gebhart/patrepeval huggingface dataset:
The Adeno-Associated Virus Type 2 Rep Protein Regulates RNA Processing via Interaction with the Transcription Template (2002)

The adeno-associated virus type 2 (AAV) large Rep proteins can act to increase the ratio of spliced to unspliced AAV RNA when they are targeted to the transcription template via a Rep binding element. The required Rep binding site is both location and orientation independent; however, Rep enhancement decreases as the distance between the promoter and the intron of the affected transcription unit increases. Only the AAV intron and an extended polyadenylation site must remain for the AAV transcription unit to manifest responsiveness to Rep. A number of promoters, when driving the AAV capsid gene transcription unit, were responsive to targeted Rep, though to various degrees. Transactivation of transcription initiation is not sufficient for the enhancement of RNA processing, because activation of the P40 transcription unit by other activators targeted to this transcription template did not result in enhancement of the ratio of spliced to unspliced AAV RNA. These results suggest that Rep may act as a trans regulator of RNA processing by modulating such functions coupled to RNA polymerase II (RNA pol II) transcription, perhaps by affecting the composition of the transcription complex either prior to or during elongation. These results reveal another way in which gene expression can be regulated by trans-acting proteins and help explain an important feature of the parvovirus life cycle.
Minimal DNA sequences that control the cell lineage-specific expression of the pro alpha 2(I) collagen promoter in transgenic mice. (1992)

The pattern of expression of the pro alpha 2(I) collagen gene is highly tissue specific in adult mice and shows its strongest expression in bones, tendons, and skin. Transgenic mice were generated harboring promoter fragments of the mouse pro alpha 2(I) collagen gene linked to the Escherichia coli beta-galactosidase or firefly luciferase genes to examine the activity of these promoters during development. A region of the mouse pro alpha 2(I) collagen promoter between -2,000 and +54 exhibited a pattern of beta-galactosidase activity during embryonic development that corresponded to the expression pattern of the endogenous pro alpha 2(I) collagen gene as determined by in situ hybridization. A similar pattern of activity was also observed with much smaller promoter fragments containing either 500 or 350 bp of upstream sequence relative to the start of transcription. Embryonic regions expressing high levels of beta-galactosidase activity included the bulbus arteriosus, valves of the developing heart, sclerotomes, meninges, limb buds, connective tissue fascia between muscle fibers, osteoblasts in newly formed bones, fibroblasts in tendons, periosteum, dermis, and peritoneal membranes. The pattern of beta-galactosidase activity was similar and included within the extracellular immunohistochemical localization pattern of transforming growth factor-beta 1 (TGF-beta 1). The -315(-)-284 region of the pro alpha 2(I) collagen promoter was previously shown to mediate the stimulatory effects of TGF-beta 1 on the pro alpha 2(I) collagen promoter in DNA transfection experiments with cultured fibroblasts. A construct containing this sequence tandemly repeated 5' to a very short alpha 2(I) collagen promoter (-40(-)+54) showed preferential activity in tail and skin of 4-wk-old transgenic mice. Except for low expression of the transgene in bone, this pattern mimics the expression of the endogenous pro alpha 2(I) collagen gene. We propose the hypothesis that the tissue-specific expression of the pro alpha 2(I) collagen gene during embryogenesis is controlled by both TGF-beta 1 and cell-specific transcription factors; one of these could interact directly or indirectly with either the -315(-)-284 or the -40(-)+54 segment.
Strong neurogenesis, angiogenesis, synaptogenesis, and antifibrosis of hepatocyte growth factor in rats brain after transient middle cerebral artery occlusion (2010)

Hepatocyte growth factor (HGF) and glial cell line-derived neurotrophic factor (GDNF) are strong neurotrophic factors. However, their potentials in neurogenesis, angiogenesis, synaptogenesis, and antifibrosis have not been compared. Therefore, we investigated these effects of HGF and GDNF in cerebral ischemia in the rat. Wistar rats were subjected to 90 min of transient middle cerebral artery occlusion (tMCAO). Immediately after reperfusion, HGF or GDNF was given by topical application. BrdU was injected intraperitoneally twice daily 1, 2, and 3 days after tMCAO. On 14 day, we histologically evaluated infarct volume, antiapoptotic effect, neurogenesis, angiogenesis, synaptogenesis, and antifibrosis. Both HGF and GDNF significantly reduced infarct size and the number of TUNEL-positive cells, but only HGF significantly increased the number of BrdU-positive cells in the subventricular zone, and 5'-bromo-2'-deoxyuridine -positive cells differentiated into mature neurons on the ischemic side. Enhancement of angiogenesis and synaptogenesis at the ischemic boundary zone was also observed only in HGF-treated rats. HGF significantly decreased the glial scar formation and scar thickness of the brain pia mater after tMCAO, but GDNF did not. Our study shows that both HGF and GDNF had significant neurotrophic effects, but only HGF can promote the neurogenesis, angiogenesis, and synaptogenesis and inhibit fibrotic change in brains after tMCAO.
Characterization of PLGA Microparticles as a Drug Carrier for 3-Ethoxycarbonyl-2H-Benzofuro[3,2-f]-1-Benzopyran-2-One. Ultrastructural Study of Cellular Uptake and Intracellular Distribution (2006)

