gebhart/patrepeval huggingface dataset:
Arachidonic acid cytochrome P450 epoxygenase pathway (2008)

Cytochrome P450 (CYP) epoxygenases convert arachidonic acid to four epoxyeicosatrienoic acid (EET) regioisomers, 5,6-, 8,9-, 11,12-, and 14,15-EET, that function as autacrine and paracrine mediators. EETs produce vascular relaxation by activating smooth muscle large-conductance Ca2+-activated K+ channels (BKCa). In addition, they have anti-inflammatory effects on blood vessels and in the kidney, promote angiogenesis, and protect ischemic myocardium and brain. CYP epoxygenases also convert eicosapentaenoic acid to vasoactive epoxy-derivatives, and endocannabinoids containing 11,12- and 14,15-EET are formed. Many EET actions appear to be initiated by EET binding to a membrane receptor that activates ion channels and intracellular signal transduction pathways. However, EETs also are taken up by cells, are incorporated into phospholipids, and bind to cytosolic proteins and nuclear receptors, suggesting that some functions may occur through direct interaction of the EET with intracellular effector systems. Soluble epoxide hydrolase (sEH) converts EETs to dihydroxyeicosatrienoic acids (DHETs). Because this attenuates many of the functional effects of EETs, sEH inhibition is being evaluated as a mechanism for increasing and prolonging the beneficial actions of EETs.
Plasma‐beam alignment technique for ferroelectric liquid crystals (2008)

Abstract— The plasma‐beam alignment procedure earlier developed for the alignment of nematic liquid crystals is successfully extended to ferroelectric liquid crystals (FLC). The highly uniform alignment of the “chevron” structure (before electrical treatment of FLC cells) and “quasi bookshelf” structure (after the electrical treatment) are realized. The contrast of bistable switching larger than 350:1 is achieved. This makes the non‐contact plasma‐beam alignment procedure especially attractive for high‐contrast bistable LCDs on an LCOS base, particularly used in PDA and e‐books. Fast switching and realization of gray scale in the plasma‐beam aligned FLC cells makes this technique also promising for full‐color displays including color LCD TV.
Highly potent and specific inhibitors of human renin (1987)

We have designed and synthesized a series of small peptides containing a perfluoroalkyl ketone group at the C-terminal position of the angiotensin I sequence as inhibitors of human renin. From this series of compounds, 8 and 10 showed strong inhibition of human renin (IC50 = 3 X 10(-9), 7 X 10(-9) M, respectively). Compound 10 did not inhibit pepsin and cathepsin D at 10(-4) M. Comparison of the IC50 of compound 8 and compound 11 (8.7 X 10(-7) M) demonstrated the marked effect of the perfluoropropyl group on the potency of inhibition on renin, presumably due to the strong electron-withdrawing effect causing the ketone in 8 to exist predominantly as the hydrate--thus mimicking the tetrahedral transition state during hydrolysis of the scissile Leu10--Val11 amide bond.
Repression of the herpes simplex virus 1 alpha 4 gene by its gene product (ICP4) within the context of the viral genome is conditioned by the distance and stereoaxial alignment of the ICP4 DNA binding site relative to the TATA box (1995)

