gebhart/patrepeval huggingface dataset:
Liver X Receptors (2002)

The Liver X receptors (LXRs), members of the nuclear receptor superfamily, play an important role in controlling lipid homeostasis by activating several genes involved in reverse cholesterol transport. These include members of the ATP binding cassette (ABC) superfamily of transporter proteins ABCA1 and ABCG1, surface constituents of plasma lipoproteins like apoE, and cholesterol ester transport protein (CETP). LXRs also play an important role in fatty acid metabolism by activating the sterol regulatory element-binding protein 1c gene (SREBP1c). hLXRα itself is an autoinducible gene, and ”auto-induction“ in response to LXR ligands is observed in multiple human cell-types including macrophages. Based on their ability to induce reverse cholesterol transport LXRs appear to be useful and novel targets for the treatment of atherosclerosis, one of the most fatal diseases in the western world. In this article, we review the biological functions of LXRs and discuss the possibility of identifyi ng LXR ligands as drugs for the treatment of atherosclerosis.
Crystal structure of an uncleaved α1‐antitrypsin reveals the conformation of its inhibitory reactive loop (1995)

The crystal structure of a recombinant human alpha 1-antitrypsin, in the uncleaved and uncomplexed state, has been determined by X-ray crystallographic methods and refined to an R-factor of 18.4% for 8.0-3.46 A data with good stereochemistry. This structure provides the first view at the inhibitory loop and the central beta-sheet A of the uncleaved alpha 1-antitrypsin. The reactive loop takes a distorted helical conformation and no pre-insertion of two residues in the reactive loop into the beta-sheet A is observed. The present structure is largely in agreement with the model predicted by Engh, Wright, and Huber [Prot. Eng. 3 (1990) 469-477].
Cyclic voltammetry theory for the disproportionation reaction and spherical diffusion (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCyclic voltammetry theory for the disproportionation reaction and spherical diffusionMichael L. Olmstead and Richard S. NicholsonCite this: Anal. Chem. 1969, 41, 6, 862–864Publication Date (Print):May 1, 1969Publication History Published online1 May 2002Published inissue 1 May 1969https://pubs.acs.org/doi/10.1021/ac60275a004https://doi.org/10.1021/ac60275a004research-articleACS PublicationsRequest reuse permissionsArticle Views726Altmetric-Citations60LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
TCR dynamics on the surface of living T cells (2001)

T lymphocyte activation by specific antigen requires prolonged TCR occupancy and sustained signaling. This is accomplished by the formation of a specialized signaling domain, the immunological synapse, at the T cell-antigen-presenting cell contact site. Surface receptors and signaling components are progressively recruited into this domain where they are organized in defined three-dimensional structures. To better understand how TCR are supplied to the signaling domain during the activation process, we measured (using confocal microscopy and photo-bleaching recovery techniques) lateral mobility of GFP-tagged TCR on living Jurkat cell surface. We show that: (i) surface-expressed TCR exhibit an intrinsic, actin cytoskeleton-independent, lateral mobility which allows them to passively diffuse over the entire T cell surface within approximately 60 min and (ii) non-stimulated TCR rapidly enter the signaling domain. Our results indicate that TCR lateral mobility per se is sufficient to ensure TCR supply to the immunological synapse in the course of sustained T cell activation.
The integration of tissue structure and nuclear function (2001)

Living cells can filter the same set of biochemical signals to produce different functional outcomes depending on the deformation of the cell. It has been suggested that the cell may be "hard-wired" such that external forces can mediate internal nuclear changes through the modification of established, balanced, internal cytoskeletal tensions. This review will discuss the potential of subnuclear structures and nuclear chromatin to participate in or respond to transduction of mechanical signals originating outside the nucleus. The mechanical interactions of intranuclear structure with the nuclear lamina will be examined. The nuclear lamina, in turn, provides a structural link between the nucleus and the cytoplasmic and cortical cytoskeleton. These mechanical couplings may provide a basis for regulating gene expression through changes in cell shape.Key words: gene expression, cell structure, nuclear structure, mechanotransduction, chromatin.
Toxic and carcinogenic agents in undiluted mainstream smoke and sidestream smoke of different types of cigarettes (1987)

