gebhart/patrepeval huggingface dataset:
Single-Shot CNN-Based Ultrasound Imaging with Sparse Linear Arrays (2020)

Sparse arrays are a topic of high interest within the ultrasound (US) imaging community, because of their promising ability to reduce costs, complexity, energy consumption, and data transfer requirements of US systems, thus addressing the main challenges of 3-D and portable 2-D systems. Undersampling a transducer array usually results in a significant increase in imaging artifacts, caused primarily by higher grating lobe (GL) levels. Thus, state-of-the-art sparse arrays design strategies focus on avoiding GLs, while compromising on the resulting image resolution and uniformity. In this work, we investigated the applicability of convolutional neural network (CNN)-based image reconstruction, having recently proven its potential in reducing GL artifacts, for reconstructing images from single unfocused acquisitions using uniformly undersampled linear array configurations on receive. The proposed reconstruction method consists of first computing a low-quality estimate from the undersampled single-shot acquisitions using a delay-and-sum (DAS) algorithm, followed by applying a real-time-capable CNN, trained specifically to reduce diffraction artifacts. Experiments were conducted within a simulation environment, in the context of plane wave imaging on a numerical test phantom dedicated to US image quality assessment. The proposed approach achieved an image comparable or better to that obtained from conventional DAS beamforming using the full array with uniformly undersampled arrays up to a factor of three, demonstrating a promising potential for sparse array imaging in general.
Internal noise-induced contrast enhancement of dark images (2012)

A contrast enhancement technique using scaling of internal noise of a dark image in discrete cosine transform (DCT) domain has been proposed in this paper. The mechanism of enhancement is attributed to noise-induced transition of DCT coefficients from a poor state to an enhanced state. This transition is effected by the internal noise present due to lack of sufficient illumination and can be modeled by a general bistable system exhibiting dynamic stochastic resonance. The proposed technique adopts a local adaptive processing and significantly enhances the image contrast and color information while ascertaining good perceptual quality. When compared with the existing enhancement techniques such as adaptive histogram equalization, gamma correction, single-scale retinex, multi-scale retinex, modified high-pass filtering, multi-contrast enhancement, multi-contrast enhancement with dynamic range compression, color enhancement by scaling, edge-preserving multi-scale decomposition and automatic controls of popular imaging tool, the proposed technique gives remarkable performance in terms of relative contrast enhancement, colorfulness and visual quality of enhanced image.
Comment on controlling dental post-operative pain and the intraoral local delivery of drugs (2015)

The results of numerous double-blind, placebo-controlled clinical trials consistently demonstrate that nonsteroidal antiinflammatory drugs should be the first line agents in treating postsurgical dental pain. Additive and potential opioid-sparing effects have also been reported in oral surgery pain by combining an optimal dose of an NSAID with acetaminophen 500 mg. While opioid combination drugs are indicated in some dental postsurgical patients, clinicians can no longer ignore the scourge of prescription opioid abuse in the United States. Other potential opioid sparing strategies include the use of locally delivered antimicrobial/antiinflammatory agents such as Bexident Post or extended duration local anesthetic agents such as liposomal bupivacaine placed directly in or in the vicinity of the extraction socket.
Mice lacking collapsin response mediator protein 1 manifest hyperactivity, impaired learning and memory, and impaired prepulse inhibition (2013)

Collapsin response mediator protein 1 (CRMP1) is one of the CRMP family members that are involved in various aspects of neuronal development such as axonal guidance and neuronal migration. Here we provide evidence that crmp1 (-/-) mice exhibited behavioral abnormalities related to schizophrenia. The crmp1 (-/-) mice exhibited hyperactivity and/or impaired emotional behavioral phenotype. These mice also exhibited impaired context-dependent memory and long-term memory retention. Furthermore, crmp1 (-/-) mice exhibited decreased prepulse inhibition, and this phenotype was rescued by administration of chlorpromazine, a typical antipsychotic drug. In addition, in vivo microdialysis revealed that the methamphetamine-induced release of dopamine in prefrontal cortex was exaggerated in crmp1 (-/-) mice, suggesting that enhanced mesocortical dopaminergic transmission contributes to their hyperactivity phenotype. These observations suggest that impairment of CRMP1 function may be involved in the pathogenesis of schizophrenia. We propose that crmp1 (-/-) mouse may model endophenotypes present in this neuropsychiatric disorder.
Supplementary Data Table S.4 from Pathology-Driven Comprehensive Proteomic Profiling of the Prostate Cancer Tumor Microenvironment (2023)

