gebhart/patrepeval huggingface dataset:
Chromatin Functional States Correlate with HIV Latency Reversal in Infected Primary CD4 + T cells (2018)

ABSTRACT Human immunodeficiency virus (HIV) infection cannot be cured due to a small reservoir of latently infected CD4 + T cells in treated patients. The “shock and kill” approach proposes to eliminate the reservoir by inducing its activation and the direct or indirect killing of infected cells. Current latency reversing agents (LRAs) do not reduce the viral reservoir in treated patients. We use a novel dual-fluorescent HIV reporter to identify and purify latent cells, and to determine the fraction of latent cells that undergo viral reactivation after infection of primary CD4 + T cells. Unexpectedly, LRAs reactivate less than 5% of latent proviruses. Analysis of HIV integration sites from induced and non-induced latent populations reveals distinct provirus integration sites between these two populations in terms of chromatin functional states. These findings challenge “shock and kill”, and suggest the need of more potent LRAs in combination with immunomodulatory approaches to eradicate HIV reservoir.
3D Microstrip Line Taper on Ultra-low Dielectric Constant Substrate (2019)

In this paper, a new microstrip three-dimensional taper is presented. This new taper enables circuit-in-substrate (CIS) integration of high-quality microwave components with a microstrip line designed on a thick, ultra-low dielectric constant substrate. The width of microstrip lines on thick low dielectric constant materials is considerably large and can create a shunt capacitive loading when using edge mount connectors. The microstrip line can be tapered in the planar direction to reduce the shunt capacitance at the cost of added mismatch. The proposed technique adds a vertical tapering of the substrate, which results in a constant impedance across the substrate and reduces the mismatch between the microstrip and the connector. For verification, the 3D microstrip line taper is fabricated and measured. Full-wave simulation results and measurements are compared to validate the proposed design.
Prediction of Total Drug Clearance in Humans Using Animal Data: Proposal of a Multimodal Learning Method Based on Deep Learning (2021)

Research into pharmacokinetics plays an important role in the development process of new drugs. Accurately predicting human pharmacokinetic parameters from preclinical data can increase the success rate of clinical trials. Since clearance (CL) which indicates the capacity of the entire body to process a drug is one of the most important parameters, many methods have been developed. However, there are still rooms to be improved for practical use in drug discovery research; "improving CL prediction accuracy" and "understanding the chemical structure of compounds in terms of pharmacokinetics". To improve those, this research proposes a multimodal learning method based on deep learning that takes not only the chemical structure of a drug but also rat CL as inputs. Good results were obtained compared with the conventional animal scale-up method; the geometric mean fold error was 2.68 and the proportion of compounds with prediction errors of 2-fold or less was 48.5%. Furthermore, it was found to be possible to infer the partial structure useful for CL prediction by a structure contributing factor inference method. The validity of these results of structural interpretation of metabolic stability was confirmed by chemists.
DNA MIcroarray-Assisted Modeling of Metabolic and Regulatory Networks With Applications to Bio-Defense (2006)

Abstract : During the course of the project four software tools for BioSPICE were developed. These include Network Component Analysis (NCA), GeneScreen, 1cDNA, and MIcroArray Experimental Spice (MIAMESpice). NCA uses available connectivity information between genes and transcriptional factors and gene expression level time course data (obtainable through DNA microarray experiments) to estimate parameters and infer a gene transcriptional network through a Matlab analysis routine. GeneScreen processes gene expression data with a collection of computational statistic routines to extract significant gene association patterns. 1cDNA estimates confidence intervals for messenger RNA, mRNA expression levels in microarray experiments, including elimination of extreme outliers, quality filtering, normalization of the log10 signal intensity ratios, and assessment of expression levels. MIAMESpice packages raw and normalized data files from a set of related microarray experiments, saving all associated data from an experiment (or set of experiments) into one archive file. Users can also enter experimental annotations, array design information, and array design files.
2, 5‐Bis( t butyl)‐2, 5‐Diaza‐1‐Germa‐Cyclopentane‐A New Precursor for Amorphous Germanium Films (2005)

