gebhart/patrepeval huggingface dataset:
Differential Transformation of Mammary Epithelial Cells by Wnt Genes (1994)

The mouse Wnt family includes at least 10 genes that encode structurally related secreted glycoproteins. Wnt-1 and Wnt-3 were originally identified as oncogenes activated by the insertion of mouse mammary tumor virus in virus-induced mammary adenocarcinomas, although they are not expressed in the normal mammary gland. However, five other Wnt genes are differentially expressed during development of adult mammary tissue, suggesting that they may play distinct roles in various phases of mammary gland growth and development. Induction of transformation by Wnt-1 and Wnt-3 may be due to interference with these normal regulatory events; however, there is no direct evidence for this hypothesis. We have tested Wnt family members for the ability to induce transformation of cultured mammary cells. The results demonstrate that the Wnt gene family can be divided into three groups depending on their ability to induce morphological transformation and altered growth characteristics of the C57MG mammary epithelial cell line. Wnt-1, Wnt-3A, and Wnt-7A were highly transforming and induced colonies which formed and shed balls of cells. Wnt-2, Wnt-5B, and Wnt-7B also induced transformation but with a lower frequency and an apparent decrease in saturation density. In contrast, Wnt-6 and two other family members which are normally expressed in C57MG cells, Wnt-4 and Wnt-5A, failed to induce transformation. These data demonstrate that the Wnt genes have distinct effects on cell growth and should not be regarded as functionally equivalent.
Recovery of Ventricular Function after Myocardial Infarction in the Reperfusion Era: The Healing and Early Afterload Reducing Therapy Study (2001)

Significant myocardial stunning with subsequent improvement of ventricular function occurred in the majority of patients after Q-wave anterior myocardial infarction. A lower peak level of creatine kinase, an estimate of the extent of necrosis, is independently predictive of recovery of function. Early functional assessment (day 1 after acute myocardial infarction) had limited ability to predict recovery of ventricular function.
Identification of undiagnosed inflammatory arthritis in a community health fair screen (2009)

Health fair screening may be an effective approach for the identification of individuals with undiagnosed IA/RA. A combination of the CSQ and autoantibody testing alone has clinically useful diagnostic accuracy for the detection of IA. Decisions regarding which methodology to use for future health fair IA/RA screening will depend on goals of screening and funding.
Detection of Y chromosome‐specific DNA in the plasma and urine of pregnant women using nested polymerase chain reaction (2001)

The present study was undertaken to evaluate a nested polymerase chain reaction (PCR) for detection of Y chromosome-specific fetal DNA in maternal plasma and urine of pregnant women during different gestational stages. DNA isolated from plasma and urine samples of 80 pregnant women (between 7 and 40 weeks' gestation) underwent amplification for Y chromosome-specific 198 bp DNA by nested PCR. The postpartum analysis of fetal gender showed that 55 women carried male and 25 female fetuses. Among the 55 women bearing male fetuses, Y chromosome-specific signals were detected in 53 (96%) plasma and 21 (38%) urine samples. Moreover, out of 25 women bearing female fetuses, 3 (12%) and 1 (4%) women had Y chromosome-specific signal in plasma and urine, respectively. Analysis of results with respect to gestational age revealed that there was no significant difference in the detection of Y chromosome-specific DNA between different trimesters in maternal plasma of women bearing male fetuses. These results showed that fetus-specific DNA was detected with high sensitivity (96%) and specificity (88%) in the maternal plasma by nested PCR, and therefore the method could be useful as a non-invasive procedure for fetal sex determination and prenatal diagnosis.
Generation and Analysis of Attack Graphs (2012)

An integral part of modeling the global view of network security is constructing attack graphs. Construction by hand, however, is tedious, error prone, and impractical for attack graphs larger than a hundred nodes. In this paper we present an automated technique for generating and analyzing attack graphs. We base our technique on symbolic model checking algorithms, letting us construct attack graphs automatically and efficiently. We also describe two analyses to help decide which attacks would be most costeffective to guard against. We implemented our technique in a tool suite and tested it on a small network example, which includes models of a firewall and an intrusion detection system.
Quantum networks for elementary arithmetic operations (1996)

