gebhart/patrepeval huggingface dataset:
Properties of promoters cloned randomly from the Saccharomyces cerevisiae genome. (1988)

Promoters were isolated at random from the genome of Saccharomyces cerevisiae by using a plasmid that contains a divergently arrayed pair of promoterless reporter genes. A comprehensive library was constructed by inserting random (DNase I-generated) fragments into the intergenic region upstream from the reporter genes. Simple in vivo assays for either reporter gene product (alcohol dehydrogenase or beta-galactosidase) allowed the rapid identification of promoters from among these random fragments. Poly(dA-dT) homopolymer tracts were present in three of five randomly cloned promoters. With two exceptions, each RNA start site detected was 40 to 100 base pairs downstream from a TATA element. All of the randomly cloned promoters were capable of activating reporter gene transcription bidirectionally. Interestingly, one of the promoter fragments originated in a region of the S. cerevisiae rDNA spacer; regulated divergent transcription (presumably by RNA polymerase II) initiated in the same region.
The α4β1 integrin can mediate leukocyte adhesion to casein and denatured protein substrates (1997)

An understanding of the binding specificity of leukocyte integrins is important to determine the range of ligands that interact with these receptors during inflammatory processes. In this study we show that the alpha4beta1 integrin can interact with casein and denatured albumin and promote leukocyte adhesion through these interactions. This was demonstrated with the use of blocking antibodies directed to alpha4beta1 and peptide adhesion competitors containing the alpha4beta1 binding tripeptide, Leu-Asp-Val (LDV). Consistent with this data, the adhesion is completely divalent cation-dependent and is stimulated by known activators of leukocyte integrin function, namely phorbol ester and the beta1 integrin activating antibody, 8A2. It is interesting to note that neither bovine alpha-casein or human albumin contain an LDV site (present in the CS-1 site of alternatively spliced fibronectin) or an IDS site (present in VCAM-1) yet they promote adhesion through this integrin. Furthermore, alpha4beta1 directly binds to Sepharose columns containing casein, casein fragments, or denatured albumin but does not bind columns containing native albumin. These data suggest that the binding specificity for the alpha4beta1 integrin is considerably broader than previously realized. This work has implications for how subsets of leukocytes may interact with damaged proteins during tissue injury and inflammation.
Effect of a proteoglycan produced by rat tumor cells on their adhesion to fibronectin-collagen substrata. (1983)

In this paper, we demonstrate that a chondroitin sulfate proteoglycan purified from a rat yolk sac tumor alters the adhesion of the tumor cells to substrata containing fibronectin or type I collagen. In the presence of the proteoglycan, these substrata were much less adhesive and did not promote cell spreading. The inhibitory effect of the proteoglycan was reversible and more pronounced during the early stages of cell attachment in vitro. The effect of the proteoglycan was selective in that it depended on the ability of the adhesive substratum to bind the proteoglycan. The proteoglycan did not inhibit the attachment of the cells to type IV collagen, which bound 12 times less proteoglycan than did type I collagen. Similarly, attachment of the cells to fibronectin fragments which did not bind the proteoglycan was not affected by it. The selective effects of the proteoglycan on the adhesion of cells to extracellular matrices suggest that such proteoglycans may promote tumor invasion by reducing interaction of cells with interstitial extracellular matrices while permitting attachment to basement membranes.
Suppression of Defense Response in Plants by the avrBs3/pthA Gene Family of Xanthomonas spp. (2006)

Effector genes of some plant-pathogenic bacteria, including some members of the avrBs3/pthA effector gene family from Xanthomonas spp., confer not only genotype-specific disease resistance but also pathogen aggressiveness or virulence. In addition, some effector gene products suppress induction of a nonspecific (or general) hypersensitive response (HR). To determine whether the Xanthomonas avrBs3/pthA gene family members apl1, avrXa7, or avrXa10 also confer suppressor activity, we introduced constructs with each effector gene into Pseudomonas fluorescens 55 that expressed the entire hrp cluster from P. syringae pv. syringae in cosmid pHIR11. When inoculated to tobacco 'Bright Yellow', P fluorescens (pHIR11) induces the HR and expression of four tobacco defense response genes: HIN1, RbohB, PAL, and PR1. When P. fluorescens double transformants that contained pHIR11 and constructs with apl1, avrXa7, or avrXa10 were infiltrated into tobacco, the HR and expression of three defense response genes, RbohB, PAL, and PR1, were suppressed. The suppression of the HR and defense gene expression was more efficient in the transformants with the apl1 and avrXa7 than the transformant with avrXa10. Although expression of other defense genes was suppressed by the double transformants, HIN1 expression was the same level as was observed after infiltration with P. fluorescens (pHIR11), suggesting that HIN1 may not be involved directly in HR. Taken together, our data suggest that avrXa7, avrXa10, and apl1, when delivered to plant cells by the P. syringae pv. syringae hrp secretion system, can suppress nonhost HR and associated phenotypes.
Nanocomposite Silica/Polyamine Films Prepared by a Reactive Layer-by-Layer Deposition (2007)

