gebhart/patrepeval huggingface dataset:
Suppression of Tumor Growth by Galectin-7 Gene Transfer (2004)

Galectin-7 is a beta-galactoside-binding animal lectin specifically expressed in stratified epithelia. Its expression is inducible by p53 and is down-regulated in squamous cell carcinomas. Other investigators previously showed that galectin-7 is a proapoptotic protein, and we showed that ectopic expression of galectin-7 in HeLa cells renders the cells more sensitive to a variety of apoptotic stimuli. In the present study, we showed that ectopic expression of galectin-7 in the human colon carcinoma cell line DLD-1 also made the cells more sensitive to apoptosis under various conditions. We also found that galectin-7-transfected DLD-1 (DLD-1-Gal7) cells grew significantly more slowly than control transfectants (DLD-1-V) under normal culture conditions in the absence of apoptosis. Moreover, a significantly lower number of colonies were formed from DLD-1-Gal7 cells than from DLD-1-V cells under anchorage-independent cell growth conditions. Most importantly, tumor formation from DLD-1-Gal7 cells was dramatically reduced compared with DLD-1-V cells when these cells were inoculated s.c. into severe combined immunodeficient mice. DLD-1-Gal7 tumors showed a significantly lower proliferation rate than DLD-1-V tumors as determined by in vivo 5-bromo-2'-deoxyuridine incorporation. DLD-1-Gal7 tumors also contained a lower density of blood vessels than DLD-1-V tumors, suggesting that ectopic expression of galectin-7 suppresses angiogenesis. This may partially account for the greater suppressive effect of galectin-7 on tumor growth in vivo than in vitro. Our results show that galectin-7 has a suppressive effect on tumor growth, suggesting that galectin-7 gene transfer or other means of specifically inducing galectin-7 expression may be a new approach for management of cancers.
Fibronectin provides a conduit for fibroblast transmigration from collagenous stroma into fibrin clot provisional matrix (1997)

After injury, the wound space is filled with a fibrin/fibronectin clot containing growth factors released by platelets and monocytes. In response to these factors, fibroblasts migrate into the fibrin clot and contribute to the formation of granulation tissue. The functional mechanisms allowing fibroblasts to leave the collagenous matrix of normal connective tissue and invade the provisional matrix of the fibrin clot have not been fully defined. To investigate these mechanisms we established a new in vitro model which simulates specific aspects of early wound healing, that is, the migration of fibroblasts from a three-dimensional collagen matrix into a fibrin clot. This transmigration could be induced by physiological concentrations of platelet releasate or platelet-derived growth factor BB (PDGF-BB) in a concentration-dependent manner. At 24 hours irradiated fibroblasts invaded the fibrin gel almost as well as non-irradiated cells, indicating that transmigration was independent of proliferation. Plasminogen and its activators appear to be necessary for invasion of the fibrin clot since protease inhibitors decreased the amount of migration. These serine proteases, however, were not necessary for exit from the collagen gel as fibroblasts migrated out of the collagen gel onto a surface coated with fibrin fibrils even in the presence of inhibitors. Removal of fibronectin (FN) from either the collagen gel or the fibrin gel markedly decreased the number of migrating cells, suggesting that FN provides a conduit for transmigration. Cell movement in the in vitro model was inhibited by RGD peptide, and by monoclonal antibodies against the subunits of the alpha5 beta1 and alpha v beta3 integrin receptor. Thus, the functional requirements for fibroblast transmigration from collagen-rich to fibrin-rich matrices, such as occurs in early wound healing, have been partially defined using an in vitro paradigm of this important biologic process.
Electroless Plating of Aluminum from a Room-Temperature Ionic Liquid Electrolyte (2007)

