gebhart/patrepeval huggingface dataset:
The human near‐term myometrial β3‐adrenoceptor but not the β2‐adrenoceptor is resistant to desensitisation after sustained agonist stimulation (2004)

1. In order to compare the beta(2)- and beta(3)-adrenoceptor (beta-AR) desensitisation process in human near-term myometrium, we examined the influence of a pretreatment of myometrial strips with either a beta(2)- or a beta(3)-AR agonist (salbutamol or SR 59119A, respectively, both at 10 microm, for 5 and 15 h) on the relaxation and the cyclic adenosine monophosphate (cAMP) production induced by these agonists. 2. To assess some of the mechanisms potentially implicated in the beta-AR desensitisation process, we studied the influence of such treatment on the number of beta(2)- and beta(3)-AR binding sites, the beta(2)- and beta(3)-AR transcripts expression and the phosphodiesterase 4 (PDE4) activity. 3. Salbutamol, but not SR 59119A, concentration-response curve (CRC) was shifted by a 15 h salbutamol preincubation, with a significant difference in -log EC(20) values (6.31+/-0.13 vs 5.58+/-0.24, for control and 15 h salbutamol pretreatment, respectively, P<0.05). Neither salbutamol nor SR 59119A CRCs were modified after a 15 h preincubation with SR 59119A. 4. A 15 h exposure of myometrial strips to salbutamol significantly reduced the salbutamol-induced (0.60+/-0.26 vs 1.54+/-0.24 pmol mg(-1) protein, P<0.05), but not the SR 59119A-induced, cAMP production. No decrease in cAMP production was observed after a 15 h SR 59119A exposure. 5. A 15 h salbutamol exposure of myometrial strips significantly reduced the beta(2)- but not the beta(3)-AR binding site density, whereas no decrease in the number of beta(2)- and beta(3)-AR binding sites was observed after a 15 h SR 59119A treatment. 6. Neither PDE4 activity nor the beta(2)- and beta(3)-AR mRNA expression levels were affected by salbutamol or SR 59119A treatments. 7. Our results indicate that beta(3)-AR, but not beta(2)-AR, are resistant to the agonist-induced desensitisation. In our model, beta(2)-AR desensitisation is mediated by a decreased number of beta(2)-AR that was not explained by transcriptional regulation of the receptor.
Cloning of Small RNAs for the Discovery of Novel MicroRNAs in Plants (2012)

Endogenous small RNAs can be grouped into several distinct classes of 21-nt-long microRNAs (miRNAs), short interfering RNAs (siRNAs), trans-acting siRNAs (tasiRNAs), and 24-nt long heterochromatic siRNAs. miRNAs are increasingly being recognized as significant effectors of gene regulation in a wide range of organisms. These molecules are typically ∼21-nt long and are amenable for cloning by streamlined protocols. Here we detail the methodology for cloning small RNAs in rice to identify novel miRNAs and other important small RNAs. Briefly, small RNA molecules are size fractionated, attached to adaptors, and subsequently converted into cDNA and PCR amplified. Current high-throughput sequencing technologies allow sequencing of the PCR products directly.
Partial Enumeration and Curvature Regularization (2013)

Energies with high-order non-sub modular interactions have been shown to be very useful in vision due to their high modeling power. Optimization of such energies, however, is generally NP-hard. A naive approach that works for small problem instances is exhaustive search, that is, enumeration of all possible labelings of the underlying graph. We propose a general minimization approach for large graphs based on enumeration of labelings of certain small patches. This partial enumeration technique reduces complex high-order energy formulations to pair wise Constraint Satisfaction Problems with unary costs (uCSP), which can be efficiently solved using standard methods like TRW-S. Our approach outperforms a number of existing state-of-the-art algorithms on well known difficult problems (e.g. curvature regularization, stereo, deconvolution), it gives near global minimum and better speed. Our main application of interest is curvature regularization. In the context of segmentation, our partial enumeration technique allows to evaluate curvature directly on small patches using a novel integral geometry approach.
From Explicit to Implicit Surfaces for Visualization, Animation and Modeling (2003)

