gebhart/patrepeval huggingface dataset:
Cartesian Parallel Manipulators With Pseudoplanar Limbs (2006)

Based on the Lie-group-algebraic properties of the displacement set, the three-degree-of-freedom (3DOF) pseudoplanar motion often termed Y motion for brevity is first introduced. Then, all possible general architectures of the mechanical generators of a given Y subgroup are obtained by implementing serial arrays of 1DOF Reuleaux pairs or hinged parallelograms. In total, five distinct mechanical generators of Y motion are revealed and seven ones having at least one parallelogram are also derived from them. In order to avoid the singularity that may occur in the limbs, all singular postures of Y-motion generators are also located by detecting the possible linear dependency of the joint twists and the group dependency of displacement sets. The parallel layout of three 4DOF limbs including Y-motion generators with orthogonal planes make up a Cartesian translational parallel manipulator, which produces a motion set of spatial translations. The 3DOF translation of the moving platform is directly controlled by the three 1DOF translations in three orthogonal prismatic fixed joints.
Rapid Inactivation of Proteins by Rapamycin-Induced Rerouting to Mitochondria (2010)

We have developed a method for rapidly inactivating proteins with rapamycin-induced heterodimerization. Cells were stably transfected with siRNA-resistant, FKBP-tagged subunits of the adaptor protein (AP) complexes of clathrin-coated vesicles (CCVs), together with an FKBP and rapamycin-binding domain-containing construct with a mitochondrial targeting signal. Knocking down the endogenous subunit with siRNA, and then adding rapamycin, caused the APs to be rerouted to mitochondria within seconds. Rerouting AP-2 to mitochondria effectively abolished clathrin-mediated endocytosis of transferrin. In cells with rerouted AP-1, endocytosed cation-independent mannose 6-phosphate receptor (CIMPR) accumulated in a peripheral compartment, and isolated CCVs had reduced levels of CIMPR, but normal levels of the lysosomal hydrolase DNase II. Both observations support a role for AP-1 in retrograde trafficking. This type of approach, which we call a "knocksideways," should be widely applicable as a means of inactivating proteins with a time scale of seconds or minutes rather than days.
Dynamics of rabies virus quasispecies during serial passages in heterologous hosts (1999)

To understand the mutations and genetic rearrangements that allow rabies virus infections of new hosts and adaptation in nature, the quasispecies structure of the nucleoprotein and glycoprotein genes as well as two noncoding sequences of a rabies virus genome were determined. Gene sequences were obtained from the brain and from the salivary glands of the original host, a naturally infected European fox, and after serial passages in mice, dogs, cats and cell culture. A relative genetic stasis of the consensus sequences confirmed previous results about the stability of rabies virus. At the quasispecies level, the mutation frequency varies, in the following order: glycoprotein region (21.9 x 10(-4) mutations per bp), noncoding sequence nucleoprotein-phosphoprotein region (7.2-7.9 x 10(-4) mutations per bp) and nucleoprotein gene region (2.9-3.7 x 10(-4) mutations per bp). These frequencies varied according to the number, type of heterologous passages and the genomic region considered. The shape of the quasispecies structure was dramatically modified by passages in mice, in which the mutation frequencies increased by 12-31 x 10(-4) mutations per bp, depending on the region considered. Non-synonymous mutations were preponderant particularly in the glycoprotein gene, stressing the importance of positive selection in the maintenance and fixation of substitutions. Two mechanisms of genomic evolution of the rabies virus quasispecies, while adapting to environmental changes, have been identified: a limited accumulation of mutations with no replacement of the original master sequence and a less frequent but rapid selective overgrowth of favoured variants.
N-(2-Aminoethyl)-5-isoquinolinesulfonamide, a newly synthesized protein kinase inhibitor, functions as a ligand in affinity chromatography. Purification of Ca2+-activated, phospholipid-dependent and other protein kinases. (1985)

