gebhart/patrepeval huggingface dataset:
The RAGE receptor and its ligands are highly expressed in astrocytes in a grade‐dependant manner in the striatum and subependymal layer in Huntington's disease (2015)

Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by an expansion of the CAG repeat in the huntingtin gene. One of the brain changes that occurs in HD is the expression of the receptor for advanced glycation end products (RAGE), a receptor protein capable of activating multiple signalling pathways by interacting with a range of ligands leading to either beneficial or harmful effects to the cell. Here, we demonstrate in human HD brains a high degree of co-localization of RAGE with its putative ligands S100B and N-carboxymethyllysine (CML) in the caudate nucleus (CN) and the subependymal layer (SEL). The level of co-staining for both RAGE-S100B and RAGE-CML was the highest in the astrocytes but was low in neurons and microglia. The immunostaining for RAGE, S100B and CML extended in a medio-lateral (SEL-CN) direction with increasing grade, such that any change in the expression and co-localization pattern between grades was less prominent in the lateral CN. Additionally, signalling molecules that are downstream of RAGE activation showed changes in their activation status in HD brains. A larger number of RAGE-positive astrocytic cells had NF-kB translocated to the nucleus and the level of phospho-ERK1/2 was also increased in HD brains. Interestingly, the level of mDia-1, that interacts directly with the cytoplasmic domain of RAGE, decreased in HD. Overall, the results suggest a correlation between the functions of RAGE and the HD pathology, but the influence of RAGE on astrocytes and the impact of this on HD progression requires further study. RAGE (receptor for advanced glycation end products) binds multiple types of ligand to produce either neurotrophic or neurotoxic effects. Immunohistochemical staining of HD human brains showed that both RAGE and its ligands were expressed primarily in astrocytes. The pattern of staining corresponded to the grade and region-wise pattern of neurodegeneration suggesting a possible role for RAGE in HD pathology.
Secondary, tertiary, and quaternary structure of T-cell-specific immunoglobulin-like polypeptide chains. (1986)

To explore the possibility that the difference in antigen recognition between B and T cells derives from a structural difference in their respective antigen-specific receptors (immunoglobulins on B cells and immunoglobulin-like molecules on T cells), we compared the extracellular segments of the T-cell receptor alpha, beta, and gamma polypeptide chains and the N-terminal segment of the T-cell T8 (Lyt-2) antigen chain with the corresponding regions of immunoglobulins whose three-dimensional structures are known. The results indicate that the four T-cell polypeptide chains are organized into immunoglobulin-like domains consisting of multistranded antiparallel beta-sheet bilayers. Invariant amino acid side chains that are conserved in diverse immunoglobulins, including those that mediate domain-domain interactions and form a constant scaffold for antibody binding sites, are also conserved in the chains encoded by the T-cell receptor genes and in the N-terminal domain of T8 (Lyt-2). It appears that the binding sites of the antigen-specific T-cell alpha beta-chain receptors and of antibodies are very similar in their overall dimensions and geometry: a T-cell alpha beta receptor molecule probably has an antigen-specific binding site that is fundamentally no different than the conventional binding site of an antibody.
The X‐ray structure of yeast 5‐aminolaevulinic acid dehydratase complexed with two diacid inhibitors (2001)

The structures of 5-aminolaevulinic acid dehydratase complexed with two irreversible inhibitors (4-oxosebacic acid and 4,7-dioxosebacic acid) have been solved at high resolution. Both inhibitors bind by forming a Schiff base link with Lys 263 at the active site. Previous inhibitor binding studies have defined the interactions made by only one of the two substrate moieties (P-side substrate) which bind to the enzyme during catalysis. The structures reported here provide an improved definition of the interactions made by both of the substrate molecules (A- and P-side substrates). The most intriguing result is the novel finding that 4,7-dioxosebacic acid forms a second Schiff base with the enzyme involving Lys 210. It has been known for many years that P-side substrate forms a Schiff base (with Lys 263) but until now there has been no evidence that binding of A-side substrate involves formation of a Schiff base with the enzyme. A catalytic mechanism involving substrate linked to the enzyme through Schiff bases at both the A- and P-sites is proposed.
Thrombopoietin supports proliferation of human primitive hematopoietic cells in synergy with steel factor and/or interleukin-3 (1996)

