gebhart/patrepeval huggingface dataset:
Mouse Models for Studies of Retinal Degeneration and Diseases (2012)

Mouse models, with their well-developed genetics and similarity to human physiology and anatomy, serve as powerful tools with which to investigate the etiology of human retinal degeneration. Mutant mice also provide reproducible, experimental systems for elucidating pathways of normal development and function. Here, I describe the tools used in the discoveries of many retinal degeneration models, including indirect ophthalmoscopy (to look at the fundus appearance), fundus photography and fluorescein angiography (to document the fundus appearance), electroretinography (to check retinal function), as well as the heritability test (for genetic characterization).
Secretion of type II phospholipase A2 and cryptdin by rat small intestinal Paneth cells (1996)

We examined the secretion of antimicrobial proteins and peptides into surgically isolated and continuously perfused segments of rat small intestine. Up to nine discrete antimicrobial molecules appeared in the intestinal perfusates following intravenous administration of bethanechol, a cholinergic agonist, or intralumenal instillation of lipopolysaccharide (LPS). Among them were three markers of Paneth cell secretion: lysozyme; type II (secretory) phospholipase A2; and at least one intestinal defensin, RIP-3, that appeared to be an alternatively processed variant of the rat neutrophil defensin RatNP-3. Both bethanechol- and LPS-stimulated intestinal lumenal perfusates (washings) contained molecules that killed Escherichia coli, Salmonella typhimurium, and Listeria monocytogenes in vitro. These molecules were more active against the avirulent S. typhimurium strain 7953S (phoP) than against its virulent parent, S. typhimurium 14028S. These data demonstrate that small intestinal Paneth cells secrete antimicrobial peptides in vivo, that this secretion is regulated by the autonomic (parasympathetic) cholinergic nervous system, and that the release of antimicrobial molecules can be triggered by the presence of bacterial LPS in the intestinal lumen.
Fracture Stimulation Utilizing a Viscoelastic-Surfactant-Based System in the Morrow Sands in Southeast New Mexico (2007)

Abstract This paper discusses the selection criteria, design methodology, and analysis of hydraulic fracturing treatments pumped using a solids-free, liquid CO2 foam-based visco-elastic surfactant (VES) fluid system in Morrow Sand reservoirs located in Southeast New Mexico (SENM). The wells discussed in the paper were completed in various Morrow Sand intervals around 10,500 ft with an average Bottom Hole Static Temperature (BHST) of 190°F. Wellbore completion constraints combined with reservoir parameters inclusive of low-pressured water sensitive formations, high rock Youngs' Modulus and unpredictable occurrence of water-bearing zones, lead to the selection of foamed VES fluids. This technology was successfully applied in the Morrow Sands in Eddy County of SENM. Fracture geometry analysis using surface treating pressures, radio-active tracers and production data, showed height growth containment and longer effective fracture half-lengths. Results also indicated successful stimulation past the cement squeezed intervals and temporary liner tie-backs run in to overcome lower pressure constraints. Finally, lower friction pressures helped in designing economical fracture stimulations for mature wellbores thereby generating an opportunity to recover otherwise bypassed hydrocarbon reserves.
Purification and Properties of Pantothenate Kinase fromBrevibacterium ammoniagenesIFO 12071 (1973)

Pantothenate kinase (ATP: pantothenate 4′-phosphotransferase, EC 2.7.1.33) was purified about 200-fold from the cell extract of Brevibacterium ammoniagenes IFO 12071 by ammonium sulfate fractionation, DEAE-cellulose chromatography, and Sephadex G-150 gel filtration. The purified enzyme gave a single band on polyacrylamide gel electrophoresis. The molecular weight was calculated approximately 45,000. The enzyme catalyzed the formation of pantothenic acid 4′-phosphate and ADP from pantothenate and ATP in the presence of Mg2+ ATP could be substituted for, partly, by ITP, GTP, and UTP. The enzyme phosphorylated not only pantothenate, but also pantothenoylcysteine, pantetheine, and pantothenyl alcohol. Apparent Km values were 6.7×10−5 m for pantothenate, 3.5×10−5 m for ATP, and 10−3 m for Mg2+. The reaction was inhibited by the intermediates of CoA biosynthesis, of which CoA itself was a most effective inhibitor. Other properties of the enzyme were also investigated.
Double duplex invasion by peptide nucleic acid: A general principle for sequence-specific targeting of double-stranded DNA (1999)

