gebhart/patrepeval huggingface dataset:
Vaginal Lactobacilli, Microbial Flora, and Risk of Human Immunodeficiency Virus Type 1 and Sexually Transmitted Disease Acquisition (1999)

A prospective cohort study was conducted to examine the relationship between vaginal colonization with lactobacilli, bacterial vaginosis (BV), and acquisition of human immunodeficiency virus type 1 (HIV-1) and sexually transmitted diseases in a population of sex workers in Mombasa, Kenya. In total, 657 HIV-1-seronegative women were enrolled and followed at monthly intervals. At baseline, only 26% of women were colonized with Lactobacillus species. During follow-up, absence of vaginal lactobacilli on culture was associated with an increased risk of acquiring HIV-1 infection (hazard ratio [HR], 2.0; 95% confidence interval [CI], 1.2-3.5) and gonorrhea (HR, 1.7; 95% CI, 1.1-2.6), after controlling for other identified risk factors in separate multivariate models. Presence of abnormal vaginal flora on Gram's stain was associated with increased risk of both HIV-1 acquisition (HR, 1.9; 95% CI, 1.1-3.1) and Trichomonas infection (HR, 1.8; 95% CI, 1.3-2.4). Treatment of BV and promotion of vaginal colonization with lactobacilli should be evaluated as potential interventions to reduce a woman's risk of acquiring HIV-1, gonorrhea, and trichomoniasis.
A General Strategy to Enantiomerically Pure Aliphatic and Olefinic Ketone Cyanohydrins by Stereoselective Alkylation of Umpoled Aldehyde Derivatives (1997)

We present the first general synthesis of optically pure (R)- and (S)-ketone cyanohydrins with olefinic and aliphatic substituents. Consecutive condensations of POCl3 with pseudoephedrine (1) and racemic crotonaldehyde cyanohydrin (3, R = 1-propenyl) lead to the respective cyanohydrin phosphate 4c. Deprotonation, followed by highly stereoselective alkylation and a single chromatographic purification step, afford diastereomerically pure ketone cyanohydrin phosphates 5a−e. From these, enantiomerically pure tertiary cyanohydrins 6a−e can be obtained by mild Lewis acid-assisted hydrolysis. Pseudoephedrine is simultaneously recovered without loss of optical purity. The unsaturated alkylation products 5a−d are readily hydrogenated with diimide to aliphatic cyanohydrin phosphates 5f−i, which can be cleaved to furnish the free optically pure cyanohydrins 6f−i. Thus a broad variety of both saturated and unsaturated ketone cyanohydrins with R > Et becomes accessible in optically pure form for the first time. The free cyanohydrins are easily converted to optically pure α-branched α-hydroxy acids.
A Study on the Aspheric Glass tens Forming Analysis in the Progressive GMP Process (2007)

In the past, precision optical glass lenses were produced through multiple processes such as grinding and polishing, but mass production of aspheric glass lenses requiring high accuracy and having complex profile was rather difficult. In such a background, the high-precision optical glass molding pressing (GMP) process was developed with an eye to mass production of precision optical glass parts by molding press. In this paper, as a fundamental research to develop the multi-cavity mold for higher productivity of a progressive GMP process used in the fabrication of an aspheric glass lens, an aspheric glass lens forming simulation was carried out.
T-cell-mediated protection of mice against virulent Mycobacterium tuberculosis (1989)

We sought to protect CBA mice against tuberculosis using in vivo transfer of a T-cell line previously shown to be capable of I-A-restricted recognition of peritoneal macrophages infected in vitro with Mycobacterium tuberculosis. This line induces total bacteriostasis in vitro. In mice that received 500 rads of irradiation 48 h before infection, the T-cell line caused significant prolongation of life when given intravenously with a challenge dose of 5 x 10(6) organisms. Similar experiments with two other T-cell lines showed that these lines offered no protection. Bacterial load at the time of death was inversely related to the time of survival. Thus, death occurred at a lower bacterial load in adoptively protected mice, implying the contribution of an immunopathological component in these animals. The protective T-cell line, which was CD4+ CD8-, had no effect on the rate of growth of strain BCG in CBA nu/nu mice or M. tuberculosis in fully T-cell-deprived mice. This could indicate that CD8+ cells play a role in this system or that there is a need for the recruitment of interleukin 2-producing cells in the recipient. Experiments with monoclonal antibodies to selectively deplete T-cell subsets in normal CBA mice showed that depletion of CD4+ cells strikingly shortened survival, whereas depletion of CD8+ cells did not. However, CD8-depleted mice died with a lower bacterial load than those found in nondepleted controls, and the lesions in CD8-depleted mice were histopathologically distinct. These results suggest that the CD8+ cells either down-regulate bacteriostasis or cause immunopathology in this model and that it is the CD4+ cells that are the major protective subset in long-term protection experiments.
Generative Data Models for Validation and Evaluation of Visualization Techniques (2016)

