gebhart/patrepeval huggingface dataset:
Immunogenic domains of hepatitis delta virus antigen: peptide mapping of epitopes recognized by human and woodchuck antibodies (1990)

Hepatitis delta virus (HDV) is a defective RNA virus which is dependent on hepatitis B virus for essential helper functions. Only a single highly basic phosphoprotein, HDV antigen (HDAg), is expressed by the HDV genome during infection in humans. Antibody directed to HDAg is important in the diagnosis of HDV infection, and it is likely but not yet proven that the immune response to HDAg provides significant protection against subsequent exposures to HDV. In an effort to map the antigenic domains of HDAg, 209 overlapping hexapeptides, spanning the entire 214 amino acid residues of the protein, were synthesized on polyethylene pins and probed by enzyme-linked immunosorbent assay with sera containing high titers of anti-HD antibodies. Domains recognized by antibodies present in serum from human chronic carriers of this virus included residues 2 to 7, 63 to 74, 86 to 91, 94 to 100, 159 to 172, 174 to 195, and 197 to 207. Antibody from an acutely superinfected woodchuck recognized similar epitopes, as well as a domain spanning residues 121 to 128. Together, residues in these antigenic domains constitute 41% of the HDAg molecule. Oligopeptides 15 to 29 residues in length and representing epitopes of HDAg found to be dominant in humans (residues 2 to 17, 156 to 184, and 197 to 211) were synthesized in bulk and found to possess significant antigenic activity by microdilution enzyme-linked immunosorbent assay. The reactivity of peptide 197-211 with human sera confirms that the entire 214 amino acids of HDAg are expressed during infection in vivo. In addition, these results suggest that synthetic peptides may be useful reagents for development of new and improved diagnostic tests for HDV infection.
Comparison of Triple Anti-Platelet Therapy (Aspirin, Clopidogrel, and Cilostazol) and Double Anti-Platelet Therapy (Aspirin and Clopidogrel) on Platelet Aggregation in Type 2 Diabetic Patients Undergoing Drug-Eluting Stent Implantation (2009)

Triple anti-platelet therapy showed more potent inhibition of maximal ADP induced platelet aggregation in type 2 diabetic patients receiving chronic anti-platelet therapy. This finding suggests that triple antiplatelet therapy may be more effective in preventing thrombotic complications after DES implantation in type 2 diabetic patients.
Empowering the Exercise: a Body-Controlled Trampoline Training Game (2014)

Video games can empower their players beyond reality, giving them extraordinary abilities. We investigate a novel cla ss of games that provide empowerment in both the real and the virtual world, in this case using a trampoline as part of the human-computer interface. We studied whether novice trampoline jumpers can learn trampolining skills wh ile playing a platform jumping game implemented using computer vision and a screen placed near the trampoline. 29 participants were divided into three groups: self-training, a game with a normal jump height, and a game with an exaggerated jump height. Performance was tested in pre, post and follow-up t ests. All groups improved their performance significantly. The game was consi dered more engaging and the mean flow questionnaire (SFSS) result with games was significantly higher than with self-training. The study shows that trampoline games can be fun, intuitive to play and basic trampolining skills can be improved while playing the game. A game is more engaging than self-training and extra empowerment, such as jump height exaggeration, enhances the experience. The e xaggeration did not adversely affect jumping performance, and half of the partici pants did not even consciously notice it, which suggests that there is considerabl e design freedom for manipulating the player’s movements in trampoline games.
Splicing program of human MENA produces a previously undescribed isoform associated with invasive, mesenchymal-like breast tumors (2012)

