gebhart/patrepeval huggingface dataset:
Application of Comparative Transcriptional Genomics to Identify Molecular Targets for Pediatric IBD (2015)

Experimental models of colitis in mice have been used extensively for analyzing the molecular events that occur during inflammatory bowel disease (IBD) development. However, it is uncertain to what extent the experimental models reproduce features of human IBD. This is largely due to the lack of precise methods for direct and comprehensive comparison of mouse and human inflamed colon tissue at the molecular level. Here, we use global gene expression patterns of two sets of pediatric IBD and two mouse models of colitis to obtain a direct comparison of the genome signatures of mouse and human IBD. By comparing the two sets of pediatric IBD microarray data, we found 83 genes were differentially expressed in a similar manner between pediatric Crohn's disease and ulcerative colitis. Up-regulation of the chemokine (C-C motif) ligand 2 (CCL2) gene that maps to 17q12, a confirmed IBD susceptibility loci, indicates that our comparison study can reveal known genetic associations with IBD. In comparing pediatric IBD and experimental colitis microarray data, we found common signatures amongst them including: (1) up-regulation of CXCL9 and S100A8; (2) cytokine-cytokine receptor pathway dysregulation; and (3) over-represented IRF1 and IRF2 transcription binding sites in the promoter region of up-regulated genes, and HNF1A and Lhx3 binding sites were over-represented in the promoter region of the down-regulated genes. In summary, this study provides a comprehensive view of transcriptome changes between different pediatric IBD populations in comparison with different colitis models. These findings reveal several new molecular targets for further study in the regulation of colitis.
Effectiveness of Analogs of the GS-Nitroxide, JP4-039, as Total Body Irradiation Mitigators (2017)

Structure-activity relationships and bioassays demonstrate that JP4-039 is an optimized small-molecule radiation mitigator.
Superconformal Filling of High Aspect Ratio through Glass Vias for Interposer Applications Using Tnbt and Ntbc Additives (2015)

The drive toward higher circuit density and higher operating frequencies in electronic packaging has led to the employment of interposers between the Si chip and the underlying package. Currently Si or glass, both are considered materials feasible for the fabrication of interposers. Through-holes are needed to make connections between the top and bottom surfaces of the interposer. This can be done with conformal Cu plating, but especially in the case of glass it is also desirable to fill the through glass vias (TGVs) with Cu to compensate for its poorer thermal conductivity compared to Si. Filling also enables formation of a flat surface for subsequent layers or for component attachment. Techniques have already been developed for filling “blind” holes/vias by Cu electroplating using combinations of suppressors and accelerators. In the case of Si, through-vias have been generated by first filling holes as blind ones. Then thinning the back side of the wafer by CMP is applied until the bottoms of the filled vias are intersected, thereby producing filled through-holes. Alternatively, sealing one end of the through vias could be made and then one could fill them as blind vias. In the case of glass, TGVs may be formed directly into the glass without the need for mechanical thinning, but this leaves the problem of filling the holes as through-holes, open on both ends. The aforementioned plating methods for filling of blind vias do not work well when directly applied to filling of TGVs, and a different approach is needed. In this report, Cu superconformal filling of through glass vias (TGV) of aspect ratios (AR) 6:1 and 10:1 for glass interposer applications is achieved by DC electroplating in the presence of the additives tetranitroblue tetrazolium Cl - (TNBT) and nitroblue tetrazolium Cl - (NTBC) in acidic CuSO 4 / Cl - formulations. Filling takes place by the so-called ‘butterfly’ mechanism that nucleates Cu plug in the TGV’s center and keeps low surface coverage. Holes of AR 6:1 are filled in 3 hours at 2.5 mA.cm -2 , using a bath composed of 40 ppm TNBT, 80 ppm Cl - , 0.88M CuSO4, and 0.3M CH 3 COOH under stagnant conditions. Increasing [TNBT] to 80 ppm and [Cl - ] to 120 ppm in the presence of 0.3 M CH 3 COOH allows filling of 10:1 AR holes in 12.5 hours at 1.0 mA.cm -2 while maintaining thin surface coverage. In the case of NTBC, 6:1 holes are filled in 4-5 h at 2.5 – 4.0 mA.cm -2 , and 10:1 holes are filled in 12-13 h at 1.0 to 1.5 mA.cm -2 in a slowly stirred bath containing 0.88 M CuSO 4 , 80 ppm Cl - , 0.6 M H 2 SO 4, and 45-50 ppm NTBC. Bath composition is necessary to avoid void-formation in the holes. Effects of composition on overvoltage and Cu surface topography are discussed. Finally, a critical discussion on some mechanistic aspects of the supeconformal filling process, taking place according to the Figure, is also presented. Figure 1
Geometric and Solid Modeling: An Introduction (1989)

