gebhart/patrepeval huggingface dataset:
Detection of the ageing-associated 5-Kb common deletion of mitochondrial DNA in blood and bone marrow of hematologically normal adults. Absence of the deletion in clonal bone marrow disorders. (1995)

In recent years, a variety of chronic degenerative diseases that mainly involve brain, heart and muscle have been shown to result from mutations in mitochondrial DNA (mtDNA). A 4977-bp deletion (mtDNA-4977, also known as the common deletion) is the most frequent abnormality in patients with mitochondrial myopathies. A low percentage of mtDNA-4977 is also found in various tissues of normal ageing individuals. Accumulation of this deletion as well as other mtDNA deletions and point mutations is thought to contribute to normal cell ageing. We examined blood and bone marrow samples of 63 hematologically normal patients undergoing sternotomy for cardiac surgery. Using short-cycle PCR, which favors the amplification of molecules carrying large deletions, we detected the common deletion in 22 (35%) of the patients. In one of the probands, a hitherto unknown 4867-bp deletion was identified (nt 8561-13429). In each sample the percentage of mtDNA-4977 was very low, since detection always required primer-shift reamplification of a primary PCR product. Because mtDNA molecules with large deletions are known to be progressively enriched through their tendency to replicate more rapidly than full-size mtDNA, the small amount of mtDNA-4977 detected is likely to be concentrated in a small fraction of cells. The common deletion was not detectable in 20 patients with myelodysplastic syndromes (MDS), 20 patients with acute myeloid leukemia (AML), and 10 patients with chronic myeloid leukemia (CML). The seeming paradox of detectability of mtDNA-4977 in hematologically normal individuals and its absence in clonal myeloid disorders is explained by varying selection against self-renewing stem cells harboring the common deletion. Selection appears to be effective under circumstances of proliferative stress (eg among continuously proliferating stem cells in clonal hematopoiesis), whereas in normal steady-state hematopoiesis, affected stem cells persist because they are rarely recruited into cell cycle and can thus tolerate mitochondrial dysfunction.
Biophysical Characterisation of Neuroglobin of the Icefish, a Natural Knockout for Hemoglobin and Myoglobin. Comparison with Human Neuroglobin (2012)

The Antarctic icefish Chaenocephalus aceratus lacks the globins common to most vertebrates, hemoglobin and myoglobin, but has retained neuroglobin in the brain. This conserved globin has been cloned, over-expressed and purified. To highlight similarities and differences, the structural features of the neuroglobin of this colourless-blooded fish were compared with those of the well characterised human neuroglobin as well as with the neuroglobin from the retina of the red blooded, hemoglobin and myoglobin-containing, closely related Antarctic notothenioid Dissostichus mawsoni. A detailed structural and functional analysis of the two Antarctic fish neuroglobins was carried out by UV-visible and Resonance Raman spectroscopies, molecular dynamics simulations and laser-flash photolysis. Similar to the human protein, Antarctic fish neuroglobins can reversibly bind oxygen and CO in the Fe(2+) form, and show six-coordination by distal His in the absence of exogenous ligands. A very large and structured internal cavity, with discrete docking sites, was identified in the modelled three-dimensional structures of the Antarctic neuroglobins. Estimate of the free-energy barriers from laser-flash photolysis and Implicit Ligand Sampling showed that the cavities are accessible from the solvent in both proteins.Comparison of structural and functional properties suggests that the two Antarctic fish neuroglobins most likely preserved and possibly improved the function recently proposed for human neuroglobin in ligand multichemistry. Despite subtle differences, the adaptation of Antarctic fish neuroglobins does not seem to parallel the dramatic adaptation of the oxygen carrying globins, hemoglobin and myoglobin, in the same organisms.
Compiling scheme to JVM bytecode: (2002)

We have added a Java virtual machine (henceforth JVM) bytecode generator to the optimizing Scheme-to-C compiler Bigloo. We named this new compiler BiglooJVM. We have used this new compiler to evaluate how suitable the JVM bytecode is as a target for compiling strict functional languages such as Scheme. In this paper, we focus on the performance issue. We have measured the execution time of many Scheme programs when compiled to C and when compiled to JVM. We found that for each benchmark, at least one of our hardware platforms ran the BiglooJVM version in less than twice the time taken by the Bigloo version. In order to deliver fast programs the generated JVM bytecode must be carefully crafted in order to benefit from the speedup of just-in-time compilers.
Rolling Bearing Analysis Codes “BRAIN” - The Estimation of Rolling Bearing Performance for an Automotive Application (1997)

