gebhart/patrepeval huggingface dataset:
Glial Cell Line-Derived Neurotrophic Factor (GDNF) Is a Proliferation Factor for Rat C6 Glioma Cells: Evidence from Antisense Experiments (2000)

Growth factors play an important role in proliferation and differentiation of malignant brain gliomas in humans. Glial cell line-derived neurotrophic factor (GDNF) has been shown recently to be highly expressed in human glioblastomas and in rat glial cell lines B49 and C6. The aim of the present study was to knockdown GDNF, its receptor GFR-alpha1, and the related family member persephin by using antisense oligonucleotides and to observe the effects on cell proliferation. To enhance cellular uptake into C6 glioma cells, 15-mer phosphorothioate oligonucleotides were complexed with the cationic lipid Lipofectamine. The complex was applied for 3 x 12 hours to C6 glioma cells, and cells were allowed to recover for 24 hours after each transfection and then analyzed. This protocol markedly reduced GDNF and GFR-alpha1 protein levels in C6 glioma cells compared with control oligonucleotides. Knockdown of C6 cells with GDNF and GFR-alpha1 but not with persephin antisense oligonucleotides significantly decreased the number of C6 glioma cells and also inhibited the incorporation of bromodeoxyuridine as a sign of reduced DNA synthesis. In conclusion, it is shown that GDNF but not persephin is a potent proliferation factor for rat glioma cells. Knockdown of GDNF using antisense oligonucleotides complexed with lipids as carriers may be useful in gene therapeutic approaches in vitro and possibly also in vivo.
<title>Registration of head CT images to physical space using multiple geometrical features</title> (1998)

We recently reported a hybrid registration technique that uses a weighted combination of multiple geometrical feature shapes. In this study we use the weighted geometrical feature (WGF) algorithm to register CT images of the head to physical space using the skin surface only, the bone surface only, and various weighted combinations of these surfaces and one fiducial point (centroid of a bone-implanted marker). We use data acquired from six patients that underwent temporal lobe craniotomies for the resection of cerebral lesions. Each patient had four external markers attached to transcutaneous posts screwed into the outer table of the skull. We evaluate and compare the accuracy of the registrations obtained using these various approaches by using as a gold standard the registration obtained using three of the four bone-implanted markers (the remaining marker is used in the various combinations). The results demonstrate that a combination of geometrical features can improve the accuracy of CT-to-physical space registration. The WGF algorithm might thus be useful in various image- guided surgical systems.
Inducible Gene Expression in Plants (1999)

Inducible control of gene expression - an overview use of the TN10-encoded tetracycline repressor to the control gene expression ecdysteroid agonist-inducible control of gene expression in plants glucocorticoid-inducible gene expression in plants tissue-specific, copper-controllable gene expression in plants nitrate inducibility of gene expression using the nitrate reductase gene promoter use of heat shock promoters to control gene expression in plants wound-inducible genes in plants developmental targeting of gene expression by the use of a senescence-specific promoter abscisic acid-inducible promoter switches in the control of gene expression potential use of hormone responsive elements to control gene expression in plants.
Genetics and Molecular Biology of the Inherited Long QT Syndrome (1994)

Two forms of the inherited long QT syndrome have been known for many years: the autosomal recessive Jervell and Lange-Nielsen form and the autosomal dominant Romano-Ward form. A gene marker at the 11p 15.5 locus has been identified for some, but not all, families with the autosomal dominant form, but as yet the gene has not been identified. It is apparent that mutations of at least four genes, and possibly more, can cause the syndrome. The molecular biology of the syndrome is not yet clarified, but abnormalities of ion channel function are likely, particularly the potassium delayed rectifier current. Proposals for the pathophysiology include an abnormality of a G protein which controls ion channel and adrenergic pathway function, as well as a disturbance of the sympathetic nervous system. The identification of the abnormal gene(s) and the gene products will provide precise information on the molecular physiology of the syndrome.
Design and Fabrication of Thermocapillary Micro Bubble Pump (2012)