The mainstream and sidestream smoke of four types of popular US cigarettes were analyzed for toxic and carcinogenic agents. The cigarettes included one without a filter tip, and one filter cigarette each with medium, low and ultra-low smoke yields. The analyses clearly demonstrated that 12 toxic agents determined in this study were significantly reduced in the mainstream smoke of filter cigarettes, as compared with smoke yields from the nonfilter cigarette. In the case of the ultra-low yield cigarette, mainstream smoke emissions were reduced by about 90%. In contrast to this finding, the emissions of the same toxic and carcinogenic components into sidestream smoke of the filter cigarettes were not greatly reduced. Sidestream smoke is the major contributor to environmental tobacco smoke, to which both smokers and non-smokers are exposed. Although the exposure of the smoker to mainstream smoke components is decreased due to proportionally greater consumption of low and ultra-low yield cigarettes, and lower rates of consumption of cigarettes with high smoke yields, the carcinogenic potential of indoor pollutants originating from tobacco products is not diminished.
Unusual macrocyclic lactone sex pheromone of Parcoblatta lata , a primary food source of the endangered red-cockaded woodpecker (2011)

Wood cockroaches in the genus Parcoblatta, comprising 12 species endemic to North America, are highly abundant in southeastern pine forests and represent an important prey of the endangered red-cockaded woodpecker, Picoides borealis. The broad wood cockroach, Parcoblatta lata, is among the largest and most abundant of the wood cockroaches, constituting >50% of the biomass of the woodpecker's diet. Because reproduction in red-cockaded woodpeckers is affected dramatically by seasonal and spatial changes in arthropod availability, monitoring P. lata populations could serve as a useful index of habitat suitability for woodpecker conservation and forest management efforts. Female P. lata emit a volatile, long-distance sex pheromone, which, once identified and synthesized, could be deployed for monitoring cockroach populations. We describe here the identification, synthesis, and confirmation of the chemical structure of this pheromone as (4Z,11Z)-oxacyclotrideca-4,11-dien-2-one [= (3Z,10Z)-dodecadienolide; herein referred to as "parcoblattalactone"]. This macrocyclic lactone is a previously unidentified natural product and a previously unknown pheromonal structure for cockroaches, highlighting the great chemical diversity that characterizes olfactory communication in cockroaches: Each long-range sex pheromone identified to date from different genera belongs to a different chemical class. Parcoblattalactone was biologically active in electrophysiological assays and attracted not only P. lata but also several other Parcoblatta species in pine forests, underscoring its utility in monitoring several endemic wood cockroach species in red-cockaded woodpecker habitats.
International survey on the use of cardiac markers. (2001)

Monitoring cardiac troponin I (cTnI) or T (cTnT) for the detection of myocardial injury in acute coronary syndromes has been endorsed by the laboratory medicine community (IFCC, AACC, National Academy of Clinical Biochemistry) (1)(2) and the cardiology community (European Society of Cardiology and American College of Cardiology) (3)(4)(5). However, little to no information is available regarding the use of troponins or changing trends from traditional enzymatic markers to the use of protein markers, such as cardiac troponins, in clinical and laboratory practice. The primary objective of this study was to survey hospital laboratories for use of cardiac troponin testing as of January 1, 1995 and January 1, 1999. More than 3000 surveys were distributed internationally at the 1999 IFCC meeting in Florence, Italy, by mail in the US to 274 randomly selected hospitals from the AACC directory, and by telephone survey to 17 hospitals in the Minneapolis-St. Paul, MN metropolitan area. The survey primarily addressed the instrumentation and assays used to measure cardiac markers as of January 1, 1995 and January 1, 1999. Results are presented as trends and descriptive findings, and no statistical analyses were performed.

