gebhart/patrepeval huggingface dataset:
The DNA replication origins of herpes simplex virus type 1 strain Angelotti (1986)

The nucleotide sequences of the origins of DNA replication (ori) of the S- and L-component (oriS, oriL) of the herpes simplex virus type 1 (HSV-1) standard genome were determined from HSV-1 strain Angelotti (ANG). In contrast to other HSV-1 strains, the ANG oriS sequence revealed an insertion of an TA-dinucleotide in an otherwise very conserved but imperfect palindromic sequence of 47 bp. The oriL sequence of the standard ANG genome was found to be identical to that of an ANG class II defective genome which exhibits a duplication of a 144 bp palindrome. A model is presented to explain the origination of the amplified ANG oriL sequences from the parental genome with a single copy of oriL via illegitimate recombination. Alignment of the ori sequences of HSV, adeno- and papovaviruses unveiled that the HSV ori region can be subdivided into two distinct sites of homology to the DNA initiation signals of papova- and adenoviruses, suggesting that the HSV origins of replication comprise elements for DNA replication by both, cellular and virus-encoded DNA polymerases.
The immunohistochemical aspects of protein Mena in cervical lesions. (2009)

We observed that Mena was not expressed in the normal cervical squamous epithelium but its expression was increased in parallel with the increasing grade of CIN, with up-regulation upon transition to CIN3 and further to invasive carcinoma. This is the first study in the literature about Mena expression in cervical lesions.
Slab-Coupled Waveguides (1974)

The slab-coupled waveguide, consisting of a dielectric rod lying on a slab that in turn covers a substrate, is a multidielectric waveguide that includes such special cases as the single-material fiber, the rib waveguide, and the strip-loaded film guide. These guides have recently become known as potentially useful either for long-distance optical transmission or for integrated optics. Simple, closed-form, approximate solutions have been found to describe the following properties of the guide: number of modes, their field configurations and propagation constants, numerical aperture, requirements for single-mode operation, field penetration in the slab, tolerance to curvature of the guide axis, dispersion, and impulse response.
Nanopore-Based Target Sequence Detection (2016)

The promise of portable diagnostic devices relies on three basic requirements: comparable sensitivity to established platforms, inexpensive manufacturing and cost of operations, and the ability to survive rugged field conditions. Solid state nanopores can meet all these requirements, but to achieve high manufacturing yields at low costs, assays must be tolerant to fabrication imperfections and to nanopore enlargement during operation. This paper presents a model for molecular engineering techniques that meets these goals with the aim of detecting target sequences within DNA. In contrast to methods that require precise geometries, we demonstrate detection using a range of pore geometries. As a result, our assay model tolerates any pore-forming method and in-situ pore enlargement. Using peptide nucleic acid (PNA) probes modified for conjugation with synthetic bulk-adding molecules, pores ranging 15-50 nm in diameter are shown to detect individual PNA-bound DNA. Detection of the CFTRΔF508 gene mutation, a codon deletion responsible for ∼66% of all cystic fibrosis chromosomes, is demonstrated with a 26-36 nm pore size range by using a size-enhanced PNA probe. A mathematical framework for assessing the statistical significance of detection is also presented.
Potter's Wheel: An Interactive Data Cleaning System (2001)

Cleaning data of errors in structure and content is important for data warehousing and integration. Current solutions for data cleaning involve many iterations of data “auditing ” to find errors, and long-running transformations to fix them. Users need to endure long waits, and often write complex transformation scripts. We present Potter’s Wheel, an interactive data cleaning system that tightly integrates transformation and discrepancy detection. Users gradually build transformations to clean the data by adding or undoing transforms on a spreadsheet-like interface; the effect of a transform is shown at once on records visible on screen. These transforms are specified either through simple graphical operations, or by showing the desired effects on example data values. In the background, Potter’s Wheel automatically infers structures for data values in terms of user-defined domains, and accordingly checks for constraint violations. Thus users can gradually build a transformation as discrepancies are found, and clean the data without writing complex programs or enduring long delays. 1
Adaptive mesh generation for global diffuse illumination (1990)

