gebhart/patrepeval huggingface dataset:
Development of a Mobility-Enabling Spinal Orthosis and Methods for Evaluating and Developing Spinal Orthoses on a Robotic Platform (2014)

Introduction: A number of decompressing spinal braces (typically pneumatic) have been introduced that attempt to mechanically emulate the "buoyancy" of water therapy by offloading upper torso load to the pelvic girdle as a treatment for lower back pain (LBP). Unfortunately, the beneficial upward force they apply on the upper torso typically makes it difficult or impossible for the patient to bend. For those cases where stabilization is not indicated, this undesirably hinders therapeutic exercise, independent living, and return to work. The cosmetic stigma of wearing an external pneumatic assembly large enough to provide significant offloading may provide additional disincentives to user compliance. Also, there was not, to our knowledge, a scientific orthosis evaluation and development platform capable of producing orthoses with predictable effects on spinal loads. Research objectives were thus to a) develop an advanced robotic test platform (RTP) for the rapid development of spinal orthoses, b) use the RTP to evaluate a commercial decompressing orthosis, c) design, build, and test on the RTP a new orthosis that provides distractive force while enabling mobility, and d) compare the test results of the new orthosis and the commercial decompressing orthosis.
Non–Small Cell Lung Cancer: Identifying Prognostic Imaging Biomarkers by Leveraging Public Gene Expression Microarray Data—Methods and Preliminary Results (2012)

This radiogenomics strategy for identifying imaging biomarkers may enable a more rapid evaluation of novel imaging modalities, thereby accelerating their translation to personalized medicine.
Vision, issues, and architecture for nomadic computing [and communications] (1995)

Computing and communications is bringing about a paradigm shift in the way these technologies are being used. The shift is in the direction of nomadic computing and communications. Nomadicity refers to the system support needed to provide a rich set of computing and communication capabilities and services to the nomad as he or she moves from place to place in a transparent, integrated and convenient form. This new paradigm is already manifesting itself as users travel to many different locations with laptops, personal digital assistants (PDAs) cellular telephones, pagers, and so on. In this article we discuss a vision of nomadicity as well as open issues, and architecture and design concerns that must be addressed as we bring about the system support necessary for nomadicity.
Towards real-time cardiovascular magnetic resonance guided transarterial CoreValve implantation: in vivo evaluation in swine (2012)

Our study shows that rtCMR-guided TAVI using the commercial CoreValve prosthesis in conjunction with a modified delivery system is feasible in swine, allowing improved procedural guidance including immediate detection of complications and direct functional assessment with reduction of radiation and omission of contrast media.
Small-Molecule Inhibitors of the MDM2-p53 Protein−Protein Interaction Based on an Isoindolinone Scaffold (2006)

From a set of weakly potent lead compounds, using in silico screening and small library synthesis, a series of 2-alkyl-3-aryl-3-alkoxyisoindolinones has been identified as inhibitors of the MDM2-p53 interaction. Two of the most potent compounds, 2-benzyl-3-(4-chlorophenyl)-3-(3-hydroxypropoxy)-2,3-dihydroisoindol-1-one (76; IC50 = 15.9 ± 0.8 μM) and 3-(4-chlorophenyl)-3-(4-hydroxy-3,5-dimethoxybenzyloxy)-2-propyl-2,3-dihydroisoindol-1-one (79; IC50 = 5.3 ± 0.9 μM), induced p53-dependent gene transcription, in a dose-dependent manner, in the MDM2 amplified, SJSA human sarcoma cell line.
Tissue-Specific and Ubiquitous Expression Patterns from Alternative Promoters of Human Genes (2010)

We describe a computational pipeline that uses microarray data to assess the level of expression and breadth of tissue profiles for transcripts with distinct first exons regulated by alternative promoters. We conclude that alternative promoters provide individualized regulation that is confirmed through expression levels, tissue preference and chromatin modifications. Although the selective use of alternative promoters often goes uncharacterized in gene expression analyses, transcripts produced in this manner make unique contributions to the cell that requires further exploration.
Rapid Delivery of Foreign Genes into Plants by Direct Rub-Inoculation with Intact Plasmid DNA of a Tomato Bushy Stunt Virus Gene Vector (1999)

