gebhart/patrepeval huggingface dataset:
Constitutive Endocytosis of CD163 Mediates Hemoglobin-Heme Uptake and Determines the Noninflammatory and Protective Transcriptional Response of Macrophages to Hemoglobin (2006)

Heme toxicity contributes to the pathogenesis of chronic inflammatory diseases, atherosclerosis, and hemolysis associated vasculopathy. Macrophage clearance of cell free hemoglobin (Hb) is thus an essential homeostatic function of these cells. We examined the transcriptional response of human PBMC derived macrophages to Hb by gene array analysis. The observed noninflammatory macrophage response was characterized by induction of an antioxidative and antiinflammatory gene expression pattern with most prominent induction of the inducible heme oxygenase (HO-1). The metabolically active Hb-CD163-HO-1 pathway resulted in synthesis of ferritin-1 of the antioxidative and antiinflammatory end products linked to heme breakdown by HO-1. This response was mediated by the Hb scavenger receptor CD163 and heme and was not related to Hb mediated depletion of reduced glutathione. In contrast to other cellular responses induced by CD163, there was no role of protein phosphorylation dependent CD163 signaling in the protective macrophage response to Hb. Instead, CD163 acted as an Hb transporter, which undergoes constitutive and ligand independent internalization and recycling between the cell surface and early endosomes. The expression of CD163 and HO-1 in macrophages of neovascularized atherosclerotic lesions suggests that the pathway described herein is active in vivo. Noninflammatory Hb clearance and intimately linked HO-1 expression may provide the long sought-after explanation for the antiinflammatory activity associated with CD163-positive macrophages.
Advanced carbon aerogels for energy applications (2011)

Carbon aerogels are a unique class of high-surface-area materials derived by sol–gel chemistry. Their high mass-specific surface area and electrical conductivity, environmental compatibility and chemical inertness make them very promising materials for many energy related applications, specifically in view of recent developments in controlling their morphology. In this perspective we will review the synthesis of monolithic resorcinol–formaldehyde based carbon aerogels with hierarchical porosities for energy applications, including carbon nanotube and graphene composite carbon aerogels, as well as their functionalization by surface engineering. Applications that we will discuss include hydrogen and electrical energy storage, desalination and catalysis.
Estimation of respiratory waveform using an accelerometer (2008)

The cardiorespiratory signal is a fundamental vital sign to assess a person's health. Additionally, the cardio-respiratory signal gives a great deal of information to healthcare providers wishing to monitor healthy individuals. This paper proposes a method to detect the respiratory waveform from an accelerometer strapped onto the chest. A system was designed and several experiments were conducted on volunteers. The acquisition is performed in different status: normal, apnea, deep breathing and also in different postures: vertical (sitting, standing) or horizontal (lying down). This method could therefore be suitable for automatic identification of some respiratory malfunction, for example during the obstructive apnea.
Vitamin E in the treatment of tardive dyskinesia (1990)

Eight subjects with persistent tardive dyskinesia were treated with vitamin E and placebo in a randomized, double-blind crossover study. Their mean score on the Abnormal Involuntary Movement Scale (AIMS) was significantly lower after treatment with vitamin E than after placebo administration.
Left Ventricular Dysfunction After Treatment With Ipilimumab for Metastatic Melanoma (2016)

Ipilimumab is a monoclonal antibody targeting cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) that is approved by the US Food and Drug Administration for the treatment of unresectable or metastatic melanoma. Ipilimumab is known to cause immune-mediated adverse reactions because of the resultant increase in T-cell activity. To date, there are no published reports of ipilimumab-related heart failure, although a recently published report describes a case of transient cardiomyopathy associated with its use. We report the case of a 60-year-old man who developed left ventricular dysfunction with an asymptomatic reduction in ejection fraction from 55%-60% at baseline to 40%-45% 4 months after completing a second course of treatment with ipilimumab for metastatic melanoma. Ipilimumab was not restarted, and the patient was initiated on lisinopril and carvedilol. Repeat echocardiograms 3 and 5 months later revealed ejection fractions of 40%-45% and 55%-60%, respectively.
High reliability 1.3 μm InP based uncooled lasers in non-hermetic packages (2002)

