gebhart/patrepeval huggingface dataset:
Proteomic Challenges: Sample Preparation Techniques for Microgram-Quantity Protein Analysis from Biological Samples (2015)

Proteins regulate many cellular functions and analyzing the presence and abundance of proteins in biological samples are central focuses in proteomics. The discovery and validation of biomarkers, pathways, and drug targets for various diseases can be accomplished using mass spectrometry-based proteomics. However, with mass-limited samples like tumor biopsies, it can be challenging to obtain sufficient amounts of proteins to generate high-quality mass spectrometric data. Techniques developed for macroscale quantities recover sufficient amounts of protein from milligram quantities of starting material, but sample losses become crippling with these techniques when only microgram amounts of material are available. To combat this challenge, proteomicists have developed micro-scale techniques that are compatible with decreased sample size (100 μg or lower) and still enable excellent proteome coverage. Extraction, contaminant removal, protein quantitation, and sample handling techniques for the microgram protein range are reviewed here, with an emphasis on liquid chromatography and bottom-up mass spectrometry-compatible techniques. Also, a range of biological specimens, including mammalian tissues and model cell culture systems, are discussed.
Impact of cyclic hypoxia on HIF‐1α regulation in endothelial cells – new insights for anti‐tumor treatments (2008)

Heterogeneities in tumor blood flow are associated with cyclic changes in pO2 or cyclic hypoxia. A major difference from O2 diffusion-limited or chronic hypoxia is that the tumor vasculature itself may be directly influenced by the fluctuating hypoxic environment, and the reoxygenation phases complicate the usual hypoxia-induced phenotypic pattern. Here, we determined the cyclic hypoxia-driven pathways that modulate hypoxia inducible factor (HIF)-1alpha abundance in endothelial cells to identify possible therapeutic targets. We found that exposure of endothelial cells to cycles of hypoxia/reoxygenation led to accumulation of HIF-1alpha during the hypoxic periods and the phosphorylation of protein kinase B (Akt), extracellular regulated kinase (ERK) and endothelial nitric oxide synthase (eNOS) during the reoxygenation phases. We identified stimulation of mitochondrial respiration and activation of the phosphoinositide-3 kinase (PI3K)/Akt pathway during intervening reoxygenation periods as major triggers of the stabilization of HIF-1alpha. We also found that the NOS inhibitor nitro-l-arginine methyl ester further stimulated the cyclic hypoxia-driven HIF-1alpha accumulation and the associated gain in endothelial cell survival, thereby mirroring the effects of a PI3K/Akt inhibitor. However, combination of both drugs resulted in a net reduction in HIF-1alpha and a dramatic in decrease in endothelial cell survival. In conclusion, this study identified cyclic hypoxia, as reported in many tumor types, as a unique biological challenge for endothelial cells that promotes their survival in a HIF-1alpha-dependent manner through phenotypic alterations occurring during the reoxygenation periods. These observations also indicate the potential of combining Akt-targeting drugs with anti-angiogenic drugs, in particular those interfering with the NO pathway.
Retinobenzoic acids. 3. Structure-activity relationships of retinoidal azobenzene-4-carboxylic acids and stilbene-4-carboxylic acids (1989)

Alkyl-substituted azobenzene-4-carboxylic acids are potent differentiation inducers of human promyelocytic leukemia cell line HL-60 to mature granulocytes. Their structure-activity relationships are very similar to those of other retinoidal benzoic acids which are generally represented by 4 and named retinobenzoic acids. The structure-activity relationships of azobenzenecarboxylic acids can also be applied to the known retinoid TTNPB (3). Thus, (E)-4-[2-(3,4-diisopropylphenyl)-1-propenyl]benzoic acid (St30 (28] and (E)-4-[2-(3-tert-butylphenyl)ethenyl]benzoic acid (St40 (29], the acyclic alkyl analogues of TTNPB, are nearly as active as retinoic acid. Among the oxidatively derived compounds (Az90, Ep series and Ox series) of azobenzene- or stilbenecarboxylic acids, Az90 (71) and Ep80 (61) have strong activities. However, all the bishydroxylated derivatives of TTNPB are inactive, while a diketo analogue Ox580 (69) has only weak potency. The activities of conformationally restricted compounds of TTNPB offer some information on the stereochemistry of the active form of these retinoidal compounds.
<title>Multiparameter sensing with fiber Bragg gratings</title> (1996)

