gebhart/patrepeval huggingface dataset:
Droplet motion in microfluidic networks: Hydrodynamic interactions and pressure-drop measurements (2009)

We present experimental, numerical, and theoretical studies of droplet flows in hydrodynamic networks. Using both millifluidic and microfluidic devices, we study the partitioning of monodisperse droplets in an asymmetric loop. In both cases, we show that droplet traffic results from the hydrodynamic feedback due to the presence of droplets in the outlet channels. We develop a recently-introduced phenomenological model [W. Engl, Phys. Rev. Lett. 95, 208304 (2005)] and successfully confront its predictions to our experimental results. This approach offers a simple way to measure the excess hydrodynamic resistance of a channel filled with droplets. We discuss the traffic behavior and the variations in the corresponding hydrodynamic resistance length L_{d} and of the droplet mobility beta , as a function of droplet interdistance and confinement for channels having circular or rectangular cross sections.
Identification of glycoinositol phospholipid-linked and truncated forms of the scrapie prion protein (1990)

Analysis of carboxy-terminal peptides derived from endoproteinase Lys-C digests of the scrapie isoform of the hamster prion protein revealed that the majority of the molecules are glycoinositol phospholipid linked through ethanolamine attached at serin-231. However, approximately 15% of PrPSc had a carboxy-terminal peptide that ends at glycine-228. It is intriguing that this glycine is part of the PrP sequence Gly-Arg-Arg, which is an established target sequence for the proteolysis and release of bioactive peptides from larger precursors. The mechanism of formation, as well as the role of the truncated carboxy terminus in the dissemination and neuropathology of scrapie, remains to be determined.
Progesterone Does Not Prevent Preterm Births in Women with Twins (2009)

Amongst this group of twin gestations weekly 17HP injections did not reduce the incidence of preterm birth or the complications associated with prematurity.
Development and evaluation of evidence based risk assessment tool (STRATIFY) to predict which elderly inpatients will fall: case-control and cohort studies (1997)

This simple risk assessment tool predicted with clinically useful sensitivity and specificity a high percentage of falls among elderly hospital inpatients.
The lower genital tract microbiota in relation to cytokine‐, SLPI‐ and endotoxin levels: application of checkerboard DNA‐DNA hybridization (CDH) (2008)

In the present study the lower genital tract microbiota in asymptomatic fertile women (n=34) was identified and quantified by culturing vaginal secretions. Also, vaginal and cervical samples were analyzed by a semiquantitative checkerboard DNA-DNA hybridization technique (CDH) based on genomic probes prepared from 13 bacterial species (Bacteroides ureolyticus, Escherichia coli, Fusobacterium nucleatum, Gardnerella vaginalis, Mobiluncus curtisii ss curtisii, Prevotella bivia, Prevotella disiens, Prevotella melaninogenica, Atopobium vaginae, Lactobacillus iners, Staphylococcus aureus ss aureus, Streptococcus anginosus, and Streptococcus agalactiae). The bacterial species found by either culture or CDH were correlated with proinflammatory cytokines (IL-1 alpha, IL-1 beta, IL-6, IL-8), secretory leukocyte protease inhibitor (SLPI), and endotoxin in the cervicovaginal samples. Grading the women into healthy, intermediate, or bacterial vaginosis (BV) as based on Gram staining of vaginal smears, the viable counts of lactobacilli (L. gasseri) and of streptococci-staphylococci combined were highest in the intermediate group. In BV, particularly the high concentrations of Actinomyces urogenitalis, Atopobium vaginae, and Peptoniphilus harei were noted (>or=10(11) per ml). The total viable counts correlated with both cervical IL-1 alpha and IL-1 beta. A strong negative correlation was observed between L. iners and total viable counts, G. vaginalis, or cervical IL-1 alpha, while it correlated positively with SLPI. Analysis of vaginal and cervical samples from 26 out of the 34 women by CDH showed that anaerobic bacteria were more frequently detected by CDH compared to culture. By this method, A. vaginae correlated with G. vaginalis, and L. iners with S. aureus. With regard to cytokines, B. ureolyticus correlated with both cervical and vaginal IL-1 alpha as well as with cervical IL-8, while F. nucleatum, S. agalactiae, S. anginosus, or S. aureus correlated with vaginal IL-1 alpha. Furthermore, all Gram-negative bacteria taken together, as measured by CDH, correlated with vaginal endotoxin and inversely with vaginal SLPI. The significance of the results is discussed. In summary, mapping of the identity and quantity of vaginal bacterial species and their association with locally produced host innate immune factors will help in defining various types of abnormal vaginal microbiota, developing new ways of assessing the risk of ascending subclinical infections, and in treating them. CDH appears to be a suitable tool for future analyses of large numbers of clinical samples with an extended number of bacterial probes.
Inhibitors Targeting JAK3 (2010)

