gebhart/patrepeval huggingface dataset:
<i>EGFR</i> mutations in lung cancer: from tissue testing to liquid biopsy (2015)

ABSTRACT The presence of EGFR mutations predicts the sensitivity to EGF receptor (EGFR)-tyrosine kinase inhibitors in a molecularly defined subset of non-small-cell lung carcinoma (NSCLC) patients. For this reason, EGFR testing of NSCLC is required to provide personalized treatment options and better outcomes for NSCLC patients. As surgery specimens are not available in the majority of NSCLC, other currently available DNA sources are small biopsies and cytological samples, providing however limited and low-quality material. In order to address this issue, the use of surrogate sources of DNA, such as blood, serum and plasma samples, which often contains circulating free tumor DNA or circulating tumor cells, is emerging as a new strategy for tumor genotyping.
Metamaterials: a new frontier of science and technology (2011)

Metamaterials, artificial composite structures with exotic material properties, have emerged as a new frontier of science involving physics, material science, engineering and chemistry. This critical review focuses on the fundamentals, recent progresses and future directions in the research of electromagnetic metamaterials. An introduction to metamaterials followed by a detailed elaboration on how to design unprecedented electromagnetic properties of metamaterials is presented. A number of intriguing phenomena and applications associated with metamaterials are discussed, including negative refraction, sub-diffraction-limited imaging, strong optical activities in chiral metamaterials, interaction of meta-atoms and transformation optics. Finally, we offer an outlook on future directions of metamaterials research including but not limited to three-dimensional optical metamaterials, nonlinear metamaterials and “quantum” perspectives of metamaterials (142 references).
On cryptography with auxiliary input (2009)

We study the question of designing cryptographic schemes which are secure even if an arbitrary function f(sk) of the secret key is leaked, as long as the secret key sk is still (exponentially) hard to compute from this auxiliary input. This setting of auxiliary input is more general than the more traditional setting, which assumes that some of information about the secret key sk may be leaked, but sk still has high min-entropy left. In particular, we deal with situations where f(sk) information-theoretically determines the entire secret key sk.
Minimum Message Length and Kolmogorov Complexity (1999)

The notion of algorithmic complexity was developed by Kolmogorov (1965) and Chaitin (1966) independently of one another and of Solomonoff's notion (1964) of algorithmic probability. Given a Turing machine T, the (prefix) algorithmic complexity of a string S is the length of the shortest input to T which would cause T to output S and stop. The Solomonoff probability of S given T is the probability that a random binary string of 0s and 1s will result in T producing an output having S as a prefix. We attempt to establish a parallel between a restricted (two-part) version of the Kolmogorov model and the minimum message length approach to statistical inference and machine learning of Wallace and Boulton (1968), in which an ‘explanation’ of a data string is modelled as a two-part message, the first part stating a general hypothesis about the data and the second encoding details of the data not implied by the hypothesis. Solomonoff's model is tailored to prediction rather than inference in that it considers not just the most likely explanation, but it also gives weights to all explanations depending upon their posterior probability. However, as the amount of data increases, we typically expect the most likely explanation to have a dominant weighting in the prediction.
Stereoselective Synthesis of the C9–C19 Fragment of Lyngbyaloside B and C via Ether Transfer (2012)

A stereoselective synthesis of the C9-C19 fragment of lyngbyaloside B and C highlighted, by an extension of our ether transfer methodology, enables the formation of tertiary ethers. 2-Naphthylmethyl ethers have been shown to proceed efficiently through ether transfer with high stereoselectivity and are easily deprotected by DDQ oxidation. Variation of the workup conditions results in the stereoselective formation of syn-1,3-diol mono- or diethers.
Effectiveness of paroxetine in the treatment of obsessive–compulsive disorders (2006)