&lt;p&gt;Full list of proteins identified from LC-MS/MS analysis of all tumour regions of interest&lt;/p&gt;
Cryogenic Etching of Porous Organosilicate Low-k Materials: Fluorine based plasma analysis (2015)

International audience
Engineered extracellular matrix components do not alter the immunomodulatory properties of mesenchymal stromal cellsin vitro (2012)

Mesenchymal stromal cells (MSCs) have emerged as promising candidates for regenerative therapies, including tissue engineering. Recently it has been reported that engineered extracellular matrix (ECM) components support the differentiation of MSCs into osteocytes and chondrocytes, indicating that ECM components may represent attractive carriers for MSC transplants to repair damaged tissues. However, little is known about the impact of engineered ECM components on the immunosuppressive properties of MSCs, which may essentially contribute to the prevention of allogeneic MSC transplant rejection. In the present study, we explored the potential of fibronectin, fibrillar collagen I, tropocollagen and collagen I/heparin to influence the immunosuppressive capacities of MSCs. We found that these ECM components do not modulate the capability of MSCs to inhibit the proliferation of anti-CD3/anti-CD28 antibody-stimulated CD4⁺ and CD8⁺ T cells and of lymphocytes in a mixed lymphocyte reaction. In addition, the potential of MSCs to impair the production of immunostimulatory IL-12 and to improve the release of immunosuppressive IL-10 by 6-sulpho LacNAc⁺ (slan) dendritic cells (DCs), representing a pro-inflammatory subset of human blood DCs, was not altered by the ECM components. Furthermore, ECM components do not influence the ability of MSCs to inhibit the slanDC-induced proliferation of CD4⁺ T cells. In conclusion, the used engineered ECMs maintain important immunosuppressive properties of MSCs, which support their suitablility as carriers for MSC transplants in tissue engineering.
Microwave Circuits Described by Two-Dimensional Vector Wave Equation and their Analysis by FD-TD Method (1991)

The paper postulates distinction of a class of microwave circuits described by two-dimensional vector wave equation. It proposes to refer to them as vector two-dimensional or 2-DV circuits to distinguish them from the circuits described by two-dimensional scalar wave equation (typically referred to as 2-D circuits). The class of 2-DV circuits includes many microwave circuits of great importance. Formal description of the 2-DV circuits is presented in a form of extension of the formulas describing 2-D circuits. The paper presents also effective way of calculating arbitrarily shaped 2-DV circuits by finite-difference time-domain method. Examples of calculations are also shown.
Ag-Bi1.6Er0.4O3 as a Potential Cathode Material for IT-SOFCs (2006)

Porous composite electrodes consisting of pure silver and Er0.4Bi1.6O3 (ESB20) were synthesized and characterized using impedance spectroscopy. Pure Ag-ESB20 electrodes were optimized according to composition and long-term stability was tested. Electrode area specific resistance (ASR) was found to increase by 80% in 140h at 600åC due to migration of the silver phase. Two approaches were used to combat silver migration. First, nano-sized 8-mol% YSZ powders were added to the electrode slurries. Stability improvement was achieved at 15vol% YSZ. Second, ESB20 starting particle size was reduced using vibratory milling. This approach yielded a 25% reduction in initial ASR, a 95% reduction in ASR growth rate under no applied bias at 650åC, and a 50% reduction in ASR growth rate under a 250mV applied bias at 650åC.
QUEST: discovering insights from survey responses (2009)

Surveys are an easy, important and reliable method to measure the pulse of the organization's stake-holders. A survey helps in identifying improvements to current products, services and business processes. With the advent of the Web, it is now easy to conduct large-scale on-line surveys. However, it is a challenge to analyze the responses to derive novel, interesting, actionable insights and to design effective improvement plans. In this paper, we describe a tool called QUEST for analyzing survey responses. QUEST's pre-packaged knowledge containers provide frequently needed analysis of survey responses. Built-in analysis in QUEST varies from summaries, reports and charts to detailed statistical and data mining analysis and optimization. The analytics is designed to answer specific business questions, detect specific types of patterns, extract specific kind of useful and actionable knowledge and automatically suggest optimal improvement plans. We present a real-life case-study where QUEST was used to analyze responses from a real-life employee satisfaction survey in an IT company.
A Good Wireless Technologies Reference (2004)

