gebhart/patrepeval huggingface dataset:
Proximate and Polyphenolic Characterization of Cranberry Pomace (2009)

The proximate composition and identification and quantification of polyphenolic compounds in dried cranberry pomace were determined. Proximate analysis was conducted based on AOAC methods for moisture, protein, fat, dietary fiber, and ash. Other carbohydrates were determined by the difference method. Polyphenolic compounds were identified and quantified by HPLC-ESI-MS. The composition of dried cranberry pomace was 4.5% moisture, 2.2% protein, 12.0% fat, 65.5% insoluble fiber, 5.7% soluble fiber, 8.4% other carbohydrates, 1.1% ash, and 0.6% total polyphenolics. It contained six anthocyanins (111.5 mg/100 g of DW) including derivatives of cyanidin and peonidin. Thirteen flavonols were identified (358.4 mg/100 g of DW), and the aglycones myricetin (55.6 mg/100 g of DW) and quercetin (146.2 mg/100 g of DW) were the most prominent. Procyanidins with degrees of polymerization (DP) of 1-6 were identified (167.3 mg/100 g of DW), the most abundant being an A-type of DP2 (82.6 mg/100 g of DW).
Alzheimer’s disease: the lipid connection (2007)

Alzheimer's disease is the most common neurodegenerative disorder. This short review summarizes the current knowledge about the role of lipids, especially cholesterol, sphingolipids, plasmalogens, and polyunsaturated fatty acids in Alzheimer's disease etiology, pathogenesis, risk-factors, prevention, treatment, and the function of the amyloid precursor protein and the amyloid peptides in lipid homeostasis.
<title>Accurate dimensional metrology with atomic force microscopy</title> (2000)

Atomic force microscopes (AFMs) generate three dimensional images with nanometer level resolution and, consequently, are used in the semiconductor industry as tools for sub-micrometer dimensional metrology. Measurements commonly performed with AFMs are feature spacing (pitch), feature height (or depth), feature width (critical dimension), and surface roughness. To perform accurate measurements, the scales of an AFM must be calibrated. We have designed and developed the calibrated AFM (C-AFM) to calibrate physical standards for other AFMs. The C- AFM has displacement metrology for all three axes traceable to the 633 nm wavelength of the Iodine-stabilized He-Ne laser. This is accomplished through the integration of a flexure x-y translation stage, heterodyne laser interferometers, and a z- axis piezoelectric actuator with an integrated capacitance sensor. This capacitance sensor is calibrated with a third interferometer. We have performed both pitch and height measurements for external customers. Recently, we performed pitch measurements on holographic gratings as part of an ongoing international comparison driven by BIPM (Bureau International des Poids et Measures). We have also completed a preliminary design of a prototype pitch/height standard and are evaluating preliminary test samples. Additionally, we are working toward the development of linewidth standards through the comparison of C-AFM width measurements with values obtained from other methods. Our step height and linewidth measurements are in good agreement with those obtained by other methods, and we are working to improve the lateral resolution and hence the uncertainty of our probe-based linewidth measurements by studying the use of nanotubes and other types of sharp tips as linewidth probes.
Substrate–water exchange in photosystem II is arrested before dioxygen formation (2014)

Light-driven oxidation of water into dioxygen, catalysed by the oxygen-evolving complex (OEC) in photosystem II, is essential for life on Earth and provides the blueprint for devices for producing fuel from sunlight. Although the structure of the OEC is known at atomic level for its dark-stable state, the mechanism by which water is oxidized remains unsettled. Important mechanistic information was gained in the past two decades by mass spectrometric studies of the H2(18)O/H2(16)O substrate-water exchange in the four (semi) stable redox states of the OEC. However, until now such data were not attainable in the transient states formed immediately before the O-O bond formation. Using modified photosystem II complexes displaying up to 40-fold slower O2 production rates, we show here that in the transient S3YZ state the substrate-water exchange is dramatically slowed as compared with the earlier S states. This further constrains the possible sites for substrate-water binding in photosystem II.
Increased clearance of IgG in mice that lack β2‐microglobulin: possible protective role of FcRn (1996)