Fewer than 5% of the surveys distributed …
Endonuclease from Escherichia coli that acts specifically upon duplex DNA damaged by ultraviolet light, osmium tetroxide, acid, or x-rays. (1977)

An endonuclease which is active upon DNA exposed to ultraviolet light at a photoproduct other than thymine dimers has been extensively purified from Escherichia coli. The small (2.7 S) enzyme is active in the presence of EDTA, has a neutral pH optimum, and is inhibited by tRNA and 1 M NaCl. It has no detectable exonuclease, DNA-N-glycosidase, or ribonuclease activities. The enzyme also nicks duplex DNA exposed to OsO4, x-rays, or acid, but it does not act upon undamaged DNA or irradiated single-stranded DNA. The majority of sites of action in DNA exposed to ultraviolet light or OsO4 appear to be alkali-stable, but those in DNA exposed to x-rays or acid are not. The incisions created by the endonuclease contain 5'-phosphate termini. The enzyme is possibly the same as E. coli endonuclease III described by Radman (Radman, M. (1976) J. Biol. Chem. 251, 1438-1445), but it is distinguishable from the other endodeoxyribonucleases described from that organism.
Materials and Optimized Designs for Human‐Machine Interfaces Via Epidermal Electronics (2013)

Thin, soft, and elastic electronics with physical properties well matched to the epidermis can be conformally and robustly integrated with the skin. Materials and optimized designs for such devices are presented for surface electromyography (sEMG). The findings enable sEMG from wide ranging areas of the body. The measurements have quality sufficient for advanced forms of human-machine interface.
On The Indistinguishability-Based Security Model of Key Agreement Protocols-Simple Cases. (2005)

Since Bellare and Rogaway&amp;apos;s work in 1994, the indistinguishability-based security models of authenticated key agreement protocols in simple cases have been evolving for more than ten years. In this paper, we review and organize the models under a unified framework with some new extensions. By providing a new ability (the Coin query) to adversaries and redefining two key security notions, the framework fully exploits an adversary&amp;apos;s capacity and can be used to prove all the commonly required security attributes of key agreement protocols with key confirmation. At the same time, the Coin query is also used to define a model which can be used to heuristically evaluate the security of a large category of authenticated protocols without key confirmation. We use the models to analyze a few identity-based authenticated key agreement protocols with pairings.
Structure-based design of specific inhibitors of Janus kinase 3 as apoptosis-inducing antileukemic agents. (1999)

A novel homology model of the kinase domain of Janus kinase (JAK) 3 was used for the structure-based design of dimethoxyquinazoline compounds with potent and specific inhibitory activity against JAK3. The active site of JAK3 in this homology model measures roughly 8 A x 11 A x 20 A, with a volume of approximately 530 A3 available for inhibitor binding. Modeling studies indicated that 4-(phenyl)-amino-6,7-dimethoxyquinazoline (parent compound WHI-258) would likely fit into the catalytic site of JAK3 and that derivatives of this compound that contain an OH group at the 4' position of the phenyl ring would more strongly bind to JAK3 because of added interactions with Asp-967, a key residue in the catalytic site of JAK3. These predictions were consistent with docking studies indicating that compounds containing a 4'-OH group, WHI-P131 [4-(4'-hydroxyphenyl)-amino-6,7-dimethoxyquinazoline], WHI-P154 [4-(3'-bromo-4'-hydroxylphenyl)-amino-6,7-dimethoxyquinazoline], and WHI-P97 [4-(3',5'-dibromo-4'-hydroxylphenyl)-amino-6,7-dimethoxyquinazolin e], were likely to bind favorably to JAK3, with estimated K(i)s ranging from 0.6 to 2.3 microM. These compounds inhibited JAK3 in immune complex kinase assays in a dose-dependent fashion. In contrast, compounds lacking the 4'-OH group, WHI-P79 [4-(3'-bromophenyl)-amino-6,7-dimethoxyquinazoline], WHI-P111 [4-(3'-bromo-4'-methylphenyl)-amino-6,7-dimethoxyquinazoline], WHI-P112 [4-(2',5'-dibromophenyl)-amino-6,7-dimethoxyquinazoline], WHI-P132 [4-(2'-hydroxylphenyl)-amino-6,7-dimethoxyquinazoline], and WHI-P258 [4-(phenyl)-amino-6,7-dimethoxyquinazoline], were predicted to bind less strongly, with estimated K(i)s ranging from 28 to 72 microM. These compounds did not show any significant JAK3 inhibition in kinase assays. Furthermore, the lead dimethoxyquinazoline compound, WHI-P131, which showed potent JAK3-inhibitory activity (IC50 of 78 microM), did not inhibit JAK1 and JAK2, the ZAP/SYK family tyrosine kinase SYK, the TEC family tyrosine kinase BTK, the SRC family tyrosine kinase LYN, or the receptor family tyrosine kinase insulin receptor kinase, even at concentrations as high as 350 microM. WHI-P131 induced apoptosis in JAK3-expressing human leukemia cell lines NALM-6 and LC1;19 but not in melanoma (M24-MET) or squamous carcinoma (SQ20B) cells. Leukemia cells were not killed by dimethoxyquinazoline compounds that were inactive against JAK3. WHI-P131 inhibited the clonogenic growth of JAK3-positive leukemia cell lines DAUDI, RAMOS, LC1;19, NALM-6, MOLT-3, and HL-60 (but not JAK3-negative BT-20 breast cancer, M24-MET melanoma, or SQ20B squamous carcinoma cell lines) in a concentration-dependent fashion. Potent and specific inhibitors of JAK3 such as WHI-P131 may provide the basis for the design of new treatment strategies against acute lymphoblastic leukemia, the most common form of childhood cancer.
Therapeutic Strategies in Alzheimer’s Disease: Ml Muscarinic Agonists (2000)

