gebhart/patrepeval huggingface dataset:
QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation – Analysis of Ranking Scores and Benchmarking Results (2022)

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at https://github.com/RagMeh11/QU-BraTS.
Differences in fluorescence profiles from breast cancer tissues due to changes in relative tryptophan content via energy transfer: tryptophan content correlates with histologic grade and tumor size but not with lymph node metastases (2014)

The correlation between histologic grade, an increasingly important measure of prognosis for patients with breast cancer, and tryptophan levels from tissues of 15 breast carcinoma patients was investigated. Changes in the relative content of key native organic biomolecule tryptophan were seen from the fluorescence spectra of cancerous and paired normal tissues with excitation wavelengths of 280 and 300 nm. Due to a large spectral overlap and matching excitation–emission spectra, fluorescence resonance energy transfer from tryptophan-donor to reduced nicotinamide adenine dinucleotides-acceptor was noted. We used the ratios of fluorescence intensities at their spectral emission peaks, or spectral fingerprint peaks, at 340, 440, and 460 nm. Higher ratios correlated strongly with high histologic grade, while lower-grade tumors had low ratios. Large tumor size also correlated with high ratios, while the number of lymph node metastases, a major factor in staging, was not correlated with tryptophan levels. High histologic grade correlates strongly with increased content of tryptophan in breast cancer tissues and suggests that measurement of tryptophan content may be useful as a part of the evaluation of these patients.
Synthesis of 7‐Substituted Benzolactam‐V8s and Their Selectivity for Protein Kinase C Isozymes. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
Simple Representation and Approximate Search of Feature Vectors for Large-Scale Object Recognition (2007)

This paper presents two methods of large-scale recognition of planar objects with a simple representation and approximate search of local feature vectors. A central problem of the use of local feature vectors is the burden of computation and memory for finding nearest neighbors. To solve this problem, the proposed methods embody the following: (1) a simple bit representation of feature vectors and hashing enable us to fast access with less memory, (2) approximate search with query perturbation allows us to find approximate nearest neighbors efficiently. From large-scale experiments using 10,000 objects in the database and 2,000 query images, it was found that only 10‐20% of correct nearest neighbors were enough for achieving recognition rate of 98.0%. The processing time for achieving this rate was 8.3 ms / query (excluding time for feature extraction). We have also tested the scalability of a proposed method using the database of 100,000 objects and obtained the result of 92.3% accuracy in 4.5 ms /query.
Highly donor-doped (110) layered perovskite materials as novel photocatalysts for overall water splitting (1999)

Highly donor-doped (110) layered perovskite materials with a generic composition of AmBmO3m+2 (m = 4, 5; A = Ca, Sr, La; B = Nb, Ti) loaded with nickel have been found to be efficient photocatalysts for overall water splitting with quantum yields as high as 23% under UV irradiation.
Photoluminescence of Si1-xGex/Si Quantum Wells with Abrupt Interfaces Formed by Segregant-Assisted Growth (1994)

Photoluminescence (PL) of Si 1- x Ge x /Si quantum wells with abrupt interfaces formed by segregant-assisted growth (SAG) is reported. It was found that SAG-grown samples show spectral red-shift compared to those grown by conventional solid-source molecular beam epitaxy due to the suppression of Ge surface segregation during growth. Crystal quality of SAG-grown samples is discussed based on the excitation variation of PL intensity.
Submicron gate Si3N4/AlGaN/GaN-metal-insulator-semiconductor heterostructure field-effect transistors (2003)

We present the characteristics of a quarter-micron gate metal-insulator-semiconductor heterostructure field-effect transistor (MISHFET) with Si/sub 3/N/sub 4/ film as a gate insulator. A detailed comparison of the MISHFET and an identical geometry HFET shows them to have the same radio frequency (RF) power gain and cut-off frequency, while the MISHFET has much lower gate-leakage currents and higher RF powers at operating frequencies as high as 26 GHz. The MISHFET gate-leakage currents are well below 100 pA at gate bias values from -10 V to +8 V. At zero gate bias, the drain saturation current is about 0.9 A/mm and it increases to 1.2 A/mm at +8 V gate bias. The output RF power of around 6 W/mm at 40 drain bias was found to be frequency independent in the range of 2 to 26 GHz. This power is 3 dB higher than that from HFET of the same geometry. The intrinsic cutoff frequency is /spl sim/63 GHz for both the HFET and the MISHFET. This corresponds to an average effective electron velocity in the MISHFET channel of 9.9/spl times/10/sup 6/ cm/s. The knee voltage and current saturation mechanisms in submicron MISHFETs and heterostructure field-effect transistors (HFET) are also discussed.
The Catalytic Diels-Alder Reaction Using Combined Catalyst System of Diphenyltin Sulfide or Lawesson’s Reagent and Silver Perchlorate (1995)