Here we describe the application of microparticles (MPs) for the delivery and release of the drug a benzopsoralen. We also evaluated the intracellular distribution and cellular uptake of the drug by using an encapsulation technique for therapeutic optimization. MPs containing the compound 3-ethoxycarbonyl-2H-benzofuro[3,2-f]-1-benzopyran-2-one (psoralen A) were prepared by the solvent evaporation technique, and parameters such as particle size, drug encapsulation efficiency, effect of the encapsulation process on the drug's photochemistry, zeta potential, external morphology, and in vitro release behavior were evaluated. The intracellular distribution of MPs as well as their uptake by tissues were monitored. Size distribution studies using dynamic ligh scattering and scanning electron microscopy revealed that the MPs are spherical in shape with a diameter of 1.4 micro m. They present low tendency toward aggregation, as confirmed by their zeta potential (+10.6 mV). The loading efficiency obtained was 75%. As a consequence of the extremely low diffusivity of the drug in aqueous medium, the drug release profile of the MPs in saline phosphate buffer (pH 7.4) was much slower than that obtained in the biological environment. Among the population of peritoneal phagocytic cells, only macrophages were able to phagocytose poly-d,l-lactic-co-glycolic acid (PLGA) MP. The use of psoralen A in association with ultraviolet light (360 nm) revealed morphological characteristics of cell damage such as cytoplasmic vesiculation, mitochondria condensation, and swelling of both the granular endoplasmatic reticulum and the nuclear membrane. These results indicate that PLGA MP could be a promising delivery system for psoralen in connection with ultraviolet irradiation therapy (PUVA).
The effects of human CYP2C8 genotype and fluvoxamine on the pharmacokinetics of rosiglitazone in healthy subjects (2006)

The importance of the CYP2C8*3 mutation in the in vivo metabolism of rosiglitazone could not be confirmed. Fluvoxamine increased the AUC(0-infinity) and t(1/2) of rosiglitazone moderately and hence may be a weak inhibitor of CYP2C8.
Prospective Study of Sex Hormone Levels and Risk of Prostate Cancer (1996)

High levels of circulating testosterone and low levels of SHBG-both within normal endogenous ranges-are associated with increased risks of prostate cancer. Low levels of circulating estradiol may represent an additional risk factor. Circulating levels of DHT and AAG do not appear to be strongly related to prostate cancer risk.
‘Subinhibitory’ Erythromycin Represses Production of <i>Pseudomonas aeruginosa</i> Lectins, Autoinducer and Virulence Factors (1999)

Pseudomonas aeruginosa infection is preceded by selective adhesion of the bacteria to the host target cells via diverse adhesins, including lectins. This step enables maximal damage to the target host cells by the bacterially secreted injurious toxins and enzymes. The production of both lectins and many of the virulence factors is positively controlled by transcription activators including signaling autoinducers (N-acyl-L-homoserine lactones). We show in this communication that erythromycin at subminimal growth inhibitory concentrations simultaneously suppresses the production of P. aeruginosa hemagglutinins (including lectins), protease, hemolysin and homoserine lactone autoinducers. The antibiotic-treated bacteria also show reduced virulence to mice, endorsing clinical observations that indicate the efficiency of low-dose erythromycin treatment of persistent drug-resistant P. aeruginosa infections.
Muscle-specific knockout of PKC-λ impairs glucose transport and induces metabolic and diabetic syndromes (2007)