We argue that there is a need for substantially more research on the use of generative data models in the validation and evaluation of visualization techniques. For example, user studies will require the display of representative and uncon-founded visual stimuli, while algorithms will need functional coverage and assessable benchmarks. However, data is often collected in a semi-automatic fashion or entirely hand-picked, which obscures the view of generality, impairs availability, and potentially violates privacy. There are some sub-domains of visualization that use synthetic data in the sense of generative data models, whereas others work with real-world-based data sets and simulations. Depending on the visualization domain, many generative data models are "side projects" as part of an ad-hoc validation of a techniques paper and thus neither reusable nor general-purpose. We review existing work on popular data collections and generative data models in visualization to discuss the opportunities and consequences for technique validation, evaluation, and experiment design. We distill handling and future directions, and discuss how we can engineer generative data models and how visualization research could benefit from more and better use of generative data models.
Evaluation of cell-free tumour DNA and RNA in patients with breast cancer and benign breast disease (2011)

High levels of DNA and RNA released by apoptotic and necrotic cells circulate in the blood of cancer patients. In the present study we determined the applicability of the quantification of nucleic acids and their genetic alterations as minimally invasive tool for breast cancer screening. The relative concentrations of DNA and RNA were determined in preoperative serum of 102 breast cancer patients, 32 patients with benign breast disease and 53 healthy women. The mean follow-up time of the cancer patients was 6.2 years. Loss of heterozygosity (LOH) at four polymorphic markers (D13S159, D13S280, D13S282 at region 13q31-33 and D10S1765 at PTEN region 10q23.31) was analyzed by PCR-based fluorescence microsatellite analyses using cell-free DNA. The serum levels of DNA (p = 0.016) and RNA (p = 0.001) could differentiate between healthy women and cancer patients, but could not discriminate malignant from benign breast lesions. A significant correlation of serum DNA with RNA levels was observed in all groups (p = 0.018). Increased serum DNA levels (but not RNA levels) in cancer patients were associated with a poorer overall (p = 0.021) and disease-free survival (p = 0.025). The occurrence of LOH at all markers significantly correlated with lymph node status (p = 0.026). In addition, the LOH frequency at D13S280 (p = 0.047) and D13S159 (p = 0.046) associated with overall and disease-free survival, respectively. In conclusion, the quantification of cell-free tumour DNA had diagnostic and prognostic values in breast cancer patients, and DNA loss at the region 13q31-33 may be an indication of lymphatic tumour cell spread.
Getting in Shape: Controlling Peptide Bioactivity and Bioavailability Using Conformational Constraints (2012)

Chemical biologists commonly seek out correlations between the physicochemical properties of molecules and their behavior in biological systems. However, a new paradigm is emerging for peptides in which conformation is recognized as the primary determinant of bioactivity and bioavailability. This review highlights an emerging body of work that directly addresses how a peptide's conformation controls its biological effects, cell penetration, and intestinal absorption. Based on this work, the dream of mimicking the potency and bioavailability of natural product peptides is getting closer to reality.
Isolation of cDNA clones for the catalytic gamma subunit of mouse muscle phosphorylase kinase: expression of mRNA in normal and mutant Phk mice. (1987)

