gebhart/patrepeval huggingface dataset:
Epigenetic regulation of Neuregulin-1 tunes white adipose stem cell differentiation (2020)

Abstract Expansion of subcutaneous adipose tissue by differentiation of new adipocytes has been linked to improvements in metabolic health. However, an expandability limit has been observed wherein new adipocytes cannot be produced, the existing adipocytes become enlarged (hypertrophic) and lipids spill over into ectopic sites. Inappropriate ectopic storage of these surplus lipids in liver, muscle, and visceral depots has been linked with metabolic dysfunction. Here we show that Neuregulin-1 (NRG1) serves as a regulator of adipogenic differentiation in subcutaneous primary human stem cells. We further demonstrate that DNA methylation modulates NRG1 expression in these cells, and a 3-day exposure of stem cells to a recombinant NRG1 peptide fragment is sufficient to reprogram adipogenic cellular differentiation to higher levels. These results define a novel molecular adipogenic rheostat with potential implications for the expansion of adipose tissue in vivo .
Confidence evaluation for robust, fast-converging disparity map refinement (2010)

To improve upon the initial disparity estimates stemming from a local correspondence method, a subsequent refinement step is commonly employed. The performance of the stereo matcher used for the initial estimation inherently depends on the underlying image content. For some regions of an image, it may be difficult or even physically impossible to establish accurate point correspondences. This results in disparity estimates of varying accuracy and reliability. In this paper, a confidence map is proposed which combines the consistency and quality of a match. It explicitly models the reliability of each disparity estimate. Such a confidence map represents valuable, additional information that can be leveraged in subsequent steps of the 3D processing chain. In this regard, this paper presents an extension of a cross bilateral filter that leverages this reliability information during a fast-converging refinement step in order to create robust and reliable disparity maps.
Evaluation and Improvement of Real-Time PCR Assays Targeting <i>lytA</i> , <i>ply</i> , and <i>psaA</i> Genes for Detection of Pneumococcal DNA (2007)

The accurate diagnosis of pneumococcal disease has frequently been hampered not only by the difficulties in obtaining isolates of the organism from patient specimens but also by the misidentification of pneumococcus-like viridans group streptococci (P-LVS) as Streptococcus pneumoniae. This is especially critical when the specimen comes from the respiratory tract. In this study, three novel real-time PCR assays designed for the detection of specific sequence regions of the lytA, ply, and psaA genes were developed (lytA-CDC, ply-CDC, and psaA, respectively). These assays showed high sensitivity (<10 copies for lytA-CDC and ply-CDC and an approximately twofold less sensitivity for psaA). Two additional real-time PCR assays for lytA and ply described previously for pneumococcal DNA detection were also evaluated. A panel of isolates consisting of 67 S. pneumoniae isolates (44 different serotypes and 3 nonencapsulated S. pneumoniae isolates from conjunctivitis outbreaks) and 104 nonpneumococcal isolates was used. The 67 S. pneumoniae isolates were reactive in all five assays. The new real-time detection assays targeting the lytA and psaA genes were the most specific for the detection of isolates confirmed to be S. pneumoniae, with lytA-CDC showing the greatest specificity. Both ply PCRs were positive for all isolates of S. pseudopneumoniae, along with 13 other isolates of other P-LVS isolates confirmed to be non-S. pneumoniae by DNA-DNA reassociation. Thus, the use of the ply gene for the detection of pneumococci can lead to false-positive reactions in the presence of P-LVS. The five assays were applied to 15 culture-positive cerebrospinal fluid specimens with 100% sensitivity; and serum and ear fluid specimens were also evaluated. Both the lytA-CDC and psaA assays, particularly the lytA-CDC assay, have improved specificities compared with those of currently available assays and should therefore be considered the assays of choice for the detection of pneumococcal DNA, particularly when upper respiratory P-LVS might be present in the clinical specimen.
Abstract CT301: Phase I study of SurVaxM in patients with survivin-expressing recurrent malignant gliomas (2015)