Quantum computers require quantum arithmetic. We provide an explicit construction of quantum networks effecting basic arithmetic operations: from addition to modular exponentiation. Quantum modular exponentiation seems to be the most difficult (time and space consuming) part of Shor's quantum factorizing algorithm. We show that the auxiliary memory required to perform this operation in a reversible way grows linearly with the size of the number to be factorized. \textcopyright{} 1996 The American Physical Society.
Synthetic Aperture Focusing using a Shear-Warp Factorization of the Viewing Transform (2006)

Synthetic aperture focusing consists of warping and adding together the images in a 4D light field so that objects lying on a specified surface are aligned and thus in focus, while objects lying of this surface are misaligned and hence blurred. This provides the ability to see through partial occluders such as foliage and crowds, making it a potentially powerful tool for surveillance. If the cameras lie on a plane, it has been previously shown that after an initial homography, one can move the focus through a family of planes that are parallel to the camera plane by merely shifting and adding the images. In this paper, we analyze the warps required for tilted focal planes and arbitrary camera configurations. We characterize the warps using a new rank- 1 constraint that lets us focus on any plane, without having to perform a metric calibration of the cameras. We also show that there are camera configurations and families of tilted focal planes for which the warps can be factorized into an initial homography followed by shifts. This shear-warp factorization permits these tilted focal planes to be synthesized as efficiently as frontoparallel planes. Being able to vary the focus by simply shifting and adding images is relatively simple to implement in hardware and facilitates a real-time implementation. We demonstrate this using an array of 30 videoresolution cameras; initial homographies and shifts are performed on per-camera FPGAs, and additions and a final warp are performed on 3 PCs.
Role of CD26/dipeptidyl peptidase IV in human immunodeficiency virus type 1 infection and apoptosis. (1994)

To examine the role of CD26/dipeptidyl peptidase IV (DPPIV; EC 3.4.14.5) in infection by human immunodeficiency virus type 1 (HIV-1), we utilized CD26 cDNA-transfected Jurkat T-cell lines. Both CD26- parental Jurkat cells and mutant CD26+ (DPPIV-) transfected Jurkat cells were readily infected with HIV-1, whereas wild-type CD26+ (DPPIV+) transfected Jurkat cells were more resistant to HIV-1 infection. Our results suggest that CD26 is not essential for HIV-1 infectivity as suggested by others but that DPPIV enzyme activity may decrease the efficiency of HIV-1 infection. Of great interest, we found that mutant CD26+ (DPPIV-) transfectants and CD26- parental Jurkat cells strongly expressed CD95 (Fas/Apo-1) and were more sensitive than wild-type CD26+ (DPPIV+) transfectants to the induction of apoptosis by anti-CD95 monoclonal antibody. These results suggest that CD26 may play a role in HIV-1-associated loss of -CD4+ cells through the process of programmed cell death.
MRL mice produce anti-Su autoantibody, a specificity associated with systemic lupus erythematosus (1993)

Certain autoimmune mouse strains exhibit features similar to human SLE. To discover genetic and immunologic events governing expression of a new SLE-associated antibody, the presence of anti-Su and its relationship to other SLE-related antibodies (anti-Sm, -ribonucleoprotein, -Ro (SS-A), -La (SS-B)) were determined in MRL and other autoimmune and nonautoimmune mice. By double immunodiffusion, sera from 34/183 (19%) 4- to 10-mo-old MRL/Mp-lpr/lpr (MRL/lpr) and 28/108 (26%) 8- to 20-mo-old MRL/Mp(-)+/+ (MRL/+) mice were positive for anti-Su antibodies. Anti-Sm antibodies were found in 60/183 (33%) and 39/108 (36%) of these animals, respectively. The two specificities were found together in individual mice more frequently than would be predicted by chance. In contrast, C57BL/6-lpr/lpr (B6/lpr) mice rarely showed either specificity. Analysis of F1 hybrids between B6/lpr and MRL/lpr and of F1 x MRL/lpr backcross mice suggested that a small number of autosomal recessive genes controlled the anti-Su and anti-Sm responses. With the exception of a single NZB serum sample, NZB, BXSB, and nonautoimmune mice were negative for all antibodies tested, and no mice were positive for anti-RNP, anti-Ro, or anti-La. MRL/lpr and MRL/+ autoimmune mice thus provide unique models for human SLE, because they express several of the SLE-specific marker autoantibodies. These models should be useful in disclosing molecular and immunologic events governing autoantibody expression in this condition.
A new model of Pneumocystis carinii infection in mice selectively depleted of helper T lymphocytes. (1990)

