gebhart/patrepeval huggingface dataset:
Enhancement of foreign gene expression by a dicot intron in rice but not in tobacco is correlated with an increased level of mRNA and an efficient splicing of the intron (1990)

The first intron of castor bean catalase gene, cat-1 was placed in the N-terminal region of the coding sequence of the beta-glucuronidase gene (gusA) and the intron-containing gusA was used with the cauliflower mosaic virus (CaMV) 35S promoter. Using this plasmid, pIG221, the effect of the intron on expression of beta-glucuronidase (GUS) activity was examined in transgenic rice calli and plants (a monocotyledon), and transgenic tobacco plants (a dicotyledon). The intron-containing plasmid increased the level of GUS enzyme activity 10 to 40-fold and 80 to 90-fold compared with the intronless plasmid, pBI221, in transgenic rice protoplasts and transgenic rice tissues, respectively. In contrast, the presence of the intron hardly influenced the expression of the GUS activity in transgenic tobacco plants. Northern blot analysis showed that the catalase intron was efficiently spliced in rice cells while transgenic tobacco plants contained both spliced and unspliced gusA transcripts in equal amounts. Furthermore, the level of the mature gusA transcript in transformed rice calli was greatly increased in the presence of the intron. The catalase intron was removed at the same splice junctions in transgenic rice and tobacco plants. These findings indicate that the stimulating effect of the intron on GUS expression is correlated with an efficient splicing of pre-mRNA and an increased level of mature mRNA.
Loss of Tumorigenicity of Murine Colon Carcinoma MC38/0 Cell Line after Transduction with a Retroviral Vector Carrying Murine IL-12 Genes (2004)

Cells of transplantable MC38 colon carcinoma of C57BL/6 mice were adapted to growth in vitro as the MC38/0 cell line. Along the establishing process, MC38/0 cells preserved their tumorigenicity. After transduction with a retroviral vector carrying murine interleukin 12 (mIL-12) genes and further selection, stable MC38/IL-12 transductant cells were obtained. These cells produced IL-12 (approx. 2500 ng/ml/5x10(5) cells/48 h) as evaluated in the optimized bioassay. After subcutaneous inoculation into syngeneic mice, the IL-12-modified cells demonstrated reduced tumorigenicity as compared to parental MC38/0 cells. Mice that rejected the MC38/IL-12 tumour became protected against subsequent challenge with MC38/0 cells. The obtained data indicate that the IL-12-transduced murine colon carcinoma cells could be used both as a model tumour for the study of mechanisms of anticancer immunity and/or as an adjuvant to cancer vaccines.
Rapid Identification of Human Adenovirus Types 3 and 7 from Respiratory Specimens via Multiplex Type-Specific PCR (2005)

The rapid diagnosis of human adenovirus (Ad) infection is crucial for the timely recognition of epidemics. Moreover, identification of the serotypes known to cause serious disease can be helpful in therapeutic intervention. A multiplex PCR assay was developed for the rapid detection of adenovirus type 3 (Ad3) and Ad7 directly from clinical specimens. For this assay, three primer pairs (primers were based on the conserved and hypervariable regions of the hexon) were designed in order to simultaneously amplify all adenoviral serotypes and discriminate between Ad3 and Ad7. In our preliminary analysis, this multiplex PCR assay generated amplicons of the consensus primers from all 106 adenoviral isolates of diverse serotypes and proved able to correctly identify Ad3 and Ad7. This assay was subsequently applied to the detection of Ad3 and Ad7 in respiratory specimens. Among the 127 nasal aspirates from which an adenovirus was grown, the sensitivity with which any serotype could be detected was 91% (115/127). Two of the 53 nasal aspirates which did not grow Ads yielded adenovirus-specific bands, which were confirmed by sequencing analysis. Among the 115 specimens which produced common adenoviral bands, the sensitivity with which Ad3 could be detected was 93% (26/28), and the sensitivity with which Ad7 could be detected was 100% (35/35). Five out of the 115 specimens were proved to harbor more than one type of Ad via sequencing analysis of the amplicons, suggesting mixed infection with at least two different serotypes. In conclusion, this multiplex PCR system can be utilized in the rapid identification of Ad3 and Ad7 directly from clinical specimens. Furthermore, this method constitutes a diagnostic strategy for the detection of coinfection by different Ad serotypes.
Expression of H-ficolin/Hakata antigen, mannose-binding lectin-associated serine protease (MASP)-1 and MASP-3 by human glioma cell line T98G (2002)