The mechanisms that regulate immunoglobulin G (IgG) catabolism are little understood. We have previously found unusually low IgG concentrations in sera of mice homozygous for a targeted disruption of the beta 2-microglobulin gene. We therefore investigated whether this might result, at least in part, from increased clearance of IgG from the systemic circulation in mice lacking beta 2-microglobulin. We compared the half-lives of radiolabelled mouse IgG1 injected intravenously into beta 2-microglobulin-/- mice and wild-type or heterozygous siblings. The clearance of 125I-labelled IgG1 was strikingly more rapid in the mice lacking beta 2-microglobulin. beta 2-microglobulin-/- mice lack functional molecules of the MHC class I-related Fc receptor, FcRn. Some mutations in mouse IgG1 that increase its clearance have recently been shown to prevent binding to FcRn in the gut. To determine whether the slower degradation of immunoglobulin in mice with beta 2-microglobulin correlated with the ability of the antibody to bind FcRn, we measured the clearance of chicken IgY, which does not bind this receptor. The 125I-labelled IgY was catabolized equally rapidly in beta 2-microglobulin-deficient and wild-type mice. We compared the half-lives of the four subclasses of mouse IgG in beta 2-microglobulin-/-, +/-, and +/+ mice to determine whether the difference we had noted for IgG1 was peculiar to this subclass. The 125I-labelled IgG of all subclasses, with the possible exception of IgG2b. was degraded more rapidly in the beta 2-microglobulin-deficient mice than in heterozygous or wild-type siblings. These data suggest that FcRn can protect IgG from degradation, and is therefore important in maintaining IgG levels in the circulation.
Simultaneous metabolic labeling of cells with multiple amino acids: Localization and dynamics of histone acetylation and methylation (2007)

Simultaneous metabolic labeling of cells with multiple amino acids combined with acetic acid urea-PAGE and MS was used to characterize histones in Kasumi-1 cells treated with the histone deacetylase inhibitor depsipeptide (DDP). The approach allowed for rapid targeting, identification, and subsequent characterization of peptides containing sites of acetylation or methylation. Multiple methylation sites were determined for histone H3 including: di- and tri-methylation of K9 and K27; mono- and di-methylation of K36 and K79; and mono-methylation of K37. The acetylation patterns for histones H4 and H3 were established. Quantitative analysis of the modification change after treatment with DDP was also performed and the dynamics of H4 acetylation determined. Functional analysis by RT-PCR showed that DDP unregulated p21 expression with a maximum after 18-h exposure. Chromatin immunoprecipitation experiments indicated that DDP treatment caused an accumulation of hyperacetylated histone H4 and H3 isoforms and a decrease in K9 di-methylation of H3 on the p21 promoter.
Towards an intelligent and personalized retrieval system (1986)

Development of an information retrieval system that can be personalized to each user requires maintaining and continually updating an interest profile for each individual user. Since people tend to be poor at self-description, it is suggested that profile development and maintenance is an area in which machine learning and knowledge based techniques can be profitably employed. This paper presents a model for such an application of AI techniques.
Tumor-Specific Gene Delivery Using Genetically Engineered Bacteria (2003)

The loco-regional control of cancer remains a major contributor to the treatment outcome for many cancer patients prescribed conventional radiotherapy or chemotherapy. Failure of treatment coupled with the realisation that cancer is essentially a genetic disease has led to development of many clinical protocols based on gene therapy. In this review, we will describe an alternative gene delivery system based on the use of non-pathogenic bacteria. Tumor regressions have been reported long ago in patients with bacterially infected tumors, suggesting that bacteria could target tumors and have local anti-tumor effects. The basis of this phenomenon is attributable to the unique properties of the tumor micro-environment. The presence of hypoxic and/or necrotic areas provides a haven for a number of anaerobic bacteria and over the past 60 years, several strains of anaerobic bacteria have been shown to localise within and cause cell lysis of experimental animal tumors. One of the most important strains in that context is Clostridium. Other bacteria have also been implicated in experimental anti-cancer settings. Of these, attenuated Salmonella strains capable of both selective amplification within tumors and expression of effector genes encoding therapeutic proteins are probably the most promising. We will discuss the potential advantages and the pitfalls of this alternative delivery approach. We will emphasize the importance of hypoxia in solid tumors and discuss the potential of radiation-inducible promoters and combined treatment modalities, involving vascular targeting and radiotherapy. We believe that this approach will act in a complementary way to current radiotherapy and chemotherapy treatments of solid tumors.
Analysis of differential gene expression in human colorectal tumor tissues by RNA arbitrarily primed-PCR: a technical assessment. (1998)

