gebhart/patrepeval huggingface dataset:
Germ cell‐specific expression of a proacrosin‐cat fusion gene in transgenic mouse testis (1992)

Acrosin is a serine proteinase located in a zymogen form, proacrosin in the acrosome of the sperm. It is released as a consequence of the acrosome reaction and is believed to be the most important enzyme in the fertilization process. In the mouse, the proacrosin gene is transcribed premeiotically in spermatocytes, but protein biosynthesis starts in haploid spermatids and is restricted to the emerging acrosome. Four lines of transgenic mice harboring 2.3 kb of 5' untranslated region of the rat proacrosin gene fused to the CAT-reporter gene were generated by microinjection of fertilized eggs. The chimeric gene was found to be present in 10-100 copies per genome in the different strains. The 5' untranslated region of rat proacrosin gene could properly direct CAT-gene expression to spermatocytes and CAT-mRNA translation to round spermatids as it is known for mouse proacrosin gene. However, CAT protein is not restricted to the acrosome; rather, it is distributed in the spermatid cytoplasm. This could be due to the lack of DNA sequences for a hydrophobic leader peptide that have been found in all mammalian proacrosins studied until now but that was not present in transgene. It can be concluded from our results that cis-acting sequences required for tissue specific proacrosin expression reside on a 2.3-kb restriction fragment and are conserved in the proacrosin genes of mouse and rat.
Positive conversion of negative signaling of CTLA4 potentiates antitumor efficacy of adoptive T-cell therapy in murine tumor models (2012)

Cytotoxic T lymphocyte-associated antigen 4 (CTLA4) has been known to be a strong tolerance-inducing inhibitory receptor on T-cell surface. Systemic blocking of CTLA4 function with blocking antibodies has been regarded as an attractive strategy to enhance antitumor immunity. However, this strategy accompanies systemic autoimmune side effects that are sometimes problematic. Therefore, we developed a novel CTLA4 mutant that could be expressed in tumor antigen-specific T cells to enhance antitumor effect without systemic autoimmunity. This mutant, named CTLA4-CD28 chimera, consists of extracellular and transmembrane domains of CTLA4, linked with cytoplasmic CD28 domain. Overexpression of CTLA4-CD28 chimera in T cells delivered stimulatory signals rather than inhibitory signals of CTLA4 and significantly enhanced T-cell reactivity. Although this effect was observed in both CD4 and CD8 T cells, the effect on CD4 T cells was predominant. CTLA4-CD28 chimera gene modification of CD4 T cells significantly enhanced antitumor effect of unmodified CD8 T cells. Nonetheless, the gene modification of CD8 T cells along with CD4 T cells further maximized antitumor effect of T cells in 2 different murine tumor models. Thus, CTLA4-CD28 chimera gene modification of both tumor antigen-specific CD4 and CD8 T cells would be an ideal way of modulating CTLA4 function to enhance tumor-specific T-cell reactivity.
Percutaneous Penetration of Fluorescein Isothiocyanate-Dextrans and the Mechanism for Enhancement Effect of Enhancers on the Intercellular Penetration. (1995)

To identify the mechanism involved in the enhancement effect of enhancers on the intercellular penetration of large polar molecules, the skin penetration of fluorescein isothiocyanate (FITC)-dextrans (average molecular weight; 4400, 9400, and 69000 Da) and the lipid removal from the intercellular spaces by enhancers were studied using hairless rat skin. Pretreatment of hairless rat skin with enhancers such as n-octanol (20%), laurocapram (2%), isopropylmyristate (IPM, 20%), oleic acid (5%) and cineol (2%), which are water-immiscible, significantly enhanced the flux of FITC-dextrans, while pretreatment with water-miscible enhancers, i.e. dimethyl sulfoxide (DMSO, 5%) and N-methyl-2-pyrrolidone (NMP) did not increase the flux compared with the control. The penetration of FITC-dextrans was approximately size dependent. n-Octanol, laurocapram, IPM and oleic acid dramatically removed ceramides which are the intercellular lipids, whereas NMP and DMSO partly extracted the sphingolipids. A linear relationship was observed between the flux and removal of ceramides (p < 0.01), indicating that the removal of intercellular lipids would cause dramatic dilations between adherent cornified cells and enhance the penetration through the intercellular pathways. When the penetration of FITC-dextrans through Wistar rat skin was compared with that via hairless rat skin, the steady state flux of FITC-dextrans through Wistar rat skin pretreated with water-immiscible enhancers was 1.2- to 4.9-fold higher, suggesting that the penetration of large polar molecules through follicles may play at least some role in the percutaneous absorption.
Automatic detection and repair of errors in data structures (2003)