Clomipramine ushered in a new age of pharmacotherapy for obsessive-compulsive disorders, and it also facilitated our understanding of the biological aspects of obsessive-compulsive disorder, focusing on the serotonergic systems. The introduction of selective serotonin reuptake inhibitors has led to great progress in the pharmacological study of obsessive-compulsive disorder based on the serotonin hypothesis. Currently, selective serotonin reuptake inhibitors are positioned as a first-line drug of obsessive-compulsive disorder pharmacotherapy in the various guidelines and algorithms. Among six different selective serotonin reuptake inhibitors (paroxetine, sertraline, fluoxetine, fluvoxamine, citalopram, escitalopram) that are available worldwide, paroxetine has the broadest treatment spectrum and promises great benefits not only for obsessive-compulsive disorder patients, but also for those with comorbid depression and/or various kinds of anxiety disorders. This paper presents several clinical trials of paroxetine carried out, and discusses and reviews the therapeutic strategies for obsessive-compulsive disorder.
Are dye‐sensitized nano‐structured solar cells stable? An overview of device testing and component analyses (2004)

The nano‐structured dye‐sensitized solar cell (DNSC) is considered as a promising technology having the potential to significantly decrease the costs of solar energy. The breakthrough was achieved in 1991 with the demonstration of a DNSC system reaching more than 7% efficiency and after a decade of intense research the commercialization is in reach. Besides efficiency, stability is equally important for the step from research to the market. Therefore, the stability of such devices has been under close investigation since the DNSC was presented. In this contribution we summarize the literature about device testing and the attempts to understand the degradation mechanisms. Solar cells developed for energy production are discussed as well as alternative systems for low power applications, e.g., DNSCs on plastic substrates. The components (substrate, nano‐structured TiO 2 , dye, electrolyte, additive and counter electrode) are analyzed towards their stability and how it affects the durability of the entire system. From this analysis, guidelines for testing and improving the stability of the DNSC are deduced.
The Humanized NOD/SCID Mouse as a Preclinical Model to Study the Fate of Encapsulated Human Islets (2010)

Despite encouraging results in animal models, the transplantation of microencapsulated islets into humans has not yet reached the therapeutic level. Recent clinical trials using microencapsulated human islets in barium alginate showed the presence of dense fibrotic overgrowth around the microcapsules with no viable islets. The major reason for this is limited understanding of what occurs when encapsulated human islets are allografted. This warrants the need for a suitable small animal model. In this study, we investigated the usefulness of NOD/SCID mice reconstituted with human PBMCs (called humanized NOD/SCID mice) as a preclinical model. In this model, human T cell engraftment could be achieved, and CD45+ cells were observed in the spleen and peripheral blood. Though the engrafted T cells caused a small fibrotic overgrowth around the microencapsulated human islets, this failed to stop the encapsulated islets from functioning in the diabetic recipient mice. The ability of encapsulated islets to survive in this mouse model might partly be attributed to the presence of Th2 cytokines IL-4 and IL-10, which are known to induce graft tolerance. In conclusion, this study showed that the hu-NOD/SCID mouse is not a suitable preclinical model to study the allograft rejection mechanisms of encapsulated human islets. As another result, the maintained viability of transplanted islets on the NOD/SCID background emphasized a critical role of protective mechanisms in autoimmune diabetes transplanted subjects due to specific immunoregulatory effects provided by IL-4 and IL-10.
Central Hemodynamic Responses During Serial Exercise Tests in Heart Failure Patients Using Implantable Hemodynamic Monitors (2003)

An added potential value of implantable hemodynamic monitors in heart failure patients may be to quantitatively determine the true hemodynamic profile during standard non-invasive clinical exercise tests and to compare that to hemodynamic effects of regular exercise during daily living. It would be of interest to study whether such information could improve the ability to predict changes in a patient's clinical condition and to improve tailoring patient management.
Deletion of 1p loci and microsatellite instability in colorectal polyps (1995)

