gebhart/patrepeval huggingface dataset:
Delayed symptom onset and increased life expectancy in Sandhoff disease mice treated with N -butyldeoxynojirimycin (1999)

Sandhoff disease is a neurodegenerative disorder resulting from the autosomal recessive inheritance of mutations in the HEXB gene, which encodes the beta-subunit of beta-hexosaminidase. GM2 ganglioside fails to be degraded and accumulates within lysosomes in cells of the periphery and the central nervous system (CNS). There are currently no therapies for the glycosphingolipid lysosomal storage diseases that involve CNS pathology, including the GM2 gangliosidoses. One strategy for treating this and related diseases is substrate deprivation. This would utilize an inhibitor of glycosphingolipid biosynthesis to balance synthesis with the impaired rate of catabolism, thus preventing storage. One such inhibitor is N-butyldeoxynojirimycin, which currently is in clinical trials for the potential treatment of type 1 Gaucher disease, a related disease that involves glycosphingolipid storage in peripheral tissues, but not in the CNS. In this study, we have evaluated whether this drug also could be applied to the treatment of diseases with CNS storage and pathology. We therefore have treated a mouse model of Sandhoff disease with the inhibitor N-butyldeoxynojirimycin. The treated mice have delayed symptom onset, reduced storage in the brain and peripheral tissues, and increased life expectancy. Substrate deprivation therefore offers a potentially general therapy for this family of lysosomal storage diseases, including those with CNS disease.
The mouse olfactory receptor gene family (2004)

In mammals, odor detection in the nose is mediated by a diverse family of olfactory receptors (ORs), which are used combinatorially to detect different odorants and encode their identities. The OR family can be divided into subfamilies whose members are highly related and are likely to recognize structurally related odorants. To gain further insight into the mechanisms underlying odor detection, we analyzed the mouse OR gene family. Exhaustive searches of a mouse genome database identified 913 intact OR genes and 296 OR pseudogenes. These genes were localized to 51 different loci on 17 chromosomes. Sequence comparisons showed that the mouse OR family contains 241 subfamilies. Subfamily sizes vary extensively, suggesting that some classes of odorants may be more easily detected or discriminated than others. Determination of subfamilies that contain ORs with identified ligands allowed tentative functional predictions for 19 subfamilies. Analysis of the chromosomal locations of members of each subfamily showed that many OR gene loci encode only one or a few subfamilies. Furthermore, most subfamilies are encoded by a single locus, suggesting that different loci may encode receptors for different types of odorant structural features. Comparison of human and mouse OR subfamilies showed that the two species have many, but not all, subfamilies in common. However, mouse subfamilies are usually larger than their human counterparts. This finding suggests that humans and mice recognize many of the same odorant structural motifs, but mice may be superior in odor sensitivity and discrimination.
Gene therapy for retinal and choroidal diseases (2002)

The eye is a small compartment separated from the systemic circulation by the blood-ocular barriers, providing advantages for intraocular gene transfer – an approach which is being investigated for several types of retinal and choroidal diseases. A compelling application is gene replacement for homozygous loss-of-function mutations in genes differentially expressed in photoreceptors or retinal pigmented epithelial (RPE) cells that result in retinal degeneration. Considerable progress has been made in this area, including demonstration of return of visual function in RPE65-/- dogs after subretinal injection of adeno-associated viral vectors encoding RPE65, providing groundwork for a clinical trial in patients with Leber’s Congenital Amaurosis. Proof of principle has been provided for intraocular gene transfer of ribozymes for dominantly inherited retinal degenerations. Survival factor gene therapy shows promise for treatments that may be used in multiple retinal degenerations. Transduction of intraocular and/or periocular cells with constructs that encode antiangiogenic proteins provides a new approach for sustained local delivery treatment of retinal and choroidal neovascularisation. While considerable investigation remains to work out critical details, there is substantial evidence suggesting that in the near future, gene therapy-based treatments will be an important addition to what is currently offered to patients with retinal and/or choroidal diseases.
Contrast-based image attention analysis by using fuzzy growing (2003)

