gebhart/patrepeval huggingface dataset:
Rapid Detection of SARS-CoV-2 Using Reverse transcription RT-LAMP method (2020)

Abstract Corona Virus Disease 2019 (COVID-19) is a recently emerged life-threatening disease caused by SARS-CoV-2. Real-time fluorescent PCR (RT-PCR) is the clinical standard for SARS-CoV-2 nucleic acid detection. To detect SARS-CoV-2 early and control the disease spreading on time, a faster and more convenient method for SARS-CoV-2 nucleic acid detecting, RT-LAMP method (reverse transcription loop-mediated isothermal amplification) was developed. RNA reverse transcription and nucleic acid amplification were performed in one step at 63 °C isothermal conditions, and the results can be obtained within 30 minutes. ORF1ab gene, E gene and N gene were detected at the same time. ORF1ab gene was very specific and N gene was very sensitivity, so they can guarantee both sensitivity and specificity for SARS-CoV-2. The sensitivity of RT-LAMP assay is similar to RT-PCR, and specificity was 99% as detecting 208 clinical specimens. The RT-LAMP assay reported here has the advantages of rapid amplification, simple operation, and easy detection, which is useful for the rapid and reliable clinical diagnosis of SARS-CoV-2.
An improved technique of perfusion of the stomach for the study of gastric secretion in the rat. (1967)

Synaptic ribbons are large, dynamic structures in the active zone complex of ribbon synapses and important for the physiological properties of these tonically active synapses. RIBEYE is a unique and major protein component of synaptic ribbons. The aim of the present study was to understand how the synaptic ribbon is built and how the construction of the ribbon could contribute to its ultrastructural plasticity. In the present study, we demonstrate that RIBEYE self-associates using different independent approaches (yeast two-hybrid analyses, protein pull downs, synaptic ribbon–RIBEYE interaction assays, coaggregation experiments, transmission electron microscopy and immunogold electron microscopy). The A-domain [RIBEYE(A)] and B-domain [RIBEYE(B)] of RIBEYE contain five distinct sites for RIBEYE–RIBEYE interactions. Three interaction sites are present in the A-domain of RIBEYE and mediate RIBEYE(A)–RIBEYE(A) homodimerization and heterodimerization with the B-domain. The docking site for RIBEYE(A) on RIBEYE(B) is topographically and functionally different from the RIBEYE(B) homodimerization interface and is negatively regulated by nicotinamide adenine dinucleotide. The identified multiple RIBEYE–RIBEYE interactions have the potential to build the synaptic ribbon: heterologously expressed RIBEYE forms large electron-dense aggregates that are in part physically associated with surrounding vesicles and membrane compartments. These structures resemble spherical synaptic ribbons. These ribbon-like structures coassemble with the active zone protein bassoon, an interaction partner of RIBEYE at the active zone of ribbon synapses, emphasizing the physiological relevance of these RIBEYE-containing aggregates. Based on the identified multiple RIBEYE–RIBEYE interactions, we provide a molecular mechanism for the dynamic assembly of synaptic ribbons from individual RIBEYE subunits.
Mitochondrial oxidative metabolism in motor neuron degeneration (<i>mnd</i>) mouse central nervous system (2002)

