gebhart/patrepeval huggingface dataset:
Three-dimensional holographic fluorescence microscopy (1997)

Most commonly used methods for three-dimensional (3D) fluorescence microscopy make use of sectioning techniques that require that the object be physically scanned in a series of two-dimensional (2D) sections along the z axis. The main drawback in these approaches is the need for these sequential 2D scans. An alternative approach to fluorescence imaging in three dimensions has been developed that is based on optical scanning holography. This novel approach requires only a 2D scan to record 3D information. Holograms of 15-microm fluorescent latex beads with longitinal separation of ~2 mm have been recorded and reconstructed. To our knowledge, this is the first time holograms of fluorescent specimens have been recorded by an optical holographic technique.
Kaposi’s sarcoma-associated herpesvirus interacts with EphrinA2 receptor to amplify signaling essential for productive infection (2012)

Kaposi's sarcoma-associated herpesvirus (KSHV), etiologically associated with Kaposi's sarcoma, uses integrins (α3β1, αVβ3, and αVβ5) and associated signaling to enter human dermal microvascular endothelial cells (HMVEC-d), an in vivo target of infection. KSHV infection activated c-Cbl, which induced the selective translocation of KSHV into lipid rafts (LRs) along with the α3β1, αVβ3, and xCT receptors, but not αVβ5. LR-translocated receptors were monoubiquitinated, leading to productive macropinocytic entry, whereas non-LR-associated αVβ5 was polyubiquitinated, leading to clathrin-mediated entry that was targeted to lysosomes. Because the molecule(s) that integrate signal pathways and productive KSHV macropinocytosis were unknown, we immunoprecipitated KSHV-infected LR fractions with anti-α3β1 antibodies and analyzed them by mass spectrometry. The tyrosine kinase EphrinA2 (EphA2), implicated in many cancers, was identified in this analysis. EphA2 was activated by KSHV. EphA2 was also associated with KSHV and integrins (α3β1 and αVβ3) in LRs early during infection. Preincubation of virus with soluble EphA2, knockdown of EphA2 by shRNAs, or pretreatment of cells with anti-EphA2 monoclonal antibodies or tyrosine kinase inhibitor dasatinib significantly reduced KSHV entry and gene expression. EphA2 associates with c-Cbl-myosin IIA and augmented KSHV-induced Src and PI3-K signals in LRs, leading to bleb formation and macropinocytosis of KSHV. EphA2 shRNA ablated macropinocytosis-associated signaling events, virus internalization, and productive nuclear trafficking of KSHV DNA. Taken together, these studies demonstrate that the EphA2 receptor acts as a master assembly regulator of KSHV-induced signal molecules and KSHV entry in endothelial cells and suggest that the EphA2 receptor is an attractive target for controlling KSHV infection.
Synthetic Cardenolides and Related Products. III. Isocardenolides (1974)

The synthesis of novel cardenolides, closely related to naturally-occurring cardiotonic agents, is described. They were obtained from 17β-[3-furyl]androstanes derived from digitoxigenin, gitoxigenin, digoxigenin, and strophanthidin by hypohalous acid or organic peracid oxidation. The preparation of β-D- and α-L-glycosidic derivatives is also reported.
Effect of Soil PH on Fluridone Activity and Persistence as Determined by Chlorophyll Measurements (1983)

Residue levels of fluridone {1-methyl-3-phenyl-5-[3-(trifluoromethyl)phenyl]-4(1 H )-pyridinone} in soil were determined indirectly by measuring the chlorophyll content of wheat ( Triticum aestivum L.) grown on a Norfolk sandy loam (Typic paleudult; fine loam, siliceous, thermic) 14, 22, 39, and 66 days after a preemergence application of the herbicide. The half-life for 0.22 and 0.45 kg/ha of fluridone was estimated to be 18 days. Phytotoxicity increased with increasing pH in newly-treated soils and in soil sampled 14 days after treatment. Higher chlorophyll levels in wheat grown in soil sampled 39 days after fluridone application indicated a decrease in biologically-active herbicide. Soil removed from the field following later cultivation produced small reductions in chlorophyll at pH 4.0 and 5.2, but at pH 7.0 significant fluridone activity was still present in the soil after 66 days. Cultivation may have increased the surface concentration of the herbicide.
Improved clonality assessment in germinal centre/post-germinal centre non-Hodgkin’s lymphomas with high rates of somatic hypermutation (2006)