Human mena (hMENA), a member of the actin cytoskeleton regulators Ena/VASP, is overexpressed in high-risk preneoplastic lesions and in primary breast tumors and has been identified as playing a role in invasiveness and poor prognosis in breast cancers that express HER2. Here we identify a unique isoform, hMENAΔv6, derived from the hMENA alternative splicing program. In an isogenic model of human breast cancer progression, we show that hMENA(11a) is expressed in premalignant cells, whereas hMENAΔv6 expression is restricted to invasive cancer cells. "Reversion" of the malignant phenotype leads to concurrent down-regulation of all hMENA isoforms. In breast cancer cell lines, isoform-specific hMENA overexpression or knockdown revealed that in the absence of hMENA(11a), overexpression of hMENAΔv6 increased cell invasion, whereas overexpression of hMENA(11a) reduced the migratory and invasive ability of these cells. hMENA(11a) splicing was shown to be dependent on the epithelial regulator of splicing 1 (ESRP1), and forced expression of ESRP1 in invasive mesenchymal breast cancer cells caused a phenotypic switch reminiscent of a mesenchymal-to-epithelial transition (MET) characterized by changes in the cytoskeletal architecture, reexpression of hMENA(11a), and a reduction in cell invasion. hMENA-positive primary breast tumors, which are hMENA(11a)-negative, are more frequently E-cadherin low in comparison with tumors expressing hMENA(11a). These data suggest that polarized and growth-arrested cellular architecture correlates with absence of alternative hMENA isoform expression, and that the hMENA splicing program is relevant to malignant progression in invasive disease.
Data Dependence Based Testability Transformation in Automated Test Generation (2006)

Source-code based test data generation is a process of finding program input on which a selected element, e.g., a target statement, is executed. There exist many test generation methods that automatically find a solution to the test generation problem. The existing methods work well for many programs. However, they may fail or are inefficient for programs with complex logic and intricate relationships between program elements. In this paper we present a testability transformation that transforms programs so that the chances of finding a solution are increased when the existing methods fail using only the original program. In our approach data dependence analysis is used to identify statements in the program that affect computation of the fitness function associated with the target statement. The transformed program contains only these statements, and it is used to explore different ways the fitness may be computed. These explorations are inexpensive when using the transformed program as compared to explorations using the original program. As a result, executions in the transformed program that lead to the evaluation of the fitness function to the target value are identified. The identified executions are then used to guide the search in the original program to find an input on which the target statement is executed. In this paper, the approach is evaluated using a case study which demonstrates the potential for this testability transformation to improve the efficacy of the test generation
Eosinophil-Derived Cationic Proteins Activate the Synthesis of Remodeling Factors by Airway Epithelial Cells (2006)

Eosinophil cationic proteins influence several biological functions of the respiratory epithelium, yet their direct contribution to airway remodeling has not been established. We show that incubation of the human bronchial epithelial cell line, BEAS-2B, or primary cultured human bronchial epithelial cells, normal human bronchial epithelial cells, with subcytotoxic concentrations (0.1, 0.3, and 1 microM) of major basic protein (MBP), or eosinophil peroxidase (EPO), augmented the transcripts of endothelin-1, TGF-alpha, TGF-beta1, platelet-derived growth factor (PDGF)-beta, epidermal growth factor receptor, metalloproteinase (MMP)-9, fibronectin, and tenascin. A down-regulation of MMP-1 gene expression was observed exclusively in BEAS-2B cells. Cationic protein-induced transcriptional effects were followed by the release of endothelin-1, PDGF-AB in the supernatants by ELISA, and by a down- and up-regulation, respectively, in the levels of MMP-1 and MMP-9 in cell lysates, by Western blot. Cell stimulation with the synthetic polycation, poly-L-arginine, reproduced some but not all effects of MBP and EPO. Finally, simultaneous cell incubation with the polyanion molecules, poly-L-glutamic acid or heparin, restored MMP-1 gene expression but incompletely inhibited MBP- and EPO-induced transcriptional effects as well as endothelin-1 and PDGF-AB release, suggesting that cationic proteins act partially through their cationic charge. We conclude that eosinophil-derived cationic proteins are able to stimulate bronchial epithelium to synthesize factors that influence the number and behavior of structural cells and modify extracellular matrix composition and turnover.
Hyaluronan Binding to Link Module of TSG-6 and to G1 Domain of Aggrecan Is Differently Regulated by pH (2008)

