gebhart/patrepeval huggingface dataset:
Delivery of therapeutic laser light using a singlemode silica fiber for a scanning fiber endoscope system (2006)

The feasibility of integrating laser-based therapy using a singlemode fiberoptic delivery system in an endoscopic procedure has been investigated. The maximum transmissible optical power in a high-resolution scanning fiber endoscope system is limited by the requirement for small-core singlemode light propagation, thus impeding the capacity for optical therapies. Since the scanning fiber endoscope can be fabricated from low-cost components, the maximum power capacity of the singlemode optical fiber can be approached in the single use of the medical device. In preparation for future tissue studies, 29.4 micron nominally thick samples of Low Density Poly-Ethylene (LDPE) were used as standardized targets. To model the transient pulse-sample interaction of a scanning fiber endoscope, a pulsed, 50mW, 404nm Coherent Cub<sup>TM</sup> laser system was used to replicate the conditions present in a scanning fiber endoscope that images by measuring the backscatter of combined red, green, and blue laser illumination. Preliminary tests indicate that thermal damage thresholds in LDPE are 120kW/cm<sup>2</sup>. Dwell time and repetition characteristics were investigated and thermal damage thresholds for full-power single pulses was approximately 1ms, using 0.125 NA lens to the LDPE film. The higher-power 405 nm laser diodes are able to be directly modulated so that small regions of interest within the scanned sample can be irradiated for diagnosis (autofluorescence) and therapy (cutting and necrosis). Future studies will integrate the violet laser light with red, green, and blue light for frame-sequential imaging, diagnosis, and therapy.
Selective Inclusion of a Hetero-Guest Pair in a Molecular Host: Formation of Stable Charge-Transfer Complexes in Cucurbit (2001)

Two different molecules are selectively included in cucurbit[8]uril to form a stable 1:1:1 ternary complex, which has been characterized by X-ray crystallography. The inclusion of a hetero-guest pair (a pyridinium derivative (blue) and 2,6-dihydroxynaphthalene (magenta)) in the molecular host is driven and stabilized by a charge-transfer interaction between the electron-rich and electron-deficient guests.
Role of bicarbonate/CO2 in the inhibition of Escherichia coli growth by cyanate (1995)

Cyanase is an inducible enzyme in Escherichia coli that catalyzes the reaction of cyanate with bicarbonate to give two CO2 molecules. The gene for cyanase is part of the cyn operon, which includes cynT and cynS, encoding carbonic anhydrase and cyanase, respectively. Carbonic anhydrase functions to prevent depletion of cellular bicarbonate during cyanate decomposition (the product CO2 can diffuse out of the cell faster than noncatalyzed hydration back to bicarbonate). Addition of cyanate to the culture medium of a delta cynT mutant strain of E. coli (having a nonfunctional carbonic anhydrase) results in depletion of cellular bicarbonate, which leads to inhibition of growth and an inability to catalyze cyanate degradation. These effects can be overcome by aeration with a higher partial CO2 pressure (M. B. Guilloton, A. F. Lamblin, E. I. Kozliak, M. Gerami-Nejad, C. Tu, D. Silverman, P. M. Anderson, and J. A. Fuchs, J. Bacteriol. 175:1443-1451, 1993). The question considered here is why depletion of bicarbonate/CO2 due to the action of cyanase on cyanate in a delta cynT strain has such an inhibitory effect. Growth of wild-type E. coli in minimal medium under conditions of limited CO2 was severely inhibited, and this inhibition could be overcome by adding certain Krebs cycle intermediates, indicating that one consequence of limiting CO2 is inhibition of carboxylation reactions. However, supplementation of the growth medium with metabolites whose syntheses are known to depend on a carboxylation reaction was not effective in overcoming inhibition related to the bicarbonate deficiency induced in the delta cynT strain by addition of cyanate. Similar results were obtained with a deltacyn strain (since cyanase is absent, this strain does not develop a bicarbonate deficiency when cyanate is added); however, as with the deltacynT strain, a higher partial CO(2) pressure in the aerating gas or expression of carbonic anhydrase activity (which contributes to a higher intercellular concentration of bicarbonate/CO(2)) significantly reduced inhibition of growth. There appears to be competition between cyanate and bicarbonate/CO(2) at some unknown but very important site such that cyanate binding inhibits growth. These results suggest that bicarbonate/CO(2) plays a significant role in the growth of E. coli other than simply as a substrate for carboxylation reactions and that strains with mutations in the cyn operon provide a unique model system for studying aspects of the metabolism of bicarbonate/CO(2) and its regulation in bacteria.
Animal models of Alzheimer's Parkinson's and Huntington's disease. A minireview. (1993)