There is an increasing demand for low cost optoelectronics for fiber-in-the-loop (FITL) and cable TV (CATV) system. The availability of a reliable, nonhermetic InP based uncooled laser and associated monitor diode could provide a significant cost reduction. In non-hermetic environment, degradation of laser performance usually occurs due to lack of proper passivation of the laser facet. Moisture and contaminants can diffuse through the laser facet passivation film, which in the presence of light, heat and bias energy sources react and corrode the facets.
Responsive nanogel-based dual fluorescent sensors for temperature and Hg2+ ions with enhanced detection sensitivity (2010)

We report on the fabrication of thermoresponsive poly(N-isopropylacrylamide) nanogel-based dual fluorescent sensors for temperature and Hg2+ ions, and the effects of thermo-induced nanogel collapse on the detection sensitivity of Hg2+ ions. Near-monodisperse thermoresponsive nanogels were prepared via emulsion polymerization of N-isopropylacrylamide (NIPAM) and a novel 1,8-naphthalimide-based polarity-sensitive and Hg2+-reactive fluorescent monomer (NPTUA, 3). At room temperature, PNIPAM nanogels labeled with a single type of naphthalimide-based dye (NPTUA) can act as ratiometric Hg2+ probes at the nanomolar level. Upon heating above the phase transition temperature, the fluorescence intensity of NPTUA-labeled nanogels in the absence of Hg2+ exhibit ∼3.4-fold increase due to that NPTUA moieties are now located in a more hydrophobic microenvironment. Moreover, it was observed that the detection sensitivity to Hg2+ can be further improved above the nanogel phase transition temperature. At a nanogel concentration of 0.05 g L−1 and in the same Hg2+ concentration range (0–3.0 equiv.), ∼10 fold and ∼57 fold increase in fluorescence emission intensity ratio changes can be achieved at 25 and 40 °C, respectively.
The epidemiological relationship between salmonella isolated from poultry meat and sewage effluents at a long-stay hospital (1991)

Between February 1988 and March 1989 chicken carcases delivered to the kitchen of a long stay psycho-geriatric hospital were screened every week for salmonella contamination. While 214 of 477 (45%) individual carcases carried one or more salmonella types, every single consignment examined contained affected carcases. Simultaneously, sewers draining the residential accommodation and excluding kitchen effluent, were also monitored. Thirty out of 79 (38%) of Moore's swabs were positive for salmonella. There was a statistically significant association between the salmonella types isolated from chicken and those isolated from sewers the following week. Following a change in kitchen policy to order only cooked chicken there was a significant reduction in the isolation of salmonella from the sewers.
Myelin basic protein-specific T lymphocyte repertoire in multiple sclerosis. Complexity of the response and dominance of nested epitopes due to recruitment of multiple T cell clones. (1993)

The human T cell response to the myelin basic protein (MBP) has been studied with respect to T cell receptor (TCR) usage, HLA class II restriction elements, and epitope specificity using a total of 215 long-term MBP-specific T cell lines (TCL) isolated from the peripheral blood of 13 patients with multiple sclerosis (MS) and 10 healthy donors. In most donors, the anti-MBP response was exceedingly heterogeneous. Using a panel of overlapping synthetic peptides spanning the entire length of human MBP, at least 26 epitopes recognized by human TCL could be distinguished. The MBP domain most commonly recognized was sequence 80-105 (31% of MS TCL, and 24% of control TCL). Sequence 29-48 was recognized more frequently by control-derived TCL (24%) than by TCL from MS patients (5%). The MBP epitopes were recognized in the context of DRB1 *0101, DRB5*0101, DRB1*1501, DRB1*0301, DRB1*0401, DRB1*1402, and DRB3*0102, as demonstrated using a panel of DR gene-transfected L cells. The TCR gene usage was also heterogeneous. V beta 5.2, a peptide of which is currently being used in a clinical trial for treatment of MS patients, was expressed by only one of our TCL. However, within this complex pattern of MBP-specific T cell responses, a minority of MS patients were found to exhibit a more restricted response with respect to their TCL epitope specificity. In these patients 75-87% of the TCL responded to a single, patient-specific cluster of immunodominant T cell epitopes located within a small (20-amino acid) domain of MBP. These nested clusters of immunodominant epitopes were noted within the amino acids 80-105, 108-131, and 131-153. The T cell response to the immunodominant epitopes was not monoclonal, but heterogeneous, with respect to fine specificity, TCR usage, and even HLA restriction. In one patient (H.K.), this restricted epitope profile remained stable for > 2 yr. The TCR beta chain sequences of TCL specific for the immunodominant region of HK are consistent with an oligoclonal response against the epitopes of this region (80-105). Further, two pairs of identical sequences were established from TCL generated from this patient at different times (June 1990 and June 1991), suggesting that some TCL specific for the immunodominant region persisted in the peripheral repertoire. The possible role of persistent immunodominant epitope clusters in the pathogenesis of MS remains to be established.
Maximal Margin Labeling for Multi-Topic Text Categorization (2004)