In this paper, a novel MEMS-fabricated thermal bubble pump is proposed. By using thermocapillary effect in a microchannel loop, bubbles are designed to move only in one direction of the loop. Driving heater with a square-wave signal, bubble nucleates and grows asymmetrically above the heater. As soon as the heating pulse is turned off, an interesting phenomenon is found. Instead of bubble collapse, bubble moves toward growing direction. Continuous bubbles grow and move periodically when square-wave pulsing signals are applied. Thermocapillary pumping phenomena are achieved successfully in the experiments. By adjusting background temperature field, thermocapillary pumping phenomena can be sustained. Detailed mechanism for pumping force will be discussed in this paper.
An Efficient, Inexpensive, and Shelf-Stable Diazotransfer Reagent:  Imidazole-1-sulfonyl Azide Hydrochloride (2007)

The design and synthesis of a new diazotransfer reagent, imidazole-1-sulfonyl azide hydrochloride, are reported. This reagent has proven to equal triflyl azide in its ability to act as a "diazo donor" in the conversion of both primary amines into azides and activated methylene substrates into diazo compounds. Crucially, this reagent can be prepared in a one-pot reaction on a large scale from inexpensive materials, is shelf-stable, and is conveniently crystalline.
Nonepitaxial Growth of Hybrid Core-Shell Nanostructures with Large Lattice Mismatches (2010)

We report a synthetic route to achieving nanoscale heterostructures consisting of a metal core and monocrystalline semiconductor shell with substantial lattice mismatches between them, which cannot be obtained by conventional epitaxial techniques. By controlling soft acid-base coordination reactions between molecular complexes and colloidal nanostructures, we show that chemical thermodynamics can drive nanoscale monocrystalline growth of the semiconductor shell with a lattice structure incommensurate with that of the core. More complex hybrid core-shell structures with azimuthal and radial nanotailoring of structures and compositions of the monocrystalline semiconductor shell are also demonstrated.
Multisite Catalysis: A Mechanistic Study of β‐Lactone Synthesis from Epoxides and CO—Insights into a Difficult Case of Homogeneous Catalysis (2003)

Carbonylation of epoxides with a combination of Lewis acids and cobalt carbonyls was studied by both theoretical and experimental methods. Only multisite catalysis opens a low-energy pathway for trans opening of oxirane rings. This ring-opening reaction is not easily achieved with a single-site metal catalyst due to structural and thermodynamic constraints. The overall reaction pathway includes epoxide ring opening, which requires both a Lewis acid and a tetracarbonylcobaltate nucleophile, yielding a cobalt alkyl-alkoxy-Lewis acid moiety. After CO insertion into the Co-C(alkyl) bond, lactone formation results from a nucleophilic attack of the alkoxy Lewis acid entity on the acylium carbon atom. A theoretical study indicates a marked influence of the Lewis acid on both ring-opening and lactone-formation steps, but not on carbonylation. Strong Lewis acids induce fast ring opening, but slow lactone formation, and visa versa: a good balance of Lewis acidity would give the fastest catalytic cycle as all steps have low barriers. Experimentally, carbonylation of propylene oxide to beta-butyrolactone was monitored by online ATR-IR techniques with a mixture of tetracarbonylcobaltate and Lewis acids, namely BF(3), Me(3)Al, Et(2)Al(+).diglyme, and a combination of Me(3)Al/dicobaltoctacarbonyl. We found that the last two mixtures are extremely active in lactone formation.
The effect of hydrogen peroxide on the degradation of methyl and ethyl tert‐butyl ether in soils (1995)