<div class="htmlview paragraph">A computer program package named “BRAIN” has been developed to simulate the kinematics and the performance of rolling bearings under various running conditions. The calculation time necessary for running BRAIN software on a PC is very short. Various outputs can be obtained using BRAIN such as running torque, roller skew angle, roller slippage, and PV values.</div> <div class="htmlview paragraph">Several experiments have been conducted to confirm the validity of BRAIN. The running torque of a four point contact ball bearing and that of a tapered roller bearing were measured. In addition, the skew of the roller in a needle bearing was measured. These experimental results were compared with the calculation results. The experiments and the calculations showed good agreement.</div>
Sustained Release of Engineered Stromal Cell–Derived Factor 1-α From Injectable Hydrogels Effectively Recruits Endothelial Progenitor Cells and Preserves Ventricular Function After Myocardial Infarction (2013)

We have developed a hydrogel delivery system that sustains the release of a bioactive endothelial progenitor cell chemokine during a 4-week period that preserves ventricular function in a rat model of myocardial infarction.
A Chlorophyll a/b-Binding Protein Gene from Soybean (Glycine max [L.] Merr.) (1994)

ular characterization of two clusters of genes encoding the type I CAB polypeptides of PSII in Nicotinnn plumbaginifolia. Plant Mo1
Involvement of the alternative oxidase in respiration of<i>Yarrowia lipolytica</i>mitochondria is controlled by the activity of the cytochrome pathway (2002)

The degree of involvement of cyanide-resistant alternative oxidase in the respiration of Yarrowia lipolytica mitochondria was evaluated by comparing the rate of oxygen consumption in the presence of cyanide, which shows the activity of the cyanide-resistant alternative oxidase, and the oxidation rate of cytochrome c by ferricyanide, which shows the activity of the main cytochrome pathway. The oxidation of succinate by mitochondria in the presence of ferricyanide and cyanide was associated with oxygen consumption due to the functioning of the alternative oxidase. The subsequent addition of ADP or FCCP (an uncoupler of oxidative phosphorylation) completely inhibited oxygen consumption by the mitochondria. Under these conditions, the inhibition of the alternative oxidase by benzohydroxamic acid (BHA) failed to affect the reduction of ferricyanide at the level of cytochrome c. BHA did not influence the rate of ferricyanide reduction by the cytochrome pathway occurring in controlled state 4, nor could it change the phosphorylation quotient ATP/O upon the oxidation of various substrates. These data indicate that the alternative system is unable to compete with the cytochrome respiratory chain for electrons. The alternative oxidase only transfers the electrons that are superfluous for the cytochrome respiratory chain.
Characteristics of a multidipole ion source (1978)

The properties of a steady-state, dc discharge multidipole ion source have been investigated. The plasma density in the source depends on the magnet geometries, the discharge voltage, and the bias voltage on the first extraction grid. Different schemes to reduce the loss of ions to the chamber wall are described. Hydrogen ion species in the extracted beam are studied by a mass analyzer.
HIF-1 Modulates Dietary Restriction-Mediated Lifespan Extension via IRE-1 in Caenorhabditis elegans (2009)

Dietary restriction (DR) extends lifespan in various species and also slows the onset of age-related diseases. Previous studies from flies and yeast have demonstrated that the target of rapamycin (TOR) pathway is essential for longevity phenotypes resulting from DR. TOR is a conserved protein kinase that regulates growth and metabolism in response to nutrients and growth factors. While some of the downstream targets of TOR have been implicated in regulating lifespan, it is still unclear whether additional targets of this pathway also modulate lifespan. It has been shown that the hypoxia inducible factor-1 (HIF-1) is one of the targets of the TOR pathway in mammalian cells. HIF-1 is a transcription factor complex that plays key roles in oxygen homeostasis, tumor formation, glucose metabolism, cell survival, and inflammatory response. Here, we describe a novel role for HIF-1 in modulating lifespan extension by DR in Caenorhabditis elegans. We find that HIF-1 deficiency results in extended lifespan, which overlaps with that by inhibition of the RSKS-1/S6 kinase, a key component of the TOR pathway. Using a modified DR method based on variation of bacterial food concentrations on solid agar plates, we find that HIF-1 modulates longevity in a nutrient-dependent manner. The hif-1 loss-of-function mutant extends lifespan under rich nutrient conditions but fails to show lifespan extension under DR. Conversely, a mutation in egl-9, which increases HIF-1 activity, diminishes the lifespan extension under DR. This deficiency is rescued by tissue-specific expression of egl-9 in specific neurons and muscles. Increased lifespan by hif-1 or DR is dependent on the endoplasmic reticulum (ER) stress regulator inositol-requiring protein-1 (IRE-1) and is associated with lower levels of ER stress. Therefore, our results demonstrate a tissue-specific role for HIF-1 in the lifespan extension by DR involving the IRE-1 ER stress pathway.
Characterization of the Viral Microbiome in Patients with Severe Lower Respiratory Tract Infections, Using Metagenomic Sequencing (2012)