Mannose-binding lectin (MBL) is a C-type lectin involved in the first line of host defense and it requires MBL-associated serine proteases (MASP) for activation of the lectin complement pathway (LCP). Recently we reported that human ficolins, L-ficolin/P35 and H-ficolin/Hakata antigen, as well as MBL activate the LCP in association with MASP. We investigated in vitro expression of complements of the lectin complement pathway in several cell lines. Out of 17 cell lines tested using RT-PCR, a human glioma cell line, T98G, expressed high levels of H-ficolin/Hakata antigen, MASP1 and MASP3 mRNAs. Similar results were obtained in four other glioma lines. In addition, mRNAs for C1r, C1s, C2, C3, C4, C5 and C6 were also detected in T98G cells, but very low amount of mRNAs for C1q and MBL. MBL mRNA was seen in two of the other glioma cell lines. An ELISA of culture supernatants showed that T98G cells secreted a considerable amount of MASP-1 and MASP-3 proteins. SDS-PAGE and immunoblotting analyses showed the secreted H-ficolin/Hakata antigen, MASP-1 and MASP-3 to be 34, 81 and 105 kDa in size respectively, similar to their serum counterparts. Since the glioma cells used are derived from astrocytes, this suggests that human astrocytes may be a source of some components of the LCP in the brain.
Levels of vascular endothelial growth factor, hepatocyte growth factor/scatter factor and basic fibroblast growth factor in human gliomas and their relation to angiogenesis (1999)

Angiogenesis is a possible target in the treatment of human gliomas. To evaluate the role of 3 growth factors, vascular endothelial growth factor (VEGF), hepatocyte growth factor/scatter factor (HGF/SF) and basic fibroblast growth factor (bFGF), in the angiogenic cascade, we determined their levels in extracts of 71 gliomas by enzyme-linked immunosorbent assay (ELISA). The levels of bFGF were only marginally different between gliomas of World Health Organization (WHO) grade II (low grade) and grades III and IV (high grade). In contrast, the mean concentrations of VEGF were 11-fold higher in high-grade tumors and those of HGF/SF 7-fold, respectively. Both were highly significantly correlated with microvessel density (p < 0.001) as determined by immunostaining for factor VIII-related antigen. In addition, VEGF and HGF/SF appeared to be independent predictive parameters for glioma microvessel density as determined by multiple regression analysis. We measured the capacity of all 3 factors to induce endothelial tube formation in a collagen gel. In this assay, bFGF was found to be an essential cofactor with which VEGF as well as HGF/SF were able to synergize independently. According to the concentrations of angiogenic factors, extracts from high-grade tumors were significantly more potent in the tube formation assay than the low-grade extracts (p = 0.02). Adding neutralizing antibodies to bFGF, VEGF and HGF/SF together with the extracts, tube formation was inhibited by up to 98%, 62% and 54%, respectively. Our findings suggest that bFGF is an essential cofactor for angiogenesis in gliomas, but in itself is insufficient as it is present already in the sparsely vascularized low-grade tumors. Upon induction of angiogenesis in high-grade tumors, bFGF may synergize with rising levels of not only VEGF but possibly also with HGF/SF, which appears here to be an independent angiogenic factor.
Mutagenically Separated PCR Assay for Rapid Detection of M41L and K70R Zidovudine Resistance Mutations in CRF01_AE (Subtype E) Human Immunodeficiency Virus Type 1 (2002)

A rapid zidovudine (ZDV) resistance genotypic assay was developed based on the mutagenically separated PCR (MS-PCR) technique to detect two ZDV-resistant mutations, M41L and K70R in CRF01_AE (subtype E). Endpoint dilution analysis revealed that the newly constructed MS-PCR assay could successfully detect three to nine copies of human immunodeficiency virus type 1 template RNA. The test against wild-type and mutant template mixtures in different ratios demonstrated that the assay could detect 10% minor population, at least. Fifty-one subtype E clinical samples were analyzed by the newly constructed MS-PCR assay and direct nucleotide sequencing. The concordance of the two assays was 92 and 100% in codons 41 and 70, respectively. The MS-PCR assay is a rapid, simple, and inexpensive assay that is highly sensitive in detecting mutant targets, including minor populations. Thus, it could be used as a powerful tool for epidemiological surveillance of drug-resistant mutations in developing countries.
Demethylation of the estrogen receptor gene in estrogen receptor-negative breast cancer cells can reactivate estrogen receptor gene expression. (1995)