Infected cell protein no. 4 (ICP4), the major regulatory protein encoded by the alpha 4 gene of herpes simplex virus 1, binds to a site (alpha 4-2) at the transcription initiation site of the alpha 4 gene. An earlier report described the construction of recombinant viruses that contained chimeric genes (alpha 4-tk) that consisted of the 5' untranscribed and transcribed noncoding domains of the alpha 4 gene fused to the coding sequences of the thymidine kinase gene and showed that disruption of the alpha 4-2 binding site by mutagenesis derepressed transcription of this gene (N. Michael and B. Roizman, Proc. Natl. Acad. Sci. USA 90:2286-2290, 1993). This experimental design was used to determine the effect of displacement of the alpha 4-2 binding site on the repression of alpha 4 gene transcription by ICP4. We report the following findings. (i) In the absence of the alpha 4-2 binding site, at 4 h after infection, alpha 4-tk RNA levels increased 10-fold relative to the corresponding RNA levels of a gene that contained the alpha 4-2 site at its natural location. Displacement of the alpha 4-2 binding site by approximately one, two, and three turns of the DNA helix, i.e., by 10, 21, and 30 nucleotides downstream of the original site, increased the concentration of alpha 4-tk RNA 2.4-, 3.5-, and 5.8-fold, respectively. (ii) Displacement of 16 nucleotides, i.e., approximately 1.5 helical turns, increased the accumulation of alpha 4-tk by 5.3-fold, i.e., more than predicted by displacement alone. (iii) At 8 h after infection in the absence of the binding site, the accumulation of alpha 4-tk RNA increased 13.6-fold. However, in cells infected with recombinants that carried displaced alpha 4-2 binding sites, RNA accumulation decreased relative to the levels seen at 4 h after infection. The insertion of DNA sequences in order to displace the alpha 4-2 binding site had no effect on accumulation of RNA in the presence of cycloheximide, i.e., in the absence of ICP4, or on maximum accumulation of alpha 4-tk RNA in the absence of the alpha 4-2 binding site.(ABSTRACT TRUNCATED AT 400 WORDS)
Characterization of the Allergen Group VI in Timothy Grass Pollen (Phl p 6) II. cDNA Cloning of Phl p 6 and Structural Comparison to Grass Group V (1995)

The complete primary structure of the major allergen Phl p 6 was determined by cDNA cloning. A cDNA library of timothy grass pollen was screened by a Phl p 6 directed mouse antiserum. Six clones were obtained. From the cDNA data we deduced a protein sequence of 110 amino acids. While the size of the leader sequences varied considerably between the different clones, only one amino acid exchange affected the mature proteins. Sequence comparison of group VI and V allergens showed a high degree of homology in the N- and C-terminal regions. The structural data strongly indicate that group VI and V are independent groups of allergens, which have derived from a common precursor gene.
Potential role of Epstein-Barr virus in Sjögren's syndrome and rheumatoid arthritis. (1992)

In the pathogenesis of Sjögren's syndrome (SS), a role for Epstein-Barr virus (EBV) has been suggested because; (a) EBV is present in salivary gland epithelial cells of healthy individuals, and exaggerated immune responses against EBV could play a role in the destruction of salivary glands in SS; (b) SS salivary gland biopsies contain increased levels of EBV DNA compared to normal salivary glands, indicating viral reactivation and inability of lymphoid infiltrates to control EBV replication in patients with SS; and (c) salivary gland epithelial cells in patients with SS express high levels of HLA-DR antigens and may present EBV associated antigens to immune T cells in patients with SS. Therefore, SS may represent a situation where genetically predisposed individuals (i.e., HLA-DR3-DQA4-DQB2) have a persistent but ineffectual T cell immune response against EBV at its site of latency. In the case of rheumatoid arthritis (RA), evidence for a potential role of EBV includes the following: (a) EBV encoded proteins share antigenic and sequence similarity to proteins found in the synovial tissues. These crossreactive proteins include EBV protein gp110 (BALF-4) and the beta chain of HLA-DR4. Also, the human and mycobacterial 65 kDa heat shock proteins have a sequence similar to that of EBV encoded proteins; (b) patients with RA have increased frequency and levels of antibodies against specific epitopes on EBV encoded EBNA-1 (BKRF-1) and EBNA-3 (BERF-1) antigens; and (c) lymphocytes from patients with RA have decreased ability to limit outgrowth of autologous EBV infected lymphocytes, probably due to defects in release of interferon gamma.(ABSTRACT TRUNCATED AT 250 WORDS)
Megahertz linewidth from a 1.5 μm semiconductor laser with HeNe laser injection (1982)

The linewidth of a 1.5 μm semiconductor laser has been reduced from &gt; 1 GHz to &lt; 1.5 MHz by injection locking the laser to the low-power narrow-linewidth output from an HeNe laser operating at 1.523 μm. A collimated-beam power of 750 μW was obtained in the injection-locked semiconductor laser mode.
Mobilising the Net (1999)

Bringing the Internet and mobile communications together, as service providers and manufacturers are now doing, will create a new mass medium for communication, interaction and transaction along with a high-volume industry supplying the associated infrastructure. A combination of technologies is creating a direct evolutionary path from today&apos;s low-bandwidth mobile connections and limited text messaging to full scale Internet access via mobile networks. Bandwidths of up to 2 Mbit/s, available through UMTS, will allow the most demanding of today&apos;s Internet applications to be carried out using portable devices. Some of the applications of this combined technology, the portable devices and the media processors are described in this paper.
Glossary of terms used in computational drug design (IUPAC Recommendations 1997) (1997)