Abstract Catalytic Diels-Alder reactions between several 1,3-dienes and α,β-unsaturated ketones are effectively promoted by the combined use of diphenyltin sulfide (Ph2Sn=S) and silver perchlorate or Lawesson’s reagent (2,4-bis(4-methoxyphenyl)-1,3-dithia-2,4-diphosphetane-2,4-disulfide) and silver perchlorate under mild conditions.
AutoTransfer: Subject Transfer Learning with Censored Representations on Biosignals Data (2022)

We investigate a regularization framework for subject transfer learning in which we train an encoder and classifier to minimize classification loss, subject to a penalty measuring independence between the latent representation and the subject label. We introduce three notions of independence and corresponding penalty terms using mutual information or divergence as a proxy for independence. For each penalty term, we provide several concrete estimation algorithms, using analytic methods as well as neural critic functions. We propose a hands-off strategy for applying this diverse family of regularization schemes to a new dataset, which we call "Auto Transfer". We evaluate the performance of these individual regularization strategies under our AutoTransfer framework on EEG, EMG, and ECoG datasets, showing that these approaches can improve subject transfer learning for challenging real-world datasets.
Stability Analysis of SIDR Model for Worm Propagation in Wireless Sensor Network (2016)

Background/Objectives: Security is essential concerns in wireless sensor network. To find the stability points when worms appear in the wireless sensor network. Methods/Statistical Analysis: By using ODE formulate the SIDR model by introducing the concept of dead nodes for wireless sensor network. Find the existence of positive equilibrium and perform the stability test with the help of Jacobian matrix. Some theorems are proposed for the analysis of model. Findings: The model explains that the inactive nodes are the nodes which die due to battery consumption and cannot be recharged because of remotely located in harsh region. Inactive nodes are not capable to transmit data from one sensor node to another sensor node. The model describes the nonlinear dynamics of Susceptible, Infectious, Dead and Recovered class of nodes. The entire dynamics of the transmission of worms can be analyzed by this mathematical model, propagating feat by worms in WSN can be determine with the help of threshold value of Ro. This model validates through extensive results by using MATLAB. Application/Improvements: Proposed model is useful to reduce the battery overhead, enhance the lifetime of wireless sensor network.Keywords: Epidemic Model, Equilibrium, Stability, Wireless Sensor Network, Worms Propagation
Characterisation of the host inflammatory response to Staphylococcus epidermidis in neonatal whole blood (2007)

These in vitro data suggest that proinflammatory responses to S epidermidis are dependent on gestational age in preterm infants, whereas the counteracting anti-inflammatory response to S epidermidis may not be directly related to gestational age. Individual host factors may have a role as well as bacterial determinants, such as biofilm production. Further studies are encouraged to investigate the different aspects of innate immune responses to CoNS in vivo.
Spatiotemporal methods for prostate cancer detection by contrast-ultrasound dispersion imaging (2012)

Prostate cancer is the most diagnosed form of cancer in men in western countries. The lack of reliable imaging solutions currently restricts treatment options to radical interventions. Reliable imaging of angiogenesis, which correlates with cancer aggressiveness, could enable efficient targeting of biopsies and focal therapies, but the complicated effects of angiogenesis on perfusion have prevented a breakthrough so far. As an alternative, contrast-ultrasound dispersion imaging (CUDI) has been proposed to obtain a better characterization of angiogenenic microvascular changes. CUDI makes use of dynamic contrast-enhanced ultrasound imaging after an intravenous contrast-agent bolus injection. Dispersion is estimated by spatiotemporal analysis of time-intensity curves (TICs) obtained at each pixel. Here we present an analytical framework for a dispersion analysis by estimation of the spatial TIC similarity. Data preprocessing is improved by a spatial Wiener deconvolution filter, which reduces the effects of the anisotropic spatial ultrasound resolution, and by TIC time windowing. In addition, we propose the TIC correlation coefficient as a new TIC similarity measure. A comparison of the resulting dispersion maps from 7 recordings with histology, obtained after radical prostatectomy, showed an increased spatial similarity in the presence of cancer in all patients. The cancer classification performance of CUDI was superior to all perfusion-related parameters and was improved by spatial filtering and windowing. Although an extended validation is required, these results confirm the promising value of CUDI for prostate cancer detection.
Prevalencia de cardiopatía isquémica, demostrada mediante tomografía por emisión de fotón único (SPECT) Tc 99m sestamibi en menores de cuarenta años y su asociación con factores de riesgo (2005)

