gebhart/patrepeval huggingface dataset:
A complete and computationally efficient numerical model of aplanatic solid immersion lens scanning microscope (2013)

This paper presents a computational model for modeling an aplanatic solid immersion lens scanning microscope. The scanning microscope model consists of three subsystems, each of which can be computed as a separate system, connected to the preceding or succeeding subsystem through the input/output only. Numerical techniques are used to enhance the computational efficiency of each subsystem. A distinct merit of the proposed model is that it can be used to simulate imaging results for diverse setups of the scanning microscope, like various polarizations, numerical aperture, and different detector pinhole sizes. It allows the study and analysis of both theoretical aspects like achievable resolution, and practical aspects like expected images for different object patterns and experimental setups. Further, due to its computational efficiency, diverse large scale structures can be easily simulated in scanning microscope and good experimental approaches determined before indulging into the time consuming and costly process of experimentation.
Fast Nonnegative Deconvolution for Spike Train Inference From Population Calcium Imaging (2010)

Fluorescent calcium indicators are becoming increasingly popular as a means for observing the spiking activity of large neuronal populations. Unfortunately, extracting the spike train of each neuron from a raw fluorescence movie is a nontrivial problem. This work presents a fast nonnegative deconvolution filter to infer the approximately most likely spike train of each neuron, given the fluorescence observations. This algorithm outperforms optimal linear deconvolution (Wiener filtering) on both simulated and biological data. The performance gains come from restricting the inferred spike trains to be positive (using an interior-point method), unlike the Wiener filter. The algorithm runs in linear time, and is fast enough that even when simultaneously imaging >100 neurons, inference can be performed on the set of all observed traces faster than real time. Performing optimal spatial filtering on the images further refines the inferred spike train estimates. Importantly, all the parameters required to perform the inference can be estimated using only the fluorescence data, obviating the need to perform joint electrophysiological and imaging calibration experiments.
An Online Survey on the Perception of Mediated Social Touch Interaction\n and Device Design (2021)

Social touch is essential for our social interactions, communication, and\nwell-being. It has been shown to reduce anxiety and loneliness; and is a key\nchannel to transmit emotions for which words are not sufficient, such as love,\nsympathy, reassurance, etc. However, direct physical contact is not always\npossible due to being remotely located, interacting in a virtual environment,\nor as a result of a health issue. Mediated social touch enables physical\ninteractions, despite the distance, by transmitting the haptic cues that\nconstitute social touch through devices. As this technology is fairly new, the\nusers' needs and their expectations on a device design and its features are\nunclear, as well as who would use this technology, and in which conditions. To\nbetter understand these aspects of the mediated interaction, we conducted an\nonline survey on 258 respondents located in the USA. Results give insights on\nthe type of interactions and device features that the US population would like\nto use.\n
A qualitative study exploring the lived experience of medication use in different disease states: Linking experiences of disease symptoms to medication adherence (2020)

Patients with symptomatic and asymptomatic diseases share similar experiences of medication adherence.
In-vitro study of organosilane coated degradable magnesium dental mesh (2016)

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Evolutionary principles and their practical application (2011)

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology.
Extended follow-up of children in a phase2b trial of the GMZ2 malaria vaccine (2021)

GMZ2/alum was well tolerated. Follow-up over 2 years confirmed a low level of vaccine efficacy with slightly higher efficacy in older children, which suggests GMZ2 may act in concert with naturally acquired immunity.
Rosuvastatin Ameliorates Obesity and Proteinuria in Zucker Diabetic Fatty Rats (2013)

Obesity and metabolic syndrome are major risk factors for the development of atherosclerosis or chronic kidney disease. In this paper, we investigated the effect of rosuvastatin and atorvastatin on endothelial function, and liver and kidney function in obese fa/fa Zucker diabetic fatty (ZDF) rats. ZDF rats were administered rosuvastatin (10 mg/kg/day p.o.) or atorvastatin (10 mg/kg/day p.o.) for 12 weeks. Rosuvastatin treatment decreased body weight and fat weight. Neither statin affected the blood sugar and total cholesterol levels, whereas they led to a significant decrease in triglyceride and liver markers (AST and ALT). Rosuvastatin, but not atorvastatin, markedly reduced elevated urinary protein excretion after 12 weeks of treatment. Endothelial function, which was evaluated by EC50 values for acetylcholine-induced relaxation of mesenteric artery rings, was altered after 12 weeks of treatment with rosuvastatin, but not atorvastatin. Our findings suggest that rosuvastatin treatment may improve obesity, proteinuria and endothelial function compared with treatment with atorvastatin. Keywords: Atorvastatin, CKD, diabetes, dyslipidemia, endothelial function, fatty liver, metabolic sindrome, obesity, proteinuria, rosuvastatin.
Long-Term Programming of Antigen-Specific Immunity from Gene Expression Signatures in the PBMC of Rhesus Macaques Immunized with an SIV DNA Vaccine (2011)