Pseudocomplementary PNAs containing diaminopurine.thiouracil base pairs have been prepared and are shown to bind with high specificity and efficiency to complementary targets in double-stranded DNA by a mechanism termed "double duplex invasion" in which the duplex is unwound and both DNA strands are targeted simultaneously, each by one of the two pseudocomplementary peptide nucleic acids (PNAs). On the basis of our results we predict that (for decameric targets) more than 80% of all sequences can be targeted by straightforward Watson-Crick base pairing by using this approach in its present form. Targeting of pseudocomplementary PNAs to the promoter of the T7 phage RNA polymerase effectively inhibits transcription initiation. These results have important implications in the development of gene therapeutic agents as well as for genetic diagnostic and molecular biology applications.
Genetically abnormal clones in histologically normal breast tissue. (1998)

Breast cancer is believed to develop as multiple genetic abnormalities accumulate, each conferring some growth advantage, but the timing and nature of the earliest steps in this progression are not yet elucidated. Proliferative breast lesions, associated with an increased risk of breast cancer although considered benign, recently were shown to contain clonal genetic abnormalities. Therefore, we hypothesized that clonal genetic abnormalities might be detectable before any phenotypic abnormalities are evident, ie, in histologically normal breast tissue. We examined DNA extracted from 95 normal-appearing breast ducts or terminal ductal-lobular units from 20 individuals at varying degrees of risk (those undergoing reduction mammoplasties, those with atypical hyperplastic proliferative lesions, and those already diagnosed with breast cancer). Using nine microsatellite markers, we sought evidence of genetic instability or of allelic imbalance (most likely representing loss of heterozygosity). We found genetically abnormal clones in 21/95 (22%) seemingly normal samples from 10/20 (50%) women from all three risk groups. In women under age 50, trends toward increased rates of abnormalities were noted with increased cancer risk. The abnormalities identified were more likely to be at sites of known or postulated tumor suppressor genes rather than at random or neutral loci. Our data indicate that genetic abnormalities potentially critical to breast tumorigenesis accumulate before pathological detection even of high-risk lesions and are detectable in tissue that is not only histologically benign but also completely normal.
The derogatis interview for sexual functioning (DISF/DISF-SR): An introductory report (1997)

The current report describes a program of research designed to demonstrate the psychometric characteristics and validity of the Derogatis Interview for Sexual Functioning (DISF/DISF-SR), a set of brief, gender-keyed, multidimensional outcome measures designed to measure quality of sexual functioning. The primary goals of the development of the DISF/DISF-SR are outlined within the context of the principal measurement parameters involved in human sexual functioning. The development and rationale for both interview (DISF) and matching self-report (DISF-SR) versions of the instrument are presented, as is the rationale for developing distinct male and female forms. The studies described evaluate the reliabilities of both modalities of the DISF/DISF-SR and demonstrate confirmation for the hypothesized internal structure of the test. Research is provided that demonstrates dimensional uniqueness in subtest-total score relationships, and several studies are reviewed that show high discriminative validity for the DISF/DISF-SR in medical and community cohorts. The initial norms for the DISF/DISF-SR are also reviewed and described.
The INNs and outs of antibody nonproprietary names (2015)

