gebhart/patrepeval huggingface dataset:
Development of integrated system for reverse engineering for biomedical devices (2004)

This report describes the work done in the general area of reverse engineering for biomedical applications, prostheses via rapid prototyping and tooling techniques, and intelligent techniques in assisted surgery. Physical 3D models can be fabricated using RP technique. The combination of RP and reverse engineering has been applied several medical areas. An integrated reverse engineering system is developed to link a hospital with RP facilities in NTU. Two case studies are reported which were conducted to test the feasibility of the system, i.e., nose prosthesis using laser scanning and skull replication using CT scanning. A novel manufacturing approach for the fabrication of extraoral facial prostheses is introduced in this paper. The approach combines or integrates 3 key manufacturing technologies, namely, laser surface digitizing/scanning, computer-aided design (CAD) and manufacturing (CAM), to provide automated fabrication of spatially and anatomically accurate prostheses.
Prediction of Significant Wave Height in Korea Strait Using Machine Learning (2021)

The prediction of wave conditions is crucial in the field of marine and ocean engineering. Hence, this study aims to predict the significant wave height through machine learning (ML), a soft computing method. The adopted metocean data, collected from 2012 to 2020, were obtained from the Korea Institute of Ocean Science and Technology. We adopted the feedforward neural network (FNN) and long-short term memory (LSTM) models to predict significant wave height. Input parameters for the input layer were selected by Pearson correlation coefficients. To obtain the optimized hyperparameter, we conducted a sensitivity study on the window size, node, layer, and activation function. Finally, the significant wave height was predicted using the FNN and LSTM models, by varying the three input parameters and three window sizes. Accordingly, FNN (W48) (i.e., FNN with window size 48) and LSTM (W48) (i.e., LSTM with window size 48) were superior outcomes. The most suitable model for predicting the significant wave height was FNN(W48) owing to its accuracy and calculation time. If the metocean data were further accumulated, the accuracy of the ML model would have improved, and it will be beneficial to predict added resistance by waves when conducting a sea trial test.
Rapid Antimicrobial Susceptibility Determination of Uropathogens in Clinical Urine Specimens by Use of ATP Bioluminescence (2008)

We describe the first direct testing of the antimicrobial susceptibilities of bacterial pathogens in human clinical fluid samples by the use of ATP bioluminescence. We developed an ATP bioluminescence assay that eliminates somatic sources of ATP to selectively quantify the bacterial load in clinical urine specimens with a sensitivity of <1,000 CFU per milliliter. There was a log-log relationship between light emission and the numbers of CFU in clinical urine specimens. A clinical study was performed to evaluate the accuracy of the ATP bioluminescence assay for determination of the antimicrobial susceptibilities of uropathogens in clinical urine specimens tested in a blinded manner. ATP bioluminescent bacterial density quantitation was used to determine the inoculation volume in growth medium with and without antibiotics. After incubation at 37 degrees C for 120 min, the ATP bioluminescence assay was repeated to evaluate the uropathogen response to antibiotics. The ability of the ATP bioluminescence assay to discriminate between antimicrobial susceptibility and resistance was determined by comparison of the results obtained by the ATP bioluminescence assay with the results obtained by standard clinical microbiology methods. Receiver operator characteristic curves were used to determine the optimal threshold for discriminating between susceptibility and resistance. Susceptibility and resistance were correctly predicted in 87% and 95% of cases, respectively, for an overall unweighted accuracy of 91%, when the results were stratified by antibiotic. For samples in which the pathogen was susceptible, the accuracy improved to 95% when the results for samples with less than a 25-fold increase in the amount of bacterial ATP in the medium without antibiotics were excluded. These data indicate that a rapid bioluminescent antimicrobial susceptibility assay may be useful for the management of urinary tract infections.
Joint sequential channel estimation and multiuser detection for uplink CDMA over multipath fading (2003)