While HIV-1-specific cellular immunity is thought to be critical for the suppression of viral replication, the correlates of protection have not yet been determined. Rhesus macaques (RM) are an important animal model for the study and development of vaccines against HIV/AIDS. Our laboratory has helped to develop and study DNA-based vaccines in which recent technological advances, including genetic optimization and in vivo electroporation (EP), have helped to dramatically boost their immunogenicity. In this study, RMs were immunized with a DNA vaccine including individual plasmids encoding SIV gag, env, and pol alone, or in combination with a molecular adjuvant, plasmid DNA expressing the chemokine ligand 5 (RANTES), followed by EP. Along with standard immunological assays, flow-based activation analysis without ex vivo restimulation and high-throughput gene expression analysis was performed. Strong cellular immunity was induced by vaccination which was supported by all assays including PBMC microarray analysis that identified the up-regulation of 563 gene sequences including those involved in interferon signaling. Furthermore, 699 gene sequences were differentially regulated in these groups at peak viremia following SIVmac251 challenge. We observed that the RANTES-adjuvanted animals were significantly better at suppressing viral replication during chronic infection and exhibited a distinct pattern of gene expression which included immune cell-trafficking and cell cycle genes. Furthermore, a greater percentage of vaccine-induced central memory CD8+ T-cells capable of an activated phenotype were detected in these animals as measured by activation analysis. Thus, co-immunization with the RANTES molecular adjuvant followed by EP led to the generation of cellular immunity that was transcriptionally distinct and had a greater protective efficacy than its DNA alone counterpart. Furthermore, activation analysis and high-throughput gene expression data may provide better insight into mechanisms of viral control than may be observed using standard immunological assays.
Radiometric Analysis from the 26-Kilowatt Electric Propulsion Space Experiment Flight (2002)

The U.S. Air Force Research Laboratory's Electric Propulsion Space Experiment (ESEX) was launched and operated in early 1999 to demonstrate the compatibility and readiness of a 30-kW class ammonia arcjet for satellite propulsion applications. As part of this flight, an array of onboard contamination sensors was used to assess the effect of the arcjet and other environments on the spacecraft. The sensors consisted of microbalances to measure material deposition, radiometers to assess material degradation due to thermal radiation or contamination, and solar cell segments to investigate solar array degradation. Over eight firings of the ESEX arcjet, and 33 min, 26 s operating time, the radiometer near the thruster, viewing the arcjet plume and body, experiences a change in the thermal properties of its coating from the firings. Radiometers with no view of the arcjet, or a view of only the plume, show no change. In general, degradation effects are observed only on sensors near the thruster exhaust nozzle, a location unlikely to be used in an operational high-power electric propulsion system. No degradation effects are observed in the backplane of the thruster. For future programs, although engineering measures may be needed for spacecraft equipment in the immediate vicinity of the thruster body, the arcjet environment is generally benign.
Protective effects of colostral antibodies to Br abortus on strain 19 vaccination and field injection. (1978)

Calves which have received no antibodies against Br abortus in their colostrum may respond to strain 19 vaccination even on the first day of life. However, calves with such antibodies may completely suppress any response to S19 vaccination. In calves which have received very high titres of passive antibodies from their dams complete suppresson of vaccinal response may be expected to occur up to about 153 days of age. Thus, if vaccination is restricted to between 90 and 180 days many calves in infected herds will not be protected by routine vaccination with S19. In calves born of and reared on infected dams the colostral antibodies also have a marked protective effect. In spite of heavy exposure to Br abortus at birth and later from infected milk only six out of 64 calves (9.4 per cent) developed persistent positive titres. The remaining calves reverted to zero titres within 12 months and an anamnestic test indicated that of these up to 15 per cent may have been latent carriers but even more remarkably, 85 per cent of such calves were not even "primed" by such heavy exposure.
Low-Complexity Channel-Likelihood Estimation for Non-Binary Codes and QAM (2012)

An approximate channel-likelihood estimation algorithm is introduced for non-binary coded, square quadrature-amplitude-modulated systems. It is shown that the proposed approximation greatly simplifies the calculation of channel-likelihoods and yet provides results close to those based on exact calculations for non-binary low-density parity-check codes over the additive white Gaussian noise channel.
Serological and immunochemical analysis of Lewis Y (Ley) blood group antigen expression in epithelial ovarian cancer (1996)