Visual attention analysis provides an alternative methodology to semantic image understanding in many applications such as adaptive content delivery and region-based image retrieval. In this paper, we propose a feasible and fast approach to attention area detection in images based on contrast analysis. The main contributions are threefold: 1) a new saliency map generation method based on local contrast analysis is proposed; 2) by simulating human perception, a fuzzy growing method is used to extract attended areas or objects from the saliency map; and 3) a practicable framework for image attention analysis is presented, which provides three-level attention analysis, i.e., attended view, attended areas and attended points. This framework facilitates visual analysis tools or vision systems to automatically extract attentions from images in a manner like human perception. User study results indicate that the proposed approach is effective and practicable.
Loss of pigment epithelium derived factor expression in glioma progression (2003)

It is possible that the absence of PEDF expression is a potent factor for the enhancement of angiogenesis in glioma.
Amphiphilic, tri-block copolymers provide potent membrane-targeted neuroprotection (2001)

SPECIFIC AIMSThe aim of our study was to investigate the potential neuroprotective effects of Poloxamer 188 (P188), one of a class of amphiphilic tri-block copolymers, on neuronal survival after st...
Characterization of His-X3-His sites in α-helices of synthetic metal-binding bovine somatotropin (1991)

Variants of bovine somatotropin have been engineered to contain synthetic metal-binding sites consisting of two solvent-exposed histidines separated by a single turn of an alpha-helix (His-X3-His variants). The affinities of these proteins for Cu(II) were characterized by measuring their partition coefficients in an aqueous two-phase polymer system. The partition coefficients were used to generate binding constants for formation of a complex between the engineered metal-binding site and Cu(II) chelated to an iminodiacetic acid derivative of polyethylene glycol. For three His-X3-His variants described here, these constants range from 2 x 10(4) to 1.6 x 10(6) M-1. The metal affinity of a His-X3-His site depends on the rigidity of the helix into which the site is engineered. The affinities of the His-X3-His sites for Cu(II) are large enough to dramatically increase not only the partitioning of these proteins in aqueous two-phase systems, but also their retention times on a metal-affinity chromatography column. Both these features can greatly facilitate the purification of engineered proteins. Criteria for choosing positions for incorporating metal-binding sites are discussed.
Role of the Transmembrane Domains of prM and E Proteins in the Formation of Yellow Fever Virus Envelope (2002)

Flavivirus envelope proteins have been shown to play a major role in virus assembly. These proteins are anchored into cellular and viral membranes by their C-terminal domain. These domains are composed of two hydrophobic stretches separated by a short hydrophilic segment containing at least one charged residue. We investigated the role of the transmembrane domains of prM and E in the envelope formation of the flavivirus yellow fever virus (YFV). Alanine scanning insertion mutagenesis has been used to examine the role of the transmembrane domains of prM and E in YFV subviral particle formation. Most of the insertions had a dramatic effect on the release of YFV subviral particles. Some of these mutations were introduced into the viral genome. The ability of these mutant viruses to produce infectious particles was severely reduced. The alanine insertions did not affect prM-E heterodimerization. In addition, replacement of the charged residues present in the middle of the transmembrane domains had no effect on subviral particle release. Taken together, these data indicate that the transmembrane domains of prM and E play a crucial role in the biogenesis of YFV envelope. In addition, these data indicate some differences between the transmembrane domains of the hepaciviruses and the flaviviruses.
THE PROTEIN KINASE C FAMILY: HETEROGENEITY AND ITS IMPLICATIONS (1989)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
A phase I and pharmacokinetic study of intravenous phenylacetate in patients with cancer. (1994)