Abstract Background: Recent studies using SurVaxM, a survivin based multi-epitope cryptic peptide mimic, show specific CD8+ T cell responses and specific CD4+ T cell stimulation. Currently SurVaxM has completed a phase I clinical trial designed to study its safety, tolerability and immunological effects in patients with survivin-positive recurrent malignant gliomas. Survivin is an intracellular inhibitor of apoptosis protein (IAP) that mediates a number of anti-apoptotic and oncogenic effects and is highly expressed in malignant gliomas and other cancers. The vaccine is immunogenic in humans with HLA-A*02, HLA-A*03, HLA-A*24 and other haplotypes and pre-clinical studies demonstrate potent and specific cytokine-supported antitumor CTL responses. Methods: Nine patients with survivin-positive, recurrent malignant gliomas and either HLA-A*02 or HLA-A*03 haplotypes received a series of 4 subcutaneous injections of SurVaxM at 2 week intervals. MRIs were performed at baseline, week 8, and at subsequent intervals. Results: SurVaxM was well tolerated with no SAE related to vaccine administration. Most AE were grade 1, including 6 of 9 patients with grade 1 localized erythema at the injection site. Three patients reported grades 1 or 2 fatigue, 2/9 experienced myalgia, possibly related to the study drug. Grade 1 lymphopenia was seen in 3/9 patients and grade 1 or 2 leukopenia was recorded in 3 patients. The only grade 3 AE, a seizure, was not related to the vaccine. The majority of patients developed specific cellular and humoral immune responses to survivin and 3 of 8 patients (all with recurrent glioblastoma), who are evaluable for clinical response, had stable disease after 17-26 months of ongoing follow-up. Five others have had progressive disease, although 4 of these maintained stable disease for 8-14 months. Conclusion: This study demonstrated the safety and tolerability of SurVaxM in patients with recurrent or progressive malignant glioma following failure of standard therapy. SurVaxM proved to be immunogenic in most patients. By activating multiple CD8+ CTL responses and CD4+ helper support, SurVaxM has a significant theoretical advantage as an active specific immunogen compared with survivin vaccines using a single class I-restricted peptide, or ones that incorporate generic helper peptides, which produce non-specific helper support. Early indicators point to a strong rationale for continued study. A phase II clinical trial of SurVaxM is planned. Citation Format: Michael J. Ciesielski, Laszlo Mechtler, Kathleen Mogensen, Jingxin Qiu, Manmeet Ahluwalia, Kelvin Lee, Alex Adjei, Robert Fenstermaker. Phase I study of SurVaxM in patients with survivin-expressing recurrent malignant gliomas. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr CT301. doi:10.1158/1538-7445.AM2015-CT301
Multiple-Band Bit-Level Switching in Two-Pump Fiber Parametric Devices (2004)

We investigated the feasibility of multiple-band switching using a two-pump fiber parametric device. The switching architecture combines band amplification, wavelength conversion, and selective signal conjugation, enabled by temporal control of one or both parametric pumps. A switching scheme with a single pump control was constructed and evaluated. Multiple-band bit-level optical switching is demonstrated over bandwidth greater than 50 nm, with a maximal conversion efficiency of 24.2 dB.
In Vitro Evaluation of New, Potent and Selective V2 Receptor Agonists (2015)

The vasopressin analogue desmopressin (dDAVP, 1) is a potent V2 receptor agonist that also activates the related V1b receptor [1]. dDAVP is approved in many countries for the treatment of diabetes insipidus, primary nocturnal enuresis, nocturia, and coagulation disorders including hemophilia A and von Willebrand’s disease. In search of novel, potent, selective and pharmacologically useful peptidic V2R agonists, we synthesized a series of C-terminally truncated [Val4]dDAVP (2) [2] analogs modified in positions 2, 3, 7 and/or at the disulfide bridge. The peptides were evaluated for in vitro potency at the humanV2 receptor (hV2R) and selectivity versus related receptors (hV1aR, hV1bR, hOTR). Here we present comprehensive in vitro data for the new compounds and describe synthetic methods used to prepare the analogues.
Textile-templated electrospun anisotropic scaffolds for tissue engineering and regenerative medicine (2010)

