gebhart/patrepeval huggingface dataset:
IKAP expression levels modulate disease severity in a mouse model of familial dysautonomia (2012)

Hereditary sensory and autonomic neuropathies (HSANs) encompass a group of genetically inherited disorders characterized by sensory and autonomic dysfunctions. Familial dysautonomia (FD), also known as HSAN type III, is an autosomal recessive disorder that affects 1/3600 live births in the Ashkenazi Jewish population. The disease is caused by abnormal development and progressive degeneration of the sensory and autonomic nervous systems and is inevitably fatal, with only 50% of patients reaching the age of 40. FD is caused by a mutation in intron 20 of the Ikbkap gene that results in severe reduction in the expression of its encoded protein, inhibitor of kappaB kinase complex-associated protein (IKAP). Although the mutation that causes FD was identified in 2001, so far there is no appropriate animal model that recapitulates the disorder. Here, we report the generation and characterization of the first mouse models for FD that recapitulate the molecular and pathological features of the disease. Important for therapeutic interventions is also our finding that a slight increase in IKAP levels is enough to ameliorate the phenotype and increase the life span. Understanding the mechanisms underlying FD will provide insights for potential new therapeutic interventions not only for FD, but also for other peripheral neuropathies.
<title>Optical coherence tomography with the "spectral radar": fast optical analysis in volume scatterers by short-coherence interferometry</title> (1996)

We present a sensor for acquisition of cross-sectional images of volume scatterers, we call it 'spectral radar'. Medical and technical applications are possible. The sensor is a modified Michelson interferometer, with a broad bandwidth light source. The scattering amplitude a(z) along one vertical axis from the surface into the bulk can be measured within one exposure. No reference arm scanning is necessary. Measurement results of stationary and non stationary scattering phantoms, human skin and of a fish eye in vitro are shown.
Solvothermal Annealing of Block Copolymer Thin Films (2013)

A two-stage annealing process for block copolymer films was introduced consisting of a solvent vapor exposure followed by a thermal cycle. By heating the film but not the chamber, changes in the ambient vapor pressure of the solvent were avoided. Films of block copolymers and homopolymers showed transient nonmonotonic swelling behavior immediately after solvent exposure that was dependent on how the thin film was cast before the anneal. Thermal cycling of the solvent-swelled block copolymer films during the solvent vapor anneal (SVA) caused the films to deswell in 1-10 s and produced well-ordered microdomains in templated 45.5 and 51.5 kg/mol polystyrene-block-polydimethylsiloxane films annealed in toluene and n-heptane vapors for total process times of 30 s to 5 min.
Towards a universal influenza vaccine: volunteer virus challenge studies in quarantine to speed the development and subsequent licensing (2013)

There are now more than 5 experimental vaccine formulations which induce T and B cell immunity towards the internally situated virus proteins matrix (M1 and M2e) and nucleoprotein (NP), and towards stem and stalk regions of the HA which have a shared antigenic structure amongst many of the 17 influenza A virus sub types. Such 'universal vaccines' could be used, at least in theory, as a prophylactic stockpile vaccine for newly emerged epidemic and novel pandemic influenza A viruses or as a supplement to conventional HA/NA vaccines. My own laboratory has approached the problem from the clinical viewpoint by identifying CD4(+) cells which are present in influenza infected volunteers who resist influenza infection. We have established precisely which peptides in M and NP proteins react with these immune CD4 cells. These experimental vaccines induce immunity in animal models but with a single exception no data have been published on protection against influenza virus infection in humans. The efficacy of the latter vaccine is based on vaccinia virus (MVA) as a carrier and was analyzed in a quarantine unit. Given the absence of induced HI antibody in the new universal vaccines a possible licensing strategy is a virus challenge model in quarantine whereby healthy volunteers can be immunized with the new vaccine and thereafter deliberately infected and clinical signs recorded alongside quantities of virus excreted and compared with unvaccinated controls.
Calibration-free WLAN location system based on dynamic mapping of signal strength (2006)

In this work we present a calibration-free system for locating wireless local area network devices, based on the radio frequency characteristics of such networks. Calibration procedures are applied in a great number of proposed location techniques and are considered to be not practical or a considerable barrier to wider adoption of such methods. Thus, we addressed issues related to some aspects of location systems through, an architecture based on wireless sniffers and by constructing a location model based on signal propagation models, in which its parameters are calculated in real time. This guarantee good self-sufficiency and adaptation capacity to the proposed system, once it does not need human intervention to work, neither from the network administrator or the wireless user being located. Moreover, a probabilistic method was used for estimating wireless devices positions, based on the previous constructed model. We later demonstrate the feasibility of our approach by reporting results of field tests in which the proposed technique was implemented and validated in a real-world indoor environment.
Vaccination of Cytotoxic T Lymphocyte-Directed Peptides Elicited and Spread Humoral and Th1-Type Immune Responses to Prostate-Specific Antigen Protein in a Prostate Cancer Patient (2005)