The human respiratory tract is heavily exposed to microorganisms. Viral respiratory tract pathogens, like RSV, influenza and rhinoviruses cause major morbidity and mortality from respiratory tract disease. Furthermore, as viruses have limited means of transmission, viruses that cause pathogenicity in other tissues may be transmitted through the respiratory tract. It is therefore important to chart the human virome in this compartment. We have studied nasopharyngeal aspirate samples submitted to the Karolinska University Laboratory, Stockholm, Sweden from March 2004 to May 2005 for diagnosis of respiratory tract infections. We have used a metagenomic sequencing strategy to characterize viruses, as this provides the most unbiased view of the samples. Virus enrichment followed by 454 sequencing resulted in totally 703,790 reads and 110,931 of these were found to be of viral origin by using an automated classification pipeline. The snapshot of the respiratory tract virome of these 210 patients revealed 39 species and many more strains of viruses. Most of the viral sequences were classified into one of three major families; Paramyxoviridae, Picornaviridae or Orthomyxoviridae. The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin.
Toward a Confocal Subcellular Atlas of the Human Proteome (2007)

Information on protein localization on the subcellular level is important to map and characterize the proteome and to better understand cellular functions of proteins. Here we report on a pilot study of 466 proteins in three human cell lines aimed to allow large scale confocal microscopy analysis using protein-specific antibodies. Approximately 3000 high resolution images were generated, and more than 80% of the analyzed proteins could be classified in one or multiple subcellular compartment(s). The localizations of the proteins showed, in many cases, good agreement with the Gene Ontology localization prediction model. This is the first large scale antibody-based study to localize proteins into subcellular compartments using antibodies and confocal microscopy. The results suggest that this approach might be a valuable tool in conjunction with predictive models for protein localization.
Self-Illuminating <sup>64</sup>Cu-Doped CdSe/ZnS Nanocrystals for in Vivo Tumor Imaging (2014)

Construction of self-illuminating semiconducting nanocrystals, also called quantum dots (QDs), has attracted much attention recently due to their potential as highly sensitive optical probes for biological imaging applications. Here we prepared a self-illuminating QD system by doping positron-emitting radionuclide (64)Cu into CdSe/ZnS core/shell QDs via a cation-exchange reaction. The (64)Cu-doped CdSe/ZnS QDs exhibit efficient Cerenkov resonance energy transfer (CRET). The signal of (64)Cu can accurately reflect the biodistribution of the QDs during circulation with no dissociation of (64)Cu from the nanoparticles. We also explored this system for in vivo tumor imaging. This nanoprobe showed high tumor-targeting ability in a U87MG glioblastoma xenograft model (12.7% ID/g at 17 h time point) and feasibility for in vivo luminescence imaging of tumor in the absence of excitation light. The availability of these self-illuminating integrated QDs provides an accurate and convenient tool for in vivo tumor imaging and detection.
Identification of CD34+ and CD34− leukemia-initiating cells in MLL-rearranged human acute lymphoblastic leukemia (2014)