Pulmonary infections with Pneumocystis carinii are an important cause of morbidity and mortality in patients with AIDS. P. carinii infections are seen in patients with decreased numbers of helper T lymphocytes, suggesting that these cells are important in preventing infection. To test this hypothesis, we sought to establish experimental infection with P. carinii in mice selectively depleted of helper T lymphocytes. Weekly injections of a monoclonal anti-CD4 antibody produced sustained depletion of helper T lymphocytes from blood and lymphoid organs. To establish pulmonary infection, lymphocyte-depleted mice were then given intratracheal inoculations of P. carinii organisms derived from the lungs of chronically infected athymic mice. Pulmonary infection with P. carinii was demonstrable in the antibody-treated mice and was centered around the conducting airways. Infection was persistent for up to 3 mo with continued antibody treatments, and yet could be cleared from the lungs if antibody treatments were discontinued. This experimental model of P. carinii infection permits the study of infection associated with a specific immune defect and implicates the helper T lymphocyte as a critical cell in host defense against this pathogen.
Mutation and mapping of genes involved in production of the antibiotic TA in Myxococcus xanthus (1992)

Transposition of TnV and Tn5lac into Myxococcus xanthus yielded 8,381 kanamycin-resistant mutants that were tested for antibiotic TA production. Twenty-four of the mutants were nonproducers of TA (less than 0.4 ng/ml), and 3 produced a higher level (2.5 micrograms/ml) than the parent strain (1.5 micrograms/ml). For most of the strains, there was 100% cotransduction between kanamycin resistance and the altered TA phenotype. Southern blot analysis of restriction digests of the mutant DNA indicated that the transposons were inserted at different sites on the M. xanthus chromosome. The TA genes were mapped by cotransduction between pairs of mutants following replacement of the initial insert of one of the pair with the tetracycline resistance transposon Tn5-132. Nine of the 13 nonproducers tested were linked over a 36-kb stretch of the chromosome. There was no linkage between one of the overproducers and any of the nonproducers tested.
Animal models of mood disorders: recent developments (2006)

Endophenotype-based modelling of depression and bipolar illness is opening up more tractable avenues for understanding the neurobiological and genetic bases of these disorders. Further, advances in the clinical dissection of the psychiatric illnesses using molecular genetics, coupled with functional neuroimaging techniques, promises to yield better translational animal models and hence more fruitful therapeutic targets.
Active odor sensing system (2002)

Pattern recognition of sensor-array signals to identify odors is a standard style of an electronic nose. Although that method is effective to compensate for each insufficient selectivity of a sensor, a more sophisticated approach is required to extend the field of artificial odor sensing system. As active sensing is an important concept for realizing a sensing system with high capability, the concept was introduced into a chemical sensing system. Since we have developed quantification of mixture composition of aromas and odor-source localization system, these active odor sensing systems are described.
Therapeutic angiogenesis for critical limb ischemia: design of the hepatocyte growth factor therapeutic angiogenesis clinical trial (2004)

The objective of the HGF-STAT clinical trial is to determine whether perfusion can be improved by gene transfer with a plasmid DNA containing hepatocyte growth factor (HGF) in the affected limb of patients with unreconstructable critical limb ischemia (CLI). CLI results in a high rate of limb loss and impaired quality of life. The current therapeutic strategies, including bypass surgery and percutaneous interventions, are only successful in treating a subset of patients. Therapeutic angiogenesis is an investigational method that seeks to favorably impact tissue perfusion in CLI. HGF-STAT is a double-blind, parallel-group, placebo-controlled, dose-response study in 100 patients with unreconstructable CLI. Eligible subjects will be randomized 1:1:1:1 to receive saline placebo or one of three dose/regimens of HGF plasmid DNA. The selection of outcome measures, including the primary endpoint, and changes in transcutaneous oxygen pressure (TcPO2) from baseline to 3 months will be discussed. In conclusion, this study will help to determine whether therapeutic angiogenesis with HGF is a viable option in the treatment of patients with CLI.
Measurements of fatty acid synthesis by incorporation of deuterium from deuterated water (1979)