Animal studies have contributed significantly to deeper understanding of several neurodegenerative disorders but fully developed models are lacking. The best models to study motor, sensory and cognitive changes and the effects of therapeutic attempts are rodents and non-human primates. This review describes neuropharmacologic, neuroanatomic and behavioral features of animal models of Alzheimer's, Parkinson's and Huntington's disease.
Melatonin Acutely Improves the Neuroendocrine Architecture of Sleep in Blind Individuals (2003)

In blind individuals, the absence of light cues results in disturbances of sleep and sleep-related neuroendocrine patterns. The Zeitgeber influence of light on the timing of sleep is assumed to be mediated by melatonin, a hormone of the pineal gland, whose secretion is inhibited by light and enhanced during darkness. Here, we investigated whether a single administration of melatonin improves sleep and associated neuroendocrine patterns in blind individuals. In a double-blind crossover study, 12 totally blind subjects received 5 mg melatonin and placebo orally 1 h before bedtime starting at 2300 h. The dose used enhanced blood melatonin concentrations to clearly supraphysiological levels. Melatonin increased total sleep time and sleep efficiency (P < 0.05, respectively) and reduced time awake (P < 0.05). The increment in total sleep time was primarily due to an increase in stage 2 sleep (P < 0.01) and a slight increase in rapid eye movement sleep (P < 0.06). Most important, melatonin normalized in parallel the temporal pattern of ACTH and cortisol plasma concentration. While after placebo, ACTH and cortisol levels did not differ between early and late sleep, melatonin induced the typical suppression of pituitary-adrenal activity during early sleep and a distinct rise during late sleep (P < 0.01, respectively). Cortisol nadir values were also decreased after melatonin (P < 0.05). We conclude from these data that in totally blind individuals the single administration of a clearly pharmacological dose of melatonin can improve sleep function by synchronizing in time the inhibition of pituitary-adrenal activity with central nervous sleep processes.
Upregulation ofFAM83Daffects the proliferation and invasion of hepatocellular carcinoma (2015)

The identification of potential oncogenes plays an important role in finding novel therapeutic targets for many cancers, including hepatocellular carcinoma (HCC), which is one of the most common cancers worldwide. In our previous research, using microarray technology, we found that FAM83D was overexpressed in HCCs. However, whether the overexpression of FAM83D contributes to hepatocarcinogenesis remains unclear. In this study, we found that FAM83D was significantly upregulated in 76.6% (167 of 218) of the HCC specimens at the mRNA level and in 69.44% (50 of 72) of the HCC specimens at the protein level compared with adjacent non-cancerous liver specimens, as indicated by RT-PCR and immunohistochemical staining, respectively. The FAM83DmRNA expression level was positively correlated with the level of alpha-fetoprotein (AFP) (≥100 ng/ml), the clinical TNM stage, the presence of a portal vein tumor thrombus (PVTT), disease-free survival (DFS) and the overall survival (OS) time of the HCC patients (P < 0.05). Knocking down FAM83D significantly promoted the growth of Huh7 and HepG2 cells, as demonstrated in an RNA interference assay. Moreover, the DNA methylation status of the FAM83D promoter was significantly reduced in the HCC specimens with overexpression of FAM83D gene. Our data suggest that the upregulation of FAM83D, a potential oncotarget gene, may be triggered by epigenetic events and can contribute to hepatocarcinogenesis.
‘Now, sir, what is your text?’ Knowing the sources (2012)

It is often said that we know so little about Shakespeare – there are so few biographical facts. But the one incontrovertible fact is the language, as seen in the texts which have survived – the First Folio of 1623, the Quarto editions of the plays, and the editions of the poems. Whether you believe that a man called Shakespeare wrote or co-wrote all or some or none of the works ascribed to him in, say, the Cambridge collected works, the fact remains that we have a body of work in (a period of) the English language which has enthralled generations, both as theatre and as literature. And the bottom line, for any linguist, must be: how on earth did he do it? How can anyone manipulate language to produce work like that? As we have seen, it cannot be reduced to such simple notions as ‘having a large vocabulary’ (the quantity myth), or ‘coining a lot of words’ (the invention myth). Nor can we avoid the language question by saying such things as ‘it is the themes he wrote about’, or ‘it is the vividness of his characters’, for others can present the same themes and characters without achieving the same impact (the translation myth). In any case, the only way we know about those themes and characters in the first place is through the language he has chosen to express them.
Virus-specific CD8+ T Lymphocytes Downregulate T Helper Cell Type 2 Cytokine Secretion and Pulmonary Eosinophilia during Experimental Murine Respiratory Syncytial Virus Infection (1997)