Phenylacetate has recently been shown to suppress tumor growth and promote differentiation in experimental models. A phase I trial of phenylacetate was conducted in 17 patients with advanced solid tumors. Each patient received a single i.v. bolus dose followed by a 14-day continuous i.v. infusion of the drug. Twenty-one cycles of therapy were administered at four dose levels, achieved by increasing the rate of the continuous i.v. infusion. Phenylacetate displayed nonlinear pharmacokinetics [Km = 105.1 +/- 44.5 (SD) microgram/ml, Vmax = 24.1 +/- 5.2 mg/kg/h and Vd = 19.2 +/- 3.3 L]. There was also evidence for induction of drug clearance. Ninety-nine % of phenylacetate elimination was accounted for by conversion to phenylacetylglutamine, which was excreted in the urine. Continuous i.v. infusion rates resulting in serum phenylacetate concentrations exceeding Km often resulted in rapid drug accumulation and dose-limiting toxicity, which consisted of reversible central nervous system depression, preceded by emesis. Three of nine patients with metastatic, hormone-refractory prostate cancer maintained stable prostatic specific antigen levels for more than 2 months; another had less bone pain. One of six patients with glioblastoma multiforme, whose steroid dosage has remained unchanged for the duration of therapy, has sustained functional improvement for more than 9 months. The use of adaptive control with feedback for the dosing of each patient enabled us to safely maintain stable phenylacetate concentrations up to the range of 200-300 micrograms/ml, which resulted in clinical improvement in some patients with advanced disease.
An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development (2006)

In order to quantify relative transcript abundances accurately using real-time RT-PCR, we recommend that combinations of several genes be used for normalization in grape berry development studies. Our data support GAPDH, actin, EF1-alpha and SAND as the most relevant reference genes for this purpose.
Mechanisms of action of new antiepileptic drugs (1997)

Many new antiepileptic drugs have been developed to treat seizure disorders. The established antiepileptic drugs reduce neuronal excitability by promoting sodium channel inactivation, inhibiting T-type calcium channels, or enhancing gamma-aminobutyric acid type A receptor-mediated inhibition. Several of the newer agents employ similar mechanisms, whereas others may enhance gamma-aminobutyric acid-ergic inhibitory systems or inhibit glutamatergic excitatory neurotransmission, and may be neuroprotective or antiepileptogenic.
A review of the newer aromatase inhibitors in the management of metastatic breast cancer (1998)

The newer aromatase inhibitors have several advantages compared to aminoglutethimide and are a useful addition to the armamentarium of therapies employed in the palliative management of advanced breast cancer.
A general planar waveguide autoregressive optical filter (1996)

A general architecture for an autoregressive (AR) planar waveguide optical filter is demonstrated for the first time. Its advantages are a flatter passband, sharper rolloff and better rejection in the stopband compared to finite impulse response (FIR) filters with the same number of stages. The architecture can be extended to an arbitrary number of stages. A modified Levinson algorithm is derived for filter synthesis and analysis which includes waveguide loss and phase errors between stages. The filter analysis algorithm allows the filter's coupling ratios and phase errors for each stage to be determined from the filter's spectral response. When combined with a postfabrication tuning process, this analysis method provides feedback for optimizing the response. Autoregressive lattice filters were designed and fabricated using Ge-doped silica waveguides. Measurements are reported which demonstrate the synthesis and analysis algorithms. The impact of fabrication tolerances on filter synthesis and of measurement uncertainties on filter analysis are investigated.
Digging the New York City Skyline: Soil Fungal Communities in Green Roofs and City Parks (2013)