Fatty acid synthesis by perfused livers of rat is measured by using D2O as tracer. The newly synthesized, deuterium-labeled fatty acids are separated from unlabeled fatty acids by gas chromatography using glass capillary columns. The areas of the deuterium-labeled peaks are proportional to the amounts of fatty acids synthesized. The absolute amounts of the individual fatty acids synthesized are obtained by use of an internal standard. The number of deuterium atoms incorporated, as determined by mass spectrometry, is proportional to the D2O concentration of the perfusate, except at very high concentrations of D2O. The relative retention times of the newly synthesized, deuterium-labeled fatty acids are proportional to their deuterium content.
Small Molecules, Big Plans—Can Low‐Molecular‐Weight Compounds Control Human Regeneration? (2004)

The name is the game. Reversine (1) is a low-molecular-weight compound that reverses the process of cell differentiation in mammals. Specialized muscle cells can be transformed into multipotent progenitor cells. This approach may have potential for targeted regeneration processes in humans.
Broad-spectrum frequency comb generation and carrier-envelope offset frequency measurement by second-harmonic generation of a mode-locked fiber laser (2003)

A frequency comb spanning more than one octave has been achieved by injecting the second-harmonic generation (780 nm) of a mode-locked fiber laser (1.56 microm) into a photonic crystal fiber. We propose and realize a novel interferometric scheme for observing the carrier-envelope offset frequency of the frequency comb. Frequency noise has been observed on the measured carrier-envelope offset frequency, which has been confirmed to be generated in the photonic crystal fiber by comparing the measured beat frequencies between cw lasers and frequency combs before and after the photonic crystal fiber. The mode-locked fiber laser is considered to be an important candidate for the light source used in realizing a compact optical frequency measurement system including applications in the telecommunication bands.
The Neutrophil-Activating Protein (NAP-1) Is Also Chemotactic for T Lymphocytes (1989)

T lymphocyte chemotactic factor (TCF) was purified to homogeneity from the conditioned media of phytohemagglutinin-stimulated human blood mononuclear leukocytes by a sequence of chromatography procedures. The amino-terminal amino acid sequence of the purified TCF showed identity with neutrophil-activating protein (NAP-1). Both TCF and recombinant NAP-1 (rNAP-1) were chemotactic for neutrophils and T lymphocytes in vitro supporting the identity of TCF with NAP-1. Injection of rNAP-1 into lymphatic drainage areas of lymph nodes in Fisher rats caused accelerated emigration of only lymphocytes in high endothelial venules. Intradermal injection of rNAP-1 caused dose-dependent accumulation of neutrophils and lymphocytes.
Mean and variance of ratio estimators used in fluorescence ratio imaging (2000)

We have derived an unbiased ratio estimator that outperforms intuitive ratio estimators.
Poly (Methylstyrene - Dimethylsiloxane) Block Copolymers As Bilevel Resists (1985)

Multi-level resist systems are rapidly becoming essential in the drive towards submicron lithography. Such systems offer many inherent advantages over single level schemes, such as planarization of underlying substrate, higher resolution and formation of high aspect ratio patterns. Other advantages, particular to specific exposure technologies, can also be found. These include minimization of backscatter and proximity effects for electron beam lithography or reduction of standing wave effects and depth of focus problems for photolithography.
A study of bite force, part 2: Relationship to various cephalometric measurements. (1995)

Maximum bilateral bite force, determined in 129 dental students, was evaluated with regard to six skeletal and eight dental measurements acquired from conventional lateral cephalometric radiographs. Statistically significant correlations for three of the skeletal measurements were found. Maximum bite force increased with regard to decreasing mandibular plane/palatal plane angle and to decreasing mandibular plane angles. Maximum bite force increased with an increasing ratio of posterior facial height to anterior facial height. Significant statistical correlation for only one of the eight dental measurements was found: maximum bite force related directly with increasing maxillary and/or mandibular dentoalveolar heights, and unexpected finding.
Spin Based Heat Engine: Demonstration of Multiple Rounds of Algorithmic Cooling (2008)