In this paper, we address the problem of statistical learning for multitopic text categorization (MTC), whose goal is to choose all relevant topics (a label) from a given set of topics. The proposed algorithm, Maximal Margin Labeling (MML), treats all possible labels as independent classes and learns a multi-class classifier on the induced multi-class categorization problem. To cope with the data sparseness caused by the huge number of possible labels, MML combines some prior knowledge about label prototypes and a maximal margin criterion in a novel way. Experiments with multi-topic Web pages show that MML outperforms existing learning algorithms including Support Vector Machines. 1 Multi-topic Text Categorization (MTC) This paper addresses the problem of learning for multi-topic text categorization (MTC), whose goal is to select all topics relevant to a text from a given set of topics. In MTC, multiple topics may be relevant to a single text. We thus call a set of topics label, and say
Recent Developments in Potential Anxiolytic Agents Targeting GABAA/BzR Complex or the Translocator Protein (18kDa) (TSPO) (2012)

Anxiety disorders are frequent and disabling disorders. For short-term treatment, benzodiazepines are useful due to their rapid onset of anxiolytic action. However, these compounds have sedative properties and may induce tolerance, abuse liability and withdrawal symptoms. First-line choices for the long-term treatment are selective serotonin reuptake inhibitors or serotonin-norepinephrine reuptake inhibitors. The major disadvantage of these compounds is their delayed onset of action. It is obvious that there is a need for novel pharmacological approaches that combine a rapid anxiolytic efficacy with the lack of tolerance induction, abuse liability and withdrawal symptoms. A very important target for the development of such compounds is the -amino-butyric-acid (GABA)A receptor. Subtype specific benzodiazepines are being developed, but also phytotherapeutic agents experience a renaissance as GABAA receptor modulators. On the other hand, GABA related compounds, e.g. tiagabine, did not show pronounced anxiolytic efficacy. Neuroactive steroids such as allopregnanolone and tetrahydrodeoxycorticosterone (THDOC) are potent modulators of GABAA receptors. To date synthetic neuroactive steroids could not be established in the treatment of anxiety disorders. Regarding endogenous neurosteroidogenesis, recently the translocator protein (18kDa) (TSPO) has been identified as a potential novel target. TSPO is supposed to play an important role for the synthesis of neuroactive steroids. TSPO ligands may promote the synthesis of neuroactive steroids via induction of cholesterol translocation to the inner mitochondrial membrane. First clinical studies revealed promising results. In this review, we discuss putative compounds affecting the GABAergic system which may provide the basis for fast acting anxiolytics with a favorable side effect profile.
Batteries based on fluoride shuttle (2011)

In search of new concepts to build batteries with high energy densities, electrochemical cells based on metal fluorides may be promising. Herein, we report the demonstration of secondary battery cells based on fluoride shuttle. In fluoride ion batteries, fluoride anion acts as charge transfer ion between a metal/metal fluoride pair where it will react with metal or evolve from metal fluoride depending on the flow of current.
RHAMM (CD168) Is Overexpressed at the Protein Level and May Constitute an Immunogenic Antigen in Advanced Prostate Cancer Disease (2009)

