gebhart/patrepeval huggingface dataset:
External memory algorithms and data structures (2001)

Data sets in large applications are often too massive to fit completely inside the computers internal memory. The resulting input/output communication (or I/O) between fast internal memory and slower external memory (such as disks) can be a major performance bottleneck. In this article we survey the state of the art in the design and analysis of external memory (or EM) algorithms and data structures, where the goal is to exploit locality in order to reduce the I/O costs. We consider a variety of EM paradigms for solving batched and online problems efficiently in external memory. For the batched problem of sorting and related problems such as permuting and fast Fourier transform, the key paradigms include distribution and merging. The paradigm of disk striping offers an elegant way to use multiple disks in parallel. For sorting, however, disk striping can be nonoptimal with respect to I/O, so to gain further improvements we discuss distribution and merging techniques for using the disks independently. We also consider useful techniques for batched EM problems involving matrices (such as matrix multiplication and transposition), geometric data (such as finding intersections and constructing convex hulls), and graphs (such as list ranking, connected components, topological sorting, and shortest paths). In the online domain, canonical EM applications include dictionary lookup and range searching. The two important classes of indexed data structures are based upon extendible hashing and B-trees. The paradigms of filtering and bootstrapping provide a convenient means in online data structures to make effective use of the data accessed from disk. We also reexamine some of the above EM problems in slightly different settings, such as when the data items are moving, when the data items are variable-length (e.g., text strings), or when the allocated amount of internal memory can change dynamically. Programming tools and environments are available for simplifying the EM programming task. During the course of the survey, we report on some experiments in the domain of spatial databases using the TPIE system (transparent parallel I/O programming environment). The newly developed EM algorithms and data structures that incorporate the paradigms we discuss are significantly faster than methods currently used in practice.
Abstract 2085: Development of a novel targeted therapy for malignant mesothelioma carcinoma by a midkine inhibitor (2017)

Abstract Malignant pleural mesothelioma is an aggressive tumor of mesenchymal origin and is increasing worldwide as a result of widespread exposure to asbestos. The median survival of patients with mesothelioma from time of diagnosis ranges between 1 and 2 years. The mortality is expected to increase, at least until 2020, which is mainly due to the long latency (30-50 years) of the disease. Despite considerable advances in the understanding of its pathogenesis and etiology, malignant mesothelioma remains largely unresponsive to standard modalities of cancer therapy. Thus, there is an urgent need for new therapeutic options for mesothelioma.Midkine (MDK) is a heparin-binding growth factor that is highly expressed in many malignant tumors, including lung cancers. We have previously reported that a MDK inhibitor, iMDK, suppresses non-small cell lung cancer expressing MDK without harming normal cells. Importantly, iMDK inhibits the PI3 kinase / Akt pathway and induces apoptosis in MDK expressing non-small cell lung cancer cells. In the present study, we have investigated the antitumor effect of iMDK against malignant mesothelioma both in vitro and in vivo. 48 hours after treatment, iMDK dose-dependently inhibited cell growth of MDK expressing malignant mesothelioma cells. iMDK also suppressed colony formation of MSTO-211H mesothelioma cells. TUNEL positive cells were significantly increased in MSTO-211H cells 48 hours after iMDK treatment in a dose-dependent manner, confirming the induction of apoptosis in mesothelioma cells by iMDK. Combination treatment of iMDK and Bcl-2 inhibitor ABT-263 is more effective than each drug alone in MSTO-211H mesothelioma cells. Moreover, systemic administration of iMDK significantly inhibited tumor growth in a mesothelioma xenograft tumor in vivo. Inhibition of MDK with iMDK provides a potential therapeutic approach for the treatment of malignant mesothelioma that is driven by MDK. Citation Format: Takuya Fukazawa, Yuitaka Maeda, Tomoki Yamatsuji, Munenori Takaoka, Masakazu Yoshida, Naomasa Ishida, Miki Iwai, Etsuko Yokota, Takuro Yukawa, Minoru Haisa, Noriko Miyake, Tomoko Ikeda, Nagio Takigawa, Jeffery Whitsett, Yoshio Naomoto. Development of a novel targeted therapy for malignant mesothelioma carcinoma by a midkine inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2085. doi:10.1158/1538-7445.AM2017-2085
An approach to nonlinear inversion with applications to cross‐well EM tomography (1993)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1993An approach to nonlinear inversion with applications to cross‐well EM tomographyAuthors: Carlos Torres‐VerdinTarek M. HabashyCarlos Torres‐VerdinSchlumberger‐Doll Research and Tarek M. HabashySchlumberger‐Doll Researchhttps://doi.org/10.1190/1.1822483 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1822483FiguresReferencesRelatedDetailsCited ByApplication of a two-and-a-half dimensional model-based algorithm to crosswell electromagnetic data inversion24 June 2010 | Inverse Problems, Vol. 26, No. 7Metalliferous mining geophysics—State of the art in the last decade of the 20th century and the beginning of the new millenniumMisac N. Nabighian and Michael W. Asten24 May 2002 | GEOPHYSICS, Vol. 67, No. 3Monitoring saltwater injection using conductivity images obtained by electromagnetic cross-hole measurements7 December 2012 | Radio Science, Vol. 30, No. 5 SEG Technical Program Expanded Abstracts 1993ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1993 Pages: 1396 publication data© 1993 Copyright © 1993 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 10 Feb 2005 CITATION INFORMATION Carlos Torres‐Verdin and Tarek M. Habashy, (1993), "An approach to nonlinear inversion with applications to cross‐well EM tomography," SEG Technical Program Expanded Abstracts : 351-354. https://doi.org/10.1190/1.1822483 Plain-Language Summary PDF DownloadLoading ...
1.8 V Power Supply 16 Mb-MRAMs With 42.3% Array Efficiency (2006)

