gebhart/patrepeval huggingface dataset:
Targeted, Systemic Non-Viral Delivery of Small Interfering RNA in vivo (2005)

Armed with the complete sequence of the human genome and an ever-increasing array of biological techniques, researchers continue to learn more about the genetic basis of diseases. For two decades, scientists and physicians have been developing therapeutic strategies for treating many diseases at the genetic level, creating the field of therapy. For those diseases caused by loss-of-function mutations in a specific gene, delivery of a wild-type copy of that gene to affected cells can reduce or eliminate the disease phenotype. Viruses, having evolved to be extremely effective at delivering nucleic acids (i.e., their own genes for viral production) to cells, have been modified to include therapeutic genes of interest. While such viral gene therapy vectors are the most efficient vectors developed, concerns about their safety and immunogenicity have prompted many to investigate non-viral vector alternatives. Cationic polymers and lipids have emerged as leading non-viral vector materials. Our laboratory has developed a class of cyclodextrin-containing polycations (CDPs) that condense DNA into complexes that can be endocytosed by cells, achieve expression of their genetic payload in those cells, and may be modified to target particular cell types within an animal. In the past five years, scientists have discovered a new mechanism for the reduction of gene expression in mammalian cells via sequence-specific cleavage of a particular messenger RNA (mRNA); this phenomenon is known as RNA interference (RNAi). Since RNAi is triggered by nucleic acids (small interfering RNA (siRNA) duplexes), I hypothesized that CDPs may be suitable vectors for the delivery of siRNA. In my thesis work, the safety of synthetic siRNA duplexes is examined both in cultured cells and in vivo. Using a number of different siRNA sequences, two different strains of mice, and three different methods of administration, I fail to observe any cytokine (IL-12 or IFN-a) responses, morphological changes, or alterations in complete blood counts (CBCs) or liver enzyme levels. The ability of CDP to serve as a delivery vehicle for siRNA is also explored. I demonstrate that CDP/siRNA complexes can be formed that are small enough to be endocytosed, can be modified to ensure stability in physiological fluid, and protect the siRNA payload from serum nuclease degradation. Finally, down-regulation of specific target genes, including genes implicated in disease, is shown in vitro and in mice. An endogenous reporter gene (luciferase) in the livers of transgenic mice is down-regulated by galactosylated CDP/siRNA formulations that target hepatocytes. The level of a chimeric oncogene, EWS-Fli1, is reduced by polyplex formulations in cultured Ewing’s sarcoma cells and by transferrin-targeted formulations in tumor-bearing mice; this in vivo down-regulation corresponds to an inhibition of tumor growth. These results suggest that CDP-containing siRNA formulations have the potential for development into therapeutics.
Small-molecule modulators of p53 family signaling and antitumor effects in p53-deficient human colon tumor xenografts (2006)

p53 deficiency is common in almost all human tumors and contributes to an aggressive chemo- or radiotherapy-resistant phenotype, therefore providing a target for drug development. Molecular targeting to restore wild-type p53 activity has been attempted in drug development and has led to the identification of CP-31398, PRIMA1, and the Nutlins. However, strategies targeting p53-activated transcriptional responses or p53 family member expression in p53-deficient tumors have yet to be explored. Here we demonstrate the use of noninvasive bioluminescence imaging in a high-throughput cell-based screen of small molecules that activate p53 responses and cell death in human tumor cells carrying a mutant p53. We isolated a number of small molecules that activate p53 reporter activity, increase expression of p53 target genes such as p21(WAF1) or death receptor 5 (KILLER/DR5) of TNF-related apoptosis-inducing ligand (TRAIL), and induce apoptosis in p53-deficient cells. Some of the compounds activate a p53 response by increasing p73 expression, and knockdown of transactivating isoforms of p73 by small interfering RNA reduces their induction of p53-responsive transcriptional activity. Some compounds do not induce significant p73 expression but induce a high p53-responsive transcriptional activity in the absence of p53. In vivo experiments demonstrate potent antitumor effects of selected compounds, using either HCT116/p53(-/-) or DLD1 human colon tumor xenografts. The results establish the feasibility of a cell-based drug screening strategy targeting the p53 transcription factor family of importance in human cancer and provide lead compounds for further development in cancer therapy.
Triisobutylaluminium and Diisobutylaluminium Hydride as Molecular Scalpels: The Regioselective Stripping of Perbenzylated Sugars and Cyclodextrins (2004)