Translocation of the mixed-lineage leukemia (MLL) gene with AF4, AF9, or ENL results in acute leukemia with both lymphoid and myeloid involvement. We characterized leukemia-initiating cells (LICs) in primary infant MLL-rearranged leukemia using a xenotransplantation model. In MLL-AF4 patients, CD34(+)CD38(+)CD19(+) and CD34(-)CD19(+) cells initiated leukemia, and in MLL-AF9 patients, CD34(-)CD19(+) cells were LICs. In MLL-ENL patients, either CD34(+) or CD34(-) cells were LICs, depending on the pattern of CD34 expression. In contrast, in patients with these MLL translocations, CD34(+)CD38(-)CD19(-)CD33(-) cells were enriched for normal hematopoietic stem cells (HSCs) with in vivo long-term multilineage hematopoietic repopulation capacity. Although LICs developed leukemic cells with clonal immunoglobulin heavy-chain (IGH) rearrangement in vivo, CD34(+)CD38(-)CD19(-)CD33(-) cells repopulated recipient bone marrow and spleen with B cells, showing broad polyclonal IGH rearrangement and recipient thymus with CD4(+) single positive (SP), CD8(+) SP, and CD4(+)CD8(+) double-positive (DP) T cells. Global gene expression profiling revealed that CD9, CD32, and CD24 were over-represented in MLL-AF4, MLL-AF9, and MLL-ENL LICs compared with normal HSCs. In patient samples, these molecules were expressed in CD34(+)CD38(+) and CD34(-) LICs but not in CD34(+)CD38(-)CD19(-)CD33(-) HSCs. Identification of LICs and LIC-specific molecules in primary human MLL-rearranged acute lymphoblastic leukemia may lead to improved therapeutic strategies for MLL-rearranged leukemia.
Using Stochastic Sampling to Create Depth-of-Field Effect in Real-Time Direct Volume Rendering (2020)

Real-time visualization of volumetric data is increasingly used by physicians and scientists. Enhanced depth perception in Direct Volume Rendering (DVR) plays a crucial role in applications such as clinical decision making. Our goal is to devise a flexible blurring method in DVR and ultimately improve depth perception in real-time DVR using synthetic depth of field (DoF) effect. We devised a permutation-based stochastic sampling method for ray casting to render images with DoF effect. Our method uses 2D blurring kernels in 3D space for each sample on a ray. Furthermore, we reduce the number of required samples for each kernel of size n 2 from n 2 to only 2 samples. This method is flexible and can be used for DoF, focus-context blurring, selective blurring, and potentially for other photographic effects such as the tilt effect.
Reading on Smart Glasses (2018)

Smart glasses are increasingly being used in professional contexts. Having key applications such as short messaging and newsreader, they enable continuous access to textual information. In particular, smart glasses allow reading while performing other activities as they do not occlude the user's world view. For efficient reading, it is necessary to understand how a text should be presented on them. We, therefore, conducted a study with 24 participants using a Microsoft HoloLens to investigate how to display text on smart glasses while walking and sitting. We compared text presentation in the top-right, center, and bottom-center positions with Rapid Serial Visual Presentation (RSVP) and line-by-line scrolling. We found that text displayed in the top-right of smart glasses increases subjective workload and reduces comprehension. RSVP yields higher comprehension while sitting. Conversely, reading with scrolling yields higher comprehension while walking. Insights from our study inform the design of reading interfaces for smart glasses.
Pincer Thioamide and Pincer Thioimide Palladium Complexes Catalyze Highly Efficient Negishi Coupling of Primary and Secondary Alkyl Zinc Reagents at Room Temperature (2008)

Abstract Pincer thioamide Pd II complex 2 was prepared, and its reaction with cyclohexylzinc chloride yielded novel pincer thioimide Pd II complex 3 besides Pd 0 species. The structures of complexes 2 and 3 were confirmed by X‐ray analysis. Both complexes are efficient catalysts for Negishi couplings involving primary and secondary alkyl zinc reagents bearing β‐hydrogen atoms. At a concentration of 0.1–0.5 mol % both catalysts readily promoted reactions at room temperature or even at 0 °C. The operational simplicity of these processes, in conjunction with the easy accessibility of both catalysts and substrates, promises synthetic utility of this new methodology. An experiment on a scale of 19.35 g carried out at very low catalyst loading of 2 (turnover number: 6 100 000) highlighted the potential application of the catalytic system. Monoalkyl and dialkyl zinc reagents displayed different reactivities and selectivities in reactions with aryl iodides catalyzed by complexes 2 or 3 , and isomerization in reactions involving acyclic secondary alkyl zinc derivatives was suppressed by using appropriate amounts of dialkyl zinc reagents. Based on preliminary kinetic profiles and reaction evidence, three possible pathways are proposed for the reactions involving acyclic secondary alkyl zinc reagents to rationalize the difference between mono‐alkyl and dialkyl zinc derivatives.
Reshaping Your Business With Web 2.0 (2008)