We consider joint channel estimation and data detection in uplink asynchronous CDMA systems employing aperiodic (long) spreading sequences in the presence of unknown multipath fading. Since maximum-likelihood sequence estimation is too complex to perform, multiuser receivers are proposed based on the sequential expectation-maximization (EM) algorithm. With prior knowledge of only the signature waveforms, the delays and the second-order statistics of the fading channel, the receivers sequentially estimate the channel using the sequential EM algorithm. The snapshot estimates of each path are further tracked by linear minimum-mean-squared-error (MMSE) filters and the user data are detected by a maximum-likelihood sequence detector, given the channel estimates. The proposed receivers that use the exact expressions have a computational complexity O(2/sup K/) per bit, where K is the number of users. Using the traditional EM algorithm, we derive low-complexity approximations which have a complexity of O(K/sup 2/) per bit. Simulation results demonstrate that the proposed receivers offer substantial performance gains over conventional pilot-symbol assisted techniques and achieve a performance close to the known-channel bounds. Furthermore, the proposed receivers even outperform the single-user RAKE receiver with Nyquist pilot-insertion rate in a single-user environment.
Endothelin in a murine model of cerebral malaria. (2006)

Cerebral malaria (CM) remains a deadly complication of Plasmodium falciparum infection, and children are at high risk of developing encephalopathy as a result of CM. This is probably a consequence of the activation of many of the inflammatory cytokines as well as the glial cells and the vascular endothelium in the brain. We have previously demonstrated that there is a striking reduction in cerebral blood flow by magnetic resonance imaging when mice are infected with Plasmodium berghei ANKA (PbA), and we now demonstrate a possible role for endothelin (ET-1) in the pathogenesis of CM. The brains of female C57BL/6 mice with PbA infection were examined at Day 5 for the expression of ET-1, endothelin converting enzyme (ECE), and the endothelin receptors A and B (ET(A) and ET(B)) by both reverse transcription-polymerase chain reaction (RT-PCR) and quantitative real-time PCR. ET-1 and ECE mRNA expression was markedly increased by RT-PCR in PbA-infected mice. Real-time quantitative PCR demonstrated a 3-fold increase in ET-1 (P < 0.05) and a significant increase in ET(A) and ET(B) expression (P < 0.05) in PbA-infected mice. Histopathology bof PbA-infected mice demonstrated a transformation in the morphology of microglial cells and clustering of these cells consistent with activation. Though the full impact of ET-1 on CM remains to be elucidated, these findings demonstrate that in the murine model, there is a significant increase in ET-1 and its components, which is associated with the vasculopathy and immunopathology of CM.
Colored Mosaic Matrix: Visualization Technique for High-Dimensional Data (2013)

Owing to a limited display resolution, it may be difficult to obtain an overview of high-dimensional data in the display area used for visualization. In this paper, we aimed to obtain an overview of high-dimensional data in a limited screen area. We developed Colored Mosaic Matrix as a method to obtain a data overview. Colored Mosaic Matrix is a visualization method for high-dimensional categorical data that uses a color representation of the features. By representing quantitative data in category units, the proposed method enables the visualization of data containing a large number of records. As a result of an experimental investigation of its readability, we found our method to be useful in obtaining a data overview.
Quantifying Behavioral Data Sets of Criminal Activity (2010)

With the increased availability of rich behavioral data sets, we present a novel combination of tools to ana-lyze to analyze this information. Using criminal offense records as an example, we employ cross-correlation measures, eigenvalue spectrum analysis, and results from random matrix theory to identify spatiotempo-ral patterns. Finally, with multivariate autoregressive models, we demonstrate a possible source of structure within the data. instructions.
Non-metastatic 2 (NME2)-mediated suppression of lung cancer metastasis involves transcriptional regulation of key cell adhesion factor vinculin (2014)