Use of BIOMED-2 primers has significantly reduced the false negative rate associated with GC/PGCL when compared with consensus primers, and the inclusion of DJH rearrangements represents a potential complementary target for clonality assessment, as SHM is thought not to occur in these types of rearrangements.
Sex differences in nociceptive withdrawal reflex and pain perception (2005)

Experimentally induced pain often reveals sex differences, with higher pain sensitivity in females. The degree of differences has been shown to depend on the stimulation and assessment methods. Since sex differences in pain develop anywhere along the physiological and psychological components of the nociceptive system, we intended to compare the nociceptive flexion reflex (NFR) as a more physiological (spinal) aspect of pain procession to the verbal pain report of intensity and unpleasantness as the more psychological (cortical) aspect. Twenty female and twenty male healthy university students were investigated by use of nociceptive flexion reflex threshold (staircase method) after electrical stimulation of the N. suralis. Furthermore, we assessed supra-threshold reflex responses (latency, amplitude and area) by applying 10 stimuli 5 mA above reflex threshold. Following each stimulation, the subjects provided pain ratings of intensity and unpleasantness on a visual analogue scale. Females exhibited marked lower nociceptive flexion reflex thresholds than males, while the supra-threshold reflex response tailored to the individual reflex threshold did not show any significant differences. The verbal pain ratings, corrected for NFR threshold, were not found to differ significantly. The large sex differences in nociception that were present in NFR threshold but not in the pain ratings corroborate the hypothesis that spinal processes contribute substantially to sex differences in pain procession.
A New Supercapacitor Design Methodology for Light Transportation Systems Saving (2011)

Light transportation systems are not new proposals since their utilization started at dawn of electric energy spreading at industrial level. The light transportation systems class includes tramways, urban and subway metro-systems as well as trolley buses. These systems are intrinsically characterized by low investment costs and high quality service in terms of environmental impact and energy efficiency. The vehicle technology, which is continuously improving, allows lighter and economical solutions. These attractive characteristics has generated a renewed interest of the researchers and transportation companies in trying to obtain better performances of these systems, being foreseeable their remarkable spreading in the next future. However, even though the perspectives appear to be particularly bright, the increase of the electrical power demand associated to the higher number of vehicles circulating at the same time, require to investigate new solutions for optimizing the whole transportation system performance and particularly the energy consumption, also by exploiting the possibility tendered by the advent of technology innovation. The improvement of the energy efficiency is a crucial issue, both in planning stage and during operating conditions, which cannot be deferred. It has to be highlighted that also for already existing light transportation systems, the energy saving can be pursued by integrating new technological components or apparatuses as energy storage systems (Chymera et al,2006), which allow contemporaneously to obtain high energy saving and to reduce the of load peaks requested to the supply system. More specifically, the storage devices employment, which may be on board (Steiner et al,2007), or located at both the substations or along the track (Barrero et al,2008), are attractive means for obtaining contemporaneously energy saving, energy efficiency, pantograph voltage stabilization and peak regularization (Hase et al,2003). Storage devices may play also a fundamental role in enhancing the dynamic response of the overall light transit system, if they are used in combination with properly controlled power converters. All these previously mentioned benefits surely are convincing arguments for persuading to upgrade the existing light transportation systems, all the more that capital costs exhibit very reduced payback periods. The high energy densities make the supercapacitors attractive means for real time energy optimization, voltage regulation and high reduction of peak powers requested to feeding substations during the acceleration and braking phases. Many solutions have been suggested in the relevant literature, both oriented to the employment of distributed
Neuronal Activity-Dependent Cell Survival Mediated by Transcription Factor MEF2 (1999)