Obesity, the metabolic syndrome, and type 2 diabetes mellitus (T2DM) are major global health problems. Insulin resistance is frequently present in these disorders, but the causes and effects of such resistance are unknown. Here, we generated mice with muscle-specific knockout of the major murine atypical PKC (aPKC), PKC-lambda, a postulated mediator for insulin-stimulated glucose transport. Glucose transport and translocation of glucose transporter 4 (GLUT4) to the plasma membrane were diminished in muscles of both homozygous and heterozygous PKC-lambda knockout mice and were accompanied by systemic insulin resistance; impaired glucose tolerance or diabetes; islet beta cell hyperplasia; abdominal adiposity; hepatosteatosis; elevated serum triglycerides, FFAs, and LDL-cholesterol; and diminished HDL-cholesterol. In contrast to the defective activation of muscle aPKC, insulin signaling and actions were intact in muscle, liver, and adipocytes. These findings demonstrate the importance of aPKC in insulin-stimulated glucose transport in muscles of intact mice and show that insulin resistance and resultant hyperinsulinemia owing to a specific defect in muscle aPKC is sufficient to induce abdominal obesity and other lipid abnormalities of the metabolic syndrome and T2DM. These findings are particularly relevant because humans who have obesity, impaired glucose tolerance, and T2DM reportedly have defective activation and/or diminished levels of muscle aPKC.
Extracorporeal Photopheresis After Lung Transplantation: A 10-Year Single-Center Experience (2008)

We report the largest single-center experience with extracorporeal photopheresis (ECP) for bronchiolitis obliterans syndrome (BOS) and recurrent acute rejection (AR) after lung transplantation. Lung transplant recipients undergoing ECP for BOS and recurrent AR were included (1997-2007). The rate of forced expiratory volume in 1 second (FEV1) decline was used as the primary measure and graft survival post-ECP as the secondary measure of efficacy. Twenty-four transplant recipients were included (BOS, n=12; recurrent AR, n=12). In recipients with BOS, decline in FEV1 was 112 mL/month before the start of ECP and 12 mL/month after 12 ECP cycles (P=0.011), mean (95% CI) change in rate of decline was 100 (28-171). Median patient survival was 7.0 (range, 3.0-13.6) years, median patient survival post-ECP 4.9 (range, 0.5-8.4) years. No ECP-related complications occurred. Extracorporeal photopheresis reduces the rate of lung function decline in recipients with BOS and is well tolerated. Furthermore, recipients with recurrent AR experience clinical stabilization. However, the underlying mechanism of ECP remains subject to further research.
Vaccinia Virus DNA Ligase Recruits Cellular Topoisomerase II to Sites of Viral Replication and Assembly (2008)

Vaccinia virus replication is inhibited by etoposide and mitoxantrone even though poxviruses do not encode the type II topoisomerases that are the specific targets of these drugs. Furthermore, one can isolate drug-resistant virus carrying mutations in the viral DNA ligase and yet the ligase is not known to exhibit sensitivity to these drugs. A yeast two-hybrid screen was used to search for proteins binding to vaccinia ligase, and one of the nine proteins identified comprised a portion (residue 901 to end) of human topoisomerase IIbeta. One can prevent the interaction by introducing a C(11)-to-Y substitution mutation into the N terminus of the ligase bait protein, which is one of the mutations conferring etoposide and mitoxantrone resistance. Coimmunoprecipitation methods showed that the native ligase and a Flag-tagged recombinant protein form complexes with human topoisomerase IIalpha/beta in infected cells and that this interaction can also be disrupted by mutations in the A50R (ligase) gene. Immunofluorescence microscopy showed that both topoisomerase IIalpha and IIbeta antigens are recruited to cytoplasmic sites of virus replication and that less topoisomerase was recruited to these sites in cells infected with mutant virus than in cells infected with wild-type virus. Immunoelectron microscopy confirmed the presence of topoisomerases IIalpha/beta in virosomes, but the enzyme could not be detected in mature virus particles. We propose that the genetics of etoposide and mitoxantrone resistance can be explained by vaccinia ligase binding to cellular topoisomerase II and recruiting this nuclear enzyme to sites of virus biogenesis. Although other nuclear DNA binding proteins have been detected in virosomes, this appears to be the first demonstration of an enzyme being selectively recruited to sites of poxvirus DNA synthesis and assembly.
Checking for Race Conditions in File Accesses (1996)

Flaws due to race conditions in which the binding of a name to an object changes between repeated references occur in many programs. We examine one type of this flaw in the UNIX operating system, and describe a semantic method for detecting possible instances of this problem. We present the results of one such analysis in which a previously undiscovered race condition flaw was found. 1. Introduction Ordinary bugs and misconfigurations prevent applications or systems from functioning correctly. By contrast, security holes or vulnerabilities enable a user (called an attacker) to gain privileges, access to data, or the ability to interfere with others&amp;apos; work via by exploitation. Much research, especially in the field of intrusion detection [5][9], draws on characteristics of these attacks [12]. But many attacks can exploit a single vulnerability, implying that the characteristics of the flaws themselves are more fundemental and should be of interest. This work focuses on a semantic chara...
Identification of a global repressor gene, rsmA, of Erwinia carotovora subsp. carotovora that controls extracellular enzymes, N-(3-oxohexanoyl)-L-homoserine lactone, and pathogenicity in soft-rotting Erwinia spp (1995)