This paper describes the design of a fiber optic sensor capable of sensing temperature and three independent components of strain simultaneously in a single, short gage length device. The sensor utilizes two fiber Bragg gratings at widely spaced wavelengths (1300 nm and 1550 nm) written at a single location in polarization maintaining optical fiber. When a broad-band light source is used to illuminate the gratings, the reflected spectrum will contain four peaks corresponding to the two polarization states for each of the two gratings. If the fiber is subjected to a change in temperature or strain, the resulting change in wavelength of the reflected peaks can be used to determine the magnitude and direction of the perturbation. In theory, the four peaks can be used to simultaneously determine the grating temperature, and three independent components of strain in the fiber.
Rosiglitazone Improves Postprandial Triglyceride and Free Fatty Acid Metabolism in Type 2 Diabetes (2005)

Rosiglitazone improves the metabolism of large triglyceride-rich lipoproteins and decreases postprandial FFA concentrations in type 2 diabetes. This may have clinical implications, as these effects may contribute to cardiovascular risk reduction.
Branhamella catarrhalis Sepsis: A Case Report and Review of the Literature (1988)

COLLEAGUES -The patient discussed in our report was a 4O-y-old African immigrant, residing in the United States since 1978, who had a history positive only for a mild case of systemic lupus erythmatosis that had been inactive for several years. The patient was receiving no chronic medication. Three weeks before admission, she had been seen in the Family Practice Center (Ohio State University, Columbus, Ohio) with an acute history of mild cough; a physical examination and chest radiograph were normal, and she responded to erythromycin therapy for bronchitis.
Presynaptic nicotinic receptors: a dynamic and diverse cholinergic filter of striatal dopamine neurotransmission (2007)

The effects of nicotine on dopamine transmission from mesostriatal dopamine neurons are central to its reinforcing properties. Only recently however, has the influence of presynaptic nicotinic receptors (nAChRs) on dopaminergic axon terminals within striatum begun to be understood. Here, rather than simply enhancing (or inhibiting) dopamine release, nAChRs perform the role of a presynaptic filter, whose influence on dopamine release probability depends on presynaptic activity in dopaminergic as well as cholinergic neurons. Both mesostriatal dopaminergic neurons and striatal cholinergic interneurons play key roles in motivational and sensorimotor processing by the basal ganglia. Moreover, it appears that the striatal influence of dopamine and ACh cannot be fully appreciated without an understanding of their reciprocal interactions. We will review the powerful filtering by nAChRs of striatal dopamine release and discuss its dependence on activity in dopaminergic and cholinergic neurons. We will also review how nicotine, acting via nAChR desensitization, promotes the sensitivity of dopamine synapses to activity. This filtering action might provide a mechanism through which nicotine promotes how burst activity in dopamine neurons facilitates goal-directed behaviour and reinforcement processing. More generally, it indicates that we should not restrict our view of presynaptic nAChRs to simply enhancing neurotransmitter release. We will also summarize current understanding of the forms and functions of the diverse nAChRs purported to exist on dopaminergic axons. A greater understanding of nAChR form and function is imperative to guide the design of ligands with subtype-selective efficacy for improved therapeutic interventions in nicotine addiction as well as Parkinson's disease.
Technology and system issues for the WDM-based fiber loop architecture (1989)

A fiber-optic subscriber loop architecture employing multichannel wavelength-division multiplexing (WDM) techniques is discussed. The architecture, which is called the passive photonic loop (PPL), eliminates the need for outside-plant multiplexing and routing electronics while maintaining complete compatibility with broadband ISDN. An experimental demonstration of the PPL employing 32-channel WDM and a combination of distributed-feedback (DFB) laser and light emitting diode (LED) transmitters is described. A family of alternative PPL implementations is identified. Tradeoffs between these alternatives are explored, and related hardware issues such as wavelength alignment and WDM-component temperature sensitivity are discussed. An economic analysis comparing the PPL with the use of dedicated fiber between the central office and customer premises is presented. The analysis predicts that the PPL can achieve a cost advantage for at least 80 to 90% of the subscribers served in today's network, given DFB-laser and dense-WDM-component cost reductions of approximately one order of magnitude from today's unit-quantity prices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effect of Intensive Compared With Moderate Lipid-Lowering Therapy on Progression of Coronary Atherosclerosis (2004)

