gebhart/patrepeval huggingface dataset:
A role for Rho in Ras transformation. (1995)

The small GTP-binding proteins Rac and Rho are key elements in the signal-transduction pathways respectively controlling the formation of lamellipodia and stress fibers induced by growth factors or oncogenic Ras. We recently reported that Rac function is necessary for Ras transformation and that expression of constitutively activated Rac1 is sufficient to cause malignant transformation. We now show that, although expression of constitutively activated V14-RhoA in Rat 1 fibroblasts does not cause transformation on its own, it strongly cooperates with constitutively active RafCAAX in focus-formation assays in NIH 3T3 cells. Furthermore, dominant-negative N19-RhoA inhibits focus formation by V12-H-Ras and RafCAAX in NIH 3T3 cells, and stable coexpression of N19-RhoA and V12-H-Ras in Rat1 fibroblasts reverts Ras transformation. Interestingly, stress fiber formation is inhibited in V12-H-Ras lines and restored by coexpression of N19-RhoA. We conclude that Rho drives at least two separate pathways, one that induces stress fiber formation and another one that is important for transformation by oncogenic Ras.
Adeno-associated virus: from defective virus to effective vector (2005)

The initial discovery of adeno-associated virus (AAV) mixed with adenovirus particles was not a fortuitous one but rather an expression of AAV biology. Indeed, as it came to be known, in addition to the unavoidable host cell, AAV typically needs a so-called helper virus such as adenovirus to replicate. Since the AAV life cycle revolves around another unrelated virus it was dubbed a satellite virus. However, the structural simplicity plus the defective and non-pathogenic character of this satellite virus caused recombinant forms to acquire centre-stage prominence in the current constellation of vectors for human gene therapy. In the present review, issues related to the development of recombinant AAV (rAAV) vectors, from the general principle to production methods, tropism modifications and other emerging technologies are discussed. In addition, the accumulating knowledge regarding the mechanisms of rAAV genome transduction and persistence is reviewed. The topics on rAAV vectorology are supplemented with information on the parental virus biology with an emphasis on aspects that directly impact on vector design and performance such as genome replication, genetic structure, and host cell entry.
Vehicle Occupant Position Sensing (1994)

&lt;div class="htmlview paragraph"&gt;Regardless of whether crash sensors are mounted in the crush zone or non-crush zone, there will always be crashes where the sensors trigger late and the occupant has moved to a position near to the airbag deployment cover where he or she may be injured by the deployment of the airbag. The required sensor triggering time is now determined by assuming that the occupant is a 50% male sitting in the mid seating position. 70% of vehicle occupants are smaller and, on average, sit closer to the airbag and thus are even more likely to be out-of-position. Finally, current sensor systems make no allowance for occupants that are wearing seatbelts, for rear facing child seats located on the front passenger seat or for unoccupied seats. There are thus strong safety reasons for occupant position sensors.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper discusses the above problems, the difficulties in sensing occupants and objects located in the vehicle and attempts to define the requirements for such devices. It also presents some of the added benefits which will result from effective sensors which can characterize the contents of the vehicle such as heating, air conditioning and entertainment systems which adjust to vehicle occupants.&lt;/div&gt;
Electrical Stimulation and High Temperature Conditioning of Broiler Carcasses (1990)

Two studies were conducted to determine the effects of post-mortem electrical stimulation and high temperature conditioning on the tenderness and post-mortem metabolism of broiler breast meat. Broiler carcasses were electrically stimulated (ES) (110 V, 1 A, 1 s on and 1 s off for 7 or 14 min) or left unstimulated (ES0), placed in a 39 C water bath (HTC) or in a water-ice slush (CTC) until 1 h post-mortem when the breast fillets were harvested. Fillets were cooked at 1 or 18 h post-mortem. Electrical stimulation and HTC had no individual effect on pectoralis major fillet tenderness, but when combined, they improved tenderness at both cooking times with the 18 h treatment yielding the lowest shear value. At 1 h post-mortem, fillets from ES- and HTC-treated carcasses had greater R values and sarcomere lengths and lower pH than ES and CTC or ES- and HTC-treated carcass fillets, which were similar and had greater R values and sarcomere lengths and lower pH than carcass fillets of the ES0 and CTC control. Although neither myofibril fragmentation index means nor SDS-PAGE banding patterns were affected by ES or HTC treatments, fragmentation index and sarcomere length were both highly correlated with shear force.
In vitro tubulogenesis of endothelial cells by relaxation of the coupling extracellular matrix-cytoskeleton (2001)