Deformable 3--D models are used extensively in Computer Graphics and Computer Vision for Visualization, Animation and Modeling. They can be represented either as traditional explicit surfaces, such as triangulated meshes, or as implicit surfaces.
An interaction network approach to study the correlation between endocrine disrupting chemicals and breast cancer (2017)

Endocrine disrupting chemicals (EDCs) are natural or synthetic exogenous substances affecting human health. Although present at low concentrations in the environment, they can cause a broad range of negative effects on the endocrine functions by mimicking the action of steroid hormones due to their structural similarity. Hormonal unbalance can play an important role in carcinogenesis at any stage of disease. In the case of the breast cancer, EDCs directly affect the transformation of normal breast cells into cancer cells by interfering with hormonal regulation and by inducing the alteration of factors that regulate gene expression. The principal aims of this work were to study the interaction networks of proteins modulated in breast cancer by either environmental EDCs or mycotoxins, and to identify the proteins with the strongest coordination role defined as hub nodes. Our studies evidenced the presence of seven and six hub proteins in two EDCs and mycotoxins networks, respectively. Then, by merging the two networks, we identified that three hub nodes (BCL2, ESR2 and CTNNB1) in the environmental EDCs network show direct interactions with three hub nodes (CASP8, RELA and MKI67) in the mycotoxins network. These data highlighted that two networks are linked through proteins involved in the apoptosis regulation and in processes related to cell proliferation and survival, and, thus, in breast cancer progression.
Metagenomics of Wastewater Influent from Wastewater Treatment Facilities across Ontario in the Era of Emerging SARS-CoV-2 Variants of Concern (2022)

We report metagenomic sequencing analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in composite wastewater influent from 10 regions in Ontario, Canada, during the transition between Delta and Omicron variants of concern. The Delta and Omicron BA.1/BA.1.1 and BA.2-defining mutations occurring in various frequencies were reported in the consensus and subconsensus sequences of the composite samples.
Novel Sulfamide Analogs of Oleoylethanolamide Showing In Vivo Satiety Inducing Actions and PPARα Activation (2006)

Long chain saturated and unsaturated alkyl sulfamide and propyl sulfamide derivatives, analogs of oleoylethanolamide, have been synthesized and evaluated in vivo and in vitro as peroxisome proliferator activated receptor alpha (PPARalpha) activators. Additionally, the anorexic effects of the new compounds have been studied in vivo in food-deprived rats. Among the active compounds N-octadecyl-N'-propylsulfamide (7) has been identified as a potent hypolipidemic compound, a potent feeding suppressant, and a concentration-dependent activator of PPARalpha.
Identification of Candidate Protein Biomarkers for CIN2+ Lesions from Self-Sampled, Dried Cervico–Vaginal Fluid Using LC-MS/MS (2021)

Molecular screening programs for cervical cancer detect the presence of human papilloma virus (HPV) in cell material or vaginal fluids. Persistent infection with high-risk HPV is a necessary pre-requisite, but the majority of infections do not lead to pathological states. Additional biomarkers are needed to increase the specificity of the molecular tests. Here, we have investigated the possibility of detecting protein biomarkers using mass spectrometry from dried self-sampled cervico-vaginal fluid deposited on FTA cards. We found significant intra-individual correlations (<i>p</i> < 2.2 × 10<sup>-16</sup>), although heterogenous protein profiles were obtained between individuals. Out of 3699 proteins found in total, 169 were detected in at least 95% of the samples. Using a discovery/replication design, 18 proteins were found to be significant in the discovery cohort, with higher values in those cases compared to controls. All of these were found to also have higher levels among the cases in the replication cohort, with one protein (DEAD-Box Helicase) remaining statistically significant. Finally, a predictive 7-protein multivariate model was developed with a sensitivity and specificity of 0.90 and 0.55, respectively. Our results demonstrate that robust measurements of protein biomarkers can be obtained from self-sampled dried CVF and that these could be used to predict cervical cancer pre-stages.
Editorial Comment (2016)