Because aluminum is a less-noble metal which has the standard electrode potential of vs normal hydrogen electrode, it is impossible to obtain the electrodeposition of aluminum from an aqueous solution. No one has reported an electroless plating method of aluminum. We succeeded in demonstrating the electroless plating of aluminum from a room-temperature ionic liquid (RTIL). It was found from measurements of inductively coupled plasma, X-ray diffraction, scanning electron microscopy (SEM), SEM-energy-dispersive X-ray analysis, and glow discharge optical emission spectroscopy that dense, smooth, and pure aluminum plating was obtained from the RTIL by the electroless plating method. Moreover, the reaction mechanism of the electroless plating of aluminum from the RTIL electrolyte was electrochemically analyzed.
Accelerometer type cardiac transducer for detection of low-level heart sounds (1993)

New applications in phonocardiography require transducers with high sensitivity, low noise, and extended frequency range. This paper compares several different cardiac transducers and describes the development of a low-mass, accelerometer type cardiac transducer which fulfills these objectives. The accelerometer weighs approximately 5 g and has a theoretical sensitivity of 125 mV/g in the frequency range 200-800 Hz. The basic design allows for easy modification of sensitivity and resonant frequency. This transducer has been effective in detecting sounds associated with turbulent blood flow in partially occluded coronary arteries.
Combinatorial mutagenesis of the reactive site region in plasminogen activator inhibitor I (1991)

Plasminogen activator inhibitor (PAI-I) rapidly inactivates tissue plasminogen activator (t-PA) and urokinase (UK) with nearly identical association rate constants. The contributions of Ser344, Ala345, and Arg346 (P3, P2, and P1 residues, respectively) in PAI-I to inhibition of UK and t-PA were evaluated using combinatorial mutagenesis of the human PAI-I cDNA. A bacteriophage lambda expression library potentially encoding the 8000 unique PAI-I species were screened for inhibitory activity against UK using a fibrin indicator gel. 390 plaques demarcated by zones of retarded fibrinolysis were analyzed to determine the DNA sequences of their associated active PAI-1 species. We found 134 unique PAI-1 variants that retained inhibitory activity towards UK; they contained a variety of amino acids in their P3 and P2 positions but only Arg or, infrequently, Lys in their P1 position. Each of the unique active PAI-1 were assayed for inhibitory activity towards UK or t-PA; many substitutions differentially affected the ability of the inhibitor to inactivate UK and t-PA. For example, replacement of Ser344 and Ala344 with Val and Pro, respectively, yielded a PAI-1 variant exhibiting an association rate constant that was unchanged for t-PA but decreased 23-fold for UK, relative to native PAI-1. In general, the PAI-1 variants were more potent inhibitors of t-PA than UK. Hence, t-PA appears more tolerant than UK of structural diversity present in the P3 and P2 positions of the PAI-1 variants.
An orthotopic model of human pancreatic cancer in severe combined immunodeficient mice: potential application for preclinical studies. (1998)

Pancreatic adenocarcinoma is one of the most incurable and least understood of all human cancers. It is the fourth leading cause of cancer-related mortality in males (after lung, prostate, and colon) and in females (after lung, breast, and colon) in the United States with <2-3% of patients surviving >5 years. In an attempt to search for more effective therapies for this disease, we report here, for the first time, an effective treatment, the combination of gemcitabine and auristatin-phenethylamine (PE), against an orthotopic implantation of a human pancreatic adenocarcinoma cell line (HPAC) in severe combined immunodeficient (SCID) mice. Tumor implantation was performed by injecting 100 microl of the HPAC cell suspension (1 x 10(6) cells) directly into the pancreas of 5-week-old SCID mice. After implantation, tumor formation was checked twice a week. All palpable tumors were detected within 21 days (100% take rate), and tumors were confirmed histologically to be pancreatic adenocarcinoma. For the subsequent efficacy trial, tumor-bearing SCID mice were randomized into four groups with five mice in each group. One served as a control, the second received gemcitabine alone (2.5 mg/kg/injection i.p.), the third received auristatin-PE alone (2.0 mg/kg/injection i.v.), and the fourth group received the combination of gemcitabine (i.p.) and auristatin-PE (1.5 mg/kg/injection i.v.). All animals were euthanized 7 days after the completion of their treatments, and the pancreases were resected. Histological examination revealed the tumors to be adenocarcinoma. The tumors were composed of diffuse sheets of cells interrupted by glandular spaces containing secretory material. Cytologically, the tumor cells were large, pleomorphic, and hyperchromatic. Many cells contained intracellular lumina containing mucin. Immunohistochemical studies showed strong p21WAF1 (p21) expression but no immunoreactivity with p53 and Her-2/neu antibodies. The mean pancreatic weight in the gemcitabine/auristatin-PE combination group was significantly (P = 0.014) lower (0.84 +/- 0.639 g) when compared with those of the control (2.91 +/- 1.19 g) and gemcitabine alone (1.84 +/- 0.796 g; P = 0.064) groups. In addition, the mean weight in the combination group approached statistical significance when compared with the auristatin-PE group alone (1.16 +/- 0.635 g; P = 0.028). We conclude that the combination of gemcitabine and auristatin-PE is an effective treatment against HPAC tumors in this xenograft model and more effective than treatment with either gemcitabine or auristatin-PE alone and could be considered for future animal studies with pancreas cancer and/or for human clinical trials.
Antigenicity and native structure of globular proteins: low frequency of peptide reactive antibodies. (1987)