During mammalian development, electrical activity promotes the calcium-dependent survival of neurons that have made appropriate synaptic connections. However, the mechanisms by which calcium mediates neuronal survival during development are not well characterized. A transcription-dependent mechanism was identified by which calcium influx into neurons promoted cell survival. The transcription factor MEF2 was selectively expressed in newly generated postmitotic neurons and was required for the survival of these neurons. Calcium influx into cerebellar granule neurons led to activation of p38 mitogen-activated protein kinase-dependent phosphorylation and activation of MEF2. Once activated, MEF2 regulated neuronal survival by stimulating MEF2-dependent gene transcription. These findings demonstrate that MEF2 is a calcium-regulated transcription factor and define a function for MEF2 during nervous system development that is distinct from previously well-characterized functions of MEF2 during muscle differentiation.
Unique ultrastructure in the elementary body of Chlamydia sp. strain TWAR (1987)

The ultrastructure of two prototype strains (TW-183 and AR-39) of Chlamydia sp. strain TWAR was described. The TWAR elementary body (EB) demonstrated a unique morphology and structure distinct from those of other chlamydial organisms. It was pleomorphic but typically pear shaped. The average size was 0.38 micron, with a long axis of 0.44 micron, a short axis of 0.31 micron, and a ratio of the long to the short axes of 1.42. The cytoplasmic mass was round, with an average diameter of 0.24 micron. There was a large periplasmic space. Small, round electron-dense bodies (0.05 micron in diameter), which were attached to the cytoplasm by a stringlike structure, were seen in the periplasmic space. These features are in contrast to those of other chlamydiae, which are typically round with a narrow or barely discernible periplasmic space. The TWAR reticulate body (RB) was morphologically and structurally similar to those of other Chlamydia species, having an average diameter of 0.51 micron and being circular in shape. The ultrastructural observations of the intracellular growth of TWAR in HeLa cells revealed that TWAR underwent the same developmental cycle as do other chlamydiae, i.e., transformation of EB to RB, multiplication by binary fission, and maturation by transformation of RB to EB via the intermediate-form stage.
Doxorubicin-Loaded PLGA Nanoparticles by Nanoprecipitation: Preparation, Characterization and In Vitro Evaluation (2007)

Nanoparticles formulated by nanoprecipitation of acid-ended poly(lactic-co-glycolic acid) were found to be able to control the release of doxorubicin in a pH-dependent manner and to effectively deliver high payloads of the drug in an active form to MDA-MB-231 breast cancer cells.
Severe Lactic Acidosis in a 14-Year-Old Female With Metastatic Undifferentiated Carcinoma of Unknown Primary (2004)

A 14-year-old girl was found to have a large, non-tender breast mass with anemia and thrombocytopenia. The diagnosis of an undifferentiated carcinoma of unknown primary was made after open breast biopsy of the mass with negative immunohistochemical studies for breast malignancies. Further evaluation showed extensive metastatic disease affecting the bone marrow, ribs, liver, and brain with magnetic resonance imaging evidence of carcinomatous meningitis. Despite 2 months of chemotherapy and intensive supportive care, the patient died of severe lactic acidosis and disseminated intravascular coagulation after exaggerated menstrual bleeding. The association of severe lactic acidosis and undifferentiated carcinoma of unknown primary in an adolescent has not been previously described.
Application-layer anycasting (2002)

The anycasting communication paradigm is designed to support server replication by allowing applications to easily select and communicate with the "best" server, according to some performance or policy criteria, in a group of content-equivalent servers. We examine the definition and support of the anycasting paradigm at the application layer, providing a service that maps anycast domain names into one or more IP addresses using anycast resolvers. In addition to being independent from network-layer support, our definition includes the notion of filters, functions that are applied to groups of addresses to affect the selection process. We consider both metric-based filters (e.g., server response time) and policy-based filters.
Regulation of Ribosome Biogenesis by the Rapamycin-sensitive TOR-signaling Pathway inSaccharomyces cerevisiae (1999)

