gebhart/patrepeval huggingface dataset:
Surface-Enhanced Raman Excitation Spectroscopy of a Single Rhodamine 6G Molecule (2008)

The surface-enhanced Raman excitation profiles (REPs) of rhodamine 6G (R6G) on Ag surfaces are studied using a tunable optical parametric oscillator excitation source and versatile detection scheme. These experiments afford the ability to finely tune the excitation wavelength near the molecular resonance of R6G (i.e., approximately 500-575 nm) and perform wavelength-scanned surface-enhanced Raman excitation measurements of a single molecule. The ensemble-averaged surface-enhanced REPs are measured for collections of molecules on Ag island films. The relative contributions of the 0-0 and 0-1 vibronic transitions to the surface-enhanced REPs vary with vibrational frequency. These results highlight the role of excitation energy in determining the resonance Raman intensities for R6G on surface-enhancing nanostructures. Single-molecule measurements are obtained from individual molecules of R6G on Ag colloidal aggregates, where single-molecule junctions are located using the isotope-edited approach. Overall, single-molecule surface-enhanced REPs are narrow in comparison to the ensemble-averaged excitation profiles due to a reduction in inhomogeneous broadening. This work describes the first Raman excitation spectroscopy studies of a single molecule, revealing new information previously obscured by the ensemble.
A Common Position-Dependent Mechanism Controls Cell-Type Patterning and GLABRA2 Regulation in the Root and Hypocotyl Epidermis of Arabidopsis1 (1998)

A position-dependent pattern of epidermal cell types is produced during root development in Arabidopsis thaliana. This pattern is reflected in the expression pattern of GLABRA2 (GL2), a homeobox gene that regulates cell differentiation in the root epidermis. GL2 promoter::GUS fusions were used to show that the TTG gene, a regulator of root epidermis development, is necessary for maximal GL2 activity but is not required for the pattern of GL2 expression. Furthermore, GL2-promoter activity is influenced by expression of the myc-like maize R gene (35S::R) in Arabidopsis but is not affected by gl2 mutations. A position-dependent pattern of cell differentiation and GL2-promoter activity was also discovered in the hypocotyl epidermis that was analogous to the pattern in the root. Non-GL2-expressing cell files in the hypocotyl epidermis located outside anticlinal cortical cell walls exhibit reduced cell length and form stomata. Like the root, the hypocotyl GL2 activity was shown to be influenced by ttg and 35S::R but not by gl2. The parallel pattern of cell differentiation in the root and hypocotyl indicates that TTG and GL2 participate in a common position-dependent mechanism to control cell-type patterning throughout the apical-basal axis of the Arabidopsis seedling.
Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA (1998)

Many examples of extreme virus resistance and posttranscriptional gene silencing of endogenous or reporter genes have been described in transgenic plants containing sense or antisense transgenes. In these cases of either cosuppression or antisense suppression, there appears to be induction of a surveillance system within the plant that specifically degrades both the transgene and target RNAs. We show that transforming plants with virus or reporter gene constructs that produce RNAs capable of duplex formation confer virus immunity or gene silencing on the plants. This was accomplished by using transcripts from one sense gene and one antisense gene colocated in the plant genome, a single transcript that has self-complementarity, or sense and antisense transcripts from genes brought together by crossing. A model is presented that is consistent with our data and those of other workers, describing the processes of induction and execution of posttranscriptional gene silencing.
Canonical Inhibitor-like Interactions Explain Reactivity of α1-Proteinase Inhibitor Pittsburgh and Antithrombin with Proteinases (2003)

The serpin antithrombin is a slow thrombin inhibitor that requires heparin to enhance its reaction rate. In contrast, alpha1-proteinase inhibitor (alpha1PI) Pittsburgh (P1 Met --> Arg natural variant) inhibits thrombin 17 times faster than pentasaccharide heparin-activated antithrombin. We present here x-ray structures of free and S195A trypsin-bound alpha1PI Pittsburgh, which show that the reactive center loop (RCL) possesses a canonical conformation in the free serpin that does not change upon binding to S195A trypsin and that contacts the proteinase only between P2 and P2'. By inference from the structure of heparin cofactor II bound to S195A thrombin, this RCL conformation is also appropriate for binding to thrombin. Reaction rates of trypsin and thrombin with alpha1PI Pittsburgh and antithrombin and their P2 variants show that the low antithrombin-thrombin reaction rate results from the antithrombin RCL sequence at P2 and implies that, in solution, the antithrombin RCL must be in a similar canonical conformation to that found here for alpha1PI Pittsburgh, even in the nonheparin-activated state. This suggests a general, limited, canonical-like interaction between serpins and proteinases in their Michaelis complexes.
Production of polyhydroxyalkanoates in sucrose-utilizing recombinant Escherichia coli and Klebsiella strains (1994)