We have isolated and characterized cDNA clones for the gamma subunit of mouse muscle phosphorylase kinase (gamma-Phk). These clones were isolated from a lambda gt11 mouse muscle cDNA library via screening with a synthetic oligonucleotide probe corresponding to a portion of the rabbit gamma-Phk amino acid sequence. The gamma-Phk cDNA clones code for a 387-amino acid protein that shares 93% amino acid sequence identity with the corresponding rabbit amino acid sequence. RNA gel blot analysis reveals that the muscle gamma-Phk probe hybridizes to two mRNA species (2.4 and 1.6 kilobases) in skeletal muscle, cardiac muscle, and brain, but does not hybridize to liver RNA. Phk-deficient I-strain (Phk) mouse muscle contains reduced levels of gamma-Phk mRNA as compared with control mice. Although the Phk defect is an X-linked recessive trait, hybridization to a human-rodent somatic cell hybrid mapping panel shows that the gamma-Phk gene is not located on the X chromosome. Rather, the gamma-Phk cross-hybridizing human restriction fragments map to human chromosomes 7 (multiple) and 11 (single). Reduced gamma-Phk mRNA in I-strain mice, therefore, appears to be a consequence of the Phk-mutant trait and does not stem from a mutant gamma-subunit gene.
Ethylene-Mediated Programmed Cell Death during Maize Endosperm Development of Wild-Type and shrunken2 Genotypes (1997)

We characterized the progression of programmed cell death during maize (Zea mays L.) endosperm development of starchy (Su; wild-type) and shrunken2 (sh2) genotypes and tested the involve ment of ethylene in mediating this process. Histological and viability staining demonstrated that endosperm cell death was initiated earlier and progressed more rapidly in sh2 endosperm compared with Su endosperm. Internucleosomal DNA fragmentation accompanied endosperm cell death and occurred more extensively in sh2 endosperm. 1-Aminocyclopropane-1-carboxylic acid levels peaked approximately 16 d after pollination (dap) in Su endosperm and gradually decreased during subsequent development, whereas two large 1-aminocyclopropane-1-carboxylic acid peaks were observed in sh2 endosperm, the first between 16 and 20 dap and the second at 36 dap. Ethylene levels were elevated in sh2 kernels compared with Su kernels, with an initial peak 20 dap approximately 3-fold higher than in Su kernels and a second peak 36 dap approximately 5-fold higher than that in Su kernels. Ethylene treatment of Su kernels resulted in earlier and more extensive endosperm cell death and DNA fragmentation. Aminoethoxyvinylglycine treatment of sh2 kernels reduced the extent of DNA fragmentation. We conclude that ethylene is involved in triggering programmed cell death in developing maize endosperm and is responsible for the aberrant phenotype of sh2 kernels.
[Expression of recombinant human stem cell factor in insect cells]. (2000)

The cDNA of human stem cell factor(hSCF) containing signal sequence was cloned into the transfer vector pVL941 of AcNPV to construct a recombinant transfer vector pVL941-SCF. Sf9 cells were cotransfected with wild type viral DNA and pVL914-SCF to produce the recombinant virus AcNPV-SCF by homologous recombination in cell. Southern-hybridization analysis suggested that the recombinant viral DNA contained hSCF cDNA fragment. The Sf9 cells infected with the recombinant baculovirus AcNPV-SCF expressed biologically active rhSCF which was secreted into the cell culture. The synergistic activities of SCF in conjunction with human interleukin-3(hIL-3) was measured by MTT colorimetric method and TF-1 cell line. The expression level of Sf9 cells reached its highest at about 1970 units/ml in the 3rd day after the infection with AcNPV-SCF. Three SCF bands with molecular masses of 18 x 10(3), 20 x 10(3) and 22 x 10(3) were detected by immunoblotting.
A Receptor Presentation Hypothesis for T Cell Help That Recruits Autoreactive B Cells (2001)