The physiological functions of hyaluronan (HA) in the extracellular matrix of vertebrate tissues involve a range of specific protein interactions. In this study, the interaction of HA with the Link module from TSG-6 (Link_TSG6) and G1 domain of aggrecan (G1), were investigated by a biophysical analysis of translational diffusion in dilute solution using confocal fluorescence recovery after photobleaching (confocal FRAP). Both Link_TSG6 and G1 were shown to bind to polymeric HA and these interactions could be competed with HA(8) and HA(10) oligosaccharides, respectively. Equilibrium experiments showed that the binding affinity of Link_TSG6 to HA was maximal at pH 6.0, and reduced dramatically above and below this pH. In contrast, G1 had maximum binding at pH 7.0-8.0 and moderate to strong binding affinity over a much broader pH range (5.5-8.0). The K(D) determined for Link_TSG6 binding to HA showed a 100-fold increase in binding affinity between pH 7.4 and 6.0, whereas G1 showed a 75-fold decrease in binding affinity over the same pH range. The sharp difference observed in their pH binding suggests that pH controls the physiological function of TSG-6, with a low affinity for HA at neutral pH, but with increased affinity as the pH falls below pH 7. TSG-6 and aggrecan interact with HA through structurally homologous domains and the difference in pH-dependent binding can be understood in terms of differences in the presence and topographical distribution of key regulatory amino acids in Link_TSG6 and in the related tandem Link domains in aggrecan G1.
Minimum error entropy luenberger observer (2005)

In this paper, we apply the information-theoretic learning (ITL) technique to the extended Luenberger observer. Instead of prespecifying the globally stable observer gains for nonlinear dynamic systems, we propose minimizing the entropy of the error between the measurement and the estimated output to update the observer gains. A stochastic gradient-based algorithm is presented and the performance of the entropy observer is demonstrated on linear and nonlinear dynamic systems. We also point out that this approach leads to the introduction of kernel methods into state estimation.
<title>Motion-estimation-based registration of geometrically distorted images for watermark recovery</title> (2001)

Image registration is essential in spread spectrum based watermark detection of a distorted image. Traditional registration approaches include the use of templates and feature matching between the distorted image and a reference image. However, neither of these techniques adequately addresses localized transformation. We propose a new registration scheme based on motion estimation between the distorted image and a reference copy. Complex wavelets provide a hierarchical framework for our motion estimation algorithm and radial basis functions provide the means to correct erroneous motion vectors. Experimental results show that our approach can estimate the distortion quite accurately and allow correct watermark detection.
The diagnostic thinking and procedure for pain of unknown origin (2020)

It is a long-term puzzle for both doctors and patients that the cause of pain is not clear, and this is very prominent in clinical work. At present, there is no unified and clear definition of pain of unknown origin (POU) and clinicians have no reference documents and guidelines.Therefore, we give a definition of POU and reviewed the typical cases with pain of unknown causes collected by our department over the years. We sorted out a set of effective diagnosis and treatment thinking and procedures.

Key words: 
Diagnosis; Pain of unknown origin (POU); Thinking
Tuning Fluorinated Benzotriazole Polymers through Alkylthio Substitution and Selenophene Incorporation for Bulk Heterojunction Solar Cells (2014)

As a high-performing, medium band gap donor polymer achieving over 7% in bulk heterojunction (BHJ) solar cells with a thick active layer, PBnDT-FTAZ has demonstrated unique photovoltaic properties that have not yet been fine-tuned. In this study, three new polymers (PSBnDT-FTAZ, PBnDT-SeFTAZ, and PSBnDT-SeFTAZ) are designed to determine how the FTAZ system would respond to further structural modifications. Specifically, we aimed to answer (a) whether alkylthio substitution could increase the open circuit voltage (Voc) of the related BHJ device and (b) whether selenophene incorporation could decrease the band gap of the FTAZ polymer and lead to an improved short circuit current (Jsc), while PBnDT-FTAZ’s other desirable attributes (high fill factor and thick active layer) could still be retained. We found that although the Voc of the alkylthio-substituted polymers (PSBnDT-FTAZ and PSBnDT-SeFTAZ) did not appreciably increase, selenophene-incorporated polymers (PBnDT-SeFTAZ and PSBnDT-SeFTAZ) indeed showed lowered band gaps of 1.7 eV. In particular, the smaller band gap of PBnDT-SeFAZ led to a larger Jsc in its BHJ solar cells than that of the original PBnDT-FTAZ solar cells. Each polymer reached moderate efficiencies (1.87–5.72%) while retaining a thick active layer (∼300 nm), demonstrating the further potential of the FTAZ system for organic photovoltaics.
A SOLR calibration procedure for the 16-term error model (2012)