The mnd mouse spontaneously develops slowly evolving motoneuron pathology leading to progressive motor impairment. There is strong evidence that a complex interplay between oxidative stress, mitochondria abnormalities and alteration of glutamate neurotransmission plays an important role in the pathogenesis of motor neuron diseases. Therefore, we investigated the presence of mitochondrial dysfunction in frontal, central (comprising the motor area) and occipital regions of the cerebral cortex and in the spinal cord of 35-week-old mnd mice. Lipid peroxide derivatives reacting with thiobarbituric acid (TBARS) were measured in the cervical, thoracic and lumbar spinal cord. In addition biochemical and behavioural analyses were carried out in mnd mice chronically treated with l-carnitine from the 11th to the 34th week of life (mndT mice). Slight but significant alterations of mitochondrial enzyme activities were seen in the mnd cortical regions. The central area was the most affected and both complex I, IV and citrate synthase were decreased with respect to controls. The rate of oxygen consumption (QO2) was markedly decreased in both the upper (cervical + upper portion of the thoracic region) and lower (lumbar + lower portion of the thoracic region) mnd spinal cord. The level of TBARS showed a rostro-caudal trend to increase, being 30% higher in the lumbar tract of mnd mice in comparison with controls. L-carnitine treatment increased the mitochondrial enzyme activities in cortical regions towards control value and was effective in enhancing QO2 and decreasing TBARS levels in the spinal cord of mndT. Behavioural testing showed that L-carnitine significantly delayed the onset of motor behaviour impairment. This beneficial effect was declining at 35 week of age, when the biochemical measurements were performed.
Potential market for LNG-fueled marine vessels in the United States (2008)

Thesis (S.M. in Ocean Systems Management)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2008.
Cross-spectral methods for processing speech (2001)

We present time-frequency methods which are well suited to the analysis of nonstationary multicomponent FM signals, such as speech. These methods are based on group delay, instantaneous frequency, and higher-order phase derivative surfaces computed from the short time Fourier transform (STFT). Unlike more conventional approaches, these methods do not assume a locally stationary approximation of the signal model. We describe the computation of the phase derivatives, the physical interpretation of these derivatives, and a re-mapping algorithm based on these phase derivatives. We show analytically, and by example, the convergence of the re-mapping to the FM representation of the signal. The methods are applied to speech to estimate signal parameters, such as the group delay of a transmission channel and speech formant frequencies. Our goal is to develop a unified method which can accurately estimate speech components in both time and frequency and to apply these methods to the estimation of instantaneous formant frequencies, effective excitation time, vocal tract group delay, and channel group delay. The proposed method has several interesting properties, the most important of which is the ability to simultaneously resolve all FM components of a multicomponent signal, as long as the STFT of the composite signal satisfies a simple separability condition. The method can provide super-resolution in both time and frequency in the sense that it can simultaneously provide time and frequency estimates of FM components, which have much better accuracy than the Heisenberg uncertainty of the STFT. Super-resolution provides the capability to accurately "re-map" each component of the STFT surface to the time and frequency of the FM signal component it represents. To attain high resolution and accuracy, the signal must be jointly estimated simultaneously in time and frequency. This is accomplished by estimating two surfaces, which are essentially the derivatives of the STFT phase with respect to time and frequency. To avoid phase ambiguities, the differentiation is performed as a cross-spectral product.
Novel shared-aperture phased arrays (1998)

The proposed phased array breaks the nexus between the surveillance and tracking functions of a radar system completely, and meets the modern challenges imposed by a dense multitarget environment where clutter, rain, or chaff are present. Compared to a conventional phased array, the novel array yields an order magnitude improvement in the time available to perform the above radar functions, and further improvements are easily attainable. © 1998 John Wiley & Sons, Inc. Microwave Opt Technol Lett 17: 189–192, 1998.
Highly regular wavelets for the detection of clustered microcalcifications in mammograms (2003)

In this paper, we consider the problem of detecting clustered microcalcification in digitized mammograms using new wavelets with a high Sobolev regularity index. We experimentally assess the superiority of the new wavelets when compared with the classical ones.
Novel approach to Abel inversion (2007)

Simple yet versatile, physically valid emissivity functions for peaked and hollow profiles with only two determinable parameters are proposed for performing Abel inversion. The advantages of the proposed functions have been explored. The inversion is very fast, accurate, convenient, and viable, in contrast to the existing methods. The validation of these functions has been confirmed by using simulated data under various conditions. The error in the process has been computed and found to depend on the functional form of the model emissivity. A comprehensive comparison has been drawn with the existing method and it has been found to offer a definite advantage over the existing technique in some respects, especially for real time applications. Limitation of this technique has also been discussed. The soft x-ray and visible light emissivity profile of SINP tokamak has been successfully obtained by using this method.
Preservative Effectiveness of Lumber-Cored Plywood Treated with Disodium Octaborate Tetrahydrate. (2002)