In urban environments, green roofs provide a number of benefits, including decreased urban heat island effects and reduced energy costs for buildings. However, little research has been done on the non-plant biota associated with green roofs, which likely affect their functionality. For the current study, we evaluated whether or not green roofs planted with two native plant communities in New York City functioned as habitats for soil fungal communities, and compared fungal communities in green roof growing media to soil microbial composition in five city parks, including Central Park and the High Line. Ten replicate roofs were sampled one year after planting; three of these roofs were more intensively sampled and compared to nearby city parks. Using Illumina sequencing of the fungal ITS region we found that green roofs supported a diverse fungal community, with numerous taxa belonging to fungal groups capable of surviving in disturbed and polluted habitats. Across roofs, there was significant biogeographical clustering of fungal communities, indicating that community assembly of roof microbes across the greater New York City area is locally variable. Green roof fungal communities were compositionally distinct from city parks and only 54% of the green roof taxa were also found in the park soils. Phospholipid fatty acid analysis revealed that park soils had greater microbial biomass and higher bacterial to fungal ratios than green roof substrates. City park soils were also more enriched with heavy metals, had lower pH, and lower quantities of total bases (Ca, K, and Mg) compared to green roof substrates. While fungal communities were compositionally distinct across green roofs, they did not differentiate by plant community. Together, these results suggest that fungi living in the growing medium of green roofs may be an underestimated component of these biotic systems functioning to support some of the valued ecological services of green roofs.
Computing by Means of Physics-Based Optical Neural Networks (2010)

We report recent research on computing with biology-based neural network models by means of physics-based opto-electronic hardware. New technology provides opportunities for very-high-speed computation and uncovers problems obstructing the wide-spread use of this new capability. The Computation Modeling community may be able to offer solutions to these cross-boundary research problems.
Diagnostic and extent of disease multigene assay for malignant thyroid neoplasms (2006)

This novel multigene assay is an excellent diagnostic and extent of disease marker for differentiated thyroid cancer and would be a helpful adjunct to FNA biopsy of thyroid nodules.
Fiber-Optic "White-Light" Birefringent Temperature Sensor (1987)

Passive multiplexing of a fiber optic temperature sensor network using spectral modulation encoding techniques in birefringent bulk materials is demonstrated. Various detection schemes are described and the consequences of the spectral dependence of optical properties for both transducer and demultiplexer are theoretically analyzed. The network organization choice is discussed and the first experimental evaluations of a breadboard network are reported (sensitivity, crosstalk, line losses effect).
Host-Pathogen Interactions in Latent Mycobacterium tuberculosis Infection: Identification of New Targets for Tuberculosis Intervention (2008)

Mycobacterium tuberculosis (M. tuberculosis) is one of the worlds' most successful and sophisticated pathogens. It is estimated that over 2 billion people today harbour latent M. tuberculosis infection without any clinical symptoms. Since most new cases of active tuberculosis (TB) arise from this (growing) number of latently infected individuals, urgent measures to control TB reactivation are required, including more effective drugs and new TB vaccines. The currently widely used BCG vaccines, as well as most new generation TB-vaccines that are being developed are designed as prophylactic or as BCG-booster vaccines. Unfortunately, many of these vaccines are unlikely to be effective in individuals already latently infected with M. tuberculosis. Here we argue that detailed analysis of M. tuberculosis genes that are switched on predominantly during the latent stage of infection may lead to the identification of new M. tuberculosis targets for drug and vaccine development. First, we will describe essential host-pathogen interactions in TB with particular emphasis on TB latency and persistent infection. Subsequently, we will focus on a novel group of late-stage specific genes, encoded by the M. tuberculosis dormancy (dosR) regulon, and summarize recent studies describing human T-cell recognition of these dormancy antigens in relation to (latent) M. tuberculosis infection. We will discuss the possible relevance of these new classes of antigens for new TB intervention strategies.
Recent Developments in the Virus Therapy of Cancer (2000)

Cancer is one of the leading causes of death in the United States. Although there has been significant progress in the areas of cancer etiology, diagnostic techniques, and cancer prevention, adequate therapeutic approaches for many cancers have lagged behind. One promising line of investigation is the virus therapy of cancer. This approach entails the use of viruses, such as retroviruses, adenovirus, and vaccinia virus, to modify tumor cells so that they become more susceptible to being killed by the host immune response, chemotherapeutic agents, or programmed cell death. This review discusses recent advances in the virus therapy of cancer from both basic science and clinical perspectives. Given the potential of viruses to kill tumor cells directly or transduce desired gene products to allow a vigorous host antitumor immune response, the virus therapy of cancer holds great promise in the treatment of cancer.
The herpes zoster subunit vaccine (2015)