Previous cytogenetic studies have indicated that a subset of large bowel adenomas have distal 1p deletions. We addressed this question by examining 70 sporadic polyps (63 adenomas, 5 hyperplastic polyps, and 2 polyps of undetermined histology) from 55 patients for alterations at eight loci on the short arm of chromosome 1 and found allelic imbalance (AI) or loss of one allele (LOH) in 14 (20%). The locus most frequently changed was MSI, which maps to 1p33-35. Fluorescence in situ hybridisation with centromeric and telomeric probes for chromosome 1, performed for 11 polyps, did not yield an abnormal number of signals, in accordance with the interpretation that the observed AI and LOH were the result of interstitial deletions in 1p. Whereas allelic imbalance at five other loci (mapping to 5q, 8p, 10p, 11p and 17q) was found less frequently, and then mainly in large (> 2 cm) tumours, the 1p alterations were equally distributed among small (< 1 cm) and large polyps. They were preferentially found in left-side tumours. Instability at microsatellite loci--the mutator phenotype--is demonstrated by shifts in the electrophoretic mobility of normal alleles. The mutator phenotype was first associated with hereditary nonpolyposis colorectal cancer but is also occasionally found in sporadic colorectal carcinomas; however, it is still uncertain when in the adenoma-carcinoma sequence in this type of genomic instability arises. We therefore looked for it at 12 dinucleotide repeat loci and found that seven tumours (six adenomas and one hyperplastic polyp) from seven patients had acquired new alleles not seen in the patients' corresponding normal DNA. Our results suggest that inactivation of a putative suppressor gene distally in chromosome arm 1p is an early event in colorectal tumourigenesis. They also show that microsatellite instability can be detected in large bowel polyps, indicating that this phenomenon, too, probably plays a pathogenic role for some colorectal tumours early in the adenoma-carcinoma sequence.
Machine Learning Interpretability: A Survey on Methods and Metrics (2019)

Machine learning systems are becoming increasingly ubiquitous. These systems’s adoption has been expanding, accelerating the shift towards a more algorithmic society, meaning that algorithmically informed decisions have greater potential for significant social impact. However, most of these accurate decision support systems remain complex black boxes, meaning their internal logic and inner workings are hidden to the user and even experts cannot fully understand the rationale behind their predictions. Moreover, new regulations and highly regulated domains have made the audit and verifiability of decisions mandatory, increasing the demand for the ability to question, understand, and trust machine learning systems, for which interpretability is indispensable. The research community has recognized this interpretability problem and focused on developing both interpretable models and explanation methods over the past few years. However, the emergence of these methods shows there is no consensus on how to assess the explanation quality. Which are the most suitable metrics to assess the quality of an explanation? The aim of this article is to provide a review of the current state of the research field on machine learning interpretability while focusing on the societal impact and on the developed methods and metrics. Furthermore, a complete literature review is presented in order to identify future directions of work on this field.
Survey of estimation techniques in image restoration (1991)

Blurred and noisy images can often be represented as nonstationary 2D stochastic processes that can be modeled by a set of linear space-varying state equations, or by an ARMA input-output equation with space-varying coefficients. Liner difference equation models for characterizing both images and their degraded observations are reviewed. The models are then expressed in state-space form suitable for Kalman filtering and in input-output equation form suitable for maximum likelihood parameter identification and ARMA smoothing. Recent methods for blur identification, image parameter identification, and simultaneous image and blur identification are reviewed. The fundamentals of image restoration are briefly summarized, and three approaches are discussed: iterative deterministic regularized restoration, restoration using optimal filtering, and adaptive restoration. Some representative results are given, and recommendations for future research topics are made.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Polyphase Ceramic for Consolidating Nuclear Waste Compositions with High Zr‐Cd‐Na Content (1990)

The development of dense polyphase tailored ceramic forms for the immobilization of high‐level nuclear wastes has been extended to an Idaho Chemical Processing Plant Fluorinel composition. The ceramic was designed to maximize waste loading and subsequent waste volume reduction without sacrificing chemical durability in aqueous environments. The ceramic, fabricated by hot isostatic pressing, consists of four main crystalline phases, calcium fluoride, zirconia, an apatite‐structured solid‐solution phase, and sphene. The form also contains a designed borosilicate glass phase, a Ni‐Cd alloy, and a minor amount of crystalline zircon. The crystalline apatite solid‐solution phase is the major host for incorporating the actinide simulants U, Ce, and Y, while the glass phase contains Cs and Sr. The calcium fluoride and sphene phases provide microstructural isolation of the radionuclide‐containing phases. Since the glass and crystalline components of the ceramic are not phase compatible at all temperatures, the exact phase content is determined by the tailoring additives, consolidation temperature, and oxidation state control during processing. The simulated HLW ceramic has a density of 3.3 g/cm 3 at a waste loading of 73 wt%.
Perchlorate and Nitrate in Leafy Vegetables of North America (2005)