To uncover mechanisms that drive spontaneous expansions of autoreactive B cells in systemic lupus erythematosus, we analyzed somatic mutations in variable region genes expressed by a panel of (NZB x SWR)F(1) hybridomas representing a large, spontaneously arising clone with specificity for chromatin. A single mutation within the Jkappa intron that was shared by all members of the lineage indicated that the clone emanated from a single mutated precursor cell and led to the prediction that a somatic mutation producing a functionally decisive amino acid change in the coding region would also be universally shared. Upon cloning and sequencing the corresponding germline V(H) gene, we found that two replacement somatic mutations in FR1 and CDR2 were indeed shared by all seven clone members. Surprisingly, neither mutation influenced Ab binding to chromatin; however, one of them produced a nonconservative amino acid replacement in a mutationally "cold" region of FR1 and created an immunodominant epitope for class II MHC-restricted T cells. The epitope was restricted by IA(q) (SWR), and the SWR MHC locus is associated with systemic lupus erythematosus in (NZB x SWR)F(1) mice. These, and related findings, provoke the hypothesis that autoreactive B cells may be recruited by a "receptor presentation" mechanism involving cognate interactions between T cells and somatically generated V region peptides that are self-presented by B cells.
Digital infrared thermal imaging of human skin (2002)

Describes computational approaches to image processing for improved interpretation and analysis. The authors discuss the physics of image formation, developments in uncooled camera technology, and the use of image processing to interpret 2-D maps of temperatures and to analyze thermal images for assessing physiological changes and responses to physical provocations and stresses such as brief exposure to low temperatures.
ROCK STRENGTH PARAMETERS FROM ANNULAR PRESSURE WHILE DRILLING AND DIPOLE SONIC DISPERSION ANALYSIS (2004)

The characterization of rock strength is perhaps the most important task in choosing the optimal type of completion in soft-sediment reservoirs. While two strategies have commonly been used to guide this decision, both have significant shortcomings. A new technique is presented that estimates formation strength parameters from annular pressure and dipole shear measurements. The highest quality rock strength properties are normally determined in a rock mechanics laboratory by stress-loading actual formation material to yield and failure. Seldom will an operator dispense with this step in fields prone to sand production. However, fewer and fewer wells are cored, and the type of completion for different zones in different wells is increasingly based on a small number of laboratory measurements in a single well. Logging measurements yielding lithology, porosity, and elastic moduli are often transformed into rock-strength parameters and used to supplement the high quality but sparse laboratory data. However, while this strategy of log calibration to laboratory data can yield the correct trend over large porosity ranges, it generally fails in predicting the strength variations in high porosity (> 27%), soft-sediment reservoirs. The new technique monitors and captures the drilling process for what it is, an in-situ stress test. As the driller penetrates each formation, the borehole magnifies the far-field stresses by an amount dependent on the wellbore pressure. This increase in loading near the wellbore causes softsediment reservoirs to yield and fail. The depth of this yielded material can be quantified using broadband dipole shear measurements. The magnitude of stress causing this radially varying damage can be estimated with a mechanical earth model and the variation in annular pressure measured between the time of drilling and logging. The methodology for this new technique is illustrated with a recent deepwater discovery.
An antigenic determinant is shared by psoriasis‐associated p27 antigen and the Fc part of human IgG (1991)

Rabbit antisera against the major internal protein, p27, of retrovirus-like particles from psoriatic urine, and against the serologically cross-reacting antigen, pso p27, from psoriatic scale, reacted with the Fc part of human IgG. Evidence indicating that the p27 antigen and the pso p27 antigen are identical has been presented in previous reports. A commercial antiserum against human IgG recognized a component in the pso p27-containing solution used as the source of antigen for immunization of the rabbits. By means of monoclonal antibodies against the pso p27 antigen, it was demonstrated that the Fc-reacting antibodies, and the antiserum against human IgG, recognized an epitope on the pso p27 antigen. The data indicated that an antigenic determinant is shared by the p27 antigen(s) and human IgG, suggesting that p27 antigen(s) may act as antigen(s) eliciting the production of antibodies with rheumatoid factor activity in psoriatic patients.
Synthesis, characterization, and some immunological properties of conjugates composed of the detoxified lipopolysaccharide of Vibrio cholerae O1 serotype Inaba bound to cholera toxin (1992)