Localized prostate cancer (CaP) can be cured using several strategies. However, the need to identify active substances in advanced tumor stages is tremendous, as the outcome in such cases is still disappointing. One approach is to deliver human tumor antigen-targeted therapy, which is recognized by T cells or antibodies. We used data mining of the Cancer Immunome Database (CID), which comprises potential immunologic targets identified by serological screening of expression libraries. Candidate antigens were screened by DNA microarrays. Genes were then validated at the protein level by tissue microarrays, representing various stages of CaP disease. Of 43 targets identified by CID, 10 showed an overexpression on the complementary DNA array in CaP metastases. The RHAMM (CD168) gene, earlier identified by our group as an immunogenic antigen in acute and chronic leukemia, also showed highly significant overexpression in CaP metastases compared with localized disease and benign prostatic hyperplasia. At the protein level, RHAMM was highest in metastatic tissue samples and significantly higher in neoplastic localized disease compared with benign tissue. High RHAMM expression was associated with clinical parameters known to be linked to better clinical outcome. Patients with high RHAMM expression in the primaries had a significantly lower risk of biochemical failure. The number of viable cells in cell cultures was reduced in blocking experiments using hormone-sensitive and hormone-insensitive metastatic CaP cell lines. Acknowledging the proven immunogenic effects of RHAMM in leukemia, this antigen is intriguing as a therapeutic target in far-advanced CaP.
The low density lipoprotein receptor in Xenopus laevis. I. Five domains that resemble the human receptor (1991)

All five functional domains of the low density lipoprotein (LDL) receptor were assembled in their modern form more than 350 million years ago, as revealed from the sequence of two cloned cDNAs from the frog Xenopus laevis. The two cDNAs appear to represent duplicated copies of the LDL receptor gene that arose when the entire genome of Xenopus duplicated approximately 30 million years ago. Both frog LDL receptors bound Xenopus LDL with high affinity and human LDL with lower affinity when expressed in monkey COS cells. The receptors also showed high affinity for rabbit beta-migrating very low density lipoprotein and canine apoE-HDLc, both of which contain apolipoprotein E. Each of the seven cysteine-rich repeats in the ligand binding domain of the Xenopus receptors resembles its counterpart in the human, indicating that these repeats had already acquired their independent structures by the time of amphibian development. The cytoplasmic tail of both Xenopus receptors is 86% identical to the human, including the FDNPVY sequence necessary for internalization in coated pits. The attainment of a fully developed receptor structure in Xenopus suggests that earlier forms of the receptor may exist in animals that are older than amphibians. An accompanying paper demonstrates that expression of both Xenopus receptor genes is controlled by a sterol regulatory element that closely resembles the human sequence (Mehta, K.D., Brown, M.S., Bilheimer, D.W., and Goldstein, J.L. (1991) J. Biol. Chem. 266, 10415-10419).
X‐ray structure of the PHF core C‐terminus: Insight into the folding of the intrinsically disordered protein tau in Alzheimer's disease (2007)

The major constituent of Alzheimer's disease paired helical filaments (PHF) core is intrinsically disordered protein (IDP) tau. In spite of a considerable effort, insoluble character of PHF together with inherent physical properties of IDP tau have precluded so far reconstruction of PHF 3D structure by X-ray crystallography or NMR spectroscopy. Here we present first crystallographic study of PHF core C-terminus. Using monoclonal antibody MN423 specific to the tertiary structure of the PHF core, the in vivo PHF structure was imprinted into recombinant core PHF tau. Crystallization of the complex led to determination of the structure of the core PHF tau protein fragment 386TDHGAE391 at 1.65A resolution. Structural analysis suggests important role of the core PHF C-terminus for PHF assembly. It is reasonable to expect that this approach will help to reveal the structural principles underlying the tau protein assembly into PHF and possibly will facilitate rationale drug design for inhibition of Alzheimer neurofibrillary changes.
Selecting Effective siRNA Target Sequences for Mammalian Genes (2005)

Short interfering RNA (siRNA) has been widely used for studying gene functions in mammalian cells but varies markedly in its gene-silencing efficacy in mammalian genes. The recently reported guidelines for selecting effective siRNA target sequences are not always useful for selecting highly effective siRNA sequences for many other mammalian genes because there are only a few consistencies among them. Hypothesizing that the positional nucleotide occurrence trends play an important role in effective gene-silencing, we examined 361 effective siRNA sequences from 227 different mammalian cDNAs in the literature and found got several nucleotide features different from the ones used in the previous guidelines. Here we first explain the problems concerning the previous guidelines from the qualitative and quantitative points of view. Then after clarifying the requirements for effective siRNA designs, we describe a new method based on a gene degradation measure defined by positional features of specific significant nucleotides. Testing the method on human cyclin B1 confirmed that it selected highly effective gene-silencing sequences and also indicated that it would be useful for other genes. It will therefore be useful for selecting new siRNA target sequences for mammalian genes.
The hepatitis C virus (HCV) induces a long-term increase in interleukin-10 production by human CD4+ T cells (H9). (2001)