Approximately one third of breast cancers grow independently of estrogen, lack detectable estrogen receptor (ER) protein, and rarely respond to hormonal treatment. Previous studies correlated the lack of ER gene expression in ER-negative breast tumor cells with hypermethylation of a CpG island in the 5' region of the ER gene. In order to determine whether demethylation of the ER gene in the ER-negative human breast cancer cell line MDA-MB-231 could affect ER transcription, cells were treated with two inhibitors of DNA methylation, 5-azacytidine or 5-aza-2'-deoxycytidine. DNA from cells treated with either drug became partially demethylated at several methylation-sensitive restriction enzyme sites, including HhaI, NotI, and SacII, within the ER CpG island. This demethylation correlated with reexpression of the ER gene as detected by reverse transcriptase-PCR and production of ER protein as detected by Western blot analysis. ER produced in drug-treated cells was functionally active as demonstrated by its ability to activate transcription of estrogen-responsive genes. These results suggest that DNA methylation of the ER CpG island may play a role in suppression of ER gene expression in ER-negative breast cancer cells.
In Vivo Activities of Evernimicin (SCH 27899) against Vancomycin-Susceptible and Vancomycin-Resistant Enterococci in Experimental Endocarditis (2000)

To assess the potential efficacy of evernimicin (SCH 27899) against serious enterococcal infections, we used a rat model of aortic valve endocarditis established with either a vancomycin-susceptible Enterococcus faecalis or a vancomycin-resistant Enterococcus faecium strain. Animals infected with either one of the test strains were assigned to receive no treatment (controls) or 5-day therapy with one of the following regimens: evernimicin 60-mg/kg of body weight intravenous (i.v.) bolus once daily, 60-mg/kg i.v. bolus twice daily (b.i.d.), 60 mg/kg/day i.v. by continuous infusion, or 120 mg/kg/day i.v. by continuous infusion. These regimens were compared with vancomycin at 150 mg/kg/day. In animals infected with E. faecalis, evernimicin at 120 mg/kg/day by continuous infusion significantly reduced bacterial counts in vegetations (final density, 5.75+/-3.38 log(10) CFU/g) compared with controls (8.51+/-1.11 log(10) CFU/g). In animals infected with 0.5 ml of an 8 x 10(7)-CFU/ml inoculum of the vancomycin-resistant E. faecium, both 60-mg/kg bolus once a day and b.i.d. dose regimens of evernimicin were very effective (viable counts, 3.45+/-1.44 and 3.81+/-1.98 log(10) CFU/g, respectively). Vancomycin was unexpectedly active against infections induced with that inoculum. In animals infected with a 10(9)-CFU/ml inoculum of the vancomycin-resistant E. faecium, the evernimicin 60-mg/kg i.v. bolus b.i.d. reduced viable counts in vegetations compared with controls (6.27+/-1.63 versus 8.34+/-0.91 log(10) CFU/g; P<0.05), whereas vancomycin was ineffective. Although resistant colonies could be selected in vitro, we were not able to identify evernimicin-resistant clones from cardiac vegetations. An unexplained observation from these experiments was the great variability in final bacterial densities within cardiac vegetations from animals in each of the evernimicin treatment groups.
Nucleocytoplasmic Transport (1996)

Active transport of proteins and RNAs between the nucleus and cytoplasm is a major process in eukaryotic cells. Recently, factors that recognize transport substrates and mediate nuclear import or export have been characterized, revealing interactions that target substrates to the nuclear pore complexes, through which translocation occurs. Translocation requires energy, and for the import process this energy is at least partly consumed by the action of the small guanosine triphosphatase Ran. In the first half of the review, some of the well-established general background information on nucleocytoplasmic transport is discussed. The second half describes recent information on the mechanistic details of nuclear import and export as well as major unresolved issues such as how directionality is conferred on either import or export. The whole review is slanted toward discussion of metazoan cells.
Reflections on "Seven Issues" (2001)