A review of Wireless Networks by P. Nicopolitidis, M.S. Obaidat, G.I. Papadimitriou, and A.S. Pomportsis
Effect of Covalent Fluorescence Labeling of Plasmid DNA on Its Intracellular Processing and Transfection with Lipid-Based Carriers (2014)

The development of biotechnological pharmaceutics, like macro- and nanocarriers, can benefit greatly from studying their characteristics in situ using advanced fluorescence microscopy methods. While choosing the optimal labeling method for visualizing the carrier or its cargo is crucial, it seldom receives attention. The possibility that high labeling densities alter the intracellular processing of the molecule is considered, but how and at which point this interference happens is not yet studied. The aim of this study was to elucidate the effect of labeling density on the cellular trafficking of labeled pDNA. Due to the drastic effect on expression levels for higher labeling densities, we tried to determine at which steps in the intracellular processing labeled pDNA behaves different than its nonlabeled counterpart. Therefore, different labeling densities, up to the manufacturer's recommended density, were tested. It was found that the cellular uptake remains unaffected, while the affinity for lipids is increased, which affects dissociation from the lipid-based complex and may affect endosomal escape. Also, nuclear injections clearly demonstrated that transcription is affected. The information and methodology, included in this work, could be helpful in determining if the labeling method and density used yields biological relevant results for the intended research question.
Biochemical Evidence for the Heptameric Complex L10(L12)6 in the Thermus thermophilus Ribosome: In Vitro Analysis of its Molecular Assembly and Functional Properties (2008)

The stalk protein L12 is the only multiple component in 50S ribosomal subunit. In Escherichia coli, two L12 dimers bind to the C-terminal domain of L10 to form a pentameric complex, L10[(L12)(2)](2), while the recent X-ray crystallographic study and tandem MS analyses revealed the presence of a heptameric complex, L10[(L12)(2)](3), in some thermophilic bacteria. We here characterized the complex of Thermus thermophilus (Tt-) L10 and Tt-L12 stalk proteins by biochemical approaches using C-terminally truncated variants of Tt-L10. The C-terminal 44-residues removal (Delta44) resulted in complete loss of interactions with Tt-L12. Quantitative analysis of Tt-L12 assembled onto E. coli 50S core particles, together with Tt-L10 variants, indicated that the wild-type, Delta13 and Delta23 variants bound three, two and one Tt-L12 dimers, respectively. The hybrid ribosomes that contained the T. thermophilus proteins were highly accessible to E. coli elongation factors. The progressive removal of Tt-L12 dimers caused a stepwise reduction of ribosomal activities, which suggested that each individual stalk dimer contributed to ribosomal function. Interestingly, the hybrid ribosomes showed higher EF-G-dependent GTPase activity than E. coli ribosomes, even when two or one Tt-L12 dimer. This result seems to be due to a structural characteristic of Tt-L12 dimer.
Pseudotime Ordering of Single Human β-Cells Reveals States of Insulin Production and Unfolded Protein Response (2018)

Proinsulin is a misfolding-prone protein, making its biosynthesis in the endoplasmic reticulum (ER) a stressful event. Pancreatic β-cells overcome ER stress by activating the unfolded protein response (UPR) and reducing insulin production. This suggests that β-cells transition between periods of high insulin biosynthesis and UPR-mediated recovery from cellular stress. We now report the pseudotime ordering of single β-cells from humans without diabetes detected by large-scale RNA sequencing. We identified major states with <i>1</i>) low UPR and low insulin gene expression, <i>2</i>) low UPR and high insulin gene expression, or <i>3</i>) high UPR and low insulin gene expression. The latter state was enriched for proliferating cells. Stressed human β-cells do not dedifferentiate and show little propensity for apoptosis. These data suggest that human β-cells transition between states with high rates of biosynthesis to fulfill the body's insulin requirements to maintain normal blood glucose levels and UPR-mediated recovery from ER stress due to high insulin production.
Cone photoreceptors are the main targets for gene therapy of NPHP5 (IQCB1) or NPHP6 (CEP290) blindness: generation of an all-cone Nphp6 hypomorph mouse that mimics the human retinal ciliopathy (2011)