Tomato bushy stunt virus (TBSV) cDNA, positioned between a modified cauliflower mosaic virus 35S promoter and the hepatitis delta virus antigenomic ribozyme with a downstream nopaline synthase gene polyadenylation signal, established infections upon rub-inoculation of plants with intact plasmids. Application of this methodology produced a TBSV DNA-based gene vector which yielded readily detectable levels of localized foreign gene expression in inoculated leaves. This is the first demonstration of an infectious DNA from a member of the Tombusviridae which permits rapid TBSV-mediated foreign-gene expression upon direct rub-inoculation of miniprep DNA onto a variety of plant species.
Unexpected high incidence of cholecystokinin-B/gastrin receptors in human medullary thyroid carcinomas (1996)

The 2 gastrointestinal peptides cholecystokinin (CCK) and gastrin, which act through CCK-A receptors (having high affinity for CCK) or CCK-B/gastrin receptors (having high affinity for CCK and gastrin), are considered to be important tumor growth factors. We have evaluated CCK-A and CCK-B/gastrin receptors in 34 human thyroid cancers using in vitro receptor autoradiography with 2 different radioligands. We demonstrate high-affinity CCK-B/gastrin receptors in medullary thyroid carcinomas, present at very high incidence (92%) but the absence of these receptors in non-medullary thyroid carcinomas or in normal thyroid glands. CCK-B/gastrin receptors are therefore likely to be the molecular substrate for the pentagastrin-stimulation test, widely used in medullary thyroid carcinomas; moreover, they represent the targets for physiologically secreted gastrin or CCK which, as growth factors, may stimulate the growth of medullary thyroid carcinomas. Furthermore, these results have diagnostic as well as therapeutic implications: radiolabeled gastrin and CCK analogs may be used for scintigraphic tumor localization in vivo, whereas CCK-B-selective antagonists may be of therapeutic value.
Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates (1990)

Polyhydroxyalkanoates (PHAs), of which polyhydroxybutyrate (PHB) is the most abundant, are bacterial carbon and energy reserve materials of widespread occurrence. They are composed of 3-hydroxyacid monomer units and exist as a small number of cytoplasmic granules per cell. The properties of the C4 homopolymer PHB as a biodegradable thermoplastic first attracted industrial attention more than 20 years ago. Copolymers of C4 (3-hydroxybutyrate [3HB]) and C5 (3-hydroxyvalerate [3HV]) monomer units have modified physical properties; e.g., the plastic is less brittle than PHB, whereas PHAs containing C8 to C12 monomers behave as elastomers. This family of materials is the centre of considerable commercial interest, and 3HB-co-3HV copolymers have been marketed by ICI plc as Biopol. The known polymers exist as 2(1) helices with the fiber repeat decreasing from 0.596 nm for PHB to about 0.45 nm for C8 to C10 polymers. Novel copolymers with a backbone of 3HB and 4HB have been obtained. The native granules contain noncrystalline polymer, and water may possibly act as a plasticizer. Although the biosynthesis and regulation of PHB are generally well understood, the corresponding information for the synthesis of long-side-chain PHAs from alkanes, alcohols, and organic acids is still incomplete. The precise mechanisms of action of the polymerizing and depolymerizing enzymes also remain to be established. The structural genes for the three key enzymes of PHB synthesis from acetyl coenzyme A in Alcaligenes eutrophus have been cloned, sequenced, and expressed in Escherichia coli. Polymer molecular weights appear to be species specific. The factors influencing the commercial choice of organism, substrate, and isolation process are discussed. The physiological functions of PHB as a reserve material and in symbiotic nitrogen fixation and its presence in bacterial plasma membranes and putative role in transformability and calcium signaling are also considered.
Rearrangement and expression of T cell antigen receptor and gamma genes during thymic development. (1986)

Rearrangement and expression of the T cell antigen receptor and the gamma genes during T cell ontogeny is a regulated process; the gamma genes are rearranged and expressed first, followed by the beta and then the alpha genes. Expression of both functional alpha and beta gene RNA first occurs at day 17 of gestation, along with the expression of T3 delta chain RNA. T cell antigen receptor gene rearrangements occur primarily or exclusively in the thymus, although some gamma gene rearrangements occur outside the thymus in fetal liver cells that may be committed T cell progenitors. There is no gross difference in the extent of beta and gamma gene rearrangements in the adult thymocyte subpopulations that were analyzed, despite the fact that some of these populations cannot respond to antigen and never emigrate from the thymus. Quantitative analysis of rearrangements in total adult thymocyte DNA shows that beta gene rearrangements generally occur on both chromosomal homologs, and that rearrangements occur preferentially to the J beta 2 gene segment cluster.
Synthesis of Unsymmetrical Triarylamines for Photonic Applications via One-Pot Palladium-Catalyzed Aminations (1997)