RNA arbitrarily primed (RAP)-PCR is a powerful tool for studying differential gene expression in cancer cells. Systematic analysis of human tumor samples may provide a list of markers with potential application to the diagnosis, prognostic assessment, and treatment of the disease. Nevertheless, because of characteristics inherent to the samples and technique, artifactual results are likely. We have assessed the effects of several factors on RAP-PCR performance to determine the sensitivity and reproducibility of the technique, as well as the accuracy of its results, under different conditions in human cell lines and in a series of 129 paired human normal colonic mucosa-colorectal carcinoma samples. Our results show that RAP-PCR provides reliable fingerprints in a relatively wide spectrum of circumstances, including variations in RNA concentration and contamination by DNA. Densitometric analysis indicated that relative band-intensity variations more than 20% were reproducible in 95% of the cases. Serial analysis of paired normal-tumor cases yielded a number of bands that were recurrently either underexpressed or overexpressed in tumor relative to normal mucosa. These differentially expressed bands are prime targets of research because they represent candidate tumor-specific up- or down-regulated genes with a relevant role in carcinogenesis.
Adenovirus as an expression vector in muscle cells in vivo. (1992)

Attempting gene transfer in muscle raises difficult problems: the nuclei of mature muscle fibers do not undergo division, thus excluding strategies involving replicative integration of exogenous DNA. As adenovirus has been reported to be an efficient vector for the transfer of an enzyme encoding gene in mice, we decided to explore its potential for muscle cells. Advantages of adenovirus vectors are their independence of host cell replication, broad host range, and potential capacity for large foreign DNA inserts. We constructed a recombinant adenovirus containing the beta-galactosidase reporter gene under the control of muscle-specific regulatory sequences. This recombinant virus was able to direct expression of the beta-galactosidase in myotubes in vitro. We report its in vivo expression in mouse muscles up to 75 days after infection. The efficiency and stability of expression we obtained compare very favorably with other strategies proposed for gene or myoblast transfer in muscle in vivo.
The HEAO A-1 X-ray source catalog (1984)

The catalog of X-ray sources detected during the NRL Large Area Sky Survey (LASS) with the HEAO 1 satellite is presented. The catalog is derived from the first six months of data from HEAO 1 and includes sources detected during one full scan. Positions and intensities for a total of 842 different sources are included, with a limiting flux of 250 nJy at 5 keV. The catalog is more than 90 percent complete at a flux level equivalent to 1.5 microjoules at 5 keV for a Crab-like spectrum. Cross-references with published literature are provided and coincidental identifications are proposed for some of the sources which have been never studied before. A cross-sectional line drawing of the sensor module of HEAO I is also provided.
Nicotinic Acetylcholine Receptors and Nicotinic Cholinergic Mechanisms of the Central Nervous System (2006)

Subtypes of neuronal nicotinic acetylcholine receptors (nAChRs) are constructed from numerous subunit combinations that compose channel-receptor complexes with varied functional and pharmacological characteristics. Structural and functional diversity and the broad presynaptic, postsynaptic, and nonsynaptic locations of nAChRs underlie their mainly modulatory roles throughout the mammalian brain. Presynaptic and preterminal nicotinic receptors enhance neurotransmitter release, postsynaptic nAChRs contribute a small minority of fast excitatory transmission, and nonsynaptic nAChRs modulate many neurotransmitter systems by influencing neuronal excitability. Nicotinic receptors have roles in development and synaptic plasticity, and nicotinic mechanisms participate in learning, memory, and attention. Decline, disruption, or alterations of nicotinic cholinergic mechanisms contribute to dysfunctions such as epilepsy, schizophrenia, Parkinson's disease, autism, dementia with Lewy bodies, Alzheimer's disease, and addiction.
Tolerance to Self Gangliosides Is the Major Factor Restricting the Antibody Response to Lipopolysaccharide Core Oligosaccharides inCampylobacter jejuniStrains Associated with Guillain-Barre Syndrome (2002)