The authors studied humoral and CD4+ T-cell responses in an HLA-A24+ prostate cancer patient vaccinated with cytotoxic T lymphocyte (CTL)-directed peptides, including a prostate-specific antigen (PSA)248-257 peptide, to understand what kinds of immune responses are elicited in peptide-vaccinated patients. The levels of immunoglobulin G (IgG) reactive to the administered PSA248-257 peptide or the PSA protein were kinetically examined. The level of IgG reactive to the PSA248-257 peptide drastically increased after the peptide vaccination, with a peak after the seventh vaccination, whereas that of IgG reactive to the PSA protein continued to increase throughout the vaccination period. IgG reactive to the PSA protein after the 13th vaccination showed no reactivity to the administered PSA peptides. However, HLA-DRB1*1302-restricted and PSA protein-recognizing TH1-type CD4+ T-cell clone and line, with different specificity, were successfully established from the post-7th and post-13th peripheral blood mononuclear cells, respectively. Both CD4+ T cells produced interferon-gamma in response to naturally processed PSA secreted from prostate cancer cells, whereas their reactivity to the administered PSA248-257 peptide was undetectable or negligible. These findings indicate that vaccination with CTL-directed peptides, including a PSA-derived peptide, was able to elicit and spread humoral and TH1-type immune responses to the PSA protein.
<title>Steganalysis of watermarking techniques using image quality metrics</title> (2001)

In this paper, we present techniques for steganalysis of images that have been potentially subjected to a watermarking algorithm. Our hypothesis is that a particular watermarking scheme leaves statistical evidence or structure that can be exploited for detection with the aid of proper selection of image features and multivariate regression analysis. We use some sophisticated image quality metrics as the feature set to distinguish between watermarked and unwatermarked images. To identify specific quality measures, which provide the best discriminative power, we use analysis of variance (ANOVA) techniques. The multivariate regression analysis is used on the selected quality metrics to build the optimal classifier using images and their blurred versions. The idea behind blurring is that the distance between an unwatermarked image and its blurred version is less than the distance between a watermarked image and its blurred version. Simulation results with a specific feature set and a well-known and commercially available watermarking technique indicates that our approach is able to accurately distinguish between watermarked and unwatermarked images.
On hybrid trellis-coded 8/4-PSK modulation systems (2003)

The authors discuss how a more robust performance can be achieved by using rate 2/3 trellis-coded 8-phase-shift-keying (PSK) signals and 4-PSK signals in a time-varying manner. It is assumed that the data are transmitted in blocks (packets) with a unique word in the packet header. Simulation results of bit error rate (BER) and performance of the recovery loop (S-curve) are presented. Several options are presented for designing the decision-directed carrier recovery and for shaping the S-curve. The cycle slip rate of the conventional system at 7.5 degrees RMS jitter is about 25% but less than 0.1% in the new schemes. This is achieved with almost no penalty in bandwidth or in BER in blocks received without cycle slips.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Clonal analysis of B cell growth and differentiation activities induced from T lymphocytes upon triggering of T3-Ti and T11 pathways. (1987)

The cellular origin of B cell growth factors (BCGF) and differentiation factors (BCDF) was investigated in the present study. For this purpose, T4+ and T8+ T cell clones were obtained from human peripheral blood, activated via stimulation of either the antigen/MHC receptor (T3-Ti molecular complex) or the antigen-independent alternative pathway (T11 molecule), and subsequently examined for their capacity to induce B cell proliferation and immunoglobulin production. The results showed that 1) BCGF is produced by both T4+ and T8+ T cells at the population level as well as at the clonal level; 2) BCDF activity, in contrast, is largely but not exclusively restricted to the T4+ subset; and 3) both the T3-Ti and T11 pathways activate individual clonal T cell populations to promote B cell growth and differentiation.
Embryonic Origins and Assembly of Blood Vessels (1989)

Embryonic blood vessels develop in two ways: angiogenesis, which is growth by budding, branching, and elongation of existing vessels, and in situ formation of endothelial vesicles that coalesce with elongating vessels. It is assumed that the former is more prevalent, with the latter restricted to vessels that form near the endoderm:mesoderm interface. Neither the relative contributions of each of these processes in the formation of specific blood vessels nor the origins of precursors (angioblasts) of these intraembryonic endothelial populations are known. Antibodies that recognize quail endothelial cells can be used to follow the movements and differentiation of endothelial cell precursors after the transplantation of putative precursor populations from quail into chick embryos. Using this method, it has been shown that all intraembryonic mesodermal tissues, except the prechordal plate, contain angiogenic precursors. After transplantation some angioblasts move in all directions away from the site of implantation, invading surrounding mesenchyme and contributing to the formation of arteries, veins, and capillaries in a wide area. Although it is clear that these invasive angioblasts, which behave unlike any other embryonic mesenchymal cell type, are found throughout the embryo, it is not known whether they represent a unique endothelial cell type in mature blood vessels. Irrespective of their original location in the donor embryo, transplanted angioblasts will form vascular channels that are appropriate for the tissues surrounding their site of implantation. These results indicate that the control over vascular assembly resides within the connective-tissue-forming mesenchyme of the embryo.
Abstract 3805: Effect of Imatinib mesylate in gastric cancer cell progression (2015)