Protection against cholera has been correlated with the level of serum vibriocidal antibodies. The specificity of these vibriocidal antibodies was mostly to the lipopolysaccharide (LPS). We synthesized conjugates of detoxified LPS with cholera toxin (CT) and other proteins in order to elicit serum LPS antibodies with vibriocidal activity. Treatment with hydrazine (deacylated LPS) reduced the endotoxic properties of the LPS to clinically acceptable levels and resulted in a molecule larger and more antigenic than the saccharide produced by acid hydrolysis. More immunogenic conjugates resulted from multipoint compared with single-point attachment of the deacylated LPS to the protein. The conjugates containing CT had low levels of pyrogen and no toxic activity upon Chinese hamster ovary cells and elicited booster responses of vibriocidal and CT antibodies when injected subcutaneously as saline solutions into mice; the vibriocidal titers were similar to those elicited by comparable doses of cellular vaccines. We suggest how serum vibriocidal antibodies might prevent cholera.
New Paradigms for Organic Catalysts: The First Organocatalytic Living Polymerization (2001)

A metal-free approach to the living ring-opening polymerization (ROP, shown schematically) of lactide has been developed using strongly basic amines such as 4-(dimethylamino)pyridine as transesterification catalysts. These organic catalysts must be used in combination with a nucleophile such as an alcohol, which is the actual initiating species.
Robot assisted knee surgery (1995)

Discusses establishing a force control strategy incorporating active motion constraint. The following subjects are considered: problems with conventional surgery; robot assisted surgery; control strategy; representing the motion constraint; design of the desired position; force control strategy; implicit force control; modified damping control; experimental results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Development of a stimuli-responsive polymer nanocomposite toward biologically optimized, MEMS-based neural probes (2011)

This paper reports the development of micromachining processes and mechanical evaluation of a stimuli-responsive, mechanically dynamic polymer nanocomposite for biomedical microsystems. This nanocomposite consists of a cellulose nanofiber network encased in a polyvinyl acetate matrix. Micromachined tensile testing structures fabricated from the nanocomposite displayed a reversible and switchable stiffness comparable to bulk samples, with a Young's modulus of 3420 MPa when dry, reducing to ∼20 MPa when wet, and a stiff-to-flexible transition time of ∼300 s. This mechanically dynamic behavior is particularly attractive for the development of adaptive intracortical probes that are sufficiently stiff to insert into the brain without buckling, but become highly compliant upon insertion. Along these lines, a micromachined neural probe incorporating parylene insulating/moisture barrier layers and Ti/Au electrodes was fabricated from the nanocomposite using a fabrication process designed specifically for this chemical- and temperature-sensitive material. It was found that the parylene layers only slightly increased the stiffness of the probe in the wet state in spite of its much higher Young's modulus. Furthermore, the Ti/Au electrodes exhibited impedance comparable to Au electrodes on conventional substrates. Swelling of the nanocomposite was highly anisotropic favoring the thickness dimension by a factor of 8 to 12, leading to excellent adhesion between the nanocomposite and parylene layers and no discernable deformation of the probes when deployed in deionized water.
Design, Synthesis, and Biological Evaluation of Halogenated N-(2-(4-Oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-8-yl)ethyl)benzamides: Discovery of an Isoform-Selective Small Molecule Phospholipase D2 Inhibitor (2010)

Phospholipase D (PLD) catalyzes the conversion of phosphatidylcholine to the lipid second messenger phosphatidic acid. Two mammalian isoforms of PLD have been identified, PLD1 and PLD2, which share 53% sequence identity and are subject to different regulatory mechanisms. Inhibition of PLD enzymatic activity leads to increased cancer cell apoptosis, decreased cancer cell invasion, and decreased metastasis of cancer cells; therefore, the development of isoform-specific, PLD inhibitors is a novel approach for the treatment of cancer. Previously, we developed potent dual PLD1/PLD2, PLD1-specific (>1700-fold selective), and moderately PLD2-preferring (>10-fold preferring) inhibitors. Here, we describe a matrix library strategy that afforded the most potent (PLD2 IC(50) = 20 nM) and selective (75-fold selective versus PLD1) PLD2 inhibitor to date, N-(2-(1-(3-fluorophenyl)-4-oxo-1,3,8-triazaspiro[4.5]decan-8-yl)ethyl)-2-naphthamide (22a), with an acceptable DMPK profile. Thus, these new isoform-selective PLD inhibitors will enable researchers to dissect the signaling roles and therapeutic potential of individual PLD isoforms to an unprecedented degree.