gebhart/patrepeval huggingface dataset:
243 GENE EXPRESSION PROFILING BY NEXT-GENERATION SEQUENCING OF cDNA SAMPLES FROM INNER CELL MASS AND TROPHECTODERM OF A SINGLE-DAY 12 PORCINE EMBRYO (2009)

Traditional microarray approaches to gene expression profiling often require RNA or cDNA amplification when working with extremely small or valuable tissue samples.This process is generally viewed as being undesirable because there is potential for bias to be introduced during amplification. Very recently, the so-called next-generation sequencing technologies were adapted for use in global gene expression profiling. Herein we report our efforts to apply these sequencing technologies to assess relative transcript abundances in pre-implantation-stage porcine embryos, without additional nucleic acid amplification before sequencing. As a proof-of-principle experiment, we have isolated total RNA from the embryonic disc (inner cell mass; ICM) and a small piece of trophectoderm (TE) from a Day 12 in vivo-produced embryo, which were estimated to be composed of 500 to 1000 cells each. The RNA was reverse transcribed using oligo-dT priming followed by second-strand cDNA synthesis. The double-stranded cDNA was then randomly sheared by sonication, and 10 ng of double-stranded cDNA fragments was used for sample preparation before sequencing. Prepared cDNA fragments (at 7 picomolar concentrations) were submitted for sequencing using the Illumina/Solexa platform as recommended. The millions of short (36 bp) reads generated by Illumina sequencing for each sample were then aligned to the swine UniGene database from NCBI, allowing for zero or one mismatches. Relative transcript abundances between cell types were profiled by considering the read counts for a given UniGene member as a percentage of the total number of reads generated for each cell type. It was demonstrated that approximately 11 000 and 9000 UniGene members were represented by a normalized average of 5 or more short reads per lane (0.001% of the total) in the ICM and TE samples, respectively. As expected, pluripotency factors, chromatin remodeling components, and cell-cell communication molecules were overrepresented in the ICM sample as compared with the TE sample. Conversely, epithelial determinants, ion transporters, and components of the steroid biosynthesis pathways were more abundant in the TE sample than in the ICM sample. Relative abundances of representative transcripts in these samples were verified by quantitative RT-PCR. In conclusion, we demonstrate the utility of next-generation sequencing technologies for gene expression profiling using even minute tissue samples and show that such analyses are possible even in species without a sequenced genome.
Temporal stability of gel relaxation-time phantoms for quality control of T1 and extracellular volume fraction measurements (2014)

Background Quantification of interstitial fibrosis by T1-mapping continues to gather momentum clinically with the recognition that extracellular volume fraction (ECV) measurements are pathologically elevated in a range of conditions. Well-known dependence of ECV estimation on imaging parameters requires quality-control by T1 phantoms[1-3]. These typically comprise agarose with NiCl[2] doping,[4] and are often used short-term, but with limited long-term data[5]. Such phantoms might assure long-term stability (over years) of methods applied in patients eg against scanner alterations. We therefore sought to assess their long-term T1 and T2 stability.
Tenascin C to regulate the function of sHER3, an endogenous inhibitor of neuregulin signaling. (2017)