Technologies for realizing high density MRAM were developed. First, new circuitry to lower the resistance of programming wires was developed. Second, both MTJ plane shape and cross-sectional structure were optimized to lower the programming current. Based on these two technologies, 16 Mb MRAM was designed, fabricated with 130 nm CMOS process and 240 nm back end MTJ process. As a result, a 1.8 V power supply MRAM with 42.3% array efficiency was successfully demonstrated
Production of human glucocerebrosidase in mice after retroviral gene transfer into multipotential hematopoietic progenitor cells. (1989)

The human glucocerebrosidase (GC) gene has been transferred efficiently into spleen colony-forming unit (CFU-S) multipotential hematopoietic progenitor cells, and production of human GC RNA and protein has been achieved in transduced CFU-S colonies. High-titer retroviral vectors containing the human GC cDNA were constructed. Mouse bone marrow cells were stimulated with hematopoietic growth factors, infected by coculture with producer cells, and injected into lethally irradiated animals. Four vectors were compared with respect to gene-transfer efficiency into CFU-S progenitors. One vector (G vector) required high concentrations of interleukins 3 and 6 during stimulation and coculture for efficient transduction of CFU-S progenitors. The remaining three vectors (NTG, GTN, and GI vectors) transduced these progenitors at infection frequencies approaching 100% using low concentrations of hematopoietic growth factors to stimulate cell division prior to and during the infection. Vectors using the viral long terminal repeat enhancer/promoter to drive the human GC cDNA produced high levels of human GC RNA in the progeny of CFU-S progenitors after gene transfer. When an internal herpes simplex thymidine kinase promoter assisted by a mutant polyoma enhancer was used to drive the human GC cDNA (NTG vector), little or no human GC RNA was detected in transduced CFU-S colonies. All three vectors producing human GC RNA in CFU-S colonies can generate human GC as detected by immunochemical analysis of CFU-S colonies. NTG vector-infected bone marrow cells were transplanted into W/Wv recipients to generate long-term reconstituted mice. The capacity of the viral long terminal repeat and the internal thymidine kinase promoter to direct synthesis of RNA in transduced bone marrow and spleen cells 5 months after bone marrow transplantation reflected the performance of these promoters in NTG-transduced CFU-S colonies.
Electroanalytical Assessment of the Effect of Ni:Fe Stoichiometry and Architectural Expression on the Bifunctional Activity of Nanoscale NiyFe1–yOx (2017)