Rapid developments in the design of algorithms for rendering globally illuminated scenes have taken place in the past five years. Net energy methods such as the hemicube and other radiosity algorithms have become very effective at computing the energy balance for scenes containing diffusely reflecting objects. Such methods first break up a scene description into a relatively large number of elements, or possibly several levels of elements. Energy transfers among these elements are then determined using a variety of means. While much progress has been made in the design of energy transfer algorithms, little or no attention has been paid to the proper generation of the mesh of surface elements. This paper presents a technique for adaptively creating a mesh of surface elements as the energy transfers are computed. The method allows large numbers of small elements to be placed at parts of the scene where the most active energy transfers occur without requiring that other parts of the scene be needlessly subdivided to the same degree. As a result, the computational effort in the energy transfer computations can be concentrated where it has the most effect.
Dynamically reconfigurable nanoscale modulators utilizing coupled hybrid plasmonics (2015)

The balance between extinction ratio (ER) and insertion loss (IL) dictates strict trade-off when designing travelling-wave electro-optic modulators. This in turn entails significant compromise in device footprint (L3dB) or energy consumption (E). In this work, we report a nanoscale modulator architecture that alleviates this trade-off while providing dynamic reconfigurability that was previously unattainable. This is achieved with the aide of three mechanisms: (1) Utilization of epsilon-near-zero (ENZ) effect, which maximizes the attainable attenuation that an ultra-thin active material can inflict on an optical mode. (2) Non-resonant coupled-plasmonic structure which supports modes with athermal long-range propagation. (3) Triode-like biasing scheme for flexible manipulation of field symmetry and subsequently waveguide attributes. By electrically inducing indium tin oxide (ITO) to be in a local ENZ state, we show that a Si/ITO/HfO2/Al/HfO2/ITO/Si coupled-plasmonic waveguide can provide amplitude modulation with ER = 4.83 dB/μm, IL = 0.03 dB/μm, L3dB = 622 nm, and E = 14.8 fJ, showing at least an order of magnitude improvement in modulator figure-of-merit and power efficiency compared to other waveguide platforms. Employing different biasing permutations, the same waveguide can then be reconfigured for phase and 4-quadrature-amplitude modulation, with actively device length of only 5.53 μm and 17.78 μm respectively.
Social Learning and Innovation in Hunter-Gatherers (2016)

This chapter provides an introduction to social learning and innovation in hunter-gatherers, summarizes major theoretical orientations on from whom and how children learn from others, and highlights new results from chapters in the book.
Evaluating three museum installations of a hypertext system (1989)

This study explores the use of a hypertext system by patrons of three museums. Data on the articles accessed, the time spent in each, the number of times the index was accessed, etc., were collected from a total of more than 5000 sessions. Results show that visitors at all three museums used the embedded menus of the Hyperties hypertext system in moving from one article to another far more than the traditional index. Article selection appears to reflect anticipated interests of patrons at each museum suggesting success in traversing the database. At the third museum, the data collection was complemented by direct observation and interviews of the museum patrons. This last approach appears to be more appropriate to analyze the usage data as well as to improve the user interface and database structure. © 1989 John Wiley & Sons, Inc.
The geographical patterns of Chinese liquors during 1995–2004 (2017)

Chinese liquors come from a variety of different regions in China. This diversity can be attributed to the difference in microorganisms, but also to the biophysical environment. The latter constitutes a significant basis for the fermentation of products, but has not been adequately understood. Using spatial statistics analysis, we studied the causes of regional differences of Chinese liquors in the perspective of climatic and socio-economic environment. Temporal changes in the density of Chinese liquor manufacturers in each prefecture-level administrative unit from1995 to 2004 revealed no changes in spatio-temporal distribution patterns of Chinese liquors. Most manufacturers were distributed in moderate climatic regions in both developed areas and less developed areas. Socio-economic factors had a significantly positive impact on the development of the Chinese liquor industry, while the climatic environment plays a crucial role in determining their difference a regional scale. Overall, this study provided scientific evidence for the importance of the biophysical environments, especially climate, to determine the geographical patterns of fermentation products.
Improved Synthesis of 2′-Amino-LNA (2003)