The production of extracellular enzymes such as pectate lyase (Pel), polygalacturonase (Peh), cellulase (Cel), and protease (Prt) is activated by the cell density (quorum)-sensing signal, N-(3-oxohexanoyl)-L-homoserine lactone (HSL); plant signals; and aep genes during postexponential growth of Erwinia carotovora subsp. carotovora 71. Studies with mutants of E. carotovora subsp. carotovora 71 derepressed in exoenzyme production led to the identification of a negative regulator gene, rsmA (rsm, repressor of secondary metabolites). Nucleotide sequencing, transcript assays, and protein analysis established that a 183-bp open reading frame encodes the 6.8-kDa RsmA. rsmA has extensive homology with the csrA gene of Escherichia coli, which specifies a negative regulator of carbon storage. Moreover, the suppression of glycogen synthesis in E. coli by rsmA indicates that the Erwinia gene is functionally similar to csrA. Southern hybridizations revealed the presence of rsmA homologs in soft-rotting and non-soft-rotting Erwinia spp. and in other enterobacteria such as Enterobacter aerogenes, E. coli, Salmonella typhimurium, Shigella flexneri, Serratia marcescens, and Yersinia pseudotuberculosis. rsmA suppresses production of Pel, Peh, Cel, and Prt, plant pathogenicity, and synthesis of HSL in E. carotovora subsp. atroseptica, E. carotovora subsp. betavasculorum, E. carotovora subsp. carotovora, and E. chrysanthemi. In the E. carotovora subsp. carotovora 71, rsmA reduces the levels of transcripts of hslI, a luxI homolog required for HSL biosynthesis. This specific effect and the previous finding that HSL is required for extracellular enzyme production and pathogenicity in soft-rotting Erwinia spp. support the hypothesis that rsmA controls these traits by modulating the levels of the cell density (quorum)-sensing signal.
「M+進行 : 油麻地」展覽與班雅明的歷史觀相遇 (2013)

「西九」的發展已討論多時，區內發展藍圖中的土地用途，除了商業、住宅用地及娛樂設施等分配比例外，還有經常提及的文化藝術發展。最近西九文化區管理局轄下的M+博物館（Museum Plus）推出了「M+進行：油麻地」的展覽活動。西九文化區管理局之前亦曾舉辦有關戲曲藝術活動，而「M+進行：油麻地」是局方安排的另一大型藝術活動。\n戲曲中心和M+博物館是西九文化區的第一期設施，預計將分別於二零一五以及二零一七年落成。西九文化區管理局行政總裁連納智希望市民逐漸認識和投入這片「你我文化新天地」，在他所言的「你我文化新天地」中，這展覽卻不光是「新」的天地，連繫的卻是個人生活的歷史片段，及記載了舊有的一段共同經歷的時光。如班雅明在《商場研究計劃》中說道：「新事物的出現，必然夾雜著舊的形式或元素」。筆者希望透過展覽活動，親身走進城市人群的景觀中，好像勾起普魯斯特或我們吃小食般的無限回憶，記起過去在這城市的點滴，召回過去的映像，認出尚未完成的願望。
Large breathing effects in three-dimensional porous hybrid matter: facts, analyses, rules and consequences (2009)

This critical review focuses on a strange behaviour of crystallized solid matter: its reversible swelling with large magnitude. This will be of interest for experts in porous solids but also for solid state chemists and physicists. Some examples, classified according to the dimensionality of the inorganic subnetwork, present the general requirements and the structural rules which govern the existence of this phenomenon. Its consequences concern specific applications related to sensors, energy savings, sustainable development and health (100 references).
Synergistic potentiation of in vivo antitumor activity of anti-human T-leukemia immunotoxins by recombinant alpha-interferon and daunorubicin. (1990)