Recent reports that peptides can frequently mimic epitopes on globular proteins are inconsistent with early studies demonstrating that antibodies to native globular proteins generally do not bind peptides. This discrepancy could result from current confusion of two different populations of antibodies in antisera: one reacting with peptides and denatured protein and the other reacting only with the native protein. To test this possibility, several hundred monoclonal antibodies to rat cytochrome c were examined by ELISA for binding the intact protein and cyanogen bromide-cleaved peptides. Inhibition by soluble native cytochrome c identified which antibodies were specific for the native protein. The vast majority of these antibodies did not bind the peptides, whereas most of the antibodies specific for denatured forms did bind them. The results are consistent with the idea that antibodies to denatured antigen are readily detected in solid-phase assays, where some antigen molecules denature as they attach to microtiter plates, and show that these antibodies are generally the ones that react with peptides. Thus, reevaluation of data suggesting that anti-native globular protein antibodies bind peptides is warranted.
Adaptive extensions to a multibranch run-to-run controller for plasma etching (1995)

Fuzzy logic and database learning mechanisms have been incorporated into a generic plasma etching run-to-run controller, resulting in a very dynamic, adaptable, and robust system. The system features an Applied 8300 reactive ion etcher controlled by a Techware II equipment controller. A TCP/IP connection links this equipment controller to the run-to-run controller residing on a SUN. The run-to-run control environment is generic in that the basic control framework and controller development results are applicable to very large scale integrated manufacturing in general. The controller is multibranch as it utilizes multiple algorithms in complementary fashion to achieve process optimization and control. The current implementation utilizes three branches: (1) a linear approximation control algorithm, (2) an optimization algorithm that utilizes (real-time) data collected in situ to determine optimal run-to-run process parameter settings, and (3) a statistical optimization algorithm that utilizes run-to-run data. We have extended the controller to accommodate an automated branch selection process that utilizes fuzzy logic to incorporate a process engineer as well as optimization and control algorithmic knowledge. We have also extended the controller to adapt to unforeseen events through utilization of a learning mechanism; this mechanism detects these unforeseen events, intelligently queries the process engineer, guides the engineer through the development of an event servicing scheme, and incorporates this new knowledge into its control knowledge base so that the event may be serviced automatically in the future. Implementation results of the controller (in the control of the etcher) confirm the robust control capabilities in the face of process shift and drift, and recipe change.
Calibrated nanoscale capacitance measurements using a scanning microwave microscope (2010)

