracks the articulated motion of the human, which improves robustness of tracking by introducing more constraints between the surface points. The second stage tracks movements of non-articulated motion. For long sequences, we stabilize the human surface in the un-seen part by directly warping the surface from the first frame to the current frame according to sequentially tracked correspondences, preventing surface from collapsing caused by error accumulation. We demonstrate our method by several real captured RGBD data, containing complex human motion. The reconstruction results show the effectiveness and robustness of our method.
Sustained activation of Ras/Raf/mitogen-activated protein kinase cascade by the tumor suppressor p53 (2000)

The p53 tumor suppressor gene can inhibit proliferation transiently, induce permanent cell-cycle arrest/senescence, or cause apoptosis depending on the cellular context. The mitogen-activated protein kinase (MAPK) cascade is known to play a crucial role in cell proliferation and differentiation. Moreover, the duration and intensity of MAPK activation can profoundly influence the biological response observed. We demonstrated that a sustained activation of MAPK cascade could be induced by wild-type p53 expression but not by p21(Waf1/Cip1). Furthermore, exposure of normal cells to DNA-damaging agents induced MAPK activation in a p53-dependent manner. Tumor-derived p53 mutants defective in DNA binding failed to activate MAPK, implying that p53 transcriptional activity is essential for this function. Finally, activation of MAPK by p53 was inhibited by expression of dominant-negative Ras (N17Ras) and Raf1 mutants, indicating that MAPK activation by p53 is mediated at a level upstream of Ras. All of these findings establish a biochemical link between p53 signaling and the Ras/Raf/MAPK cascade.
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector (2016)

The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated genes (Cas) adaptive immune system defends microbes against foreign genetic elements via DNA or RNA-DNA interference. We characterize the class 2 type VI CRISPR-Cas effector C2c2 and demonstrate its RNA-guided ribonuclease function. C2c2 from the bacterium Leptotrichia shahii provides interference against RNA phage. In vitro biochemical analysis shows that C2c2 is guided by a single CRISPR RNA and can be programmed to cleave single-stranded RNA targets carrying complementary protospacers. In bacteria, C2c2 can be programmed to knock down specific mRNAs. Cleavage is mediated by catalytic residues in the two conserved Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) domains, mutations of which generate catalytically inactive RNA-binding proteins. These results broaden our understanding of CRISPR-Cas systems and suggest that C2c2 can be used to develop new RNA-targeting tools.
Antibody mapping to domains of botulinum neurotoxin serotype A in the complexed and uncomplexed forms (1997)

The domain organization of the botulinum neurotoxin serotype A was studied by using antibody mapping of 44 monoclonal single-chain variable fragments. The analysis was carried out on (i) the individual domains of botulinum neurotoxin holotoxin (binding, translocation, and catalytic), (ii) botulinum neurotoxin holotoxin, (iii) the botulinum neurotoxin holotoxin in complex with the nontoxic portion, and (iv) botulinum neurotoxin holotoxin and nontoxic portion of the complex recombined in vitro. All 44 antibodies mapped to individual domains of botulinum neurotoxin. Forty of the 44 single-chain variable fragments bound the botulinum neurotoxin holotoxin relative to the isolated domains, suggesting that 4 epitopes are covered when the individual domains are in the holotoxin form. Only 20 of the antibodies showed a positive reaction to the toxin while in complex with the nontoxic portion. All of the covered epitopes were mapped to the binding domain of botulinum neurotoxin, which suggested that the binding domain is in direct contact with the nontoxic portion in the complex. Based on the antibody mapping to the different domains of the botulinum neurotoxin holotoxin and the entire complex, a model of the botulinum neurotoxin complex is proposed.
Identification of Amino Acid Residues of Anthrax Protective Antigen Involved in Binding with Lethal Factor (2002)

Protective antigen (PA) and lethal factor (LF) are the two components of anthrax lethal toxin. PA is responsible for the translocation of LF to the cytosol. The binding of LF to cell surface receptor-bound PA is a prerequisite for the formation of lethal toxin. It has been hypothesized that hydrophobic residues P184, L187, F202, L203, P205, I207, I210, W226, and F236 of domain 1b of PA play an important role in the binding of PA to LF. These residues are normally buried in the 83-kDA version of PA, PA83, as determined by the crystal structure of PA. However, they become exposed due to the conformational change brought about by the cleavage of PA83 to PA63 by a cell surface protease. Mutation of the above-mentioned residues to alanine resulted in mutant proteins that were able to bind to the cell surface receptors and also to be specifically cleaved by the cellular proteases. All the mutant proteins except the F202A, L203A, P205A, and I207A mutants were able to bind to LF and were also toxic to macrophage cells in combination with LF. It was concluded that residues 202, 203, 205, and 207 of PA are essential for the binding of LF to PA.
Multicast Communication on Network Computers (1985)

Channel-oriented packet casting is a predominant feature of Micros, an operating system designed to explore control and communication techniques for network computers containing thousands of hosts.
Broad spectrum inhibition of HIV-1 infection by sulfated K5 Escherichia coli polysaccharide derivatives (2003)