The cloned poly-3-hydroxybutyrate (PHB) synthesis pathway from Alcaligenes eutrophus has been introduced into sucrose-utilizing strains of Escherichia coli, Klebsiella aerogenes, and Klebsiella oxytoca. The plasmid-borne genes were well expressed in these environments and were able to mediate the production of significant amounts of PHB when the bacteria were grown with sucrose as the sole carbon source. The molecular weight of the PHB polymer made in K. aerogenes and E. coli was approximately 1 x 10(6) to 2 x 10(6). Sucrose uptake in K. aerogenes was measured and found to be similar to that found for other Klebsiella strains, but sucrose uptake in the E. coli strain was not detectable. K. aerogenes is able to utilize sugarcane molasses as the sole carbon source to accumulate PHB at the rate of approximately 1 g of PHB per liter of culture fluid per h. A K. oxytoca fadR strain was able to incorporate 3-hydroxyvalerate into a poly-(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-co-V) polymer to levels as high as 56 mol% when grown in a medium containing propionate. Total PHB-co-V levels could be enhanced by adding propionate at the beginning of stationary phase rather than at the time of inoculation.
Nanoparticle-Based Immunotherapy for Cancer (2014)

The design of nanovaccines capable of triggering effective antitumor immunity requires an understanding of how the immune system senses and responds to threats, including pathogens and tumors. Equally important is an understanding of the mechanisms employed by tumor cells to evade immunity and an appreciation of the deleterious effects that antitumor immune responses can have on tumor growth, such as by skewing tumor cell composition toward immunologically silent tumor cell variants. The immune system and tumors engage in a tug-of-war driven by competition where promoting antitumor immunity or tumor cell death alone may be therapeutically insufficient. Nanotechnology affords a unique opportunity to develop therapeutic compounds than can simultaneously tackle both aspects, favoring tumor eradication. Here, we review the current status of nanoparticle-based immunotherapeutic strategies for the treatment of cancer, ranging from antigen/adjuvant delivery vehicles (to professional antigen-presenting cell types of the immune system) to direct tumor antigen-specific T-lymphocyte-targeting compounds and their combinations thereof.
Role of alginate lyase in cell detachment of Pseudomonas aeruginosa (1994)

The exopolysaccharide alginate of Pseudomonas aeruginosa was shown to be important in determining the degree of cell detachment from an agar surface. Nonmucoid strain 8822 gave rise to 50-fold more sloughed cells than mucoid strains 8821 and 8830. Alginate anchors the bacteria to the agar surface, thereby influencing the extent of detachment. The role of the P. aeruginosa alginate lyase in the process of cell sloughing was investigated. Increased expression of the alginate lyase in mucoid strain 8830 led to alginate degradation and increased cell detachment. Similar effects were seen both when the alginate lyase was induced at the initial stage of cell inoculation and when it was induced at a later stage of growth. It appears that high-molecular-weight alginate polymers are required to efficiently retain the bacteria within the growth film. When expressed from a regulated promoter, the alginate lyase can induce enhanced sloughing of cells because of degradation of the alginate. This suggests a possible role for the lyase in the development of bacterial growth films.
Equine infectious anemia virus and human immunodeficiency virus DNA synthesis in vitro: characterization of the endogenous reverse transcriptase reaction (1991)

The endogenous reverse transcriptase reaction of equine infectious anemia virus (EIAV) has been studied, and conditions allowing synthesis of full-length minus-strand DNA have been determined. In contrast to results reported for other retroviruses, synthesis of EIAV full-length minus-strand DNA was not impaired by high concentrations of Nonidet P-40, a nonionic detergent used to make the virion envelope permeable. All components of the reaction were titrated for maximum synthesis of complete minus strands, and a time course under the standardized conditions was determined. Minor subgenomic bands were observed in some cases, and both the size and proportion varied with reaction conditions. Conditions established for full-length EIAV DNA synthesis also allowed full-genome-length human immunodeficiency virus type 1 DNA synthesis. The human immunodeficiency virus type 1 DNA product contained a greater proportion of reverse transcripts that were shorter than the complete virus genome. Also in contrast to EIAV, the endogenous synthesis of high-molecular-weight human immunodeficiency virus type 1 DNA was drastically reduced at Nonidet P-40 concentrations above 0.02%. These results indicated that a detergent-stable core is not a property shared by all lentiviruses. The EIAV virion synthetic machinery is unusually stable and provides a convenient system for further in vitro study of reverse transcription.
New NRD guide oscillator (2005)

A new millimeter-wave Gunn oscillator is described. The present structure makes use of NRD guide and metal resonant cap. Some experimental results of 8mm and 6mm guide oscillators show that the new Gunn oscillator has a future as an integrated millimeter-wave source.
Integration of Multianalyte Sensing Functions on a Capillary-Assembled Microchip:  Simultaneous Determination of Ion Concentrations and Enzymatic Activities by a “Drop-and-Sip” Technique (2006)