We present a system that accepts a specification of key data structure consistency constraints, then dynamically detects and repairs violations of these constraints, enabling the program to continue to execute productively even in the face of otherwise crippling errors. Our experience using our system indicates that the specifications are relatively easy to develop once one understands the data structures. Furthermore, for our set of benchmark applications, our system can effectively repair inconsistent data structures and enable the program to continue to operate successfully.
Viscoelasticity of the Vessel Wall: The Role of Collagen and Elastic Fibers (2001)

The aortic wall contains collagen fibrils, smooth muscle cells, and elastic fibers as the primary load-bearing components. It is well known that the collagen fibrils bear loads in the circumferential direction, whereas elastic fibers provide longitudinal as well as circumferential support. Stiffening of the vessel wall is associated with loss of elastic tissue and increases in the collagen content: however, little is known about the mechanism of vessel wall stiffening with age. The purpose of this review is to attempt to relate structural changes that occur to the collagen and elastic fibers to changes in the viscoelastic behavior that are associated with aging. Analysis of the viscoelastic mechanical properties of collagen fibrils from tendon, skin, and aortic wall suggest that the collagen fibrils of aortic wall are different than those of other tissues. The elastic spring constant of the collacen fibrils in vessel walls is significantly less than that found in tendon, suggesting that the presence of type III collagen in aortic wall increases the flexibility of the collagen fibrils. Furthermore, it is hypothesized that changes in the interface between collagen fibrils, elastic fibers, and smooth muscle during aging and in connective tissue disorders leads to changes in the viscoelasticity of the vessel wall.
Implantation of neural stem cells embedded in hyaluronic acid and collagen composite conduit promotes regeneration in a rabbit facial nerve injury model (2008)

The implantation of neural stem cells (NSCs) in artificial scaffolds for peripheral nerve injuries draws much attention. NSCs were ex-vivo expanded in hyaluronic acid (HA)-collagen composite with neurotrophin-3, and BrdU-labeled NSCs conduit was implanted onto the ends of the transected facial nerve of rabbits. Electromyography demonstrated a progressive decrease of current threshold and increase of voltage amplitude in de-innervated rabbits after implantation for one, four, eight and 12 weeks compared to readouts derived from animals prior to nerve transection. The most remarkable improvement, observed using Electrophysiology, was of de-innervated rabbits implanted with NSCs conduit as opposed to de-innervated counterparts with and without the implantation of HA-collagen, NSCs and HA-collagen, and HA-collagen and neurotrophin-3. Histological examination displayed no nerve fiber in tissue sections of de-innervated rabbits. The arrangement and S-100 immunoreactivity of nerve fibers in the tissue sections of normal rabbits and injured rabbits after implantation of NSCs scaffold for 12 weeks were similar, whereas disorderly arranged minifascicles of various sizes were noted in the other three arms. BrdU+ cells were detected at 12 weeks post-implantation. Data suggested that NSCs embedded in HA-collagen biomaterial could facilitate re-innervations of damaged facial nerve and the artificial conduit of NSCs might offer a potential treatment modality to peripheral nerve injuries.
The Nrf2-ARE Signalling Pathway: Promising Drug Target to Combat Oxidative Stress in Neurodegenerative Disorders (2005)

A large body of evidence indicates that oxidative stress is a salient pathological feature in many neurodegenerative diseases, including Amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease. In addition to signs of systemic oxidative stress, at the biochemical and neuropathological level, neuronal degeneration in these disorders has been shown to coincide with several markers of oxidative damage to lipids, nucleic acids, and proteins in affected brain regions. Neuroinflammatory processes, often associated with the induction of free radical generating enzymes and the accumulation of reactive astrocytes and microglial cells, are considered as a major source of oxidative stress. Given the pathogenic impact of oxidative stress and neuroinflammation, therapeutic strategies aimed to blunt these processes are considered an effective way to confer neuroprotection. Recently, the nuclear transcription factor Nrf2, that binds to the antioxidant response element (ARE) in gene promoters, has been reported to constitute a key regulatory factor in the co-ordinate induction of a battery of endogenous cytoprotective genes, including those encoding for both antioxidant- and anti-inflammatory proteins. In the present review, besides discussing recent evidence underscoring the thesis that the Nrf2-ARE signalling pathway is an attractive therapeutic target for neurodegenerative diseases, we advocate the view that chemopreventive agents might be suitable candidates to serve as lead compounds for the development of a new class of neuroprotective drugs.
Tegument-Specific, Virus-Reactive CD4 T Cells Localize to the Cornea in Herpes Simplex Virus Interstitial Keratitis in Humans (2000)