2'-Amino-LNA phosphoramidite (10) was synthesised by means of a new strategy, which is convergent with the synthesis of 2'-oxy-LNA up until a late stage intermediate (1).
Transition Metal Chelators Reduce Directly Measured Myocardial Free Radical Production During Reperfusion (1998)

Transition metals such as iron and copper are present in the myocardium and can act as catalysts for the formation of oxygen free radicals during reperfusion after myocardial ischemia. Previous studies suggested that transition metal chelators such as desferrioxamine reduce the production of such radicals and may thereby attenuate postischemic myocardial dysfunction. These studies used spin trapping agents, commonly nitrone compounds, which may themselves influence the severity of the ischemia and reperfusion events being studied. We evaluated two transition metal chelators, desferrioxamine, an iron chelator, and bathocuproine, a copper chelator, by using a new electron paramagnetic resonance technique that does not require the administration of spin traps. We measured ascorbate free radical, an index of free radical production, in the great cardiac vein effluent. Twenty-eight open-chest dogs underwent 20 min of coronary artery occlusion and 30 min of reperfusion. Ten dogs received no drug, 10 dogs received 750 mg bathocuproine, i.v., and eight dogs received 700 mg desferrioxamine, i.v. Both bathocuproine and desferrioxamine blunted the postreperfusion increase in ascorbate free radical generation: no drug, 36+/-8% increase; desferrioxamine, 13+/-5% increase; bathocuproine, 21+/-6% increase (p < 0.05 vs. baseline). Thus direct free radical measurements indicate that chelation of the transition metals iron and copper reduces free radical generation during reperfusion.
Compact far ultraviolet emission source with rich spectral emission 1150–3100 Å (1977)

A new compact far uv emission source suitable for laboratory or space applications is described. The source is small, rugged, lightweight, spectrally rich, and bright in the 1150-3200-A region. It has met rigid spacecraft environmental tests and also is a very useful transfer standard for absolute sensitivity calibrations of spectrometric instruments.
Zinc-Catalyzed Cycloisomerizations. Synthesis of Substituted Furans and Furopyrimidine Nucleosides (2008)

5-Endo-dig cycloisomerization of 1,4- and 1,2,4- mostly aryl-substituted but-3-yn-1-ones in the presence of a catalytic amount of zinc chloride etherate (10 mol %) in dichloromethane at room temperature gave 2,5-di- and 2,3,5-trisubstituted furans in high yields (85-97%). DSC studies confirmed that a solely thermal process does not take place. A relevant catalytic process, employing mu-oxo-tetranuclear zinc cluster Zn4(OCOCF3)6O, yielded bicyclic furopyrimidine nucleosides, when starting from acetyl-protected 5-alkynyl-2'-deoxyuridines (85-86%). Furopyrimidine was deprotected or simultaneously converted into pyrrolopyrimidine nucleoside. The time/concentration dependence for the reaction of 1-phenyl-4-(4-methylphenyl)butynone to 2-(4-methylphenyl)-5-phenylfuran displayed first-order kinetics with the rate dependent on catalyst concentration. The plot of ln k(obs) versus ln[ZnCl2] indicated first-order cycloisomerization, as referred to ZnCl2 concentration, using both NMR and UV-vis reaction monitoring. The crystal structure of propyl furopyrimidine nucleoside (orthorhombic, P2(1)2(1)2(1), a/b/c = 5.684(2)/6.682(2)/36.02(2) A, Z = 4) shows C2'- endo deoxyribose puckering, and the base is found in the anti position in crystalline form.
DNA triple‐helix formation: An approach to artificial gene repressors? (1992)