Tumor metastasis refers to spread of a tumor from site of its origin to distant organs and causes majority of cancer deaths. Although >30 metastasis suppressor genes (MSGs) that negatively regulate metastasis have been identified so far, two issues are poorly understood: first, which MSGs oppose metastasis in a tumor type, and second, which molecular function of MSG controls metastasis. Herein, integrative analyses of tumor-transcriptomes (n=382), survival data (n=530) and lymph node metastases (n=100) in lung cancer patients identified non-metastatic 2 (NME2) as a key MSG from a pool of >30 metastasis suppressors. Subsequently, we generated a promoter-wide binding map for NME2 using chromatin immunoprecipitation with promoter microarrays (ChIP-chip), and transcriptome profiling. We discovered novel targets of NME2 which are involved in focal adhesion signaling. Importantly, we detected binding of NME2 in promoter of focal adhesion factor, vinculin. Reduced expression of NME2 led to enhanced transcription of vinculin. In comparison, NME1, a close homolog of NME2, did not bind to vinculin promoter nor regulate its expression. In line, enhanced metastasis of NME2-depleted lung cancer cells was found in zebrafish and nude mice tumor models. The metastatic potential of NME2-depleted cells was remarkably diminished upon selective RNA-i-mediated silencing of vinculin. Together, we demonstrate that reduced NME2 levels lead to transcriptional de-repression of vinculin and regulate lung cancer metastasis.
High-Speed Deposition of New Dielectric Film Having the Low Refractive Index for the Rewritable HD DVD Media (2005)

We have developed a new low refractive index material “SiOC”, which enables high deposition rates for the rewritable HD DVD media. The SiOC film is formed using the SiC target with Ar and O2 gas mixture by the sputter deposition method using RF or DC power supply. The resultant deposition rate per sputter power is about three times higher than the rate of the deposition using a SiO2 target. The obtained thin film consists of substantial amount of carbon (C) as well as silicon (Si) and oxygen (O). However, the film shows almost the same optical characteristics as SiO2. We demonstrated that the single-layer type HD DVD rewritable media with 20 GB using SiOC film had good recording characteristics similar to the disc using a SiO2 film. We believe that this media can be manufactured at a cost similar to conventional rewritable DVDs in mass production.
Push−Pull Tests to Quantify In Situ Degradation Rates at a Phytoremediation Site (2005)

Nine push-pull tests (PPTs) were performed to determine in-situ aerobic respiration rates at a creosote-contaminated site and to assess the contribution of hybrid poplar trees to the remediation of polynuclear aromatic hydrocarbons (PAH) in groundwater. PPTs were conducted by injecting a solution containing dissolved oxygen and naphthalene (reactive tracers) with bromide (nonreactive tracer) into wells constructed in a shallow unconfined aquifer. The objective of this study was to determine seasonal variation and spatial differences (contaminated versus uncontaminated areas and treed versus untreed areas) in the rate of consumption of dissolved oxygen. First-order aerobic respiration rates varied from 0.0 (control well) to 1.25 hr(-1), which occurred at a planted area in early summer (June). Rates measured in winter at treed areas were greater by a factor of 3-5 when compared to winter rates determined at nontreed areas of the site. Rates at treed regions were found to increase by over 4 times in summer relative to winter at the same location.
Plutonium Immobilization Process: Puck Handling Module Supervisory Control System (2008)

This paper discusses the Supervisory Control and Data Acquisition for green puck handling. Also discussed is the overall control scheme implemented by the supervisory computer, the individual inspections completed on the puck, and the checks and balances between the computer, tray loading system and robot.
Enhanced protein expression through strain selection, gene disruption, improved vector design and co-expression of endogenous chaperones (2006)

Results An analysis of a series of haploid laboratory yeast strains revealed significant intra-strain variability and unstable plasmid segregation. By combining classic chemical mutagenesis and selection a family of highly efficient Saccharomyces cerevisiae strains has been developed for the commercial production of biopharmaceutical products. When combined with a stable [1], high copy number [2], episomal expression vector system and a strong constitutive promoter, secreted recombinant protein expression titres in excess of 4 g/L were achieved (see Figure 1). Specific genetic modifications to the host were also introduced to increase product yield and control posttranslational modifications, such as proteolysis and glycosylation.
An Improved Functional Link Architecture for Nonlinear AEC (2022)