Frank Halasz revisits his papers "Reflections on NoteCards: Seven Issues for the Next Generation of Hypermedia Systems" and "Seven Issues: Revisited" from a Web perspective. His goal is to better understand how the Web has shaped and often overshadowed how we look at the tremendous possibilities of hypertext.
Increased γ- and Decreased δ-Oscillations in a Mouse Deficient for a Potassium Channel Expressed in Fast-Spiking Interneurons (1999)

Kv3.1 is a voltage-gated, fast activating/deactivating potassium (K(+)) channel with a high-threshold of activation and a large unit conductance. Kv3.1 K(+) channels are expressed in fast-spiking, parvalbumin-containing interneurons in cortex, hippocampus, striatum, the thalamic reticular nucleus (TRN), and in several nuclei of the brain stem. A high density of Kv3.1 channels contributes to short-duration action potentials, fast afterhyperpolarizations, and brief refractory periods enhancing the capability in these neurons for high-frequency firing. Kv3.1 K(+) channel expression in the TRN and cortex also suggests a role in thalamocortical and cortical function. Here we show that fast gamma and slow delta oscillations recorded from the somatomotor cortex are altered in the freely behaving Kv3.1 mutant mouse. Electroencephalographic (EEG) recordings from homozygous Kv3.1(-/-) mice show a three- to fourfold increase in both absolute and relative spectral power in the gamma frequency range (20-60 Hz). In contrast, Kv3.1-deficient mice have a 20-50% reduction of power in the slow delta range (2-3 Hz). The increase in gamma power is most prominent during waking in the 40- to 55-Hz range, whereas the decrease in delta power occurs equally across all states of arousal. Our findings suggest that Kv3. 1-expressing neurons are involved in the generation and maintenance of cortical fast gamma and slow delta oscillations. Hence the Kv3. 1-mutant mouse could serve as a model to study the generation and maintenance of fast gamma and slow delta rhythms and their involvement in behavior and cognition.
Language Identification Using Pitch Contour Information (2006)

An approach to automatic language identification (LID) using pitch contour information is proposed. A segment of pitch contour is approximated by a set of Legendre polynomials so that coefficients of the polynomials form a feature vector to represent this pitch contour. A Gaussian mixture model (GMM) method based on feature vectors extracted from pitch contours is suggested for the LID. Our experiments show that only two or three coefficients are necessary to obtain reasonably good identification rates. We also find that the length of the segmented pitch contour is another useful feature for LID, so that it is included to improve the performance further. Pair-wise language identification experiments on the OGI-TS corpus show that our proposed approach is very promising We also find that tonal languages and pitch accent languages achieve better performance in our system.
Raltitrexed (Tomudex™) (1998)

Raltitrexed (Tomudex) is a new specific, mixed non-competitive inhibitor of thymidylate synthase indicated for use in the therapy of advanced colorectal cancer. Phase I and II studies defined a maximum tolerated dose of 3.0 mg/m(2) administered as a 15-min i.v. infusion every 3 weeks: this dose proved active in a range of malignancies, but most significantly in advanced colorectal cancer. Phase III studies in patients with advanced colorectal cancer indicate similar efficacy with raltitrexed monotherapy and combination therapy with 5-fluorouracil + low or high dose leucovorin (5-FU + LV) (Mayo or Machover regimens, respectively). Major toxicity in the various studies of raltitrexed included gastrointestinal effects, haematological suppression, asthenia and reversible asymptomatic increases in hepatic transaminases. However, patients receiving 5-FU + LV experienced more severe leucopaenia and mucositis than patients receiving raltitrexed: this translated into fewer toxicity-related dosage reductions. Raltitrexed is therefore as effective as but better tolerated and accepted than 5-FU + LV. Thus, raltitrexed offers the first alternative to 5-FU-based therapy in advanced colorectal cancer; furthermore, the mode of action of the drug offers the potential for synergy with agents that act via other molecular mechanisms.
Nucleotide sequence and mutation rate of the H strain of hepatitis C virus. (1991)