We designed a simple procedure for the purification of Ca2+-activated, phospholipid-dependent protein kinase (protein kinase C) from rabbit brain, using affinity chromatography with a new affinity adsorbent. The adsorbent was synthesized by attaching the amino residue of N-(2-aminoethyl)-5-isoquinolinesulfonamide (H-9) to cyanogen bromide-activated Sepharose. H-9 is a potent competitive inhibitor of protein kinase C, cGMP-, and cAMP-dependent protein kinase with respect to ATP and exhibits inhibition constants of 18, 0.87, and 1.9 microM, respectively (Hidaka, H., Inagaki, M., Kawamoto, S., and Sasaki, Y. (1984) Biochemistry, 23, 5036). A 960-fold purification was achieved in the two-step procedure, which entailed DEAE-cellulose and the affinity chromatography. The resultant preparation was essentially homogeneous, as indicated by polyacrylamide gel electrophoresis under conditions of denaturation with sodium dodecyl sulfate. The affinity of protein kinase C for the H-9-Sepharose was high, and the enzyme could not be eluted either by a high concentration of sodium chloride or by 40% glycerol. The protein kinase C could be eluted from H-9-Sepharose by the buffer containing both 0.2 M NaCl and 20% glycerol, thereby suggesting that the binding between protein kinase C and H-9-Sepharose was due to both hydrophobic and electrostatic interactions. H-9 coupled to Sepharose retained both cyclic nucleotide-dependent protein kinases and protein kinase C, and these enzymes could be eluted separately by the buffer containing L-arginine, a potent inhibitor of these three kinases. The novel aspects of these three multifunctional protein kinases can thus be investigated using isoquinolinesulfonamide derivatives.
Detection of Steel Fatigue Cracks with Strain Sensing Sheets Based on Large Area Electronics (2015)

Reliable early-stage damage detection requires continuous monitoring over large areas of structure, and with sensors of high spatial resolution. Technologies based on Large Area Electronics (LAE) can enable direct sensing and can be scaled to the level required for Structural Health Monitoring (SHM) of civil structures and infrastructure. Sensing sheets based on LAE contain dense arrangements of thin-film strain sensors, associated electronics and various control circuits deposited and integrated on a flexible polyimide substrate that can cover large areas of structures. This paper presents the development stage of a prototype strain sensing sheet based on LAE for crack detection and localization. Two types of sensing-sheet arrangements with size 6 × 6 inch (152 × 152 mm) were designed and manufactured, one with a very dense arrangement of sensors and the other with a less dense arrangement of sensors. The sensing sheets were bonded to steel plates, which had a notch on the boundary, so the fatigue cracks could be generated under cyclic loading. The sensors within the sensing sheet that were close to the notch tip successfully detected the initialization of fatigue crack and localized the damage on the plate. The sensors that were away from the crack successfully detected the propagation of fatigue cracks based on the time history of the measured strain. The results of the tests have validated the general principles of the proposed sensing sheets for crack detection and identified advantages and challenges of the two tested designs.
Silicon Analogues of the RXR‐Selective Retinoid Agonist SR11237 (BMS649): Chemistry and Biology (2009)

C/Si switch: Twofold sila-substitution (C/Si exchange) in the RXR-selective retinoids 4 a (SR11237) and 5 a leads to 4 b (disila-SR11237) and 5 b, respectively. Chemistry and biology of the C/Si pairs are reported.SR11237 (BMS649, 4 a) is a pan-RXR-selective retinoid agonist. Its silicon analogue, disila-SR11237 (4 b; twofold C/Si exchange), was prepared in a multistep synthesis by starting from 1,2-bis(ethynyldimethylsilyl)ethane. In addition, the related C/Si analogues 5 a and 5 b, with an indane (disila-indane) instead of a tetraline (disila-tetraline) skeleton, were synthesized. The C/Si pairs 4 a/4 b and 5 a/5 b were studied for their interaction with retinoid receptors and were demonstrated to be highly potent RXR-selective ("rexinoid") agonists. Interestingly, twofold C/Si exchange in the indane moiety of 5 a resulted in a 10-fold increase in biological activity of the corresponding silicon-containing rexinoid 5 b, possibly resulting from an increased receptor affinity or a divergent allosteric effect on co-regulator-binding surfaces. The crystal structures of the ternary complexes formed by 5 a and 5 b, respectively, with the ligand-binding domain of hRXRalpha and a peptide of the co-activator TIF2/GRIP1 revealed additional interactions of the disila analogue 5 b with the H7 and H11 residues, supporting the first option of increased binding affinity. This is the first demonstration of an increase in binding affinity of a ligand to a nuclear receptor by C/Si replacement, thereby adding this C/Si switch strategy to the repertoire of nuclear receptor ligand design.
Angiogenesis inhibitor TNP-470 (AGM-1470) potently inhibits the tumor growth of hormone-independent human breast and prostate carcinoma cell lines. (1993)

