gebhart/patrepeval huggingface dataset:
In Vivo and Scanning Electron Microscopy Imaging of Upconverting Nanophosphors in<i>Caenorhabditis</i><i>elegans</i> (2005)

We show here that upconversion phosphors can be imaged both by infrared excitation and in a scanning electron microscope. We have synthesized and characterized for this work up-converting phosphor nanoparticles nonaggregated nanocrystals of size range 50-200 nm. We have investigated the optical properties of 50-200 nm nanoparticles and found a square dependence of the emitted visible fluorescence on the infrared excitation and verified that under electron excitation similar narrow band emission spectra can be obtained as is seen with IR upconversion. The viability of the nanoparticles for biological imaging was confirmed by imaging the digestive system of the nematode worm Caenorhabditis elegans, and we have confirmed using energy-dispersive X-ray analysis that the up-conversion nanoparticles can be identified in a scanning electron microscope at high spatial resolution.
GENEALOGY OF PRINCIPAL STRAINS OF THE YEAST GENETIC STOCK CENTER (1986)

We have constructed a genealogy of strain S288C, from which many of the mutant and segregant strains currently used in studies on the genetics and molecular biology of Saccharomyces cerevisiae have been derived. We have determined that its six progenitor strains were EM93, EM126, NRRL YB-210 and the three baking strains Yeast Foam, FLD and LK. We have estimated that approximately 88% of the gene pool of S288C is contributed by strain EM93. The principal ancestral genotypes were those of segregant strains EM93-1C and EM93-3B, initially distributed by C. C. Lindegren to several laboratories. We have analyzed an isolate of lyophilized culture of strain EM93 and determined its genotype as MATa/MAT alpha SUC2/SUC2 GAL2/gal2 MAL/MAL mel/mel CUP1/cup1 FLO1/flo1. Strain EM93 is therefore the probable origin of genes SUC2, gal2, CUP1 and flo1 of S288C. We give details of the current availability of several of the progenitor strains and propose that this genealogy should be of assistance in elucidating the origins of several types of genetic and molecular heterogeneities in Saccharomyces.
Evolutionary origins of eukaryotic sodium/proton exchangers (2005)

More than 200 genes annotated as Na+/H+ hydrogen exchangers (NHEs) currently reside in bioinformation databases such as GenBank and Pfam. We performed detailed phylogenetic analyses of these NHEs in an effort to better understand their specific functions and physiological roles. This analysis initially required examining the entire monovalent cation proton antiporter (CPA) superfamily that includes the CPA1, CPA2, and NaT-DC families of transporters, each of which has a unique set of bacterial ancestors. We have concluded that there are nine human NHE (or SLC9A) paralogs as well as two previously unknown human CPA2 genes, which we have named HsNHA1 and HsNHA2. The eukaryotic NHE family is composed of five phylogenetically distinct clades that differ in subcellular location, drug sensitivity, cation selectivity, and sequence length. The major subgroups are plasma membrane (recycling and resident) and intracellular (endosomal/TGN, NHE8-like, and plant vacuolar). HsNHE1, the first cloned eukaryotic NHE gene, belongs to the resident plasma membrane clade. The latter is the most recent to emerge, being found exclusively in vertebrates. In contrast, the intracellular clades are ubiquitously distributed and are likely precursors to the plasma membrane NHE. Yeast endosomal ScNHX1 was the first intracellular NHE to be described and is closely related to HsNHE6, HsNHE7, and HsNHE9 in humans. Our results link the appearance of NHE on the plasma membrane of animal cells to the use of the Na+/K(+)-ATPase to generate the membrane potential. These novel observations have allowed us to use comparative biology to predict physiological roles for the nine human NHE paralogs and to propose appropriate model organisms in which to study the unique properties of each NHE subclass.
How accurate are Stoney’s equation and recent modifications (2000)