Abstract
Time-resolved fluorescence resonance energy transfer studies of DNA bending in double-stranded oligonucleotides and in DNA-protein complexes (2002)

Time-resolved Förster resonance energy transfer (trFRET) has been used to obtain interdye distance distributions. These distributions give the most probable distance as well as a parameter, sigma, that characterize the width of the distribution. This latter parameter contains information not only on the flexibility of the dyes tethered to macromolecules, but on the flexibility of the macromolecules. Both the most probable interdye distance as well as sigma provide insight into DNA static bending and DNA flexibility. Time-resolved fluorescence anisotropy and static anisotropy measurements can be combined to provide a measure of the cone angle within which the tethered dyes appear to wobble. When this motion is an order of magnitude faster than the average lifetime that characterizes transfer, an average value of the dipolar orientational parameter kappa2 can be calculated for various mutual dye orientations. The resulting kappa2 distribution is very much narrower than the limiting values of 0 and 4, allowing more precise distances and distance changes to be determined. Static and time-resolved fluorescence data can be combined to constrain the analyses of DNA-protein kinetics to provide thermodynamic parameters for binding and for conformational changes along a reaction coordinate. The parameter sigma can be used to model multiple DNA-protein complexes with varying DNA bend angles in a global fitting of trFRET data. Such a global fitting approach has shown how the range of bends in single base DNA variants, when bound by the TATA binding protein (TBP), can be understood in terms of two limiting forms. Time-resolved FRET, combined with steady-state FRET, can be used to show not only how osmolytes affect the binding of DNA to proteins, but also how DNA bending depends on osmolyte concentration in the DNA-protein complexes.
Protocols for cloning and analysis of blunt-ended PCR-generated DNA fragments. (1994)

Methods are presented for the improved yield and analysis of blunt-ended cloning of PCR-generated DNA fragments.(1) We show that Pfu DNA polymerase polishing of Taq DNA polymerase-generated fragments increases the yield and efficiency of cloning.Using a triple primer set consisting of two outside, asymmetrically distanced primers and one fragment-specific primer, one can determine both the presence and orientation of cloned inserts.Application of these methods allows one to generate and clone a fragment in 1 day and analyze putative clones the next, thereby saving a substantial amount of both time and effort. VECTOR PREPARATIONSeveral vectors and derivatives have been created for PCR cloning.These include the standard pBluescript-type multiple cloning sites (e.g., pBluescrip-tlI, pBC, pCR-ScriptAmp, and pCR-ScriptCam) (Stratagene, La Jolla CA) and the abbreviated multiple cloning sites as contained in the pCR-Script Direct plasmids (Stratagene) (2-4~ (see Fig. 1).The abbreviated multiple cloning sites allow the end user to incorporate common restriction enzyme sites into their PCR primer sets without the problem of having the same target sequence occurring in the plasmid vector.It is recommended that the chloramphenicol derivatives be used when subcloning DNA fragments generated from ampicillin-resistance encoding plasmids.This ensures that recombinant colonies after Escherichia coli transformation are not the result of parental plasmid transformation. Bidirectional Cloning VectorsBlunt-ended cloning procedures capture blunted PCR fragments for bidirec-FIGURE 1 Vectors for bidirectional and directional cloning of PCR fragments.Several vectors have been developed for directional and bidirectional cloning.These include derivatives that encode either chloramphenicol or ampicillin resistance with modified multiple cloning sites optimized for specific cloning operations (e.g., general subcloning or protein expression).
Annexin A5 protein expression is associated with the histological differentiation of uterine cervical squamous cell carcinoma in patients with an increased serum concentration (2012)