Electrocatalysis of the oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) was assessed for a series of Ni-substituted ferrites (Ni<sub>y</sub>Fe<sub>1-y</sub>Ox, where y = 0.1 to 0.9) as expressed in porous, high-surface-area forms (ambigel and aerogel nanoarchitectures). We then correlate electrocatalytic activity with Ni:Fe stoichiometry as a function of surface area, crystallite size, and free volume. In order to ensure in-series comparisons, calcination at 350 °C/air was necessary to crystallize the respective Ni<sub>y</sub>Fe<sub>1-y</sub>Ox nanoarchitectures, which index to the inverse spinel structure for Fe-rich materials (y ≤ 0.33), rock salt for the most Ni-rich material (y = 0.9), and biphasic for intermediate stoichiometry (0.5 ≤ y ≤ 0.67). In the intermediate Ni:Fe stoichiometric range (0.33 ≤ y ≤ 0.67), the OER current density at 390 mV increases monotonically with increasing Ni content and increasing surface area, but with different working curves for ambigels versus aerogels. At a common stoichiometry within this range, ambigels and aerogels yield comparable OER performance, but do so by expressing larger crystallite size (ambigel) versus higher surface area (aerogel). Effective OER activity can be achieved without requiring supercritical-fluid extraction as long as moderately high surface area, porous materials can be prepared. We find improved OER performance (η decreases from 390 to 373 mV) for Ni<sub>0.67</sub>Fe<sub>0.33</sub>Ox aerogel heat-treated at 300 °C/Ar, owing to an increase in crystallite size (2.7 to 4.1 nm). For the ORR, electrocatalytic activity favors Fe-rich Ni<sub>y</sub>Fe<sub>1-y</sub>Ox materials; however, as the Ni-content increases beyond y = 0.5, a two-electron reduction pathway is still exhibited, demonstrating that bifunctional OER and ORR activity may be possible by choosing a nickel ferrite nanoarchitecture that provides high OER activity with sufficient ORR activity. Assessing the catalytic activity requires an appreciation of the multivariate interplay among Ni:Fe stoichiometry, surface area, crystallographic phase, and crystallite size.
The Challenge of Drugging Undruggable Targets in Cancer: Lessons Learned from Targeting BCL-2 Family Members (2007)

The genomic and proteomic revolutions have provided us with an ever-increasing number of mechanistic insights into cancer pathogenesis. Mutated genes and pathologic protein products have emerged as the basis for modern anticancer drug development. With the increasing realization of the importance of disrupting oncogenic protein-protein interaction, new challenges have emerged for classical small molecule and protein-based drug modalities, i.e., the critical need to target flat and extended protein surfaces. Here, we highlight two distinct technologies that are being used to bridge the pharmacologic gap between small molecules and protein therapeutics. With the BCL-2 family of survival proteins as their substrate for intracellular targeting, we conclude that peptide stapling and fragment-based drug discovery show promise to traverse the critical surface features of proteins that drive human cancer.
Heterotypic Neuraminidase Antibodies Against Different A(H1N1) Strains are Elicited after Seasonal Influenza Vaccination (2019)

Neuraminidase (NA) content is not standardized in current seasonal influenza vaccines; neither anti-NA antibodies (anti-NA Abs) are measured nor is it well-defined as a correlate of humoral protection. In this work, the presence of NA1 antibodies against classical A(H1N1) and A(H1N1) pdm09 subtypes was studied before and after vaccination with seasonal vaccines containing A/California/07/2009 strain (A(H1N1) pdm09 subtype). By Enzyme-Linked Lectin Assay (ELLA; Consortium for the Standardization of Influenza Seroepidemiology), we analyzed serum samples from two different cohorts (adults and elderly). The presence of anti-NA Abs at titers ≥1/40 against classical A(H1N1) and A(H1N1) pdm09 subtypes were frequently found in both age groups, in 81.3% and 96.3% of adults and elderly, respectively. The higher titers of anti-NA Abs (NAI titers) were detected more frequently against classical A(H1N1) strains according to the expected age when the first flu infection takes place. In this way, an Original Antigenic Sin phenomenon related to NA seems to be part of the immune response against flu. Seasonal-vaccination induced homologous seroconversion against NA of A(H1N1) pdm09 subtype in 52.5% and 55.0%, and increased the Geometric Mean Titers (GMTs) in 70.0% and 78.8% of adults and elderly, respectively. Seasonal vaccination also induced a heterotypic anti-NA Abs response against classical A(H1N1) strains (seroconversion at least in 8.8% and 11.3% of adults and elderly, respectively, and an increase in GMTs of at least 28.0% in both age groups). These anti-NA Abs responses occur even though the seasonal vaccine does not contain a standardized amount of NA. This work demonstrates that seasonal vaccines containing the A(H1N1) pdm09 subtype induce a broad antibody response against NA1, that may be a target for future influenza vaccines. Our study is one of the first to analyze the presence of Abs against NA and the response mediated by NAI titers after seasonal influenza vaccination.
Rising incidence of second cancers in patients with low‐risk (T1N0) thyroid cancer who receive radioactive iodine therapy (2011)