An important step in drug development is the assignment of an International Nonproprietary Name (INN) by the World Health Organization (WHO) that provides healthcare professionals with a unique and universally available designated name to identify each pharmaceutical substance. Monoclonal antibody INNs comprise a -mab suffix preceded by a substem indicating the antibody type, e.g., chimeric (-xi-), humanized (-zu-), or human (-u-). The WHO publishes INN definitions that specify how new monoclonal antibody therapeutics are categorized and adapts the definitions to new technologies. However, rapid progress in antibody technologies has blurred the boundaries between existing antibody categories and created a burgeoning array of new antibody formats. Thus, revising the INN system for antibodies is akin to aiming for a rapidly moving target. The WHO recently revised INN definitions for antibodies now to be based on amino acid sequence identity. These new definitions, however, are critically flawed as they are ambiguous and go against decades of scientific literature. A key concern is the imposition of an arbitrary threshold for identity against human germline antibody variable region sequences. This leads to inconsistent classification of somatically mutated human antibodies, humanized antibodies as well as antibodies derived from semi-synthetic/synthetic libraries and transgenic animals. Such sequence-based classification implies clear functional distinction between categories (e.g., immunogenicity). However, there is no scientific evidence to support this. Dialog between the WHO INN Expert Group and key stakeholders is needed to develop a new INN system for antibodies and to avoid confusion and miscommunication between researchers and clinicians prescribing antibodies.
Information flow control for standard OS abstractions (2007)

Decentralized Information Flow Control (DIFC) is an approach to security that allows application writers to control how data flows between the pieces of an application and the outside world. As applied to privacy, DIFC allows untrusted software to compute with private data while trusted security code controls the release of that data. As applied to integrity, DIFC allows trusted code to protect untrusted software from unexpected malicious inputs. In either case, only bugs in the trusted code, which tends to be small and isolated, can lead to security violations. We present Flume , a new DIFC model that applies at the granularity of operating system processes and standard OS abstractions (e.g., pipes and file descriptors). Flume was designed for simplicity of mechanism, to ease DIFC's use in existing applications, and to allow safe interaction between conventional and DIFC-aware processes. Flume runs as a user-level reference monitor onLinux. A process confined by Flume cannot perform most system calls directly; instead, an interposition layer replaces system calls with IPCto the reference monitor, which enforces data flowpolicies and performs safe operations on the process's behalf. We ported a complex web application (MoinMoin Wiki) to Flume, changingonly 2% of the original code. Performance measurements show a 43% slowdown on read workloadsand a 34% slowdown on write workloads, which aremostly due to Flume's user-level implementation.
<title>Differential field-widened spatial heterodyne spectrometer for investigations at high spectral resolution of the diffuse far-ultraviolet 1548-A emission line from the interstellar medium</title> (1993)

In this paper we describe the design of the Spatial Heterodyne Spectrometer that we are developing for velocity-resolved observations of the diffuse interstellar C IV emission, and we describe a new implementation of the Spatial Heterodyne Spectroscopy (SHS) concept that reduces contamination due to grating scattering and unwanted orders in wide field applications. Laboratory tests of this concept at visible and ultraviolet wavelengths demonstrate that this SHS technique is suitable for the study of faint, diffuse emission lines at any wavelength, particularly in the ultraviolet, where the full advantages of interference spectroscopy have not been realized. Specifically, the development of SHS will provide the opportunity to map both the distribution and radial velocities of the hot (10<SUP>5</SUP> K) component of the interstellar medium. An SHS spectrometer capable of obtaining the first velocity-resolved (20 km s<SUP>-1</SUP>) line profiles of the C IV (lambda) 1548 emission line in the Cygnus loop and in the hot component of the interstellar medium at high Galactic latitude is currently being developed for suborbital observations. Our long term goal is the development of SHS for a radial-velocity-resolved sky survey of the 104+5) K `coronal gas' component of the interstellar medium using a small satellite with an approximately one year operational lifetime.
Cannabinoid System as a Potential Target for Drug Development in the Treatment of Cardiovascular Disease (2003)