The angiogenesis inhibitor O-(chloroacetyl-carbamoyl)fumagillol (TNP-470) showed antitumor activity in three human cancer xenograft systems. TNP-470 potently inhibited the tumor growth of hormone-independent prostate cancer PC-3 cells and breast cancer MDA-MB-231 cells dose dependently at weekly s.c. doses of 50-200 mg/kg with maximum inhibition of 96 and 88% (tumor growth, 4 and 12% of that in the respective control). In experiments of combination therapy with chemotherapeutic agents, the combination of TNP-470 (100 mg/kg) and cisplatin (5 mg/kg) showed an additive antitumor effect (from treated versus control, 38 and 22% to 5%) against PC-3 carcinoma. 5-Fluorouracil and Adriamycin alone did not significantly inhibit MDA-MB-231 tumor growth (treated versus control, 131 and 64%, respectively). TNP-470 also inhibited tumor growth of WiDr colon cancer; although the inhibition was less marked (treated versus control, 39%) than that observed with the hormone-independent cancers used in this study. In an in vitro study, all the cell lines tested were considerably insensitive to TNP-470 in monolayer cultures (50% inhibitory concentration, approximately 5 micrograms/ml), whereas TNP-470 inhibited the anchorage-independent growth of PC-3 and MDA-MB-231 cells (50% inhibitory concentration, 0.05 and 470 ng/ml, respectively). The inhibitory activity of TNP-470 against anchorage-independent growth correlated well with the in vivo antitumor activity among the cell lines tested. Thus, this inhibitory action may partly contribute to the potent antitumor activity of the angiogenesis inhibitor TNP-470, at least in the case of PC-3 and MDA-MB-231. These results suggest that hormone-independent prostate and breast cancers may be appropriate target diseases for TNP-470 clinical trials.
Oxidative Nucleobase Modifications Leading to Strand Scission (1998)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidative Nucleobase Modifications Leading to Strand ScissionCynthia J. Burrows and James G. MullerView Author Information Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112-0850 Cite this: Chem. Rev. 1998, 98, 3, 1109–1152Publication Date (Web):April 1, 1998Publication History Received18 December 1997Revised20 February 1998Published online1 April 1998Published inissue 7 May 1998https://pubs.acs.org/doi/10.1021/cr960421shttps://doi.org/10.1021/cr960421sresearch-articleACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views6532Altmetric-Citations1513LEARN 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 SUBJECTS:Adducts,Genetics,Guanine,Nucleobases,Oxidation Get e-Alerts
Correction for distortion in a beam outline transfer device in radiotherapy CT‐based simulation (1993)

In using a CT scanner as a radiation therapy simulator, it would be helpful to be able to transfer the beam outline from the computer plan to the patient's skin. A beam outline transfer device has been constructed and installed on a Siemens' DRH CT scanner gantry. The planned treatment beam geometry from a 3-D computerized simulation and planning system can be projected onto the patient's skin surface accurately and efficiently. The positioning accuracy achieved is within +/- 0.1 cm over a 20 cm x 20 cm field. Integrating the device into the CT scanner, simplifies the device and reduces the cost over an externally mounted device. Two unsuccessful methods to correct the projection distortions are also mentioned. In order to achieve the reported beam outline transfer accuracy, a system based on our empirically derived calibration procedure is described.
Cloning and Functional Identification of a Neuronal Glutamine Transporter (2000)