To explain the remarkable regioselective de-O-benzylating properties of diisobutylaluminium hydride (DIBAL-H) and triisobutylaluminium (TIBAL) towards polybenzylated sugars or cyclodextrins, we propose a plausible mechanistic rationale critically involving the kinetic formation of a product-generating 2:1 Al-benzylated sugar complex. For the reaction to occur, one pair of adjacent oxygen atoms should first be able to form a chelation complex with the first equivalent of aluminium reagent, either a highly fluxional complex with tetracoordinate aluminium species or a pentacoordinate one. The second equivalent then induces the regioselectivity of the de-O-alkylation by coordinating preferentially to one of the oxygen atoms of the selected pair.
Taxonomy of bacterial fish pathogens (2011)

Bacterial taxonomy has progressed from reliance on highly artificial culture-dependent techniques involving the study of phenotype (including morphological, biochemical and physiological data) to the modern applications of molecular biology, most recently 16S rRNA gene sequencing, which gives an insight into evolutionary pathways (= phylogenetics). The latter is applicable to culture-independent approaches, and has led directly to the recognition of new uncultured bacterial groups, i.e. "Candidatus", which have been associated as the cause of some fish diseases, including rainbow trout summer enteritic syndrome. One immediate benefit is that 16S rRNA gene sequencing has led to increased confidence in the accuracy of names allocated to bacterial pathogens. This is in marked contrast to the previous dominance of phenotyping, and identifications, which have been subsequently challenged in the light of 16S rRNA gene sequencing. To date, there has been some fluidity over the names of bacterial fish pathogens, with some, for example Vibrio anguillarum, being divided into two separate entities (V. anguillarum and V. ordalii). Others have been combined, for example V. carchariae, V. harveyi and V. trachuri as V. harveyi. Confusion may result with some organisms recognized by more than one name; V. anguillarum was reclassified as Beneckea and Listonella, with Vibrio and Listonella persisting in the scientific literature. Notwithstanding, modern methods have permitted real progress in the understanding of the taxonomic relationships of many bacterial fish pathogens.
MEMS-switched reconfigurable antennas (2002)

The integration and use of RF MEMS switches in microstrip patch antennas and feed structures were investigated for developing reconfigurable multi-band antennas. The current application focuses on the development of a dual L/X-band antenna that would support several satellite or UAV-based communications and radar applications such as SAR, terrain mapping, GMTI, AMTI, etc. A reconfigurable patch module (RPM) was designed and fabricated consisting of a 3/spl times/3 array of patches connected together using MEMS switches (we simulated MEMS switches with ideal OPEN/CLOSED switches). This RPM could be used as a basic element in a tile/conformal architecture. Stripline power dividers and blind via transitions were developed to demonstrate feed structures that could be located below the radiating aperture.
Regional Cardiac Dilatation after Acute Myocardial Infarction (1979)

To assess the early topographic changes after acute transmural myocardial infarction, we studied 28 patients during the first two weeks after infarction by serial two-dimensional echocardiography. Regional end-diastolic segment lengths and wall thicknesses for anterior and posterior left ventricular walls were calculated. Eight patients showed infarct expansion, with disproportionate dilatation and transmural thinning in the infarcted zone, that was significantly different (P less than 0.005) from changes in non-infarcted regions. This regional expansion led to an overall left ventricular dilatation in these eight patients of 25 per cent compared to 5 per cent in the 20 patients without infarct expansion. Although the eight patients with regional expansion did not have significantly higher peak creatine kinase or Killip classification, they had a significantly greater eight-week mortality (four of eight versus none of 20, P less than 0.004). Thus, regional cardiac dilatation may be an early, lethal consequence of transmural infarcts, and appears to be an important mechanism of acute cardiac dilatation after myocardial infarction.
Preparation of Genomic DNA from Mammalian Tissue (1998)