A scanning microwave microscope (SMM) for spatially resolved capacitance measurements in the attofarad-to-femtofarad regime is presented. The system is based on the combination of an atomic force microscope (AFM) and a performance network analyzer (PNA). For the determination of absolute capacitance values from PNA reflection amplitudes, a calibration sample of conductive gold pads of various sizes on a SiO(2) staircase structure was used. The thickness of the dielectric SiO(2) staircase ranged from 10 to 200 nm. The quantitative capacitance values determined from the PNA reflection amplitude were compared to control measurements using an external capacitance bridge. Depending on the area of the gold top electrode and the SiO(2) step height, the corresponding capacitance values, as measured with the SMM, ranged from 0.1 to 22 fF at a noise level of ~2 aF and a relative accuracy of 20%. The sample capacitance could be modeled to a good degree as idealized parallel plates with the SiO(2) dielectric sandwiched in between. The cantilever/sample stray capacitance was measured by lifting the tip away from the surface. By bringing the AFM tip into direct contact with the SiO(2) staircase structure, the electrical footprint of the tip was determined, resulting in an effective tip radius of ~60 nm and a tip-sample capacitance of ~20 aF at the smallest dielectric thickness.
Structurally Efficient Three-dimensional Metamaterials with Controllable Thermal Expansion (2016)

The coefficient of thermal expansion (CTE) of architected materials, as opposed to that of conventional solids, can be tuned to zero by intentionally altering the geometry of their structural layout. Existing material architectures, however, achieve CTE tunability only with a sacrifice in structural efficiency, i.e. a drop in both their stiffness to mass ratio and strength to mass ratio. In this work, we elucidate how to resolve the trade-off between CTE tunability and structural efficiency and present a lightweight bi-material architecture that not only is stiffer and stronger than other 3D architected materials, but also has a highly tunable CTE. Via a combination of physical experiments on 3D fabricated prototypes and numeric simulations, we demonstrate how two distinct mechanisms of thermal expansion appearing in a tetrahedron, can be exploited in an Octet lattice to generate a large range of CTE values, including negative, zero, or positive, with no loss in structural efficiency. The novelty and simplicity of the proposed design as well as the ease in fabrication, make this bi-material architecture well-suited for a wide range of applications, including satellite antennas, space optical systems, precision instruments, thermal actuators, and MEMS.
The Core of the Polycomb Repressive Complex Is Compositionally and Functionally Conserved in Flies and Humans (2002)

The Polycomb group (PcG) genes are required to maintain homeotic genes in a silenced state during development in drosophila and mammals and are thought to form several distinct silencing complexes that maintain homeotic gene repression during development. Mutations in the PcG genes result in developmental defects and have been implicated in human cancer. Although some PcG protein domains are conserved between flies and humans, substantial regions of several PcG proteins are divergent and humans contain multiple versions of each PcG gene. To determine the effects of these changes on the composition and function of a PcG complex, we have purified a human Polycomb repressive complex from HeLa cells (hPRC-H) that contains homologues of PcG proteins found in drosophila embryonic PRC1 (dPRC1). hPRC-H was found to have fewer components than dPRC1, retaining the PcG core proteins of dPRC1 but lacking most non-PcG proteins. Preparations of hPRC-H contained either two or three different homologues of most of the core PcG proteins, including a new Ph homologue we have named HPH3. Despite differences in composition, dPRC1 and hPRC-H have similar functions: hPRC-H is able to efficiently block remodeling of nucleosomal arrays through a mechanism that does not block the ability of nucleases to access and cleave the arrays.
Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients (2002)

Current theories of CF pathogenesis predict different predisposing "local environmental" conditions and sites of bacterial infection within CF airways. Here we show that, in CF patients with established lung disease, Pseudomonas aeruginosa was located within hypoxic mucopurulent masses in airway lumens. In vitro studies revealed that CF-specific increases in epithelial O(2) consumption, linked to increased airway surface liquid (ASL) volume absorption and mucus stasis, generated steep hypoxic gradients within thickened mucus on CF epithelial surfaces prior to infection. Motile P. aeruginosa deposited on CF airway surfaces penetrated into hypoxic mucus zones and responded to this environment with increased alginate production. With P. aeruginosa growth in oxygen restricted environments, local hypoxia was exacerbated and frank anaerobiosis, as detected in vivo, resulted. These studies indicate that novel therapies for CF include removal of hypoxic mucus plaques and antibiotics effective against P. aeruginosa adapted to anaerobic environments.
Design and Synthesis of Potent, Long-Acting Lipidated Relaxin-2 Analogs (2018)