The TOR (target of rapamycin) signal transduction pathway is an important mechanism by which cell growth is controlled in all eucaryotic cells. Specifically, TOR signaling adjusts the protein biosynthetic capacity of cells according to nutrient availability. In mammalian cells, one branch of this pathway controls general translational initiation, whereas a separate branch specifically regulates the translation of ribosomal protein (r-protein) mRNAs. In Saccharomyces cerevisiae, the TOR pathway similarly regulates general translational initiation, but its specific role in the synthesis of ribosomal components is not well understood. Here we demonstrate that in yeast control of ribosome biosynthesis by the TOR pathway is surprisingly complex. In addition to general effects on translational initiation, TOR exerts drastic control over r-protein gene transcription as well as the synthesis and subsequent processing of 35S precursor rRNA. We also find that TOR signaling is a prerequisite for the induction of r-protein gene transcription that occurs in response to improved nutrient conditions. This induction has been shown previously to involve both the Ras-adenylate cyclase as well as the fermentable growth medium-induced pathways, and our results therefore suggest that these three pathways may be intimately linked.
Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells (2011)

We describe a microchip designed to quantify the levels of a dozen cytoplasmic and membrane proteins from single cells. We use the platform to assess protein-protein interactions associated with the EGF-receptor-mediated PI3K signaling pathway. Single-cell sensitivity is achieved by isolating a defined number of cells (n = 0-5) in 2 nL volume chambers, each of which is patterned with two copies of a miniature antibody array. The cells are lysed on-chip, and the levels of released proteins are assayed using the antibody arrays. We investigate three isogenic cell lines representing the cancer glioblastoma multiforme, at the basal level, under EGF stimulation, and under erlotinib inhibition plus EGF stimulation. The measured protein abundances are consistent with previous work, and single-cell analysis uniquely reveals single-cell heterogeneity, and different types and strengths of protein-protein interactions. This platform helps provide a comprehensive picture of altered signal transduction networks in tumor cells and provides insight into the effect of targeted therapies on protein signaling networks.
Comparison between Use of Lysol and Effective Microorganism to Manage Odour at Municipal Waste Transfer Station (2017)

Ampang Jajar Transfer Station (AJTS) in Pulau Pinang, Malaysia receives wastes from North and Central Seberang Perai, which are consolidated at AJTS before final disposal at Pulau Burung Sanitary Landfill located 40 km south. AJTS is located in an industrial area with the closest residences, Flat Ampang Jajar, about 300 m away. Efforts have been in place to manage odour nuisance by spraying solutions of Effective Microorganism (EM) and Lysol at the operation area of the AJTS. This study was conducted with the objective of verifying the effectiveness of EM and Lysol in odour control and their suitable spraying frequency. Solid wastes taken from AJTS were characterised in the laboratory for solids and moisture content, while its leachate was analysed for chemical oxygen demand (COD) and volatile fatty acids. A portion of the collected sample was also tested for odour concentration with and without EM and Lysol application. Laboratory analysis indicated that AJTS waste is highly degradable with 72% moisture content and 76% volatile solids, thus susceptible to odour production during decomposition. Acetic, butyric and propionic acid were present at concentrations of 3618 ppm, 581 ppm and 549 ppm respectively, higher than their respective odour threshold detection value of 0.21 ppm, 0.001 ppm and 0.16 ppm. The sour and rancid smell attributed with the waste sample is contributed partly by the VFA content. AJTS sample in laboratory conditions was treated more effectively by Lysol (57% odour reduction) compared to EM (24% odour reduction). Lysol reduces malodour by masking the unpleasant "sour garbage" odour with a "soapy" scent instead, leading to a perceived "mildly unpleasant" (-1) hedonic tone. The current spraying of Lysol twice every 6 h at the AJTS is sufficient to manage odour to acceptable levels for 7 h after spray.
Shotgun identification of protein modifications from protein complexes and lens tissue (2002)