No AccessJournal of UrologyAdult Urology1 Nov 2016Editorial Comment Benjamin T. Ristau and Alexander Kutikov Benjamin T. RistauBenjamin T. Ristau More articles by this author and Alexander KutikovAlexander Kutikov More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2016.05.128AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Editorial Comment." The Journal of Urology, 196(5), p. 1355 References 1 : Some renal masses did not “read the book”: a case of a high grade hybrid renal tumor masquerading as a renal cyst on non-contrast imaging. Urol Case Rep2015; 3: 219. Google Scholar © 2016 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 196Issue 5November 2016Page: 1355 Advertisement Copyright & Permissions© 2016 by American Urological Association Education and Research, Inc.MetricsAuthor Information Benjamin T. Ristau More articles by this author Alexander Kutikov More articles by this author Expand All Advertisement PDF downloadLoading ...
Susceptibility to Acute Rheumatic Fever Based on Differential Expression of Genes Involved in Cytotoxicity, Chemotaxis, and Apoptosis (2013)

It is unknown why only some individuals are susceptible to acute rheumatic fever (ARF). We investigated whether there are differences in the immune response, detectable by gene expression, between individuals who are susceptible to ARF and those who are not. Peripheral blood mononuclear cells (PBMCs) from 15 ARF-susceptible and 10 nonsusceptible (control) adults were stimulated with rheumatogenic (Rh+) group A streptococci (GAS) or nonrheumatogenic (Rh-) GAS. RNA from stimulated PBMCs from each subject was cohybridized with RNA from unstimulated PBMCs on oligonucleotide arrays to compare gene expression. Thirty-four genes were significantly differentially expressed between ARF-susceptible and control groups after stimulation with Rh+ GAS. A total of 982 genes were differentially expressed between Rh+ GAS- and Rh- GAS-stimulated samples from ARF-susceptible individuals. Thirteen genes were differentially expressed in the same direction (predominantly decreased) between the two study groups and between the two stimulation conditions, giving a strong indication of their involvement. Seven of these were immune response genes involved in cytotoxicity, chemotaxis, and apoptosis. There was variability in the degree of expression change between individuals. The high proportion of differentially expressed apoptotic and immune response genes supports the current model of autoimmune and cytokine dysregulation in ARF. This study also raises the possibility that a "failed" immune response, involving decreased expression of cytotoxic and apoptotic genes, contributes to the immunopathogenesis of ARF.
A large screen identifies beta-lactam antibiotics which can be repurposed to target the syphilis agent (2023)

Syphilis, caused by the spirochete <i>Treponema pallidum</i> subsp. <i>pallidum</i> (hereafter called <i>T. pallidum</i>), is re-emerging as a worldwide sexually transmitted infection. A single intramuscular dose of benzathine penicillin G is the preferred syphilis treatment option. Both supply shortage concerns and the potential for acquired antibiotic resistance further the need to broaden the repertoire of syphilis therapeutics. We reasoned that other β-lactams may be equally or more effective at targeting the disease-causing agent, <i>Treponema pallidum</i>, but have yet to be discovered due to a previous lack of a continuous in vitro culture system. Recent technical advances with respect to in vitro <i>T. pallidum</i> propagation allowed us to conduct a high-throughput screen of almost 100 β-lactams. Using several molecular and cellular approaches that we developed or adapted, we identified and confirmed the efficacy of several β-lactams that were similar to or outperformed the current standard, benzathine penicillin G. These options are either currently used to treat bacterial infections or are synthetic derivatives of naturally occurring compounds. Our studies not only identified additional potential therapeutics in the resolution of syphilis, but provide techniques to study the complex biology of <i>T. pallidum</i>-a spirochete that has plagued human health for centuries.
Stable, synthetic analogs of diadenosine tetraphosphate inhibit rat and human P2X3 receptors and inflammatory pain (2016)

Stable, synthetic Ap4A analogs (AppNHppA and AppCH2ppA) being weak partial agonist provoke potent high-affinity desensitization-mediated inhibition of homomeric P2X3Rs at low concentrations. Therefore, both analogs demonstrate clear potential as potent analgesic agents for use in the management of chronic pain associated with heightened P2X3R activation.
New Design of Ultra High Cell Density Metal Substrates (2002)