A reduced tension between the endothelial cells and the extracellular matrix, originating in the support or within the cells is sufficient to trigger an intracellular signaling cascade leading to tubulogenesis, an event mimicking one of the last steps of angiogenesis.
Edible Film Coating to Minimize Eggshell Breakage and Reduce Post‐Wash Bacterial Contamination Measured by Dye Penetration in Eggs (2002)

ABSTRACT: The mechanical and bacterial barrier properties of washed (tap water, sodium carbonate, Na 2 CO 3 , sodium hypochlorite, NaOCl) noncoated eggs and eggs coated with soy protein isolate (SPI), whey protein isolate (WPI), carboxylmethyl cellulose (CMC), or wheat gluten (WG) were evaluated. All coated eggshells showed greater puncture strength than those of noncoated eggs. The film‐coated eggs reduced post‐wash bacterial penetration as measured by dye penetration method. WPI coating completely inhibited blue dye penetration on average. These results suggest that WPI coatings can be used to reduce breakage of eggshell and egg microbial contamination.
Effects of methotrexate on trophoblast proliferation and local immune responses (1998)

Methotrexate is a folic acid analogue that has been used successfully for the treatment of ectopic pregnancy and, in conjunction with misoprostol, for medical abortions of early intrauterine pregnancies. To administer the most efficacious treatment requires knowledge of the mechanism underlying the induction of methotrexate-induced abortion. This study was designed to ascertain trophoblast integrity, proliferation and differentiation following administration of methotrexate. In addition, to determine if methotrexate affects the local uterine immune response, we ascertained the numbers and identities of decidual leukocytes following treatment. Ten women with undesired intrauterine pregnancies of 42-49 days gestation were recruited to receive methotrexte 50 mg/m2 i.m. A suction aspiration was performed 7 days later. Tissues from gestational age-matched elective surgical abortions were used as controls. Additionally, specimens from women who received methotrexate and misoprostol for abortion in a clinical trial of oral methotrexate in combination with misoprostol, who had a suction abortion because of continued embryonic cardiac activity 14 days after the methotrexate, were evaluated. Immunoreactivity to proliferating cell nuclear antigen and cyclin D3 antibodies was used to demonstrate a marked reduction in the proliferation index of cytotrophoblasts from methotrexate-treated abortions. Methotrexate treatment failures and non-treated pregnancies had a much higher proliferation index. There was no direct destruction of the syncytiotrophoblast, as indicated by the continued presence of human placental lactogen and beta-human chorionic gonadotrophin proteins. A decrease in the total number of leukocyte cells was observed in the decidua of methotrexate-treated samples, with the large granular lymphocyte (LGL) cells showing the greatest decline in numbers. Our conclusions from this study are that methotrexate acts primarily to derail the normal developmental programme of the trophoblast stem cell population, as well as to decrease LGL cell numbers in the decidua.
Automated Refactoring of Legacy Java Software to Enumerated Types (2007)

Java 1.5 introduces several new features that offer significant improvements over older Java technology. In this paper we consider the new enum construct, which provides language support for enumerated types. Prior to Java 1.5, programmers needed to employ various patterns (e.g., the weak enum pattern) to compensate for the absence of enumerated types in Java. Unfortunately, these compensation patterns lack several highly-desirable properties of the enum construct, most notably, type safety. We present a novel fully-automated approach for transforming legacy Java code to use the new enumeration construct. This semantics-preserving approach increases type safety, produces code that is easier to comprehend, removes unnecessary complexity, and eliminates brittleness problems due to separate compilation. At the core of the proposed approach is an interprocedural type inferencing algorithm which tracks the flow of enumerated values. The algorithm was implemented as an Eclipse plug-in and evaluated experimentally on 17 large Java benchmarks. Our results indicate that analysis cost is practical and the algorithm can successfully refactor a substantial number of fields to enumerated types. This work is a significant step towards providing automated tool support for migrating legacy Java software to modern Java technologies.
Transformation of a partial nopaline synthase gene into tobacco suppresses the expression of a resident wild-type gene. (1991)