Large-scale genomics has enabled proteomics by creating sequence infrastructures that can be used with mass spectrometry data to identify proteins. Although protein sequences can be deduced from nucleotide sequences, posttranslational modifications to proteins, in general, cannot. We describe a process for the analysis of posttranslational modifications that is simple, robust, general, and can be applied to complicated protein mixtures. A protein or protein mixture is digested by using three different enzymes: one that cleaves in a site-specific manner and two others that cleave nonspecifically. The mixture of peptides is separated by multidimensional liquid chromatography and analyzed by a tandem mass spectrometer. This approach has been applied to modification analyses of proteins in a simple protein mixture, Cdc2p protein complexes isolated through the use of an affinity tag, and lens tissue from a patient with congenital cataracts. Phosphorylation sites have been detected with known stoichiometry of as low as 10%. Eighteen sites of four different types of modification have been detected on three of the five proteins in a simple mixture, three of which were previously unreported. Three proteins from Cdc2p isolated complexes yielded eight sites containing three different types of modifications. In the lens tissue, 270 proteins were identified, and 11 different crystallins were found to contain a total of 73 sites of modification. Modifications identified in the crystallin proteins included Ser, Thr, and Tyr phosphorylation, Arg and Lys methylation, Lys acetylation, and Met, Tyr, and Trp oxidations. The method presented will be useful in discovering co- and posttranslational modifications of proteins.
Lysine-scanning Mutagenesis Reveals an Amendable Face of the Cyclotide Kalata B1 for the Optimization of Nematocidal Activity (2010)

Cyclotides are a family of macrocyclic peptides that combine the unique features of a head-to-tail cyclic backbone and a cystine knot motif, the combination of which imparts them with extraordinary stability. The prototypic cyclotide kalata B1 is toxic against two economically important gastrointestinal nematode parasites of sheep, Haemonchus contortus and Trichostrongylus colubriformis. A lysine scan was conducted to examine the effect of the incorporation of positive charges into the kalata B1 cyclotide framework. Each of the non-cysteine residues in this 29-amino acid peptide was successively substituted with lysine, and the nematocidal and hemolytic activities of the suite of mutants were determined. Substitution of 11 residues within kalata B1 decreased the nematocidal activity dramatically. On the other hand, six other residues that are clustered on the surface of kalata B1 were tolerant to Lys substitution, and indeed the introduction of positively charged residues into this region increased nematocidal activity. This activity was increased further in double and triple lysine mutants, with a maximal increase (relative to the native kalata B1) of 13-fold obtained with a triple lysine mutant (mutated at positions Thr-20, Asn-29, and Gly-1). Hemolytic activity correlated with the nematocidal activity of all lysine mutants. Our data clearly highlight the residues crucial for nematocidal and hemolytic activity in cyclotides, and demonstrate that the nematocidal activity of cyclotides can be increased by incorporation of basic amino acids.
Abstract 14813: Pre-Treatment With Thienopyridines Reduces The Amount of Myonecrosis in Acute Coronary Syndrome Patients Invasively Managed: Insights from the CHAMPION trials (2010)

Introduction: Clopidogrel pretreatment is beneficial in acute coronary syndrome (ACS) patients managed invasively but its effect on the extent of myonecrosis after PCI has not been explored. We inv...
Emission spectra of single quantum well lasers with inhomogeneous current injection (1988)

Emission spectra of a tandem-type GaAs single quantum well laser diode were investigated under pulsed operating conditions. By controlling the two injection current levels, we could force the device to operate not only at the lowest (n=1) quantized state transition but also at the second (n=2) transition. Anomalous pulse responses, moreover, were found for the two lasing modes which were simultaneously observed in time-integrated spectra. The dynamic emission behavior was utilized to achieve a variety of intensity combinations of the two radiation modes at the widely different wavelengths.
New polyacrylamide gel‐based methods of sample preparation for optical microscopy: immobilization of DNA molecules for optical mapping (1996)

New methods have been developed for rapid immobilization of biological macromolecules and other microscopic objects from aqueous solution at gel/gel, gel/solid and gel/solution interfaces using thin polyacrylamide gels covalently bound to glass surfaces. When quickly spread over a dry gel, an aqueous sample loses most of its water and low-molecular-weight solutes due to migration of these components into the gel. All optically observable objects thus become concentrated at the gel surface and may be easily located by light microscopy. Based on this, a procedure for binding DNA at a positively charged gel/solution interface was developed. A mild immobilization of the DNA molecules was obtained, allowing 'all in focus' observations of DNA digestion by restriction endonucleases with an apparent rate close to that in solution.