Stoney’s equation has been—and still is—extensively used to evaluate the macrostress acting in a coating deposited on a thick substrate. In principle, the formula applies only in the “thin-film approximation,” that is, for coatings much thinner than the substrate. The main purpose of this communication is to demonstrate that, based on a general theory of elastic interactions in multilayer laminates, the correct formula for the stress can be expressed in terms of Stoney’s equation and a correction factor equal to (1+γ δ3)/(1+δ), where γ designates the ratio of the biaxial moduli and δ is the ratio of the layer thicknesses. In this light, it is shown that (a) Stoney’s equation does not cause serious errors for thickness ratios δ⩽0.1; (b) Atkinson’s recently proposed modification, which does not require information on the coating’s modulus, yields much improved results for thickness ratios up to δ≃0.4; and (c) Brenner–Senderoff-type expressions can be very misleading and should be avoided.
Specific Metal‐Catalysed Protein Oxidation Reactions in Chronic Degenerative Disorders of Ageing: Focus on Alzheimer's Disease and Age‐Related Cataracts (2001)

Abnormalities of protein aggregation and deposition may play an important role in the pathophysiology of a diverse set of chronically progressive degenerative disorders including Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease and age-related cataracts. We propose that aberrant metalloprotein reactions may be a common denominator in these diseases. In these instances, an abnormal reaction between a protein and redox active metal ions (especially copper or iron) promotes the generation of reactive oxygen species, and possibly, protein radicalization. These products then lead to chemical modification of the protein, alterations in protein structure and solubility, and oxidative damage to surrounding tissue. In this review, we explore these ideas by focusing on two common diseases of ageing, Alzheimer's disease and age-related cataracts. Understanding the metalloprotein biochemistry in both diseases may lead to a better understanding of the underlying pathophysiology in both disorders and suggest novel targets for therapeutic agents.
Microscopy and viscometry of blood flowing under uniform shear rate(rheoscopy) (1969)

Transparent cone and plate in a Wells-Brookfield LVT viscometer allow direct microscopic observation ( x 60–400 magnification) of blood flowing under specific rates of shear (0.6–1,380 set –1 ) while simultaneously measuring shear stress. The viscometer is placed on the stage of an inverted microscope; observation in bright-field and dark-field illumination is made through a thin optical quartz inserted in the plate. The range of shear rates is extended by the use of different cone angles and can be adapted to any desired level by driving the viscometer motor with a sine-wave generator with variable output. The use of the instrument confirmed recent theories about the role of reversible red cell aggregation upon the rheology of blood at low shear rates. The influence of quantified flow forces on reversible red cell aggregation and irreversible platelet aggregation can be examined directly. blood rheology; microscopy of blood flow; platelet aggregation; red cell aggregation Submitted on August 5, 1968
Salamander: a push-based distribution substrate for internet applications (1997)

The Salamander distribution system is a widearea network data dissemination substrate that has been used daily for overayear by several groupware and webcasting Internet applications. Speci-cally, Salamander is designed to support push-based applications and provides a variety of delivery semantics. These semantics range from basic data delivery, used by the Internet Performance Measurement and Analysis (IPMA) project, to collaborative group communication used by the Upper Atmospheric Research Collaboratory (UARC) project. The Salamander substrate is designed to accommodate the large variation in Internet connectivity and client resources through the use of applicationspeci
Molecular cloning and expression of cDNA encoding rat skeletal muscle cytosolic sialidase. (1993)

We have isolated a cDNA clone encoding the cytosolic sialidase of rat skeletal muscle. Degenerate oligonucleotides, based on amino acid sequence data for the purified enzyme, were used as primers to amplify fragments of the gene from rat skeletal muscle cDNA by the polymerase chain reaction. The amplified cDNA fragment was then applied as probe to screen a rat skeletal muscle cDNA library. The longest cDNA clone thus isolated was incomplete at the 5'-end, and therefore an amplified cDNA from the 5'-end portion of the gene was further generated by polymerase chain reaction. These two cDNAs were used to construct a cDNA encoding the entire sequence of rat sialidase. The composite sequence encodes an open reading frame of 379 amino acids that include all sequenced peptides. Although the deduced amino acid sequence is not largely similar to those of bacterial and parasite sialidases, it contains two Asp blocks, the conserved sequence of the sialidases from these microorganisms. When the cDNA was inserted into an expression vector followed by transformation in Escherichia coli, sialidase activity appeared in the cell extract. The sialidase could be completely immunoprecipitated by antiserum against the cytosolic sialidase of rat skeletal muscle.
A synchrotron radiation microtomography system for the analysis of trabecular bone samples (1999)

