gebhart/patrepeval huggingface dataset:
In Vitro, Ex Vivo , and In Vivo Methodological Approaches for Studying Therapeutic Targets of Osteoporosis and Degenerative Joint Diseases: How Biomarkers Can Assist? (2005)

Although our approach to the clinical management of osteoporosis (OP) and degenerative joint diseases (DJD)-major causes of disability and morbidity in the elderly-has greatly advanced in the past decades, curative treatments that could bring ultimate solutions have yet to be found or developed. Effective and timely development of candidate drugs is a critical function of the availability of sensitive and accurate methodological arsenal enabling the recognition and quantification of pharmacodynamic effects. The established concept that both OP and DJD arise from an imbalance in processes of tissue formation and degradation draws attention to need of establishing in vitro, ex vivo, and in vivo experimental settings, which allow obtaining insights into the mechanisms driving increased bone and cartilage degradation at cellular, organ, and organism levels. When addressing changes in bone or cartilage turnover at the organ or organism level, monitoring tools adequately reflecting the outcome of tissue homeostasis become particularly critical. In this context, bioassays targeting the quantification of various degradation and formation products of bone and cartilage matrix elements represent a useful approach. In this review, a comprehensive overview of widely used and recently established in vitro, ex vivo, and in vivo set-ups is provided, which in many cases effectively take advantage of the potentials of biomarkers. In addition to describing and discussing the advantages and limitations of each assay and their methods of evaluation, we added experimental and clinical data illustrating the utility of biomarkers for these methodological approaches.
Design of Environment‐Sensitive Supramolecular Assemblies for Intracellular Drug Delivery: Polymeric Micelles that are Responsive to Intracellular pH Change (2003)

Drug smuggling: Micelles made up of block copolymers and the anticancer drug adriamycin (ADR), which is linked to the polymer by a pH-sensitive linker, have been prepared (see picture). Treatment of cancer cells with the micelles shows that the micelles are transported into the cell by endocytosis, thus bypassing the cell-membrane transporters. In the cell, the decrease in pH value triggers the release of the ADR, which retains its cytotoxic effect. The released ADR fluoresces which allows its localization within the cells to be detected. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z50653_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Cross-family dimerization of transcription factors Fos/Jun and ATF/CREB alters DNA binding specificity. (1991)

The Fos/Jun and ATF/CREB families of transcription factors function in coupling extracellular signals to alterations in expression of specific target genes. Like many eukaryotic transcription factors, these proteins bind to DNA as dimers. Dimerization is mediated by a structure known as the "leucine-zipper" motif. Although Fos/Jun and ATF/CREB were previously thought to interact preferentially with different DNA regulatory elements (the AP-1/TRE and ATF/CRE sites, respectively), we find that members of these two families form selective cross-family heterodimers. The resulting heterodimers display distinguishable DNA binding specificities from each other and from their parental homodimers. These findings indicate that the Fos/Jun and ATF/CREB families of transcription factors are not as distinct as was previously thought. We suggest that they can be grouped into a superfamily of transcription factors.
Deletion of chromosome 15 (q11 – 13) in a Prader‐Labhart‐Willi syndrome clinic population (1984)

Deletion of the long arm of chromosome 15 has recently been reported in a number of patients with the Prader-Labhart-Willi syndrome who were studied with prometaphase banding. We performed cytogenetic analysis on 12 patients with this disorder in whom the clinical diagnosis was certain. A specific cytogenetic anomaly, del(15q11-13) was found in all of the 12 patients. In nine of the 12, the deletion was noted in all cells examined; in two, there was mosaicism, some cells having the deletion and others being normal; one patient had a 7;15 translocation. No clinical differences were evident between individuals with mosaicism for the translocation and those with the typical deletion in all cells examined. The finding that all of our patients with Prader-Labhart-Willi syndrome have a cytogenetic anomaly, with some patients having mosaicism, distinguishes the results of this study from those of previous reports. Prometaphase chromosome analysis is recommended in all individuals clinically suspected of having Prader-Labhart-Willi syndrome and should be considered in hypotonic infants without a specific diagnosis.
Cellular Cholesterol Depletion Triggers Shedding of the Human Interleukin-6 Receptor by ADAM10 and ADAM17 (TACE) (2003)

