gebhart/patrepeval huggingface dataset:
Immunodominant Epitopes in Herpes Simplex Virus Type 2 Glycoprotein D Are Recognized by CD4 Lymphocytes from Both HSV-1 and HSV-2 Seropositive Subjects (2008)

In human recurrent cutaneous herpes simplex, there is a sequential infiltrate of CD4 and then CD8 lymphocytes into lesions. CD4 lymphocytes are the major producers of the key cytokine IFN-gamma in lesions. They recognize mainly structural proteins and especially glycoproteins D and B (gD and gB) when restimulated in vitro. Recent human vaccine trials using recombinant gD showed partial protection of HSV seronegative women against genital herpes disease and also, in placebo recipients, showed protection by prior HSV1 infection. In this study, we have defined immunodominant peptide epitopes recognized by 8 HSV1(+) and/or 16 HSV2(+) patients using (51)Cr-release cytotoxicity and IFN-gamma ELISPOT assays. Using a set of 39 overlapping 20-mer peptides, more than six immunodominant epitopes were defined in gD2 (two to six peptide epitopes were recognized for each subject). Further fine mapping of these responses for 4 of the 20-mers, using a panel of 9 internal 12-mers for each 20-mers, combined with MHC II typing and also direct in vitro binding assay of these peptides to individual DR molecules, showed more than one epitope per 20-mers and promiscuous binding of individual 20-mers and 12-mers to multiple DR types. All four 20-mer peptides were cross-recognized by both HSV1(+)/HSV2(-) and HSV1(-)/HSV2(+) subjects, but the sites of recognition differed within the 20-mers where their sequences were divergent. This work provides a basis for CD4 lymphocyte cross-recognition of gD2 and possibly cross-protection observed in previous clinical studies and in vaccine trials.
High-Density Electron Anions in a Nanoporous Single Crystal: [Ca 24 Al 28 O 64 ] 4 + (4 e - ) (2003)

We removed approximately 100% of clathrated oxygen ions from the crystallographic cages in a single crystal of 12CaO.7Al2O3, leading to the formation of high-density (approximately 2 x 10(21) cm-3) electrons highly localized in the cages. The resulting electron forms a structure that we interpret as an F+ center and migrates throughout the crystal by hopping to a neighboring cage with conductivity approximately 100 siemens per centimeter, demonstrating that the encaged electron behaves as an anion. The electron anions couple antiferromagnetically with each other, forming a diamagnetic pair or singlet bipolaron. The resulting [Ca24Al28O64]4+(4e-) may be regarded as a thermally and chemically stable single crystalline "electride."
Recombinant Mycobacterium tuberculosis protein associated with mammalian cell entry (2001)

The ability to gain entry and resist the antimicrobial intracellular environment of mammalian cells is an essential virulence property of Mycobacterium tuberculosis. A purified recombinant protein expressed by a 1362 bp locus (mce1) in the M. tuberculosis genome promoted uptake into HeLa cells of polystyrene latex microspheres coated with the protein. N-terminus deletion constructs of Mce1 identified a domain located between amino acid positions 106 and 163 that was needed for this cell uptake activity. Mce1 contained hydrophobic stretches at the N-terminus predictive of a signal sequence, and colloidal gold immunoelectron microscopy indicated that the corresponding native protein is expressed on the surface of the M. tuberculosis organism. The complete M. tuberculosis genome sequence revealed that it contained four homologues of mce (mce1, mce2, mce3, mce4) and that they were all located within operons composed of genes arranged similarly at different locations in the chromosome. Recombinant Mce2, which had the highest level of identity (67%) to Mce1, was unable to promote the association of microspheres with HeLa cells. Although the exact function of Mce1 is still unknown, it appears to serve as an effector molecule expressed on the surface of M. tuberculosis that is capable of eliciting plasma membrane perturbations in non-phagocytic mammalian cells.
Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry of Anthocyanin-poly-flavan-3-ol Oligomers in Cranberry Fruit (Vaccinium macrocarpon, Ait.) and Spray-Dried Cranberry Juice (2004)

