gebhart/patrepeval huggingface dataset:
Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates (2017)

The requirement for bone-marrow aspirates for genomic profiling of multiple myeloma poses an obstacle to enrolment and retention of patients in clinical trials. We evaluated whether circulating cell-free DNA (cfDNA) analysis is comparable to molecular profiling of myeloma using bone-marrow tumour cells. We report here a hybrid-capture-based Liquid Biopsy Sequencing (LB-Seq) method used to sequence all protein-coding exons of KRAS, NRAS, BRAF, EGFR and PIK3CA in 64 cfDNA specimens from 53 myeloma patients to >20,000 × median coverage. This method includes a variant filtering algorithm that enables detection of tumour-derived fragments present in cfDNA at allele frequencies as low as 0.25% (median 3.2%, range 0.25-46%). Using LB-Seq analysis of 48 cfDNA specimens with matched bone-marrow data, we detect 49/51 likely somatic mutations, with subclonal hierarchies reflecting tumour profiling (96% concordance), and four additional mutations likely missed by bone-marrow testing (>98% specificity). Overall, LB-Seq is a high fidelity adjunct to genetic profiling of bone-marrow in multiple myeloma.
Manifesto of the Communist Party (with Friedrich Engels) (1996)

A spectre stalks the land of Europe – the spectre of communism. The powers that be – Pope and Tsar, Metternich and Guizot, French Radicals and German police – are in holy alliance for a witchhunt.
Assessment of Left Ventricular Diastolic Function using Phonocardiogram Signals: A Comparison with Echocardiography (2020)

This paper presents a fully-automated end-to-end phonocardiogram(PCG)-based wearable system capable of providing echocardiography-like metrics for left ventricular (LV) diastolic function assessment. Proxy metrics for five echocardiographic parameters were calculated based on physiologically-motivated features extracted from PCG signals using noise-subtraction, heartbeat-segmentation, and quality-assurance algorithms. The clinical value of these proxy metrics was evaluated using the latest American Society of Echocardiography/European Association of Cardiovascular Imaging guidelines for evaluation of LV diastolic function. When tested on a group of n=34 patients, proxy metrics successfully identified LV diastolic dysfunction in a n=29 subset with 87.5% accuracy, and elevated LV filling pressures in a n=17 subset with 75% accuracy.
A methodology for wafer scale integration of linear pipelined arrays (2002)

A methodology for designing large one-dimensional pipelined array processing architectures where a large number of defects can be expected is presented. Central to the methodology is a functional separation at each processing element between the processing core and the inter-cell communication path. Using an 'interconnection harness' which provides the inter-cell communication medium and straps or links the underlying processing cores into a working array, 100% utilisation of the 'healthy' processing elements can be achieved. The harness which snakes across the wafer and forms the backbone of this architecture is made highly reliable and capable of sustaining up to a maximum of N single errors in an N cell array.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<i>In vitro</i> prostanoid release from spinal cord following peripheral inflammation: effects of substance P, NMDA and capsaicin (1999)

1. Spinal prostanoids are implicated in the development of thermal hyperalgesia after peripheral injury, but the specific prostanoid species that are involved are presently unknown. The current study used an in vitro spinal superfusion model to investigate the effect of substance P (SP), N-methyl-d-aspartate (NMDA), and capsaicin on multiple prostanoid release from dorsal spinal cord of naive rats as well as rats that underwent peripheral injury and inflammation (knee joint kaolin/carrageenan). 2. In naive rat spinal cords, PGE2 and 6-keto-PGF1alpha, but not TxB2, levels were increased after inclusion of SP, NMDA, or capsaicin in the perfusion medium. 3. Basal PGE2 levels from spinal cords of animals that underwent 5-72 h of peripheral inflammation were elevated relative to age-matched naive cohorts. The time course of this increase in basal PGE2 levels coincided with peripheral inflammation, as assessed by knee joint circumference. Basal 6-keto-PGF1alpha levels were not elevated after injury. 4. From this inflammation-evoked increase in basal PGE2 levels, SP and capsaicin significantly increased spinal PGE2 release in a dose-dependent fashion. Capsaicin-evoked increases were blocked dose-dependently by inclusion of S(+) ibuprofen in the capsaicin-containing perfusate. 5. These data suggest a role for spinal PGE2 and NK-1 receptor activation in the development of hyperalgesia after injury and demonstrate that this relationship is upregulated in response to peripheral tissue injury and inflammation.
Functionalized gold nanorod nanocomposite system to modulate differentiation of human mesenchymal stem cells into neural-like progenitors (2017)