八ホウ酸二ナトリウム四水和物(DOT, Timbor®)を注入したParaserianthes falcataria(ファルカータ)をコア材としたランバーコア合板の防腐性能を室内標準試験によって評価した。ファルカータに0.12～0.5%DOT水溶液を加圧注入した結果,いずれの濃度においても良好な注入性を示し,各濃度における注入量の平均は607～651kg/m3であった。DOTを加圧注入したファルカータ試験体の中央部付近においてもDOTは浸透していたが,木口端部から内部へ進むにしたがいDOT吸収量(BAE)が減少し,試験体の中央部付近(木口端部から20cm)における吸収量は,木口端部における吸収量の60～70%程度であった。DOTで処理したランバーコア合板の防腐性能を調べた結果,コア材中のDOT吸収量がオオウズラタケに対して2kg/m3 BAE以上,カワラタケに対して1kg/m3 BAE以上で,高い防腐性能を示すことがわかった。また,単板塗布処理あるいは接着剤混入処理にも供試菌の侵入を防止する効果が認められた。
Metformin: an old but still the best treatment for type 2 diabetes (2013)

The management of T2DM requires aggressive treatment to achieve glycemic and cardiovascular risk factor goals. In this setting, metformin, an old and widely accepted first line agent, stands out not only for its antihyperglycemic properties but also for its effects beyond glycemic control such as improvements in endothelial dysfunction, hemostasis and oxidative stress, insulin resistance, lipid profiles, and fat redistribution. These properties may have contributed to the decrease of adverse cardiovascular outcomes otherwise not attributable to metformin's mere antihyperglycemic effects. Several other classes of oral antidiabetic agents have been recently launched, introducing the need to evaluate the role of metformin as initial therapy and in combination with these newer drugs. There is increasing evidence from in vivo and in vitro studies supporting its anti-proliferative role in cancer and possibly a neuroprotective effect. Metformin's negligible risk of hypoglycemia in monotherapy and few drug interactions of clinical relevance give this drug a high safety profile. The tolerability of metformin may be improved by using an appropiate dose titration, starting with low doses, so that side-effects can be minimized or by switching to an extended release form. We reviewed the role of metformin in the treatment of patients with type 2 diabetes and describe the additional benefits beyond its glycemic effect. We also discuss its potential role for a variety of insulin resistant and pre-diabetic states, obesity, metabolic abnormalities associated with HIV disease, gestational diabetes, cancer, and neuroprotection.
Signature-based search algorithm (2003)

Most existing search algorithms for motion compensation have been specifically tailored to exploit the interframe redundancy in image sequences that contain small amounts of motion. With large amounts of motion, the performance of these algorithms is significantly reduced. A class of signature-based search algorithms is proposed as an alternative to these algorithms. A specific example, called the frequency labeling search algorithm, is developed in detail. Experimental results show that this algorithm gives compression rates 3-5 times that achieved by other algorithms in the presence of substantial amounts of motion. The accuracy of the technique can be adjusted to suit different applications by changing the number of coefficients used in the signature and the size of the candidate set. While it is computationally more expensive than other approaches, the cost of the frequency labeling technique falls within the range reasonable for real-time applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Management of Respiratory Syncytial Virus With Lower Respiratory Tract Infection in Infants and Children (2002)