In practice, hands-free devices commonly employ low-cost electronic components. Unfortunately, the nonlinear distortion arising from them affects the performance of acoustic echo cancellers. To address this issue, this paper proposes a new adaptive filtering algorithm based on nonlinear acoustic echo cancellation (NAEC) framework for improving its echo cancellation performance. The advanced method employs a novel combination of an adaptive filter based on sub-filter and proportionate adaptation, and presents an enhanced NAEC framework. In addition to that, both convergence and steady-state analysis of the proposed NAEC algorithm are presented. The performance evaluation made in the presence of speech and colored noise inputs has shown an average improvement of 3–4 dB compared to the existing algorithms.
Ultralow emittance electron beams from a laser-wakefield accelerator (2012)

Using quadrupole scan measurements we show laser-wakefield accelerated electrons to have a normalized transverse emittance of ${0.21}_{\ensuremath{-}0.02}^{+0.01}\ensuremath{\pi}\text{ }\mathrm{mm}\text{ }\mathrm{mrad}$ at 245 MeV. We demonstrate a multishot and a single-shot method, the mean emittance values for both methods agree well. A simple model of the beam dynamics in the plasma density downramp at the accelerator exit matches the source size and divergence values inferred from the measurement. In the energy range of 245 to 300 MeV the normalized emittance remains constant.
Physics-Informed Supervised Residual Learning for 2-D Inverse Scattering Problems (2023)

In this communication, we propose a new physics-constrained approach to solve 2-D inverse scattering problems (ISPs) by extending physics-informed supervised residual learning (PhiSRL) with Born approximation (BA). By embedding the fixed-point iteration method in residual neural network (ResNet), PhiSRL aims to solve ISPs iteratively by applying the convolutional neural networks (CNNs) to learn the update rules of reconstructions. PhiSRL is employed to invert lossy scatterers by introducing BA to linearize ISPs and further reduce the computational burden of forward modeling. Both numerical and experimental results validate the effectiveness of the proposed approach.
Center variation in screening for and management of metabolic syndrome in pediatric liver transplant recipients: A survey of SPLIT centers (2019)

Transplant providers intend to screen for and initiate management of PTMS components in these children, but protocols and practices vary substantially. This highlights opportunities for multi-center collaboration on protocols or interventions to improve screening and management.
Comparison of immunofluorescence and hemagglutination inhibition tests and enzyme-linked immunosorbent assay for detection of serum antibody in rats infected with hemorrhagic fever with renal syndrome virus (1986)

Serum antibodies against the B-1 strain of hemorrhagic fever with renal syndrome (HFRS) virus in wild and experimental rats were investigated by the indirect immunofluorescent antibody (IF) test, the hemagglutination inhibition (HI) test, and an enzyme-linked immunosorbent assay (ELISA). In the newly developed ELISA, monoclonal antibodies to the B-1 strain were applied as coating antibody. In sera from wild rats, the results obtained by the ELISA agreed quite well with those obtained by the HI test, but some serum samples that gave a negative reaction in the HI test gave a positive reaction in the IF test, although their IF titers were very low. In serum samples from experimental rats that had been kept in an animal house infected with HFRS virus, a group with high titers and a group with low or negative titers were clearly differentiated by all the tests.
Supplementary Methods from Targets of the Tumor Suppressor &lt;i&gt;miR-200&lt;/i&gt; in Regulation of the Epithelial–Mesenchymal Transition in Cancer (2023)

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Entanglement Degradation of Biphotons Propagating in Turbulent Medium (2007)

We study the entanglement of transverse spatial coordinates of biphotons propagating through a turbulent medium. The degree of entanglement is quantified by calculating the second moments of the spatial coordinates.
Timing dependence of peripheral pulse‐wave‐triggered pulsed arterial spin labeling (2013)