A 2D multifunctional nanocomposite system of gold nanorods (AuNRs) was developed. Gold nanorods were functionalized via polyethylene glycol with a terminal amine, and, were characterized using transmission and scanning electron microscopy, ultra violet-visible and X-ray photoelectron spectroscopy, and Zeta-potential. The system was cytocompatible to and maintained the integrity of Schwann cells. The neurogenic potential of adipose tissue - derived human mesenchymal stem cells (hMSCs) was evaluated in vitro. The expression pattern and localization of Vimentin confirmed the mesenchymal origin of cells and tracked morphological changes during differentiation. The expression patterns of S100β and glial fibrillary acidic protein (GFAP), were used as indicator for neural differentiation. Results suggested that this process was enhanced when the cells were seeded on the AuNRs compared to the tissue-culture surface. The present study indicates that the design and the surface properties of the AuNRs enhances neural differentiation of hMSCs and hence, would be beneficial for neural tissue engineering scaffolds.
Editorial Vol.1(2) (2016)

NSBM Journal of Management is published by the National School of Business Management (NSBM), Colombo.The principal objective of the journal is to provide a medium for disseminating findings of study and research addressing issues, practices and developments in Management. Scholars and practioners are invited to publish their work in the field of Management taking either a positivistic or a nonpositivistic approach. Thereby, the journal promotes free and unbiased opinion, networking and sharing of experiences on matters of importance to organizations and society.
Side effects from amiodarone (1991)

Amiodarone causes many side effects involving all organ systems. Although most of the side effects are mild and do not limit the use of the drug, there are several that are serious. Since many of these toxic reactions develop only after a prolonged period of therapy, careful follow-up on a regular basis is essential.
BCL-XL directly modulates RAS signalling to favour cancer cell stemness (2017)

In tumours, accumulation of chemoresistant cells that express high levels of anti-apoptotic proteins such as BCL-X<sub>L</sub> is thought to result from the counter selection of sensitive, low expresser clones during progression and/or initial treatment. We herein show that BCL-X<sub>L</sub> expression is selectively advantageous to cancer cell populations even in the absence of pro-apoptotic pressure. In transformed human mammary epithelial cells BCL-X<sub>L</sub> favours full activation of signalling downstream of constitutively active RAS with which it interacts in a BH4-dependent manner. Comparative proteomic analysis and functional assays indicate that this is critical for RAS-induced expression of stemness regulators and maintenance of a cancer initiating cell (CIC) phenotype. Resistant cancer cells thus arise from a positive selection driven by BCL-X<sub>L</sub> modulation of RAS-induced self-renewal, and during which apoptotic resistance is not necessarily the directly selected trait.
Fluoride Ion Capture from Water with a Cationic Borane (2006)

The reaction of the [Li(THF)4]+ salt of dimesityl-1,8-naphthalenediylborate with [Me2NCH2]I affords a borane (1-(Mes2B)-8-(Me2NCH2)-C10H6) which can be converted into a cationic borane [3]+ ([1-(Mes2B)-8-(Me3NCH2)-C10H6]+) by methylation with MeOTf. This cationic borane promptly complexes fluoride to afford the corresponding zwitterionic ammonium/fluoroborate 3-F (1-(Mes2FB)-8-(Me3NCH2)-C10H6). Cation [3]+ fails to react with chloride, bromide, and iodide indicating that fluoride complexation is selective. Structural, spectroscopic, and computational studies carried out on 3-F show the existence of an unusual C-H...F-B hydrogen bond. Remarkably, [3]+ captures fluoride from water under biphasic conditions (H2O/CHCl3) to form 3-F. The high fluoride affinity of [3]+ can be correlated to the Coulombic forces which stabilize the B-F bond against heterolysis.
Code time division multiple access: an indoor cellular system (2003)

