gebhart/patrepeval huggingface dataset:
Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis. (2006)

The identification of genes affected by cross-hybridization of mouse liver RNA on human oligonucleotide microarrays makes it feasible to use functional genomics approaches to study the chimeric SCID-beige/Alb-uPA mouse model of HCV infection. This approach used to study cross-species hybridization on oligonucleotide microarrays can be adapted to other chimeric systems of viral disease to facilitate selective analysis of human gene expression.
<title>Photorefractive beamsplitter for free-space optical interconnection systems</title> (1997)

A photorefractive beamsplitter (PRBS) is introduced as an alternative to a polarizing beamsplitter (PBS) for coupling optical power into reflective modulators in a free-space optical interconnection (FSOI) system. The PRBS uses a single diffraction grating recorded in a photorefractive material to redirect the incident laser light into the first diffraction order and onto the modulators. Reflected interconnection light not matching the Bragg angle criteria transmits through the beamsplitter uncoupled. Experimental results show that the PRBS provides better uniform transmission for off-axis beams than the currently used PBS.
Secure Network Coding With Erasures and Feedback (2015)

Secure network coding assumes that the underlying network channels are error-free; thus, if our channels introduce errors, we need to first apply a channel code to correct them, and then build security on top of the resulting error-free network. In this paper, we develop achievability protocols and outer bounds for the secure network coding setting, where the edges are subject to packet erasures, and public feedback of the channel state is available to both Eve and the legitimate network nodes. We show that by leveraging erasures and feedback, we can achieve secrecy rates that are in some cases multiple times higher than the alternative of separate channel-error-correction followed by secure network coding; moreover, we develop outer bounds and prove optimality of our proposed schemes in some special cases.
Decomposition Analysis of Wastewater Pollutant Discharges in Industrial Sectors of China (2001–2009) Using the LMDI I Method (2012)

China's industry accounts for 46.8% of the national Gross Domestic Product (GDP) and plays an important strategic role in its economic growth. On the other hand, industrial wastewater is also the major source of water pollution. In order to examine the relationship between the underlying driving forces and various environmental indicators, values of two critical industrial wastewater pollutant discharge parameters (Chemical Oxygen Demand (COD) and ammonia nitrogen (NH(4)-N)), between 2001 and 2009, were decomposed into three factors: i.e., production effects (caused by change in the scale of economic activity), structure effects (caused by change in economic structure) and intensity effects (caused by change in technological level of each sector), using additive version of the Logarithmic Mean Divisia Index (LMDI I) decomposition method. Results showed that: (1) the average annual effect of COD discharges in China was -2.99%, whereas the production effect, the structure effect, and the intensity effect were 14.64%, -1.39%, and -16.24%, respectively. Similarly, the average effect of NH(4)-N discharges was -4.03%, while the production effect, the structure effect, and the intensity effect were 16.18%, -2.88%, and -17.33%, respectively; (2) the production effect was the major factor responsible for the increase in COD and NH(4)-N discharges, accounting for 45% and 44% of the total contribution, respectively; (3) the intensity effect, which accounted for 50% and 48% of the total contribution, respectively, exerted a dominant decremental effect on COD and NH(4)-N discharges; intensity effect was further decomposed into cleaner production effect and pollution abatement effect with the cleaner production effect accounting for 60% and 55% of the reduction of COD and NH(4)-N, respectively; (4) the major contributors to incremental COD and NH(4)-N discharges were divided among industrial sub-sectors and the top contributors were identified. Potential restructuring and regulation measures were proposed for pollutant reduction.
Surface characterization techniques for determining the root-mean-square roughness and power spectral densities of optical components (2002)

Surface topography and light scattering were measured on 15 samples ranging from those having smooth surfaces to others with ground surfaces. The measurement techniques included an atomic force microscope, mechanical and optical profilers, confocal laser scanning microscope, angle-resolved scattering, and total scattering. The samples included polished and ground fused silica, silicon carbide, sapphire, electroplated gold, and diamond-turned brass. The measurement instruments and techniques had different surface spatial wavelength band limits, so the measured roughnesses were not directly comparable. Two-dimensional power spectral density (PSD) functions were calculated from the digitized measurement data, and we obtained rms roughnesses by integrating areas under the PSD curves between fixed upper and lower band limits. In this way, roughnesses measured with different instruments and techniques could be directly compared. Although smaller differences between measurement techniques remained in the calculated roughnesses, these could be explained mostly by surface topographical features such as isolated particles that affected the instruments in different ways.
Phosphoramidate, Phosphorothioate, and Methylphosphonate Analogs of Oligodeoxynucleotide : Inhibitors of Replication of Human Immunodeficiency Virus (1989)