Scattering parameter measurements in the presence of crosstalk is a well documented problem. The available calibration methods, suited for the general 16-term error model, capable of taking the crosstalk into account, suffer from the required Thru-Standard, which has to be perfectly known. This information is hard to acquire in some cases. An approach which makes the advantage of the 7-term SOLR (Short-Open-Load-Reciprocal) accessible to the 16-term error model is discussed in this article. The mathematical description, the feasibility for multiport applications, measurement results and a brief sensitivity analysis will be presented.
Monotonic Penalized-Likelihood Image Reconstruction for X-Ray Fluorescence Computed Tomography (2006)

In this work, we derive a monotonic penalized-likelihood algorithm for image reconstruction in X-ray fluorescence CT (XFCT) when the attenuation maps at the energies of the fluorescence X-rays are unknown. XFCT is not a transmission tomography modality but rather a stimulated emission tomography modality, and it is thus necessary to correct for attenuation of the incident and fluorescence photons if accurate images are to be obtained. This is challenging because the attenuation map is, in general, known only at the stimulating beam energy and not at the various fluorescence energies. We have developed a penalized-likelihood image reconstruction strategy for this problem. The approach alternates between updating the distribution of a given element and updating the attenuation map for that element's fluorescence X-rays. As derived, the approach is guaranteed to increase the penalized likelihood at each iteration.
23.7 Self-powered 30&#x03BC;W-to-10mW Piezoelectric energy-harvesting system with 9.09ms/V maximum power point tracking time (2014)

Energy harvesting is a key technology in various small-size applications such as wireless sensor nodes, mobile devices, and implantable bio-devices to improve battery lifetime or to substitute for batteries. Piezoelectric (PE) transducers are popular energy harvesters that can be used to supply AC power at the μW to mW scale to electronic devices using ambient vibrational energy. To use PE energy effectively, the harvesting systems need a highly efficient AC-DC converter and a DC-DC converter with maximum power point tracking (MPPT). However, existing sub-mW converters do not include an integrated MPPT algorithm [1, 2] or use the perturb and observe MPPT method which has long tracking time [3, 4]. This long tracking time reduces the power extraction from the transducer because the maximum power point (MPP) of the input power can be changed frequently according to the environment. In this paper, a low-power harvesting system is presented that finds the MPP of the input power in one cycle of the vibration of the PE transducer.
Review (2000)

There have been many recent potential useful additions to our existing portfolio of platelet function tests. In particular, the development of reliable, sophisticated, but simple to use, whole blood tests (e.g. CSA, PFA-100, Hemodyne, etc.) that mirror physiological conditions provides the ability to screen potential samples rapidly before our existing tests are utilized. These tests should provide us with a rapid, but reliable, means of assessing whether there is a primary haemostatic defect. The in vivo bleeding time may therefore be potentially replaced by simple in vitro tests. Many of the instruments (e.g. Ultegra, PFA-100, CSA, Hemodyne and TEG) have been or will be utilized as point-of-care instruments for assessing bleeding risk or monitoring anti-GpIIb/IIIa or anti-platelet therapy. For the first time therefore, simple platelet function testing may not require the specialized pathology laboratory and will increase cost effectiveness. Flow cytometry now offers a powerful approach to studying a number of different platelet activation markers and will increasingly reveal the true clinical picture of platelet activation in various disorders. Clinically useful flow cytometric assays will also have the potential of being fully automated within existing cell counters. Also, many of the new tests will be able to predict whether certain types of patients exhibit a prothrombotic tendency. For the first time, we will be able to reliably and accurately assess both platelet hypofunction and hyperfunction. With the advent of the millenium, we can now look forward to a completely new approach to both the diagnosis and management of patients with the full spectrum of platelet disorders.
Development of the High Temperature Silicon Pressure Sensor (2004)