Guillain-Barré syndrome following Campylobacter jejuni infection is frequently associated with anti-ganglioside autoantibodies mediated by molecular mimicry with ganglioside-like oligosaccharides on bacterial lipopolysaccharide (LPS). The regulation of antibody responses to these T-cell-independent antigens is poorly understood, and only a minority of Campylobacter-infected individuals develop anti-ganglioside antibodies. This study investigates the response to gangliosides and LPS in strains of mice by using a range of immunization strategies. In normal mice following intraperitoneal immunization, antibody responses to gangliosides and LPS are low level but can be enhanced by the antigen format or coadministration of protein to recruit T-cell help. Class switching from the predominant immunoglobulin M (IgM) response to IgG3 occurs at low levels, suggesting B1-cell involvement. Systemic immunization results in poor responses. In GalNAc transferase knockout mice that lack all complex gangliosides and instead express high levels of GM3 and GD3, generation of anti-ganglioside antibodies upon immunization with either complex gangliosides or ganglioside-mimicking LPS is greatly enhanced and exhibits class switching to T-cell-dependent IgG isotypes and immunological memory, indicating that tolerance to self gangliosides is a major regulatory factor. Responses to GD3 are suppressed in knockout mice compared with wild-type mice, in which responses to GD3 are induced specifically by GD3 and as a result of polyclonal B-cell activation by LPS. The anti-ganglioside response generated in response to LPS is also dependent on the epitope density of the ganglioside mimicked and can be further manipulated by providing secondary signals via lipid A and CD40 ligation.
Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein (2002)

Enhancer of Zeste [E(z)] is a Polycomb-group transcriptional repressor and one of the founding members of the family of SET domain-containing proteins. Several SET-domain proteins possess intrinsic histone methyltransferase (HMT) activity. However, recombinant E(z) protein was found to be inactive in a HMT assay. Here we report the isolation of a multiprotein E(z) complex that contains extra sex combs, suppressor of zeste-12 [Su(z)12], and the histone binding proteins RbAp46/RbAp48. This complex, which we termed Polycomb repressive complex (PRC) 2, possesses HMT activity with specificity for Lys 9 (K9) and Lys 27 (K27) of histone H3. The HMT activity of PRC2 is dependent on an intact SET domain in the E(z) protein. We hypothesize that transcriptional repression by the E(z) protein involves methylation-dependent recruitment of PRC1. The presence of Su(z)12, a strong suppressor of position effect variegation, in PRC2 suggests that PRC2 may play a widespread role in heterochromatin-mediated silencing.
Left atrial appendage thrombus outside of a “successful” ligation (2007)

A 79-year-old woman with severe aortic stenosis underwent aortic valve replacement surgery, and had ligation of the left atrial appendage (LAA) using an epicardial approach. On a post-operative echocardiographic evaluation, the distal portion of the LAA was excluded, leaving no communication with the left atrium. The proximal portion of the LAA, however, was in continuity with the circulation and a large thrombus was present within it. While previous reports of incomplete LAA ligation have involved disruption of the suture line, this present report describes a case of incomplete ligation due to persistence of the proximal portion of the appendage. Thus, thrombus formation occurred despite a 'successful' epicardial exclusion of the distal LAA.
Chimeric immune receptors (CIRs) specific to JC virus for immunotherapy in progressive multifocal leukoencephalopathy (PML) (2007)

Progressive multifocal leukoencephalopathy (PML) is a deadly brain disease caused by the polyomavirus JC (JCV). The aim of this study is to develop 'designer T cells' armed with anti-JCV TCR-based chimeric immune receptors (CIRs) by gene modification for PML immunotherapy. Two T cell lines specific to two dominant CTL epitopes derived from JCV VP1 protein (termed p36 and p100) from an HLA-A0201+ PML survivor were generated for TCR cloning. Two distinct dominant TCR alpha chains (Valpha6 and Valpha12) and a unique TCR beta chain (Vbeta5.1) were cloned from the p36-specific cell line, while only one alpha (Valpha8.6) and one beta (Vbeta2) chains were dominant in the p100-specific line. Retroviral constructs encoding CIRs were created with the extracellular domains of TCR alpha and beta chains fused to the transmembrane and cytoplasmic portions of CD3zeta (ValphaCalphaCD3zeta or VbetaCbetaCD3zeta). Cellular expression and screening for binding specific peptide-HLA-A0201 tetramer confirmed the reactivity of the p100 TCRalphabeta and of one of the two pairs of p36 TCRalphabeta (Valpha12 and Vbeta5.1). Functional tests confirmed CIR-expressing T cells secreted cytokines and expressed potent cytotoxicity on contact with A0201+ B-lymphoblastoid line loaded with peptides and/or with HLA-A0201+ cells expressing native JCV VP1 protein. In conclusion, anti-JCV designer T cells were generated.
Interaction of prostate specific membrane antigen with clathrin and the adaptor protein complex-2 (2007)