T lymphocytes play a pivotal role in the immune response during viral infections. In a murine model of experimental respiratory syncytial virus (RSV) infection, mice sensitized to either of the two major glycoproteins of RSV develop distinct patterns of cytokine secretion and lung inflammation upon subsequent RSV infection. Mice sensitized to RSV-G (attachment) glycoprotein exhibit a strong interleukin (IL)-4 and IL-5 response and develop pulmonary eosinophilia, whereas mice sensitized to RSV-F (fusion) glycoprotein develop a predominantly T helper cell (Th)1 response and pulmonary inflammation characterized by mononuclear cell infiltration. In this study, we examined the potential role of virus-specific CD8+ T cytolytic T cells on the differentiation and activation of functionally distinct CD4+ T cells specific to these viral glycoproteins. Mice primed with recombinant vaccinia virus expressing RSV-F glycoprotein mounted a strong RSV-specific, MHC class I-restricted cytolytic response, whereas priming with recombinant vaccinia virus expressing RSV-G glycoprotein failed to elicit any detectable cytolytic response. Priming for a RSV-specific CD8+ T cell response, either with a recombinant vaccinia virus expressing RSV-G glycoprotein in which a strong CD8+ T cell epitope from RSV-M2 (matrix) protein has been inserted or with a combination of vaccinia virus expressing the matrix protein and the RSV-G glycoprotein, suppressed the eosinophil recruitment into the lungs of these mice upon subsequent challenge with RSV. This reduction in pulmonary eosinophilia correlated with the suppression of Th2 type cytokine production. The importance of CD8+ T cells in this process was further supported by the results in CD8+ T cell deficient, beta 2 microglobulin KO mice. In these mice, priming to RSV-F glycoprotein (which in normal mice primed for a strong cytolytic response and a pulmonary infiltrate consisting primarily of mononuclear cells on RSV challenge) resulted in the development of marked pulmonary eosinophilia that was not seen in mice with an intact CD8+ T cell compartment. These results indicate that CD8+ T cells may play an important role in the regulation of the differentiation and activation of Th2 CD4+ T cells as well as the recruitment of eosinophils into the lungs during RSV infection.
Src: Marker or Actor in Prostate Cancer Aggressiveness (2014)

A key question for urologic practitioners is whether an apparently organ-confined prostate cancer (PCa) is actually aggressive or not. The dilemma is to specifically identify among all prostate tumors the very aggressive high-grade cancers that will become life-threatening by developing extra-prostatic invasion and metastatic potential and the indolent cancers that will never modify a patient's life expectancy. A choice must be made between several therapeutic options to achieve the optimal personalized management of the disease that causes as little harm as possible to patients. Reliable clinical, biological, or pathological markers that would enable distinctions to be made between aggressive and indolent PCas in routine practice at the time of initial diagnosis are still lacking. The molecular mechanisms that explain why a PCa is aggressive or not are also poorly understood. Among the potential markers and/or actors in PCa aggressiveness, Src and other members of the Src kinase family, are valuable candidates. Activation of Src-dependent intracellular pathways is frequently observed in PCa. Indeed, Src is at the cross-roads of several pathways [including androgen receptor (AR), TGFbeta, Bcl-2, Akt/PTEN or MAPK, and ERK …], and is now known to influence some of the cellular and tissular events that accompany tumor progression: cell proliferation, cell motility, invasion, epithelial-to-mesenchymal transition, resistance to apoptosis, angiogenesis, neuroendocrine differentiation, and metastatic spread. Recent work even suggests that Src could also play a part in PCa initiation in coordination with the AR. The aim of this review is to gather data that explore the links between the Src kinase family and PCa progression and aggressiveness.
Pexelizumab, an Anti-C5 Complement Antibody, as Adjunctive Therapy to Primary Percutaneous Coronary Intervention in Acute Myocardial Infarction (2003)