Because K5 derivatives are unlikely to penetrate into cells they may represent potential topical microbicides for the prevention of sexual HIV-1 transmission.
A time diversity CDMA scheme employing orthogonal modulation for time varying channels (2002)

In order to increase the channel capacity of CDMA (code division multiple access) mobile and personal communication systems, a new time diversity CDMA scheme that employs orthogonal modulation is proposed. The time diversity CDMA scheme with orthogonal modulation reduces the required Eb/(No+Io) by 5 dB at Pe = 10/sup -2/ in Rayleigh fading environments with fDT (the product of Doppler frequency and one symbol duration) values ranging from 0.002 to 0.02. This improvement in required Eb/(No+Io) significantly increases the channel capacity of CDMA communication systems that have time varying channels. Computer simulation results show that the required time delay values of the time diversity scheme are resonably short (20-100 symbols for 10 kbps transmission) for fDT values ranging from 0.002 to 0.02.
Impact of Glycosylation on Effector Functions of Therapeutic IgG (2010)

Human IgG has only one conserved glycosylation site located in the Cγ2 domain of the Fc region that accounts for the presence of two sugar moieties per IgG. These IgG sugar cores play a critical role in a number of IgG effector functions. In the present review, we describe the main characteristics of IgG Fc glycosylation and some abnormalities of serum IgG glycosylation. We also discuss how glycosylation impacts on monoclonal antibodies (mAbs) and IVIg effector functions and how these molecules can be engineered. Several therapeutic antibodies have now been engineered to be no- or low-fucose antibodies and are currently tested in clinical trials. They exhibit an increased binding to activating FcγRIIIA and trigger a strong antibody-dependent cell cytotoxicity (ADCC) as compared to their highly-fucosylated counterparts. They represent a new generation of therapeutic antibodies that are likely to show a better clinical efficacy in patients, notably in cancer patients where cytotoxic antibodies are needed.
Globalisation - the effect on directors' fees and tax : tax (2014)

Globalisation has created wonderful opportunities for businesses to expand their reach across the borders of various jurisdictions and significantly increase their market share. In addition, it has enabled many individuals and companies to invest in operations beyond the jurisdictions in which they reside or are registered. Markets are no longer compartmentalised based on jurisdiction and, as a consequence, multi-national companies have had to adapt the manner in which they control and manage their operations.
Isolation and characterization of sulfhydryl oxidase from bovine milk. (1975)

A method is described for purification of sulfhydryl oxidase from bovine milk which consistently yields preparations with greater than 3000-fold purification over skim milk. A concentration-dependent association-dissociation of the enzyme was adapted to the development of an isolation procedure. Purified preparations exhibited two zones, both of which displayed activity, upon polyacrylamide disc gel electrophoresis, but only one zone following disc gel electrophoresis in sodium dodecyl sulfate. Its mobility indicated a subunit weight of 89,000. Several lines of evidence suggest that iron is an integral part of the enzyme. Treatment of the enzyme with EDTA resulted in complete loss of activity which could be subsequently restored by dialysis against 1 muM ferrous sulfate. Furthermore, atomic absorption analysis and neutron activation analysis of separate enzyme preparations each indicated 0.5 atom of iron per subunit. Chemical analyses of sulfhydryl oxidase accounted for 97% of the sample weight, of which 89% could be attributed to amino acid residues and 11% to carbohydrate residues. Five half-cystine residues per subunit were indicated by cysteic acid analysis and by sulfhydryl group determination following reaction with sodium borohydride. Comparison of this value to the total sulfhydryl groups without reduction tentatively suggests the presence of one disulfide bond. Sulfhydryl oxidase was found to catalyze the oxidation of sulfhydryl groups in both small compounds and proteins, using O2 as oxidant and producing, in equimolar quantities, H2O2 and the corresponding disulfide. A Michaelis constant of 90 muM was obtained using reduced glutathione as substrate, under conditions of optimal pH and temperature, viz., pH 7.0 and 35 degrees. Substrate inhibition was apparent at GSH concentrations above 0.8 mM. In the presence of sulfhydryl oxidase, reductively denatured RNase was reoxidized and fully reactivated within 1 hour, whereas in the absence of the oxidase under otherwise identical conditions, full recovery of RNase activity required 24 hours. The presence of reducing agent was not required for this activity, nor was prior reduction of the sulfhydryl oxidase. Based on the observed activity, it appears that the enzyme could be involved in the biosynthesis of disulfide bonds in certain proteins.
Assessment of Dental Caries with Digital Imaging Fiber-Optic Translllumination (DIFOTI<sup>TM</sup>): In vitro Study (1997)