It is the view of the author that the streams of geometric and solid modeling are converging, and that as the importance of this convergence is anticipated and recognized, the need for the development of techniques to bridge the gap between the two becomes critical. This book is devoted to filling that need. Geometric and Solid Modeling deals with the concepts and tools needed to design and implement solid-modeling systems and their infrastructure and substrata, making this information remarkably accessible--to the novice as well as to the experienced designer. The essential algorithms and the underlying theory needed to design these systems are given primary emphasis. Techniques for the study and implementation of geometric algorithms are taken from computer science, numerical analysis, and symbolic computation, among other areas. Special attention is given to geometric investigations of implicit and parametric surfaces, with the focal point being the possible integration of geometric and solid modeling.
Relation of Oral Hairy Leukoplakia to Infection with the Human Immunodeficiency Virus and the Risk of Developing AIDS (1987)

We investigated the relation of oral hairy leukoplakia (HL) to human immunodeficiency virus (HIV) infection and to the presence or development of AIDS. All 155 patients with HL seen in our clinic were immunosuppressed homosexual men. Of 101 serum samples obtained from patients in this group who did not have AIDS, 100 showed antibodies to HIV. HIV was recovered from peripheral blood mononuclear cells of 22 of 28 patients tested. Most serum samples examined by immunoblot assay reacted with the viral envelope and gag gene precursors gp160 and p55. Of the 155 patients, 12 had AIDS at the time of diagnosis, and the syndrome developed in an additional 43 patients in one to 31 months. Survival analysis showed that the probability of AIDS developing in patients with HL was 48% by 16 months and 83% by 31 months. We conclude that oral HL is highly predictive of the development of AIDS.
Early to mid-term results of total knee arthroplasty in hemophilic knees: a review of 34 cases (2008)

Total knee arthroplasty (TKA) in hemophilic knees is getting renewed attention as both surgical techniques ans implants and medical management of hemophilia have improved.
Model-Based Tools for the Integration of Design and Diagnosis into a Common Process - A Project Report (2002)

The growing importance of on-board diagnosis for automobiles demands for a close integration of diagnostic tasks in the entire design process. This report describes work carried out to date within the European project 'Integrated Design Process for onboard Diagnosis' (IDD). It presents an analysis of the current design process and the model of a new process which allows for a better integration of diagnosis related tasks, such as diagnosability analysis, failure-modes-and-effects analysis (FMEA), on-board diagnosis design, in the overall design process of mechatronic subsystems. We then discuss in what way model-based technology can provide tools to support the actual integration and, in particular, present an approach to model-based diagnosability analysis.
Hermite finite elements for high accuracy electromagnetic field calculations: A case study of homogeneous and inhomogeneous waveguides (2016)

Maxwell's vector field equations and their numerical solution represent significant challenges for physical domains with complex geometries. There are several limitations in the presently prevalent approaches to the calculation of field distributions in physical domains, in particular, with the vector finite elements. In order to quantify and resolve issues, we consider the modeling of the field equations for the prototypical examples of waveguides. We employ the finite element method with a new set of Hermite interpolation polynomials derived recently by us using group theoretic considerations. We show that (i) the approach presented here yields better accuracy by several orders of magnitude, with a smoother representation of fields than the vector finite elements for waveguide calculations. (ii) This method does not generate any spurious solutions that plague Lagrange finite elements, even though the C1-continuous Hermite polynomials are also scalar in nature. (iii) We present solutions for propagating modes in inhomogeneous waveguides satisfying dispersion relations that can be derived directly, and investigate their behavior as the ratio of dielectric constants is varied both theoretically and numerically. Additional comparisons and advantages of the proposed method are detailed in this article. The Hermite interpolation polynomials are shown to provide a robust, accurate, and efficient means of solving Maxwell's equations in a variety of media, potentially offering a computationally inexpensive means of designing devices for optoelectronics and plasmonics of increasing complexity.
Synthetic Stimulator of Interferon Genes (STING) Agonists Induce a Cytokine-Mediated Anti-Hepatitis B Virus Response in Nonparenchymal Liver Cells (2022)