Herpes stromal keratitis (HSK) is a prevalent and frequently vision-threatening disease associated with herpes simplex virus type 1 (HSV-1) infection. In mice, HSK progression occurs after viral clearance and requires T cells and neutrophils. One model implicates Th1-like CD4 T cells with cross-reactivity between the HSV-1 protein UL6 and a corneal autoantigen. HSK can be prevented by establishing specific immunological tolerance. However, HSK can also occur in T-cell receptor-transgenic X SCID mice lacking HSV-specific T cells. To study the pathogenesis of HSK in the natural host species, we measured local HSV-specific T-cell responses in HSK corneas removed at transplant surgery (n = 5) or control corneas (n = 2). HSV-1 DNA was detected by PCR in two specimens. HSV-specific CD4 T cells were enriched in three of the five HSK specimens and were not detectable in the control specimens. Reactivity with peptide epitopes within the tegument proteins UL21 and UL49 was documented. Responses to HSV-1 UL6 were not detected. Diverse HLA DR and DP alleles restricted these local responses. Most clones secreted gamma interferon, but not interleukin-5, in response to antigen. HSV-specific CD8 cells were also recovered. Some clones had cytotoxic-T-lymphocyte activity. The diverse specificities and HLA-restricting alleles of local virus-specific T cells in HSK are consistent with their contribution to HSK by a proinflammatory effect.
Steroids and Oocyte Maturation—A New Look at an Old Story (2003)

Female fertility requires precise regulation of oocyte meiosis. Oocytes are arrested early in the meiotic cycle until just before ovulation, when ovarian factors trigger meiosis, or maturation, to continue. Although much has been learned about the late signaling events that accompany meiosis, until recently less was known about the early actions that initiate maturation. Studies using the well-characterized model of transcription-independent steroid-induced oocyte maturation in Xenopus laevis now show that steroid metabolism, classical steroid receptors, G protein-mediated signaling, and novel G protein-coupled receptors, all may play important roles in regulating meiosis. Furthermore, steroids appear to promote similar events in mammalian oocytes, implying a conserved mechanism of maturation in vertebrates. Interestingly, testosterone is a potent promoter of mammalian oocyte maturation, suggesting that androgen actions in the oocyte might be partially responsible for the polycystic ovarian phenotype and accompanying infertility associated with high androgen states such as polycystic ovarian syndrome or congenital adrenal hyperplasia. A detailed appreciation of the steroid-activated signaling pathways in frog and mammalian oocytes may therefore prove useful in understanding both normal and abnormal ovarian development in humans.
RNA-Ascorbate Interaction (1998)

Ascorbic acid and divalent iron salts have been widely used to investigate the effects of reactive oxygen species in different biological targets such as nucleic acids, proteins and lipids. This study was designed to examine the interaction of yeast RNA with vitamin C in aqueous solution at physiological pH with drug/RNA(P)(P=phosphate) molar ratios of r=1/80, 1/40, 1/20, 1/10, 1/4 and 1/2. Absorption spectra and Fourier transform infrared (FTIR) difference spectroscopy were used to determine the ascorbate binding mode, binding constant, sequence selectivity and RNA secondary structure in aqueous solution. Spectroscopic evidence showed that at low drug concentration (r=1/80 and 1/40), no major ascorbate-RNA interaction occurs, while at higher drug concentrations (r>1/40), a major drug-RNA complexation was observed through both G-C and A-U base pairs and the backbone phosphate groups with k=31.80 M(-1). Evidence for this comes from large perturbations of the G-C vibrations at 1698 and 1488 cm(-1) and the A-U bands at 1654 and 1608 cm(-1) as well as the phosphate antisymmetric stretch at 1244 cm(-1). At r>1/10, minor structural changes occur for the ribose-phosphate backbone geometry with RNA remaining in the A-family structure. The drug distributions around double helix were about 55% with G-C, 33% A-U and 12% with PO2 groups. A comparison between ascorbate-RNA and ascorbate-DNA complexes showed minor differences. The ascorbate binding (H-bonding) is via anion CO and OH groups.
Computational Identification and Characterization of Novel Genes from Legumes (2004)