The degradation of the gasoline oxygenates, methyl tert‐butyl ether (MTBE) and ethyl tert‐butyl ether (ETBE) in soil systems was evaluated. The data indicated that MTBE and ETBE were chemically oxidized to tertiary butanol and acetone when H 2 O 2 was added to soil microcosms containing aquifer material from an organic rich site. Identical reactions were observed when H 2 O 2 was added to solutions containing soluble ferrous iron and either MTBE or ETBE. Chemical oxidation was influenced by the H 2 O 2 concentration, pH, and the presence of ferrous iron but was independent of the iron concentration. Naturally occurring aerobic microcosms in the soil were able to degrade ETBE but not MTBE. Chemical oxidation coupled with an aerobic‐anaerobic‐biological cycle is proposed to describe a degradation pathway for ETBE in H 2 O 2 amended soils.
Automatic rate adaptation (2010)

Rate adaptation is a fundamental primitive in wireless networks. Since wireless channel strength varies quickly and unpredictably, senders have to constantly measure the channel and correspondingly adapt the bitrate so that the transmitted packet gets correctly decoded. Prior approaches to this problem can be divided into two classes: those that require constant and expensive feedback from the receiver about channel strength, or those that use coarse and often inaccurate inference based on packet losses to measure channel strength and decide what bitrate to use.
Integration, Regulation, and Long-Term Stability of R2 Retrotransposons (2015)

R2 elements are sequence specific non-LTR retrotransposons that exclusively insert in the 28S rRNA genes of animals. R2s encode an endonuclease that cleaves the insertion site and a reverse transcriptase that uses the cleaved DNA to prime reverse transcription of the R2 transcript, a process termed target primed reverse transcription. Additional unusual properties of the reverse transcriptase as well as DNA and RNA binding domains of the R2 encoded protein have been characterized. R2 expression is through co-transcription with the 28S gene and self-cleavage by a ribozyme encoded at the R2 5' end. Studies in laboratory stocks and natural populations of Drosophila suggest that R2 expression is tied to the distribution of R2-inserted units within the rDNA locus. Most individuals have no R2 expression because only a small fraction of their rRNA genes need to be active, and a contiguous region of the locus free of R2 insertions can be selected for activation. However, if the R2-free region is not large enough to produce sufficient rRNA, flanking units - including those inserted with R2 - must be activated. Finally, R2 copies rapidly turnover within the rDNA locus, yet R2 has been vertically maintained in animal lineages for hundreds of millions of years. The key to this stability is R2's ability to remain dormant in rDNA units outside the transcribed regions for generations until the stochastic nature of the crossovers that drive the concerted evolution of the rDNA locus inevitably reshuffle the inserted and uninserted units, resulting in transcription of the R2-inserted units.
Radical scavenging activity and cytotoxicity of ferulic acid. (2003)

Ferulic acid and eugenol were examined for their superoxide (O2-), hydroxyl radical (.OH) and nitric oxide (NO)-scavenging ability, using ESR spectroscopy with spin trap agents DMPO and carboxy-PTIO/NOC-7. Ferulic acid more efficiently scavenged .OH and NO than eugenol. The O2- scavenging activity of ferulic acid was comparable with that of eugenol. Ferulic acid significantly reduced the NO production by lipopolysaccharide (LPS)-stimulated mouse macrophage-like cells (Raw 264.7 cells) compared to eugenol. The cytotoxic activity of ferulic acid against Raw 264.7 cells was comparable with that against human submandibular gland carcinoma (HSG) cells and the cytotoxicity of ferulic acid was about 10-fold smaller than that of eugenol. The stoichiometric factor (n) (number of moles of peroxy radical trapped by moles of the relevant phenol) of ferulic acid and eugenol was investigated, using the induction period methods of the methyl methacrylate polymerization system. The n-value of ferulic acid (1.5) was higher than that of eugenol (1.0) and was similar to that of 2, 6-di-t-butyl-4-methylphenol (BHT). Ferulic acid as well as eugenol may produce a dimer during the induction period due to an n-value less than 2. These results suggested that ferulic acid may be useful for preventing cell damage perhaps caused by O2-, and in particular by .OH and NO, in living systems.
Death by Design (1997)