In the present study, immunotoxins (ITs) containing ricin A chain (RA) and anti-human T leukemia monoclonal antibodies SN1 and SN2 were used with or without alpha-interferon (IFN) and/or daunorubicin (DNR) for in vivo tumor suppression. SN1 and SN2 are directed toward two unique human T-leukemia-associated cell surface antigens, TALLA and GP37, respectively. As the tumor model, we used nude mice bearing ascitic tumors of Ichikawa, a human T acute lymphoblastic leukemia cell line. In initial studies, we investigated the effect of the IT injection schedule on the efficacy of ITs in the in vivo suppression of the ascitic tumors. Four doses of 20 micrograms each of SN1-RA and SN2-RA completely suppress the tumor growth in 100% of the treated mice when the IT treatment is initiated either 1 or 2 days after tumor inoculation of 1.6 x 10(7) Ichikawa cells into the mice. Subsequently, we investigated the potentiating effects of IFN and DNR on the in vivo antitumor activity of ITs. To this end, we chose to initiate the treatment 4 days after the tumor inoculation when IT treatment alone is only partially effective. ITs (10 micrograms each of SN1-RA and SN2-RA) plus IFN (2 x 10(5) IU) or ITs plus IFN plus DNR (5 micrograms) completely suppress tumor growth in 100% of the treated mice while similar treatment with any one of the three agents is only partially effective. Similar treatment with ITs plus DNR or IFN plus DNR results in complete suppression of tumor growth in 80% of the treated mice. These results were reproducible in a repeated experiment. To gain information about the mechanisms involving the IFN potentiation of IT activity, we carried out several experiments. The cell surface expression of TALLA and GP37 was slightly augmented by the in vitro incubation of Ichikawa cells with IFN as measured by fluorescence-activated cell sorter analysis. The degree of the increase in either TALLA or GP37 was significantly smaller than that of HLA class I antigens in the same experiment. In in vitro experiments, IFN did not show any significant cytotoxic activity against Ichikawa cells or augment the cytotoxic activity of ITs against Ichikawa cells. On the other hand, injections of IFN into nude mice augmented activity of macrophages and NK cells; however, Ichikawa leukemia cells were rather resistant to the NK cell lysis.(ABSTRACT TRUNCATED AT 400 WORDS)
In Vitro Formation of Enteric Neural Network Structure in a Gut-Like Organ Differentiated from Mouse Embryonic Stem Cells (2006)

Using an embryoid body (EB) culture system, we developed a functional organ-like cluster--a "gut"--from mouse embryonic stem (ES) cells (ES gut). Each ES gut exhibited spontaneous contractions but did not exhibit distinct peristalsis-like movements. In these spontaneously contracting ES guts, dense distributions of interstitial cells of Cajal (c-kit [a transmembrane receptor that has tyrosine kinase activity]-positive cells; gut pacemaker cells) and smooth muscle cells were discernibly identified; however, enteric neural ganglia were absent in the spontaneously differentiated ES gut. By adding brain-derived neurotrophic factor (BDNF) only during EB formation, we for the first time succeeded in in vitro formation of enteric neural ganglia with connecting nerve fiber tracts (enteric nervous system [ENS]) in the ES gut. The ES gut with ENS exhibited strong peristalsis-like movements. During EB culture in BDNF(+) medium, we detected each immunoreactivity associated with the trk proto-oncogenes (trkB; BDNF receptors) and neural crest marker, proto-oncogene tyrosine-protein kinase receptor ret precursor (c-ret), p75, or sox9. These results indicated that the present ENS is differentiated from enteric neural crest-derived cells. Moreover, focal stimulation of ES guts with ENS elicited propagated increases in intracellular Ca(2+) concentration ([Ca(2+)](i)) at single or multiple sites that were attenuated by atropine or abolished by tetrodotoxin. These results suggest in vitro formation of physiologically functioning enteric cholinergic excitatory neurons. We for the first time succeeded in the differentiation of functional neurons in ENS by exogenously adding BDNF in the ES gut, resulting in generation of distinct peristalsis-like movements.
Physical limitations on frequency and power parameters of transistors (2005)

A simple analysis shows that the ultimate performance limits of a transistor are set by the product <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ev_{s}/2\pi</tex> , where <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E</tex> is the semiconductor's dielectric breakdown strength and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">v_{s}</tex> is its minority carrier saturated drift velocity. This product, having a value of about <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2 \times 10^{11}</tex> volts/ second for silicon, emphasizes that a semiconductor material has a maximum capability for energizing the electric charges that process a signal. If the device operating frequency is high, the frequency time period is short and only a small amount of energy can be given to a charge carrier. Consequently, the power and power amplification must be relatively low. At low frequencies the inverse is true. That is, device physics demands an inverse relation between frequency and power parameters that is independent of the thermal dissipation arguments commonly given to explain the trade-off between these parameters. The analysis leads to an effective means for making comparisons between existing devices. This is illustrated.