There are a number of different procedures for the preparation of genomic DNA. They all start with some form of cell lysis, followed by deproteination and recovery of DNA. The main differences between various approaches lie in the extent of deproteination and in molecular weight of the DNA produced. The isolation procedure described here is relatively brief and relies on the powerful proteolytic activity of proteinase K combined with the denaturing ability of the ionic detergent SDS.
Modeling of planar circuits including the effect of space-varying surface impedances (1991)

Microstrip circuit calculations including the effect of lumped impedances can be carried out by describing the lumped elements mathematically with the help of Delta -functions. This approach is based on the assumption of impedances with infinitesimally small extension in one dimension. This approach is generalized for impedances of finite extent. Space-varying surface impedances are introduced that are incorporated into the mixed space-spectral domain analysis. The circuit is embedded in layered media and is fed by an arbitrary number of planar lines. Examples for microstrip lines with an absorbing impedance region are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fecal microbiota transplantation for severe enterocolonic fistulizing Crohn’s disease (2013)

The concept of fecal microbiota transplantation (FMT) has been used in traditional Chinese medicine at least since the 4(th) century. Evidence from recent human studies strongly supports the link between intestinal bacteria and inflammatory bowel disease. We proposed that standardized FMT might be a promising rescue therapy for refractory inflammatory bowel disease. However, there were no reports of FMT used in patients with severe Crohn's disease (CD). Here, we report the successful treatment of standardized FMT as a rescue therapy for a case of refractory CD complicated with fistula, residual Barium sulfate and formation of intraperitoneal large inflammatory mass. As far as we know, this is the first case of severe CD treated using FMT through mid-gut.
LFA-1 interaction with ICAM-1 and ICAM-2 regulates Th2 cytokine production. (1998)

The role of CD28/B7 and LFA-1/ICAM costimulation in proliferation and Th1/Th2 differentiation of naive CD4+ T cells was addressed using T cells from DO11.10 TCR transgenic mice stimulated by dendritic cells. The blockade of either CD28/B7 or LFA-1/ICAM interactions partially inhibited T cell proliferation. By comparison, blocking CD28/B7 costimulation inhibited IL-4 and IL-5 (Th2 cytokine) production, whereas blocking LFA-1/ICAM-1 or LFA-1/ICAM-2 led to a significant increase (15- to 40-fold) of Th2 cytokines. The combination of anti-ICAM-1 and anti-ICAM-2 mAbs had a synergistic effect with a 100- to 1000-fold increase of Th2 cytokine production. Thus, these two costimulatory pathways have opposing roles in the regulation of Th2 development.
Progressive paresthesia and weakness after intrathecal chemotherapy. (2008)

A 53-year-old woman was diagnosed with acute lymphoblastic leukemia (ALL) confirmed by bone marrow biopsy to be pre-B ALL. The patient underwent a hyperfractionated cyclophosphamide, doxorubicin, vincristine, and dexamethosone (hyper-CVAD) regimen, except the doxorubicin was withheld. She received two intrathecal injections of cytarabine and methotrexate and two months later presented to Tulane University Hospital with paresthesias and weakness causing her to be wheelchair bound.
Mobile Application Development: Web vs. Native (2011)

A few short years ago, most mobile devices were, for want of a better word, "dumb." Sure, there were some early smartphones, but they were either entirely e-mail focused or lacked sophisticated touch screens that could be used without a stylus. Even fewer shipped with a decent mobile browser capable of displaying anything more than simple text, links, and maybe an image. This meant if you had one of these devices, you were either a businessperson addicted to e-mail or an alpha geek hoping that this would be the year of the smartphone. Then Apple changed everything with the release of the iPhone, and our expectations for mobile experiences were completely reset.
A security pass for messages (2011)