A portion of the nopaline synthase gene under the control of the cauliflower mosaic virus 35S promoter was used to transform a tobacco plant that had previously been transformed with a wild-type nopaline synthase (nos) gene. Unexpectedly, in all nine primary transformants tested the wild-type nos expression was virtually completely suppressed. In contrast, plants transformed with the control vector DNA, which differed only in the absence of the partial nos gene, did not show any inhibition of nos expression. Progeny plants were analyzed for the stability of the gene-silencing phenotype. All of the progeny that carried both the wild-type and partial nos genes had no detectable nopaline synthase activity. In addition, wild-type nos mRNA could not be detected in these plants. In most plants in which the wild-type gene was segregated away from the partial nos gene, wild-type levels of activity were detected. Although DNA methylation has been shown to be correlated with a decrease in promoter activity in plants, none of the progeny appeared to carry a methylated nos promoter. The underlying mechanism causing this gene suppression phenomenon is unclear at this time.
Ultrafine fibrous cellulose membranes from electrospinning of cellulose acetate (2002)

Abstract Three solvents, that is, acetone, acetic acid, and dimethylacetamide (DMAc), with a range of solubility parameter δ, surface tension γ, viscosity η and boiling temperature were used to generate mixtures for electrospinning cellulose acetate (CA) (degree of substitution, DS = 2.45). Although none of these solvents alone enables continuous formation of fibers, mixing DMAc with either acetone or acetic acid produced suitable solvent systems. The 2:1 acetone:DMAc mixture is the most versatile mixture because it allows CA in the 12.5–20% concentration range to be continuously electrospun into fibrous membranes. These CA solutions have η between 1.2 and 10.2 poise and γ around 26 dyne/cm and produce smooth fibers with diameters from 100 nm to ∼1 μm. Fiber sizes generally decrease with decreasing CA concentrations. The nature of the collectors affects the morphology as well as packing of fibers. Fibers collected on paper have more uniform sizes, smooth surfaces, and fewer defects, whereas fibers collected on water are more varied in size. Electrically conductive solid collectors, such as Al foil and water, favor more tightly packed and less porous membranes. Porous collectors, like paper and copper mesh, produce highly porous membranes. The pores in membranes collected on the Al foil and paper are much better interconnected in the planar directions than those in membranes collected on water. There is evidence that electrospinning induces order in the fibers. Deacetylation of CA membranes is more efficient and complete in NaOH/ethanol than in aqueous NaOH, producing DS values between 0.15 and 2.33 without altering fiber surfaces, packing, or organization. The fully regenerated cellulose membranes are similarly hydrophilic as commodity cellulose fibrous matrices but absorb nearly 10 times as much water. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2119–2129, 2002
Membrane introduction Mass Spectrometry: Trends and applications (2000)