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to characterize the structural diversity of a series of anthocyanin-polyflavan-3-ol oligomers in cranberry fruit and spray dried juice. MALDI-TOF mass spectra provide evidence for a series of compounds corresponding to anthocyanins; cyanidin-hexose, cyanidin- pentose, peonidin-hexose and peonidin-pentose linked to polyflavan-3-ols through a CH3-CH bridge. Deionizing the isolated anthocyanin-polyflavan-3-ol oligomers with cation exchange resin prior to mass spectral analysis allowed the detection of exclusively [M]+ ions because the singly charged oxonium cation does not require cationization. MALDI-TOF mass spectra of the anthocyanin-polyflavan-3-ols that eluate from Sephadex LH-20 columns with water/ethanol (1:1) contained oligomers with a degree of polymerization (DP) of 1 to 2. MALDI-TOF MS of the Sephadex-ethanol eluate contained a series of masses corresponding to DPI to DP4 and the Sephadex-ethanol:methanol (1:1) eluate contained a series of masses corresponding to DP3 to DP5. The anthocyanin-polyflavan-3-ol oligomers also show structural variation in the nature of the interflavan bond (A-type vs. B-type). Anthocyanin-polyflavan-3-ol oligomers incorporating a CH3-CH bridge have been described in red wines and in model reactions as a condensation reaction between anthocyanins and flavan-3-ols via acetaldehyde. Our results indicate that oligomeric anthocyanins may also be present in cranberry fruit and unfermented spray dried cranberry juice.
Synthesis and Anthelmintic Activity of some New Isothiocyanates, Carbamates and N'-Furoylthioureas derived from 6-Amino-3-aryl/heteroaryl-2H-1, 4- benzoxazines (1986)

Chemistry Division, IDPL Research Centre, Indian Drugs and Pharmaceuticals Limited, Hyderabad-500 037 <em>Manuscript received 1 July 1985, revised 6 January 1986, accepted 2 August 1986</em> Several new isothiocyanates (3a - k), carbamates (4a - k) and N<em>'</em>-furoylthioureas (4a —k) derived from 6-amino-3-aryl/heteroaryl-2<em>H</em>-1,4-benzoxazines have been synthesised and screened for their anthelmintic activity.
DNA Analogues with Nonphosphodiester Backbones (1995)

This review discusses the recent developments of DNA analogues with nonphosphodiester backbones in terms of DNA structure and antisense and antigene potential. A larger number of derivatives are now available in which the phosphodiester linkage has been replaced but the deoxyribose retained. However, only a few of these (e.g. the ones having a thioformacetal or a carboxamide linkage) appear to be good structural DNA mimics. Two successful attempts to replace the entire deoxyribose phosphate backbone have been reported, the morpholino derivatives and the peptide nucleic acids (PNA), which contain an N-(2-aminoethyl)glycine-based pseudopeptide backbone. Most information is available on the PNA, which is a very promising DNA mimic. In conclusion, the deoxyribose phosphate backbone is not essential for a potent structural DNA mimic and not even required for a helical duplex structure.
Up-Regulation of TWIST in Prostate Cancer and Its Implication as a Therapeutic Target (2005)

Androgen-independent metastatic prostate cancer is the main obstacle in the treatment of this cancer. Unlike a majority of solid cancers, prostate cancer usually shows poor response to chemotherapeutic drugs. In this study, we have shown a potential novel target, TWIST, a highly conserved bHLH transcription factor, in the treatment of prostate cancer. Using malignant and nonmalignant prostate tissues, we found that TWIST expression was highly expressed in the majority (90%) of prostate cancer tissues but only in a small percentage (6.7%) of benign prostate hyperplasia. In addition, the TWIST expression levels were positively correlated with Gleason grading and metastasis, indicating its role in the development and progression of prostate cancer. Furthermore, down-regulation of TWIST through small interfering RNA in androgen-independent prostate cancer cell lines, DU145 and PC3, resulted in increased sensitivity to the anticancer drug taxol-induced cell death which was associated with decreased Bcl/Bax ratio, leading to activation of the apoptosis pathway. More importantly, inactivation of TWIST suppressed migration and invasion abilities of androgen-independent prostate cancer cells, which was correlated with induction of E-cadherin expression as well as morphologic and molecular changes associated with mesenchymal to epithelial transition. These results were further confirmed on the androgen-dependent LNCaP cells ectopically expressing the TWIST protein. Our results have identified TWIST as a critical regulator of prostate cancer cell growth and suggest a potential therapeutic approach to inhibit the growth and metastasis of androgen-independent prostate cancer through inactivation of the TWIST gene.
Photovoltaic Sample-and-Hold Circuit Enabling MPPT Indoors for Low-Power Systems (2011)