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection in infants and children requiring pediatric hospitalizations. Infants with chronic lung, cardiac, or neuromuscular conditions are at increased risk for RSV infection. Early RSV is associated with subsequent diagnosis of reactive airway disease. The management of RSV with lower respiratory track infection in infants and children remains controversial. Bronchodilators may have some short-term benefit, but are not recommended as standard practice for infants and children. Antiviral therapy may be used for high-risk and severely ill patients. Corticosteroids may be effective in cases of moderate to severe RSV with lower respiratory track infection. Monoclonal antibodies have shown some promise in achieving passive immunity for those at greatest risk, including preterm infants younger than 1 year or infants younger than 2 years with chronic lung disease. Emergency management remains primarily supportive, with vigilant monitoring of oxygenation and hydration status. Interventions include supplemental oxygen therapy, ventilation, and fluid and nutrition therapy. Respiratory syncytial virus prophylaxis for high-risk patients includes intramuscular injections of palivizumab (Synagis) each month during RSV season, from November through April. Prevention strategies include washing hands, cleaning environment surfaces, and isolating infants and children with RSV in the emergency care area.
A Point Mutation in the Polyhedrin Gene of a Baculovirus, Autographa californica MNPV, Prevents Crystallization of Occlusion Bodies (1987)

The polyhedrin gene region of the Autographa californica nuclear polyhedrosis virus(AcMNPV) morphology mutant M29 has been characterized by genetic and physical techniques. Recombination analysis of mutants M29 and AcM5polyl demonstrated that wild-type polyhedrin recombinants could be obtained and that the DNA restriction patterns of the recombinant viruses were identical to wild-type AcMNPV DNA. Marker rescue experiments using the wild-type AcMNPV EcoRI I fragment indicated that the morphology mutation responsible for the M29 phenotype was located in the 0.0 to 5.9 % region of the genome. Direct DNA sequencing of the BamHIF fragment from M29 showed a single point mutation at position 253 of the polyhedrin gene. This mutation caused a substitution of phenylalanine for leucine at amino acid 84 of the M29 polyhedrin protein. These results indicated the necessity of amino acid conservation in the polyhedrin amino acid sequence for proper folding and assembly of the polypeptide into occlusion bodies.
Red Blood Cell Development (2014)

This animation describes the formation of red blood cells from proerythroblast.
The Challenges of PFAS Remediation. (2018)

Many military bases and their surrounding communities are impacted by contamination with per- and polyfluoroalkyl substances (PFAS) from Aqueous Film-Forming Foams (AFFFs). Soil sorption technologies provide a promising solution to immobilize PFAS in the soil and prevent groundwater and drinking water contamination. This article is the result of a collaborative effort between Battelle and the U.S. EPA's review of the most promising technologies.
Laptop Education: Impact on Learning and Achievement (2010)

The purpose of this study was to examine how 1:1 Laptop initiatives in the 10th, 11th, and 12th grade affected student achievement and student academic performance over the 2008–2009 school year at a selected small rural, Minnesota high school. The two variables in this study were: perceived student performance skills based on survey results from both student and teacher participants, and pre-existing Minnesota graduation testing results and grade point averages from Fertile-Beltrami School District students. The three questions that were researched in this study were: (1) What effects does a 1:1 Laptop initiative have on student academic performance based on perceptions of participating sophomores, juniors, and seniors? (2) What effects does a 1:1 Laptop initiative have on student academic performance based on perceptions of participating faculty? (3) What effect does the 1:1 Laptop initiative for students in grades 10th, 11th, and 12th in the Fertile-Beltrami School District have on student achievement based on Minnesota graduation testing and local assessments in math and reading? The research was conducted in a small, rural setting with students in grades 10–12. The study population consisted of 105 students that attend the small, rural school during the 2008–2009 school year. A survey instrument created by the Mitchell Institute was used by the school district to collect data on student perceptions of the impact of 1:1 computing on academic achievement and learning, as well as student engagement in school. A survey instrument created by the Mitchell Institute was also used to collect data on faculty perceptions on the impact of 1:1 computing on student achievement and learning, as well as faculty's integration of technology. Evidence from this study indicates that the integration of 1:1 computing positively impacts student engagement in learning and student achievement. Evidence from this study further indicates that the amount of impact is directly related to the amount of integration by faculty. Students and faculty indicate that skills and engagement is improved through the use of 1:1 computing.
A camera neural model (2002)