A novel organometallic precursor has been synthesized and used for the deposition of amorphous germanium by thermal OM CVD (organometallic chemical vapour deposition) at temperatures below 300 °C. The films are of high purity with an oxygen content below the detection limit of about ≤ 1018 cm−3. OM CVD from a novel precursor 2, 5-Bis(tbutyl)-2, 5-diaza-1-germa-cyclopentane is a promising alternative for the deposition of a-Ge at low temperature. Oxygen, nitrogen, and carbon impurities of the films are very low, but their electrical properties do not reach the quality of the best plasma CVD material. Work is in progress to solve these problems.
Potential Biocontrol Activities of Populus Endophytes against Several Plant Pathogens Using Different Inhibitory Mechanisms (2022)

The plant microbiome can be used to bolster plant defense against abiotic and biotic stresses. Some strains of endophytes, the microorganisms within plants, can directly inhibit the growth of plant fungal pathogens. A previously isolated endophyte from wild <i>Populus</i> (poplar), WPB of the species <i>Burkholderia vietnamiensis</i>, had robust in vitro antifungal activity against pathogen strains that are highly virulent and of concern to Pacific Northwest agriculture: <i>Rhizoctonia solani</i> AG-8, <i>Fusarium culmorum</i> 70110023, and <i>Gaemannomyces graminis</i> var. <i>tritici</i> (Ggt) ARS-A1, as well as activity against the oomycete, <i>Pythium ultimum</i> 217. A direct screening method was developed for isolation of additional anti-fungal endophytes from wild poplar extracts. By challenging pathogens directly with dilute extracts, eleven isolates were found to be inhibitory to at least two plant pathogen strains and were therefore chosen for further characterization. Genomic analysis was conducted to determine if these endophyte strains harbored genes known to be involved in antimicrobial activities. The newly isolated <i>Bacillus</i> strains had gene clusters for production of bacillomycin, fengicyn, and bacillibactin, while the gene cluster for the synthesis of sessilin, viscosin and tolaasin were found in the <i>Pseudomonas</i> strains. The biosynthesis gene cluster for occidiofungin (<i>ocf</i>) was present in the <i>Burkholderia vietnamiensis</i> WPB genome, and an <i>ocf</i> deletion mutant lost inhibitory activity against 3 of the 4 pathogens. The new isolates lacked the gene cluster for occidiofungin implying they employ different modes of action. Other symbiotic traits including nitrogen fixation, phosphate solubilization, and the production of auxins and siderophores were investigated. Although it will be necessary to conduct in vivo tests of the candidates with pathogen-infected agricultural crops, the wild poplar tree microbiome may be a rich source of beneficial endophyte strains with potential for biocontrol applications against a variety of pathogens and utilizing varying modes of action.
Reliability-based generation and view synthesis in layered depth video (2008)

In this paper, a system for video rendering on multiscopic 3D displays is considered where the data is represented as layered depth video (LDV). This representation consists of one full or central video with associated per-pixel depth and additional residual layers. Thus, only one full view with additional residual data needs to be transmitted. The LDV data is used at the receiver to generate all intermediate views for the display. The paper presents the LDV layer extraction as well as the view synthesis, using a scene reliability-driven approach. Here, unreliable image regions are detected and in contrast to previous approaches the residual data is enlarged to reduce artifacts in unreliable areas during rendering. To provide maximum data coverage, the residual data remains at its original positions and will not be projected towards the central view. The view synthesis process also uses this reliability analysis to provide higher quality intermediate views than previous approaches. As a final result, high quality intermediate views for an existing 9-view auto-stereoscopic display are presented, which prove the suitability of the LDV approach for advanced 3D video (3DV) systems.
Preemptive versus postoperative lumiracoxib for analgesia in ambulatory arthroscopic knee surgery (2008)