Prostate-specific membrane antigen (PSMA) is an integral membrane glycoprotein expressed in prostatic epithelia and is being evaluated as a therapeutic target in prostate cancer. It undergoes constitutive receptor-mediated endocytosis via clathrin-coated pits, which is enhanced in the presence of monoclonal antibodies directed against it. We describe distinct interactions of PSMA with clathrin and the clathrin adaptor protein-2 (AP-2) complex, two components of clathrin-coated pits. The intracellular N-terminal domain of PSMA interacts with the N-terminal globular domain of clathrin heavy chain. Deletion analysis revealed an important determinant of this interaction residing within the proximal portion of the clathrin heavy chain N-terminal domain (amino acids 1-85) distinct from the clathrin binding sites of other known clathrin-binding proteins. Furthermore, PSMA interacts with the ear domain of alpha-adaptin (an AP-2 subunit), and a glutamic acid residue at position 7 in the cytoplasmic tail of PSMA is essential for this interaction. These data indicate that PSMA exhibits a high affinity, specific association with the clathrin-based endocytic machinery by distinct interactions with both clathrin and AP-2. Thus, although PSMA is a new member of the dual AP and clathrin binding proteins, its alpha-adaptin and clathrin heavy chain binding determinants are distinct from those of other members.
Identification of Putative Agouti-Related Protein(87−132)-Melanocortin-4 Receptor Interactions by Homology Molecular Modeling and Validation Using Chimeric Peptide Ligands (2004)

Agouti-related protein (AGRP) is one of only two naturally known antagonists of G-protein-coupled receptors (GPCRs) identified to date. Specifically, AGRP antagonizes the brain melanocortin-3 and -4 receptors involved in energy homeostasis. Alpha-melanocyte stimulating hormone (alpha-MSH) is one of the known endogenous agonists for these melanocortin receptors. Insight into putative interactions between the antagonist AGRP amino acids with the melanocortin-4 receptor (MC4R) may be important for the design of unique ligands for the treatment of obesity related diseases and is currently lacking in the literature. A three-dimensional homology molecular model of the mouse MC4 receptor complex with the hAGRP(87-132) ligand docked into the receptor has been developed to identify putative antagonist ligand-receptor interactions. Key putative AGRP-MC4R interactions include the Arg111 of hAGRP(87-132) interacting in a negatively charged pocket located in a cavity formed by transmembrane spanning (TM) helices 1, 2, 3, and 7, capped by the acidic first extracellular loop (EL1) and specifically with the conserved melanocortin receptor residues mMC4R Glu92 (TM2), mMC4R Asp114 (TM3), and mMC4R Asp118 (TM3). Additionally, Phe112 and Phe113 of hAGRP(87-132) putatively interact with an aromatic hydrophobic pocket formed by the mMC4 receptor residues Phe176 (TM4), Phe193 (TM5), Phe253 (TM6), and Phe254 (TM6). To validate the AGRP-mMC4R model complex presented herein from a ligand perspective, we generated nine chimeric peptide ligands based on a modified antagonist template of the hAGRP(109-118) (Tyr-c[Asp-Arg-Phe-Phe-Asn-Ala-Phe-Dpr]-Tyr-NH(2)). In these chimeric ligands, the antagonist AGRP Arg-Phe-Phe residues were replaced by the melanocortin agonist His/D-Phe-Arg-Trp amino acids. These peptides resulted in agonist activity at the mouse melanocortin receptors (mMC1R and mMC3-5Rs). The most notable results include the identification of a novel subnanomolar melanocortin peptide template Tyr-c[Asp-His-DPhe-Arg-Trp-Asn-Ala-Phe-Dpr]-Tyr-NH(2) that is equipotent to alpha-MSH at the mMC1, mMC3, and mMC5 receptors but is 30-fold more potent than alpha-MSH at the mMC4R. Additionally, these studies identified a new and novel >200-fold MC4R versus MC3R selective peptide Tyr-c[Asp-D-Phe-Arg-Trp-Asn-Ala-Phe-Dpr]-Tyr-NH(2) template. Furthermore, when the His-DPhe-Arg-Trp sequence is used to replace the hAGRP Arg-Phe-Phe residues in the "mini"-AGRP (hAGRP87-120, C105A) template, a potent nanomolar agonist resulted at the mMC1R and MC3-5Rs.