Leber congenital amaurosis (LCA), a severe autosomal recessive childhood blindness, is caused by mutations in at least 15 genes. The most common molecular form is a ciliopathy due to NPHP6 (CEP290) mutations and subjects have profound loss of vision. A similarly severe phenotype occurs in the related ciliopathy NPHP5 (IQCB1)-LCA. Recent success of retinal gene therapy in one form of LCA prompted the question whether we know enough about human NPHP5 and NPHP6 disease to plan such treatment. We determined that there was early-onset rapid degeneration of rod photoreceptors in young subjects with these ciliopathies. Rod outer segment (OS) lamination, when detectable, was disorganized. Retinal pigment epithelium lipofuscin accumulation indicated that rods had existed in the past in most subjects. In contrast to early rod losses, the all-cone human fovea in NPHP5-and NPHP6-LCA of all ages retained cone nuclei, albeit with abnormal inner segments and OS. The rd16 mouse, carrying a hypomorphic Nphp6 allele, was a good model of the rod-dominant human extra-foveal retina. Rd16 mice showed normal genesis of photoreceptors, including the formation of cilia, followed by abnormal elaboration of OS and rapid degeneration. To produce a model of the all-cone human fovea in NPHP6-LCA, we generated rd16;Nrl 2/ 2 double-mutant mice. They showed substantially retained cone photoreceptors with disproportionate cone function loss, such as in the human disease. NPHP5-and NPHP6-LCA across a wide age spectrum are thus excellent candidates for cone-directed gene augmentation therapy, and the rd16;Nrl 2/2 mouse is an appropriate model for pre-clinical proof-of-concept studies.
BACK TO NATURE (2001)

The fruitfly has inspired a new approach to network design, and DNA and evolution are providing ways of solving big computing problems. Daniel Ballin and Robert Ghanea-Hercock explain how researchers are going back to nature to rethink the development of complex systems
Collimated Fibers with Bragg Gratings for Strain Sensing of Rapidly Rotating Mechanical Structures (2015)

Standard single mode fibers terminated with small diameter collimators are coupled to fiber Bragg gratings to demonstrate a generic approach for optical strain measurement in rapidly rotating structures which does not require optical ingress via the central rotation axis. Strain has been measured dynamically for a drum rotating at rates of up to 5000 rpm, and results agree very well with numerical calculations.
Robust Separation of Signal Domain From Single Channel Mixed Signal Output of Automotive Urea Based Selective Catalytic Reduction Systems (2013)

There is a class of sensor constrained, uncertain, chemical reactor systems that pose unique challenges with regard to the feedback signal. We refer specifically to the urea based selective catalytic reduction (SCR) of nitrogen oxides (NOx) in the engine exhaust of diesel powertrains. These catalysts rely on adsorbed ammonia (NH3), produced from aqueous urea, for the catalytic reduction of NOx to N2. Typically, underinjection of urea will result in the slip of NOx, whereas overinjection will induce NH3 slip. The ideal control objective of such a plant is, therefore, to regulate urea injection such that the net slip over the catalyst is minimized. Meeting these control objectives is made difficult due to the presence of an output sensor that is cross sensitive to both NOx and NH3, thereby producing a mixed feedback signal. This signal confounding poses significant challenges with regard to the stability and robustness of both closed loop control as well as on board diagnostics. In the absence of a robust NH3 sensor, it becomes necessary to create alternate methods of signal disambiguation. However, so far in open literature, there has not been a detailed discussion of this problem nor has a concrete solution been proposed to robustly and continuously identify the nature of slip as NOx or NH3. In this paper, we discuss the systematic development of a new method that allows a robust and continuous determination of the slip regime from the mixed signal output of a standard NOx sensor. The full scope of the practical problem is discussed and the performance of the proposed method is shown via experimental data.
All fired up over fire detectors (1993)