This paper describes Digital Imaging Fiber-Optic TransIllumination (DIFOTI-TM), a new method for the reliable detection of dental caries. Images of teeth obtained through visible-light, fiber-optic transillumination (FOTI) are acquired with a digital CCD camera, and sent to a computer for analysis with dedicated algorithms. The algorithms were developed to facilitate the location and diagnosis of carious lesions by the operator in real time, and provide quantitative characterization for monitoring of the lesions. The DIFOTI method has been tested by imaging teeth in vitro. The results suggest the superior sensitivity of DIFOTI for detection of approximal, occlusal and smooth-surface caries vis-à-vis radiological imaging.
Applied virtual reality for simulation of endoscopic retrograde cholangio-pancreatography (ERCP). (1996)

Researchers from the Georgia Institute of Technology and the Medical College of Georgia (GIT/MCG) have developed an interactive computer simulation of Endoscopic Retrograde Cholangio-Pancreatography (ERCP). ERCP is a minimally invasive technique for evaluating and treating pathologic conditions of the biliary and pancreatic ducts. While ERCP provides the patient with substantial advantages over traditional methods, ERCP requires advanced skills and extensive experience to minimize the risk of complications. Computer simulation offers many advantages for efficiently and safely training physicians in ERCP. The GIT/MCG proof of concept simulation provides realistic training with both visual and force feedback while an endoscopist practices the ERCP procedure.
An introduction to nuclear magnetic resonance in biomedicine. (1990)

In this paper the author illustrates the historical aspects of the development, first, of the fundamental principles of nuclear magnetic resonance and, second, the extension of these principles to magnetic resonance imaging and in vivo spectroscopy.
Immunohistochemical study of androgen receptors in metastatic prostate cancer. Comparison of receptor content and response to hormonal therapy (1991)

A longstanding goal has been to determine whether androgen receptor (AR) levels could be used to predict the clinical response of metastatic prostate cancer to androgen withdrawal therapy. A major limitation of previous studies was the use of homogenized tissue, which yields an average AR content for all cells. By AR immunohistochemical study using an antibody specific for AR the authors assessed nuclear AR content specifically in the malignant epithelial cells of prostate needle biopsy specimens of 17 patients with Stage D prostate cancer. The authors found that prostate cancer contains AR-positive and AR-negative malignant cells before androgen withdrawal therapy, but the percentage of AR-positive cells did not predict the time to tumor progression after therapy. There was no significant correlation between the percentage of AR-positive malignant cells and the time to tumor progression. When patients were divided into two groups based on the median time to progression, the percentage of AR-positive nuclei was not significantly different in poor responders versus good responders. When patients were divided into two groups based on the median percentage of receptor-positive nuclei, Kaplan-Meier estimates of the progression-free interval revealed no significant difference between the group of patients with AR-poor tumors and patients with AR-rich tumors. Potential explanations for these results are discussed. The authors conclude that the percentage of AR-positive nuclei is not a sufficient criterion to predict tumor behavior.
Identification of a human pancreatic duct tissue-specific antigen. (1983)

Antiserum raised against a pancreatic duct mucin was absorbed with type AB red blood cells and used in the indirect immuno-glucose oxidase procedure to examine tissue specificity. All mucin-producing organs were stained by this antiserum. Absorption of the antiserum with mucinous ovarian cystadenocarcinoma fluid eliminated generalized mucin staining, and only pancreatic ducts and colonic goblet cells were positive. Further absorption with purified colonic mucin revealed a pancreatic duct tissue-specific determinant(s). This tissue-specific determinant(s) was detected in the RIP-1 and RIP-2 human pancreatic adenocarcinomas carried as xenografts in athymic nude mice. Because the majority of pancreatic adenocarcinomas are believed to arise from ductal tissue, pancreatic duct mucin may have a useful role as a marker in detection and differential diagnosis.
Oxygen vacancy clusters on ceria: Decisive role of ceriumfelectrons (2009)

Defects such as oxygen vacancies dominate the electronic and chemical properties of ceria. However, fundamental understanding of such defects, especially clusters of vacancies, is sparse. In this work, we use density-functional theory with the addition of the Hubbard $U$ term to investigate various oxygen vacancies, including the vacancy monomer, dimer, trimer, and tetramer, in which subsurface vacancies can also be involved. We show that the individual surface and subsurface vacancies have very similar stabilities; the vacancy dimer consisting of two surface vacancies, which is not reported experimentally, is stable in theory; between the two vacancy trimers observed in experiments, the triangular surface vacancy cluster is more stable than the double linear surface vacancy cluster containing a subsurface vacancy, which agrees with some experiments but disagrees with some others; and the linear vacancy tetramer emerges as the most stable among the possible tetramers containing subsurface vacancies, although it is less stable than those containing no subsurface vacancies. These findings are rationalized in terms of the electronic change upon the removal of oxygen, namely, the localization of resulting excess electrons on $\text{Ce}\text{ }f$ orbitals. We identify a correlation between the energy levels of the occupied $f$ states of reduced Ce ions and their coordination numbers, which proves pivotal in interpreting formation energy and stability of various vacancies. Comparisons are made with experiments and apparent discrepancies are discussed. Results for gold adsorption on the vacancy clusters are presented, and the implications these have in catalysis are briefly discussed.