Cardiovascular diseases, specifically myocardial infarction and end-stage heart failure represent some of the major pathologies that threaten human life. Here we present a novel approach for a bioactive cardiac patch based on a combination of biomedical and textile manufacturing techniques in concert with nano-biotechnology based tissue-engineering stratagems. The technological goal is to create BioNanoTextiles™ (BNT) by using "conventional" fabrics as templates for creating three-dimensional nanofibrous scaffolds. Electrospinning nanofibrous scaffolds templated after "ordinary" textiles is a novel way to create complex-patterned, 3-D scaffolds intrinsically mimicking some of the anisotropic structural features of the ventricular wall's extracellular matrix. In preliminary studies, we established that this approach will yield anisotropic 3-D scaffolds with mechanical properties dependent upon the yarn type of the textile-templates. These scaffolds are biocompatible, as inferred from their support of H9C2 cardiac myoblast adhesion which promotes their proliferation as well as cardiac-like anisotropic organization. The use of textile manufacturing strategies will enhance the complexity of the 3-D scaffold structures and enable their commercialization, while providing an opportunity for the textile industry to advance established "low-tech" manufacturing technologies into the realm of "high-tech" BioNanoTextiles.
Developing Antidote Controlled Antiplatelet Therapies By Targeting The Vwf ‐ Gp Ib‐Ix‐V Interaction (2007)

Peer Reviewed
Novel dispersion tolerant interferometry method for accurate measurements of displacement (2015)

We demonstrate that the recently proposed master-slave interferometry method is able to provide true dispersion free depth profiles in a spectrometer-based set-up that can be used for accurate displacement measurements in sensing and optical coherence tomography. The proposed technique is based on correlating the channelled spectra produced by the linear camera in the spectrometer with previously recorded masks. As such technique is not based on Fourier transformations (FT), it does not require any resampling of data and is immune to any amounts of dispersion left unbalanced in the system. In order to prove the tolerance of technique to dispersion, different lengths of optical fiber are used in the interferometer to introduce dispersion and it is demonstrated that neither the sensitivity profile versus optical path difference (OPD) nor the depth resolution are affected. In opposition, it is shown that the classical FT based methods using calibrated data provide less accurate optical path length measurements and exhibit a quicker decays of sensitivity with OPD.
Seismic characterization of reservoirs containing multiple fracture sets (2007)

Natural fractures in reservoirs play an important role in determining fluid flow during production, and knowledge of the orientation and density of fractures is required to optimize production. Variations in reflection amplitude as a function of azimuth and incidence angle are sensitive to the presence of fractures, but current models used to invert the seismic response often make simplified assumptions that prevent fractured reservoirs from being characterized correctly. For example, many models assume a single set of perfectly aligned fractures, whereas most reservoirs contain several fracture sets with variable orientation within a given fracture set. In this paper, the variation in the reflection coefficient of seismic P‐waves as a function of azimuth and offset is used to determine the components of a second‐rank fracture compliance tensor. The variation in the trace of this tensor as a function of position in the reservoir can be used to estimate the variation in fracture density and permeability of the fracture network, and may be used to choose the location of infill wells in the field. The use of this tensor to estimate the anisotropy of the permeability tensor, the orientation of deviated wells, and the relative orientation of neighboring infill wells to ensure adequate drainage is discussed.
CX3CR1+ mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22 (2014)

Interleukin (IL)-22-producing group 3 innate lymphoid cells (ILC3) promote mucosal healing and maintain barrier integrity, but how microbial signals are integrated to regulate mucosal protection offered by these cells remains unclear. Here, we show that in vivo depletion of CX₃CR1⁺ mononuclear phagocytes (MNPs) resulted in more severe colitis and death after infection with Citrobacter rodentium. This phenotype was rescued by exogenous IL-22, which was endogenously produced by ILC3 in close spatial proximity to CX₃CR1⁺ MNPs that were dependent on MyD88 signaling. CX₃CR1⁺MNPs from both mouse and human tissue produced more IL-23 and IL-1β than conventional CD103(+) dendritic cells (cDCs) and were more efficient than cDCs in supporting IL-22 production in ILC3 in vitro and in vivo. Further, colonic ILC3 from patients with mild to moderate ulcerative colitis or Crohn's disease had increased IL-22 production. IBD-associated SNP gene set analysis revealed enrichment for genes selectively expressed in human intestinal MNPs. The product of one of these, TL1A, potently enhanced IL-23- and IL-1β-induced production of IL-22 and GM-CSF by ILC3. Collectively, these results reveal a critical role for CX₃CR1⁺ mononuclear phagocytes in integrating microbial signals to regulate colonic ILC3 function in IBD.
Pharmacological activities of imidazo[1,2-alpha]pyrazine derivatives. (1995)