The expression of Ley blood group antigen in epithelial ovarian cancer tissues and cell lines has been studied using a Ley-specific monoclonal antibody (MAb 3S193). In ovarian cancer specimens, Ley was expressed in 75% of the 140 tumor specimens examined, with strong or moderate expression being observed in 56% of the samples. Seven of the 11 ovarian cancer cell lines studied were Ley-positive. Using immunochemical approaches, Ley epitopes were found to be expressed on 4 types of carrier molecules: CA125 ovarian cancer antigen, MUC-1 mucins, lower m.w. glycoproteins and glycolipids. In cell lines, Ley was more commonly expressed on MUC-1 mucin than on CA125, whereas in tumor specimens Ley was commonly found on both CA125 and MUC-1. The biochemical nature of the smaller Ley glycoproteins was not determined, but it was shown that they were not CEA and LAMP-1, known Ley carriers in some other tumor types. Glycolipids carrying Ley epitopes were detected in both ovarian cancer cell lines and tumor specimens. The presence of Ley epitopes on a number of different molecular carriers, including 2 major ovarian cancer antigens (CA125 and MUC-1), explains the high incidence of Ley in ovarian cancer. The high expression of Ley in ovarian cancer and the availability of specific murine and humanized MAbs make Ley an attractive candidate target for clinical studies.
Role of an RNase III Binding Site in Transcription Termination at λ nutL by HK022 Nun Protein (2006)

The phage HK022 Nun protein excludes phage lambda by binding nascent lambda pL and pR transcripts at nutL and nutR, respectively, and inducing transcription termination just downstream of these sites. Termination is more efficient at nutL than at nutR. One difference between nutL and nutR is the presence of RNase III processing sites (rIII) located immediately promoter distal to lambda nutL. We found that deletion of rIII dramatically reduced Nun transcription arrest in vitro but had little effect on termination in vivo. However, consistent with the in vitro results, overexpression of a transcript carrying nutL and rIII efficiently titrated Nun, allowing lambda to grow on a strain that expressed Nun, whereas a transcript carrying only nutL or nutL-rIII with nucleotides 97 to 141 deleted was ineffective. Rnc70, an RNase III mutant that binds but does not cleave rIII, also prevented Nun-mediated lambda exclusion. We propose that rIII enhances the on-rate of Nun at nutL, stimulating Nun-mediated arrest in vitro. We have shown that a specific element in rIII, i.e., box C (G89GUGUGUG), strongly enhances arrest on rIII+ templates. Nun-rIII interactions do not stimulate Nun termination in vivo, presumably because formation of the Nun-nutL complex is normally not rate-limiting in the cell. In contrast to Nun, N is not occluded by Rnc70 and is not efficiently titrated by a nutL-rIII transcript.
A Roadmap for Reaching the Potential of Brain‐Derived Computing (2020)

Neuromorphic computing is a critical future technology for the computing industry, but it has yet to achieve its promise and has struggled to establish a cohesive research community. A large part of the challenge is that full realization of the potential of brain inspiration requires advances in both device hardware, computing architectures, and algorithms. This simultaneous development across technology scales is unprecedented in the computing field. This article presents a strategy, framed by market and policy pressures, for moving past these current technological and cultural hurdles to realize its full impact across technology. Achieving the full potential of brain‐derived algorithms as well as post‐complementary metal–oxide‐semiconductor (CMOS) scaling neuromorphic hardware requires appropriately balancing the near‐term opportunities of deep learning applications with the long‐term potential of less understood opportunities in neural computing.
Nouvelles méthodes pour la recherche sémantique et esthétique d'informations multimédia (2013)

In the internet era, computerized classification and discovery of image properties (objects, scene, emotions generated, aesthetic traits) is of crucial importance for the automatic retrieval of the huge amount of visual data surrounding us. But how can computers see the meaning of an image? Multimedia Information Retrieval (MMIR) is a research field that helps building intelligent systems that automatically recognize the image content and its characteristics. In general, this is achieved by following a chain process: first, low-level features are extracted and pooled into compact image signatures. Then, machine learning techniques are used to build models able to distinguish between different image categories based on such signatures. Such model will be finally used to recognize the properties of a new image. Despite the advances in the field, human vision systems still substantially outperform their computer-based counterparts. In this thesis we therefore design a set of novel contributions for each step of the MMIR chain, aiming at improving the global recognition performances. In our work, we explore techniques from a variety of fields that are not traditionally related with Multimedia Retrieval, and embed them into effective MMIR frameworks. For example, we borrow the concept of image saliency from visual perception, and use it to build low-level features. We employ the Copula theory of economic statistics for feature aggregation. We re-use the notion of graded relevance, popular in web page ranking, for visual retrieval frameworks. We explain in detail our novel solutions and prove their effectiveness for image categorization, video retrieval and aesthetics assessment.
Dermatology and Aesthetic Medicine Applications (2018)