We experimentally demonstrate multiple rounds of heat-bath algorithmic cooling in a 3 qubit solid-state nuclear magnetic resonance quantum information processor. By pumping entropy into a heat bath, we are able to surpass the closed system limit of the Shannon bound and purify a single qubit to 1.69 times the heat-bath polarization. The algorithm combines both high fidelity coherent control and a deliberate interaction with the environment. Given this level of quantum control in systems with larger reset polarizations, nearly pure qubits should be achievable.
Formation and Occurrence of Flavor Compounds in Wine and Distilled Alcoholic Beverages (1986)

The most probable mechanisms involved in the formation of carbonyl compounds, fusel alcohols, fatty acid esters, and free fatty acids by yeast in fermentation are discussed. Isopentyl alcohol, phenethyl alcohol, and their acetates in addition to the ethyl esters from hexanoate to laurate formed by different yeasts in sugar fermentation were determined. The bivariate distributions of the concentrations indicate that the mutual relationships of the compounds depend significantly on the yeast used and on the capacity of the yeast to produce alcohols and esters. The wine yeast used in this work produced smaller amounts of ethyl esters of fatty acids from acetic acid to octanoic acid under aerobic fermentation conditions than under strictly anaerobic conditions; on the other hand, ethyl laurate and ethyl 9-hexadecenoate were formed more abundantly in anaerobic conditions. Furthermore, qualitatively-similar flavor compositions were obtained in a Spanish sherry and a Finnish berry wine of sherry type. Hence, the formation of the most dominant compounds occurring in beverages depend more on the yeast selected than the raw materials used in fermentation.
Further evidence that CENP-C is a necessary component of active centromeres: studies of a dic(X; 15) with simultaneous immunofluorescence and FISH (1995)

The stability of certain dicentric chromosomes in humans seems to result from inactivation of one centromere, yielding a functionally monocentric chromosome. Centromere protein C (CENP-C) was previously shown to be present at active centromeres but absent from the inactive centromere of one homologous dicentric rearrangement. We have combined indirect immunofluorescence detection of CENP-C and fluorescence in situ hybridization with chromosome-specific alpha-satellite DNA probes in a simultaneous assay to unequivocally identify the active and inactive centromeres of a dicentric (X;15) translocation. In both fibroblast and lymphoblast cell lines containing the translocation, the X chromosome centromere consistently had a primary constriction and CENP-C immunofluorescence, and is therefore the active centromere. CENP-C was never detected at the chromosome 15 centromere, which appears to be inactive. The inactivation pattern is apparently stable and observed in all cells with the translocation. Immunofluorescence with CREST serum revealed staining at both centromeres of the translocation, and thus was not specific to the active centromere. This study demonstrates the specificity of CENP-C to the active centromere in a non-homologous rearrangement and further establishes CENP-C as an essential component of a functional human centromere.
Hepatic acute-phase proteins control innate immune responses during infection by promoting myeloid-derived suppressor cell function (2010)

Acute-phase proteins (APPs) are an evolutionarily conserved family of proteins produced mainly in the liver in response to infection and inflammation. Despite vast pro- and antiinflammatory properties ascribed to individual APPs, their collective function during infections remains poorly defined. Using a mouse model of polymicrobial sepsis, we show that abrogation of APP production by hepatocyte-specific gp130 deletion, the signaling receptor shared by IL-6 family cytokines, strongly increased mortality despite normal bacterial clearance. Hepatic gp130 signaling through STAT3 was required to control systemic inflammation. Notably, hepatic gp130-STAT3 activation was also essential for mobilization and tissue accumulation of myeloid-derived suppressor cells (MDSCs), a cell population mainly known for antiinflammatory properties in cancer. MDSCs were critical to regulate innate inflammation, and their adoptive transfer efficiently protected gp130-deficient mice from sepsis-associated mortality. The hepatic APPs serum amyloid A and Cxcl1/KC cooperatively promoted MDSC mobilization, accumulation, and survival, and reversed dysregulated inflammation and restored survival of gp130-deficient mice. Thus, gp130-dependent communication between the liver and MDSCs through APPs controls inflammatory responses during infection.