Abstract Imatinib is a powerful tyrosine kinase inhibitor that specifically targets BCR-ABL, KIT, and PDGFR kinases that is used in the treatment of chronic myelogenous leukemia (CML), gastrointestinal stromal tumors (GIST), and other cancers. But, imatinib mesylate has not yet been reported about anti-cancer effect in gastric cancer. This study was undertaken to evaluate the in vitro effect of imatinib mesylate in gastric cancer cells and to define molecular mechanism underlying these effects. This study was to determine the expression of PDGFR molecules in gastric cancer cells (AGS, MKN28, MKN45, SNU638) by semi-quantitative polimerase chain reaction (PCR). The effects of imatinib mesylate on gastric cancer cells were examined in four human gastric cancer cell lines. The results showed expression of PDGFR in all four gastric cancer cells. We measured the sensitivity of gastric cancer cell line (AGS, MKN28, MKN45, SNU638) to imatinib mesylate using MTT assay. Cell viability of cell treated with imatinib mesylate was decreased in high dose. But cell viability was not change in high dose. Next, the results showed expression of PDGFR and suppression of its phosphorylation by imatinib mesylate in all four gastric cancer cells. Cell cycle analysis for sub-G1 and G2/M fraction also detected the increased cell death in the cells treated with imatinib mesylates. Results by Western blotting indicated that imatinib mesylates promotes apoptosis of gastric cancer cells by both activating caspase-3 and -9 and inducing PARP cleavage. And expression of p-AKT level was decreased. Cell migration and invasion that imatinib treated cells is decreased in low dose. Cell viability assay revealed that the combination of imatinib mesylate and chemo-reagent synergistically inhibited cell growth compared to cells treated with any of the agent alone. In conclusion, inhibition the PDGFR by imatinib mesylates lead to apoptosis of gastric cancer cell lines. And Imatinib suppressed motility and invasion of gastric cancer cells. The results suggest that imatinib mesylate may be useful in the treatment of gastric cancer. Note: This abstract was not presented at the meeting. Citation Format: Jung Lim Kim, Bo Ram Kim, Yoo Jin Na, Seong Hye Park, Yoon A Jeong, Sang Cheul Oh. Effect of Imatinib mesylate in gastric cancer cell progression. [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 3805. doi:10.1158/1538-7445.AM2015-3805
Elucidation of the Structures of Residual and Dissolved Pine Kraft Lignins Using an HMQC NMR Technique (2003)

Comparative studies on the structures of residual and dissolved lignins isolated from pine kraft pulp and pulping liquor have been undertaken using the (1)H-(13)C HMQC NMR technique, GPC, and sugar analysis to elucidate the reaction mechanisms in kraft pulping and the lignin reactivity. A modified procedure for the isolation of enzymatic residual lignins has resulted in an appreciable decrease in protein contaminants in the residual lignin preparations (N content < 0.2%). The very high dispersion of HMQC spectra allows identification of different lignin moieties, which signals appear overlapped in 1D (13)C NMR spectra. Elucidation of the role of condensation reactions indicates that an increase in the degree of lignin condensation during pulping results from accumulation of original condensed lignin moieties rather than from the formation of new alkyl-aryl structures. Among aryl-vinyl type moieties, only stilbene structures are accumulated in lignin in appreciable amounts. Benzyl ether lignin-carbohydrate bonds involving primary hydroxyl groups of carbohydrates have been detected in residual and dissolved lignin preparations. Structures of the alpha-hydroxyacid type have been postulated to be among the important lignin degradation products in kraft pulping. The effect of the isolation method on the lignin structure and differences between the residual and dissolved lignins are discussed.
Leukemia inhibitory factor differentiation-inhibiting activity/human interleukin for DA cells augments proliferation of human hematopoietic stem cells (1990)