X-ray computed microtomography is particularly well suited for studying trabecular bone architecture, which requires three-dimensional (3-D) images with high spatial resolution. For this purpose, we describe a three-dimensional computed microtomography (microCT) system using synchrotron radiation, developed at ESRF. Since synchrotron radiation provides a monochromatic and high photon flux x-ray beam, it allows high resolution and a high signal-to-noise ratio imaging. The principle of the system is based on truly three-dimensional parallel tomographic acquisition. It uses a two-dimensional (2-D) CCD-based detector to record 2-D radiographs of the transmitted beam through the sample under different angles of view. The 3-D tomographic reconstruction, performed by an exact 3-D filtered backprojection algorithm, yields 3-D images with cubic voxels. The spatial resolution of the detector was experimentally measured. For the application to bone investigation, the voxel size was set to 6.65 microm, and the experimental spatial resolution was found to be 11 microm. The reconstructed linear attenuation coefficient was calibrated from hydroxyapatite phantoms. Image processing tools are being developed to extract structural parameters quantifying trabecular bone architecture from the 3-D microCT images. First results on human trabecular bone samples are presented.
The role of myostatin in muscle wasting: an overview (2011)

Myostatin is an extracellular cytokine mostly expressed in skeletal muscles and known to play a crucial role in the negative regulation of muscle mass. Upon the binding to activin type IIB receptor, myostatin can initiate several different signalling cascades resulting in the upregulation of the atrogenes and downregulation of the important for myogenesis genes. Muscle size is regulated via a complex interplay of myostatin signalling with the insulin-like growth factor 1/phosphatidylinositol 3-kinase/Akt pathway responsible for increase in protein synthesis in muscle. Therefore, the regulation of muscle weight is a process in which myostatin plays a central role but the mechanism of its action and signalling cascades are not fully understood. Myostatin upregulation was observed in the pathogenesis of muscle wasting during cachexia associated with different diseases (i.e. cancer, heart failure, HIV). Characterisation of myostatin signalling is therefore a perspective direction in the treatment development for cachexia. The current review covers the present knowledge about myostatin signalling pathways leading to muscle wasting and the state of therapy approaches via the regulation of myostatin and/or its downstream targets in cachexia.
FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms (2012)

Quantitative and systems biology approaches benefit from the unprecedented depth of next-generation sequencing. A typical experiment yields millions of short reads, which oftentimes carry particular sequence tags. These tags may be: (a) specific to the sequencing platform and library construction method (e.g., adapter sequences); (b) have been introduced by experimental design (e.g., sample barcodes); or (c) constitute some biological signal (e.g., splice leader sequences in nematodes). Our software FLEXBAR enables accurate recognition, sorting and trimming of sequence tags with maximal flexibility, based on exact overlap sequence alignment. The software supports data formats from all current sequencing platforms, including color-space reads. FLEXBAR maintains read pairings and processes separate barcode reads on demand. Our software facilitates the fine-grained adjustment of sequence tag detection parameters and search regions. FLEXBAR is a multi-threaded software and combines speed with precision. Even complex read processing scenarios might be executed with a single command line call. We demonstrate the utility of the software in terms of read mapping applications, library demultiplexing and splice leader detection. FLEXBAR and additional information is available for academic use from the website: http://sourceforge.net/projects/flexbar/.
Expression profiling by microarrays in colorectal cancer (Review) (2005)