The smooth muscle relaxant activity and other pharmacological properties of imidazo[1,2-alpha]pyrazine derivatives were compared with those of theophylline. Imidazo[1,2-alpha]pyrazine derivatives exhibited a potent smooth muscle relaxant activity regardless of the agent which had elicited the contraction and thus showed a broad spectrum of non specific smooth muscle relaxant activity. In the isolated guinea-pig atria, imidazo[1,2-alpha]pyrazine derivatives exhibited potent inotropic and chronotropic activities. As opposed to theophylline, the imidazo[1,2-alpha]pyrazine derivatives tested were unable to antagonize the adenosine-induced inhibition of spontaneous contractile activity of rabbit ileum. Furthermore, as opposed to theophylline, these derivatives did not exhibit a marked diuretic activity. Thus it appears that they do not act as adenosine receptor antagonists. Imidazo[1,2-alpha]pyrazine derivatives inhibited the total cAMP-phosphodiesterase (cAMP-PDE) and the total cGMP-phosphodiesterase (cGMP-PDE) activities of bovine trachea but with relatively low potencies, sharing a discrepancy between their activity on isolated tissues and their ability to inhibit PDE. It is suggested that imidazo[1,2-alpha]pyrazine derivatives may selectively inhibit type III and/or type IV phosphodiesterase isoenzymes involved in the regulation of the mechanical activity of cardiac and smooth muscle tissues.
Identification of an interleukin-15 antagonist peptide (2008)

La interleucina-15 (IL-15) es una citocina pro-inflamatoria que se expresa en muchas enfermedades autoinmunes e inflamatorias. Nosotros hemos identificado la secuencia 36-45 KVTAMKCFLL de la IL-15 humana, que es reconocida por la proteina de fusion hIL-15Rα-Fc soluble. Esta secuencia sintetizada como un peptido de 10 aa , se une a la IL-15Rα y bloquea la actividad biologica de la IL-15 en dos lineas celulares dependientes de IL-15. Ademas, este peptido inhibe la trascripcion de la IL-6 inducida por IL-15Rα en una linea celular humana de carcinoma de prostata; una senalizacion inversa descrita para la IL-15 unida a la membrana. Nosotros tambien examinamos la formacion de dimeros de este peptido y encontramos que cuando la Cys fue remplazada por Ala o Ser se pierde el efecto antagonista del peptido y que el dimero formado a traves de la Cys libre es mas activo que el monomero. Este peptido es el primer antagonista peptidico de la IL-15 descrito hasta el momento y puede ser un potencial agente terapeutico para el tratamiento de enfermedades relacionadas con la expresion de la IL-15
Single-mode quantum cascade lasers employing a candy-cane shaped monolithic coupled cavity (2011)

We demonstrate single-mode quantum cascade lasers emitting at ∼4.5 μm by employing a monolithic “candy-cane” shaped coupled-cavity consisting of a straight section connecting at one end to a spiral section. The fabrication process is identical to those for simple Fabry-Perot-type ridge lasers. Continuously tunable single-mode emission across ∼8 cm−1 with side mode suppression ratio up to ∼25 dB and a single-mode operating current range of more than 70% above the threshold current is achieved when the lasers are operated in pulsed-mode from 80 K to 155 K.
Operational deployment of compressive sensing systems for seismic data acquisition (2017)

Abstract Compressive sensing (CS) provides a new basis for sampling that can increase sampling efficiency for seismic data acquisition by an order of magnitude. A major challenge for this new technology is to show that theoretical increases in sampling efficiency can be translated to real efficiency gains in the field. Along with efficiency gains, data quality must be preserved in order to gain acceptance of a new acquisition technology. CS designs require solution of large optimization problems that are consistent with compressive sampling theory. We refer to our optimization framework for CS-based acquisition design and processing as compressive seismic imaging (CSI). We illustrate our CSI framework on example projects for ocean-bottom node, narrow-azimuth marine streamer, and land vibroseis acquisition. The ocean-bottom-node project was conducted in the UK North Sea during the difficult winter season. A CSI dual-source design was used to significantly reduce shooting time for this project. The project was completed on time, under budget, and with data quality that exceeded the quality of an overlapping uniformly sampled survey. The narrow-azimuth marine CSI survey project was acquired in offshore Australia for field development purposes. Nonuniform CSI sampling was used to increase sampling efficiency for both sources and cables, resulting in significant improvements in data quality and lateral resolution. The land vibroseis project was conducted on the North Slope of Alaska. In this case, the goal was to acquire a development survey of sufficient size within a short time window. Nonuniform CSI sampling was used to support the use of 10 or more vibrators shooting simultaneously, along with improving sampling efficiency for both sources and receivers. Compared to conventional designs, the CSI survey achieved an order of magnitude improvement in field acquisition efficiency and step-function improvements in data quality. These examples show that theoretical improvements in sampling efficiency from CS can make real and significant impacts on seismic data acquisition and processing.
Process for removing NO/sub chi/ and SO/sub chi/ from a gaseous mixture (1989)