Certain sequences of double-helical DNA can be recognized and tightly bound by oligonucleotides. The effects of such triple-helical structures on DNA binding proteins have been studied. Stabilities of DNA triple-helices at or near physiological conditions are sufficient to inhibit DNA binding proteins directed to overlapping sites. Such proteins include restriction endonucleases, methylases, transcription factors, and RNA polymerases. These and other results suggest that oligonucleotide-directed triple-helix formation could provide the basis for designing artificial gene repressors. The general question of whether biological systems employ RNA molecules for recognition and regulation of double-helical DNA is discussed.
Coexpression of the partial androgen receptor enhances the efficacy of prostate-specific antigen promoter-driven suicide gene therapy for prostate cancer cells at low testosterone concentrations. (2001)

The prostate specific antigen (PSA) promoter/enhancer has been clearly demonstrated to be tissue specific, and has been applied to prostate-specific gene therapy. However, the transcription of the PSA gene is strictly androgen dependent, and its promoter activity is very weak at low concentrations of testosterone, which are generally observed in prostatic cancer patients treated with androgen deprivation. In this study, we used a partial androgen receptor (ARf) containing amino acids 232-429 and 481-657 to transactivate the PSA gene without androgens. We made two expression vectors, ARfPPLUC and ARfPPTK. They contained ARf cDNA driven by cytomegalovirus promoter and cDNAs of either firefly luciferase (LUC) or herpes simplex virus thymidine kinase (TK) driven by PSA promoter/enhancer (PP). The expressed ARf enhanced the PP activity by about 110-fold in the PSA-producing prostate cancer cell line, LNCaP, under low testosterone concentrations. Moreover, in a PSA-nonproducing prostate cancer cell line, DU145, ARf also enhanced the PP activity by about 60-fold in an androgen-independent manner. In a growth inhibition assay, ARfPPTK treated with ganciclovir was found to inhibit the cell growth of LNCaP cells much more effectively than PPTK. Furthermore, in contrast to PPTK, ARfPPTK also had an inhibitory effect on DU145 cells. This system is thus considered to provide a useful therapeutic option in patients with prostate cancer who are receiving hormonal therapy.
Capillarity‐Driven Assembly of Carbon Nanotubes on Substrates into Dense Vertically Aligned Arrays (2007)

Carbon nanotubes are assembled into dense, vertically aligned arrays on substrates by using capillary forces. Modulating the interactions between the nanotubes and the underlying substrate provides control over the assembly of the nanotube array; capillary forces can either cause bending (left) or translation (right) of the nanotube array. The use of this densification strategy enables a four-fold increase in current density through nanotube arrays. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2007/c2883_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Overlapping sequential pulses. A new waveform for transthoracic defibrillation. (1994)

Sequential overlapping pulse shock waveforms facilitate defibrillation compared with single pulse shocks of the same total energy. This is due at least in part to the changing orientation of the electrical vector during the multiple pulse shock.
Angiogenic Factors (1987)

Within the past 2 years, several angiogenic factors have been fully purified, their amino acid sequences determined, and their genes cloned. These polypeptides include acidic and basic fibroblast growth factor, angiogenin, and transforming growth factors alpha and beta. Other less well characterized angiogenesis factors have also been isolated, some of which are lipids. This article traces the discovery of the angiogenic factors and describes their possible significance in understanding growth regulation of the vascular system. When evaluated according to their putative targets, they appear to fall into two groups: those that act directly on vascular endothelial cells to stimulate locomotion or mitosis, and those that act indirectly by mobilizing host cells (for example, macrophages) to release endothelial growth factors. In addition to their presence in tumors undergoing neovascularization, the same angiogenic peptides are found in many normal tissues where neovascularization is not occurring. This suggests that physiological expression of angiogenic factors is tightly regulated. In addition to the persistent angiogenesis induced by tumors, it now appears that a variety of nonneoplastic diseases, previously thought to be unrelated, can be considered as "angiogenic diseases" because they are dominated by the pathologic growth of capillary blood vessels.
Synthesis and in vitro activity of a new carbapenem, RS-533. (1983)