We have studied the effects of recombinant human thrombopoietin (TPO; mpl ligand) on the proliferation of human primitive hematopoietic progenitors in vitro. CD34+ cells were enriched for cell-cycle-dormant primitive progenitors by separation on the basis of expression of c-kit and CD38. In the presence of varying combinations of TPO, Steel factor (SF), and interleukin-3 (IL-3), CD34+/c-kit(low)/CD38neg/low cells produced fewer colonies than CD34+/c-kit(low)/CD38high cells. However, when cultured in suspension for 7 days and replated in methylcellulose culture for measurement of colony-forming cells, the former population generated more colony-forming cells than the latter. In suspension culture of CD34+/c-kit(low)/CD38neg/low cells, TPO acted synergistically with SF and/or IL-3 in support of the production of colony-forming cells for granulocyte/macrophage colonies, erythroid colonies, and mixed colonies. Culture studies of individual CD34+/c-kit(low)/CD38neg/low cells provided the evidence for the direct nature of the effects of TPO. When combined with SF, TPO showed stronger stimulation of production of progenitors in suspension culture than other early-acting factors, such as IL-6, IL-11, and granulocyte colony-stimulating factor (G-CSF). TPO may be an important cytokine for in vitro manipulation of human hematopoietic stem cells.
Weighted Likelihood Estimation of Ability in Item Response Theory (1989)

Applications of item response theory, which depend upon its parameter invariance property, require that parameter estimates be unbiased. A new method, weighted likelihood estimation (WLE), is derived, and proved to be less biased than maximum likelihood estimation (MLE) with the same asymptotic variance and normal distribution. WLE removes the first order bias term from MLE. Two Monte Carlo studies compare WLE with MLE and Bayesian modal estimation (BME) of ability in conventional tests and tailored tests, assuming the item parameters are known constants. The Monte Carlo studies favor WLE over MLE and BME on several criteria over a wide range of the ability scale.
The biomechanical properties of deep freezing and freeze drying bones and their biomechanical changes after in-vivo allograft (1995)

This study measured the physical properties in bending of the rat femur and compression of the rat first tail vertebra subjected to deep freezing at -80 degrees C for 2 weeks, 6 weeks, 12 weeks and freeze drying. This study also measured the mechanical changes after in vivo allograft of fresh bone, deep freezing(2, 6, 12 weeks) and freeze drying. Analysis for deep freezing groups showed a mean 7.2% decrease in bending strength and 11.0% decrease in compressive strength when compared with the control group, but there was no statistical difference in the duration of deep freezing. The groups of in vivo graft after deep freezing showed 23.1% and 22.2% decrease in bending and compressive strength. There was no statistical difference in the duration of deep freezing. The freeze drying group showed a 9.7% decrease in bending strength and no significant difference in compressive strength. The group of in vivo graft after freeze drying showed a 30.1% and a 41.3% decrease in bending and compressive strength. The above results suggested that there would be some mechanical limitation in using freeze dried graft for supporting implants.
Asthma heterogeneity and severity (2016)

Asthma is a common, chronic inflammatory airways disease characterized by a clinical syndrome of bronchial hyperresponsiveness, inflammation, and reversible airflow obstruction. Individuals with asthma can vary widely in clinical presentation, severity, and pathobiology. The incident factors, pathogenesis, prognosis, and treatment of asthma remain incompletely understood. Utilizing measurable characteristics of asthmatic patients, including demographic, physiologic, and biologic markers, can however identify meaningful phenotypic categories in asthma. Identification of these phenotypes may help improve precision therapeutics targeted toward an individual's' disease, and may identify strategies for preventing progression of disease severity.
Glucuronoyl esterase – Novel carbohydrate esterase produced by Schizophyllum commune (2006)

The cellulolytic system of the wood‐rotting fungus Schizophyllum commune contains an esterase that hydrolyzes methyl ester of 4‐ O ‐methyl‐ d ‐glucuronic acid. The enzyme, called glucuronoyl esterase, was purified to electrophoretic homogeneity from a cellulose‐spent culture fluid. Its substrate specificity was examined on a number of substrates of other carbohydrate esterases such as acetylxylan esterase, feruloyl esterase and pectin methylesterase. The glucuronoyl esterase attacks exclusively the esters of MeGlcA. The methyl ester of free or glycosidically linked MeGlcA was not hydrolysed by other carbohydrate esterases. The results suggest that we have discovered a new type of carbohydrate esterase that might be involved in disruption of ester linkages connecting hemicellulose and lignin in plant cell walls.
Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications (2004)

The detection of double-stranded (ds) DNA by SYBR Green I (SG) is important in many molecular biology methods including gel electrophoresis, dsDNA quantification in solution and real-time PCR. Biophysical studies at defined dye/base pair ratios (dbprs) were used to determine the structure-property relationships that affect methods applying SG. These studies revealed the occurrence of intercalation, followed by surface binding at dbprs above approximately 0.15. Only the latter led to a significant increase in fluorescence. Studies with poly(dA)* poly(dT) and poly(dG)* poly(dC) homopolymers showed sequence-specific binding of SG. Also, salts had a marked impact on SG fluorescence. We also noted binding of SG to single-stranded (ss) DNA, although SG/ssDNA fluorescence was at least approximately 11-fold lower than with dsDNA. To perform these studies, we determined the structure of SG by mass spectrometry and NMR analysis to be [2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]. For comparison, the structure of PicoGreen (PG) was also determined and is [2-[N-bis-(3-dimethylaminopropyl)-amino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]+. These structure-property relationships help in the design of methods that use SG, in particular dsDNA quantification in solution and real-time PCR.
The effect of sildenafil on gastric emptying in patients with end-stage renal failure and symptoms of gastroparesis (2004)