The HZ/su vaccine appears very promising in immunocompetent patients in the ZoE-50 controlled trial. The unblinding of the current ZoE-50 trial and publication of results from the accompanying ZoE-70 trial will reveal more about its mechanism of action and its efficacy against PHN, particularly in subjects >70 years. Phase III trial results in immunocompromised patients are eagerly awaited.
RNA-guided endonuclease provides a therapeutic strategy to cure latent herpesviridae infection (2014)

Latent viral infection is a persistent cause of human disease. Although standard antiviral therapies can suppress active viral replication, no existing treatment can effectively eradicate latent infection and therefore a cure is lacking for many prevalent viral diseases. The prokaryotic immune system clustered regularly interspaced short palindromic repeat (CRISPR)/Cas evolved as a natural response to phage infections, and we demonstrate here that the CRISPR/Cas9 system can be adapted for antiviral treatment in human cells by specifically targeting the genomes of latent viral infections. Patient-derived cells from a Burkitt's lymphoma with latent Epstein-Barr virus infection showed dramatic proliferation arrest and a concomitant decrease in viral load after exposure to a CRISPR/Cas9 vector targeted to the viral genome.
Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: Application to prolyl endopeptidase and thermolysin (2000)

A method of analysis of a local fitness landscape for a current biopolymer is presented. Based on the assumption of additivity of mutational effects in the biopolymer, we assigned a site-fitness to each residue at each site. The assigned values of site-fitnesses were obtained by the least-squares method to minimize discrepancies between experimental fitnesses and theoretical ones. As test cases, we analyzed a section of a local landscape for the thermostability of prolyl endopeptidase and that for the enzymatic activity of thermolysin. These sections were proved to be of the rough Mt. Fuji-type with straight theta values of larger than 1.0, where straight theta is defined as the ratio of the "mean slope" to the "degree of roughness" on the fitness surface. Furthermore, we theoretically explained discrepancies between the fitnesses of multiple mutants and those predicted based on strict additivity of the component mutations by using a model of the rough Mt. Fuji-type landscape. According to this model, the discrepancies depend on the local landscape property (such as the straight theta value) and the location of the wild type on the landscape and the mean change in fitness by the component mutations. Our results suggest that this model may provide a good approximation of real sections of local landscapes for current biopolymers phenomenologically.
Human Protein C Receptor Is Present Primarily on Endothelium of Large Blood Vessels (1997)

These studies suggest that EPCR may be important in enhancing protein C activation on large vessels. The presence of high levels of EPCR on arterial vessels may help explain why partial protein C deficiency is a weak risk factor for arterial thrombosis.
Targeting the Extracellular Membrane-Proximal Domain of Membrane-Bound IgE by Passive Immunization Blocks IgE Synthesis In Vivo (2008)

The classical allergic reaction starts seconds or minutes after Ag contact and is committed by Abs produced by a special subset of B lymphocytes. These Abs belong to the IgE subclass and are responsible for Type I hyperreactivity reactions. Treatment of allergic diseases with humanized anti-IgE Abs leads primarily to a decrease of serum IgE levels. As a consequence, the number of high-affinity IgE receptors on mast cells and basophils decreases, leading to a lower excitability of the effector cells. The biological mechanism behind anti-IgE therapy remains partly speculative; however, it is likely that these Abs also interact with membrane IgE (mIgE) on B cells and possibly interfere with IgE production. In the present work, we raised a mouse mAb directed exclusively against the extracellular membrane-proximal domain of mIgE. The interaction between the monoclonal anti-mIgE Ab and mIgE induces receptor-mediated apoptosis in vitro. Passive immunization experiments lead to a block of newly synthesized specific IgEs during a parallel application of recombinant Bet v1a, the major birch pollen allergen. The decrease of allergen-specific serum IgE might be related to tolerance-inducing mechanisms stopping mIgE-displaying B cells in their proliferation and differentiation.