Photovoltaic (PV) energy harvesting is commonly used to power autonomous devices, and maximum power point tracking (MPPT) is often used to optimize its efficiency. This paper describes an ultra low-power MPPT circuit with a novel sample-and-hold and cold-start arrangement, enabling MPPT across the range of light intensities found indoors, which has not been reported before. The circuit has been validated in practice and found to cold-start and operate from 100 lux (typical of dim indoor lighting) up to 5000 lux with a 55 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> amorphous silicon PV module. It is more efficient than non-MPPT circuits, which are the state-of-the-art for indoor PV systems. The proposed circuit maximizes the active time of the PV module by carrying out samples only once per minute. The MPPT control arrangement draws a quiescent current draw of only 8 μA, and does not require an additional light sensor as has been required by previously reported low-power MPPT circuits.
Patterns of Vascular Cell Adhesion Molecule-1 and Intercellular Adhesion Molecule-1 Expression in Rabbit and Mouse Atherosclerotic Lesions and at Sites Predisposed to Lesion Formation (1999)

The recruitment of mononuclear leukocytes and formation of intimal macrophage-rich lesions at specific sites of the arterial tree are key events in atherogenesis. Inducible endothelial cell adhesion molecules may participate in this process. In aortas of normal chow-fed wild-type mice and rabbits, vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1), but not E-selectin, were expressed by endothelial cells in regions predisposed to atherosclerotic lesion formation. En face confocal microscopy of the mouse ascending aorta and proximal arch demonstrated that VCAM-1 expression was increased on the endothelial cell surface in lesion-prone areas. ICAM-1 expression extended into areas protected from lesion formation. Hypercholesterolemia induced atherosclerotic lesion formation in rabbits, LDL receptor and apolipoprotein E knockout mice, and Northern blot analysis demonstrated increased steady-state mRNA levels of VCAM-1 and ICAM-1, but not of E-selectin. Immunohistochemical staining revealed that VCAM-1 and ICAM-1 were expressed predominantly by endothelium in early lesions and by intimal cells in more advanced lesions. In early and advanced lesions, staining was most intense in endothelial cells at and adjacent to lesion borders. ICAM-1 staining extended into the uninvolved aorta. These expression patterns were highly reproducible in both species. The only difference was that VCAM-1 expression in endothelium over the central portions of lesions was found frequently in rabbits and rarely in mice. The expression of VCAM-1 by arterial endothelium in normal animals may represent a pathogenic mechanism or a phenotypic marker of predisposition to atherogenesis.
An improved dynamic power distribution control scheme for PWM controlled converter modules (2003)

PWM gain scheduling control is applied to a load-sharing system driven by different line sources whose voltages vary over a wide range. This system can distribute total output current among converter modules with various current ratings. The large-signal behavior of such a system is verified, based primarily on computer simulation. Based on the small-signal analysis, the design procedure for the current and voltage error amplifiers is shown in detail. The system relative stability is investigated to ensure that the performance requirements are satisfied. It is pointed out that the loop-gain function in a multiple-loop system is not as useful as that in a single-loop system. In other words. the current and voltage error amplifiers or compensators need to be selected based on the system characteristic equation, which is uniquely defined for a system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hyperactive Antifreeze Protein from Winter Flounder Is a Very Long Rod-like Dimer of α-Helices (2005)