Annexin A5 (ANXA5) is a calcium-dependent phospholipid-binding protein belonging to the annexin family and is expressed abnormally in several types of carcinoma. In the present study, ANXA5 protein expression was evaluated by western blot analysis in a series of 60 human uterine cervical squamous cell carcinomas (UCSCCs) to search for molecular alterations that may be able to serve as useful diagnostic/prognostic markers. The upregulation of ANXA5 expression was observed in 48/60 UCSCC cases (80%), whereas a weak expression was observed in the 25 normal uterine cervical tissues. ANXA5 expression was also analyzed by immunohistochemical staining, western blot and reverse transcription-polymerase chain reaction (RT-PCR) assays of the UCSCC and uterine cervical normal tissue lesions. All dysplastic tissues showed significantly increased ANXA5 expression compared with the weak signal observed in normal epithelia. A close association was observed between the ANXA5 expression levels and the histological grade of UCSCC. Compared with moderately and well-differentiated tumors, there was a significant increase in ANXA5 expression in poorly differentiated tumors. Furthermore, ANXA5 concentrations in the blood serum of the patients were significantly increased. Our findings clearly identify ANXA5 as an effective differentiation marker for the histopathological grading of UCSCCs and for the detection of epithelial dysplasia. The results from our study support the critical role of ANXA5 in the molecular profiling of UCSCC.
Energy Minimization via Graph Cuts: Settling What is Possible (2005)

The recent explosion of interest in graph cut methods in computer vision naturally spawns the question: what energy functions can be minimized via graph cuts? This question was first attacked by two papers of Kolmogorov and Zabih, in which they dealt with functions with pair-wise and triplewise pixel interactions. In this work, we extend their results in two directions. First, we examine the case of k-wise pixel interactions; the results are derived from a purely algebraic approach. Second, we discuss the applicability of provably approximate algorithms. Both of these developments should help researchers best understand what can and cannot be achieved when designing graph cut based algorithms.
Suppression of transient receptor potential melastatin 7 channel induces cell death in gastric cancer (2008)

Ca2+ and Mg2+ have a fundamental role in many cellular processes and ion channels are involved in normal physiologic processes and in the pathology of various diseases. The aim here was to show that the presence and potential role of transient receptor potential melastatin 7 (TRPM7) channels in the growth and survival of AGS cells, the most common human gastric adenocarcinoma cell line. The patch-clamp technique for whole-cell recording was used in AGS cells. TRPM7-specific small interfering RNAs were used for specific inhibition of TRPM7. Whole-cell voltage-clamp recordings revealed the TRPM7-like currents that activated spontaneously following loss of intracellular Mg2+. The current had a non-linear current-voltage relationship with the characteristic steep outward rectification associated with TRPM7 channels. Reverse transcription-polymerase chain reaction, western blotting, and immunoreactivity all showed abundant expression of TRPM7 messenger RNA and protein in AGS cells. Transfection of AGS cells with TRPM7 siRNA significantly reduced the expression of TRPM7 mRNA and protein as well as the amplitude of the TRPM7-like currents. Furthermore, we found that Mg2+ is critical for the growth and survival in AGS cells. Blockade of TRPM7 channels by La3+ and 2-APB or suppression of TRPM7 expression by siRNA inhibited the growth and survival of these cells. Human gastric adenocarcinoma cells express TRPM7 channel whose presence is essential for cell survival. The protein is a likely potential target for the pharmacological treatment of gastric cancer.
Improving Neural Question Generation Using Answer Separation (2019)

Neural question generation (NQG) is the task of generating a question from a given passage with deep neural networks. Previous NQG models suffer from a problem that a significant proportion of the generated questions include words in the question target, resulting in the generation of unintended questions. In this paper, we propose answer-separated seq2seq, which better utilizes the information from both the passage and the target answer. By replacing the target answer in the original passage with a special token, our model learns to identify which interrogative word should be used. We also propose a new module termed keyword-net, which helps the model better capture the key information in the target answer and generate an appropriate question. Experimental results demonstrate that our answer separation method significantly reduces the number of improper questions which include answers. Consequently, our model significantly outperforms previous state-of-the-art NQG models.
A case for “StopGo”: Reprogramming translation to augment codon meaning of GGN by promoting unconventional termination (Stop) after addition of glycine and then allowing continued translation (Go) (2007)