In previous studies trace levels of perchlorate were found in lettuce (Lactuca sativa L.) irrigated with Colorado River water, which is contaminated with low levels of perchlorate from aerospace and defense related industries. In this paper, we report the results of a survey conducted across North America to evaluate the occurrence of perchlorate in leafy vegetables produced outside the lower Colorado River region, and evaluate the relative iodide uptake inhibition potential to perchlorate and nitrate in these leafy vegetables. Conventionally and organically produced lettuce and other leafy vegetable samples were collected from production fields and farmers' markets in the central and coastal valleys of California, New Mexico, Colorado, Michigan, Ohio, New York, Quebec, and New Jersey. Results show that 16% of the conventionally produced samples and 32% of the organically produced samples had quantifiable levels of perchlorate using ion chromatography. Estimated perchlorate exposure from organically produced leafy vegetables was approximately 2 times that of conventional produce, but generally less than 10% of the reference dose recommended by the National Academy of Sciences. Furthermore, the iodide uptake inhibition potential of perchlorate was less than 1% of that of the nitrate present. These data are consistent with those of other reported perchlorate survey work with lettuce, bottled water, breast milk, dairy milk, and human urine, and suggest a wide national presence of perchlorate.
En Route to an Efficient Catalytic Asymmetric Synthesis of AS-3201 (2007)

A catalytic asymmetric synthesis of AS-3201 via catalytic asymmetric amination with a novel lanthanum−amide complex is described. The amination reaction proceeded efficiently with as little as 1 mol % of catalyst loading, allowing for an efficient access to the key intermediate for the synthesis of AS-3201, a potent aldose reductase inhibitor.
Initial Characterization of Osteoblast Differentiation and Loss of RUNX2 Stability in the Newly Established SK11 Human Embryonic Stem Cell‐Derived Cell Line (2014)

We describe a novel model for investigation of genetically normal human osteoblasts in culture. SK11 is a clonal progenitor cell line derived from human embryonic stem cells. Initially selected based on the expression of chondrogenic markers when differentiated in micromass culture, SK11 cells display typical mRNA expression patterns of bone phenotypic genes under osteogenic conditions. These include osterix, α1(I) collagen, alkaline phosphatase, osteonectin, osteopontin, and osteocalcin. Similar to well-characterized murine osteoblast cultures, the osteoblast master regulator RUNX2 was present during the first few days after plating, but the protein disappeared during the first week of culture. Loss of RUNX2 expression is considered an important regulatory feature for osteoblast maturation. Indeed, following ∼2 weeks of differentiation, SK11 cultures exhibited robust calcium deposition, evidenced by alizarin red staining. We also introduced a lentiviral vector encoding doxycycline (dox)-inducible FLAG-tagged RUNX2 into SK11 cells. Dox-mediated enhancement of RUNX2 expression resulted in accelerated mineralization, which was further increased by co-treatment with BMP-2. Like the endogenous RUNX2, expression of the virally coded FLAG-RUNX2 was lost during the first week of culture despite persistent dox treatment. By following RUNX2 decay after dox withdrawal from day-5 versus day-3 cultures, we demonstrated a developmentally regulated decrease in RUNX2 stability. Availability of culture models for molecular investigation of genetically normal human osteoblasts is important because differences between murine and human osteoblasts, demonstrated here by the regulation of matrix Gla Protein, may have significant biomedical implications.
Advanced Tools for Advanced Wells: Rotary Closed-Loop Drilling System-Results of Prototype Field Testing (1998)