A wideband communications system for indoor cellular applications is proposed that is based on an accessing scheme called code time division multiple access (CTDMA). It combines some of the most important advantages of code-division multiple access (CDMA) and time-division multiple access (TDMA): a constant-envelope transmitted signal, a perfect separation of the users in one cell and a cluster size of one. Simulation results of such a system offering an information data rate of 144 kb/s, applying frequency division duplex and occupying a total bandwidth of 2*20 MHz are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Functional Analysis and Transcriptomic Profiling of iPSC-Derived Macrophages and Their Application in Modeling Mendelian Disease (2015)

Our protocol-derived IPSDM are comparable with HMDM at phenotypic, functional, and transcriptomic levels. Tangier disease-IPSDM recapitulated hallmark features observed in HMDM and revealed novel inflammatory phenotypes. IPSDMs provide a powerful tool for study of macrophage-specific function in human genetic disorders as well as molecular studies of human macrophage activation and polarization.
Streaming and Exploration of Dynamically Changing Dense 3D Reconstructions in Immersive Virtual Reality (2016)

We introduce a novel framework that enables large-scale dense 3D scene reconstruction, data streaming over the network and immersive exploration of the reconstructed environment using virtual reality. The system is operated by two remote entities, where one entity – for instance an autonomous aerial vehicle – captures and reconstructs the environment as well as transmits the data to another entity – such as human observer – that can immersivly explore the 3D scene, decoupled from the view of the capturing entity. The performance evaluation revealed the framework’s capabilities to perform RGB-D data capturing, dense 3D reconstruction, streaming and dynamic scene updating in real time for indoor environments up to a size of 100m2, using either a state-of-the-art mobile computer or a workstation. Thereby, our work provides a foundation for enabling immersive exploration of remotely captured and incrementally reconstructed dense 3D scenes, which has not shown before and opens up new research aspects in future.
The Isolation and Detection of Non-Collagenous Proteins from the Compact Bone of the Dinosaur<i>Iguanodon</i> (2000)

This report describes the isolation of guanidinium chloride extractable protein from demineralised bone extracts obtained from the 125-130 mya dinosaur Iguanodon. Protein products were isolated in the Mr. range 5,000-66,000 using SDS-PAGE and represent the first electrophoretically defined proteins isolated from dinosaur tissues. The levels of glycine, aspartate and serine tentatively suggest the presence of phosphoproteins. Hydroxylysine and hydroxyproline were not detected, confirming the presence of non-collagenous material. In addition the absence of ornithine confirmed lack of bacterial contamination. The relatively high level of leucine in the 2MNaCl NaCl fractions together with the abolition of alcian blue reactivity following protease-free chondroitinase digestion suggests the presence of proteoglycans. The study is of interest in describing the early proteins laid down in mineralised tissues for epitactic crystal growth and may provide evidence on evolutionary aspects of bone proteins.
Isolation of recombinant phage clones expressing mycobacterial T cell antigens by screening a recombinant DNA library with human CD4+ Th1 clones (1998)

A Vgt11 recombinant DNA library of Mycobacterium leprae was screened to isolate recombinant phage clones expressing mycobacterial antigens important for T cell reactivity. The library was plated on a lawn of Escherichia coli Y1090 and recombinant antigens were expressed from isolated phage clones in 96-well plates. Pools of recombinant antigens from 12 wells were tested in T cell proliferation assays with MHC class II restricted human CD4 Th1 clones secreting interferon-Q and cytotoxic for antigen pulsed antigen presenting cells. By screening 1750 pools of recombinant antigens with a mixture of eight Th1 clones, we identified two recombinant phage clones that expressed recombinant mycobacterial antigens stimulatory for T cells. MHC restriction analysis and reactivity to a battery of mycobacterial antigens suggested that the two responding Th1 clones recognized mycobacterial antigens/epitopes with different MHC class II (HLA-DR) restriction requirements. Our results suggest that the methodology described in this paper is suited to isolate recombinant phage clones expressing mycobacterial recombinant antigens stimulatory for T cells of protective phenotype. Such antigens may be useful in designing new vaccines and diagnostic reagents against mycobacterial diseases.
Texture-Constrained Active Shape Models (2002)