Background: Coronary artery disease is the first cause of death among Mexican population. Between the multiple risk factors it outstands the age, with greater predisposition since 45 years old. Nevertheless, there are few studies in young people. Myocardial perfusion scan is a non invasive study with great sensitivity and specificity. It allows to detect obstructive coronary lesions. Objective: To determine the ischemic heart disease and the myocardial infarction prevalence in young people and to identify its risk factors. Patients and methods: A retrospective and transversal study in 125 patients younger than 40 years was made. The expedients of the patients who had underwent one day technetium-99 m-sestamibi protocol in the myocardial perfusion study were analysed. General data, somatometry, emotional profile analysis, and lipids and glucose profiles were collected. Results: 53% of the population were women and 47% men, with mean age of 31.9 years old and body mass index of 25.1 kg/m 2 . 46% of the studies were abnormal, and from them 35% were compatible with ischemic heart disease and 11% with myocardial infarction. The patients characteristics were: age 31.6 ± 6 vs 32.6 ± 5.9 years old; BMI 25.4 ± 7.0 vs 24.4 ± 3.34 kg/m 2 ; height 161.6 ± 9.8 vs 165.5 ± 9.7 cm; systolic arterial pressure 139.1 ± 29.2 vs 115 ± 13.4 mmHg; diastolic arterial pressure 84.5 ± 17.4 vs 75 ± 9.4 mmHg; civil status: married 65.5 vs singles 57% (p = 0.005); greater depression 32 vs anxiety 28% in the group of patients with ischemic heart disease and myocardial infarction, respectively. Besides, in the myocardial infarction population we found chronic renal failure in 21% of the cases (p = 0.030), arterial hypertension in 21% (p = 0.025) and drug addiction in 21% (p = 0.002). The rest of the results did not show any significant difference.
Demonstrating the Merits of Integrating Multipath Signals into 5G LoS-Based Positioning Systems for Navigation in Challenging Environments (2023)

Constrained environments, such as indoor and urban settings, present a significant challenge for accurate moving object positioning due to the diminished line-of-sight (LoS)communication with the wireless anchor used for positioning. The 5th generation new radio (5G NR) millimeter wave (mmWave) spectrum promises high multipath resolvability in the time and angle domain, enabling the utilization of multipath signals for such problems rather than mitigating their effects. This paper investigates the benefits of integrating multipath signals into 5G LoS-based positioning systems with onboard motion sensors (OBMS). We provide a comprehensive analysis of the positioning system's performance in various conditions of erroneous 5G measurements and outage scenarios, which offers insights into the system's behavior in challenging environments. To validate our approach, we conducted a road test in downtown Toronto, utilizing actual OBMS measurements gathered from sensors installed in the test vehicle. The results indicate that utilization of multipath signals for wireless positioning operating in multipath-rich environments (e.g. urban and indoor) can bridge 5G LoS signal outages, thus enhancing the reliability and accuracy of the positioning solution. The redundant measurements obtained from the multipath signals can enhance the system's robustness, particularly when low-cost 5G receivers with a limited resolution for angle or range measurements are present. This holds true even when only considering the utilization of single-bounce reflections (SBRs).
The Histone Deacetylase Inhibitor Depsipeptide Mediates Distinct Patterns of Histone Acetylation in Cells Overexpressing Bcl-2. (2004)

Abstract Post-translational modifications of histone proteins including acetylation and methylation are known to be important in the regulation of gene expression, and histone modification patterns are found to be altered in many tumor types. We have established a liquid chromatography/mass spectrometry (LC/MS) analysis technique that allows for detailed interrogation of histone protein post-translational patterns. Application of this technique to histone proteins isolated from Chronic Lymphocytic Leukemia (CLL) patient cells and CD19-selected normal B cells has demonstrated that primary CLL cells have a pattern of H2A modification distinct from normal B cells, and that changes in each of the histone proteins H2A, H2B, H3 and H4 occur following treatment with HDAC inhibitors. We have used this and other techniques to understand how factors that influence apoptotic threshold, such as Bcl-2, can also cause changes in histone post-translational modifications induced by depsipeptide and other HDAC inhibitors. To initially explore this, we utilized the 697 lymphoblastoid cell line transfected either with an empty vector (697-neo) or a vector driving a ten-fold overexpression of Bcl-2 protein (697-Bcl-2). Cells were exposed to varying concentrations of depsipeptide for 4 or 24 hours and analyzed for growth inhibition, cell death, HDAC inhibition, and p21 induction. The results of these studies are summarized in the following table: Effects of Depsipeptide Treatment on 697 Cells at 24 Hours Relative % Cell Growth Apoptotic Cells (%) Relative HDAC Inhibition (%) p21, fold increase 697-neo untreated 100 8.2 0 1.0 697-neo 3.8 nM DDP 66.3 9.0 74.0 1.5 697-neo 38 nM DDP 41.0 57.5 97.0 2.3 697-Bcl-2 untreated 100 7.6 0 1.0 697-Bcl-2 3.8 nM DDP 90.4 7.5 77.3 1.9 697-Bcl-2 38 nM DDP 80.6 10.4 94.6 3.9 Over-expression of Bcl-2 completely blocked apoptosis induced by depsipeptide, as compared to the empty vector cell line. Despite this, growth inhibition, HDAC inhibition and p21 protein induction was observed in the Bcl-2 over-expressing cell line. Specific acetylation of H4 was analyzed by LC/MS and demonstrated that baseline histone acetylation patterns were identical between the 697-neo and 697-Bcl-2 cell lines. With depsipeptide treatment, however, distinct differences were noted in the pattern of acetylation between the two cell lines at 24 hours. Specifically, 697-neo showed increases in the di-, tri-, and tetra-acetylated H4 forms, with the tri-acetylated form predominating. In the 697-Bcl-2 cells the di-acetylated form was the most abundant followed closely by tri- and tetra- acetylated forms, and in contrast to the 697-neo cells, a penta-acetylated form is strongly detected. Our data suggest that molecular characteristics of tumor cells that alter apoptotic thresholds may influence changes in histone acetylation following HDAC inhibitor treatment. Exploration of the relationship between histone acetylation and Bcl-2 over-expression is currently under study.
Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding (2004)