e23002 Background: HER3 expression is associated with poor prognosis in melanoma patients but the mechanistic basis has not been determined. An endogenous secreted isoform of HER3, p85-sHER3, has been shown by us to inhibit neuregulin-1 mediated, Akt-dependent breast and ovarian cancer cell growth in vitro. Here we demonstrate that p85-sHER3 also regulates neuregulin-dependent melanoma cell migration via an Akt- independent, tenascin C-dependent mechanism. Methods: Immunoblot analysis and RT-PCR were used to study HER3 and p85-sHER expression. Cell proliferation and chamber assays were conducted to determine the effect of p85-sHER3 on melanoma cell growth and migration. Mass spectrometry (MS) was performed to identify sHER3-interacting proteins. CRSPR in vitro editing methods were used to knock out tenascin C (TNC) expression. Results: HER3 and p85-sHER3 were expressed in 5 of 6 human melanoma-derived cell lines tested, with exception of SK-MEL-103 which did not express either gene product. Exogenous addition of 10 nM p85-sHER3 inhibited growth in 3 cells lines, although Akt phosphorylation was not reduced. Protein extracts from M14-MEL cell conditioned media were characterized by MS, and identified p85-sHER3 and TNC. Their association was confirmed by co-immunoprecipitation. sHER3 was further shown to inhibit neuregulin stimulated cell migration in 2 cell lines which exhibited high levels of TNC. CRSPR knockout of TNC in these cell lines (but not in control lines) eliminated sHER3 inhibition of neuregulin stimulated melanoma cell migration. Conclusions: Our results suggest that p85-sHER3, predominantly secreted by HER3-expressing melanoma cells, inhibits melanoma cell proliferation and migration via an Akt-independent mechanism, which is likely achieved through interaction(s) with TNC. TNC promotes an intermediate adhesive state favoring cell migration and this state appears to be mediated by Rho-associated kinase signaling. The Rho inhibitor, CCG-203971 has been shown to inhibit melanoma cell migration. Together, these results suggest the existence of a TNC and HER3-dependent signaling pathway in melanoma that regulates cell migration, and therefore may be correlated with poor patient survival.
What are the costs of heart failure? (2011)

Heart failure , a syndrome associated with increasing prevalence, high mortality, and frequent hospital admissions, imposes a significant economic burden on western healthcare systems that is expected to further increase in the future due to the ageing population. Hospitalizations are responsible for the largest part of treatment costs and, thus, the main target for strategies aiming at cost reduction. Current literature suggests that evidence-based therapy with drugs, devices, and modern disease management programmes improves clinical outcomes of the large population of heart failure patients in a largely cost-effective manner. However, comprehensive knowledge about the cost of treatment is important to guide clinicians in the responsible allocation of today's limited health-care resources. This review provides information about the total cost of heart failure and the contribution of different treatment components to the overall costs.
Hierarchical routing on unstructured identifiers (2008)

The power point presentation presents the existing solution and methods for the problems in the IP routing paradigm such as small changes in host, reduced, id/loc split with overlapping identifier scopes and caching for higher performance.
Application of Artificial Intelligence Techniques to Predict the Well Productivity of Fishbone Wells (2019)

Fishbone multilateral wells are applied to enhance well productivity by increasing the contact area between the bottomhole and reservoir region. Fishbone wells are characterized by reduced operational time and a competitive cost in comparison to hydraulic fracturing operations. However, limited models are reported to determine the productivity of fishbone wells. In this paper, several artificial intelligence methods were applied to estimate the performance of fishbone wells producing from a heterogeneous and anisotropic gas reservoir. The well productivity was determined using an artificial neural network, a fuzzy logic system and a radial basis network. The models were developed and validated utilizing 250 data sets, with the inputs being the permeability ratio (Kh/Kv), flowing bottomhole pressure and lateral length. The results showed that the artificial intelligence models were able to predict the fishbone well productivity with an acceptable absolute error of 7.23%. Moreover, a mathematical equation was extracted from the artificial neural network, which is able to provide a simple and direct estimation of fishbone well productivity. Actual flow tests were used to evaluate the reliability of the developed model, and a very acceptable match was obtained between the predicted and actual flow rates, wherein an absolute error of 6.92% was achieved. This paper presents effective models for determining the well performance of complex multilateral wells producing from heterogeneous reservoirs. The developed models will help to reduce the uncertainty associated with numerical methods, and the extracted equation can be inserted into commercial software, thereby significantly reducing deviation between the actual data and simulated results.
Colocación de vías centrales de inserción periférica mediante métodos de imagen. Experiencia en un hospital infantil (2012)

Poster: SERAM 2012 / S-0792 / Colocacion de vias centrales de insercion periferica mediante metodos de imagen. Experiencia en un hospital infantil by: Albi Rodriguez, I. Solis Muniz, E. Garcia Esparza, M. A. Lopez Pino, S. I. Sirvent, G. Gomez Mardones; Madrid/ES
Evaluation of diabetic retinopathy severity on ultrawide field colour images compared with ultrawide fluorescein angiograms (2023)