This patent describes a combination denitrogenation and desulfurization process. It comprises the steps of: contacting a gaseous mixture comprising nitrogen oxides and sulfur oxides in the presence of oxygen and in the absence of a catalyst, with ammonia in a molar amount equal to the sum of about 1.0 to about 3.0 times the moles of the nitrogen oxides plus about 0.01 to about 2.0 times the moles of the sulfur oxides to reduce the nitrogen oxides to nitrogen, at a temperature ranging from about 1300{sup 0} to about 2200{sup 0}F; passing the gaseous effluent resulting comprising the nitrogen, the sulfur oxides and unreacted ammonia to a gas desulfurization zone maintained at desulfurization conditions, including a temperature ranging from about 100{sup 0} to about 400{sup 0}F, to react the sulfur oxides with ammonia at a molar ratio of at least 1 mole of ammonia per mole of the sulfur oxides to produce a gaseous effluent and an ammonium salt of an acid of sulfur; and recovering the ammonium salt.
Studies in Polyphenol Chemistry and Bioactivity. 3.<sup>1</sup><sup>,</sup><sup>2</sup> Stereocontrolled Synthesis of Epicatechin-4α,8-epicatechin, an Unnatural Isomer of the B-Type Procyanidins (2001)

Oligomeric procyanidins containing 4alpha-linked epicatechin units are rare in nature and have hitherto not been accessible through stereoselective synthesis. We report herein the preparation of the prototypical dimer, epicatechin-4alpha,8-epicatechin (6), by reaction of the protected 4-ketones 11a,b with aryllithium reagents derived by halogen/metal exchange from the aryl bromides 26a,b. Removal of the 4-hydroxyl group from the resulting tertiary benzylic alcohols 27a,b was effected by tri-n-butyltin hydride and trifluoroacetic acid in a completely stereoselective manner, resulting in hydride delivery exclusively from the beta face. If benzyl was chosen for protection of the 3-hydroxyls, all protective groups could subsequently be removed in a single step by hydrogenolysis. tert-Butyldimethylsilyl groups, on the other hand, permitted selective deprotection of the 3-hydroxyls in preparation for their subsequent acylation with tri-O-benzylgalloyl chloride. Only monogalloylation at the "bottom" 3-hydroxyl took place when 28c was acylated under the previously reported conditions, reflecting the increased steric hindrance of the "top" 3-hydroxyl group in 28c compared with its 4beta,8-isomer 3. The preparation of compounds 14 and 17 containing phloroglucinol trimethyl ether in the 4alpha and 4beta linkages to epicatechin is also described. The 8-position of the bromine atom in 19, previously conjectured in analogy to the structurally characterized tetramethyl ether 20, was confirmed by transformation of both compounds into the common derivative 25.
Processing and Characterization of a New Composite Metal Foam (2006)

New closed cell composite metal foam has been processed using both casting and powder metallurgy (PM) techniques. The foam is comprised of steel hollow spheres packed into a dense arrangement, with the interstitial spaces between spheres occupied with a solid metal matrix. Using the casting technique, an aluminum alloy infiltrates the interstitial spaces between steel spheres. In the PM technique, steel spheres and steel powder are sintered to form a solid, closed cell structure. The measured densities of the Al-Fe composite foam, low carbon steel foam, and stainless steel foam are 2.4, 2.6, and 2.9 g/cm3 with relative densities of 42, 34, and 37%, respectively.The composite metal foams composite materials developed in this study displayed superior compressive strength as compared to any other foam being produced with similar materials. The compressive strength of the cast Al-Fe foam averaged 67 MPa over a region of 10 to 50% strain, while the low carbon steel PM foam averaged 76 MPa over the same strain region, and the stainless steel PM foam averaged 136 MPa over the same region. Densification began at approximately 50% for the cast foam and ranged from 50 to 55% for the PM foams. The strength to density ratio of the product of both techniques exceeded twice that of foams processed using other techniques with similar materials.