In patients with ST-elevation MI undergoing percutaneous coronary intervention, pexelizumab had no measurable effect on infarct size. However, the significant reduction in mortality suggests that pexelizumab may benefit patients through alternative novel mechanisms and provides impetus for additional investigation.
Inhibition of the P2X7 Receptor Reduces Cystogenesis in PKD (2011)

The P2X7 receptor participates in purinergic signaling, which may promote the progression of ADPKD. We examined the effects of a P2X7 receptor antagonist and a P2X7 receptor agonist on cyst development in a zebrafish model of polycystic kidney disease in which we knocked down pkd2 by morpholinos. We used live wt-1b pronephric-specific GFP-expressing zebrafish embryos to directly observe changes in the pronephros. Exposure of pkd2-morphant zebrafish to a P2X7 receptor antagonist (oxidized ATP [OxATP]) significantly reduced the frequency of the cystic phenotype compared with either exposure to a P2X7 receptor agonist (BzATP) or with no treatment (P < 0.01). Histology confirmed improvement of glomerular cysts in OxATP-treated pkd2 morphants. OxATP also reduced p-ERK activity and cell proliferation in pronephric kidneys in pkd2 morphants. Inhibition of P2X7 with an additional specific antagonist (A-438079), and through morpholino-mediated knockdown of p2rx7, confirmed these effects. In conclusion, blockade of the P2X7 receptor reduces cyst formation via ERK-dependent pathways in a zebrafish model of polycystic kidney disease, suggesting that P2X7 antagonists may have therapeutic potential in ADPKD.
Succinate Dehydrogenase-dependent Nutritional Requirement for Succinate in Mutants of Escherichia coli K12 (1978)

Lipoic acid (lip) and 2-oxoglutarate dehydrogenase (sucA) mutants of Escherichia coli K12 exhibit a requirement for exogenous succinate during aerobic growth on glucose minimal medium. Reversion studies have shown that this requirement can be suppressed by gal-linked mutations which inactivate succinate dehydrogenase. Biochemical and genetic studies confirmed that the succinate dehydrogenase gene (sdh) is affected and that suppression is mediated by the same intergenic and indirect mechanism that generates succinate independence in partial revertants of lipoamide dehydrogenase mutants (Creaghan & Guest, 1977). A series of isogenic strains containing all combinations of mutations affecting 2-oxoglutarate dehydrogenase (sucA), succinate dehydrogenase (sdh), isocitrate lyase (aceA) and fumarate reductase (frd) in a background lacking succinate semialdehyde dehydrogenase, was constructed to assess the importance of these enzymes as sources of endogenous succinate (succinyl-CoA) during aerobic and anaerobic growth on glucose. Only strains combining a deficiency in 2-oxoglutarate dehydrogenase with the presence of an active succinate dehydrogenase required succinate for aerobic growth. In all mutants, including the triple mutant (frd sucA aceA), the succinate requirement was suppressed by inactivating succinate dehydrogenase. The aerobic growth rates of succinate-independent strains were most affected by lack of isocitrate lyase but only two mutants (sdh sucA aceA and frd sdh sucA aceA) grew faster with added succinate: the growth yields were lowered by deficiencies in isocitrate lyase and also succinate dehydrogenase. It is concluded that very little succinate is needed for biosynthesis during aerobic growth on glucose and the requirement for relatively high concentrations of succinate (2 mM) by mutants lacking 2-oxoglutarate dehydrogenase or related functions stems from the presence of active succinate dehydrogenase. Anaerobically, either isocitrate lyase or fumarate reductase is essential for succinate-independent growth on glucose.
Electrical Stimulation of Nerve Cells Using Conductive Nanofibrous Scaffolds for Nerve Tissue Engineering (2009)

Fabrication of scaffolds with suitable chemical, mechanical, and electrical properties is critical for the success of nerve tissue engineering. Electrical stimulation was directly applied to electrospun conductive nanofibrous scaffolds to enhance the nerve regeneration process. In the present study, electrospun conductive nanofibers were prepared by mixing 10 and 15 wt% doped polyaniline (PANI) with poly (epsilon-caprolactone)/gelatin (PG) (70:30) solution (PANI/PG) by electrospinning. The fiber diameter, pore size, hydrophilicity, tensile properties, conductivity, Fourier transform infrared (FTIR), and X-ray photoelectron spectroscopy spectra of nanofibers were determined, and the in vitro biodegradability of the different nanofibrous scaffolds was also evaluated. Nanofibrous scaffolds containing 15% PANI was found to exhibit the most balanced properties to meet all the required specifications for electrical stimulation for its enhanced conductivity and is used for in vitro culture and electrical stimulation of nerve stem cells. 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay and scanning electron microscopy results showed that conductive nanofibrous scaffolds are suitable substrates for the attachment and proliferation of nerve stem cells. Electrical stimulation through conductive nanofibrous PANI/PG scaffolds showed enhanced cell proliferation and neurite outgrowth compared to the PANI/PG scaffolds that were not subjected to electrical stimulation.
Poliovirus Requires a Precise 5′ End for Efficient Positive-Strand RNA Synthesis (2000)