Programmed cell death (apoptosis) is recognized, increasingly, as a contributing cause of cardiac myocyte loss with ischemia/reperfusion injury, myocardial infarction, and long-standing heart failure. Although the exact mechanisms initiating apoptosis in these in vivo settings remain unproven, insights into the molecular circuitry controlling apoptosis more widely suggest the potential to protect mammalian ventricular muscle from apoptosis through one or more of these pathways, by pharmacological means or, conceivably, gene transfer.
Dynamic multidimensional imaging of the human left atrial appendage (2007)

Regardless of AF history, there is broad variation in LAA morphology, anatomical relationships, dimensions, angulation, and motility. These observations may have importance for the development of technologies for therapy delivery in this region.
Methods of induced pluripotent stem cells for clinical application (2015)

Reprograming somatic cells using exogenetic gene expression represents a groundbreaking step in regenerative medicine. Induced pluripotent stem cells (iPSCs) are expected to yield novel therapies with the potential to solve many issues involving incurable diseases. In particular, applying iPSCs clinically holds the promise of addressing the problems of immune rejection and ethics that have hampered the clinical applications of embryonic stem cells. However, as iPSC research has progressed, new problems have emerged that need to be solved before the routine clinical application of iPSCs can become established. In this review, we discuss the current technologies and future problems of human iPSC generation methods for clinical use.
Biofuels from lignin and novel biodiesel analysis (2009)

The first part of the thesis presents a study based on the forest biorefinery concept, which involves converting a pulp mill into a multi-purpose biofuels, biomaterials, and biopower production facility in which these products are produced in an environmentally compatible and sustainable manner. A key challenge in this process is the recovery of lignin from process streams such that it can be utilized in a variety of innovative green chemistry processes &#13;\n\tThe first study examines the fundamental chemical structure of LignoBoost derived lignin recovered from Kraft pulping streams using an acid precipitation/washing methodology. Functional group analysis and molecular weight profiles were determined by nuclear magnetic resonance (NMR) and size exclusion chromatography. These findings gave valuable insight into the physical properties and the determining chemical properties of this currently underutilized, renewable bioresource. &#13;\n\tThe second study is based on the future second generation bioethanol production process, where ethanol produced from lignocellulosic materials will bring about the co-production of significant amounts of under-utilized lignin. The study examines the potential of conventional heterogeneous and novel homogeneous catalysts for the selective cleavage of the aryl-O-aryl and aryl-O-aliphatic linkages of ethanol organosolv lignin to convert it from a low grade fuel to potential fuel precursors or other value added chemicals. The experimental data demonstrated that aryl-O-aryl and aryl-O-aliphatic linkages could be cleaved and the hydrogenated lignin had a decrease in oxygen functionality and the formation of products with lower oxygen content.&#13;\n\tThe second part of this thesis reports the development and optimization of a novel qualitative method for the determination of the various types of hydroxyl groups present in biodiesel production streams. In the first study, the use of 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane as a phosphitylation reagent for quantitative ³¹P-NMR analysis of the hydroxyl groups in biodiesel process samples has been developed. Subsequently a characteristic chemical shifts library is developed with model compounds to provide quantitative data on the concentration of biodiesel precursors, intermediates and final product. The last part of this thesis depicts the results of an industrial trial based on the novel biodiesel analytical method developed earlier.
TROY, a Newly Identified Member of the Tumor Necrosis Factor Receptor Superfamily, Exhibits a Homology with Edar and Is Expressed in Embryonic Skin and Hair Follicles (2000)