Patients with chronic hepatitis C present an imbalance of Th1/Th2 cytokine production. Therefore, we investigated whether the exposure of the CD4+ T cell line H9 to HCV could induce activation of cells through synthesis of IL-10. Three infection protocols were performed to enhance HCV propagation. Viral particles were prepared by ultracentrifugation of serum from patients. From 3 to 81 days post-infection (p.i.), HCV-RNA was monitored both in supernatants and cells by nested RT-PCR, IL-10 protein in medium by ELISA, and IL-10 mRNA in cells by semi-quantitative RT-PCR. The expression of tetraspanins was analyzed by flow cytometry. The PKC signal pathway was studied using specific inhibitors. The H9 cells express CD81. HCV-RNA (+) was detected in cells until 21 days p.i, and in culture media over 39 days p.i. Up to day 81 p.i., HCV exposure induced a specific, 2-fold increase of IL-10 production by H9 cells. IL-10 production was inhibited by a PKC inhibitor (Calphostin C). This study shows that even if the infection of H9 T cells did not result in any viral progeny, HCV induced the activation of IL-10 secretion, which supports the role of IL-10 in HCV pathogenesis.
A Reversible Gel for Chiral Separations (2004)

The use of a guanosine gel as a chiral selector in capillary electrophoresis is introduced. Guanosine gels are reversible organized media that are formed through the self-association of guanosine compounds. Their degree of organization and their physicochemical properties can be modulated through variations in guanosine monomer concentration, pH, temperature, and cation content. Baseline resolution of the d and l enantiomers of propranolol was achieved using a reversible biogel formed by 5'-guanosine monophosphate as the run buffer in capillary electrophoresis. Conditions were optimized to provide enantiomeric resolution of 2.1-2.3 in less than 5 min. The reversibility of the gel network offers potential advantages for chiral separations, including the possibility of using thermal or chemical dissociation of the gel network to remove the nucleoside monomers from the separated enantiomers, thereby eliminating the chiral selector as a source of physical contamination of the enantiomerically pure products and spectral background in UV absorbance detection.
Methods for Skin Absorption (2024)

Choice of Membranes for In Vitro Skin Uptake Studies and General Experimental Techniques. Penetrant Characteristics Influencing Skin Absorption. Instrumentation and Methodology for In Vitro Skin Diffusion Cells. Preparation of Biological Membranes. Methodology for the Execution of In Vitro Skin Penetration Determinations. In-Vivo Methods for Determining Percutaneous Absorption and Metabolism of Xenobiotics: Indirect Methods. Physical Resources Needed for In Vivo Animal Studies. Detection Methods. Data Interpretation and Analysis in Percutaneous Absorption Studies. Specialized Techniques: Congenitally Athymic (Nude) Animal Models. Specialized Technique: The Isolated Perfused Porcine Skin Flap (IPPSF). Validity of Skin Absorption and Metabolism Studies.
Portal to the interior: viral pathogenesis and natural compounds that restore mucosal immunity and modulate inflammation. (2003)

Most antigens, particularly viruses, enter the body through the mucosal epithelia where they are carried by afferent lymphatics to regional lymph nodes for presentation to the immune system. Although they share immunological similarities, immune processes that protect the mucosa are distinct from innate and acquired immunity. The barrier formed by the intestinal mucosa is the most studied, with its microenvironment having a marked influence on both local and systemic immune responses. A healthy microenvironment and resilient neighboring tissue provide protection against inflammation known to dampen mucosal immunity, promote carcinogenesis, contribute to systemic inflammatory processes, and result in autoimmune diseases. Numerous natural substances improve this microenvironment and thereby enhance immunity against microbial infections. Since mucosal immunity forms the first line of defense against many commonly transmitted pathogens, restoring and maintaining mucosal immunity is critical for disease prevention and intervention. This article discusses the nature of mucosal immunity and its relationship to viral infections and other conditions, and reviews natural compounds that help restore mucosal immunity.