Composite material nanofilms of controlled thickness constituted by ceramics and polymers find more and more applications to improve the properties and functionalities of material surfaces. In this paper we present a new way to deposit such composite coatings by alternated contacts of a surface with a polyamine solution (either poly(allylamine), poly(ethyleneimine), poly-l-lysine, or poly(diallydimethylammonium)chloride and silicic acid. The experiments are mainly realized by spraying of solutions onto the surface. The polyamines deposited in the first spraying step catalyze silica formation upon further spraying of a silicic acid-containing solution. The film thickness increases linearly with the number of deposition steps, the thickness increment being of the order of a few nanometers per silicic acid/polyamine layer. Infrared spectroscopy in the total attenuated reflection mode reveals spectra that are close to those of pure silica particles. The film morphology is further investigated by means of atomic force microscopy and environmental scanning electron microscopy. This reactive layer-by-layer deposition constitutes a new way to build, in an easy way, nanocomposite coatings with precise control of their thickness.
Integrated Digital Microfluidic Platform for Voltammetric Analysis (2013)

Digital microfluidics (DMF) is an emerging technique for manipulating small volumes of liquids. DMF is particularly well suited for analytical applications as it allows automated handling of discrete samples, and it has been integrated with several inline analysis techniques. However, examples of the integration of DMF with electroanalytical methods are notably scarce, and those that have been reported rely on external electrodes that impose limitations on complexity. To combine the full capabilities of DMF with voltammetry, we designed a platform featuring a three-electrode electrochemical cell integrated in a microfabricated DMF device, removing the need for external electrodes and allowing for complete droplet control. The performance of the DMF/voltammetry system is comparable to that of a commercial screen printed electrode, and the new platform was applied to generating a calibration series for acetaminophen with a limit of detection of 76 μM and good precision (4% average RSD), all with minimal human intervention. We propose that this platform and variations thereof may be a useful new tool for microscale electroanalysis and will be a complementary system to existing inline analysis techniques for DMF.
A Thermoelectric Blood Flow Recorder in the Form of a Needle (1933)

The needle flow recorder described here was primarily designed to measure rate of blood flow through the internal jugular vein of man. Preliminary work on animals has shown that the device possesses certain characteristics that would seem to promise it a sphere of usefulness in a variety of problems where blood flow is an important variable. The advantages of the device are as follows: Its use entails only a minimal trauma. It can be applied to the study of flow through relatively inaccessible structures. The method makes it possible to measure qualitatively the changes in blood flow through a vascular tissue without isolating or cannulizing the afferent or efferent vessels, and thus enables one to study the blood flow through a tissue or organ, the blood supply of which is not capable of being completely isolated. It also makes possible relative determinations of the blood flow through various parts of the same organ or region. This has not been possible by any method previously described. The thermoelectric methods for measurement of volume flow of blood previously reported require cannulization of a vessel and the passing of heparinized blood through a water jacket, the temperature of which is thermoelectrically determined (Bronk and Gesell); or the isolation of a vessel, the heating of the blood therein by means of a high frequency current, and the determination of the temperature gradient along the vessel (Rein2); or the insertion of an organ or region into a calorimeter.The theory upon which the instrument operates is extremely simple. The cooling power of a stream depends, among other things, upon its velocity.
Cloning and mutagenesis of genes encoding the cytochrome bd terminal oxidase complex in Azotobacter vinelandii: mutants deficient in the cytochrome d complex are unable to fix nitrogen in air (1990)