The Janus kinase (JAK) JAK3 plays a vital role in the intracellular signaling cascade downstream of select cytokine receptors in immune cells. Inhibition of JAK3 is expected to result in potent immunosuppression, and thus JAK3 appears to be a rational pharmaceutical target. Nonclinical and clinical data relating to transplantation have become available for several molecules targeting inhibition of JAK3. Recent studies suggest that some of these agents lack potency and selectivity for JAK3 or the JAK family. Published data on these relatively nonselective agents must, therefore, be interpreted with caution. Clinical trials on CP-690,550 in calcineurin-inhibitor-free regimens have provided preliminary evidence that JAK3 inhibition is a promising approach to prevent acute allograft rejection. However, dose-limiting adverse events, such as opportunistic viral infections and hematological aberrations, have been observed. Further evaluations of this class of agents are warranted to ascertain the dose/concentration range for individual agents and the combination regimens that optimize clinical efficacy and minimize adverse effects.
Probing Protein Stability with Unnatural Amino Acids (1992)

Unnatural amino acid mutagenesis, in combination with molecular modeling and simulation techniques, was used to probe the effect of side chain structure on protein stability. Specific replacements at position 133 in T4 lysozyme included (i) leucine (wt), norvaline, ethylglycine, and alanine to measure the cost of stepwise removal of methyl groups from the hydrophobic core, (ii) norvaline and O-methyl serine to evaluate the effects of side chain solvation, and (iii) leucine, S,S-2-amino-4-methylhexanoic acid, and S-2-amino-3-cyclopentylpropanoic acid to measure the influence of packing density and side chain conformational entropy on protein stability. All of these factors (hydrophobicity, packing, conformational entropy, and cavity formation) significantly influence protein stability and must be considered when analyzing any structural change to proteins.
Determination of the transcript profile of human endometrium (2003)

The response of the human endometrium to the ovarian hormones, estrogen and progesterone, has been the focus of decades of research. In order to understand this critical aspect of endometrial physiology, we undertook a genome-wide analysis of transcript abundance and changes in transcript level between normal endometrium in the proliferative and secretory phases of the menstrual cycle. A high-density, oligonucleotide gene array, comprising 60 000 gene targets, was used to define the gene expression profile of proliferative and secretory phase endometrium. Results from the arrays were verified using real-time PCR. The expression levels of 149 transcripts differed significantly between the two phases of the cycle determined by stringent range limits (99.99%), calculated using local variance values. These transcripts include previously documented steroidally responsive genes (such as placental protein 14 and stromelysin-3) and novel transcripts not previously linked to either endometrial physiology or steroid regulation (such as intestinal trefoil factor and a number of expressed sequence tags). Examination of the 5' promoter regions of these genes identified many putative estrogen and progesterone receptor DNA binding domains, suggesting a direct response of these genes to the ovarian hormones.
A variable structure controller for a tentacle manipulator (2002)