Chronic hepatitis B (CHB) remains a major public health problem worldwide, with limited treatment options, but inducing an antiviral response by innate immunity activation may provide a therapeutic alternative. We assessed the cytokine-mediated anti-hepatitis B virus (HBV) potential for stimulating the cyclic GMP-AMP synthase-stimulator of interferon genes (STING) pathway using STING agonists in primary human hepatocytes (PHH) and nonparenchymal liver cells (NPCs). The natural STING agonist, 2',3'-cyclic GMP-AMP, the synthetic analogue 3',3'-c-di(2'F,2'dAMP), and its bis(pivaloyloxymethyl) prodrug had strong indirect cytokine-mediated anti-HBV effects in PHH regardless of HBV genotype. Furthermore, STING agonists induced anti-HBV cytokine secretion <i>in vitro,</i> in both human and mouse NPCs, and triggered hepatic T cell activation. Cytokine secretion and lymphocyte activation were equally stimulated in NPCs isolated from control and HBV-persistent mice. Therefore, STING agonists modulate immune activation regardless of HBV persistence, paving the way toward a CHB therapy.
Spinal cord hydrolysate ameliorate immunological reaction in experimental allergic encephalomyelitis (2009)

The aim of this study was to use the hydrolysate of pig spinal cord proteins to induce oral tolerance in the animal model of sclerosis multiplex - experimental allergic encephalomyelitis. The female Lewis rats were fed with hydrolysate of pig spinal cord proteins in two doses for one week before immunization, which was induced by injection of guinea pig spinal cord homogenate. At the peak of clinical symptoms (the 13th day post immunization) the rats were sacrificed and the spleen removed. Splenocytes were suspended in a culture medium and placed in microculture plates. The cells were stimulated with homogenate. The cells were cultured for seven days. Proliferation of splenocytes was estimated by means of methyl-3H thymidine incorporation. In supernatants of cultures of splenocytes the level of cytokines INF-gamma, IL-10, IL-4, and TGF-gamma was measured. It was demonstrated that homogenate-induced splenocytes of hydrolysate-fed rats gave rise to low proliferation as compared to the controls used. The IFN-gamma was inhibited in hydrolysate-fed animals. The hydrolysate of pig spinal cord proteins has a modulatory effect on the immune reaction, particularly on the orally-induced antigen-specific modulation of autoimmune response.
Potential photoresponse of membranes containing a lipophilic crowned spirobenzopyran (1999)

Potential response and its photoresponse for plasticized-poly(vinyl chloride) membranes containing a lipophilic crowned spirobenzopyran were surveyed and compared with those for membrane systems of a spirobenzopyran deriative not carrying any crown ether moiety. On UV-light irradiation, an intriguing type of time-course change was found with the membrane potential for the crowned spirobenzopyran system in the presence of alkali metal ions, i.e., the potential first increases and then decreases. The photoresponse profile for the crowned spirobenzopyran system was affected considerably by the sort of metal ions and the pH conditions of aqueous phases. This phenomenon is explained by an ion-exchange mechanism specific to crowned spirobenzopyran, that is, fast proton exchange followed by slow metal-ion exhange of its merocyanine form. The system for the corresponding spirobenzopyran without crown ether moiety exhibited a steady potential photoresponse that depends on the pH conditions of aqueous phases.
Seabed Current Boundary Layers in Wave‐Plus‐Current Flow Conditions (1988)

The current boundary layer has been investigated with measurements of tidal current and wave velocity made at 0.24, 0.61, 1.22, 1.83, and 3.66 m above a rough seafloor. The logarithmic boundary‐layer flow model was fitted to the measurements determining the roughness (z0) and friction velocity (u*) parameters. The data presented here cover a wide range of combined current and wave conditions and are of high quality. The measurements and analysis results demonstrate clearly the existence of large boundary‐layer current gradients in the tidal environment. Large values of (z0) and (u*) were found that depend on the ratio of the wave‐flow component to the current flow component as well as the upstream bottom roughness. Boundary layers in the flow near the seabed can affect the design of offshore structures such as offshore pipelines.
INTRAVESICAL APPLICATION OF A STABLE OXYBUTYNIN SOLUTION IMPROVES THERAPEUTIC COMPLIANCE AND ACCEPTANCE IN CHILDREN WITH NEUROGENIC BLADDER DYSFUNCTION (1998)