Interleukin-6 (IL-6) activates cells by binding to the membrane-bound IL-6 receptor (IL-6R) and subsequent formation of a glycoprotein 130 homodimer. Cells that express glycoprotein 130, but not the IL-6R, can be activated by IL-6 and the soluble IL-6R which is generated by shedding from the cell surface or by alternative splicing. Here we show that cholesterol depletion of cells with methyl-beta-cyclodextrin increases IL-6R shedding independent of protein kinase C activation and thus differs from phorbol ester-induced shedding. Contrary to cholesterol depletion, cholesterol enrichment did not increase IL-6R shedding. Shedding of the IL-6R because of cholesterol depletion is highly dependent on the metalloproteinase ADAM17 (tumor necrosis factor-alpha-converting enzyme), and the related ADAM10, which is identified here for the first time as an enzyme involved in constitutive and induced shedding of the human IL-6R. When combined with protein kinase C inhibition by staurosporine or rottlerin, breakdown of plasma membrane sphingomyelin or enrichment of the plasma membrane with ceramide also increased IL-6R shedding. The effect of cholesterol depletion was confirmed in human THP-1 and Hep3B cells and in primary human peripheral blood monocytes, which naturally express the IL-6R. For decades, high cholesterol levels have been considered harmful. This study indicates that low cholesterol levels may play a role in shedding of the membrane-bound IL-6R and thereby in the immunopathogenesis of human diseases.
Imaging Texture and Porosity in Mudstones and Shales: Comparison of Secondary and Ion-Milled Backscatter SEM Methods (2010)

Abstract Observations from a number of unconventional reservoirs lead us to conclude that four major pore types exist in fine-grained reservoir and non-reservoir rocks, that they are effectively connected, and that pore sizes from nanometers to microns must be considered when evaluating size distributions. This paper uses SEM imaging of Haynesville, Horn River, Barnett and Marcellus Shales to illustrate that pore types other than those hosted by organics are present in unconventional shale gas reservoirs, and that they are continuous and connected to kerogen-hosted pores. In addition, we present evidence that the maximum size of pores originating in organic matter is determined by the size of the kerogen mass (in the case of organic particles) or the geometry of enclosing crystals (in the case of amorphous, pore-filling kerogen). Pairs of secondary and ion-milled backscatter SEM images address the misconception that large pores observed in secondary electron images are grain pullouts. 2-D image analysis and 3-D volumetric reconstructions to study pore distributions should take rock microtexture and the various pore types into consideration. A combined method using thin section textural analysis, XRD, and SEM imaging is recommended to address scaling issues when choosing samples for 2-D and 3-D volumetric analysis.
A Scaleable and Defined System for Generating Neural Stem Cells from Human Embryonic Stem Cells (2006)

The ability to differentiate human ESCs (hESCs) to defined lineages in a totally controlled manner is fundamental to developing cell-based therapies and studying human developmental mechanisms. We report a novel, scaleable, and widely applicable system for deriving and propagating neural stem cells from hESCs without the use of animal products, proprietary formulations, or genetic manipulation. This system provides a definitive platform for studying human neural development and has potential therapeutic implications.
Glimpses through the clouds: collocates in a new light (2008)

This paper demonstrates a web-based, interactive data visualisation, allowing users to quickly inspect and browse the collocational relationships present in a corpus. The software is inspired by tag clouds, first popularised by on-line photograph sharing website Flickr (www.flickr.com). A paper based on a prototype of this Collocate Cloud visualisation was given at Digital Resources for the Humanities and Arts 2007. The software has since matured, offering new ways of navigating and inspecting the source data. It has also been expanded to analyse additional corpora, such as the British National Corpus (http://www.natcorp.ox.ac.uk/), which will be the focus of this talk.
The evaluation of complex-dependent alterations in human factor VIIa. (1992)