In this paper we introduce the concept of Message Keys by proposing that their function is similar to that of an employee's security pass in that they identify legitimate messages. We describe numerous types and forms of keys, their usage, advantages and disadvantages. Further we describe the requirements of three different types of key issuing facilities and the types of keys typically issued by each. We explore the dynamics of user confidence in systems that utilize user feedback or training, and identify the benefits of supplementing user feedback with an automated "Message Keys" system. We discuss two different implementation architectures, user acceptance, and system scalability. Finally we argue that exposing a user to spam in their Spam folder is still exposing the user to Spam, and that the best way to avoid this exposure is to avoid false positives.
Adenosine Deaminase Acts as a Natural Antagonist for Dipeptidyl Peptidase 4-Mediated Entry of the Middle East Respiratory Syndrome Coronavirus (2013)

Middle East respiratory syndrome coronavirus (MERS-CoV) replicates in cells of different species using dipeptidyl peptidase 4 (DPP4) as a functional receptor. Here we show the resistance of ferrets to MERS-CoV infection and inability of ferret DDP4 to bind MERS-CoV. Site-directed mutagenesis of amino acids variable in ferret DPP4 thus revealed the functional human DPP4 virus binding site. Adenosine deaminase (ADA), a DPP4 binding protein, competed for virus binding, acting as a natural antagonist for MERS-CoV infection.
Presence and possible role of vascular endothelial growth factor in thyroid cell growth and function (1998)

Angiogenesis is an important component in the development of thyroid goitre. Vascular endothelial growth factor (VEGF) represents a family of specific endothelial cell mitogens involved in normal angiogenesis and in tumour development. The purpose of this study was to determine the distribution of VEGF in thyroid tissues during goitre formation, and to study the actions of VEGF on the regulation of thymidine incorporation and iodine uptake by thyroid follicular cells. Goitre was induced in adult rats by administration of methimazole together with a low iodine diet. Thyroid from normal or goitrous rats was removed, fixed and sectioned. Immunocytochemistry performed for VEGF using the avidin-biotin system showed that VEGF is present in normal thyroid and is located mainly in the vascular endothelium and interfollicular stromal tissue. After administration of goitrogen for 2 weeks, which caused a two- to threefold increase in thyroid weight, staining of VEGF was less apparent within the interfollicular stroma, but strongly increased throughout the thyroid follicular and endothelial cells. Uptake of [125I] and incorporation of [3H]thymidine by Fisher rat thyroid cells (FRTL-5) were measured after 72 h culture with or without TSH or VEGF, or both. In the absence of TSH, incubation with VEGF caused a significant reduction in [3H]thymidine incorporation, but did not significantly alter [125I] uptake. Incubation with TSH (1 mU/ml) caused a fourfold increase in [3H]thymidine incorporation that was diminished by co-incubation with 10 ng/ml or greater VEGF. Similarly, 10 ng/ml or greater VEGF significantly reduced the ability of TSH to increase [125I] uptake. The antagonistic effects of VEGF on TSH-stimulated [3H]thymidine incorporation or [125I] uptake were significantly reduced in the presence of an anti-VEGF antiserum. A DNA fragment representing mRNA encoding the VEGF receptor, flt-1, was identified in FRTL-5 cells by reverse transcription PCR analysis, and the abundance of this fragment was increased in FRTL-5 cells cultured in the medium containing TSH (1 mU/ml) or fibroblast growth factor (FGF)-2 (25 ng/ml). These results indicated that VEGF and one of its receptors, Flt-1, are present in epithelial cells of the thyroid, and that VEGF could contribute to the regulation of development and function of thyroid epithelial cells.
The RXR homolog Ultraspiracle is an essential component of the Drosophila ecdysone receptor (1998)

Pulses of the steroid hormone ecdysone function as key temporal signals during insect development, coordinating the major postembryonic developmental transitions, including molting and metamorphosis. In vitro studies have demonstrated that the EcR ecdysone receptor requires an RXR heterodimer partner for its activity, encoded by the ultraspiracle (usp) locus. We show here that usp exerts no apparent function in mid-third instar larvae, when a regulatory hierarchy prepares the animal for the onset of metamorphosis. Rather, usp is required in late third instar larvae for appropriate developmental and transcriptional responses to the ecdysone pulse that triggers puparium formation. The imaginal discs in usp mutants begin to evert but do not elongate or differentiate, the larval midgut and salivary glands fail to undergo programmed cell death and the adult midgut fails to form. Consistent with these developmental phenotypes, usp mutants show pleiotropic defects in ecdysone-regulated gene expression at the larval-prepupal transition. usp mutants also recapitulate aspects of a larval molt at puparium formation, forming a supernumerary cuticle. These observations indicate that usp is required for ecdysone receptor activity in vivo, demonstrate that the EcR/USP heterodimer functions in a stage-specific manner during the onset of metamorphosis and implicate a role for usp in the decision to molt or pupariate in response to ecdysone pulses during larval development.
An efficient route for synthesis of 5,6‐diphenylimidazo‐[2,1‐b]thiazoles as antibacterial agents (2000)