The winter flounder (Pseudopleuronectes americanus) produces short, monomeric alpha-helical antifreeze proteins (type I AFP), which adsorb to and inhibit the growth of ice crystals. These proteins alone are not sufficiently active to protect this fish against freezing at -1.9 degrees C, the freezing point of seawater. We have recently isolated a hyperactive antifreeze protein from the plasma of the flounder with activity 10-100-fold higher than type I AFP. It is comparable in activity to the AFPs produced by insects, and is capable of conferring freeze resistance to the flounder. This novel AFP has a molecular mass of 16,683 Da and a remarkable amino acid composition that is >60% alanine. CD spectra indicate that the protein is almost entirely alpha-helical at 4 degrees C but partially denatures at 20 degrees C, resulting in a species with a moderately reduced helix content that is stable at up to 50 degrees C. This transformation correlates with irreversible loss of activity. Analytical ultracentrifugation (sedimentation velocity and equilibrium) indicates that the predominant species in solution is dimeric (molecular weight, 32,275). Size-exclusion chromatography reveals a 2-fold higher apparent molecular weight suggesting that this molecule has an unusually large Stokes radius. The axial ratio of the dimer calculated from the sedimentation velocity data is 18:1, confirming that this protein has an extraordinarily long, rod-like structure, consistent with a novel dimeric alpha-helical arrangement. The structural model that best fits these data is one in which the approximately 195 amino acids of each monomer form one approximately 290-A long alpha-helix and associate via a unique dimerization motif that is distinct from that of the leucine zipper and any other coiled-coil.
The Magic of Duplicates and Aggregates (1990)

We present a formal treatment of multisets (that arise when duplicates are not eliminated) and aggregate operators for deductive and relational databases. We define the semantics rigorously and extend the magic-sets technique to programs containing multisets and aggregates. The work presented here is an important step in demonstrating the applicability of the magic-sets technique for optimizing queries in commercial query languages such as SQL.
Effectiveness of Diabetic Therapeutic Footwear in Preventing Reulceration (2004)

Therapeutic footwear has been used for decades as one of many strategies to prevent reulceration in patients with diabetes and foot risk factors. The findings of several studies reporting statistically significant protective effects from therapeutic footwear may have been influenced by several design issues. When considering the appropriateness of therapeutic footwear recommendations for moderate-risk patients, clinicians and patients should jointly explore individual strategies to decrease events that lead to foot ulcers.
Local Reflex Mechanisms: Influence on Basal Genioglossal Muscle Activation in Normal Subjects (1998)

Local, topical receptor mechanisms located in the nasopharynx importantly modulate upper airway dilator muscle activity in humans during normal tidal breathing. Therefore, the mechanisms exist for the airway to respond to local events which would tend to compromise airway patency.
ANTERIOR TRANSPERITONEAL LUMBAR FUSION (1971)

1. Anterior transperitoneal lumbar fusion is a successful method of stabilising painful mechanical derangements which have not responded to the usual conservative measures. 2. The operation in this series was done mainly for backache; it should not be contemplated if there is definite evidence of nerve root compression, because sequestrated disc material cannot be removed from the spinal canal from the anterior route. 3. Careful technique has resulted in few complications attributable to the operation. 4. This method is sometimes thought to be inapplicable in cases of spondylolisthesis with a displacement of more than one-third. However, in this series we have seen the block type of graft used with a good measure of clinical and radiological success. 5. There is no doubt that for those patients who have had previous unsuccessful laminectomies or posterior fusions anterior interbody fusion offers an excellent prospect of recovery.
Neural Summarization by Extracting Sentences and Words (2016)

Traditional approaches to extractive summarization rely heavily on humanengineered features. In this work we propose a data-driven approach based on neural networks and continuous sentence features. We develop a general framework for single-document summarization composed of a hierarchical document encoder and an attention-based extractor. This architecture allows us to develop different classes of summarization models which can extract sentences or words. We train our models on large scale corpora containing hundreds of thousands of document-summary pairs 1 . Experimental results on two summarization datasets demonstrate that our models obtain results comparable to the state of the art without any access to linguistic annotation.
Quantitative hopanoid analysis enables robust pattern detection and comparison between laboratories (2015)