Intravesical instillation of a specially prepared oxybutynin solution is safe and reliable in children with persistent detrusor hyperactivity or side effects on oral oxybutynin therapy. Eliminating the complex crushing preparation of the solution by the child or parent has made this therapy easy to use and acceptable in the long term.
Active Notch signaling is required for arm regeneration in a brittle star (2020)

Cell signaling pathways play key roles in coordinating cellular events in development. The Notch signaling pathway is highly conserved across all multicellular animals and is known to coordinate a multitude of diverse cellular events, including proliferation, differentiation, fate specification, and cell death. Specific functions of the pathway are, however, highly context-dependent and are not well characterized in post-traumatic regeneration. Here, we use a small-molecule inhibitor of the pathway (DAPT) to demonstrate that Notch signaling is required for proper arm regeneration in the brittle star Ophioderma brevispina, a highly regenerative member of the phylum Echinodermata. We also employ a transcriptome-wide gene expression analysis (RNA-seq) to characterize the downstream genes controlled by the Notch pathway in the brittle star regeneration. We demonstrate that arm regeneration involves an extensive cross-talk between the Notch pathway and other cell signaling pathways. In the regrowing arm, Notch regulates the composition of the extracellular matrix, cell migration, proliferation, and apoptosis, as well as components of the innate immune response. We also show for the first time that Notch signaling regulates the activity of several transposable elements. Our data also suggests that one of the possible mechanisms through which Notch sustains its activity in the regenerating tissues is via suppression of Neuralized1.
Natural compounds as potential PI3K-AKT1 signaling pathway inhibitors by means of pharmacophore modeling (2016)

AKT1, a modulator of PI3K-AKT1 pathway, is dysregulated in several human diseases, and understanding deeper its role in the complexity of biological systems remains an important goal. The research has been focused on development and study of potential synthetic-natural allosteric inhibitors for AKT1, and recent studies have shown how some natural compounds may play this role (1). We are interested in a screening of small bioactive molecules, in order to identify the potential “lead compounds”, for next experimental assays, searching those potentially able to inhibit AKT1 and its signaling mechanisms, trying to re-establish the normal balance and safeguarding of human health. The workflow executed is the following: 1) search in PDB database of a model structure for AKT1 (comparing different structures and choosing the most suitable for our purposes), through algorithm BLAST. 2) pharmacophore modeling by means of ZINCpharmer web-server, to investigate all purchasable compounds of the ZINC database, using the Pharmer as efficient and exact pharmacophore search technology (2). 3) screening of possible natural AKT1 inhibitors, using the pharmacophore generated by ZINCpharmer, choosing only the best candidates for next steps. 4) molecular validation of selected compounds, to analyze the ligand-protein interactions. 5) study of physical-chemical properties of selected compounds to trace their origin. 6)prediction of their biosynthetic pathways and Pharmacokinetics/Pharmacodynamics models, by means of ADMET/toxicity predictor server in order to direct the design of next experimental assays. Our attention is focused on the study of natural compounds that can show many health benefits, through the realization and analysis of “pharmacophore modeling”, essential step in drug discovery (3). We selected the PDB structure 3O96 as the reference complex (protein-ligand), and we analyzed it by means of ZINCpharmer, to generate three different “pharmacophore models” with three different list of natural compounds. It is performed a thorough screening of compounds applying other filters, to find some good candidates as possible natural AKT1 allosteric inhibitors. The compounds that match a well-defined pharmacophore have been analyzed through direct molecular docking, for selecting only the best candidates and studying the protein-ligand interactions. Selected compounds have been investigated in more details, to trace their origin, by their chemical-physical properties. This information can help us to predict some plausible enzyme-catalyzed reaction pathways, investigated with PathPred server and KEGG compound database, in order to highlight the most important reactions for biosynthesis of compounds and obtain PharmacoKinetics/PharmacoDynamics (PK/PD) models through ADME predictor server and to realize of next experimental assays. (Abstract truncated at 3,000 characters - the full version is available in the pdf file)
Nanotechnologies for Water Environment Applications (2009)