We compared the efficacy and safety of preemptive vs postoperative dosing of lumiracoxib 400 mg in patients undergoing minor ambulatory arthroscopic knee surgery. Eligible patients were randomized to preemptive lumiracoxib, postoperative lumiracoxib, and placebo. The main efficacy parameter was pain intensity (PI) (0-100 mm visual analog scale) in the target knee upon movement, 2 hours after surgery. Other efficacy variables included PI in the target knee at rest and upon movement at 1, 3, 4, and 24 hours, time to first rescue medication intake. In the lumiracoxib preemptive and postoperative groups, the estimated treatment difference compared to placebo for primary endpoint was -4.0 (95% CI: -9, -1; p = 0.007) and -3.5 (95% CI: -8.5, 0; p = 0.052), respectively. There was no statistical significant difference between two active treatment groups (p = 0.602). Both preemptive and postoperative lumiracoxib resulted in significantly lower PI scores at rest and after movement at all time-points and no statistically significant difference was observed between the active treatments. Time to rescue medication intake was comparable for both active treatments. The proportion of adverse events was similar among all groups. We conclude that the efficacy of lumiracoxib 400 mg is not affected by the timing of administration (preemptive or postoperative).
Design and fabrication of micro-optical elements for the generation of various novel beams and its applications in optical tweezers (2006)

Light assisted micro-manipulation techniques have provided a non-invasive technique to investigate microscopic world. Employing micro-optical elements for laser beam shaping can aggrandize the trapping capabilities of conventional optical tweezers system. In the paper we report the design parameters and fabrication techniques of diversified micro-optical elements. High quality Laguerre-Gaussian beams, Bessel beams, self-imaged bottle beams and fractional Bessel beams were achieved using such micro-optical elements. We further integrated these micro-elements in conventional optical tweezers systems for various trapping applications. Such micro-elements were high efficient (in terms of power conversion) which is an important criteria to be incorporated with the optical trapping systems. Due to its micro-size such micro-elements are potential candidates to be integrated with lab-on-a-chip techniques to realize next generation "miniaturized optical trap".
Carnosol and Related Substances Modulate Chemokine and Cytokine Production in Macrophages and Chondrocytes (2016)

Phenolic diterpenes present in Rosmarinus officinalis and Salvia officinalis have anti-inflammatory and chemoprotective effects. We investigated the in vitro effects of carnosol (CL), carnosic acid (CA), carnosic acid-12-methylether (CAME), 20-deoxocarnosol and abieta-8,11,13-triene-11,12,20-triol (ABTT) in murine macrophages (RAW264.7 cells) and human chondrocytes. The substances concentration-dependently reduced nitric oxide (NO) and prostaglandin E₂ (PGE₂) production in LPS-stimulated macrophages (i.e., acute inflammation). They significantly blunted gene expression levels of iNOS, cytokines/interleukins (IL-1α, IL-6) and chemokines including CCL5/RANTES, CXCL10/IP-10. The substances modulated the expression of catabolic and anabolic genes in chondrosarcoma cell line SW1353 and in primary human chondrocytes that were stimulated by IL-1β (i.e., chronic inflammation In SW1353, catabolic genes like MMP-13 and ADAMTS-4 that contribute to cartilage erosion were down-regulated, while expression of anabolic genes including Col2A1 and aggrecan were shifted towards pre-pathophysiological homeostasis. CL had the strongest overall effect on inflammatory mediators, as well as on macrophage and chondrocyte gene expression. Conversely, CAME mainly affected catabolic gene expression, whereas ABTT had a more selectively altered interleukin and chemokine gene exprssion. CL inhibited the IL-1β induced nuclear translocation of NF-κBp65, suggesting that it primarily regulated via the NF-κB signalling pathway. Collectively, CL had the strongest effects on inflammatory mediators and chondrocyte gene expression. The data show that the phenolic diterpenes altered activity pattern of genes that regulate acute and chronic inflammatory processes. Since the substances affected catabolic and anabolic gene expression in cartilage cells in vitro, they may beneficially act on the aetiology of osteoarthritis.
Functional Problems and Arthrofibrosis Following Total Knee Arthroplasty (2007)