Sildenafil did not improve gastric emptying in patients with ESRF and gastric paresis. Sildenafil may have opposing effects on gastric peristalsis (causing gastric relaxation) compared with its effects on pyloric relaxation. Studies combining sildenafil with prokinetic drugs are of interest.
Directed Mutagenesis of Chloroplast Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (1996)

The structure of active-site loop 6 plays a role in determining the CO2/O2 specificity of chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1.39). Rubisco from the green alga Chlamydomonas reinhardtii differs from higher plant Rubisco within the loop 6 region, and the C. reinhardtii enzyme has a CO2/O2 specificity 25% lower than that of higher plant enzymes. To examine whether differences in sequence may account for differences in catalytic efficiency, we focused on a conserved pair of residues that are in van der Waals contact at the base of loop 6. C. reinhardtii Rubisco contains Leu-326 and Met-349, whereas higher plant enzymes contain Ile-326 and Leu-349. By employing in vitro mutagenesis and chloroplast transformation, L326I and M349L substitutions were created within the Rubisco large subunit of C. reinhardtii. M349L had little effect, but L326I destabilized the holoenzyme in vivo and in vitro. When present together, the M349L substitution partially alleviated the instability resulting from the L326I substitution, but caused a 21% decrease in CO2/O2 specificity and a 74% decrease in the Vmax of carboxylation. Interactions between loop 6 and other structural regions are likely to be responsible for both holoenzyme stability and catalytic efficiency in higher plant Rubisco enzymes.
3D domain swapping: A mechanism for oligomer assembly (1995)

3D domain swapping is a mechanism for forming oligomeric proteins from their monomers. In 3D domain swapping, one domain of a monomeric protein is replaced by the same domain from an identical protein chain. The result is an intertwined dimer or higher oligomer, with one domain of each subunit replaced by the identical domain from another subunit. The swapped "domain" can be as large as an entire tertiary globular domain, or as small as an alpha-helix or a strand of a beta-sheet. Examples of 3D domain swapping are reviewed that suggest domain swapping can serve as a mechanism for functional interconversion between monomers and oligomers, and that domain swapping may serve as a mechanism for evolution of some oligomeric proteins. Domain-swapped proteins present examples of a single protein chain folding into two distinct structures.
Memory CD8 T-Cell Differentiation during Viral Infection (2004)

Memory CD8 T cells are an important component of protective immunity against viral infections, and understanding their development will aid in the design of optimal vaccines. Recent work has shed light on the complex differentiation process that occurs during a CD8 T-cell response to viral infection
Gene Transfer of the Na+,K+-ATPase β1 Subunit Using Electroporation Increases Lung Liquid Clearance (2004)

The development of nonviral methods for efficient gene transfer to the lung is highly desired for the treatment of several pulmonary diseases. We have developed a noninvasive procedure using electroporation to transfer genes to the lungs of rats. Purified plasmid (100-600 microg) was delivered to the lungs of anesthetized rats through an endotracheal tube, and a series of square-wave pulses were delivered via electrodes placed on the chest. Relatively uniform gene expression was observed in multiple cell types and layers throughout the lung, including airway and alveolar epithelial cells, airway smooth muscle cells, and vascular endothelial cells, and this finding was dose- and pulse length-dependent. Most important, no inflammatory response was detected. To demonstrate efficacy of this approach, the beta1 subunit of the Na(+),K(+)-ATPase was transferred to the lungs of rats with or without electroporation, and 3 days later, alveolar fluid clearance was measured. Animals electroporated with the beta1 subunit plasmid showed a twofold increase in alveolar fluid clearance and Na(+),K(+)-ATPase activity as compared with animals receiving all other plasmids, with or without electroporation. These results demonstrate that electroporation is an effective method to increase clearance by introducing therapeutic genes (Na(+),K(+)-ATPase) into the rat lung.
Oil Bodies and Oleosins in Seeds (1992)

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context ...Read More
Serum levels of collagenase, stromelysin‐1, and timp‐1 (1994)