Sponsored by the Nanotechnology Task Committee of the Environmental Council of the Environmental and Water Resources Institute of ASCE.
Homology of the NifS family of proteins to a new class of pyridoxal phosphate‐dependent enzymes (1993)

Iterative profile sequence analysis reveals a remote homology of peroxisomal serine-pyruvate aminotransferases from mammals to the small subunit of soluble hydrogenases from cyanobacteria, an isopenicillin N epimerase, the NifS gene products from bacteria and yeast, and the phosphoserine aminotransferase family. All members of this new class whose function is known are pyridoxal phosphate-dependent enzymes, yet they have distinct catalytic activities. Upon alignment, a lysine around position 200 remains invariant and is predicted to be the pyridoxal phosphate-binding residue. Based on the detected homology, it is predicted that NifS has also a pyridoxal phosphate-dependent serine (or related) aminotransferase function associated with nitrogen economy and/or protection during nitrogen fixation.
Ultrasonic Characterization of Flaws in Composites Using Plate Waves Dispersion Data (1997)

Leaky Lamb wave (LLW) propagation in composite materials has been studied extensively since it was first observed in 1982. The wave is induced using a pitch-catch arrangement and the plate wave modes are detected by searching minima in the reflected spectra.
ChemInform Abstract: SYNTHESIS OF (+)‐CIS‐1‐METHOXY‐4β‐CARBOMETHOXY‐4A,5,8,8A‐TETRAHYDROISOCHROMAN, A SYNTHON FOR THE PREPARATION OF ALKALOIDS AND IRIDOIDS (1980)

Abstract Die anodische Oxidation von Furfurylalkohol (I) in Gegenwart von Methanol ergibt das Dihydrodimethoxyderivat (II), das zum Dihydropyranon (III) recyclisiert wird.
Chest Pain with a Surprising Course (1999)

This Clinical Problem-Solving case is based on a presentation at the Beth Israel Deaconess Medical Center Morbidity and Mortality Conference. A 73-year-old man with insulin-dependent diabetes mellitus and a history of coronary artery disease came to the emergency department because of chest pain of one hour's duration that radiated to the jaw and back, shortness of breath, diaphoresis, and a nonproductive cough. The pain was similar to the angina he usually experienced, except for an intermittent pleuritic component with accompanying discomfort on the right side of the chest. An electrocardiogram showed right bundle-branch block with T-wave inversion in leads . . .
Rapamycin prevents tobacco-carcinogen induced lung tumorigenesis and selectively reduces lung-associated Foxp3 positive cells (2007)

B8 Inhibitors of the serine/threonine kinase mTOR can prevent tumorigenesis in many model systems, but the use of mTOR inhibitors for cancer prevention in humans is theoretically limited by the risk of secondary malignancies, which was observed in patients receiving rapamycin as part of multi-drug immunosuppressive therapy. However, little is known about immune modulation by rapamycin as a single agent. Previously, we showed that physiologic concentrations of rapamycin inhibited lung tumorigenesis driven by a tobacco-specific carcinogen, NNK. Here we characterize immune modulation in this system. NNK alone acutely depleted multiple lineages of immune splenic cells without suppressing immune function. In contrast to these nominal systemic effects, NNK doubled the percentage of cells expressing the Treg marker Foxp3 in lung tissues prior to tumor development and caused a dose-dependent increase in tumor-infiltrating Foxp3+ cells at 12 weeks. NNK administration did not increase the overall number of CD3+ cells, suggesting that the effect of NNK was specific for Foxp3+ cells. Rapamycin rapidly decreased splenic Foxp3+/CD4+ cells, and was associated with depletion of Foxp3+ cells in lung tissues. At 12 wk, rapamycin inhibited tumorigenesis, decreased the number of tumor-associated Foxp3+ cells by 88%, modestly decreased systemic CD4+ and CD8+ cells, and did not induce an immunosuppressive Th2 phenotype. Thus, single-agent rapamycin prevents lung infiltration of Foxp3+ cells that occurs early in tumorigenesis without causing profound immunosuppression.
GLUTARIC ACID: A POTENTIAL FOOD ACIDULANT (1976)

ABSTRACT Some physical and chemical properties of glutaric acid which pertain to its potential use as a food acid were studied. Comparisons were made between it and some approved food acids regarding solubility, hygroscopicity, acidity and rate of sucrose inversion. Results reveal favorable chemical and physical properties, making it an attractive prospect for a new food acidulant.