b]15.1 Effects of LLLT on Skin</strong> <strong>15.1.1 Skin rejuvenation</strong> Skin aging is a process that can present itself relatively early on in life, sometimes even as soon as 20 - 30 years of age. Common signs and symptoms associated with skin aging include skin wrinkling, skin dyspigmentation, telangiectasia, and reduced tissue elasticity. At the histological and molecular level, common noticeable features include a reduction in collagen content, fragmentation of collagen fibers, elastotic degeneration of elastic fibers, the appearance of dilated and tortuous dermal vessels, disorientation and atrophy of the epidermis, and up-regulation of matrix metalloproteinases (MMPs), especially MMP-1 and MMP-2. Skin aging can be influenced by both time (normal aging) and environmental factors, but the single most influential factor responsible for accelerated skin aging is believed to be ultraviolet (UV) radiation-induced photodamage.
Non-intrusive estimation of the level of reverberation in speech (2014)

We show corroborating evidence that, among a set of common acoustic parameters, the clarity index C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">50</sub> provides a measure of reverberation that is well correlated with speech recognition accuracy. We also present a data driven method for non-intrusive C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">50</sub> parameter estimation from a single channel speech signal. The method extracts a number of features from the speech signal and uses a binary regression tree, trained on appropriate training data, to estimate the C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">50</sub> . Evaluation is carried out using speech utterances convolved with real and simulated room impulse responses, and additive babble noise. The new method outperforms a baseline approach in our evaluation.
Systolic MOLLI T1 mapping with heart-rate-dependent pulse sequence sampling scheme is feasible in patients with atrial fibrillation (2016)

Systolic MOLLI T1 mapping with heart-rate-dependent pulse sequence scheme can improve image quality and avoid T1 underestimation. It is feasible and with further validation may extend clinical applicability of T1 mapping to patients with atrial fibrillation.
Optical spectroscopy of a singleAl0.36In0.64As/Al0.33Ga0.67Asquantum dot (2001)

We report results of interband spectroscopy of a single ${\mathrm{Al}}_{0.36}{\mathrm{In}}_{0.64}{\mathrm{A}\mathrm{s}/\mathrm{A}\mathrm{l}}_{0.33}{\mathrm{Ga}}_{0.67}\mathrm{As}$ self-assembled quantum dot. The single dot spectroscopy has been carried out at low temperature as a function of the excitation power and magnetic field up to 8 T. The emission spectra as a function of excitation power show two distinct groups of transitions that we associate with the recombination from ground and excited quantum dot levels with a spacing of \ensuremath{\sim}70 meV. The application of magnetic field allows us to identify the exciton emission as well as the emission from the biexciton, and charged exciton complexes with binding energies of \ensuremath{\sim}5 meV. The binding energies compare favorably with results of calculations.
Full efficacy and long-term immunogenicity induced by the SARS-CoV-2 vaccine candidate MVA-CoV2-S in mice (2022)

Two doses of the MVA-CoV2-S vaccine candidate expressing the SARS-CoV-2 spike (S) protein protected K18-hACE2 transgenic mice from a lethal dose of SARS-CoV-2. This vaccination regimen prevented virus replication in the lungs, reduced lung pathology, and diminished levels of pro-inflammatory cytokines. High titers of IgG antibodies against S and receptor-binding domain (RBD) proteins and of neutralizing antibodies were induced against parental virus and variants of concern, markers that correlated with protection. Similar SARS-CoV-2-specific antibody responses were observed at prechallenge and postchallenge in the two-dose regimen, while the single-dose treatment does not avoid vaccine breakthrough infection. All vaccinated animals survived infection and were also protected to SARS-CoV-2 reinfection. Furthermore, two MVA-CoV2-S doses induced long-term memory S-specific humoral and cellular immune responses in C57BL/6 mice, 6 months after immunization. The efficacy and immunological benefits of the MVA-CoV2-S vaccine candidate against COVID-19 supports its consideration for human clinical trials.
Fair Bandwidth allocation between service providers in a geostationary satellite network (2002)

We consider the problem of how a geostationary satellite should assign bandwidth to several service providers (operators) so as to meet some minimum requirements, on one hand, and to perform the allocation in a fair way, on the other hand. In the paper, we firstly address practical issues (such as integrity constraints), whereafter we provide a computational method for obtaining an optimal fair allocation in polynomial time taking the practical issues into account.