The genome of Azotobacter vinelandii contains DNA sequences homologous to the structural genes for the Escherichia coli cytochrome bd terminal oxidase complex. Two recombinant clones bearing cydA- and cydB-like sequence were isolated from an A. vinelandii gene library and subcloned into the plasmid vector pACYC184. Physical mapping demonstrated that the cydA- and cydB-like regions in A. vinelandii are contiguous. The cydAB and flanking DNA was mutagenized by the insertion of Tn5-B20. Mutations in the cydB-hybridizing region resulted in the loss of spectral features associated with cytochromes b595 and d. A new locus, cydB, encoding cytochromes b595 and d in A. vinelandii is proposed. A second region adjacent to cydB was also involved in expression of the cytochrome bd complex in A. vinelandii, since mutations in this region resulted in an increase in the levels of both cytochrome b595 and cytochrome d. The regions involved in expression of the cytochrome bd complex and cydB are transcribed in the same direction. Mutants deficient in cytochromes b595 and d were unable to grow on N-deficient medium when incubated in air but could fix nitrogen when the environmental O2 concentration was reduced to 1.5% (vol/vol). It is proposed that the branch of the respiratory chain terminated by the cytochrome bd complex supports the high respiration rates required for the respiratory protection of nitrogenase.
Synthetic Polymer Fracturing Fluid for High-Temperature Applications (2003)

Abstract High-temperature fracturing fluids based on guar degrade rapidly at temperatures above 300°F, complicating stimulation of high-temperature wells. A synthetic polymer was developed that overcomes the hydrolytic stability limitations of polysaccharides while maintaining the ability to crosslink and break the fluid. This paper presents the initial laboratory development of a fracturing fluid using the synthetic polymer. Hydration is rapid compared to guar, eliminating the need for special hydration tanks or equipment when mixed on-the-fly. Crosslinking is achieved with conventional zirconium crosslinkers to yield a highly viscoelastic gel. Static and dynamic fluid-loss test data are presented and compared to guar-based fluids. Dynamic effects on fluid-loss rates were negligible compared to a borate-crosslinked guar fluid over a wide range of matrix permeabilities. Rheological characterization up to 400°F was performed with a Fann Model 50 viscometer and clearly demonstrated the synthetic frac fluid's high stability relative to guar. Additionally, effects of various breaker types are presented.
Live Attenuated Varicella Virus Vaccine (1984)

We conducted a double-blind, placebo-controlled efficacy trial of the live attenuated Oka/Merck varicella vaccine among 956 children between the ages of 1 and 14 years, with a negative clinical history of varicella. Of the 914 children who were serologically confirmed to be susceptible to varicella, 468 received vaccine and 446 received placebo. The vaccine produced few clinical reactions and was well tolerated. There was no clinical evidence of viral spread from vaccinated children to sibling controls. Approximately eight weeks after vaccination, 94 per cent of the initially seronegative children who received vaccine had detectable antibody to varicella. During the nine-month surveillance period, 39 clinically diagnosed cases of varicella, 38 of which were confirmed by laboratory tests, occurred among study participants. All 39 cases occurred in placebo recipients; no child who received vaccine contracted varicella. The vaccine was 100 per cent efficacious in preventing varicella in this population of healthy children (P less than 10(-9).
Proinflammatory cytokines in patients with congestive heart failure (2004)

Objective:To study the change of the serum level of proinflammatory cytokines(PIC): tumor necrosis factor-α(TNF-α), interleukin-6(IL-6), interleukin-1β (IL-1β) and nitric oxide(NO), and to assess their effects on congestive heart failure and their relationship between each other.Method:IL-6 was measured by enzyme-linked immunosorbent assay,and TNF-α, IL-1β by radioimmuno assay, NO by colorimetry in 45 patients with various degrees of CHF and 17 age-matched control subjects. The patients were devided into 3 groups(cardiac function classⅡ, Ⅲ, Ⅳ,according to NYHA classficiation), and divided into “cachectic” and “noncachectic” groups based on body weight patients with CHF were identified as “cachexia” when their body weight was less than 85 percent of ideal body weight.Result:The levels of above serum analytes were significantly elevated in patients with CHF as compared with control subjects. NO, IL-6 were obviously risen in patients with cardiac function class(NYHA)Ⅱ、Ⅲ、Ⅳ, and TNF-α rose in ones with NYHA class Ⅲ and Ⅳ, but IL-1β only rose in ones with class Ⅳ. There were no significant difference between various etiology CHF groups and between “cachectic” and “noncachectic” groups.Serum TNF-α was positively related with serum IL-6(r= 0.5829,P 0.01).Conclusion:The level of serum IL-6, IL-1β, TNF-α, NO are closely related with severity of CHF, and can serve as the markers to judge the severity and the prognosis of CHF. IL-6, IL-1β and TNF-α may play an important role in the incidence and progress of heart failure.
ApoStream™, a new dielectrophoretic device for antibody independent isolation and recovery of viable cancer cells from blood (2012)