Genome-wide gene profiling studies using microarrays have the potential to improve diagnosis and treatment of human cancers. Microarrays have identified many genes that are deregulated in colorectal cancer compared to normal tissue. Groups of genes that are predictive of tumor stage or presence of metastases, hence putatively associated with cancer progression have also been revealed. Microarray studies have identified genes whose expression are impacted by chemotherapies for colorectal cancer, thus could potentially be used to predict response to treatments. Unique gene expression profiles have also been used to classify metastases of uncertain origin. The wide application of microarrays generates exciting prospects in translational research. However, to date overlaps of candidate gene lists associated with specific clinical/biological phenotypes remain disturbingly poor between studies. Overfitting, bias, reporting of only the best results, and fidelity of probe annotations could present limitations for the interpretation of results shown in microarray publications. Making raw data from these microarray experiments publicly available for analysis by other investigators using different analytical algorithms or for in silico studies may facilitate the most thorough mining of data from these expensive studies. Validations of the results using other more precise techniques and at the biological level represent critical follow-up goals for microarray studies.
Frustrated Lewis Pair Inspired Carbon Dioxide Reduction by a Ruthenium Tris(aminophosphine) Complex (2012)

Frustrating ruthenium: the ruthenium complex 1 is shown to bind carbon dioxide or aldehyde in a manner similar to a frustrated Lewis pair. Compound 2 catalyzes the reduction of CO(2) in the presence of pinacolborane (HBpin), yielding MeOBpin and O(Bpin)(2) (Ru red, P orange, N green, O light red, C black).
Point-to-Point Protocol extensions for bridging (1991)

This document defines an extension of the Internet Point-to-Point
Protocol (PPP) described in RFC 1171, targeting the use of Point-to-
Point lines for Remote Bridging. [STANDARDS-TRACK]
FOLFIRINOX versus Gemcitabine for Metastatic Pancreatic Cancer (2011)

International audience
Leukemic stem cell persistence in chronic myeloid leukemia patients with sustained undetectable molecular residual disease (2011)

Sustained undetectable molecular residual disease (UMRD) is obtained in a minority of patients with chronic myeloid leukemia treated with tyrosine kinase inhibitors. It remains unclear whether these patients are definitively cured of their leukemia or whether leukemic stem cells (LSCs) persist in their BM. We have evaluated the presence of BCR-ABL-expressing marrow LSCs in 6 patients with chronic myeloid leukemia with sustained UMRD induced by IFN-α (n = 3), imatinib mesylate after IFN-α failure (n = 2), and dasatinib after imatinib intolerance (n = 1). Purified CD34(+) cells were used for clonogenic and long-term culture-initiating cell assays performed on classic or HOXB4-expressing MS-5 feeders. Using this strategy, we identified BCR-ABL-expressing LSCs in all patients. Interestingly, long-term culture-initiating cell assays with MS-5/HOXB4 stromal feeders increased detected numbers of LSCs in 3 patients. The relation between LSC persistency and a potential risk of disease relapse for patients with durable UMRD (on or off tyrosine kinase inhibitor therapy) warrants further investigation.
Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber (1995)

A bacterial spore was revived, cultured, and identified from the abdominal contents of extinct bees preserved for 25 to 40 million years in buried Dominican amber. Rigorous surface decontamination of the amber and aseptic procedures were used during the recovery of the bacterium. Several lines of evidence indicated that the isolated bacterium was of ancient origin and not an extant contaminant. The characteristic enzymatic, biochemical, and 16S ribosomal DNA profiles indicated that the ancient bacterium is most closely related to extant Bacillus sphaericus.
Scaling Distributed Machine Learning with the Parameter Server (2014)

Big data may contain big values, but also brings lots of challenges to the computing theory, architecture, framework, knowledge discovery algorithms, and domain specific tools and applications. Beyond the 4-V or 5-V characters of big datasets, the data processing shows the features like inexact, incremental, and inductive manner. This brings new research opportunities to research community across theory, systems, algorithms, and applications. Is there some new "theory" for the big data? How to handle the data computing algorithms in an operatable manner? This report shares some view on new challenges identified, and covers some of the application scenarios such as micro-blog data analysis and data processing in building next generation search engines.
Role of Nuclear Architecture in Epigenetic Alterations in Cancer (2010)