A general and simple implementation of simultaneous multiparametric sensing in a single microchip is presented by using a capillary-assembled microchip (CAs-CHIP) integrated with the plural different reagent-release capillaries (RRCs), acting as various biochemical sensors. A novel "drop-and-sip" technique of fluid handling is performed with a microliter droplet of a model sample solution containing proteases (trypsin, chymotrypsin, thrombin, elastase) and divalent cations (Ca2+, Zn2+, Mg2+) that passes through the microchannel with the aid of a micropipette as a vacuum pump, concurrently filling each RRC via capillary force. To avert the evaporation of the nanoliter sample volume in each capillary, PDMS oil is dropped on the outlet hole of the CAs-CHIP exploiting the capillary force that results in spontaneous sealing of all the RRCs. In addition, this high-speed sample introduction alleviates the possibility of protein adsorption and capillary cross-contamination, allowing a reliable and multianalyte determination of a sample containing many different proteases and divalent cations by using the fluorescence image analysis. Presented results suggested the possible application of this microchip in the field of drug discovery and systems biology.
Wide‐angle film diffuser (2007)

Abstract— A unique roll‐to‐roll mass‐producible high‐transmission wide‐angle diffuser (WAD™) film for use in LCD backlights is reported. WAD™ diffuser films include optical structures that efficiently manage forward light scattering and significantly reduces backward light scattering. WAD™ technology facilitates backlights with significantly higher brightness and thinner backlight profiles.
Elevated levels of connective tissue growth factor, WISP-1, and CYR61 in primary breast cancers associated with more advanced features. (2001)

To gain insight into the role of the CCN genes in human breast carcinomas, we quantified connective tissue growth factor (CTGF), WISP-1, CYR61, and human NOV (NOVH) mRNA expression levels in samples from 44 primary breast tumors and seven normal breasts using quantitative real-time PCR assay. Overexpression of CTGF, WISP-1, CYR61, and NOVH was found in 55 (24 of 44), 46 (20 of 44), 39 (17 of 44), and 11% (5 of 44) primary breast tumors, respectively. Statistical univariate analysis was performed to explore the links between expression of the CCN genes and clinical and pathological parameters. Interestingly, significant associations were found between CTGF expression versus stage, tumor size, lymph node status, and age at diagnosis; WISP-1 mRNA levels versus stage, tumor size, lymph node, and HER-2/neu overexpression; and CYR61 expression with stage, tumor size, lymph node, age, and estrogen receptor expression. In contrast to CTGF, WISP-1, and CYR61, no significant correlation was found between NOVH expression and any of the clinical and pathological factors. Furthermore, multivariate classification tree model analysis showed that stage and lymph node involvement were important for predicting CTGF expression in breast cancers; the stage, age, and HER-2/neu status were key factors for WISP-1 expression; and the stage, age, and estrogen receptor were valuable predictors for CYR61 expression. In summary, these results suggest that CTGF, WISP-1, and CYR61 may play a role in the progression of breast cancer and might serve as a valuable tool for monitoring tumor status of breast cancer patients.
Inhibition of Leaf Senescence by Autoregulated Production of Cytokinin (1995)

Controlling expression of IPT , a gene encoding isopentenyl transferase (the enzyme that catalyzes the rate-limiting step in cytokinin biosynthesis), with a senescence-specific promoter results in the suppression of leaf senescence. Transgenic tobacco plants expressing this chimeric gene do not exhibit the developmental abnormalities usually associated with IPT expression because the system is autoregulatory. Because sufficient cytokinin is produced to retard senescence, the activity of the senescence-specific promoter is attenuated. Senescence-retarded leaves exhibit a prolonged, photosynthetically active life-span. This result demonstrates that endogenously produced cytokinin can regulate senescence and provides a system to specifically manipulate the senescence program.
Changes in Salicylic Acid and Antioxidants during Induced Thermotolerance in Mustard Seedlings (1998)

Heat-acclimation or salicylic acid (SA) treatments were previously shown to induce thermotolerance in mustard (Sinapis alba L.) seedlings from 1.5 to 4 h after treatment. In the present study we investigated changes in endogenous SA and antioxidants in relation to induced thermotolerance. Thirty minutes into a 1-h heat-acclimation treatment glucosylated SA had increased 5.5-fold and then declined during the next 6 h. Increases in free SA were smaller (2-fold) but significant. Changes in antioxidants showed the following similarities after either heat-acclimation or SA treatment. The reduced-to-oxidized ascorbate ratio was 5-fold lower than the controls 1 h after treatment but recovered by 2 h. The glutathione pool became slightly more oxidized from 2 h after treatment. Glutathione reductase activity was more than 50% higher during the first 2 h. Activities of dehydroascorbate reductase and monodehydroascorbate reductase decreased by at least 25% during the first 2 h but were 20% to 60% higher than the control levels after 3 to 6 h. One hour after heat acclimation ascorbate peroxidase activity was increased by 30%. Young leaves appeared to be better protected by antioxidant enzymes following heat acclimation than the cotyledons or stem. Changes in endogenous SA and antioxidants may be involved in heat acclimation.
Introducing Colorimetric Analysis with Camera Phones and Digital Cameras: An Activity for High School or General Chemistry (2013)