&lt;div class="htmlview paragraph"&gt;To meet the most stringent emissions standards such as Super Ultra Low Emission Vehicle (SULEV) in California, substrates with high cell densities and ultra thin foils are needed, mounted in a close-coupled position. A new substrate design has been developed incorporating increased thermal and mechanical load in association with reduced thermal mass and improved heat transfer due to higher cell density. This paper describes the development of the new design using finite element calculation and practical test results from component and engine test benches.&lt;/div&gt;
Effect of gas flow on a helium/oxygen endoscopic plasma jet (2022)

Abstract This experimental study characterized the effect of carrier gas flow on an endoscopic plasma jet. This system generates and transports helium plasma in a tube over several meters, along with a separate channel transporting oxygen to enhance plasma reactivity on site. The resulting plasma plume exiting the tube allows treatment of tissue surfaces in an endoscopic setting with a view to perform therapeutic operations in the gastrointestinal tract. In a closed cavity simulating the tract, the carrier gas flow was studied by a combined approach investigating plasma plume chemistry, fluid dynamics, and plasma effects on the surface of a hydrogel tissue model reporting oxidation. These three aspects are shown to be closely inter-related. Plasma plume length, intensity, and shape strongly depend on helium content, velocity, turbulence, and environment. Optical emission spectroscopy was used to show that the helium gas flow rate increases the amount of helium and reactive oxygen species (ROS) in the plume. Schlieren imaging was used to visualize the transition of the fluid from buoyant to laminar and finally turbulent depending on flow rate, with a backflow in a closed cavity. Finally, the frontal and radial treatment of the cavity was assessed by measuring ROS delivery to a KI-starch agarose gel model. Helium flow rate had a noticeable effect on the treatment distribution profile and treatment intensity, with different maxima for frontal and radial treatments. This combined approach, in an accurate simulation of the target configuration (i.e. a closed, cylindrical cavity), is necessary to optimize treatment, as its outcome depends on a balance between ROS production, transport, and distribution.
Bubble flow in the downflow section of an airlift tower (1979)

Abstract Characterization of the two‐phase flow in the downflow section of the airlift tower is necessary for accurate modeling of the airlift tower. A Split‐cylinder airlift tower was investigated for superficial gas velocities ranging from 0.0683 to 0.3315 m/sec for an air–water system. Statistical cross‐covariance techniques were used to yield velocities, void fractions, and flow rates corresponding to upward and downward components of bubble flow in the downflow section of the airlift tower. From these results the fraction of incoming air entrained in the downflow section was determined as a function of superficial gas velocity and position.
Systematic investigation of influence factor on parallel transmit pulse performance at 9.4 Tesla (2015)

This work systematically investigates the factors that could pose negative influence on the transmit pulse performance at 9.4 tesla. These factors are B1 mapping inaccuracy, B0 inhomogeneity, actual RF and gradient pulse deviations, among which B1 mapping inaccuracy and actual RF pulse deviations are deemed as the major influence factor. Comparative measurements with and without consideration of these factors during the pulse design process, including one in vivo experiment, are performed.
Overlap of Genetic Risk between Interstitial Lung Abnormalities and Idiopathic Pulmonary Fibrosis (2019)