Leukemia inhibitory factor (LIF)/differentiation-inhibiting activity (DIA)/human interleukin for DA cells (HILDA) is a cytokine with biologic activities involving a variety of different types of target cells. Here we have tested LIF/DIA for possible effects on the growth and differentiation of normal human hematopoietic cells in culture. As a single agent, LIF/DIA had no effect on colony formation by CD34- positive human bone marrow cells. However, LIF/DIA was as effective as either interleukin-6 (IL-6) or granulocyte colony-stimulating factor (G- CSF) in the enhancement of IL-3-dependent colony formation of very primitive blast colony-forming cells. Studies using neutralizing antibodies against IL-6 or G-CSF demonstrated that this was not due to induction in culture of either of the other known synergistic factors for blast cell colony formation. A 1-day delay in the time course of appearance of blast cell colonies grown in the presence of LIF/DIA relative to those grown in the presence of IL-6 suggests that the different synergistic factors may operate through different mechanisms, although we cannot rule out that high doses of LIF/DIA might yield accelerated blast cell colony formation. Our findings provide evidence that LIF/DIA may play an important role, along with IL-6 and G-CSF, in the regulation of early hematopoietic stem cells.
Protein‐tyrosine Kinase Inhibitors (2004)

Gleevec® (imatinib mesylate) is a protein kinase inhibitor, the first marketed drug whose mechanism of action (MOA) is through inhibition of a protein kinase, functioning as a signal transduction inhibitor (STI). In 2002, it received approval from the FDA as the first-line treatment of CML and for the indication of GIST. Synthesis of imatinib mesylate involves assembly of nitrophenylpyrimidine 10 from condensation of 3-dimethylamino-enone 6 and guanidine 9 in the presence of NaOH in refluxing isopropanol. Amide formation was accomplished by treatment of aniline 11 with 4-(4-methypiperazinomethyl)-benzoyl chloride to deliver imatinib. Iressa® (gefitinib) is an epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI). It works by disrupting molecular signals that turn normal cells into tumors. As such, it does not damage healthy cells or cause side effects as harsh as those associated with standard chemotherapy treatments. Iressa® won FDA approval early in 2003.
Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis (1993)

Five different genetic elements have been found to be associated with genetic rearrangements in Mycobacterium tuberculosis complex strains. Of these elements, the insertion sequence IS6110 is presently the most frequently used genetic marker for strain differentiation of M. tuberculosis. In the present study we compared five genetic elements for their potentials to differentiate a given cluster of M. tuberculosis strains. Because of the presence of only a single copy of IS6110 or two IS6110 copies at the same chromosomal locus, a large number of strains could not be differentiated by IS6110 fingerprinting. Most strains, including the low-copy-number IS6110 strains, could be differentiated by fingerprinting with the 36-bp direct repeat or the polymorphic GC-rich repetitive DNA element. Less discriminative power was obtained with the major polymorphic tandem repeat and the insertion element IS1081. One strain which did not contain IS6110 DNA was encountered. Until now, this element has invariantly been found to be present in all M. tuberculosis complex strains. On the basis of classical taxonomic criteria and sequencing of the 16S rRNA gene, this strain was shown to be a genuine M. tuberculosis strain. Therefore, the use of this element as a target for polymerase chain reaction-facilitated detection of M. tuberculosis should be reconsidered.
Tracking and mitigating piracy (2006)

The DVD piracy problem is analyzed as a benchmark case study of propagation of potentially sensitive information through the small-world social network and the scale-free Internet. The fundamental mathematical concept is that of a hybrid network, that is, two graphs, one with positive curvature the other with negative curvature, connected with an exchange mechanism. It is shown that this propagation model on a hybrid network matches real traces of DVD piracy. Some anti-piracy measures based on control concepts are suggested.
De novo expression of intercellular-adhesion molecule 1 in melanoma correlates with increased risk of metastasis. (1989)

The 89-kDa cell surface glycoprotein, P3.58, is detectable on advanced human melanomas in situ but not on benign melanocytes or early melanomas. cDNA cloning of P3.58 from melanoma cells was accomplished by screening a lambda zap expression vector library with monoclonal antibodies produced against the denatured antigen. Nucleotide sequencing of the clones revealed that P3.58 is identical to the intercellular-adhesion molecule 1. No qualitative differences in P3.58 mRNA species could be seen between melanoma cells and hematopoietic cells and no differences in gene organization were observed between peripheral blood leukocytes and melanoma cells. Inspection of the deduced amino acid sequence of P3.58 indicated the presence of the consensus sequence characteristic for complement-binding proteins. The acquisition of this cell-adhesion molecule during the process of tumor progression is speculated to contribute to the development of metastasis in melanoma.
Perspectives on the production of polyhydroxyalkanoates in plants (1992)

Poly-β-hydroxybutyrate (PBH) was recently shown to be produced in genetically engineered plants which expressed the genes from Alcaligenes eutrophus responsible for the formation of PHB from acetoacetyl-CoA. The transgenic plants accumulated PHB as granules which were similar in size and appearance to the bacterial PHB granules. These observations suggest that large scale production of PHB and other polyhydroxyalkanoates in genetically altered crop plants may be feasible.