Seyler, Thorsten M. MD; Marker, David R. BS; Bhave, Anil PT; Plate, Johannes F. BS; Marulanda, German A. MD; Bonutti, Peter M. MD; Delanois, Ronald E. MD; Mont, Michael A. MD Author Information
Resequencing Study Confirms That Host Defense and Cell Senescence Gene Variants Contribute to the Risk of Idiopathic Pulmonary Fibrosis (2019)

<b>Rationale:</b> Several common and rare genetic variants have been associated with idiopathic pulmonary fibrosis, a progressive fibrotic condition that is localized to the lung. <b>Objectives:</b> To develop an integrated understanding of the rare and common variants located in multiple loci that have been reported to contribute to the risk of disease. <b>Methods:</b> We performed deep targeted resequencing (3.69 Mb of DNA) in cases (<i>n</i> = 3,624) and control subjects (<i>n</i> = 4,442) across genes and regions previously associated with disease. We tested for associations between disease and <i>1</i>) individual common variants via logistic regression and <i>2</i>) groups of rare variants via sequence kernel association tests. <b>Measurements and Main Results:</b> Statistically significant common variant association signals occurred in all 10 of the regions chosen based on genome-wide association studies. The strongest risk variant is the <i>MUC5B</i> promoter variant rs35705950, with an odds ratio of 5.45 (95% confidence interval, 4.91-6.06) for one copy of the risk allele and 18.68 (95% confidence interval, 13.34-26.17) for two copies of the risk allele (<i>P</i> = 9.60 × 10<sup>-295</sup>). In addition to identifying for the first time that rare variation in <i>FAM13A</i> is associated with disease, we confirmed the role of rare variation in the <i>TERT</i> and <i>RTEL1</i> gene regions in the risk of IPF, and found that the <i>FAM13A</i> and <i>TERT</i> regions have independent common and rare variant signals. <b>Conclusions:</b> A limited number of common and rare variants contribute to the risk of idiopathic pulmonary fibrosis in each of the resequencing regions, and these genetic variants focus on biological mechanisms of host defense and cell senescence.
Sigesbeckia orientalis L. Extract Alleviated the Collagen Type II–Induced Arthritis Through Inhibiting Multi-Target–Mediated Synovial Hyperplasia and Inflammation (2020)

Excessive proliferation and inflammation of synovial fibroblasts accelerate and decorate the pathological process of rheumatoid arthritis (RA). <i>Sigesbeckia orientalis</i> L. (SO) is one of the main plant sources for Sigesbeckiae Herba (SH) which has been used traditionally in treating various forms of arthritis and rheumatic pain. However, the anti-arthritic mechanisms of SO are still not clearly understood. In this study, we investigated the therapeutic effects and the underlying mechanisms of SO against collagen type II (C II)-induced RA in rats as well as the interleukin (IL)-1β-induced human synovial SW982 and MH7A cells. For the <i>in vivo</i> studies, thirty-six Wistar male rats were randomly arranged to six groups based on the body weight, and then C II-induced to RA model for 15 days, followed by treatment with the 50% ethanolic extract of SO (SOE, 0.16, 0.78, and 1.56 g/kg) for 35 days. The results suggested that SOE significantly inhibited the formation of pannus (synovial hyperplasia to the articular cavity) and attenuated the cartilage damaging and bone erosion in the CIA-induced rats' hind paw joints. Moreover, SOE decreased the production of C-reactive protein (CRP) in the serum and the expression of IL-6 and IL-1β in the joint muscles, as well as recovered the decreased regulatory T lymphocytes. The results obtained from the <i>in vitro</i> studies showed that SOE (50, 100, and 200 µg/ml) not only inhibited the proliferation, migration, and invasion of human synovial SW982 cells but also decreased the IL-1β-induced expression of IL-6 and IL-8 both in SW982 and MH7A cells. Besides, SOE reduced the expression of COX-2, NLRP3, and MMP9, and increased the expression of MMP2 in the IL-1β-induced SW982 cells. Furthermore, SOE blocked the activation of NF-κB and reduced the phosphorylation of MAPKs and the expression of AP-1. In conclusion, SOE attenuated the C II-induced RA through inhibiting of MAPKs/NF-κB/AP-1-mediated synovial hyperplasia and inflammation.
Twisted intramolecular charge-transfer phenomenon as a quantitative probe of polymerization kinetics (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTwisted intramolecular charge-transfer phenomenon as a quantitative probe of polymerization kineticsJ. Paczkowski and D. C. NeckersCite this: Macromolecules 1991, 24, 10, 3013–3016Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/ma00010a059https://doi.org/10.1021/ma00010a059research-articleACS PublicationsRequest reuse permissionsArticle Views235Altmetric-Citations60LEARN 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
Indications, timing, and patient selection (2009)