The increased risk of a SPM in patients with low-risk (T1N0) WDTC, along with a lack of data demonstrating improved survival outcomes with adjuvant RAI, provide a compelling argument in favor of rationing the use of RAI in this patient population.
Concentrated dyes as a source of two‐dimensional fluorescent field for characterization of a confocal microscope (2007)

The axial spread function is a useful tool for evaluation of a confocal microscope. It can be obtained experimentally by scanning a uniform fluorescent layer whose thickness is significantly below the resolution limit. Previous researchers have created thin fluorescent films by chemical synthesis. We show here that concentrated fluorescent dyes with a strong absorption at the excitation wavelength can serve as a good approximation of thin fluorescent films. The vertical intensity profiles of such dyes are symmetrical and represent the true axial resolution of a microscope. Solutions of dyes sufficiently opaque to test confocal microscopes with high-NA objectives can be prepared from sodium fluorescein, acid fuchsin and acid blue 9 for excitation at 488 nm, 543 nm and 633 nm, respectively.
Combining diagnostic test results to increase accuracy (2000)

When multiple diagnostic tests are performed on an individual or multiple disease markers are available it may be possible to combine the information to diagnose disease. We consider how to choose linear combinations of markers in order to optimize diagnostic accuracy. The accuracy index to be maximized is the area or partial area under the receiver operating characteristic (ROC) curve. We propose a distribution-free rank-based approach for optimizing the area under the ROC curve and compare it with logistic regression and with classic linear discriminant analysis (LDA). It has been shown that the latter method optimizes the area under the ROC curve when test results have a multivariate normal distribution for diseased and non-diseased populations. Simulation studies suggest that the proposed non-parametric method is efficient when data are multivariate normal.The distribution-free method is generalized to a smooth distribution-free approach to: (i) accommodate some reasonable smoothness assumptions; (ii) incorporate covariate effects; and (iii) yield optimized partial areas under the ROC curve. This latter feature is particularly important since it allows one to focus on a region of the ROC curve which is of most relevance to clinical practice. Neither logistic regression nor LDA necessarily maximize partial areas. The approaches are illustrated on two cancer datasets, one involving serum antigen markers for pancreatic cancer and the other involving longitudinal prostate specific antigen data.
A human neuronal model of Niemann Pick C disease developed from stem cells isolated from patient’s skin (2013)

After 3 passages in selective medium, MASC isolated either from skin biopsies or previously established skin fibroblast cultures displayed an antigenic pattern characteristic of mesenchymal stem cells and expressed the stem cell markers Oct-4, Nanog, Sox-2 and nestin. A massive lysosomal accumulation of cholesterol was observed only in cells isolated from NPC patients. After the induction of neural differentiation, remarkable morphologic changes were observed and cells became positive to markers of the neuronal lineage NeuN and MAP2. Differentiated cells from NPC patients displayed characteristic features of NPC disease, they showed intracellular accumulation of unesterified cholesterol and GM2 ganglioside and presented morphological differences with respect to cells derived from healthy donors.In conclusion, we generated a human neuronal model of NPC disease through the induction of differentiation of stem cells obtained from patient's easily accessible sources. The strategy described here may be applied to easily generate human neuronal models of other neurodegenerative diseases.
Evidence for damage-dependent hygienic behaviour towards Varroa destructor-parasitised brood in the western honey bee, Apis mellifera (2011)