<b>Rationale:</b> Interstitial lung abnormalities (ILAs) are associated with the highest genetic risk locus for idiopathic pulmonary fibrosis (IPF); however, the extent to which there are unique associations among individuals with ILAs or additional overlap with IPF is not known.<b>Objectives:</b> To perform a genome-wide association study (GWAS) of ILAs.<b>Methods:</b> ILAs and a subpleural-predominant subtype were assessed on chest computed tomography (CT) scans in the AGES (Age Gene/Environment Susceptibility), COPDGene (Genetic Epidemiology of Chronic Obstructive Pulmonary Disease [COPD]), Framingham Heart, ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-points), MESA (Multi-Ethnic Study of Atherosclerosis), and SPIROMICS (Subpopulations and Intermediate Outcome Measures in COPD Study) studies. We performed a GWAS of ILAs in each cohort and combined the results using a meta-analysis. We assessed for overlapping associations in independent GWASs of IPF.<b>Measurements and Main Results:</b> Genome-wide genotyping data were available for 1,699 individuals with ILAs and 10,274 control subjects. The <i>MUC5B</i> (mucin 5B) promoter variant rs35705950 was significantly associated with both ILAs (<i>P</i> = 2.6 × 10<sup>-27</sup>) and subpleural ILAs (<i>P</i> = 1.6 × 10<sup>-29</sup>). We discovered novel genome-wide associations near <i>IPO11</i> (rs6886640, <i>P</i> = 3.8 × 10<sup>-8</sup>) and <i>FCF1P3</i> (rs73199442, <i>P</i> = 4.8 × 10<sup>-8</sup>) with ILAs, and near <i>HTRE1</i> (rs7744971, <i>P</i> = 4.2 × 10<sup>-8</sup>) with subpleural-predominant ILAs. These novel associations were not associated with IPF. Among 12 previously reported IPF GWAS loci, five (<i>DPP9</i>, <i>DSP</i>, <i>FAM13A</i>, <i>IVD</i>, and <i>MUC5B</i>) were significantly associated (<i>P</i> < 0.05/12) with ILAs.<b>Conclusions:</b> In a GWAS of ILAs in six studies, we confirmed the association with a <i>MUC5B</i> promoter variant and found strong evidence for an effect of previously described IPF loci; however, novel ILA associations were not associated with IPF. These findings highlight common genetically driven biologic pathways between ILAs and IPF, and also suggest distinct ones.
Yet another pattern recognition receptor involved in the chemotherapy-induced anticancer immune response: Formyl peptide receptor-1 (2016)

Several pattern recognition receptors including toll-like receptors and purinergic receptors are implicated in the anticancer immune response elicited by anthracyclines or oxaliplatin. Recently, formyl peptide receptor-1 (FPR1) has been involved in this response as well. FPR1 is required for the correct positioning of dendritic cells (DC) close to dying cancer cells. A genetic defect in FPR1 abrogates cross-presentation of tumor antigens by DC, thereby compromising therapy-elicited immunosurveillance.
Computational Statistics in the Earth Sciences (2017)

Based on a course taught by the author, this book combines the theoretical underpinnings of statistics with the practical analysis of Earth sciences data using MATLAB. The book is organized to introduce the underlying concepts, and then extends these to the data, covering methods that are most applicable to Earth sciences. Topics include classical parametric estimation and hypothesis testing, and more advanced least squares-based, nonparametric, and resampling estimators. Multivariate data analysis, not often encountered in introductory texts, is presented later in the book, and compositional data is treated at the end. Datasets and bespoke MATLAB scripts used in the book are available online, as well as additional datasets and suggested questions for use by instructors. Aimed at entering graduate students and practicing researchers in the Earth and ocean sciences, this book is ideal for those who want to learn how to analyse data using MATLAB in a statistically-rigorous manner.
Modified CT Limits Analysis for Practical Well Intervention Design (2002)

Abstract An alternative to the standard graphical presentation of CT operating limits is proposed in this paper to facilitate design of CT well interventions and to guide operational decisions in critical, at-risk procedures. Typical issues in intervention design include maximum safe overpull and maximum safe circulating and annular fluid pressures and the interplay between these parameters. However, CT job designers are sometimes unfamiliar with the interrelation between tension and fluid pressures. In particular, the relationship between surface weight and actual tubing stress is often overlooked. This interrelation can be explained and interpreted via the concepts of effective and real force. Based on a presentation of effective and real force, this paper proposes a graphical presentation of CT limits which references effective force, specifically surface weight. Using this modified stress graph, safe operating limits can be more clearly inferred from actual job parameters such as surface weight and pressure.
Development and Validation of a Mobile Application to Detect Visual Dysfunction Following Mild Traumatic Brain Injury (2021)

iPad measures of NPC were highly correlated with clinical measures, while visual acuity measured with the iPad showed modest correlation. Nonetheless, the suite of visual assessments provide value as screening tools, and when used in combination with reading fluency assessment and self-reported CI may be effective in identifying visual dysfunction following mild traumatic brain injury.