Most of the techniques proposed for camera calibration consist of identifying a set of physical parameters (focal length, optical center position, coefficient of radial distortion). The determination and inversion of such a model in the case of strong or unstructured distortions is not straightforward. Instead we propose a new approach that uses artificial neural networks' abilities of interpolation and extrapolation to perform the global identification of any optical system, provided a set of pairs of calibration points given in a camera-centered frame of reference and their corresponding image in the image plane are available. A methodological framework is given that deals with the architecture of the neural network the training algorithm and the choice of the learning database. Validity and robustness of the method are shown by comparing reconstruction errors obtained by the neural model, by a theoretical prediction and by classical estimations on both linear and nonlinear lenses.
Business Building Blocks as Coordination Mechanism for Enterprise Transformations (2013)

Enterprise architecture management (EAM) aims at aligning business and IT. Therefore, EAM analyzes the current and defines the target state. In order to reach the target state, EAM plans and monitors transformations affecting business processes, information systems and the underlying IT infrastructure. Thereby, domains are a widely used tool in order to reduce the complexity. The domains structure the enterprise architecture, e.g. according to the business fields a company is working in. Resources and responsibilities are assigned to these domains and transformations are then coordinated within domains. This approach, however, poses the risk that business requirements are solved redundantly although an existing IT system from another domain could have been reused. It even hinders an integration of the IT systems used in the different business fields. This paper describes an approach for coordinating transformations based on so-called business building blocks (BBBs). BBBs define the essential business elements independent from their implementation, with a granularity suitable for reuse within and across domains. Our approach determines who is responsible for providing a solution to a certain business requirement by assigning clear responsibilities to the corresponding BBB. This business outcome-driven approach helps focusing on business requirement solutions instead of managing system solutions. Ideally, there is exactly one responsible authority per BBB. In the paper, we provide a description of our BBB identification method and relate the suggested approach into one of the currently most widely adopted EA frameworks, i.e. The Open Group Architecture Framework (TOGAF). We report about the experiences we made when using this method in various EAM projects and recommend best practices.
Seamless image stitching algorithm using radiometric lens calibration for high resolution optical microscopy (2009)

Image mosaicing method is an image-based rendering and visualization method which is a common procedure in the generation of panoramic (composite) images and applications, such as creating virtual reality, super resolution, object insertion and object removal, etc. Specifically, the image stitching approach becomes common in super resolution digital imaging microscopy, where it is required to achieve both high magnification and a large field of view. This work presents the algorithm for the stitching of different overlapped high resolution views of the whole scene obtained from high magnification optical microscopes into a large radiometric balanced image through maximization of a cross-correlation function. To seamlessly blend and reduce the possibility of intensity and color mismatching of multiple source images in mosaicing, a radiometric calibration of the microscope optical system is employed. The algorithm was tested with grayscale and color images, and showed convincing and robust results in image stitching and blending.
Dual camera intelligent sensor for high definition 360 degrees surveillance (2005)

A novel integrated multi-camera video-sensor (panoramic scene analysis – PSA) system is proposed for surveillance applications. In the proposed set-up, an omnidirectional imaging device is used in conjunction with a pan tilt zoom (PTZ) camera leading to an innovative kind of sensor that is able to automatically track at a higher zoom level any moving object within the guarded area. In particular, the catadioptric sensor is calibrated and used in order to track every single moving object within its 360 degree field of view. Omnidirectional image portions are eventually rectified and pan, tilt and zoom parameters of the moving camera are automatically adjusted by the system in order to track detected objects. In addition a co-operative strategy was developed for the selection of the object to be tracked by the PTZ sensor in the case of multiple targets.