Summary In the next few years, a revolutionary well-steering system will arrive to face the "advanced wells" challenge. After an extensive period of field testing, the "rotary closed-loop system" (RCLS) seems very close to having the capability of operating in any extended-reach, deep horizontal, or complex multilateral well and in a high-pressure/high-temperature (HPHT) environment. Additionally, mainly because of the elimination of a sliding operation, conventional directional wells will, in many cases, also greatly benefit. The RCLS was designed to control automatically well geometry during directional drilling, even while rotating the drill-string. Hydraulically powered, electronically controlled, expandable ribs, which generate a radial steering contact force to the borehole wall, adjust the wellpath. All parts, except a short steering sleeve, work continuously in rotation. The RCLS may be operated with or without a downhole motor. Several subsystems, e.g., the hydraulic components, most electronic modules, and the bottom-to-surface communication, were field tested during 1994 and 1995. The first field trial of the complete unit, drilling a total of 1067 m, was conducted in late 1995 at Montrose, Scotland. The field test program was continued in early 1996 to compare RCLS drilling and directional performance with the introduction of broadened operating parameters. During this prototype testing period, the efficacy of all major functions was fully verified.
An on-line dynamic light-scattering instrument for protein chromatography (1991)

Conference Article| April 01 1991 An on-line dynamic light-scattering instrument for protein chromatography Paul Claes; Paul Claes 1Oros Instruments Limited, 715 Banbury Avenue, Slough, Berks. SL1 4LJ, U.K. Search for other works by this author on: This Site PubMed Google Scholar Martin Dunford; Martin Dunford 1Oros Instruments Limited, 715 Banbury Avenue, Slough, Berks. SL1 4LJ, U.K. Search for other works by this author on: This Site PubMed Google Scholar Andrew Kenney; Andrew Kenney 1Oros Instruments Limited, 715 Banbury Avenue, Slough, Berks. SL1 4LJ, U.K. Search for other works by this author on: This Site PubMed Google Scholar Penny Vardy Penny Vardy 1Oros Instruments Limited, 715 Banbury Avenue, Slough, Berks. SL1 4LJ, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1991) 19 (2): 487–488. https://doi.org/10.1042/bst0190487 Article history Received: December 20 1990 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation Paul Claes, Martin Dunford, Andrew Kenney, Penny Vardy; An on-line dynamic light-scattering instrument for protein chromatography. Biochem Soc Trans 1 April 1991; 19 (2): 487–488. doi: https://doi.org/10.1042/bst0190487 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: DLS, dynamic light scattering This content is only available as a PDF. © 1991 Biochemical Society1991 Article PDF first page preview Close Modal You do not currently have access to this content.
Effects of electrical stimulation of cutaneous afferents on corticospinal transmission of tremor signals in patients with Parkinson's disease (2013)

It has been hypothesized that propriospinal neurons (PNs) in the C3-C4 spinal cord mediates cortical motor commands to the peripheral muscles during tremor in patients with Parkinson's disease (PD). However, there has been no direct evidence so far to support the role of PN in transmitting tremor commands. In this paper, we report the positive correlation of cutaneous afferents with reduction in tremor amplitude and frequency in PD patients. Resting tremor and EMGs of biceps, triceps, flexor digitorum superficialis (FDS), extensor digitorum (ED), flexor carpi ulnaris (FCU) and extensor carpi radialis (ECR) muscles were recorded while transcutaneous electrical stimulation (TES) was applied to the dorsal hand skin of PD subjects. We observed instant suppression of tremor amplitude and EMGs occurring immediately at the start of electrical stimulation. However at the end of stimulation, the tremor amplitude and EMGs showed a quick recovery to the level prior to stimulation. Spectral analysis indicated that cutaneous afferents also have a long-lasting memory effect on the tremor frequency, i.e. the tremor frequency post stimulation did not recover to the value prior to stimulation. Preliminary results implied that the reduction in tremor amplitude and EMGs could be due to the inhibitory effects of cutaneous afferents to PNs, supporting the hypothesis that the PN network is involved in transmission of cortical tremor commands to peripheral muscles.