Factor VIIa is a plasma glycoprotein which, when bound to the integral membrane glycoprotein tissue factor, forms an enzymatic complex that is essential for normal hemostasis. We have developed a fluorescent substrate (6-(Mes-D-Leu-Gly-Arg)amino-1-naphthalenediethylsulfamide) which can be used to directly measure the enzymatic activity of factor VIIa in the presence and absence of tissue factor and phospholipid. The sensitivity of this substrate allows for detection of factor VIIa at concentrations below 10(-9) M. The kinetics of substrate hydrolysis by factor VIIa were evaluated and it was observed that the binding of factor VIIa to tissue factor increases the catalytic efficiency (kcat/Km) of factor VIIa substrate hydrolysis greater than 100-fold. The increase in enzymatic efficiency of factor VIIa, when complexed to tissue factor, is mediated primarily by an increase in kcat. These data suggest that tissue factor induces an alteration in the catalytic site of factor VIIa, which allows for more efficient hydrolysis of the small fluorescent substrate. Measurements conducted using various phospholipids and detergents demonstrated that the increase in catalytic efficiency of factor VIIa, when complexed to tissue factor, is independent of the supporting surface. The differential rate of substrate hydrolysis when factor VIIa is complexed to tissue factor was used to estimate the binding of factor VIIa to tissue factor. From these data an apparent dissociation constant for factor VIIa binding to tissue factor was calculated to be between 1.1 and 2.1 nM with a binding stoichiometry of 1.04:1 (factor VIIa:tissue factor). When the reactivity of this small fluorescent substrate toward single-chain factor VII was investigated, both in the presence and absence of tissue factor, no substrate hydrolysis was observed.
Switch of Coenzyme Specificity of Mouse Lung Carbonyl Reductase by Substitution of Threonine 38 with Aspartic Acid (1997)

Mouse lung carbonyl reductase, a member of the short-chain dehydrogenase/reductase (SDR) family, exhibits coenzyme specificity for NADP(H) over NAD(H). Crystal structure of the enzyme-NADPH complex shows that Thr-38 interacts with the 2'-phosphate of NADPH and occupies the position spatially similar to an Asp residue of the NAD(H)-dependent SDRs that hydrogen-bonds to the hydroxyl groups of the adenine ribose of the coenzymes. Using site-directed mutagenesis, we constructed a mutant mouse lung carbonyl reductase in which Thr-38 was replaced by Asp (T38D), and we compared kinetic properties of the mutant and wild-type enzymes in both forward and reverse reactions. The mutation resulted in increases of more than 200-fold in the Km values for NADP(H) and decreases of more than 7-fold in those for NAD(H), but few changes in the Km values for substrates or in the kcat values of the reactions. NAD(H) provided maximal protection against thermal and urea denaturation of T38D, in contrast to the effective protection by NADP(H) for the wild-type enzyme. Thus, the single mutation converted the coenzyme specificity from NADP(H) to NAD(H). Calculation of free energy changes showed that the 2'-phosphate of NADP(H) contributes to its interaction with the wild-type enzyme. Changing Thr-38 to Asp destabilized the binding energies of NADP(H) by 3.9-4.5 kcal/mol and stabilized those of NAD(H) by 1.2-1.4 kcal/mol. These results indicate a significant role of Thr-38 in NADP(H) binding for the mouse lung enzyme and provide further evidence for the key role of Asp at this position in NAD(H) specificity of the SDR family proteins.
Influence of Lactoferrin on Host-Microbe Interactions (1997)