Integrate Web 2.0 trends and technologies into the enterprise

Written by a team of experts from the Web 2.0 community and Oracle Corporation, this innovative guide provides a blueprint for leveraging the new culture of participation in an enterprise environment. Reshaping Your Business with Web 2.0 offers proven strategies for the successful adoption of an enterprise 2.0 paradigm and covers the technical solutions that best apply in specific situations. You will find clear guidelines for using Web 2.0 technologies and standards in a productive way to align with business goals, increase efficiency, and provide measurable bottom line growth.

Foster collaboration and accelerate information dissemination with blogs and wikis
Implement folksonomic strategies to achieve business intelligence, analytics, and semantic web goals
Capture and broadcast connection graphs and activity streams via social networks
Bring together application data, business analytics, unstructured information, and collaborative interactions in enterprise mashups
Enable rich Internet applications with Ajax, Ruby on Rails, Flash, FLEX, and other technologies
Connect your Web 2.0 ecosystem through Web services, such as REST and JSON
Ensure security and compliance management


 

Table of contents
Foreword
Introduction
Part 1: The Behaviors
Chapter 1: Participation Culture: Opportunities and Pitfalls
Chapter 2: Many Voices: We're All Publishers
Chapter 3: The Power of Crowds: Varieties of Collaboration
Chapter 4: Social Networking: Discriminating Connectedness
Part 2: The Technologies
Chapter 5: Mashups: A Behavior and a Technology
Chapter 6: AJAX and Beyond: Merging the Desktop with the Web
Chapter 7: The APIs: Interfaces and Ecosystems
Chapter 8: Security and Compliance: Maintaining Control While Providing Flexibility
Part III: Best Practices
Chapter 9: Putting Web 2.0 to Use in the Enterprise: Higher Value From Greater Participation
Chapter 10: The Semantic Web: New Paradigms and the Future
References
Index
Transmission des informations numériques et phoniques entre une haveuse et la surface (1994)

National audience
Sensitivity and specificity of the ImPACT Test Battery for concussion in athletes (2005)

This study explored the diagnostic utility of the composite scores of Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) and Post Concussion Symptom Scale scores (PCSS). Recently concussed high school athletes (N=72) were tested within 72 h of sustaining a concussion, and data were compared to non-concussed high school athletes with no history of concussion (N=66). Between-groups MANOVA revealed a significant multivariate effect of concussion on test performance (p<.001); univariate ANOVAS revealed all six measures contributed to the between-groups differences. A discriminant function analyses was conducted to measure the ability of the five ImPACT composite scores, as well as the PCSS to classify concussion status. One discriminant function was identified that consisted of the Visual Memory, Processing Speed, and Impulse Control composite scores PCSS, which correctly classified 85.5% of the cases. Approximately 82% of participants in the concussion group and 89% of participants in the control group were correctly classified. Using these data, the sensitivity of ImPACT was 81.9%, and the specificity was 89.4%. As part of a formal concussion management program, ImPACT is a useful tool for the assessment of the neurocognitive and neurobehavioral sequelae of concussion, and can also provide post-injury cognitive and symptom data that can assist a practitioner in making safer return to play decisions.
USE OF EXTRACT OF THE SUPRARENAL CORTEX IN PYOGENIC INFECTIONS (1934)

The suprarenal gland is a composite structure consisting of two entirely distinct systems of tissue that differ both phylogenetically and ontogenetically. In the selachians the medulla and cortex are separate glands, the latter appearing as the interrenal body. In the higher vertebrates the cortex develops from the celomic epithelium near the germinal ridge and comes to lie between the wolffian body and the aorta. The medulla is derived from the cells of the ganglionic germ layer of the sympathetic nervous system that wander into the folds of the cortical substance. Morphologically and embryologically the cortex and medulla differ widely, and it was apparent to many investigators that they must differ as widely in function. By removing the interrenal body from members of the order Selachii (shark and skates), Biedl<sup>1</sup>was the first to demonstrate that the cortical substance is essential to life. Wheeler and Vincent,<sup>2</sup>Houssay and Lewis,