We have developed a microfluidic mixer for studying protein folding and other reactions with a mixing time of 8 mus and sample consumption of femtomoles. This device enables us to access conformational changes under conditions far from equilibrium and at previously inaccessible time scales. In this paper, we discuss the design and optimization of the mixer using modeling of convective diffusion phenomena and a characterization of the mixer performance using microparticle image velocimetry, dye quenching, and Forster resonance energy-transfer (FRET) measurements of single-stranded DNA. We also demonstrate the feasibility of measuring fast protein folding kinetics using FRET with acyl-CoA binding protein.
Control of Thick Airfoil, Deep Dynamic Stall Using Steady Blowing (2014)

The utility of constant blowing as an aerodynamic load control concept for wind turbine blades was explored experimentally. A NACA 0018 airfoil model equipped with control slots near the leading edge and at mid-chord was investigated initially under quasi-static conditions at Reynolds numbers ranging from to . Blowing from the leading-edge slot showed a significant potential for load control applications. Leading-edge stall was either promoted or inhibited depending on the momentum coefficient, and a corresponding reduction or increase in lift on the order of was obtained. Control from the mid-chord slot counteracted trailing-edge stall but was ineffective at preventing leading-edge separation. The impact of blowing from the leading-edge slot on dynamic stall was explored by means of unsteady surface pressure measurements and simultaneous particle image velocimetry above the suction surface. At a sufficiently high momentum coefficient, the formation and shedding of the dynamic stall vortex were fully suppressed. This led to a significant reduction in lift hysteresis and form drag while simultaneously mitigating moment coefficient excursions.
Alignment induced aberration fields of next generation telescopes (2007)

There is a long list of new ground-based optical telescopes being considered around the world. While many are conventional Cassegrain and Ritchey-Chretien designs, some are from a family of 3-mirror offset field (but still obscured) optical forms that trace back to designs developed in the 1970s. The nodal theory of aberrations, developed in the late 1970s, provides valuable insights into the response of these systems to alignment errors and provides simple, linear solutions to real-time or at-assembly alignment algorithms. The application of nodal aberration techniques to the alignment of two and three mirror astronomical telescopes will be presented.
Effect of Human Pancreatic Polypeptide and Its C-Terminal Hexapeptide on Pancreatic Secretion in Man and in the Dog (1982)

Human pancreatic polypeptide (HPP) and its C-terminal hexapeptide (HP-PP) were infused intravenously in graded doses into healthy human subjects and dogs with chronic pancreatic fistula during submaximal stimulation with secretin. Plasma levels of PP were measured by radioimmunoassay, and pancreatic volume flow and bicarbonate and protein outputs were monitored. PP and HP-PP in humans did not affect secretion-induced volume flow or bicarbonate secretion, but at the highest doses it reduced the protein outputs. In dogs both HPP and HP-PP inhibited dose-dependently the pancreatic volume flow and bicarbonate and protein outputs. There was a linear correlation between the dose of HPP infused and the increments in plasma PP levels in these experiments. The inhibition of pancreatic secretion occurred at doses of exogenous HPP which produced blood plasma PP concentrations not significantly different from those normally seen after a meat meal. We conclude that there is a marked difference in the effect of HPP on the exocrine pancreas in man and the dog, that PP may play a role as a physiological inhibitor of pancreatic protein secretion in man and of both bicarbonate and protein secretion in the dog, and that the effect of HPP on the exocrine pancreas can be mimicked by its C-terminal hexapeptide.