The antimicrobial spectrum of lactoferrin (Lf) includes statsis, cidal, cationic, phagocytic, and colonization/decolonization effects on susceptible microorganisms. The selective interaction of Lf with microbial surface seems to play an essential role in regulating many of these events. Lf bound to specific outer membrane (OM) pore-forming proteins (porins) of various enteric bacteria. The magnitude of Lf-microbe interaction showed a direct relationship with the bacterial susceptibility to Lf. Although most bacteria expressed porins, certain strains showed resistance to Lf effects and did not demonstrate specific Lf binding. This Lf “resistance” was attributed to the shielding of porin accessibility by the carbohydrate O-antigenic chains of lipopolysaccharide (LPS). Mutants with progressive deletions in O-side-chain and core polysaccharide demonstrated increased Lf binding and progressive susceptibility to Lf effects. Lf interaction with bacterial surface affected the porin channels in the OM and potentiated the diffusion of antibiotics. Lf also affected the intestinal colonization of Escherichia coli. Lf inhibited the expression of various bacterial fimbriae and also blocked bacterial interaction with host subepithelial matrix components, such as fibronectin, fibrinogen, various collagens, and laminin. Our studies suggested that specific interaction with cell target involved the anion-binding ligands of Lf, followed by coordinate binding and oxidation of Fe2+ to Fe3+ on bacterial surface. This metal transition in the presence of suitable oxygen species seems to fulfill the necessary components of Haber-Weiss reaction and promote a targeted radical generation, with iron (Fe) serving as the Lf prosthetic group on the bacterial surface.
Adaptive multiple-candidate hierarchicalsearch for block matching algorithm (1995)

A new adaptive multiple-candidate hierarchical search for the estimation of motion vectors is presented. This technique can eliminate the undesirable problem of local minima in coarse-to-fine hierarchical block matching algorithms. Computer simulations show that the algorithm is very efficient as compared with the traditional coarse-to-fine hierarchical search. Also, it is close to the performance of the exhaustive full search, with a significant reduction on computation.
High Efficiency, Homology-Directed Genome Editing in Caenorhabditis elegans Using CRISPR-Cas9 Ribonucleoprotein Complexes (2015)

Homology-directed repair (HDR) of breaks induced by the RNA-programmed nuclease Cas9 has become a popular method for genome editing in several organisms. Most HDR protocols rely on plasmid-based expression of Cas9 and the gene-specific guide RNAs. Here we report that direct injection of in vitro-assembled Cas9-CRISPR RNA (crRNA) trans-activating crRNA (tracrRNA) ribonucleoprotein complexes into the gonad of Caenorhabditis elegans yields HDR edits at a high frequency. Building on our earlier finding that PCR fragments with 35-base homology are efficient repair templates, we developed an entirely cloning-free protocol for the generation of seamless HDR edits without selection. Combined with the co-CRISPR method, this protocol is sufficiently robust for use with low-efficiency guide RNAs and to generate complex edits, including ORF replacement and simultaneous tagging of two genes with fluorescent proteins.
Flow Cytometry Protocols (1997)

In Flow Cytometry Protocols, leading researchers and experimenters update the complex and technically sophisticated field of flow cytometry with detailed accounts of their many new, improved, and well-tested protocols and applications. Among the cutting-edge methods presented here are techniques for the detection of terminal transferase ion leukemia, intracellular cytokines, intracellular/intranuclear antigens in leukemia and tumors, and cyclins. Protocols for performing functional studies include methods for assessing viability, transmembrane potential, oxidative metabolism, environmental particulate uptake, drug resistance, and cellular pharmacokinetics. The methods for examining DNA address cell cycle analysis, DNA/RNA analysis of solid malignancies, solid-tumor DNA ploidy analysis, apoptosis, and a method that combines FISH with flow cytometry. Advanced methods for chromosome sorting and 5-6 color analysis are also detailed. Flow Cytometry Protocols contains methods that take advantage of the recently developed instrumentation and the vast array of novel probes that have led to advances in the field of flow cytometry, as well as to significantly improved standard methods. This eminently practical new book will play a key role in bringing researchers up-to-date in this unique and productive technology
Site of inhibitory action of isoniazid in the synthesis of mycolic acids in Mycobacterium tuberculosis (1975)