Isolation and enumeration of circulating tumor cells (CTCs) are used to monitor metastatic disease progression and guide cancer therapy. However, currently available technologies are limited to cells expressing specific cell surface markers, such as epithelial cell adhesion molecule (EpCAM) or have limited specificity because they are based on cell size alone. We developed a device, ApoStream(™) that overcomes these limitations by exploiting differences in the biophysical characteristics between cancer cells and normal, healthy blood cells to capture CTCs using dielectrophoretic technology in a microfluidic flow chamber. Further, the system overcomes throughput limitations by operating in continuous mode for efficient isolation and enrichment of CTCs from blood. The performance of the device was optimized using a design of experiment approach for key operating parameters such as frequency, voltage and flow rates, and buffer formulations. Cell spiking studies were conducted using SKOV3 or MDA-MB-231 cell lines that have a high and low expression level of EpCAM, respectively, to demonstrate linearity and precision of recovery independent of EpCAM receptor levels. The average recovery of SKOV3 and MDA-MB-231 cancer cells spiked into approximately 12 × 10(6) peripheral blood mononuclear cells obtained from 7.5 ml normal human donor blood was 75.4% ± 3.1% (n = 12) and 71.2% ± 1.6% (n = 6), respectively. The intra-day and inter-day precision coefficients of variation of the device were both less than 3%. Linear regression analysis yielded a correlation coefficient (R(2)) of more than 0.99 for a spiking range of 4-2600 cells. The viability of MDA-MB-231 cancer cells captured with ApoStream was greater than 97.1% and there was no difference in cell growth up to 7 days in culture compared to controls. The ApoStream device demonstrated high precision and linearity of recovery of viable cancer cells independent of their EpCAM expression level. Isolation and enrichment of viable cancer cells from ApoStream enables molecular characterization of CTCs from a wide range of cancer types.
Design, modeling and preliminary control of a compliant hexapod robot (2002)

We present the design, modeling and preliminary control of RHex, an autonomous dynamically stable hexapod possessing merely six actuated degrees of freedom (at the hip attachment of each leg). Our design emphasizes mechanical simplicity as well as power and computational autonomy, critical components for legged robotics applications. A compliant hexapod model, used to build a simulation environment closely informed the design and construction of the physical machine and promises to inform, similarly, our future analysis as well. Simulations and experiments show that RHex can achieve dynamically stable walking, running and turning with very simple clock driven open-loop control strategies.
Soluble polyarylenes containing alternating binaphthylene and biphenylene structural units (1992)

Abstract This article describes the synthesis of a novel series of soluble polyarylenes containing alternating binapthylene and biphenylene structural units. They were obtained by the cation‐radical polymerization of bis(1‐naphthyl) biphenyls. The following monomers were synthesized and polymerized : 4,4′‐bis(1‐naphthyl) biphenyl ( 9 ), 3,3′‐bis(1‐naphthyl) biphenyl ( 10 ), 2,2′‐bis(1‐naphthyl)biphenyl ( 11 ), and 2,5‐bis(1‐naphthyl)biphenyl ( 14 ). All polymerizations were performed in nitrobenzene using FeCl 3 as oxidant. Polymers with number average molecular weights of up to 4000 g/mol were obtained.
Local Expression of C-Type Natriuretic Peptide Suppresses Inflammation, Eliminates Shear Stress–Induced Thrombosis, and Prevents Neointima Formation Through Enhanced Nitric Oxide Production in Rabbit Injured Carotid Arteries (2002)