The ectoparasitic mite Varroa destructor and honey bee pathogenic viruses have been implicated in the recent demise of honey bee colonies. Several studies have shown that the combination of V. destructor and deformed wing virus (DWV) poses an especially serious threat to honey bee health. Mites transmitting virulent forms of DWV may cause fatal DWV infections in the developing bee, while pupae parasitised by mites not inducing or activating overt DWV infections may develop normally. Adult bees respond to brood diseases by removing affected brood. This hygienic behaviour is an essential part of the bees' immune response repertoire and is also shown towards mite-parasitised brood. However, it is still unclear whether the bees react towards the mite in the brood cell or rather towards the damage done to the brood. We hypothesised that the extent of mite-associated damage rather than the mere presence of parasitising mites triggers hygienic behaviour. Hygienic behaviour assays performed with mites differing in their potential to transmit overt DWV infections revealed that brood parasitised by 'virulent' mites (i.e. mites with a high potential to induce fatal DWV infections in parasitised pupae) were removed significantly more often than brood parasitised by 'less virulent' mites (i.e. mites with a very low potential to induce overt DWV infections) or non-parasitised brood. Chemical analyses of brood odour profiles suggested that the bees recognise severely affected brood by olfactory cues. Our results suggest that bees show selective, damage-dependent hygienic behaviour, which may be an economic way for colonies to cope with mite infestation.
Changes in Brain Glucose Metabolism as a Key to the Pathogenesis of Alzheimer’s Disease (1994)

The article discusses some aspects demonstrating that a decrease in acetylcholine synthesis in senile dementia of the Alzheimer type (SDAT) is a consequence of the strong decline in glucose turnover in the brain. This becomes obvious by the fact that acetylcoenzyme A, the key substrate of acetylcholine synthesis, is exclusively synthesized in the glycolytic pathway in the brain. This means that a single molecule of glucose synthesizes only two molecules of acetylcoenzyme A but 38 molecules of ATP. This is critically changed if glucose metabolism of the brain decreases in SDAT. beta-Amyloid precursor protein (beta-APP) of chromosome 21 is a regular protein of repair of any cellular membrane in the body. It is integrated into the cellular membranes and split off by proteases in the beta-region. This process is ATP-dependent. If in SDAT ATP synthesis is critically lowered by a decreased glucose turnover, beta-APP cannot be built into the cellular membranes and the beta-APP molecule is not split off in the beta-region either. The consequence is a generation of beta-amyloid from beta-APP fragments, which are progressively accumulated in senile plaques and vascular walls. The missing repair of cellular membranes and synapses in the brain results in nerve cell atrophy and a shrinkage of the brain. It is concluded that the cholinergic deficit, nerve cell atrophy and the amyloid accumulation in the brain are secondary phenomena caused by the 50-70% decline of glucose metabolism in SDAT.
<title>Microscopic and mesoscopic spectral bioimaging</title> (1996)

Light microscopy has become a versatile tool for investigating biological phenomena as they unfold, using cells as living microcuvettes. The progress is based on improvements in a number of technological fields, including optics, electronics, reagent chemistry and computer science. The non-destructiveness, spatial resolution and speed of optical imaging can provide high versatility for investigating biological structure and function at the tissue or even whole organism level as well. Having previously reported on some new approaches to meeting the challenges posed by the fluorescence-based imaging of cells and tissues, we concentrate here on imaging with increased spectral content and resolution. We improved and applied two techniques of spectral selection: (1) acousto-optic tunable filtering, allowing for multiwavelength fluorescence microscopy with diffraction-limited spatial imaging and sub- millisecond temporal resolution, and (2) 2D Sagnac interferometry-based Fourier spectroscopy, yielding advanced spectral imaging capabilities. Enhanced implementations of existing optical technologies, coupled with image processing, were key in these approaches. We present an overview of the methods, and summarize some of our results in applying these advances to imaging biological specimens. The extension of spectral selection approaches to the mesoscopic domain, suitable for in vivo imaging is also illustrated, by fluorescence-based tumor visualization in the near infrared spectral region. Finally, some future directions are discussed.