Recent advances in membrane introduction mass spectrometry (MIMS) are reviewed. On-line monitoring is treated by focusing on critical variables, including the nature and dimensions of the membrane, and the analyte vapor pressure, diffusivity, and solubility in the membrane barrier. Sample introduction by MIMS is applied in (i) on-line monitoring of chemical and biological reactors, (ii) analysis of volatile organic compounds in environmental matrices, including air, water and soil, and (iii) in more fundamental studies, such as measurements of thermochemical properties, reaction mechanisms, and kinetics. New semipermeable membranes are discussed, including those consisting of thin polymers, low vapor pressure liquids, and zeolites. These membranes have been used to monitor polar compounds, selectively differentiate compounds through affinity-binding, and provide isomer differentiation based on molecular size. Measurements at high spatial resolution, for example, using silicone-capped hypodermic needle inlets, are also covered, as is electrically driven sampling through microporous membranes. Other variations on the basic MIMS experiment include analyte preconcentration through cryotrapping (CT-MIMS) or trapping in the membrane (trap-and-release), as well as differential thermal release methods and reverse phase (i.e., organic solvent) MIMS. Method limitations center on semivolatile compounds and complex mixture analysis, and novel solutions are discussed. Semivolatile compounds have been monitored with thermally assisted desorption, ultrathin membranes and derivatization techniques. Taking advantage of the differences in time of membrane permeation, mixtures of structurally similar compounds have been differentiated by using sample modulation techniques and by temperature-programmed desorption from a membrane interface. Selective ionization techniques that increase instrument sensitivity towards polar compounds are also described, and comparisons are made with other direct sampling (nonchromatographic) methods that are useful in mixture analysis.
Structural characterization of intrinsically curved AT-rich DNA sequences (1994)

AT-rich DNA sequences other than AnTm tracts (n + m > or = 4) are known to be intrinsically curved. The AATAT-element constitutes one known example of these sequences. In this paper, the elucidation of the structural basis of the curvature induced by this sequence element was addressed. As judged by the patterns of cleavage by the hydroxyl radical and DNase I, the AATAT sequence shows a narrow minor groove. Furthermore, the 5' adenine residue of the AA dinucleotide contained within the sequence is hyperreactive to diethylpyrocarbonate. Similar structural properties are shown by several sequences inducing intrinsic DNA curvature, such as an A5-tract or the closely related ATAAT, AATATA and TAATAT sequences, which are also shown here to induce curvature. On the other hand, other related sequences, such as TATAA and ATATA, that do not induce curvature, show different structural characteristics.
Visual arrestin interaction with rhodopsin. Sequential multisite binding ensures strict selectivity toward light-activated phosphorylated rhodopsin (1993)

Visual arrestin plays an important role in regulating light responsiveness via its ability to specifically bind to the phosphorylated and light-activated form of rhodopsin. Previously, we utilized an in vitro translation system to express and characterize the full-length (404 amino acids) and two truncated forms of visual arrestin. Here we have extended these studies to include a total of 33 different truncation and deletion mutants of arrestin, ranging from 69 to 391 amino acids in length. Mutants were produced by cutting within the open reading frame of the bovine arrestin cDNA with selective restriction enzymes followed by in vitro translation of the transcribed truncated mRNAs. Mutant arrestin binding to dark, light-activated, dark phosphorylated, and light-activated phosphorylated rhodopsin as well as to opsin, phosphoopsin, and truncated rhodopsin was then extensively characterized. In addition, the sensitivity of arrestin/rhodopsin interactions to conditions of increasing ionic strength was measured. These studies suggest the localization of multiple functional domains within the arrestin molecule that include: 1) a "phosphorylation recognition" domain, which interacts with the phosphorylated carboxyl terminus of rhodopsin, was localized predominately between residues 158-185; 2) an "activation recognition" domain, which interacts with those portions of the rhodopsin molecule that change conformation upon light activation, was found to consist of at least three regions within the first 191 residues of the arrestin molecule; 3) a hydrophobic interaction domain, localized between residues 191 and 365, appears to be mobilized upon binding of arrestin to activated phosphorylated rhodopsin; 4) a regulatory domain, localized in the COOH-terminal region of arrestin (residues 365-391), was found to play a role in controlling the conformational change in arrestin necessary for mobilization of the hydrophobic interaction domain; and 5) The NH2 terminus of arrestin (residues 2-16) was found to be important for interacting with the regulatory COOH-terminal region as well as maintaining the conformation of the NH2-terminal half of arrestin. A mechanism which ensures strict arrestin binding selectivity toward phosphorylated light-activated rhodopsin is proposed.
Accuracy and Survival Benefit of Cytological Prediction of Endometrial Carcinoma on Routine Cervical Smears (1993)