Abstract Objective. To measure serum levels of collagenase (MMP‐1), stromelysin‐1 (MMP‐3), and tissue inhibitor of matrix metalloproteinases‐1 (TIMP‐1) in normal subjects and in patients with osteoarthritis (OA), and to assess how these correlate with biochemical and clinical indicators of disease activity in OA. Methods. Specific immunoassays were used to measure MMPs, TIMP‐1, and antigenic keratan sulfate (KS). The total area of cartilage affected by the disease was measured (expressed as an articular index). Results. In the normal population (n = 118), the serum concentration of MMP‐3, but not of MMP‐1 or TIMP‐1, increased with age and was approximately 2 times higher in males than in females. In the OA patients (n = 33), the serum levels of MMP‐3, but not of MMP‐1 or TIMP‐1, were significantly elevated and correlated strongly with the articular index but poorly with objective and subjective functional capacity scores as well as with serum levels of antigenic KS and systemic parameters of inflammation. Conclusion. These findings illustrate the importance of matching patients and normal controls for age and sex in further studies of MMP‐3 and are consistent with the hypothesis that MMP‐3 might play an important role in the degradation of joint cartilage in OA. Further, serum levels of MMP‐3 may prove useful for monitoring therapy for OA.
Syntheses of semiconductor nanoparticles using single‐molecular precursors (2001)

Methods for the preparation of II-VI, III-V, and II-V as well as other compound semiconductor nanoparticles using main group single-molecular precursors have been developed. The work involves the design and synthesis of compounds containing all the elements required within the desired nanoparticulate material. Precursors are tailored to give reproducible, clean decomposition at moderate temperatures, leading to high quality, defect free, mono-dispersed nanoparticles. In this article we cover key aspects of precursor and nanoparticle synthesis. One of the more successful and reproducible series of single-source precursors used, and the one on which we have concentrated our research efforts, is the bis(dialkyldithio-/diseleno-carbamato)cadmium(II)/zinc(II) compounds, M(E(2)CNR(2))(2) (M = Zn or Cd, E = S or Se, and R = alkyl) for the preparation of chalcogenide nanoparticulate materials. Preliminary mechanistic studies suggest that the precursor to nanoparticle deposition route is strongly influenced by the alkyl substituent groups present, and may well determine the phase and quality of the final metal chalcogenide nanoparticles produced. Herein we discuss the synthesis of semiconductor nanoparticles using such single-molecular precursors.
A 5mW multi-standard Bluetooth LE/IEEE 802.15.6 SoC for WBAN applications (2014)

In this work we present Bodysense, a low-power radio with sensor interface for WBAN applications. The SoC comprises a transceiver operating in the frequency range 2.36-2.483GHz and adhering to the IEEE 802.15.6 Narrow Band (NB) and Bluetooth Low-Energy (BLE) standards. The chip was fabricated in a 65nm technology and absorbs 5.5mA/5mA when operating in Rx/Tx mode. The receiver noise figure of 6dB leads to excellent sensitivity in both standards (-94/-96 for the BLE/NB). The π/4-DQPSK transmitter has a measured EVM and ACPR of 6.8% and -30dBc that exceed the NB specifications.
Effect of a recA mutation on cholera toxin gene amplification and deletion events (1986)

The cholera toxin operon (ctxAB) is located on a 7-kilobase pair variable genetic element which undergoes genetic duplication and amplification events in Vibrio cholerae. Amplification of the ctx genetic element was investigated by substituting the resident ctx loci of two V. cholerae strains with a DNA fragment encoding resistance to kanamycin. Although these strains were not normally resistant to greater than 150 micrograms of kanamycin per ml, spontaneous derivatives could be obtained that grew well on 3 mg of kanamycin per ml. Southern blot analysis of these highly resistant isolates demonstrated that the ctx element was amplified approximately 20-fold. This amplification process was completely inhibited in the absence of a functional recA gene. The V. cholerae RecA protein, therefore, is essential for cholera toxin gene amplification. Spontaneous deletions of the ctx structural genes were observed in both recA+ and recA- V. cholerae strains, although such deletions occurred at a 21-fold-lower frequency in the latter case. Structural analysis of these ctx amplification and deletion events supports a model for their formation that involves unequal crossing over between repetitive sequences located upstream and downstream of the ctx operon.
The sol-gel process (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe sol-gel processLarry L. Hench and Jon K. WestCite this: Chem. Rev. 1990, 90, 1, 33–72Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://pubs.acs.org/doi/10.1021/cr00099a003https://doi.org/10.1021/cr00099a003research-articleACS PublicationsRequest reuse permissionsArticle Views54674Altmetric-Citations3577LEARN 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
Northern blotting (1996)

Northern blotting is the main method for examining the expression of genes through measurement of an mRNA. Tissue specificity and the factors which regulate expression can both be determined by Northern blotting. A cDNA radioactively labelled with 32P is the most-commonly-used hybridization probe. Convenient, non-radioactive detection protocols are, however, increasingly available. A combination of anti-sense oligonucleotides as probes, together with chemiluminescence-based detection provides a rapid and simplified approach to Northern blotting, increasing the accessibility of this important procedure for nutritional studies.