Patient H is an American patient who was infected with hepatitis C virus (HCV) in 1977. The patient became chronically infected and has remained so for the past 13 years. In this study, we compared the nucleotide and predicted amino acid sequences of the HCV genome obtained from plasma collected in 1977 with that collected in 1990. We find that the two HCV isolates differ at 123 of the 4923 (2.50%) nucleotides sequenced. We estimate that the mutation rate of the H strain of HCV is approximately 1.92 x 10(-3) base substitutions per genome site per year. The nucleotide changes were exclusively base substitutions and were unevenly distributed throughout the genome. A relatively high rate of change was observed in the region of the HCV genome that corresponds to the non-structural protein 1 gene region of flaviviruses, where 44 of 960 (4.6%) nucleotides were different. Within this region there was a 39-nucleotide domain in which 28.2% of the nucleotides differed between the two isolates. In contrast, relatively few nucleotide substitutions were observed in the 5' noncoding region, where only 2 of 276 (0.7%) nucleotides were different. Our results suggest that the mutation rate of the HCV genome is similar to that of other RNA viruses and that genes appear to be evolving at different rates within the virus genome.
A dynamic collimation system for penumbra reduction in spot‐scanning proton therapy: Proof of concept (2014)

The spread of the lateral penumbra of low-energy SS proton treatments may be greatly reduced with the use of this system at the cost of only a small penalty in delivery time.
L-Thymidine is phosphorylated by herpes simplex virus type 1 thymidine kinase and inhibits viral growth (1992)

We have demonstrated that herpes simplex 1 (HSV1) thymidine kinase (TK) shows no stereospecificity for D- and L-beta-nucleosides. In vitro, L enantiomers are not recognized by human TK, but function as specific substrates for the viral enzyme in the order: L-thymidine (L-T) >> 2'-deoxy-L-guanosine (L-dG) > 2'-deoxy-L-uridine (L-dU) > 2'-deoxy-L-cytidine (L-dC) > 2'-deoxy- L-adenosine (L-dA). HSV1 TK phosphorylates both thymidine enantiomers to their corresponding monophosphates with identical efficiency and the Ki of L-T (2 microM) is almost identical to the Km for the natural substrate D-T (2.8 microM). The L enantiomer reduces the incorporation of exogenous [3H]T into cellular DNA in HeLa TK-/HSV1 TK+ but not in wild-type HeLa cells, without affecting RNA, protein synthesis, cell growth, and viability. L-T markedly reduces HSV1 multiplication in HeLa cells. Our observations could lead to the development of a novel class of antiviral drugs characterized by low toxicity.
Meridional analysis for calculating the expected spherocylindrical refraction in eyes with toric intraocular lenses (2007)

Calculation of the expected spherocylindrical refraction with toric IOLs was achieved using meridional analysis.
Fluidics Cube for Biosensor Miniaturization (2001)

To create a small, portable, fully automated biosensor, a compact means of fluid handling is required. We designed, manufactured, and tested a "fluidics cube" for such a purpose. This cube, made of thermoplastic, contains reservoirs and channels for liquid samples and reagents and operates without the use of any internal valves or meters; it is a passive fluid circuit that relies on pressure relief vents to control fluid movement. We demonstrate the ability of pressure relief vents to control fluid movement and show how to simply manufacture or modify the cube. Combined with the planar array biosensor developed at the Naval Research Laboratory, it brings us one step closer to realizing our goal of a handheld biosensor capable of analyzing multiple samples for multiple analytes.
Performance of a photorefractive joint transform correlator for fingerprint identification (1995)

A photorefractive joint transform correlator is connected to a PC-based image processing board and tested for fingerprint recognition. Distortions due to rotation, scale, and partial hiding are considered: ± 4 deg in rotation, ± 7% in scale, and up to 80% hiding can be handled by the correlator. The performance of the correlator operating with a realtime fingerprint acquisition camera is then measured. The captured fingerprint is generally distorted with respect to its original counterpart stored in the PC memory. These distortions are mostly due to the positioning and pressure of the finger on the glass prism of the camera. We evaluate the recognition performance qualitatively and statistically with these distortions on a limited data bank and demonstrate 80% successful recognition rate.
Existence of a photonic gap in periodic dielectric structures (1990)

Using a plane-wave expansion method, we have solved Maxwell's equations for the propagation of electromagnetic waves in a periodic lattice of dielectric spheres (dielectric constant ${\mathrm{\ensuremath{\epsilon}}}_{\mathit{a}}$) in a uniform dielectric background (${\mathrm{\ensuremath{\epsilon}}}_{\mathit{b}}$). Contrary to experiment, we find that fcc dielectric structures do not have a ``photonic band gap'' that extends throughout the Brillouin zone. However, we have determined that dielectric spheres arranged in the diamond structure do possess a full photonic band gap. This gap exists for refractive-index contrasts as low as 2.