Abstract Modified oligodeoxynucleotides complementary to RNA of human immunodeficiency virus (HIV-1) were tested for their ability to inhibit virally induced syncytium formation and expression of viral p24 protein. The modification of oligomers include replacement of phophodiester backbone with phosphorothioate, methylphosphonate and various phosphoramidates. Cells infected for four days, then treated with the antisense oligomers also showed inhibition of viral expression.
Conformation Change in a Self-recognizing Autotransporter Modulates Bacterial Cell-Cell Interaction (2010)

Bacteria mostly live as multicellular communities, although they are unicellular organisms, yet the mechanisms that tie individual bacteria together are often poorly understood. The adhesin involved in diffuse adherence (AIDA-I) is an adhesin of diarrheagenic Escherichia coli strains. AIDA-I also mediates bacterial auto-aggregation and biofilm formation and thus could be important for the organization of communities of pathogens. Using purified protein and whole bacteria, we provide direct evidence that AIDA-I promotes auto-aggregation by interacting with itself. Using various biophysical and biochemical techniques, we observed a conformational change in the protein during AIDA-AIDA interactions, strengthening the notion that this is a highly specific interaction. The self-association of AIDA-I is of high affinity but can be modulated by sodium chloride. We observe that a bile salt, sodium deoxycholate, also prevents AIDA-I oligomerization and bacterial auto-aggregation. Thus, we propose that AIDA-I, and most likely other similar autotransporters such as antigen 43 (Ag43) and TibA, organize bacterial communities of pathogens through a self-recognition mechanism that is sensitive to the environment. This could permit bacteria to switch between multicellular and unicellular lifestyles to complete their infection.
Classification of disease severity in retinitis pigmentosa (2019)

We present a simple, objective and easy to use disease severity classification for RP which can be used to categorise and compare patients.
Nonlinear dynamics in a high‐gain amplifier: the dc SQUID (2000)

Abstract We study the detection of very weak time‐periodic magnetic signals via a double‐junction (dc) Superconducting Quantum Interference Device (SQUID). The device, represented by two coupled nonlinear differential equations for the quantum mechanical junction phase differences, admits long‐time static or oscillatory solutions, the transition between them being easily controlled by experimentally accessible parameters. Gain is maximal when the device is tuned to the onset of the oscillatory solutions; i.e., when the minima in the 2D potential function disappear. We concentrate on the SQUID dynamics near this critical point and compute the oscillation frequency via a center manifold reduction of the full 2D dynamics. Knowing this frequency permits its exploitation as a detection/classification tool in magnetic remote sensing applications.
Diffractive optics: an introduction to the feature issue (1995)

This special feature of Applied Optics contains 20 papers on the design, applications, and fabrication of diffractive optics. The companion feature in the Journal of the Optical Society of America A (May 1995) contains papers on diffractive optics modeling. Many of these papers result from presentations at the second OSA topical meeting on diffractive optics, June 6-9, 1994, in Rochester, New York.
Photocurrent Generation in Nanostructured Organic Solar Cells (2008)

Photocurrent generation in nanostructured organic solar cells is simulated using a dynamical Monte Carlo model that includes the generation and transport properties of both excitons and free charges. Incorporating both optical and electrical properties, we study the influence of the heterojunction nanostructure (e.g., planar vs bulk junctions) on donor-acceptor organic solar cell efficiencies based on the archetype materials copper phthalocyanine (CuPc) and C(60). Structures considered are planar and planar-mixed heterojunctions, homogeneous and phase-separated donor-acceptor (DA) mixtures, idealized structures composed of DA pillars, and nanocrystalline DA networks. The thickness dependence of absorption, exciton diffusion, and carrier collection efficiencies is studied for different morphologies, yielding results similar to those experimentally observed. The influences of charge mobility and exciton diffusion length are studied, and optimal device thicknesses are proposed for various structures. Simulations show that, with currently available materials, nanocrystalline network solar cells optimize both exciton diffusion and carrier collection, thus providing for highly efficient solar energy conversion. Estimations of achievable energy conversion efficiencies are made for the various nanostructures based on current simulations used in conjunction with experimentally obtained fill factors and open-circuit voltages for conventional small molecular weight materials combinations.
Cerebrovascular Disease and Carotid Artery Stenting (2012)

Abstract Carotid artery disease is common in patients with atherosclerosis in other vascular beds (ie, coronary and peripheral arteries) and has a wide spectrum of clinical presentations (asymptomatic carotid bruit, TIA, or stroke). Given the dire consequences of stroke and the fact that stroke may not be preceded by warning symptoms or signs such as TIA, there has been great interest in predicting and identifying patients at risk. Identification of carotid artery stenosis has been an important component of this process. Carotid endarterectomy is superior to medical therapy for patients with symptomatic carotid artery disease and a high-grade stenosis, including carotid territory or retinal TIAs or nondisabling stroke with an ipsilateral high-grade carotid artery stenosis. The increased morbidity and mortality associated with carotid endarterectomy in high-risk patients formed the rationale for the application of carotid artery stenting. Pertinent clinical trials are also reviewed.
High‐Throughput Multiplex Sequencing of miRNA (2012)