When evaluating UWF-FA images using the ETDRS colour severity scale, DRSS is graded as more severe in a substantial number of eyes than when evaluating UWF-CI. It is uncertain how the DRSS levels using UWF-FA translate to clinical outcomes, but the additional lesions detected might provide added prognostic value. These and other recent data emphasise the need of obtaining outcome data based on UWF-FA and the potential need to develop DRSS specifically tailored for UWF-FA images.
Experimental challenge of a North American bat species, big brown bat ( Eptesicus fuscus ), with SARS‐CoV‐2 (2020)

The recently emerged novel coronavirus, SARS-CoV-2, is phylogenetically related to bat coronaviruses (CoVs), specifically SARS-related CoVs from the Eurasian bat family Rhinolophidae. As this human pandemic virus has spread across the world, the potential impacts of SARS-CoV-2 on native North American bat populations are unknown, as is the ability of North American bats to serve as reservoirs or intermediate hosts able to transmit the virus to humans or to other animal species. To help determine the impacts of the pandemic virus on North American bat populations, we experimentally challenged big brown bats (Eptesicus fuscus) with SARS-CoV-2 under BSL-3 conditions. We inoculated the bats both oropharyngeally and nasally, and over the ensuing three weeks, we measured infectivity, pathology, virus concentrations in tissues, oral and rectal virus excretion, virus transmission, and clinical signs of disease. We found no evidence of SARS-CoV-2 infection in any examined bat, including no viral excretion, no transmission, no detectable virus in tissues, and no signs of disease or pathology. Based on our findings, it appears that big brown bats are resistant to infection with the SARS-CoV-2. The potential susceptibility of other North American bat species to SARS-CoV-2 remains to be investigated.
Quantitative and Selective Analysis of Feline Growth Related Proteins Using Parallel Reaction Monitoring High Resolution Mass Spectrometry (2016)

Today immunoassays are widely used in veterinary medicine, but lack of species specific assays often necessitates the use of assays developed for human applications. Mass spectrometry (MS) is an attractive alternative due to high specificity and versatility, allowing for species-independent analysis. Targeted MS-based quantification methods are valuable complements to large scale shotgun analysis. A method referred to as parallel reaction monitoring (PRM), implemented on Orbitrap MS, has lately been presented as an excellent alternative to more traditional selected reaction monitoring/multiple reaction monitoring (SRM/MRM) methods. The insulin-like growth factor (IGF)-system is not well described in the cat but there are indications of important differences between cats and humans. In feline medicine IGF-I is mainly analyzed for diagnosis of growth hormone disorders but also for research, while the other proteins in the IGF-system are not routinely analyzed within clinical practice. Here, a PRM method for quantification of IGF-I, IGF-II, IGF binding protein (BP) -3 and IGFBP-5 in feline serum is presented. Selective quantification was supported by the use of a newly launched internal standard named QPrEST™. Homology searches demonstrated the possibility to use this standard of human origin for quantification of the targeted feline proteins. Excellent quantitative sensitivity at the attomol/μL (pM) level and selectivity were obtained. As the presented approach is very generic we show that high resolution mass spectrometry in combination with PRM and QPrEST™ internal standards is a versatile tool for protein quantitation across multispecies.
Randomized phase I and pharmacological study of weekly or 2-weekly gemcitabine and cisplatin in advanced non-small cell lung cancer (2002)

inhibitory effect were not significantly different between hetEMs and homEMs, although there was a trend towards an increased AUC and acid-inhibitory effect in hetEMs.Therefore we compared the acid-inhibitory effect of LPZ and OPZ to baseline.Compared with baseline median 24 h pH and % of time pH > 4 at day 1 were significantly increased in hetEMs, but not in homEMs for both LPZ and OPZ.At day 6 the differences in acid-inhibitory effect between hetEMs and homEMs were not significant.At day 1 of administration acid inhibitory effect of LPZ 15 mg and OPZ 10 mg is affected by CYP2C19 polymorphism.Compared with baseline, there was at day 1 a significant acid-inhibitory effect in hetEMs, but not in homEMs.
Comparison of NOx Removal Efficiencies in Compost Based Biofilters Using Four Different Compost Sources (2001)