Although cannabinoids have been recreationally employed for thousands of years, it was not until the discovery of their specific receptors, in the early nineties, that the molecular basis of cannabinoid activity have began to be understood. Growing research in this field has demonstrated not only that the action of cannabinoids in mammals is mainly receptor-mediated, but also that endogenous cannabinoids, such as anandamide, are produced, metabolized, and taken up across the cell membrane through a facilitated uptake process. The exogenous administration of cannabinoids, as well as the manipulation of their endogenous levels have been related to a variety of effects, such as analgesia, impairment of cognition and learning, appetite enhancement and peripheral vasodilation. Hence, the endocannabinoid system, including the CB1 and CB2 receptors, the metabolizing enzyme fatty acid amide hydrolase and the anandamide transporter, is a potential target for the development of novel therapeutic drugs in the treatment of various conditions, such as pain, feeding disorders and vascular disease among others. Although most of the research in the field of cannabinoids has been focused on their effects in the central nervous system, a growing line of evidence indicates that cannabinoids can also play a major role in the control of physiopathological functions in the cardiovascular system. In this context, endocannabinoids have been proposed as novel possible hypotensive agents, and have been involved in the hypotension observed in septic shock, acute myocardial infarction and cirrhosis. In addition, a protective role for endocannabinoids has been described in ischemia.
MicroRNA‑186 promotes cell proliferation and inhibits cell apoptosis in cutaneous squamous cell carcinoma by targeting RETREG1 (2019)

MicroRNAs (miRs), a class of small non-coding RNAs, have been demonstrated to be involved in the development and progression of human malignancies, including cutaneous squamous cell carcinoma (CSCC). miR-186 serves a suppressive role in certain common types of human cancer; however, its exact function in CSCC has not been reported previously. In the present study, the expression of miR-186 was significantly increased in CSCC tissues compared with adjacent non-tumour tissues. Overexpression of miR-186 significantly promoted CSCC cell proliferation while inhibiting cell apoptosis. Reticulophagy regulator 1 (RETREG1), a gene that is significantly downregulated in CSCC tissues and cell lines, was identified as a novel target of miR-186. In addition, the expression of RETREG1 was inversely correlated with miR-186 expression in CSCC tissues. Furthermore, the expression of RETREG1 was negatively regulated by miR-186 in CSCC cells, and restoration of RETREG1 attenuated the effects of miR-186 on CSCC cells. Taken together, the results of the current study suggest that miR-186 serves an oncogenic role in CSCC and may be used as a potential therapeutic target for the treatment of this disease.
mRNA For Genes Associated with Antigen Presentation are Expressed by Human Middle Meatal Epithelial Cells in Culture (2004)

Primary human epithelial cells obtained from the middle meatus express genes associated with antigen presentation function. The pattern of gene expression is modulated by cytokine stimulation and changes as the cells differentiate at the ALI. These findings suggest that mature middle meatal epithelial cells have the cellular machinery to interact with T cells and therefore may be direct participants in the modulation of T-cell activity in chronic sinusitis.
Nanotube composite carbon fibers (1999)

Single walled carbon nanotubes (SWNTs) were dispersed in isotropic petroleum pitch matrices to form nanotube composite carbon fibers with enhanced mechanical and electrical properties. We find that the tensile strength, modulus, and electrical conductivity of a pitch composite fiber with 5 wt % loading of purified SWNTs are enhanced by ∼90%, ∼150%, and 340% respectively, as compared to the corresponding values in unmodified isotropic pitch fibers. These results serve to highlight the potential that exits for developing a spectrum of material properties through the selection of the matrix, nanotube dispersion, alignment, and interfacial bonding.
Retention of hemostatic and immunological properties of frozen plasma and COVID‐19 convalescent apheresis fresh‐frozen plasma produced and freeze‐dried in Canada (2021)

Changes in protein activities or clotting times arising from freeze-drying were <15%. Although C3a levels in TFDP were elevated, they were less than literature values for transfusable plasma. SARS-CoV-2-neutralizing antibody titers and viral protein binding levels were largely unaffected by freeze-drying. In vitro characteristics of TFDP or CC-TFDP were comparable to their originating plasma, making future clinical studies appropriate.
Effect of Manganese on Lignin Degradation by Pleurotus ostreatus during Solid-State Fermentation (1993)