Abstract The reaction of 4,5‐diphenylimidazol‐2‐thione ( 1 ) with aromatic ketones 2a‐i using the acidified acetic acid method afforded the 4,5‐diphenyl(2‐imidazolylthio)acetophenones 3a‐h in good yields. While, the cyclized product 4i was obtained directly upon reaction of 1 with α‐acetyl naphthalene. Compounds 3a‐h were cyclized directly to the corresponding 3‐aryl‐5,6‐diphenylimidazo[2,1‐ b ]thiazoles (4a‐c) and ( 4e‐h ). In the same manner the reaction of 1 with aliphatic and/or alicyclic ketones gave the 3‐(4,5‐diphenyl‐2‐imidazolylthio)acetone derivatives 5a‐d , 2‐(4,5‐diphenylimidazolylthio)cycloalkanones 8a,d and the tricyclic compounds 9b‐c respectively. The cyclized compounds 6a‐d and 9a,d were obtained by cyclization of 5a‐d and 8a,b respectively. Oxidation of 1 gives the corresponding bis(4,5‐diphenyl‐2‐imidazolyl)‐disulfide ( 10 ) in 90% yield. Some of the synthesized compounds were tested for antifungal and antibacterial activity.
Molecular Mechanisms, Emerging Etiological Insights and Models to Test Potential Therapeutic Interventions in Alzheimers Disease (2004)

Alzheimer's disease (AD) is a common cause of dementia, resulting from accumulated beta-amyloid protein deposits in the brain. As the population ages the incidence of AD is also on the rise. The incidence is very high in the developed countries where life expectancy is high, but it is also rising rapidly in the developing countries. Caring for patients suffering from AD is a major economic burden. The mechanisms underlying the neuropathology of AD are slowly being unravelled. Here we explore the many models and theories, which have been proposed over the years. We then discuss a potential therapeutic agent, vaccinia virus complement control protein (VCP), involved in modulating the complement system in AD. VCP has been shown in in vitro studies to block the complement activation caused by the beta peptide. Traumatic injuries to the brain are well known risk factors associated with the development of AD. VCP can also enhance functional recovery resulting from traumatic brain injury and may be able to slow the progression of traumatic brain injury to AD. Here we describe strategies for testing this hypothesis and evaluating other agents such as VCP.
Development and antitumor activity of a BCL-2 targeted single-stranded DNA oligonucleotide (2014)

PNT100 is a 24-base, chemically unmodified DNA oligonucleotide sequence that is complementary to a region upstream of the BCL-2 gene. Exposure of tumor cells to PNT100 results in suppression of proliferation and cell death by a process called DNA interference. PNT2258 is PNT100 that is encapsulated in protective amphoteric liposomes developed to efficiently encapsulate the PNT100 oligonucleotide, provide enhanced serum stability, optimized pharmacokinetic properties and antitumor activity of the nanoparticle both in vivo and in vitro. PNT2258 demonstrates broad antitumor activity against BCL-2-driven WSU-DLCL2 lymphoma, highly resistant A375 melanoma, PC-3 prostate, and Daudi-Burkitt's lymphoma xenografts. The sequence specificity of PNT100 was demonstrated against three control sequences (scrambled, mismatched, and reverse complement) all encapsulated in a lipid formulation with identical particle characteristics, and control sequences did not demonstrate antiproliferative activity in vivo or in vitro. PNT2258 is currently undergoing clinical testing to evaluate safety and antitumor activity in patients with recurrent or refractory non-Hodgkin's lymphoma and additional studies are planned.