This is a preprint of a paper intended for publication in a journal or proceedings. Since changes may be made before publication, this preprint should not be cited or reproduced without permission of the author. This document was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, or any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility for any third party&amp;apos;s use, or the results of such use, of any information, apparatus, product or process disclosed in this report, or represents that its use by such third party would not infringe privately owned rights. The views expressed in this paper are not necessarily those of the U.S. Government or the sponsoring agency.
Importance of the DNA “Bond” in Programmable Nanoparticle Crystallization* (2020)

In this chapter, the authors observe the reorganization of nanoparticle superlattices using time-resolved synchrotron small-angle X-ray scattering in systems with different DNA sequences, salt concentrations, and densities of DNA linkers on the surface of the nanoparticles. The agreement between bulk crystallization and the behavior of free oligonucleotides may bear important consequences for constructing novel classes of crystals and incorporating new interparticle bonds in a rational manner. The authors evaluate the formation and reorganization of these crystals in a time-resolved manner using small-angle X-ray scattering to study how crystallization dynamics are affected by each design variable. They develop a predictive model that allows one to compare the range of temperatures over which crystallization will occur for different conditions. The authors explain reorganization kinetics based upon how the rates of hybridization and dehybridization change as a function of design variables including temperature, nucleobase sequence, oligonucleotide density, and solution ionic strength.
Effectiveness of Glycerol Mono-oleate as a Biosealant. (2008)

In conclusion, these results illustrate a significant hemostatic effect post liver biopsy at multiple time points using GMO. Furthermore, GMO displays bacterial deterrent properties.
Artificial intelligence in real-time control 1998 : a proceedings volume from the 7th IFAC Symposium, Grand Canyon National Park, Arizona, USA, 5-8 October 1998 (1999)

Chapter headings and selected papers: Architectures for Real-Time Expert Systems. Handling timing in a time-critical reasoning system in a case study (L. Motus). Hybrid Systems. Behavioral programming: enabling a middle-out approach to learning and intelligent systems (M.S. Branicky). Evolutionary. How fast can a species adapt and still be evolutionary stable (T.L. Vincent). Real-World Tasks. A study and implementation of intelligent node based on LonWorks technology (Junjie Wang). Special Session on Distributed Control & Panel Discussion. Flow control with electric actuators (C.C. Federspiel). Visualization & Imaging. Spectroscopic imaging sensors in materials process control (J.F. Maguire). Evolutionary. Synthetic optimization approach of combining regional guided order principle and biological evolution strategies and its applications (Chang-Yun Shen). Theoretical Issues & Topics. Compactness of a set of membership functions in L2 space and its application to fuzzy optimal control (Takashi Mitsuishi). Fuzzy or Rough Sets. Predictive control by multiple-step linearization of Takagi-Sugeno fuzzy models (S. Mollov et al.). Framework for approximate time rough control systems an integrated fuzzy sets-rough sets approach (J.F. Peters et al.). Generic Principles and Strategies. Fault-tolerant process control and some future directions (Jianbo Meng). Nonlinear process modeling using a dynamically recurrent neural network (Shi-Rong Liu). Real-World Tasks. Mimicking a fuzzy flight controller using B-splines (A. Aznar Fernandez-Montesinos et al.).
1532. Increased Risk of Bacterial, Fungal and Other Viral Infections During CMV Infection: Decreased Cytokine Production in Response to Toll-Like Receptor Ligands (2018)