Peptide hormone relaxin-2, a member of the insulin family of peptides, plays a key role in hemodynamics and renal function and has shown preclinical efficacy in multiple disease models, including acute heart failure, fibrosis, preeclampsia, and corneal wound healing. Recently, serelaxin, a recombinant version of relaxin-2, has been studied in a large phase 3 clinical trial (RELAX-AHF-2) for acute decompensated heart failure patients with disappointing outcome. The poor in vivo half-life of relaxin-2 may have limited its therapeutic efficacy and long-term cardiovascular benefit. Herein, we have developed a semisynthetic methodology and generated potent, fatty acid-conjugated relaxin analogs with long-acting pharmacokinetic (PK) profile in rodents. The enhanced PK properties translated into improved and long-lasting pharmacodynamic effect in pubic ligament elongation (PLE) studies. The resultant novel relaxin analog, R9-13, represents the first long-acting relaxin-2 analog and could potentially improve the clinical efficacy and outcome for this important peptide hormone. This semisynthetic methodology could also be applied to other cysteine-rich peptides and proteins for half-life extension.
Supragingival plaque removal with and without dentifrice: a randomized controlled clinical trial (2012)

The aim of this study was to compare the efficacy of dental plaque removal by brushing with and without conventional dentifrice. Twenty-four students aged 17 to 28 years participated in this randomized controlled clinical trial. Quadrants 1-3 or 2-4 were randomly allocated to the test group (brushing without dentifrice) or control group (brushing with dentifrice). After 72 h of cessation of oral hygiene, Quigley & Hein (Turesky) plaque index was assessed before and after brushing by a calibrated and blind examiner. Overtime and intergroup comparisons were performed by Student's paired sample t-test at 5% significance level. The results showed that both groups after toothbrushing presented statistically significant reductions in plaque, with no differences between them (from 3.06 ± 0.54 to 1.27 ± 0.26 versus from 3.07 ± 0.52 to 1.31 ± 0.23). A separate analysis of the buccal and lingual aspects also showed no significant differences between groups. It may be concluded that the use of a conventional dentifrice during toothbrushing does not seem to enhance plaque removal capacity.
Vibrio factors cause rapid fluid accumulation in suckling mice (1983)

Non-O-1 and O-1 Vibrio cholerae and Vibrio fluvialis isolated from clinical and environmental sources were examined for virulence factor production in 3-day-old suckling mice and in Y-1 tissue culture. The responses of the suckling mice to intragastrically administered bacterial cultures were measured by intestinal fluid accumulation (FA), diarrhea, and mortality. Regardless of the O-serovar, source of isolation, or ability to produce cholera toxin, all strains of V. cholerae stimulated increased FA, which was measurable in the mice at 4 h post-inoculation. The factor(s) causing these symptoms was found to be distinct from cholera toxin by the kinetics of FA and serological difference from cholera toxin based on in vivo neutralization tests. In most instances, FA was followed by high rates of mortality. Y-1 mouse adrenal tumor cell assays also showed that many V. cholerae produced extracellular heat-labile cytotoxic factor(s), and many cholera toxin-negative strains also caused a cytotonic-like morphological response. The majority of V. fluvialis strains produced smaller amounts of cytotoxic factor(s) but no cytotoxic reactions. The factor which stimulates rapid FA in suckling mice could be one of several virulence-associated factors contributing to diarrheal disease by nontoxigenic vibrios, but this is not verified at present.
Crystal Structure of the Aequorea victoria Green Fluorescent Protein (1996)

The green fluorescent protein (GFP) from the Pacific Northwest jellyfish Aequorea victoria has generated intense interest as a marker for gene expression and localization of gene products. The chromophore, resulting from the spontaneous cyclization and oxidation of the sequence -Ser65 (or Thr65)-Tyr66-Gly67-, requires the native protein fold for both formation and fluorescence emission. The structure of Thr65 GFP has been determined at 1.9 angstrom resolution. The protein fold consists of an 11-stranded beta barrel with a coaxial helix, with the chromophore forming from the central helix. Directed mutagenesis of one residue adjacent to the chromophore, Thr203, to Tyr or His results in significantly red-shifted excitation and emission maxima.