The cholinergic hypofunction in Alzheimer's disease (AD) appears to be linked with two other major hallmarks of this disease, beta-amyloid and hyperphosphorylated tau protein. Formation of beta-amyloids might impair the coupling of M1 muscarinic acetylcholine receptors (mAChR) with G-proteins. This can lead to decreased signal transduction, a decrease of trophic and non-amyloidogenic amyloid precursor protein (APPs) and generation of more beta-amyloids, aggravating further the cholinergic deficiency. This review is an attempt to explore the M1 mAChR regulation of beta-amyloid metabolism, tau hyperphosphorylation and cognitive functions. The therapeutic potential of M1-selective muscarinic agonists including AF102B, AF150(S), AF267B (the AF series) is evaluated and compared, when possible, with several FDA-approved acetylcholinesterase inhibitors. These M1 agonists can elevate APPs, decrease tau protein phosphorylation/hyperphosphorylation in vitro and in vivo and restore cognitive impairments in several animal models for AD. Except for the M1 agonists, no other compounds were reported yet with combined effects; e.g., amelioration of cognition dysfunction and beneficial modulation of APPs/beta-amyloid together with tau hyperphosphorylation/phosphorylation. This property of M1 agonists to alter different aspects associated with AD pathogenesis could represent the most remarkable clinical value of such drugs.
Mitogenic stimulation of human tumor-infiltrating lymphocytes by secreted factor(s) from human tumor cell lines. (1990)

Tumor-infiltrating lymphocytes (TILs) have shown in vivo antitumor efficacy in both animal and human studies. Functions thought necessary for antitumor activity include cytolysis, homing, and proliferation at tumor sites. TILs, which are T lymphocytes grown ex vivo directly from tumors, bear interleukin 2 (IL-2) receptors capable of transducing the IL-2 mitogenic signal. However, IL-2 is not normally synthesized by solid tumor cells. This study was aimed at exploring the possible presence of T-cell mitogens of tumor origin. To this end four TIL lines derived from four melanoma patients were studied for their ability to use the environments of cultured tumor cell lines as mitogenic sources. The presence of four irradiated cultured human tumor cell lines, three of which were derived from the same melanoma patients as the TILs, were found to stimulate proliferation of human TILs in the absence of IL-2. Further investigation showed that the observed proliferative stimulation by the fourth tumor line was due to secreted factor(s) as mitogenic activity was present in the serum-free tumor cell supernatant. Both immunologic analyses of this medium and proliferative assays in which TILs were stimulated with recombinant lymphokine standards suggest the presence of a yet uncharacterized T-cell mitogen.
Biological correlates of migraine and cluster headaches: an overview of their potential use in diagnosis and treatment (2010)