The paper presents a class of tentacle arms based on the use of flexible composite materials in conjunction with active-controllable electrorheological (ER) fluids. The model consists of a finite number of segments, each segment having a specific structure and control. The dynamic behaviour of the arm is obtained using Lagrange's principle developed for infinite-dimensional systems. This model is represented by a set of integral-differential equations. An approximate model is then derived as a set of differential equations with variable coefficients. Two cases are discussed: the sliding mode with the bang-bang control; and the direct mode in which the controller is based on the use of the direct evolution of the system on the switching line by switching the fluid viscosity. The numerical simulations are presented. A nonlinear observer is introduced to estimate the inaccessible state variable distributed on the length of the arm. The conditions which assure the convergence to zero of the errors are proved.
Divergent Insulin and Platelet-derived Growth Factor Regulation of Focal Adhesion Kinase (pp125FAK) Tyrosine Phosphorylation, and Rearrangement of Actin Stress Fibers (1995)

Insulin treatment of Chinese hamster ovary cells expressing high levels of the human insulin receptor resulted in the tyrosine dephosphorylation of the 125-kDa focal adhesion kinase (pp125FAK). The decrease in pp125FAK tyrosine phosphorylation paralleled a decrease in the cellular content of actin stress fibers, and these changes were independent of the extracellular matrix on which the cells were grown. The reduction in both pp125FAK tyrosine phosphorylation and actin stress fibers occurred in an insulin concentration-dependent manner, with significant effects at approximately 0.3 nM and a maximal effect at 3 nM. However, in the continuous presence of insulin, the decreases in the tyrosine phosphorylation state of pp125FAK and actin stress fiber content were transient. Maximal reduction of pp125FAK tyrosine phosphorylation was observed following 15 min of insulin treatment, with a return to unstimulated control levels by 60 min. Similarly, actin stress fiber content was maximally reduced by 15 min of insulin treatment and fully recovered by 60 min. In contrast to insulin, platelet-derived growth factor stimulation increased actin stress fiber content and enhanced pp125FAK tyrosine phosphorylation. These data demonstrate a novel signaling role for insulin in inducing the tyrosine dephosphorylation of pp125FAK and a concomitant reorganization of actin stress fibers, which underlies at least one aspect of signaling divergence between the insulin and platelet-derived growth factor receptor tyrosine kinases.
Immunization of chimpanzees confers protection against challenge with human immunodeficiency virus. (1991)

Sustained high titers of neutralizing antibodies were elicited in three chimpanzees after sequential injections of different human immunodeficiency virus 1 (HIV-1) antigen preparations derived from the HIV-1 BRU strain that included whole inactivated virus or purified recombinant proteins and then synthetic peptides identical to the major HIV-1 neutralizing epitope V3. The animals were challenged i.v. with 40 chimpanzee infectious doses (equivalent to 100 tissue culture 50% infectious doses) of a stock of HIV-1 IIIB isolate. After 6 mo of follow-up, all three animals appeared uninfected by serologic and virologic criteria, including polymerase chain reaction analysis and failure to isolate virus from peripheral blood lymphocytes, bone marrow, and lymph node tissue. Of two chimpanzees monitored for 1 yr, virus was isolated initially from one animal at 32 weeks, but the second chimpanzee was virus negative by all assays through 12 mo; the third animal has remained virus negative through 9 mo of follow-up. These results indicate that it is possible to elicit protection against, or significantly delay infection of, HIV-1 by immunization, thus laying the foundation for development of an HIV-1 vaccine.
Mutational Analysis of the A-Kinase Anchoring Protein (AKAP)-binding Site on RII (1996)

Compartmentalization of the type II cAMP-dependent protein kinase is conferred by interaction of the regulatory subunit (RII) with A-Kinase Anchoring Proteins (AKAPs). The AKAP-binding site involves amino-terminal residues on each RII protomer and is formed through dimerization. A site-directed mutagenesis strategy was utilized to assess the contribution of individual residues in either RII isoform, RIIalpha or RIIbeta, for interaction with various anchoring proteins. Substitution of long-chain or bulky hydrophobic groups (leucines or phenylalanines) for isoleucines at positions 3 and 5 in RIIalpha decreased AKAP-binding up to 24 +/- 3 (n = 8)-fold, whereas introduction of valines had minimal effects. Replacement with hydrophilic residues (serine or asparigine) at both positions abolished AKAP binding. Mutation of proline 6 in RIIalpha reduced binding for four AKAPs (Ht31, MAP2, AKAP79, and AKAP95) from 2.3 to 20-fold (n = 4) whereas introduction of an additional proline at position 6 in RIIbeta increased or conferred binding toward these anchoring proteins. Therefore, we conclude that beta-branched side chains at positions 3 and 5 are favored determinants for AKAP-binding and prolines at positions 6 and 7 increase or stabilize RIIalpha interaction with selected anchoring proteins.
A capacity comparison for SONET self-healing ring networks (2002)