Hopanoids are steroid-like lipids from the isoprenoid family that are produced primarily by bacteria. Hopanes, molecular fossils of hopanoids, offer the potential to provide insight into environmental transitions on the early Earth, if their sources and biological functions can be constrained. Semiquantitative methods for mass spectrometric analysis of hopanoids from cultures and environmental samples have been developed in the last two decades. However, the structural diversity of hopanoids, and possible variability in their ionization efficiencies on different instruments, have thus far precluded robust quantification and hindered comparison of results between laboratories. These ionization inconsistencies give rise to the need to calibrate individual instruments with purified hopanoids to reliably quantify hopanoids. Here, we present new approaches to obtain both purified and synthetic quantification standards. We optimized 2-methylhopanoid production in Rhodopseudomonas palustris TIE-1 and purified 2Me-diplopterol, 2Me-bacteriohopanetetrol (2Me-BHT), and their unmethylated species (diplopterol and BHT). We found that 2-methylation decreases the signal intensity of diplopterol between 2 and 34% depending on the instrument used to detect it, but decreases the BHT signal less than 5%. In addition, 2Me-diplopterol produces 10× higher ion counts than equivalent quantities of 2Me-BHT. Similar deviations were also observed using a flame ionization detector for signal quantification in GC. In LC-MS, however, 2Me-BHT produces 11× higher ion counts than 2Me-diplopterol but only 1.2× higher ion counts than the sterol standard pregnane acetate. To further improve quantification, we synthesized tetradeuterated (D4) diplopterol, a precursor for a variety of hopanoids. LC-MS analysis on a mixture of (D4)-diplopterol and phospholipids showed that under the influence of co-eluted phospholipids, the D4-diplopterol internal standard quantifies diplopterol more accurately than external diplopterol standards. These new quantitative approaches permit meaningful comparisons between studies, allowing more accurate hopanoid pattern detection in both laboratory and environmental samples.
Evidence for Colinearity among Genetic Linkage Maps in Cucumber (2007)

Cucumber ( Cucumis sativus L. var. sativus ; 2n = 2x = 14), has a narrow genetic base (3% to 8% polymorphism). Nevertheless, several genetic maps exist for this species. It is important to know the degree of colinearity among these maps. Thus, the positions of random amplified polymorphic DNAs, sequenced characterized amplified regions, simple sequence repeat, restriction fragment length polymorphisms, and fluorescent amplified fragment length polymorphism markers were compared in four maps. A previously unreported map was constructed in a narrow cross (processing line 2A × Gy8; C. s. var. sativus ; ≈7% polymorphism) and compared with the three published maps [two narrow-based (processing type; C. s. var. sativus ; 8% to 12% polymorphism) and a broad-based ( C. s. var. sativus × C. s. var. hardwickii (R.) Alef. ≈12%)]. Common makers were identified in seven linkage groups, providing evidence for microsynteny. These common markers were used as anchor markers for map position comparisons of yield component quantitative trait loci. The relative order of anchor markers in each of six linkage groups (linkage groups 1, 2, and 4–7) that had two or more anchor markers within each group was colinear, and instances of microsynteny were detected. Commonalities in the position of some yield component quantitative trait loci exist in linkage groups 1 and 4 of the maps examined, and the general synteny among these maps indicates that identification and mapping of additional anchor markers would lead to successful map merging to increase cucumber map saturation for use in cucumber breeding.
Large scale chemical synthesis, purification and crystallization of RNA-DNA chimeras (1992)

RNA-DNA chimeras, in which both DNA and RNA monomers are site-specifically substituted in the same strand, may be prepared only by chemical synthesis. Biochemical studies have revealed a number of surprising and subtle effects resulting from the insertion of either a ribonucleotide into a DNA strand or a deoxyribonucleotide into an RNA strand. The availability of large quantities of these chimeras allows for their crystallization and subsequent x-ray structure determination. We describe a flexible and efficient method for the large-scale preparation of these compounds, their purification, and their crystallization. The methodology is based on a combination of existing DNA phosphoramidite synthons and those recently introduced for the preparation of biochemically active RNA1. We demonstrate that these two different synthons are compatible, produce large quantities of nucleic acid needed for physical studies, and that high resolution diffraction quality crystals may be grown from these chimeras. Of the duplex chimeras synthesized and crystallized, [r(G)d(CGTATACGC)]2, [d(GCGT)r(A)d(TACGC)]2 and [r(GCG)d(TATACCC) + d(GGGTATACGC)] form A-helices and d(CG)r(CG)d(CG)]2 forms a left-handed Z-helix.