Poliovirus infectious RNA can be synthesized in vitro using phage DNA-dependent RNA-polymerases. These synthetic transcripts contain several extra nucleotides at the 5' end, which are deleted during replication to generate authentic viral genomes. We removed those 5'-end extra nucleotides utilizing a hammerhead ribozyme to produce transcripts with accurate 5' ends. These transcripts replicate substantially more rapidly in cell culture, demonstrating no lag before replication; they also replicate more efficiently in Xenopus laevis oocytes and in in vitro translation-replication cell extracts. In both systems, an exact 5' end is necessary for synthesis of positive-strand RNA but not negative-strand RNA.
Tumor Necrosis Factor- Inhibits Leydig Cell Steroidogenesis through a Decrease in Steroidogenic Acute Regulatory Protein Expression (1998)

The aim of the present study was to identify the sites of the inhibitory action of TNFα (tumor necrosis factor alpha) on LH/hCG-stimulated testosterone formation. By using cultured porcine Leydig cells as a model, TNFα was shown to inhibit testosterone secretion when testicular cells were stimulated with hCG but not when incubated with 22R-hydroxycholesterol (a cholesterol substrate derivative that readily passes through cell and mitochondrial membranes). Such an observation suggested that the cytokine may affect cholesterol transport and/or availability to cytochrome P450scc in the mitochondria. Specifically, we report here that TNFα reduced in a dose- and time-dependent manner hCG-induced StAR (steroidogenic acute regulatory protein) levels. The maximal and half-maximal effects were obtained with 20 ng/ml (1.2 nm) and 1.6 ng/ml (0.09 nm) of TNFα, respectively. Maximal inhibitory effects of TNFα on StAR messenger RNA and protein levels were obtained after 48 h of treatment. Additionally, the presence of TNFα receptors P55 in terms of protein (identified through cross-linking experiments) and messenger RNA (identified through RT-PCR analysis) suggested that the effects of the cytokine are directly exerted on the testicular steroidogenic cell type.
PD-1 is a regulator of virus-specific CD8+ T cell survival in HIV infection (2006)

Here, we report on the expression of programmed death (PD)-1 on human virus-specific CD8(+) T cells and the effect of manipulating signaling through PD-1 on the survival, proliferation, and cytokine function of these cells. PD-1 expression was found to be low on naive CD8(+) T cells and increased on memory CD8(+) T cells according to antigen specificity. Memory CD8(+) T cells specific for poorly controlled chronic persistent virus (HIV) more frequently expressed PD-1 than memory CD8(+) T cells specific for well-controlled persistent virus (cytomegalovirus) or acute (vaccinia) viruses. PD-1 expression was independent of maturational markers on memory CD8(+) T cells and was not directly associated with an inability to produce cytokines. Importantly, the level of PD-1 surface expression was the primary determinant of apoptosis sensitivity of virus-specific CD8(+) T cells. Manipulation of PD-1 led to changes in the ability of the cells to survive and expand, which, over several days, affected the number of cells expressing cytokines. Therefore, PD-1 is a major regulator of apoptosis that can impact the frequency of antiviral T cells in chronic infections such as HIV, and could be manipulated to improve HIV-specific CD8(+) T cell numbers, but possibly not all functions in vivo.
Expansion of Polystyrene Using Water as the Blowing Agent (2007)

The expansion of polystyrene using water as the blowing agent has been investigated. Hydrophilic particles are dispersed in styrene before the suspension polymerization. During this polymerization the necessary amount of water is absorbed and/or adsorbed by these additives. The different additives used in this work are ordinary corn starch and high-amylose starch, zeolite A and Y, and SiO2. Factors that influence the density and the morphology of the expanded product are the type of additive, the additive and water content, the polymerization conditions, and the expansion procedure. High frequency electric field heating and hot air have been used for the expansion. The lowest density is obtained with high frequency electric field heating.