Glutamine is the preferred precursor for the neurotransmitter pool of glutamate, the major excitatory transmitter in the mammalian central nervous system. We have isolated a complementary DNA clone (designated GlnT) encoding a plasma membrane glutamine transporter from glutamatergic neurons in culture, and its properties have been examined using the T7 vaccinia system in fibroblasts. When GlnT is transfected into CV-1 cells, L-glutamine is the preferred substrate. Transport is Na(+)-dependent and inhibited by alpha-methylaminoisobutyric acid, a specific inhibitor of neutral amino acid transport system A. Kinetic analysis of glutamine uptake by GlnT is saturable, with a Michaelis constant (K(m)) of 489 +/- 88 microM at pH 7.4. Glutamine uptake mediated by GlnT is pH-sensitive with a 5-fold greater efficiency of uptake at pH 8.2 than at pH 6.6. Only the maximal velocity of transport increases without a significant change in K(m). The distribution of GlnT mRNA and protein in the central nervous system is widespread and is expressed on neurons that use glutamate as their neurotransmitter. In cultured cerebellar granule cells, GlnT is expressed only on neurons and is absent from astrocytes. GlnT expression increases concomitantly with the morphologic and functional differentiation of these cells in vitro, consistent with its role of supplying glutamatergic neurons with their neurotransmitter precursor. GlnT is the first member of the system A family of neutral amino acid transporters with 11 putative membrane-spanning domains and is a potential target to modulate presynaptic glutamatergic function.
Fission yeast retrotransposon Tf1 integration is targeted to 5' ends of open reading frames (2000)

Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100-420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed.
CDDO-me induces apoptosis and inhibits Akt, mTOR and NF-kappaB signaling proteins in prostate cancer cells. (2007)

These studies provide a rationale for clinical evaluation of CDDO-Me as adjuvant therapy for treatment of advanced and fatal form of prostate cancer.
Classification and treatment of functional incontinence in children (2000)

Functional urinary incontinence in children may be caused by disturbances of the filling phase, the voiding phase or a combination of both. Detrusor overactivity may cause frequency and urgency, with or without urge incontinence. Girls present with symptoms of detrusor overactivity more often than boys, but sometimes other symptoms, e.g. urinary tract infections or constipation, prevail. Frequent contractions of the detrusor may cause the pelvic floor muscles to become overactive, resulting in staccato or fractionated voiding. When incontinence is the result of a voiding disorder the term 'dysfunctional voiding' is used. Bladder function in these children may be normal, but instability may be present. In children with a 'lazy' bladder, voiding occurs with no detrusor contractions, and postvoid residual volumes and overflow incontinence are the main characteristics. Diagnosis is based on the medical and voiding history, a physical examination, bladder diaries and uroflowmetry. The upper urinary tract should be evaluated in children with recurrent infections and dysfunctional voiding (reflux). Uroflowmetry can be combined with pelvic floor electromyography to detect overactivity of the pelvic floor muscles. Urodynamic studies are usually reserved for patients with dysfunctional voiding and those not responding to anticholinergic drugs. Treatment is usually a combination of 'standard therapy', behavioural therapy, bladder training, physiotherapy and medical treatment. The role of alpha-blockers needs to be evaluated further. Also, neuromodulation may have a place in treatment but the exact indications need to be defined. Clean intermittent self-catheterization is sometimes necessary in children with a lazy bladder and large residual volumes who do not respond to a more conservative approach. Future research needs to be directed towards improving understanding of the pathophysiology, epidemiology, classification and treatment modalities of functional incontinence in children.
Antifungal agents: chemotherapeutic targets and immunologic strategies (1996)

Free access1 February 1996 Share on Antifungal agents: chemotherapeutic targets and immunologic strategiesAuthors: N H Georgopapadakou, T J WalshAuthors Info & AffiliationsDOI: https://doi.org/10.1128/aac.40.2.279 PDF/EPUB
Hydrothermal Synthesis and Optical, Magnetic, and Supercapacitance Properties of Nanoporous Cobalt Oxide Nanorods (2009)