The SONET technology employed in reducing the complexity, cost and number of transmission systems of a public network makes the creation of the telecommunication superhighway system for transporting signals for a wide range of services at high speed possible. But SONET technology can also create a certain degree of complexity in building a cost-efficient SONET network, especially in the case of SONET SHR (self-healing ring). It is a challenge to the network planner to find an efficient way to select the most economical SONET ring, or combination of rings, for demands between a set of nodes that are expected to be connected in a certain type of ring configuration. To gain the full benefit of the economics and services SONET might have to offer, effective ways for ring selection must be found. Routing decisions, especially for bidirectional rings, play a key role in deciding the ring capacities which the ring is supposed to meet. We present two efficient demand loading algorithms for BSHR, and analyze the results from their application on a variety of demand patterns, to find criterion for ring selection.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Design and fabrication of 1D and 2D micro scanners actuated by double layered PZT bimorph beams (2002)

Micro scanners including 1D scanner beams and 2D scanning micromirrors are designed and fabricated. In order to yield great actuation force and large scanning angle, double layered PZT beams were developed in this study. In the case of 1D scanner beams (750/spl times/230 /spl mu/m/sup 2/), the optical scanning angle was 41.2 degree while driven dynamically with 5 V (AC) at 2706 Hz. Under the applied bias of 10 V (DC), the optical deflection angle reached 34.3 degree. Combined with four double layered PZT bimorph beams, a 2D scanning micromirror was fabricated successfully.
Immune response of heifers to vaginal submucosal or subcutaneous vaccination and intravaginal challenge with Ureaplasma diversum. (1994)

Twenty beef heifers were randomly assigned to five equal groups and vaccinated: Group 1--in vaginal submucosa (VM) with Ureaplasma diversum ultrasonicated whole cells (WC) in complete Freund's adjuvant (CFA); Group 2--in VM with U. diversum cell membranes (CM) in CFA; Group 3--subcutaneously (SC) with CM in CFA; Group 4--in VM with CM alone; and Group 5--in VM with phosphate buffered saline (PBS) in CFA. A second vaccination with the same antigens in incomplete Freund's adjuvant was given after four weeks, and three weeks later, all heifers were challenged intravaginally with 3.6 x 10(7) colony-forming units (CFU) of U. diversum strain 2312. Immunoglobulins that reacted with U. diversum were measured in serum and cervicovaginal mucus (CVM) by an enzyme-linked-immunosorbent assay. In groups 1 and 2, vaccination by the VM route with WC or CM antigens, stimulated high levels of U. diversum-reactive IgG1 and IgG2 antibodies in serum as well as CVM, but a low IgA response only in CVM. In group 4, VM vaccination with CM (no adjuvant) elicited a minimal IgG1 and IgG2 response in serum and CVM. In group 3, SC vaccination with CM antigen stimulated high IgG1 and IgG2 reactivity in both serum and CVM, but no IgA reactivity. Very little IgM reactivity was detected in the four vaccinated groups. Intravaginal challenge resulted in characteristic granular vulvitis in all vaccinated and control heifers, with all animals remaining culture-positive for the 35 day observation period. The infection stimulated a marked increase in the specific IgA response in CVM of the three groups vaccinated with either, adjuvanted antigen.(ABSTRACT TRUNCATED AT 250 WORDS)
Value of tumor-antigen (TA-4) of squamous cell carcinoma in predicting the extent of cervical cancer (1982)