I was surprised to read Bob Peat's claim (Physics in action, June p23) that the detection of fires by detecting gaseous products-of-combustion is "a novel concept pioneered by AEA Technology". Experimental work on this idea, using broadly the same type of sensor discussed by Bob Peat (i.e. metal-oxide semiconductor gas sensors), was initiated by British Coal (then the National Coal Board) as long ago as 1977. Fire detection instruments using this principle were introduced underground in UK coal mines around 1980 (the semiconductor sensor employed was a commercially available device). Indeed the most common coal mine fire detector currently in use, which incorporates both this semiconductor and a commercial electrochemical carbon monoxide sensor, has been available for the last 10 years.
Synthesis of Some 4-Chloro-5-cyano-2-dialkylamino-6H-1,3-oxazin-6-ones and their Reactions with Trialkyl Phosphites to Give Dialkyl (5-Cyano-2-dialkylamino-6-oxo-6H-1,3-oxazin-4-yl)phosphonates (1992)

The reaction of the salts of alkyl dicyanoacetates and N-(dichloromethylene) dialkylammonium chlorides in chloroform leads to 4-chloro-5-cyano-2-dialkylamino-6H -1,3-oxazin-6-ones. The chloro atom of these compounds can be easily substituted in a Michaelis-Arbuzov reaction with trialkyl phosphites, giving dialkyl (5-cyano-2-dialkylamino-6-oxo-6-H-1,3-oxazin-4-yl)phosphonates in good yields.
Graph Neural Network-based Clustering Enhancement in VANET for Cooperative Driving (2022)

The significantly increasing number of vehicles brings convenience to daily life while also introducing significant challenges to the transportation network and air pollution. It has been proved that platooning/clustering-based driving can significantly reduce road congestion and exhaust emissions and improve road capacity and energy efficiency. This paper aims to improve the stability of vehicle clustering to enhance the lifetime of cooperative driving. Specifically, we use a Graph Neural Network (GNN) model to learn effective node representations, which can help aggregate vehicles with similar patterns into stable clusters. To the best of our knowledge, this is the first generalized learnable GNN-based model for vehicular ad hoc network clustering. In addition, our centralized approach makes full use of the ubiquitous presence of the base stations and edge clouds. It is noted that a base station has a vantage view of the vehicle distribution within the coverage area as compared to distributed clustering approaches. Specifically, eNodeB-assisted clustering can greatly reduce the control message overhead during the cluster formation and offload to eNodeB the complex computations required for machine learning algorithms. We evaluated the performance of the proposed clustering algorithms on the open-source highD dataset. The experiment results demonstrate that the average cluster lifetime and cluster efficiency of our GNN-based clustering algorithm outperforms state-of-the-art baselines.
Direct laser writing of vapour-responsive photonic arrays (2021)

Using direct laser writing, arrays of optically responsive ionogel structures were fabricated. To demonstrate their responsive nature, visible colour changes in the presence of different solvent vapours were investigated. This represents a new departure for photonic structural colouration, in which the fabricating structure shows a programmable, controllable, and dynamic stimuli response.
Hydrazide Reactive Peptide Tags for Site-Specific Protein Labeling (2011)

New site-specific protein labeling (SSPL) reactions for targeting-specific, short peptides could be useful for the real-time detection of proteins inside of living cells. One SSPL approach matches bioorthogonal reagents with complementary peptides. Here, hydrazide reactive peptides were selected from phage-displayed libraries using reaction-based selections. Selection conditions included washes of varying pH and treatment with NaCNBH(3) in order to specifically select reactive carbonyl-containing peptides. Selected peptides were fused to T4 lysozyme or synthesized on filter paper for colorimetric assays of the peptide-hydrazide interaction. A peptide-lysozyme protein fusion demonstrated specific, covalent labeling by the hydrazide reactive (HyRe) peptides in crude bacterial cell lysates, sufficient for the specific detection of an overexpressed protein fusion. Chemical synthesis of a short HyRe tag variant and subsequent reaction with two structurally distinct hydrazide probes produced covalent adducts observable by MALDI-TOF MS and MS/MS. Rather than isolating reactive carbonyl-containing peptides, we observed reaction with the N-terminal His of HyRe tag 114, amino acid sequence HKSNHSSKNRE, which attacks the hydrazide carbonyl at neutral pH. However, at the pH used during selection wash steps (<6.0), an alternative imine-containing product is formed that can be reduced with sodium cyanoborohydride. MSMS further reveals that this low pH product forms an adduct on Ser6. Further optimization of the novel bimolecular reaction described here could provide a useful tool for in vivo protein labeling and bioconjugate synthesis. The reported selection and screening methods could be widely applicable to the identification of peptides capable of other site-specific protein labeling reactions with bioorthogonal reagents.