In a signal sequence trap screening of the murine brain, we identified a new member of the tumor necrosis factor receptor superfamily designated TROY. TROY is a type I membrane protein of 416 amino acids with characteristic cysteine-rich motifs in the extracellular domain and a tumor necrosis factor receptor-associated factor (TRAF) 2 binding sequence in the cytoplasmic domain of 223 amino acids. In fact, activation of nuclear factor kappaB was induced by the overexpression of TROY and inhibited by dominant negative forms of TRAF2, TRAF5, and TRAF6, indicating that TRAFs and nuclear factor kappaB are involved in the signal transduction of TROY. We also cloned a cDNA for a human counterpart, which showed a 75% homology with mouse TROY at the amino acid level. The extracellular domain of TROY exhibits an extensive homology with that of Edar, a receptor that specifies hair follicle fate. TROY mRNA is strongly expressed in brain and embryo and moderately expressed in the heart, lung, and liver but not the spleen. In the embryo, the expression level is particularly strong in the skin. Interestingly, in situ hybridization analysis of the embryo showed that TROY mRNA was exclusively expressed in the epithelium of many tissues. On the other hand, in neonatal mice, TROY is expressed in hair follicles like Edar as well as in the cerebrum, suggesting pleiotropic functions of TROY in development as well as in the adult mice. The Troy gene is located near the waved coat (Wc) locus, a mutant related to abnormalities in skin and hair.
In Vivo Formation of Dihydroxylated and Glutathione Conjugate Metabolites Derived from Thalidomide and 5-Hydroxythalidomide in Humanized TK-NOG Mice (2012)

The formation of dihydroxythalidomide and glutathione (GSH) conjugate(s) of 5-hydroxythalidomide was investigated in chimeric mice modified with "humanized" liver: novel humanized TK-NOG mice were prepared by the introduction of thymidine kinase, followed by induction with ganciclovir, and human liver cells were transplanted. Following oral administration of racemic thalidomide (100 mg/kg), plasma concentrations of 5-hydroxy- and dihydroxythalidomide were higher in humanized mice than in controls. After administration of 5-hydroxythalidomide (10 mg/kg), higher concentrations of dihydroxythalidomide were detected. These results indicate that livers of humanized mice mediate thalidomide oxidation, leading to catechol and/or the GSH conjugate in vivo and suggest that thalidomide activation occurs.
A chemical genetic screen in Mycobacterium tuberculosis identifies carbon-source-dependent growth inhibitors devoid of in vivo efficacy (2010)

Candidate antibacterials are usually identified on the basis of their in vitro activity. However, the apparent inhibitory activity of new leads can be misleading because most culture media do not reproduce an environment relevant to infection in vivo. In this study, while screening for novel anti-tuberculars, we uncovered how carbon metabolism can affect antimicrobial activity. Novel pyrimidine-imidazoles (PIs) were identified in a whole-cell screen against Mycobacterium tuberculosis. Lead optimization generated in vitro potent derivatives with desirable pharmacokinetic properties, yet without in vivo efficacy. Mechanism of action studies linked the PI activity to glycerol metabolism, which is not relevant for M. tuberculosis during infection. PIs induced self-poisoning of M. tuberculosis by promoting the accumulation of glycerol phosphate and rapid ATP depletion. This study underlines the importance of understanding central bacterial metabolism in vivo and of developing predictive in vitro culture conditions as a prerequisite for the rational discovery of new antibiotics.
An efficient general-purpose least-squares refinement program for macromolecular structures (1987)

A package of programs has been developed for efficient restrained least-squares refinement of macromolecular crystal structures. The package has been designed to be as flexible and general purpose as possible. The process of refinement is divided into basic units and an independent computer program handles each task. Each functional unit communicates with other programs in the package by way of files of well defined format. To modify or replace any program, the user need only understand the function of that particular element. Stereochemical restraints are defined in a general way that can be applied to proteins, nucleic acids, prosthetic groups, solvent atoms and so on. Guide values for bond lengths and bond angles are specified in a straightforward direct manner. Designated groups of atoms can be held constant or constrained to behave as a rigid body during refinement. In order to make the package as efficient as possible, the fast Fourier transform algorithm is used for all the crystallographic transformations. To highlight potential errors in the refined structure the user can list those atoms that have the worst bond lengths and angles, or have the largest positional, temperature-factor or occupancy gradients. It is also possible to check that protein and solvent atoms do not sterically clash with symmetry-related neighbors. Applications of the program package to a bacteriochlorophyll-containing protein, thermolysin-inhibitor complexes and mutants of bacteriophage T4 lysozyme are described.