Current diagnostic criteria for headaches are based on the International Classification for Headache Disorders, second edition, which is largely built on data obtained from clinical examinations and patients' medical histories. Despite decades of vigorous basic and clinical research, we still lack reliable clinical laboratory diagnostic markers for headaches, which clearly obstructs the physician's ability to optimize and follow the patient's response to treatment protocols as well as holds back the discovery and implementation of new therapeutic modalities. In this paper, we review and discuss current efforts to identify and characterize biochemical and immunological changes in biological fluids and tissue that may be specifically associated with the etiology and/or pathophysiology of migraine and cluster headaches; we also discuss some of the recent genetic findings and ion channel modulation studies that may help to distinguish among various headache populations.
Quality scores and SNP detection in sequencing-by-synthesis systems (2008)

Promising new sequencing technologies, based on sequencing-by-synthesis (SBS), are starting to deliver large amounts of DNA sequence at very low cost. Polymorphism detection is a key application. We describe general methods for improved quality scores and accurate automated polymorphism detection, and apply them to data from the Roche (454) Genome Sequencer 20. We assess our methods using known-truth data sets, which is critical to the validity of the assessments. We developed informative, base-by-base error predictors for this sequencer and used a variant of the phred binning algorithm to combine them into a single empirically derived quality score. These quality scores are more useful than those produced by the system software: They both better predict actual error rates and identify many more high-quality bases. We developed a SNP detection method, with variants for low coverage, high coverage, and PCR amplicon applications, and evaluated it on known-truth data sets. We demonstrate good specificity in single reads, and excellent specificity (no false positives in 215 kb of genome) in high-coverage data.
Coding image sequences for interactive retrieval (1989)

An image coding technique for digital storage of motion picture information is presented that is optimated for use in interactive systems where high quality still frames, random access, and database linkages are required.
Lysophosphatidic acid is a chemoattractant for Dictyostelium discoideum amoebae. (1993)

The naturally occurring phospholipid lysophosphatidic acid (LPA) can induce a number of physiological responses in vertebrate cells, including platelet aggregation, smooth muscle contraction, and fibroblast proliferation. LPA is thought to activate a specific G-protein-coupled receptor, thereby triggering classic second messenger pathways such as stimulation of phospholipase C and inhibition of adenylate cyclase. Here we report that 1-oleoyl-LPA, at submicromolar concentrations, evokes a chemotactic response in amoebae of the cellular slime mold Dictyostelium discoideum. LPA-induced chemotaxis is specific in that other lysophospholipids, phosphatidic acid, and monoacylglycerol have no effect. We show that the response to LPA is not secondary to the accumulation of extracellular cAMP, a well-established chemoattractant for nutrient-starved D. discoideum. Compared with cAMP-induced chemotaxis, LPA-induced chemotaxis has a somewhat lower efficiency and is not accompanied by the characteristic cellular elongation and orientation along the gradient. These results indicate that LPA has a previously unsuspected role as a chemoattractant for D. discoideum and imply that its biological function as a "first messenger" is not restricted to vertebrate cells.
Disruption of FADS2 gene in mice impairs male reproduction and causes dermal and intestinal ulceration (2009)

Delta-6 desaturase (D6D) catalyzes the first step in the synthesis of highly unsaturated fatty acids (HUFA) such as arachidonic (AA), docosapentaenoic (DPAn-6), and docosahexaenoic (DHA) acids, as well as the last desaturation of DPAn-6 and DHA. We created D6D-null mice (-/-), which enabled us to study HUFA deficiency without depleting their precursors. In -/-, no in vivo AA synthesis was detected after administration of [U-(13)C]linoleic acid (LA), indicating absence of D6D isozyme. Unexpectedly, all of the -/- developed ulcerative dermatitis when fed a purified diet lacking D6D products but containing ample LA. The -/- also exhibited splenomegaly and ulceration in duodenum and ileocecal junction. Male -/- lacked normal spermatozoa with a severe impairment of spermiogenesis. Tissue HUFAs in -/- declined differentially: liver AA and DHA by 95%, and a smaller decrease in brain and testes. Dietary AA completely prevented dermatitis and intestinal ulcers in -/-. DPAn-6 was absent in -/- brain under AA supplementation, indicating absence of D6D isozyme for DPAn-6 synthesis from AA. This study demonstrated a distinct advantage of the D6D-null mice (-/-) to elucidate (1) AA function without complication of LA deprivation and (2) DHA function in the nervous system without AA depletion or DPAn-6 replacement seen in traditional models.