Next-generation sequencing offers many advantages over other methods of microRNA (miRNA) expression profiling, such as sample throughput and the capability to discover novel miRNAs. As the sequencing depth of current sequencing platforms exceeds what is necessary to quantify miRNAs, multiplexing several samples in one sequencing run offers a significant cost advantage. Although previous studies have achieved this goal by adding bar codes to miRNA libraries at the ligation step, this was recently shown to introduce significant bias into the miRNA expression data. This bias can be avoided, however, by bar coding the miRNA libraries at the PCR step instead. Here, we describe a user-friendly PCR bar-coding method of preparing multiplexed microRNA libraries for Illumina-based sequencing. The method also prevents the production of adapter dimers and can be completed in one day.
Experimental Investigation and Design of Rotating Packed Beds for Distillation (2018)

Improved separation efficiency and flexibility are of major importance in the downstream processing of liquid mixtures in the chemical industry, in order to respond to fluctuating demand and raw material quality. The application of the high gravity (HiGee) concept in Rotating Packed Beds (RPBs) has the potential to meet these requirements for the separation of liquid mixtures. The current work provides an analysis of the potential improvements gained by RPBs. The flexibility of RPBs is analyzed based on an experimental investigation, which evaluates the effect of rotational speed, different rotor configurations and F-factors on separation efficiency. Batch distillation experiments were performed in a single-stage pilot plant RPB with the ethanol-water system under total reflux conditions at atmospheric pressure. An analysis of the number of transfer units (NTU) reveals that separation efficiency in RPBs is not necessarily proportional to the rotational speed. There is rather an optimal rotational speed for each investigated rotor configuration. A maximum of 3.7 transfer units was achieved for a rotor with outer packing diameter of 0.36 m and an axial height of 0.01 m. Special emphasize in this experimental study is placed on the analysis of the contributions to mass transfer from the packing and the casing, which can contribute significantly to the overall mass transfer in RPBs.
Conformational study of the potent peptide hormone antagonist [1-penicillamine,2-leucine]oxytocin in aqueous solution (1981)

[1-Penicillamine,2-leucine]oxytocin is a conformationally restricted analogue of oxytoxin in which the half-cystine-1 and tyrosine-2 residues of the native hormone are replaced by half-penicillamine (beta, beta-dimethyl-half-cystine) and leucine, respectively. This analogue is a surprisingly potent oxytocin antagonist [Hruby, V. J., Deb, K. K., Yamamoto, D. M., Hadley, M. E., & Chan, W. Y. (1979) J. Med. Chem. 22,7]. Extensive proton magnetic resonance experiments were performed to determine the conformational properties of this analogue in aqueous solution, and the results were compared with the previously published model for the conformation of [1-penicillamine]oxytocin. The results are consistent with a conformation similar to that of [1-penicillamine]oxytocin except that, while [1-penicillamine]oxytocin in aqueous solution possesses two 1 comes from 3 (C7) type turns involving the isoleucine-3 peptide amide proton and the half-penicillamine-1 carbonyl and the asparagine-5 peptide amide proton and the isoleucine-3 carbonyl, [1-penicillamine,2-leucine)oxytocin has only the latter 1 comes from 3 turn. This difference between the antagonists is reflected in the different phi and psi angles in the three N-terminal residues of the two inhibitor analogues and in differences in the preferred side-chain conformations for several residues. One particular result of these conformational differences is that, whereas for [1-penicillamine]oxytocin the tyrosine-2 side chain is unable to assume the rotamer for maximal binding to the uterine receptor, [1-penicillamine,2-leucine]oxytoxin retains conformational and dynamic properties at residues two and three which are more similar to those of oxytocin. It is postulated that these conformational and dynamic properties are consistent with the stronger binding and, hence, greater antagonist activity for this penicillamine analogue relative to [1-penicillamine]oxytocin.
Modulation of ERCC1-XPF Heterodimerization Inhibition via Structural Modification of Small Molecule Inhibitor Side-Chains (2022)