Syntheses of unsymmetrically substituted triarylamines have been achieved by a one-pot procedure using C−N bond-forming reactions, where two aryl bromides are sequentially added to an arylamine in the presence of a palladium catalyst. This methodology has been utilized to synthesize a number of substituted analogs of 4,4‘-bis(m-tolylphenylamino)biphenyl, which may be useful as the hole transport component of vapor-deposited organic light-emitting diodes. The variations in the substitution are anticipated to lead to a variety of band gaps, band offsets, and glass transition temperatures in this class of materials.
PSII Inhibitory Activity of Resorcinolic Lipids from Sorghum bicolor (2002)

Resorcinolic lipids were isolated from the root extracts of Sorghum bicolor and identified as 4,6-dimethoxy-2-[(8'Z,11'Z)-8',11',14'-pentadecatriene]resorcinol (4), 4-methoxy-6-ethoxy-2-[(8'Z,11'Z)-8',11',14'-pentadecatriene]resorcinol (5), and 4-hydroxy-6-ethoxy-2-[(10'Z,13'Z)-10',13',16'-heptadecatriene]resorcinol (6). Compounds 4 and 5 inhibited photosynthetic oxygen evolution (IC50 0.09 and 0.20 microM, respectively). Compound 4 could not be enzymatically converted to a quinone, suggesting that the quinone moiety is not required for its photosystem II inhibitory activity. Compounds 5 and 6 are reported for the first time.
Proto‐oncogene c‐jun and c‐fos messenger RNAs increase in the liver of carnitine‐deficient juvenile visceral steatosis (jvs) mice (1992)

We determined the mRNA levels of c-jun and c-fos in the liver of C3H-H-2 degrees jvs mice. Both were higher in jvs mice than in normal mice. The level of c-jun mRNA increased gradually after birth, but in the control mice there was almost no change. In addition, alpha-fetoprotein and aldolase A mRNA levels were also higher than in normal littermates. These results suggest that the pattern of the gene expression in jvs mice partly resembles the one that occurs in undifferentiated hepatocytes and/or hepatocellular carcinoma.
Extracellular superoxide dismutase in human tissues and human cell lines. (1984)

Extracellular-superoxide dismutase is a tetrameric copper-containing glycoprotein that previously has been demonstrated to be the major superoxide dismutase of human extracellular fluids. The occurrence of this enzyme in various human tissues that were removed from two accidental death victims and in 19 different human cultured cell lines was determined. All investigated tissues were found to contain extracellular-superoxide dismutase. There was a larger variation between tissues in the concentration of this enzyme than in CuZn superoxide dismutase and Mn superoxide dismutase. No relation could be demonstrated between the content of extracellular-superoxide dismutase and the content of the other superoxide dismutase isoenzymes in the various tissues. In uterus there was more extracellular-superoxide dismutase than Mn superoxide dismutase, but in all other tissues the content of extracellular-superoxide dismutase was lower than the content of the other isoenzymes. The concentration of extracellular-superoxide dismutase was higher in all investigated human tissues than in human plasma. 19 human cultured cell lines were found to be devoid of or to contain very little extracellular-superoxide dismutase. Most tissues contained more extracellular-superoxide dismutase than did the investigated cell lines.
Immunogenicity of Thrombopoietin Mimetic Peptide GW395058 in BALB/c Mice and New Zealand White Rabbits: Evaluation of the Potential for Thrombopoietin Neutralizing Antibody Production in Man (1999)