Abstract Chapter 6 discusses indications, timing, and patient selection in CRRT.
Infant‐Directed Speech Is Modulated by Infant Feedback (2008)

When mothers engage in infant‐directed (ID) speech, their voices change in a number of characteristic ways, including adopting a higher overall pitch. Studies have examined these acoustical cues and have tested infants' preferences for ID speech. However, little is known about how these cues change with maternal sensitivity to infant feedback in the context of interaction. In this study, each mother watched her infant (located in an adjacent sound booth) on a video screen and talked to him or her through a microphone. The mother believed that her infant could hear her voice and she attempted to make her infant happy through her vocalizations. In reality, the infant could not hear her voice. The mother's ID speech was analyzed in real time for changes in mean pitch. For half of the infant–mother dyads an experimenter surreptitiously positively engaged the infant when the voice analysis revealed a rise in pitch, thereby producing positive reinforcement to the mother for natural higher pitched ID speech. The other half were reinforced for lower pitched ID speech. Mothers raised their pitch significantly more in the former than the latter condition, illustrating that the pitch of ID speech is dynamically affected by feedback from the infant.
Influence of doping on charge carrier collection in normal and inverted geometry polymer:fullerene solar cells (2013)

Abstract While organic semiconductors used in polymer:fullerene photovoltaics are generally not intentionally doped, significant levels of unintentional doping have previously been reported in the literature. Here, we explain the differences in photocurrent collection between standard (transparent anode) and inverted (transparent cathode) low band-gap polymer:fullerene solar cells in terms of unintentional p-type doping. Using capacitance/voltage measurements, we find that the devices exhibit doping levels of order 10 16 cm −3 , resulting in space-charge regions ~100 nm thick at short circuit. As a result, low field regions form in devices thicker than 100 nm. Because more of the light is absorbed in the low field region in standard than in inverted architectures, the losses due to inefficient charge collection are greater in standard architectures. Using optical modelling, we show that the observed trends in photocurrent with device architecture and thickness can be explained if only charge carriers photogenerated in the depletion region contribute to the photocurrent.
Kinetic Spectrophotometric Methods for the Determination of Isatin (2013)

Simple, rapid and sensitive kinetic spectrophotometric methods are described for the analysis of isatin in pure form and in mixture. The procedures were based on the kinetic investigations and studies were done upon the oxidation of isatin with potassium permanganate in basic medium. Various parameters affecting the colour developments were investigated and parameters were optimized. The reliability and the analytical performance of the proposed methods were validated for its linearity, range, accuracy and precision. The calibration curves were linear over the range of 5-50 g mL -1 . The limit of detection and limit of quantitation of the two methods ranges from 3.4 10 -4 -0.878 and 1.05 10 -3 -2.663, respectively. The possible mechanism of the reaction is also proposed.
Chapitre 15. Naples, une réforme difficile (2016)

« Les premiers chrétiens étaient tout aussi chrétiens ; comme nous, et peut-être mieux : mais ils n’avaient de cimetières qu’en dehors des villes. C’est une loi de la nature que de ne nuire à personne. Pourquoi en exempte-t-on les morts ? » Antonio Genovesi, un des plus célèbres penseurs des Lumières napolitaines, titulaire de la chaire d’économie politique de l’université, exprime ainsi, dans un opuscule paru en 1764, une opinion désormais partagée par un nombre croissant de réformateurs : l...