Inhibition of DNA repair enzymes is an attractive target for increasing the efficacy of DNA damaging chemotherapies. The ERCC1-XPF heterodimer is a key endonuclease in numerous single and double strand break repair processes, and inhibition of the heterodimerization has previously been shown to sensitize cancer cells to DNA damage. In this work, the previously reported ERCC1-XPF inhibitor 4 was used as the starting point for an <i>in silico</i> study of further modifications of the piperazine side-chain. A selection of the best scoring hits from the <i>in silico</i> screen were synthesized using a late stage functionalization strategy which should allow for further iterations of this class of inhibitors to be readily synthesized. Of the synthesized compounds, compound 6 performed the best in the <i>in vitro</i> fluorescence based endonuclease assay. The success of compound 6 in inhibiting ERCC1-XPF endonuclease activity <i>in vitro</i> translated well to cell-based assays investigating the inhibition of nucleotide excision repair and disruption of heterodimerization. Subsequently compound 6 was shown to sensitize HCT-116 cancer cells to treatment with UVC, cyclophosphamide, and ionizing radiation. This work serves as an important step towards the synergistic use of DNA repair inhibitors with chemotherapeutic drugs.
Organolanthanide tetrahydroborates. Ligation geometry and coordinative saturation (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganolanthanide tetrahydroborates. Ligation geometry and coordinative saturationTobin J. Marks and Gregory W. GrynkewichCite this: Inorg. Chem. 1976, 15, 6, 1302–1307Publication Date (Print):June 1, 1976Publication History Published online1 May 2002Published inissue 1 June 1976https://pubs.acs.org/doi/10.1021/ic50160a011https://doi.org/10.1021/ic50160a011research-articleACS PublicationsRequest reuse permissionsArticle Views142Altmetric-Citations55LEARN 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
Facilitating the Formation of Disulfide Bonds in the Escherichia coli Periplasm via Coexpression of Yeast Protein Disulfide Isomerase (1999)

Sacchromyces cerevisiae protein disulfide isomerase (yPDI) was expressed in the E. coli periplasm by using plasmids encoding the OmpA-yPDI-(His)(6) fusion gene under the control of the araBAD, trc, or T7 promoter. The expression levels of yeast PDI under these promoters were compared. Our results showed that yeast PDI expressed into the periplasm could catalyze the formation of disulfide bonds in alkaline phosphatase, restoring the phoA(+) phenotype in dsbA(-) mutants. The yeast PDI was purified from the Escherichia coli periplasm and shown to exhibit catalytic properties comparable to those of the rat enzyme with reduced RNase as substrate. In vivo, coexpression of the yeast PDI increased the yield of bovine pancreatic trypsin inhibitor (BPTI) in E. coli by 2-fold, similar to the effect seen previously with the coexpression of the rat enzyme. However yeast PDI was more effective than rat PDI in facilitating the expression of active tissue plasminogen activator (tPA). These results point to differences in the substrate specificity of various PDI enzymes, at least in the context of the E. coli periplasm.
Ressentiment in Australian policy debate (2014)

This paper argues Australian policy debate is characterised by an unwarranted sense of dissatisfaction and grievance. The argument is illustrated with reference to key policy issues under debate in Australia at present. The concept of 'ressentiment' is used to show how the trend of focusing on perceptions of wrong and injury among policy protagonists may preclude crucial constraints from future policy discussion.
Ammonium-directed dihydroxylation of 3-aminocyclohex-1-enes: development of a metal-free dihydroxylation protocol (2008)

Treatment of 3-aminocyclohex-1-enes with mCPBA in the presence of trichloroacetic acid gives the corresponding 1,2-anti-2,3-syn-1-trichloroacetoxy-2-hydroxy-3-aminocyclohexane with high levels of diastereoselectivity (90% de). This is consistent with a mechanism of oxidation involving hydrogen-bonded delivery of the oxidant by the allylic ammonium ion formed in situ, followed by highly regioselective ring-opening of the intermediate epoxide by trichloroacetic acid. The effect of conformational constraints upon the oxidation reaction is also examined.
Neurally adjusted ventilatory assist versus pressure support ventilation in patient-ventilator interaction and clinical outcomes: a meta-analysis of clinical trials (2019)

NAVA is more beneficial in patient-ventilator interaction than PSV, and could decrease the duration of ventilation.
Hydroboration. 61. Diisopinocampheylborane of high optical purity. Improved preparation and asymmetric hydroboration of representative cis-disubstituted alkenes (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydroboration. 61. Diisopinocampheylborane of high optical purity. Improved preparation and asymmetric hydroboration of representative cis-disubstituted alkenesHerbert C. Brown, Manoj C. Desai, and Prabhakar K. JadhavCite this: J. Org. Chem. 1982, 47, 26, 5065–5069Publication Date (Print):December 1, 1982Publication History Published online1 May 2002Published inissue 1 December 1982https://pubs.acs.org/doi/10.1021/jo00147a004https://doi.org/10.1021/jo00147a004research-articleACS PublicationsRequest reuse permissionsArticle Views3002Altmetric-Citations123LEARN 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
Rapid DNA Extraction from Dried Blood Spots on Filter Paper: Potential Applications in Biobanking (2014)

Our simple and convenient DBS storage and extraction methods are suitable for diagnostic screening by using very small volumes of blood collected on filter paper, and can be used in biobanks for blood sample storage.