The value of a tumor-antigen (TA-4) of squamous cell carcinoma in evaluating the extent of disease was studied in patients who primarily had surgical treatments with a diagnosis of cervical squamous cell carcinoma. Pretreatment serum TA-4 levels were determined by a radioimmunoassay method. The extent of disease was determined by surgical evaluation and postoperative histologic examinations. Furthermore, all patients were followed for at least two years, and those patients who developed recurrence at the sites which were unresectable by radical hysterectomy were retrospectively regarded as the unresectable case. It was found that serum TA-4 levels reflected the extent of disease, and that high pretreatment TA-4 levels indicated the presence of the widespread tumor which was unresectable by radical hysterectomy.
The dipeptidyl peptidase‐4 inhibitor PHX1149 improves blood glucose control in patients with type 2 diabetes mellitus (2008)

Addition of the DPP4 inhibitor PHX1149 to a stable regimen of metformin or metformin plus a glitazone in patients with type 2 diabetes was well tolerated and improved blood glucose control.
Development of the insulin secretion mechanism in fetal and neonatal rat pancreatic B-cells: response to glucose, K+, theophylline, and carbamylcholine (1998)

We studied the development of the insulin secretion mechanism in the pancreas of fetal (19- and 21-day-old), neonatal (3-day-old), and adult (90-day-old) rats in response to stimulation with 8.3 or 16.7 mM glucose, 30 mM K+, 5 mM theophylline (Theo) and 200 µM carbamylcholine (Cch). No effect of glucose or high K+ was observed on the pancreas from 19-day-old fetuses, whereas Theo and Cch significantly increased insulin secretion at this age (82 and 127% above basal levels, respectively). High K+ also failed to alter the insulin secretion in the pancreas from 21-day-old fetuses, whereas 8.3 mM and 16.7 mM glucose significantly stimulated insulin release by 41 and 54% above basal levels, respectively. Similar results were obtained with Theo and Cch. A more marked effect of glucose on insulin secretion was observed in the pancreas of 3-day-old rats, reaching 84 and 179% above basal levels with 8.3 mM and 16.7 mM glucose, respectively. At this age, both Theo and Cch increased insulin secretion to close to two-times basal levels. In islets from adult rats, 8.3 mM and 16.7 mM glucose, Theo, and Cch increased the insulin release by 104, 193, 318 and 396% above basal levels, respectively. These data indicate that pancreatic B-cells from 19-day-old fetuses were already sensitive to stimuli that use either cAMP or IP3 and DAG as second messengers, but insensitive to stimuli such as glucose and high K+ that induce membrane depolarization. The greater effect of glucose on insulin secretion during the neonatal period indicates that this period is crucial for the maturation of the glucose-sensing mechanism in B-cells.
Combinatorial targeting and discovery of ligand-receptors in organelles of mammalian cells (2012)

Phage display screening allows the study of functional protein-protein interactions at the cell surface, but investigating intracellular organelles remains a challenge. Here we introduce internalizing-phage libraries to identify clones that enter mammalian cells through a receptor-independent mechanism and target-specific organelles as a tool to select ligand peptides and identify their intracellular receptors. We demonstrate that penetratin, an antennapedia-derived peptide, can be displayed on the phage envelope and mediate receptor-independent uptake of internalizing phage into cells. We also show that an internalizing-phage construct displaying an established mitochondria-specific localization signal targets mitochondria, and that an internalizing-phage random peptide library selects for peptide motifs that localize to different intracellular compartments. As a proof-of-concept, we demonstrate that one such peptide, if chemically fused to penetratin, is internalized receptor-independently, localizes to mitochondria, and promotes cell death. This combinatorial platform technology has potential applications in cell biology and drug development.
jRapture (2000)

We describe the design of jRapture: a tool for capturing and replaying Java program executions in the field. jRapture works with Java binaries (byte code) and any compliant implementation of the Java virtual machine. It employs a lightweight, transparent capture process that permits unobtrusive capture of a Java programs executions. jRapture captures interactions between a Java program and the system, including GUI, file, and console inputs, among other types, and on replay it presents each thread with exactly the same input sequence it saw during capture. In addition, jRapture has a profiling interface that permits a Java program to be instrumented for profiling ó after its executions have been captured. Using an XML-based profiling specification language a tester can specify various forms of profiling to be carried out during replay.