Arterial spin labeling (ASL) has been developed into a useful technique that is capable of quantifying noninvasively local cerebral blood flow (CBF) using the water molecules in arterial blood as diffusible tracers. Pulsed ASL (PASL) is more strongly affected than continuous ASL (CASL) by cardiac pulsation, because the tag bolus is shorter than the cardiac cycle in most cases. No reports have yet clarified the effects of multiple cardiac phases on the quantification of CBF in PASL when triggering is used. Fourteen subjects participated in this study. Peripheral pulse-wave-triggered (PPWT)-ASL was performed at various time points at the carotid artery (delay 0 ms, second point, foot, peak and tail) and compared with nontriggered (NT)-ASL. Regions of interest (ROIs) were applied based on the anterior, middle and posterior cerebral artery (ACA, MCA, PCA) territories, and CBFs were compared among different time points and ROIs. PPWT-ASL strongly affects CBF values compared with NT-ASL in ACA and MCA territories, especially when measured at the foot of the carotid artery flow phase. CBF_NT was assumed to lie approximately between the minimum and maximum CBFs, with clear statistical significance in several ROIs at several time points of PPWT-ASL, and CBF_NT was assumed to resemble 'randomly triggered' PPWT-ASL. In conclusion, PPWT-ASL strongly affects CBF values compared with NT-ASL, particularly at the foot of the carotid artery flow in ACA and MCA territories.
The length of the linker between the epidermal growth factor‐like domains in factor VIIa is critical for a productive interaction with tissue factor (2014)

Formation of the factor VIIa (FVIIa)-tissue factor (TF) complex triggers the blood coagulation cascade. Using a structure-based rationale, we investigated how the length of the linker region between the two epidermal growth factor (EGF)-like domains in FVIIa influences TF binding and the allosteric activity enhancement, as well as the interplay between the γ-carboxyglutamic acid (Gla)-containing and protease domains. Removal of two residues from the native linker was compatible with normal cofactor binding and accompanying stimulation of the enzymatic activity, as was extension by two (Gly-Ser) residues. In sharp contrast, truncation by three or four residues abolished the TF-mediated stabilization of the active conformation of FVIIa and abrogated TF-induced activity enhancement. In addition, FVIIa variants with short linkers associated 80-fold slower with soluble TF (sTF) as compared with wild-type FVIIa, resulting in a corresponding increase in the equilibrium dissociation constant. Molecular modeling suggested that the shortest FVIIa variants would have to be forced into a tense and energetically unfavorable conformation in order to be able to interact productively with TF, explaining our experimental observations. We also found a correlation between linker length and the residual intrinsic enzymatic activity of Ca(2+)-free FVIIa; stepwise truncation resulting in gradually higher activity with des(83-86)-FVIIa reaching the level of Gla-domainless FVIIa. The linker appears to determine the average distance between the negatively charged Gla domain and a structural element in the protease domain, presumably of opposite charge, and proximity has a negative impact on apo-FVIIa activity.
Smooth Fictitious Play in $N\times 2$ Potential Games (2019)

The paper shows that smooth fictitious play converges to a neighborhood of a pure-strategy Nash equilibrium with probability 1 in almost all $N\times 2$ ($N$-player, two-action) potential games. The neighborhood of convergence may be made arbitrarily small by taking the smoothing parameter to zero. Simple proof techniques are furnished by considering regular potential games.
Fluorogenic Bifunctional <i>trans</i>‐Cyclooctenes as Efficient Tools for Investigating Click‐to‐Release Kinetics (2020)

The inverse electron demand Diels-Alder pyridazine elimination reaction between tetrazines and allylic substituted trans-cyclooctenes (TCOs) is a key player in bioorthogonal bond cleavage reactions. Determining the rate of elimination of alkylamine substrates has so far proven difficult. Here, we report a fluorogenic tool consisting of a TCO-linked EDANS fluorophore and a DABCYL quencher for accurate determination of both the click and release rate constants for any tetrazine at physiologically relevant concentrations.
Anterior Cruciate Ligament Reconstruction With Transtibial Medial Meniscus Root Repair (2023)

The author(s) attests that consent has been obtained from any patient(s) appearing in this publication. If the individual may be identifiable, the author(s) has included a statement of release or other written form of approval from the patient(s) with this submission for publication.
"Not my bug!" and other reasons for software bug report reassignments (2011)

Bug reporting/fixing is an important social part of the soft-ware development process. The bug-fixing process inher-ently has strong inter-personal dynamics at play, especially in how to find the optimal person to handle a bug report. Bug report reassignments, which are a common part of the bug-fixing process, have rarely been studied.