Summary: Among 359 women who received a cytology report of endometrial malignancy from the Victorian Cytology Service during 1982–87, the positive predictive value for a later histological diagnosis of endometrial malignancy was 64%. The positive predictive value was significantly higher for the group of women in whom the cytopathologists made definite predictions of endometrial malignancy as compared to the group where the cytologic features were only suggestive of endometrial malignancy (75% vs. 50%, X2 = 23.4; p > 0.001). The sensitivity of cervical cytology performed within two years of the diagnosis of endometrial malignancy was 28%. The odds ratio of death from endometrial cancer among women where the cytology may have allowed for an early diagnosis in comparison to women where cytology did not hasten the diagnosis was 0.78 (95% confidence interval = 0.25–2.47; p < 0.05). We conclude that while cervical cytology can predict the presence of malignancy for a small proportion of women with endometrial cancer, there remains no evidence that a cervical cancer screening program will make a major impact on reducing the morbidity and mortality from endometrial cancer.
High Dynamic Range Image and Video Compression - Fidelity Matching Human Visual Performance (2007)

Vast majority of digital images and video material stored today can capture only a fraction of visual information visible to the human eye and does not offer sufficient quality to fully exploit capabilities of new display devices. High dynamic range (HDR) image and video formats encode the full visible range of luminance and color gamut, thus offering ultimate fidelity, limited only by the capabilities of the human eye and not by any existing technology. In this paper we demonstrate how existing image and video compression standards can be extended to encode HDR content efficiently. This is achieved by a custom color space for encoding HDR pixel values that is derived from the visual performance data. We also demonstrate how HDR image and video compression can be designed so that it is backward compatible with existing formats.
Genomic organization of the 5′ end of human β-ENaC and preliminary characterization of its promoter (2002)

The mRNA for the beta-subunit of the epithelial Na(+) channel (beta-ENaC) is regulated developmentally and, in some tissues, in response to corticosteroids. To understand the mechanisms of transcriptional regulation of the human beta-ENaC gene, we characterized the 5' end of the gene and its 5'-flanking regions. Adaptor-ligated human kidney and lung cDNA were amplified by 5' rapid amplification of cDNA ends, and transcription start sites of two 5' variant transcripts were determined by nuclease protection or primer extension assays. Cosmid clones that contain the 5' end of the gene were isolated, and analysis of these clones indicated that alternate first exons approximately 1.5 kb apart and approximately 45 kb upstream of a common second exon formed the basis of these transcripts. Genomic fragments that included the proximal 5'-flanking region of either transcript were able to direct expression of a reporter gene in lung epithelia and to bind Sp1 in nuclear extracts, confirming the presence of separate promoters that regulate beta-ENaC expression.
The Chicken β-Globin 5′HS4 Boundary Element Blocks Enhancer-Mediated Suppression of Silencing (1999)

A constitutive DNase I-hypersensitive site 5' of the chicken beta-globin locus, termed 5'HS4 or cHS4, has been shown to insulate a promoter from the effect of an upstream enhancer and to reduce position effects on mini-white expression in Drosophila cells; on the basis of these findings, it has been designated a chromatin insulator. We have examined the effect of the cHS4 insulator in a system that assays both the level of gene expression and the rate of transcriptional silencing. Because transgenes flanked by insulator elements are shielded from position effects in Drosophila cells, we tested the ability of cHS4 to protect transgenes from position effects in mammalian cells. Flanking of an expression vector with the cHS4 insulator in a colony assay did not increase the number of G418-resistant colonies. Using lox/cre-based recombinase-mediated cassette exchange to control integration position, we studied the effect of cHS4 on the silencing of an integrated beta-geo reporter at three genomic sites in K562 erythroleukemia cells. In this assay, enhancers act to suppress silencing but do not increase expression levels. While cHS4 blocked enhancement at each integration site, the strength of the effect varied from site to site. Furthermore, at some sites, cHS4 inhibited the enhancer effect either when placed between the enhancer and the promoter or when placed upstream of the enhancer. These results suggest that the activity of cHS4 is not dominant in all contexts and is unlikely to prevent silencing at all genomic integration sites.