For patients with coronary heart disease, intensive lipid-lowering treatment with atorvastatin reduced progression of coronary atherosclerosis compared with pravastatin. Compared with baseline values, patients treated with atorvastatin had no change in atheroma burden, whereas patients treated with pravastatin showed progression of coronary atherosclerosis. These differences may be related to the greater reduction in atherogenic lipoproteins and C- reactive protein in patients treated with atorvastatin.
Phase I Study of Alternate-Week Administration of Tipifarnib in Patients with Myelodysplastic Syndrome (2008)

Alternate-week tipifarnib is active and well tolerated in patients with MDS at doses up to and including 600 mg orally twice daily. The biological activity of tipifarnib is not dependent on dose.
Application of human FcRn transgenic mice as a pharmacokinetic screening tool of monoclonal antibody (2014)

1. For drug discovery, useful screening tools are essential to select superior candidates. Here, we evaluated the applicability of transgenic mice expressing human neonatal Fc receptor (FcRn) (hFcRn Tgm) as a pharmacokinetic screening tool of therapeutic monoclonal antibodies (mAbs) and Fc-fusion proteins that overcomes the species difference in FcRn binding. 2. Marketed 11 mAbs and 2 Fc-fusion proteins were intravenously administered to hFcRn Tgm and WT mice. The half-lives in hFcRn Tgm and WT mice were compared with those in human obtained from literature. The linear half-lives in human and monkey were also calculated by nonlinear pharmacokinetic analysis. For comparison, correlations of half-lives between monkey and human were also evaluated. 3. The half-lives of mAbs and Fc-fusion proteins after intravenous administration ranged from 1.1 to 13.2 days in hFcRn Tgm and from 1.2 to 30.3 days in WT mice. The half-lives in human correlated more closely with those in hFcRn Tgm than in WT mice and monkey. 4. Our results suggest that hFcRn Tgm are a valuable and useful tool for pharmacokinetic screening of mAbs and Fc-fusion proteins in the preclinical stage. Furthermore, we believe that hFcRn Tgm are broadly applicable to preclinical pharmacokinetic screening of mAbs-based therapeutics.
Expanding tRNA recognition of a tRNA synthetase by a single amino acid change (2003)

Aspartyl-tRNA synthetase (AspRS) occurs in two types: the discriminating enzyme (D-AspRS) forms only Asp-tRNA(Asp), whereas the nondiscriminating enzyme (ND-AspRS) also synthesizes Asp-tRNA(Asn), which is a required intermediate for protein synthesis in many organisms. We attempted to expand the tRNA recognition of the discriminating Thermococcus kodakaraensis AspRS to that of a ND-AspRS by in vitro mutagenesis. An alignment of 26 archaeal AspRS proteins revealed two positions (26 and 85 in the T. kodakaraensis sequence) whose amino acid identity changes according to the enzymes' tRNA specificity. In their anticodon-binding domain, D-AspRS proteins contain W26 (or Q26) and K85, compared with H26 and P85 in the ND-AspRSs. T. kodakaraensis AspRS gained the ability to form Asp-tRNA(Asn) in vitro when the W26H or K85P changes were introduced independently or in combination. In the aminoacylation of tRNA(Asn) or tRNA(Asp) transcripts, the mutant enzymes displayed at least a 100- to 500-fold change in tRNA specificity, as judged by the ratio of the k(cat)K(m) values of Asp-tRNA(Asp) vs. Asp-tRNA(Asn) formation. That T. kodakaraensis mutant AspRSs mischarge tRNA(Asn) was also manifested in the higher level (1.7%) of aspartylation of unfractionated Pyrococcus tRNA compared with that achieved by the wild-type enzyme (0.9%). Northern blot analysis of the Asp-tRNA separated by acidurea gel electrophoresis confirmed the in vitro synthesis of Asp-tRNA(Asn). A structure-based model points to a direct interaction of K85 in T. kodakaraensis AspRS with the anticodon nucleotide C36 of tRNA(Asp). Thus, a switch between D-AspRS and ND-AspRS enzymes could have evolved with only limited amino acid changes.
Regulation of B Cell Functions by the Sialic Acid-Binding Receptors Siglec-G and CD22 (2012)