The Fabaceae, the third largest family of plants and the source of many crops, has been the target of many genomic studies. Currently, only the grasses surpass the legumes for the number of publicly available expressed sequence tags (ESTs). The quantity of sequences from diverse plants enables the use of computational approaches to identify novel genes in specific taxa. We used BLAST algorithms to compare unigene sets from Medicago truncatula, Lotus japonicus, and soybean (Glycine max and Glycine soja) to nonlegume unigene sets, to GenBank's nonredundant and EST databases, and to the genomic sequences of rice (Oryza sativa) and Arabidopsis. As a working definition, putatively legume-specific genes had no sequence homology, below a specified threshold, to publicly available sequences of nonlegumes. Using this approach, 2,525 legume-specific EST contigs were identified, of which less than three percent had clear homology to previously characterized legume genes. As a first step toward predicting function, related sequences were clustered to build motifs that could be searched against protein databases. Three families of interest were more deeply characterized: F-box related proteins, Pro-rich proteins, and Cys cluster proteins (CCPs). Of particular interest were the >300 CCPs, primarily from nodules or seeds, with predicted similarity to defensins. Motif searching also identified several previously unknown CCP-like open reading frames in Arabidopsis. Evolutionary analyses of the genomic sequences of several CCPs in M. truncatula suggest that this family has evolved by local duplications and divergent selection.
Effect of hydrostatic pressure on the mitochondrial ATP synthase (1988)

The effects of hydrostatic pressure on three different preparations of mitochondrial H+-ATPase were investigated by studies of the hydrolytic activity, of the spectral shift and quantum yield of the intrinsic protein fluorescence, and of filtration chromatography. Both membrane-bound and detergent-solubilized forms of the mitochondrial F0-F1 complex were reversibly inactivated in the pressure range of 600-1800 bar, whereas with soluble F1-ATPase the inactivation was irreversible. Pressure inactivation of soluble F1-ATPase was facilitated by decreasing the protein concentration, indicating that dissociation is an important factor. In the presence of 30% glycerol, soluble F1-ATPase becomes inactivated by pressure in a reversible fashion, recovering the original activity. ATPase activity measured in an aqueous medium returns to the original values when incubated under high pressure in a glycerol-containing medium without substrate and is even enhanced when Mg-ATP is present. ATP hydrolysis returns to 80% of its original value in the case of the F0-F1 complex. Fluorescence studies under pressure revealed a red shift in the spectral distribution of the emission of tyrosine fluorescence of soluble F1-ATPase. A decrease in the quantum yield of intrinsic fluorescence was also observed upon subjection to pressure. The fluorescence intensity decreased monotonically as a function of pressure when the sample was in an aqueous medium, whereas it presented a biphasic behavior in a 30% glycerol medium. Gel filtration studies demonstrated that the hydrodynamic properties of the F1-ATPase are preserved if the enzyme is subjected to pressure in the presence of glycerol but they are modified when the same procedure is performed in an aqueous medium.(ABSTRACT TRUNCATED AT 250 WORDS)
Tabu Search: A Tutorial (1990)

Tabu search is a “higher level” heuristic procedure for solving optimization problems, designed to guide other methods (or their component processes) to escape the trap of local optimality. Tabu search has obtained optimal and near optimal solutions to a wide variety of classical and practical problems in applications ranging from scheduling to telecommunications and from character recognition to neural networks. It uses flexible structures memory (to permit search information to be exploited more thoroughly than by rigid memory systems or memoryless systems), conditions for strategically constraining and freeing the search process (embodied in tabu restrictions and aspiration criteria), and memory functions of varying time spans for intensifying and diversifying the search (reinforcing attributes historically found good and driving the search into new regions). Tabu search can be integrated with branch-and-bound and cutting plane procedures, and it has the ability to start with a simple implementation that can be upgraded over time to incorporate more advanced or specialized elements.
5.8-GHz circularly polarized rectifying antenna for wireless microwave power transmission (2002)