It is widely accepted that cancer results from an array of epigenetic and genetic alterations, particularly aberrant epigenetic patterns that are a hallmark of every cancer type studied. Another well-known feature of cancer cells is the array of abnormalities in their nuclear structure. Although it is known that nuclear structure has an important role in the regulation of gene expression, we know little about the direct relationship between nuclear structural alterations and aberrant epigenetic patterns in cancer. Here, we discuss some of the recent studies from our lab and others to understand the relationship between alterations of nuclear architecture and aberrant epigenetic patterns in cancer cells. Although the precise relationship remains elusive, we suggest that changes in nuclear structure and composition could alter long-range genomic interactions and cause global epigenetic changes during tumorigenesis. We emphasize the need for further studies to elucidate the direct relationship between nuclear structure alterations and aberrant epigenetic patterns in cancers.
Analog design automation: Where are we? Where are we going? (2002)

A high-level survey of the state of CAD (computer-aided design) for analog and mixed-signal ICs is presented, focusing on synthesis-related work (cell-level and system-level synthesis). Both circuit synthesis and layout and system synthesis and layout are considered. Experimental results from some of the Carnegie Mellon University (CMU) tools in each niche of the analog CAD spectrum are used as concrete examples of what the author does (and does not yet) believe can be automated. It is noted that the growing presence of analog functions on chip and the market pressure to decrease design time for new mixed-signal ASICs (application-specific integrated circuits) have forced industry and academia to confront a range of challenging analog design automation problems. The author offers some opinions on how well he is doing and where he appears to be heading.
Complete remission through blast cell differentiation inPLZF/RARα-positive acute promyelocytic leukemia: in vitro and in vivo studies (2002)

Acute leukemia with the t(11;17) expressing the PLZF-RARalpha gene fusion is a rare variant of acute promyelocytic leukemia (APL) that has been associated with poor clinical response to all-trans retinoic acid (ATRA) treatment. However, some recent reports have put into question the absolute refractoriness of this leukemia to ATRA. We describe here a patient with PLZF/RARalpha APL who was treated at relapse with ATRA and low-dose hydroxyurea. Complete hematologic remission was obtained through differentiation of leukemic blasts, as proven by morphologic, immunophenophenotypic, and genetic studies carried out in sequential bone marrow samples. Moreover, in vitro studies indicated that blast differentiation was potentiated by the addition of the histone deacetylase inhibitor tricostatin A, but not of hydroxyurea, to ATRA. Our findings indicate that the maturation block may be overcome and terminal differentiation obtained in this leukemia subset and support the view that sensitivity/refractoriness of this form to ATRA should be revisited.
Verifying Haskell programs by combining testing and proving (2003)

We propose a method for improving confidence in the correctness of Haskell programs by combining testing and proving. Testing is used for debugging programs and specification before a costly proof attempt. During a proof development, testing also quickly eliminates wrong conjectures. Proving helps us to decompose a testing task in a way that is guaranteed to be correct. To demonstrate the method, we have extended the Agda/Alfa proof assistant for dependent type theory with a tool for random testing. As an example, we show how the correctness of a BDD-algorithm written in Haskell is verified by testing properties of component functions. We also discuss faithful translations from Haskell to type theory.
Derivation, characterization, and phenotypic variation of hepatic progenitor cell lines isolated from adult rats (2002)

Liver progenitor cells (LPCs) cloned from adult rat livers following allyl alcohol injury express hematopoietic stem cell and early hepatic lineage markers when cultured on feeder layers; under these conditions, neither mature hepatocyte nor bile duct, Ito, stellate, Kupffer cell, or macrophage markers are detected. These phenotypes have remained stable without aneuploidy or morphological transformation after more than 100 population doublings. When cultured without feeder layers, the early lineage markers disappear, and mature hepatocyte markers are expressed; mature hepatocytic differentiation and cell size are also augmented by polypeptide and steroidal growth factors. In contrast to hepatocytic potential, duct-like structures and biliary epithelial markers are expressed on Matrigel. Because they were derived without carcinogens or mutagens, these bipotential LPC lines provide novel tools for models of cellular plasticity and hepatocarcinogenesis, as well as lines for use in cellular transplantation, gene therapy, and bioreactor construction.