B cell antigen receptor (BCR) engagement can lead to many different physiologic outcomes. To achieve an appropriate response, the BCR signal is interpreted in the context of other stimuli and several additional receptors on the B cell surface participate in the modulation of the signal. Two members of the Siglec (sialic acid binding immunoglobulin like lectin) family, CD22 and Siglec-G have been shown to inhibit the BCR signal. Recent findings indicate that the ability of these two receptors to bind sialic acids might be important to induce tolerance to self-antigens. Sialylated glycans are usually absent on microbes but abundant in higher vertebrates and might therefore provide an important tolerogenic signal. Since the expression of the specific ligands for Siglec-G and CD22 is tightly regulated and since Siglecs are not only able to bind their ligands in trans but also on the same cell surface this might provide additional mechanisms to control the BCR signal. Although both Siglec-G and CD22 are expressed on B cells and are able to inhibit BCR mediated signaling, they also show unique biological functions. While CD22 is the dominant regulator of calcium signaling on conventional B2 cells and also seems to play a role on marginal zone B cells, Siglec-G exerts its function mainly on B1 cells and influences their lifespan and antibody production. Both Siglec-G and CD22 have also recently been linked to TLR (toll like receptor) signaling and may provide a link in the regulation of the adaptive and innate immune response of B cells.
3-Hydroxypropionyl-Coenzyme A Synthetase from Metallosphaera sedula , an Enzyme Involved in Autotrophic CO 2 Fixation (2007)

A modified 3-hydroxypropionate cycle has been proposed as the autotrophic CO2 fixation pathway for the thermoacidophilic crenarchaeon Metallosphaera sedula. The cycle requires the reductive conversion of 3-hydroxypropionate to propionyl-coenzyme A (propionyl-CoA). The specific activity of the 3-hydroxypropionate-, CoA-, and MgATP-dependent oxidation of NADPH in autotrophically grown cells was 0.023 micromol min(-1) mg protein(-1). The reaction sequence is catalyzed by at least two enzymes. The first enzyme, 3-hydroxypropionyl-CoA synthetase, catalyzes the following reaction: 3-hydroxypropionate + ATP + CoA --> 3-hydroxypropionyl-CoA + AMP + PP(i). The enzyme was purified 95-fold to a specific activity of 18 micromol min(-1) mg protein(-1) from autotrophically grown M. sedula cells. An internal peptide sequence was determined and a gene encoding a homologous protein identified in the genome of Sulfolobus tokodaii; similar genes were found in S. solfataricus and S. acidocaldarius. The gene was heterologously expressed in Escherichia coli, and the His-tagged protein was purified. Both the native enzyme from M. sedula and the recombinant enzyme from S. tokodaii not only activated 3-hydroxypropionate to its CoA ester but also activated propionate, acrylate, acetate, and butyrate; however, with the exception of propionate, the affinities for these substrates were reduced. 3-Hydroxypropionyl-CoA synthetase is up-regulated eightfold in autotrophically versus heterotrophically grown M. sedula, supporting its proposed role during CO2 fixation in this archaeon and possibly other members of the Sulfolobaceae family.
Polyethylene Glycol–Derivatized Cysteine-Substitution Variants of Recombinant Staphylokinase for Single-Bolus Treatment of Acute Myocardial Infarction (2000)

The staphylokinase variant SY161-P5, derivatized with one linear polyethylene glycol molecule of M:(r) 5000, is a promising fibrin-selective agent for single-bolus coronary thrombolysis.
DEEP BRAIN STIMULATION FOR THE TREATMENT OF EPILEPSY (2009)

During the last decade, deep brain stimulation (DBS) has been used to treat several neurologic disorders, including epilepsy. Promising results have been reported with stimulation in different brain regions. At present however, several issues remain unanswered. As an example, it is still unclear whether particular seizure types and syndromes should be treated with DBS in different targets or with different stimulation parameters. In addition, clinical, electrophysiological and anatomical features capable of predicting a good postoperative outcome are still unknown. We review the published literature on DBS, cortical and cerebellar stimulation for the treatment of epilepsy focusing predominantly on the rationale and clinical outcome in each target.
Connectivity : local area networks (1992)

The authority on networking and the entire enterprise market. Contains an overview of the major methods of computer intercommunication. Presents details from understanding basic wiring to selecting an operating system. Includes a glossary of connectivity terms. Covers NetWare, LAN Manager, LAN Server, UNIX, and IBM 3270. Disk included.
Transitory effects of glucose starvation on the synthesis of dolichol-linked oligosaccharides in mammalian cells. (1981)