A pressure sensor for high temperature was fabricated by using a SDB(Silicon-Direct-Bonding) wafer with a Si/<TEX>$SiO_{2}$</TEX>/ Si structure. High pressure sensitivity was shown from the sensor using a single crystal silicon of the first layer as a piezoresistive layer. It also was made feasible to use under the high temperature as of over <TEX>$120^{\circ}C$</TEX>, which is generally known as the critical temperature for the general silicon sensor, by isolating the piezoresistive layer dielectrically and thermally from the silicon substrate with a silicon dioxide layer of the second layer. The pressure sensor fabricated in this research showed very high sensitivity as of <TEX>$183.6{\mu}V/V{\cdot}kPa$</TEX>, and its characteristics also showed an excellent linearity with low hysteresis. This sensor was usable up to the high temperature range of <TEX>$300^{\circ}C$</TEX>.
Beyond the socket (2017)

GPUs achieve high throughput and power efficiency by employing many small single instruction multiple thread (SIMT) cores. To minimize scheduling logic and performance variance they utilize a uniform memory system and leverage strong data parallelism exposed via the programming model. With Moore's law slowing, for GPUs to continue scaling performance (which largely depends on SIMT core count) they are likely to embrace multi-socket designs where transistors are more readily available. However when moving to such designs, maintaining the illusion of a uniform memory system is increasingly difficult. In this work we investigate multi-socket non-uniform memory access (NUMA) GPU designs and show that significant changes are needed to both the GPU interconnect and cache architectures to achieve performance scalability. We show that application phase effects can be exploited allowing GPU sockets to dynamically optimize their individual interconnect and cache policies, minimizing the impact of NUMA effects. Our NUMA-aware GPU outperforms a single GPU by 1.5×, 2.3×, and 3.2× while achieving 89%, 84%, and 76% of theoretical application scalability in 2, 4, and 8 sockets designs respectively. Implementable today, NUMA-aware multi-socket GPUs may be a promising candidate for scaling GPU performance beyond a single socket.
The use of risk criteria in comparing transport modalities (2011)

For the transportation of dangerous substances, several transport modalities are possible. The choice for a specific transportation mode is often based on practical assumptions, like "we have a railroad available" or "we have a shipping contract". But suppose you have a choice for different types of transport, which one would be the safest for your substance? TNO has developed a method to compare the different transport modalities by using standard risk criteria like cumulated Individual Risk (a.k.a. Locational Risk) and Societal Risk. The evaluation was done for two typical substances: ammonia and propane, which are both transported often in the Netherlands. By using a standard QRA (Quantitative Risk Assessment) tool, the individual risk contours, the societal risk (FN) curve, and societal risk maps were generated and compared. A number of important assumptions were made in the study: 1. Since loading / unloading are essential steps in the distribution process, the risk of these activities were included for all batch based transportation methods (so not for pipeline transport) 2. The currently prevailing legislative failure rates and accident distances have been applied (calculated for the number of required ships/cars/wagons and typical dimensions). Although there is no consensus on "correct" failure rates or consequence distances, the statutory rules and values were applied. For the Individual Risk contour, one tends to use the "distance to 10-6 risk value" in comparing risks of transport. Due to the important contribution of loading and unloading activities at the beginning and endpoints of the route, one really should evaluate the cumulated contours for interference with vulnerable objects. For Societal Risk, the Dutch prescribed approach would be to compare the FN-curve for the highest kilometer section of the route. The study pointed out that this approach may give misleading results in comparing situations for different route tracks. Furthermore, because stationary equipment is subjected to stricter allowance rules (a lower guide value of societal risk curve), comparison of the combined effect of the transport and stationary loading & unloading activities is complicated. The use of societal risk maps, where (cumulated) risk is observed from the point of view of the receiver, appeared a very valuable addition in ranking risks.