The synthesis and in vitro antimicrobial activity of a new synthetic carbapenem, (5R,6S)-6-[(R)-1-hydroxyethyl]-2-[(S)-1-acetimidoylpyrrolidin -3-ylthio]-1-carbapen-2-em-3-carboxylic acid (RS-533), are described. The MIC values of related penems and carbapenems are also given for comparison with those of the new carbapenem.
Large-scale prediction of phenotype: Concept (2000)

The capability to gather organism wide data has far outstripped the ability to understand it. Transforming large-scale data into a "better" cell requires tools that integrate physiology with its environment. One such tool is large-scale mathematical models that marry stoichiometry and kinetics with metabolic regulation and control. It is straightforward to determine stoichiometry (at least for central pathways), and kinetics can be roughly approximated where need be. However, the molecular details of the "metabolic wiring" managing the cell are often missing. Presented here is a surrogate for these missing details based on a simple premise; over evolutionary time, biological systems have developed objective-based programs that frugally manage gene expression and enzyme activity. Mathematically, this notion can be represented as sets of nonlinear control or "management" problems which, when solved in parallel with the model balances, offer a prediction of how gene expression and enzyme activity are modulated, in the absence of specific mechanistic details. We present a model of Escherichia coli central carbon metabolism, describing batch aerobic growth on glucose, in which transcription, translation, and activity of the gene products of 45 genes is "managed" using this approach. The model consists of 122 species (metabolites, enzymes, mRNA pools, and biomass) and describes 46 reactions (17 reversible). The model is identified (kinetic parameters as well as management structure) from metabolic flux ratio (METAFoR) analysis and physiological measurements. Simulations of a pyruvate kinase knockout strain are compared with experiments and it is shown the model is capable of accurately capturing the metabolic reprogramming resulting from the deletion. Analysis of the mRNA expression pattern, translational pattern and enzyme activity pattern of the wild-type versus mutant indicates a combination of expression and specific activity shifts are responsible for observed differences. While being only a first step toward large-scale physiological modeling, this work is important in two ways. First, it strengthens the hypothesis that unknown mechanism can be reasonably approximated using objective-based management criteria. Second, it provides a dynamic means to couple large-scale analysis technologies with physiology at the single-gene, single-protein level.
Site specific constraints on shell selection behavior in the hermit crab,Clibanarius vittatus (1992)

Site‐specific constraints on shell selection behavior in the hermit crab Clibanarius vittatus were studied with both laboratory and field experiments at two sites along the Louisiana coast. At both sites, crabs selected larger Stramonita haemastoma shells in field experiments. Although discarded shells were often no smaller than selected shells, they did show heavy damage by predators. Crabs in both populations inhabited shells that were on average larger than those of living 5. haemastoma as well as those discarded in experiments. Although these results suggest that larger, undamaged shells may be a limiting resource, crabs collected from a site with few intermediate sized 5. haemastoma actually selected smaller shells in the laboratory. Clibanarius vittatus also selected the stronger, higher spired shell of S. haemastoma over Polinices duplicatus in both laboratory and field experiments, suggesting predation risk plays a role in shell choice. Although crabs in P. duplicatus shells were no more vulnerable in laboratory experiments to the stone crab, Menippe adina, they may be more vulnerable to other, less effective predators, or prone to dessication stress. Taken together, these results suggest that site‐specific constraints on shell selection behavior exist. Size preferences may depend on the size distributions and dynamics of gastropods, or the predators that produce empty gastropod shells. Sites with higher abundances of crabs may also have a higher fraction of individuals forced to occupy less preferred shells like P. duplicatus. These site‐specific constraints may be just as important as differences in shell architecture in explaining shell use patterns.
Short in-fibre Bragg grating structure for simultaneous measurement of strain and temperature (2005)

The study of a single short length Bragg grating for sensing applications is presented. The dependences of the central wavelength, reflected optical power and spectral width of a 250 &mu;m length grating on strain and temperature are analyzed. The obtained results indicate the feasibility of this novel sensing head for simultaneous measurement of strain and temperature.