Administration of exogenous proteins and peptides as therapeutics carries with it the potential for immune system recognition and the development of neutralizing antibodies to endogenous regulatory proteins. PEGylation of proteins typically reduces their immunogenicity in vivo. GW395058 is a PEGylated peptide thrombopoietin receptor (TPOr) agonist being evaluated for the treatment of chemotherapy-induced thrombocytopenia. Although GW395058 shares no homology with TPO, it does compete with TPO for binding to a common receptor, and a similarity in local structure could result in shared epitopes. Thus GW395058 could elicit TPO-neutralizing antibodies. In this study, we evaluated the immunogenicity of GW395058 in mice, the potential of rabbit antibodies elicited by immunizations with the non-PEGylated parent peptide AF15705 to cross-react with recombinant human (rHu) TPO, and the potential of mouse anti-rHuTPO antibodies elicited by repeated dosing with rHuTPO to cross-react with AF15705. GW395058-dosed mice failed to produce antibodies to AF15705 or rHuTPO. Mouse anti-rHuTPO did not cross-react with AF15705 and rabbit anti-AF15705 antibodies failed to cross-react with rHuTPO. GW395058 caused no immune-mediated lesions in mice, but rHuTPO suppressed megakaryocytopoiesis and caused B-lymphocyte hyperplasia in lymphoid tissues consistent with antigenic stimulation. These data suggest that the potential for an immune response to GW395058 in man would be low.
Automatic endless polarization control with integrated-optical Ti:LiNbO_3 polarization transformers (1988)

In coherent-optical transmission systems continuous or endless polarization matching between the superposed beams must be ensured. We describe a practical closed-loop polarization-control system with two integrated-optical retarders acting as polarization transformers. They have variable retardations and variable eigenmodes, i.e., adjustable birefringence magnitude and orientation as in a Babinet-Soleil compensator. In theory, one retarder would be sufficient. However, a second device is added to correct nonideal behavior of the first. The intensity losses during polarization control are less than 0.15 dB.
Determination of the loading values for high levels of drugs and sugars conjugated to proteins by matrix-assisted ultraviolet laser desorption/ionization mass spectrometry (1993)

The loading values of high levels of anti-cancer drugs and sugars conjugated to human serum albumin were determined by matrix-assisted ultraviolet (UV) laser desorption/ionization mass spectrometry. The values were compared with those obtained by UV spectrometry, radioactivity labeling or by chemical analysis, and were found to be consistent. The matrix-assisted UV laser desorption/ionization method has been demonstrated to be a routine and reliable method for obtaining high loading values and therefore was applied to the determination of the loading of two experimental drugs, for treating AIDS and septic shock, respectively, when conjugated to bovine serum albumin, which could not be routinely determined by UV spectrometry since the chromophores of the drugs and protein overlap.
Context-specific Bayesian clustering for gene expression data (2001)

The recent growth in genomic data and measurement of genome-wide expression patterns allows to examine gene regulation by transcription factors using computational tools. In this work, we present a class of mathematical models that help in understanding the connections between transcription factors and functional classes of genes based on genetic and genomic data. These models represent the joint distribution of transcription factor binding sites and of expression levels of a gene in a single model. Learning a combined probability model of binding sites and expression patterns enables us to improve the clustering of the genes based on the discovery of putative binding sites and to detect which binding sites and experiments best characterize a cluster. To learn such models from data, we introduce a new search method that rapidly learns a model according to a Bayesian score. We evaluate our method on synthetic data as well as on real data and analyze the biological insights it provides.
Activation of nuclear transcription factor kappa B (NF‐κB) is essential for dopamine‐induced apoptosis in PC12 cells (2001)

The etiology of Parkinson's disease is still unknown, though current investigations support the notion of the pivotal involvement of oxidative stress in the process of neurodegeneration in the substantia nigra (SN). In the present study, we investigated the molecular mechanisms underlying cellular response to a challenge by dopamine, one of the local oxidative stressors in the SN. Based on studies showing that nuclear factor kappa B (NF-kappaB) is activated by oxidative stress, we studied the involvement of NF-kappaB in the toxicity of PC12 cells following dopamine exposure. We found that dopamine (0.1-0.5 m M) treatment increased the phosphorylation of the IkappaB protein, the inhibitory subunit of NF-kappaB in the cytoplasm. Immunoblot analysis demonstrated the presence of NF-kappaB-p65 protein in the nuclear fraction and its disappearance from the cytoplasmic fraction after 2 h of dopamine exposure. Dopamine-induced NF-kappaB activation was also evidenced by electromobility shift assay using radioactive labeled NF-kappaB consensus DNA sequence. Cell-permeable NF-kappaB inhibitor SN-50 rescued the cells from dopamine-induced apoptosis and showed the importance of NF-kappaB activation to the induction of apoptosis. Furthermore, flow cytometry assay demonstrated a higher level of translocated NF-kappaB-p65 in the apoptotic nuclei than in the unaffected nuclei. In conclusion, our findings suggest that NF-kappaB activation is essential to dopamine-induced apoptosis in PC12 cells and it may be involved in nigral neurodegeneration in patients with Parkinson's disease.
The Role and Influence of Gut Microbiota in Pathogenesis and Management of Obesity and Metabolic Syndrome (2014)