Abstract — In this paper, we propose a texture-constrained active shape model (TC-ASM) to localize a face in an image. TC-ASM effectively incorporates not only the shape prior and local appearance around each landmark, but also the global texture constraint over the shape. Therefore, it performs stable to initialization, accurate in shape localization and robust to illumination variation, with low computational cost. Extensive experiments are provided to demonstrate our algorithm. I.
A perspective on active machinery isolation (2003)

A summary of general considerations in active vibration isolation obtained from experience in developing a testbed system is given. Application of this approach is illustrated by a description of the testing facility and the results achieved to date. These include broadband active vibration isolation of 20 dB over a decade-wide frequency band on the nearly-full-scale testbed. Significant features of the testing facility are a small diesel engine mounted on a representatively complex structural foundation, the correspondingly complex open-loop transfer function of the system, and the use of a hybrid analog/digital controller to partition the compensation filter frequency coverage.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Sustainable Synthesis of Pure Silica Zeolites from a Combined Strategy of Zeolite Seeding and Alcohol Filling (2019)

Currently, the synthesis of pure silica zeolites always requires the presence of organic structure-directing agents (OSDAs), which direct the assembly pathway and ultimately fill the pore space. A sustainable route is now reported for synthesizing pure silica zeolites in the absence of OSDAs from a combined strategy of zeolite seeding and alcohol filling, where the zeolite seeds direct crystallization of zeolite crystals from amorphous silica, while the alcohol is served as pore filling in the zeolites. Very importantly, the alcohol could be fully washed out from zeolite pores by water at room temperature, which completely avoids calcination at high temperature for removal of OSDAs in the synthesis of pure silica zeolites.
Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation (2012)

The ARTISTIC trial is registered with the International Standard Randomised Controlled Trial Number ISRCTN25417821.
Asymmetric Induction and Enantiodivergence in Catalytic Radical C–H Amination via Enantiodifferentiative H-Atom Abstraction and Stereoretentive Radical Substitution (2019)

Control of enantioselectivity remains a major challenge in radical chemistry. The emergence of metalloradical catalysis (MRC) offers a conceptually new strategy for addressing this and other outstanding issues. Through the employment of <i>D</i><sub>2</sub>-symmetric chiral amidoporphyrins as the supporting ligands, Co(II)-based MRC has enabled the development of new catalytic systems for asymmetric radical transformations with a unique profile of reactivity and selectivity. With the support of new-generation HuPhyrin chiral ligands whose cavity environment can be fine-tuned, the Co-centered d-radicals enable to address challenging issues that require exquisite control of fundamental radical processes. As showcased with asymmetric 1,5-C-H amination of sulfamoyl azides, the enantiocontrol of which has proven difficult, the judicious use of HuPhyrin ligand by tuning the bridge length and other remote nonchiral elements allows for controlling both the degree and sense of asymmetric induction in a systematic manner. This effort leads to successful development of new Co(II)-based catalytic systems that are highly effective for enantiodivergent radical 1,5-C-H amination, producing both enantiomers of the strained five-membered cyclic sulfamides with excellent enantioselectivities. Detailed deuterium-labeling studies, together with DFT computation, have revealed an unprecedented mode of asymmetric induction that consists of enantiodifferentiative H-atom abstraction and stereoretentive radical substitution.
A novel BIST scheme for circuit aging measurement of aerospace chips (2018)

The avionics working environment is bad, easy to accelerate aging of circuits. Circuit aging is one of the important factors that influence the reliability of avionics, so circuit aging testing is of great significance to improve the reliability of avionics. As continuing aging would degrade circuit performance, aging can be monitored through precise measurement of performance degradation. However, previous methods for predicting circuit performance have limited prediction accuracy. In this paper, we propose a novel Built-In Self-Test (BIST) scheme for circuit aging measurement, which constructs self-oscillation loops employing parts of critical paths and activates oscillations by specific test patterns. An aging signature counter is then used to capture the oscillation frequency and in turn measure the aging state of the circuit. We propose to implement this measurement process by BIST. Experimental results show that the proposed in-field aging measurement is robust with respect to process variations and can achieve a precision of about 90%. The application of this scheme has a certain value to improve the reliability of avionics systems.
Physical Map and Gene Survey of the <i>Ochrobactrum anthropi</i> Genome Using Bacterial Artificial Chromosome Contigs (1999)