The cellular mycolate synthetase activity of Mycobacterium tuberculosis H37Ra was previously shown to be very sensitive to isoniazid (Wang, L., and K. Takayama. 1972. Antimicrob. Agents Chemother. 2: 438-441). We have now examined the question of how isoniazid inhibits the synthesis of mycolic acids. The saponifiable 14-C-labeled lipids of control and isoniazid-treated cells (1.0 mug/ml, 60 min) were compared on a Sephadex LH-20 column, and it appeared that the synthesis of the intermediate-sized fatty acids was partially inhibited. These fatty acids were fractionated as their methyl esters by Sephadex LH-20 column chromatograp-y and gas-liquid (6% Dexsil) chromatography. Mass sectral analysis of the fractionated lipids revealed several series of fatty acids: fraction II, C39-C56; fraction III, C27-C40. The long-chain fatty acids in three kinds of isoniazid-treated cells were examined: (a) long-term exposure (48 hr, 0.5 mug/ml), (b) short-term exposure (60 min, 1.0 mug/ml), and (c) variable exposure at low concentration (0-90 min, 0.2 mug/ml). Both long- and short-term exposure experiments showed that isoniazid inhibited the synthesis of saturated fatty acids greater than C26 and of unsaturated fatty acids greater than C24. The variable-exposure experiment at low isoniazid concentration showed that the syntheses of mycolic acids and long-chain fatty acid fractions II and III were inhibited to the same extent. These fatty acids may thus be precursors of mycolic acids.
In vivo EXCITATION OF PHOTOSENSITIZERS BY INFRARED LIGHT (1995)

Use of near infrared instead of visible light would markedly improve tissue penetration, making larger tumors candidates for photochemotherapy. Because common photesensitizers exhibit virtually no absorption in this wavelength region, conditions are required where the simultaneous action of two photons is possible. Healthy tissue (rat ears), sensitized by hematoporphyrin derivative, sulfonated chloroaluminum phthalocyanine or pheophorbide alpha, was irradiated (1064 nm, 10 ns) with power densities up to 200 MW cm-2 and total energy densities up to 200 kJ cm-2. No reproducible photodynamic lesions were observed, but there was sensitizer fluorescence that depended quadratically on the excitation intensity.
Intrinsic microvasculature of the sciatic nerve in the rat (2012)

Microvasculature associated with the sciatic nerve was examined using high-resolution micro-CT scanning in one group of rats and surgical exploration in another. The results indicate that blood supply to the sciatic nerve is an "open-ended" system in which the vessels run longitudinally within the epineurium and connect with external vasculature primarily at junction points. Although the range of vasculature found extended down to 4-5 μ, only a few isolated vessels of this size were found, with no capillary "mesh" as such, possibly because of the close proximity of the intrinsic vessel to nerve fibers within the epineurium. While the study did not include direct measurements of flow or nerve function, the "open-ended" pattern of vasculature found has important implications regarding the relationship between the two. Specifically, the nerve is less vulnerable to a severe or complete disruption in blood supply than it would be under a close-ended system such as that of the heart or brain, where a severe disruption can occur with the obstruction of only a single vessel. Indeed, the pattern of vasculature found, subject to further study of vasculature at the capillary level, suggests that flow within the intrinsic vessels may be in either direction, depending on circumstances, somewhat like flow within the circle of Willis in the cerebral circulation.
Overexpression of Interleukin (IL)-7 Leads to IL-15–independent Generation of Memory Phenotype CD8+ T Cells (2002)

Transgenic (TG) mice expressing a high copy number of interleukin (IL)-7 cDNA under the control of the major histocomaptability complex (MHC) class II promoter display a 10-20-fold increase in total T cell numbers. Here, we show that the increase in T cell numbers in IL-7 TG mice is most apparent at the level of memory phenotype CD44hi CD122hi CD8+ cells. Based on studies with T cell receptor (TCR) TG mice crossed to IL-7 TG mice, increased levels of IL-7 may provide costimulation for TCR recognition of self-MHC ligands and thus cause naive CD8+ cells to proliferate and differentiate into memory phenotype cells. In addition, a marked increase in CD44hi CD122hi CD8+ cells was found in IL-7 TG IL-15(-) mice. Since these cell are rare in normal IL-15(-) mice, the dependency of memory phenotype CD8+ cells on IL-15 can be overcome by overexpression of IL-7.