We previously observed that adenovirus-mediated expression of C-type natriuretic peptide (CNP) markedly inhibits neointima formation after balloon injury in rat carotid arteries, suggesting that CNP has multiple effects over its modest inhibitory effect on cellular proliferation. We hypothesized that local expression of CNP might have antithrombotic and antiinflammatory effects. Balloon-injured rabbit carotid arteries were infected with an adenovirus expressing human CNP (AdCNP), human tissue factor pathway inhibitor (AdTFPI), or bacterial β-galactosidase (AdLacZ) or infused with saline. Seven days later, shear stress–induced thrombosis was evaluated by cyclic flow variation (CFV), reflecting recurrent cycles of thrombus formation and dislodgment. CFV was observed in all AdLacZ-infected and saline-infused arteries but not in arteries infected with AdCNP or AdTFPI even in the presence of epinephrine. Injury increased the expressions of intracellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1) and infiltration of macrophages. However, these effects were markedly reduced in AdCNP-treated arteries but not in AdTFPI-infected ones. In AdCNP-infected arteries, injury-induced expression of inducible NO synthase (iNOS) was enhanced, leading to increased NO generation. Interestingly, when the enhanced NO production was inhibited, neither inhibitory effect was observed, and suppression of neointima formation by CNP was canceled. Our study demonstrates that overexpression of CNP shows antithrombotic and antiinflammatory effects and reduces neointima formation mainly through enhanced NO production.
Cloning and characterization of a functionally distinct corticotropin-releasing factor receptor subtype from rat brain. (1995)

The present study reports the isolation of a cDNA clone that encodes a second member of the corticotropin-releasing factor (CRF) receptor family, designated as the CRF2 receptor. The cDNA was identified using oligonucleotides of degenerate sequence in a PCR paradigm. A PCR fragment obtained from rat brain was utilized to isolate a full-length cDNA from a rat hypothalamus cDNA library that encoded a 411-amino acid protein with approximately 70% identity to the known CRF1 receptor over the entire coding region. When expressed in mouse Ltk- cells, this receptor stimulates cAMP production in response to CRF and known CRF-like agonists. CRF and the nonmammalian CRF-related peptides sauvagine and urotensin I stimulate adenylate cyclase activity in a dose-dependent manner with a rank order of potency different from that of the CRF1 receptor: sauvagine > urotensin > or = rat/human CRF > ovine CRF. Tissue distribution analysis of the mRNAs by reverse transcriptase-PCR shows CRF2 receptor mRNA is present in rat brain and detectable in lung and heart. In situ hybridization studies indicate specific expression within the brain in the ventromedial nuclei of the hypothalamus, the lateral septum, the amygdala, and entorhinal cortex, but there is unremarkable expression in the pituitary. An additional splice variant of the CRF2 receptor with a different N-terminal domain has been identified by PCR, encoding a putative protein of 431 amino acids. Thus, the data demonstrate the presence of another functional CRF receptor, with significant differences in the pharmacological profile and tissue distribution from the CRF1 receptor, which would predict important functional differences between the two receptors.
Implementing transparent shared memory on clusters using virtual machines (2005)

Shared memory systems, such as SMP and ccNUMA topologies, simplify programming and administration. On the other hand, clusters of individual workstations are commonly used due to cost and scalability considerations. We have developed a virtual-machine-based solution, dubbed vNUMA, that seeks to provide a NUMA-like environment on a commodity cluster, with a single operating system instance and transparent shared memory. In this paper we present the design of vNUMA and some preliminary evaluation.
Acyclovir in the prevention of duodenal ulcer recurrence. (1990)

This study tests the hypothesis that reactivation of a latent herpes simplex virus infection may be a cause of recurrent duodenal ulceration. Patients with recently healed duodenal ulcer were entered into a double blind, randomised study of maintenance treatment with the antiviral drug acyclovir (400 mg bid) versus placebo, to determine if suppression of herpes virus infection would influence the natural history of the ulcer disease. One hundred and fifteen patients entered the trial and 76 patients completed it according to the protocol. Endoscopy was performed when ulcer symptoms recurred and at the end of the 25 week trial period. In the acyclovir group the cumulated relapse rate was 63% compared with 56% in the placebo group (NS). This result suggests that reactivation of herpes simplex virus is not a cause of recurrent duodenal ulcer.