Bacterial artificial chromosome (BAC) clones are effective mapping and sequencing reagents for use with a wide variety of small and large genomes. This report describes research aimed at determining the genome structure of Ochrobactrum anthropi, an opportunistic human pathogen that has potential applications in biodegradation of hazardous organic compounds. A BAC library for O. anthropi was constructed that provides a 70-fold genome coverage based on an estimated genome size of 4.8 Mb. The library contains 3072 clones with an average insert size of 112 kb. High-density colony filters of the library were made, and a physical map of the genome was constructed using a hybridization without replacement strategy. In addition, 1536 BAC clones were fingerprinted with HindIII and analyzed using IMAGE and Fingerprint Contig software (FPC, Sanger Centre, U.K.). The FPC results supported the hybridization data, resulting in the formation of two major contigs representing the two major replicons of the O. anthropi genome. After determining a reduced tiling path, 138 BAC ends from the reduced tile were sequenced for a preliminary gene survey. A search of the public databases with the BLASTX algorithm resulted in 77 strong hits (E-value < 0.001), of which 89% showed similarity to a wide variety of prokaryotic genes. These results provide a contig-based physical map to assist the cloning of important genomic regions and the potential sequencing of the O. anthropi genome.
Nitrate reductase and molybdenum cofactor in annual ryegrass as affected by salinity and nitrogen source (1997)

The influence of salinity on the activity of nitrate reductase (NR, EC 1.6.6.1) and the level of the molybdenum cofactor (MoCo) as affected by the source and concentration of nitrogen was studied in annual ryegrass ( Lolium multiflorum cv. Westerwoldicum). Plants grown in sand were irrigated with nutrient solution with an electrical conductivity of 2 or 11.2 dS m −1 , containing nitrogen (0.5 or 4.5 m M ) in the form of NH 4 NO 3 or NaNO 3 Salinity‐treated (11.2 dS m −1 ) plants produced less biomass and more organic nitrogen while accumulating more NO − 3 than control plants. Increased nitrogen concentration in the irrigation solutions enhanced biomass and organic nitrogen production as well as NO − 3 accumulation irrespective of the electrical conductivity. Salinity inhibited shoot growth and increased shoot NR activity of plants receiving 4.5 m M NH 4 NO 3 or NaNO 3 . Similar effects were observed in roots of plants grown in 4.5 m M NaNO 3 . Nitrate added to a complementation medium containing ryegrass MoCo and the NR apoprotein of Neurospora crassa mutant nit‐1 stimulated the activity of the reconstituted NR (NADPH‐nitrate reductase, EC 1.6.6.3). Increased salinity and nitrogen in the nutrient solutions caused an increase of MoCo content in roots and shoots. Similar results were observed for NR activity in the shoots. The increase of MoCo in response to salinity was more pronounced than that of NR, especially in the roots. We conclude that the pool size of MoCo in ryegrass is not constant, but varies in response to nutritional and environmental factors.
Expert Gate: Lifelong Learning with a Network of Experts (2017)

In this paper we introduce a model of lifelong learning, based on a Network of Experts. New tasks / experts are learned and added to the model sequentially, building on what was learned before. To ensure scalability of this process, data from previous tasks cannot be stored and hence is not available when learning a new task. A critical issue in such context, not addressed in the literature so far, relates to the decision which expert to deploy at test time. We introduce a set of gating autoencoders that learn a representation for the task at hand, and, at test time, automatically forward the test sample to the relevant expert. This also brings memory efficiency as only one expert network has to be loaded into memory at any given time. Further, the autoencoders inherently capture the relatedness of one task to another, based on which the most relevant prior model to be used for training a new expert, with fine-tuning or learning-without-forgetting, can be selected. We evaluate our method on image classification and video prediction problems.