Lignin degradation by Pleurotus ostreatus was studied under solid-state fermentation (SSF) in chemically defined medium containing various levels of Mn. Degradation of [C]lignin prepared from cotton branches to soluble products, as well as its mineralization to CO(2), was enhanced by the addition of Mn. The effect of malonate on lignin mineralization was most marked during the first 10 days of SSF, in a treatment amended with 73 muM Mn. A high concentration of Mn (4.5 mM) caused inhibition of both fungal growth and mineralization rates during the first 2 weeks of incubation. Addition of malonate reversed this effect because of chelation of Mn. Mn was found to precipitate in all treatments, with or without the addition of malonate. alpha-Keto-gamma-methiolbutyric acid cleavage to ethylene, an indication of OH production, was observed as early as 3 days of incubation in all treatments.
Radioactive source detection by sensor networks (2005)

Detection limits of sensor networks for moving radioactive sources are characterized, using Bayesian methods in conjunction with computer simulation. These studies involve point sources moving at constant velocity, emulating vehicular conveyance on a straight road. For networks involving ten nodes, respective Bayesian methods are implementable in real time. We probe the increased computational requirements incurred by larger numbers of nodes and source trajectory parameters. The complexity appears quadratic in the number of nodes and, also, numerous trajectory parameters may be used. We investigate the consequences of different levels of background radiation. Simulations are shown to be useful for ranking candidate node layouts. We study the detection capabilities of individual sensors and the scalability of detection with sensor density; near the detection limit, increasing the number of sensors can accrue subproportional network sensitivity.
Mitochondrial and Chloroplast Phage-Type RNA Polymerases in Arabidopsis (1997)

In addition to the RNA polymerases (RNAPs) transcribing the nuclear genes, eukaryotic cells also require RNAPs to transcribe the genes of the mitochondrial genome and, in plants, of the chloroplast genome. The plant Arabidopsis thaliana was found to contain two nuclear genes similar to genes encoding the mitochondrial RNAP from yeast and RNAPs of bacteriophages T7, T3, and SP6. The putative transit peptides of the two polymerases were capable of targeting fusion proteins to mitochondria and chloroplasts, respectively, in vitro. The results indicate that the mitochondrial RNAP in plants is a bacteriophage-type enzyme. A gene duplication event may have generated the second RNAP, which along with the plastid-encoded eubacteria-like RNAP could transcribe the chloroplast genome.
Scott Wiring for Direct Repair of Lumbar Spondylolysis (2003)

The Scott wiring technique is recommended for the treatment of symptomatic lumbar spondylolysis in patients younger than 25 years because it gave "good" or "excellent" results in approximately 86% of the patients with a mean follow-up period of 10.9 years.
Selection and characterization of HER2/neu-binding affibody ligands (2004)

Affibody (affibody) ligands that are specific for the extracellular domain of human epidermal growth factor receptor 2 (HER2/neu) have been selected by phage display technology from a combinatorial protein library based on the 58 amino acid residue staphylococcal protein A-derived Z domain. The predominant variants from the phage selection were produced in Escherichia coli, purified by affinity chromatography, and characterized by biosensor analyses. Two affibody variants were shown to selectively bind to the extracellular domain of HER2/neu (HER2-ECD), but not to control proteins. One of the variants, denoted His6-ZHER2/neu:4, was demonstrated to bind with nanomolar affinity (approximately 50 nM) to the HER2-ECD molecule at a different site than the monoclonal antibody trastuzumab. Furthermore, radiolabeled His6-ZHER2/neu:4 affibody showed specific binding to native HER2/neu, overexpressed on the SKBR-3 tumor cell line. Such affibody ligands might be considered in tumor targeting applications for radionuclide diagnostics and therapy of adenocarcinomas such as breast and ovarian cancers.
Encyclopedia Of Controlled Drug Delivery (1999)

Covers all aspects of controlled drug delivery, including human, agricultural and animal applications. The 70 entries, written by an international team of renowned experts, offers A-to-Z coverage of controlled drug delivery systems for researchers in the pharmaceutical and biotechnology industries, agriculture companies, medical device companies, clinical research organizations and medical schools.