The distribution of lipid-linked oligosaccharide intermediates in cultured mammalian cells has been studied under conditions of glucose deprivation. It was found that at low to moderate cell densities within 20 min of glucose starvation, the major species of lipid-linked oligosaccharide shifted from mainly a single species containing three glucose, nine mannose, and two N-acetylglucosamine residues to a pattern dominated by two species containing either five mannose and two N-acetylglucosamine residues or two mannose and two N-acetylglucosamine residues. At high cell densities, this effect was not evident. Continued glucose starvation at low density resulted in a second shift in distribution in which the proportions of these two species decreased and that of the original major species (Glc3Man9GlcNAc2) increased. Addition of glucose or mannose, but not pyruvate, glutamine, galactose, inositol, or glycine, prevented the shift to the Man5GlcNAc2 and Man2GlcNAc2 species. The intermediates that accumulate during glucose starvation were identified by their elution position on gel filtration columns, sensitivity to digestion with alpha-mannosidase, resistance to digestion with endo-beta-N-acetylglucosaminidase H, and by the products of Smith degradation. These data suggest that a regulatory point in the lipid-linked oligosaccharide synthetic pathway exists at the reaction in which Man5GlcNAc2-P-P-dolichol is converted to Man6GlcNAc2-P-P-dolichol.
ZPinch of a Gas Jet (1978)

A modified version of the vacuum spark experiment, in which a jet of argon is injected from the anode, is described. Experiments on a 1.26-kJ system have shown a strong pinching of the plasma with good reproducibility. The pinched plasma (\ensuremath{\sim} 20 ns lifetime) is submillimeter in size with estimated temperature of 6-9 keV and density \ensuremath{\gtrsim} ${10}^{18}$e/${\mathrm{cm}}^{3}$. Advantages of such a device for the study of high-density plasmas and scaling up are discussed. Results are compared to vacuum spark and exploding wire experiments performed on the same system.
Practical management of organic acidemias (2019)

Organic acidemias or acidurias (OAs) are a group of metabolic disorders which result in organic acids detected in the urine (or plasma). They include the systemic OAs, the cerebral OAs, and the ketogenic/ketolytic OAs. In general, all types of OA can be treated using a similar conceptual organization. The goals of therapy (acute and chronic) include reversal/prevention of catabolism, limitation of non-tolerated precursors, scavenging of toxic intermediates, replacement of the deficient product, use of cofactors when able and treatment of complications using standard methods. In the future, this framework will also include replacement of dysfunctional enzyme with a functional one. Here we review how this conceptional framework applies to the systemic OAs (propionic acidemia, methylmalonic aciduria without homocystinuria, and isovaleric acidemia), the cerebral OA (glutaric aciduria 1) and the ketogenic/ketolytic OA (HMG-CoA lyase deficiency). We review the current recommendations and use examples of how to use this conceptional framework.
Influenza A Vaccine Based on the Extracellular Domain of M2: Weak Protection Mediated via Antibody-Dependent NK Cell Activity (2004)

Vaccination of mice with a peptide corresponding to the extracellular part of M2 protein coupled to the immunodominant domain of hepatitis B core can protect mice from a lethal challenge with influenza A virus. As the extracellular part of M2 protein is highly conserved in all known human influenza A strains, such a vaccine may protect against all human influenza A strains, which would represent a major advantage over current vaccine strategies. The present study demonstrates that protection is mediated exclusively by Abs, a very important feature of a successful preventive vaccine. However, these Abs neither bind efficiently to the free virus nor neutralize virus infection, but bind to M2 protein expressed on the surface of virus-infected cells. The presence of NK cells is important for protection, whereas complement is not, supposing that protection is mediated via Ab-dependent, cell-mediated cytotoxicity. The absence of neutralizing Abs results in much weaker protection than that achieved by vaccination with UV-inactivated influenza virus. Specifically, whereas neutralizing Abs completely eliminate signs of disease even at high viral challenge doses, M2-specific Abs cannot prevent infection, but merely reduce disease at low challenge doses. M2-specific Abs fail to protect from high challenge doses, as vaccinated mice undergo lethal infection under these conditions. In conclusion, protection mediated by M2-hepatitis B core vaccine would be insufficient during the yearly epidemics, for which full protection is desirable, and overall is clearly inferior to protection achieved by immunization with classical inactivated viral preparations.