Nanoporous cobalt oxide nanorods were synthesized by a hydrothermal method. Transmission electron microscopy analysis showed that the individual Co3O4 nanorods have a nanoporous structure, consisting of the textured aggregations of nanocrystals. Optical properties of Co3O4 nanorods were characterized by Raman and UV−vis spectroscopy. Magnetic property measurement shows that Co3O4 nanorods have a low Néel transition temperature of 35 K. We observed quite significant exchange bias for nanoporous Co3O4 nanorods, indicating the existence of magnetic coupling between the nanocrystals in Co3O4 nanorods. When applied as electrode materials in supercapacitors, Co3O4 demonstrated a high capacitance of 280 F/g.
Comparative genomic hybridization (CGH)‐arrays pave the way for identification of novel cancer‐related genes (2004)

Comparative genomic hybridization (CGH) has already made a significant impact on cancer cytogenetics. However, CGH to metaphase chromosomes can provide only limited resolution at the 5-10 Mb level. To circumvent this limitation, array-based CGH has been devised. Since spotted DNAs in a CGH-array contain sequence information directly connected with the genome database, we can easily note particular biological aspects of genes that lie within regions involved in copy-number aberrations. High-density, sub-megabase arrays can reveal nonrandom chromosome copy-number aberrations responsible for neoplastic transformation that have been masked under complex karyotypes in epithelial solid tumors. High-density CGH-array therefore paves the way for identification of disease-related genetic aberrations that have not yet been detected by existing technologies, and array-based CGH technology should soon be practical for diagnosis of cancer or genetic diseases in the clinical setting.
Super-Resolution Stereo- and Multi-View Synthesis from Monocular Video Sequences (2007)

This paper presents a new approach for generation of super-resolution stereoscopic and multi-view video from monocular video. Such multi-view video is used for instance with multi-user 3D displays or auto-stereoscopic displays with head-tracking to create a depth impression of the observed scenery. Our approach is an extension of the realistic stereo view synthesis (RSVS) approach which is based on structure from motion techniques and image-based rendering to generate the desired stereoscopic views for each point in time. The extension relies on an additional super- resolution mode which utilizes a number of frames of the original video sequence to generate a virtual stereo frame with higher resolution. The algorithm is tested on several TV broadcast videos, as well as on sequences captured with a single handheld camera and sequences from the well known BBC documentation "Planet Earth". Finally, some simulation results will show that RSVS is quite suitable for super-resolution 2D-3D conversion.
Simultaneous Topography-guided PRK Followed by Corneal Collagen Cross-Linking for Keratoconus (2009)

Simultaneous PRK followed by CXL seems to be a promising treatment capable of offering functional vision in patients with keratoconus.
Development of a GFP reporter gene for Chlamydomonas reinhardtii chloroplast (2002)

Reporter genes have been successfully used in chloroplasts of higher plants, and high levels of recombinant protein expression have been reported. Reporter genes have also been used in the chloroplast of Chlamydomonas reinhardtii, but in most cases the amounts of protein produced appeared to be very low. We hypothesized that the inability to achieve high levels of recombinant protein expression in the C. reinhardtii chloroplast was due to the codon bias seen in the C. reinhardtii chloroplast genome. To test this hypothesis, we synthesized a gene encoding green fluorescent protein (GFP) de novo, optimizing its codon usage to reflect that of major C. reinhardtii chloroplast-encoded proteins. We monitored the accumulation of GFP in C. reinhardtii chloroplasts transformed with the codon-optimized GFP cassette (GFPct), under the control of the C. reinhardtii rbcL 5'- and 3'-UTRs. We compared this expression with the accumulation of GFP in C. reinhardtii transformed with a non-optimized GFP cassette (GFPncb), also under the control of the rbcL 5'- and 3'-UTRs. We demonstrate that C. reinhardtii chloroplasts transformed with the GFPct cassette accumulate approximately 80-fold more GFP than GFPncb-transformed strains. We further demonstrate that expression from the GFPct cassette, under control of the rbcL 5'- and 3'-UTRs, is sufficiently robust to report differences in protein synthesis based on subtle changes in environmental conditions, showing the utility of the GFPct gene as a reporter of C. reinhardtii chloroplast gene expression.