When a eukaryotic mRNA sequence specifying an amino acid motif known as 2A is directly followed by a proline codon, two nonoverlapping proteins are synthesized. From earlier work, the second protein is known to start with this proline codon and is not created by proteolysis. Here we identify the C-terminal amino acid of an upstream 2A-encoded product from Perina nuda picorna-like virus that is glycine specified by the last codon of the 2A-encoding sequence. This is an example of recoding where 2A promotes unconventional termination after decoding of the glycine codon and continued translation beginning with the 3' adjacent proline codon.
Exercise training enhances basic fibroblast growth factor-induced collateral blood flow (1998)

This study evaluated whether daily exercise would enhance the peripheral collateral vessel development found in response to exogenous basic fibroblast growth factor (bFGF) infusion. After bilateral femoral occlusion, male Sprague-Dawley rats (approximately 325 g) received intra-arterial infusions of either bFGF (1 microg/day; n = 15) or carrier solution (n = 13) via osmotic pumps for 2 wk. Subgroups of each treatment were kept sedentary (cage activity) or trained by walking at 20 m/min at 15% grade, two times a day, 5 days/wk for 4 wk. Training markedly increased citrate synthase activity in the active muscle (P < 0.001). Muscle function and blood flows (85Sr microsphere) were evaluated using an isolated hindquarter perfused at 100 mmHg via the abdominal aorta. The significant increase in blood flow to the entire hindlimb in the sedentary animals, caused by bFGF infusion (P < 0.05), was further increased (P < 0.01) in the bFGF-trained group. The quantitatively largest increases in blood flows were observed in the collateral-dependent tissues of the distal hindlimb. Blood flows to the entire calf muscle group increased approximately 140% in carrier-trained (P < 0.001), approximately 180% in bFGF sedentary (P < 0.001), and approximately 240% in the bFGF-trained (P < 0.001) groups compared with the carrier sedentary group. The increases in collateral blood flow were functionally important, as improvements in calf muscle performance correlated with measured blood flows. Our results demonstrate that exogenous bFGF administration in combination with a moderate-intensity exercise program greatly increases collateral-dependent blood flow and improves muscle performance. That physical activity enriched the bFGF response is consistent with the hypothesis that hemodynamic factors are important contributors to collateral vessel enlargement.
Labeling of glucose transporters at the cell surface in 3T3-L1 adipocytes. Evidence for both translocation and a second mechanism in the insulin stimulation of transport. (1988)

In order to determine whether translocation of intracellular glucose transporters to the plasma membrane upon insulin stimulation accounts entirely for the increase in glucose transport, a method was developed to measure the relative amount of transporter at the cell surface. Glycoproteins at the cell surface, including the glucose transporter, were labeled by oxidation with galactose oxidase and then reduction by borotritide at 4 degrees C; subsequently the glucose transporter was isolated by immunoprecipitation and sodium dodecyl sulfate gel electrophoresis. Insulin stimulation of 3T3-L1 adipocytes resulted in a 2.6-fold increase in transporter at the cell surface. Under the same conditions, the rate of 2-deoxyglucose uptake was increased 11-fold. These results both provide further evidence that translocation of the glucose transporter occurs in response to insulin and indicate that it does not account for the full stimulation. Most likely, insulin also increases the intrinsic activity of the transporter.
Several small Josephson junctions in a resonant cavity: Deviation from the Dicke model (2002)

We have studied quantum mechanically a system of several small identical Josephson junctions in a lossless single-mode cavity for different initial states, under conditions such that the system is at resonance. This system is analogous to a collection of identical atoms in a cavity, which is described under appropriate conditions by the Dicke model. We find that our system can be well approximated by a reduced Hamiltonian consisting of two levels per junction. The reduced Hamiltonian is similar to the Dicke Hamiltonian, but contains an additional term resembling a dipole-dipole interaction between the junctions. This extra term can be understood as a natural consequence of degenerate second-order (L\"owdin) perturbation theory. For typical, physically reasonable values of the junction-cavity coupling, we find that this perturbation treatment is an adequate way to include the junction energy levels beyond the lowest two. As in the Dicke model, we find that, when N junctions are present in the cavity, the junction-cavity interaction is enhanced by $\sqrt{N},$ with a corresponding decrease in the Rabi oscillation period. We find that this enhancement survives even if the junctions differ slightly from one another, as expected in a realistic system. Since coherence effects thus reduce the Rabi period, it may become smaller than the decoherence time due to dissipation, making these oscillations observable.