A common task in chemistry is the determination of concentration of unknown compounds. The Beer–Lambert law, also commonly referred to as Beer’s law, enables the quantitation of the concentration of an absorbing analyte in solution. Results from experiments using solutions of blue food dye, lemon–lime sports drink, and iron(III) chloride demonstrated that absorbance versus concentration data are linear for data collected using digital cameras and camera phones. The key to obtaining reliable data is collecting a single image of samples, standards, and blanks arranged in front of a uniform light source, such as a light box or a computer screen. The approach provides a facile method for performing colorimetric analysis in a wide range of settings, from the high school chemistry laboratory, in the field, and the research laboratory.
Reactions of 4-Methyl-1,3-pentadiene1,2 (1944)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of 4-Methyl-1,3-pentadiene1,2G. Bryant Bachman and Roger E. HattonCite this: J. Am. Chem. Soc. 1944, 66, 9, 1513–1514Publication Date (Print):September 1, 1944Publication History Published online1 May 2002Published inissue 1 September 1944https://pubs.acs.org/doi/10.1021/ja01237a029https://doi.org/10.1021/ja01237a029research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Genomics and Proteomics in Reverse Vaccines (2005)

This chapter contains sections titled: Problem of Orphan Vaccine Infectious Diseases Change of Paradigm: Reverse Vaccinology Examples of Reverse Vaccines Additional Gene Selection Criteria in Reverse Vaccinology: Role of Transcriptomics and Proteomics Conclusions References
Age‐Dependent Vulnerability of the Striatum to the Mitochondrial Toxin 3‐Nitropropionic Acid (1993)

The mechanisms of delayed onset and cell death in Huntington's disease (HD) are unknown. One possibility is that a genetic defect in energy metabolism may result in slow excitotoxic neuronal death. Therefore, we examined the effects of age on striatal lesions produced by local administration of the mitochondrial toxin 3-nitropropionic acid in rats. In vivo chemical shift magnetic resonance imaging showed marked increases in striatal lactate concentrations that significantly correlated with increasing age. Histologic and neurochemical studies showed a striking age dependence of the lesions, with 4- and 12-month-old animals being much more susceptible than 1-month-old animals. Continuous systemic administration of low doses of 3-nitropropionic acid for 1 month resulted in striatal lesions showing growth-related changes in dendrites of striatal spiny neurons using the Golgi technique. These results show that a known mitochondrial toxin can produce selective axon-sparing striatal lesions showing both the age dependence and striatal spiny neuron dendritic changes that characterize HD.
Examination of the Matrix Isolation Fourier Transform Infrared Spectra of Organic Compounds, Part I (1987)

Data are presented that describe the IR spectra of organic compounds obtained under matrix isolation conditions. Among the types of compounds examined are amides, lactones, lactams, esters, acids, alcohols, and phenols. Trends, as a function of structure, established in vapor-phase IR are shown to exist under MI conditions. The frequency (cm −1 ) of the stretching absorption for hydroxyl groups and carbonyl groups associated with the types of compounds listed above under MI conditions is shown to be intermediate between the vapor-phase position (highest energy) and the solid-solution position (lowest energy). In some cases the three phases differ by as much as 300 cm −1 (OH group in carboxylic acids) and by as little as 15 cm −1 (carbonyl group in carboxylic acid esters).
Hybrid positioning system combining angle-based localization, pedestrian dead reckoning and map filtering (2010)

We present a hybrid indoor positioning solution combining angle-based localization, pedestrian dead reckoning, and map filtering. The angle-based localization system provides absolute location estimates, whereas pedestrian dead reckoning (PDR) results in accurate shape and length of the traversed route without absolute location and heading information. PDR movement and angle-based location estimates are fused together with a building vector map in a fusion filter, which in this study is implemented through a particle filter. When the fusion filter has been initialized with absolute position data and has converged, it can run also on PDR and map filtering, independently of the angle-based localization system, in areas that are not illuminated by multi-antenna arrays. In principle the same fusion design could accommodate location estimates also from other positioning sources, for example WiFi, or GPS in outdoor-to-indoor transitions. By combining information from various positioning modalities, different types of indoor environments can be provided with seamless positioning coverage with reasonable accuracy and infrastructural investments.