This paper reports a new circularly polarized (CP) high-gain high-efficiency rectifying antenna (rectenna). The CP rectenna can be rotated and still maintain a constant dc output voltage. The high-gain antenna has an advantage of reducing the total number of rectenna elements to cover a fixed area. The rectenna is etched on Rogers Duroid 5870 substrate with /spl epsi//sub r/=2.33 and 10 mil thickness. A high-gain dual-rhombic-loop antenna and a reflecting plane are used to achieve a CP antenna gain of 10.7 dB and a 2:1 voltage standing-wave ratio bandwidth of 10%. The rectenna's pattern has an elliptical cross section with orthogonal beamwidths of 40/spl deg/ and 60/spl deg/. The rectenna circuit has a coplanar stripline band-reject filter that suppresses the re-radiated harmonics by 20 dB. A highly efficient Schottky diode is used for RF-to-dc conversion with an efficiency of approximately 80% for an input power level of 100 mW and a load resistance of 250 /spl Omega/.
An integrated process for partial oxidation of alkanes (2003)

The partial oxidation of alkanes via bromination followed by the reaction with solid metal oxide mixtures (MO) is shown to give an array of products that can be tuned by varying the MO and the reaction conditions.
Telomerase inhibitors based on quadruplex ligands selected by a fluorescence assay (2001)

The reactivation of telomerase activity in most cancer cells supports the concept that telomerase is a relevant target in oncology, and telomerase inhibitors have been proposed as new potential anticancer agents. The telomeric G-rich single-stranded DNA can adopt in vitro an intramolecular quadruplex structure, which has been shown to inhibit telomerase activity. We used a fluorescence assay to identify molecules that stabilize G-quadruplexes. Intramolecular folding of an oligonucleotide with four repeats of the human telomeric sequence into a G-quadruplex structure led to fluorescence excitation energy transfer between a donor (fluorescein) and an acceptor (tetramethylrhodamine) covalently attached to the 5' and 3' ends of the oligonucleotide, respectively. The melting of the G-quadruplex was monitored in the presence of putative G-quadruplex-binding molecules by measuring the fluorescence emission of the donor. A series of compounds (pentacyclic crescent-shaped dibenzophenanthroline derivatives) was shown to increase the melting temperature of the G-quadruplex by 2-20 degrees C at 1 microM dye concentration. This increase in T(m) value was well correlated with an increase in the efficiency of telomerase inhibition in vitro. The best telomerase inhibitor showed an IC(50) value of 28 nM in a standard telomerase repeat amplification protocol assay. Fluorescence energy transfer can thus be used to reveal the formation of four-stranded DNA structures, and its stabilization by quadruplex-binding agents, in an effort to discover new potent telomerase inhibitors.
Effect of multiple copies of cohesins on cellulase and hemicellulase activities of Clostridium cellulovorans mini-cellulosomes. (2007)

Cellulosomes in Clostridium cellulovorans are assembled by the interaction between the repeated cohesin domains of a scaffolding protein (CbpA) and the dockerin domain of enzyme components. In this study, we determined the synergistic effects on cellulosic and hemicellulosic substrates by three different recombinant mini-cellulosomes containing either endoglucanase EngB or endoxylanase XynA bound to mini-CbpA with one cohesin domain (mini-CbpA1), two cohesins (mini-CbpA12), or four cohesins (mini-CbpA1234). The assembly of EngB or XynA with mini-CbpA increased the activity against carboxymethyl cellulose, acid-swollen cellulose, Avicel, xylan, and corn fiber 1.1-1.8-fold compared with that for the corresponding enzyme alone. A most distinct improvement was shown with corn fiber, a natural substrate containing xylan, arabinan, and cellulose. However, there was little difference in activity between the three different mini-cellulosomes when the cellulosomal enzyme concentration was held constant regardless of the copy number of cohesins in the cellulosome. A synergistic effect was observed when the enzyme concentration was increased to be proportional to the number of cohesins in the mini-cellulosome. The highest degree of synergy was observed with mini-CbpA1234 (1.8-fold) and then mini-CbpA12 (1.3-fold), and the lowest synergy was observed with mini-CbpA1 (1.2-fold) when Avicel was used as the substrate. As the copy number of cohesin was increased, there was more synergy. These results indicate that the clustering effect (physical enzyme proximity) of the enzyme within the mini-cellulosome is one of the important factors for efficient degradation of plant cell walls.