The obesity epidemic has drastically impacted the state of health care in the United States. Aside from poor diet hygiene and genetics, there are many other factors thought to play a role in the emergence of obesity and the metabolic syndrome. There has been a paradigm shift toward further investigating the gut microbiota and its implications in the pathogenesis of a variety of disease states, including inflammatory bowel disease, Clostridium difficile, and most recently obesity and the metabolic syndrome. This article is intended to evaluate the role of gut microbiota in the pathogenesis of obesity and metabolic syndrome and its influence in future management.
Nuclear factor‐κB activation and differential expression of survivin and Bcl‐2 in human grade 2–4 astrocytomas (2008)

NF-kappaB and factors involved in its intracellular activation were up-regulated in gliomas. NF-kappaB-activated antiapoptotic genes were hyperexpressed in tumor samples, but showed a differential expression with higher levels of Bcl-2 in LGAs and higher levels of Survivin in GBMs.
A synergistic effect between anti‐idiotype antibodies and anti‐neoplastic drugs in the therapy of a murine B‐cell tumor (1986)

Abstract Antibodies directed against idiotypic determinants of the cell‐surface IgM of a B lymphoma, 38c, were effective in delaying development of the tumor and in some instances in preventing its growth. The efficacity of the anti‐idiotype antibodies was markedly increased when they were injected in combination with anti‐neoplastic drugs. Since chemotherapy, as such, is limited by the general toxicity of the drugs it was of advantage to apply them in low doses. The drug doses used were mostly ineffective by themselves, yet were active in combination with the antibody in a more than additive fashion. We performed studies designed to elucidate the mechanism of the synergy between the anti‐idiotype antibodies and the drugs. The data suggest that the activity of the antibody is partly indirect and is mediated through the host's effector cells. In the case of one drug, daunomycin, the activity is also, at least in part, mediated through peritoneal exudate cells (PEC). Daunomycin injected intraperitoneally activated PEC. Such activated PEC, when injected into recipient mice, could replace the drug in its synergy with the antibody. In conclusion, it was shown that it is possible to increase the effectiveness either of antibodies to tumor cells or of cytotoxic drugs by combination therapy.
Efficient Total Syntheses of Resin Glycosides and Analogues by Ring-Closing Olefin Metathesis (1999)

A highly efficient entry into the resin glycoside family of natural products is outlined which takes advantage of the inherently modular character of ring-closing metathesis (RCM) for the formation of their macrolactone substructures. Starting from only three well accessible sugar building blocks and (6S)-undec-1-en-6-ol (7) (prepared by enantioselective addition of dipentylzinc to hexenal in the presence of a catalyst formed from Ti(OiPr)4 and bis-(R,R)-trifluoromethanesulfonamide (9)), it was possible to achieve total syntheses of tricolorin A (1), tricolorin G (2), and jalapinolic acid (58) as well as the synthesis of the disaccharidic unit 48 which constitutes a common structural motif of all simonin, operculin, tuguajalapin, orizabin, mammoside, quamoclin, and stoloniferin resin glycosides. Furthermore, various analogues of these naturally occurring glycolipids have been obtained in a straightforward manner from the same set of substrates. This highlights the flexibility of the chosen approach and opens the door for a synthesis-driven mapping of the structure/activity profile of this structurally demanding class of oligosaccharides. The macrocyclization reactions via RCM have been performed using carbene 22 introduced by Grubbs, the cationic allenylidene complex 23, or the particularly convenient precatalyst [(p-cymene)RuCl2(PCy3)] 24. All these ruthenium-based systems catalyze the ring closure of the highly functionalized diene substrates with comparable efficiency and turned out to be compatible with an array of functional groups including unprotected secondary hydroxyl functions.
Human Kallikrein 6 (hK6): A New Potential Serum Biomarker for Diagnosis and Prognosis of Ovarian Carcinoma (2003)

Serum hK6 concentration seems to be a new biomarker for ovarian carcinoma and may have value for disease diagnosis and prognosis.