In the solid-organ transplant (SOT) setting, CMV is an immunomodulatory virus that indirectly increases the risk for bacterial, fungal and viral infections. However, the pathogenesis of this phenomenon is poorly understood. The aim of our study was to determine whether inflammatory responses to different Toll-like receptor ligands are blunted during CMV infection in SOT patients. CMV D+/R− SOT patients had blood drawn at the end of CMV prophylaxis and then weekly after onset of CMV viremia. PBMCs were extracted and incubated for 24 hours in the presence of bacterial (LPS), fungal (Zymosan [ZYM]), and viral (Resiquimod [R848]) ligands. Proinflammatory (IL1β), Th1 (IFNγ), Th2 (IL4), immunoregulatory (IL10), and chemotactic (MCP1) cytokines were measured in the supernatant by multiplex ELISA. Thirty-eight SOT patients were followed for at least 9 months. Patients who developed subsequent CMV infection had lower cytokines in response to bacterial, fungal and viral ligands (LPS, ZYM, and R848) at the end of prophylaxis compared with those with no CMV infection. These results were independent of immunosuppression and peripheral blood cell counts. Specifically, these trends were significantly different with respect to IFNγ, IL1β, and IL10 production in response to LPS (P = 0.003, 0.003, and 0.039, respectively), R848 (P < 0.001, 0.039, and <0.001, respectively) and ZYM (P = 0.039, 0.003, and 0.003, respectively), as well as for MCP1 in response to R848 or ZYM (P = 0.039 for both). In the cohort with CMV infection, cytokine responses to TLR ligands were even lower during the acute CMV infection when compared with the end of prophylaxis, although this was significant only for IL10 production after R848 stimulation (P = 0.034). There was no influence of CMV viral load or duration of viremia on cytokine levels. Response to non-CMV antigens during CMV infection was blunted supporting the clinical observation in transplant recipients that CMV infection increases susceptibility to bacterial, fungal, and other viral infections. However, inherent differences in patients that are neither directly related to CMV nor to their net level of immunosuppression also contribute to this increased susceptibility, as cytokine levels at the end of prophylaxis were lower among patients with compared with those without subsequent CMV infection. All authors: No reported disclosures.
Composition of the Essential Oil of Two Nepeta Species and in vitro Evaluation of their Activity against Helicobacter pylori (2001)

The chemical composition of the essential oils obtained from the aerial parts of Nepeta camphorata and Nepeta argolica ssp. dirphya were analysed by GC-MS. A total of 52 components were identified and significant differences (qualitative and quantitative) were observed between the two samples. 1,8-Cineol and two nepetalactones were found to be the major components of the oil of N. camphorata and N. argolica ssp. dirphya respectively. The in vitro activity, of the two oils and the three above mentioned isolated compounds, against 25 clinically isolated and commercial strains of Helicobacter pylori was investigated and some activity was found.
Sox17 modulates Wnt3A/β-catenin-mediated transcriptional activation of the Lef-1 promoter (2010)

Wnt/β-catenin-dependent activation of lymphoid enhancer factor 1 (Lef-1) plays an important role in numerous developmental processes. In this context, transcription of the Lef-1 gene is increased by Wnt-mediated TCF4/β-catenin activation on the Lef-1 promoter through mechanisms that remain poorly defined. In mouse airway submucosal gland progenitor cells, Wnt3A transiently induces Lef-1 gene expression, and this process is required for epithelial cell proliferation and glandular morphogenesis. In the present study, we sought to identify additional candidate transcriptional regulators of the Lef-1 gene during glandular morphogenesis. To this end, we found that Sox17 expression is dramatically downregulated in early glandular progenitor cells that induce Lef-1 expression. Wnt stimulation of undifferentiated primary airway epithelial cells induced similar changes in Sox17 and Lef-1 expression. Reporter assays revealed that ectopic expression of Sox17 suppresses Wnt3A/β-catenin activation of the Lef-1 promoter in cell lines. EMSA and ChIP analyses defined several Sox17- and TCF4-binding sites that collaborate in transcriptional control of the Lef-1 promoter. More specifically, Sox17 bound to four sites in the Lef-1 promoter, either directly or indirectly through TCF complexes. The DNA- or β-catenin-binding domains of Sox17 controlled context-specific binding of Sox17/TCF complexes on the Lef-1 promoter. Combinatorial site-directed mutagenesis of Sox17- or TCF-binding sites in the Lef-1 promoter demonstrated that these sites control Wnt/β-catenin-mediated induction and/or repression. These findings demonstrate for the first time that Sox17 can directly regulate Wnt/β-catenin-dependent transcription of the Lef-1 promoter and reveal new context-dependent binding sites in the Lef-1 promoter that facilitate protein-protein interactions between Sox17 and TCF4.