gebhart/patrepeval huggingface dataset:
Abstract 11195: Is Personalized Computational Model of Atrial Fibrillation Really Personalized? (2021)

Introduction: Computational modeling-guided, personalized electrophysiology (EP) intervention for atrial fibrillation (AF) is an emerging paradigm of precision medicine. In the published models, advanced imaging and invasive mapping achieve personalization of cardiac anatomy. However, EP cellular personalization is less developed, and parameters are often assumed to be uniform across individual patients Hypothesis: Anatomical personalization alone is not sufficient to recapitulate the individual clinical features of AF in personalized models. Methods: For each of 57 patients (66±10 yr, 30 persistent) referred for catheter ablation of AF, we constructed a personalized 3-D model using pre-ablation CT, invasive mapping, and Courtemanche-Ramirez-Nattel atrial cell model. In the pre-ablation model, we performed virtual ramp pacing with cycle lengths at 200-120ms within the coronary sinus to induce AF. AF was defined as being inducible when it persists for &gt;15s. Simulation was repeated for 5 different published sets of EP parameters of ionic currents. In total, &gt;10k simulations were performed on an NVIDIA V100 GPU cluster, using the Lattice Boltzmann method with spatial resolution of 0.5mm and temporal resolution of 0.05ms, achieving a runtime of 24s per 1s of simulation ( Fig. A ). Results: While 100% AF inducibility was expected in the personalized pre-ablation models, AF inducibility varied between 27% and 96% depending on the set of ionic parameters used ( Fig. B ). The large variability of AF inducibility indicates that those models are highly sensitive to EP parameters, therefore anatomical personalization alone cannot adequately constrain the individual features of AF. Conclusions: The patient-specificity of the current paradigm of modeling-guided, personalized EP intervention is limited. There is an unmet clinical need for incorporation of personalized EP as well as anatomical parameters to achieve true precision medicine.
<title>3D speckle-shift hologram and its storage capacity</title> (1999)

Here a method for data storage by means of multiplexing 3D holograms is considered. The method consists in shifting the recording material with respect to a reference speckle wave. The experimental data on the dependence of the diffraction efficiency of the hologram with respect to the shift is presented. The general scheme of data storage in 3D-speckle shift hologram is considered and presented. It's shown that this kind of hologram substantially outperforms all other types for the number of cells (pixels) in which information can be stored. At the same time, the noises that are inherent in a 3D-speckle shift hologram restrict the density of the information storage.
Laser dismantling with a compact all-diffractive optical system (1997)

We propose a novel approach to the design and fabrication of focussing systems for laser material processing applications, especially for thoses where compactness, light weight, low volume and low-cost fabrication and mass-replication are desired, such as for laser-based dismantling systems. The focussing systems for laser-based dismantling applications we describe in this paper are designed to be remotely operated by a robot within irradiated environments for decommissioning of nuclear facilities. The laser cutting systems we developped are based solely on surface relief Diffractive Optical Elements (DOE:s), designed and optimized by computer and fabricated by conventional microlithographic technologies. The entire design and simulation procedures have been performed with proprietay CAD/CAM tools, especially developped for DOE:s. Two different dismantling systems have been designed, fabricated and tested.
Circulating tumor DNA association with residual cancer burden after neoadjuvant chemotherapy in triple-negative breast cancer in TBCRC 030 (2023)

NAT for TNBC reduced ctDNA TFx by 285-fold in responders and 24-fold in non-responders. In 58% (22/38) of patients, ctDNA TFx dropped below the detection level of a commercially available test, emphasizing the need for sensitive tests. Additional studies will determine if ctDNA-guided approaches can improve outcomes.
A description scheme for video based on feature extraction in the compressed domain (2002)

Feature extraction in the compressed domain enables fast but somewhat inaccurate computation. We describe a video description scheme that makes use of a combination of features extracted in the compressed domain so as to compensative for the lack of accuracy of each individual extraction.
Pilot Plant Operations in Kita-Akita City for Producing Bioethanol from Lignocellulosic Biomass (2017)

Since June 2009, we have been operating a pilot plant to evaluate a process for producing bio-ethanol from lignocellulosic biomass, wherein lignin is removed using soda-anthraquinone（ soda-AQ） cooking as a pretreatment for enzymatic saccharification. By the end of September 2012, we completed all pilot plant operations and obtained the following results. Using a semi-batch cooking method, Sugi （Cryptomeria japonica） soda-AQ pulp was produced at an yield of 44%. The Sugi pulp was hydrolyzed using a commercial cellulase to obtain a sugar yield of 97%. The produced sugar solution was concentrated from 3.1% to 7.4% using a reverse osmosis membrane and then fermented using a yeast to obtain an ethanol yield of 96.5%. The volume of ethanol produced was then calculated to be 216 L from 1 BDT of Sugi chips.
Unsupervised analysis of activity sequences using event-motifs (2006)

We present an unsupervised framework to discover characterizations of everyday human activities, and demonstrate how such representations can be used to extract points of interest in event-streams. We begin with the usage of Suffix Trees as an efficient activity-representation to analyze the global structural information of activities, using their local event statistics over the entire continuum of their temporal resolution. Exploiting this representation, we discover characterizing event-subsequences and present their usage in an ensemble-based framework for activity classification. Finally, we propose a method to automatically detect subsequences of events that are locally atypical in a structural sense. Results over extensive data-sets, collected from multiple sensor-rich environments are presented, to show the competence and scalability of the proposed framework.
Predicting Response of Printed Potentiometric Nitrate Sensors Using Image Based Machine Learning (2020)

Solid-contact nitrate sensors have wide applications in agriculture. In manufacturing, fabrication is an essential step and strongly affects the sensor performance. We focus on controlling the fabrication process to develop an economical thin-film nitrate sensor with an ion-selective membrane (ISM). However, direct long-time measurement of sensor performance for monitoring fabrication is expensive and costs human labor. Thus, in this work, we propose an automatic system to predict the temporal potentiometric response based on non-contact images acquired in real time. Our prediction systems are generated by exploiting image-processing techniques and machine learning approaches. To improve the prediction accuracy, we also fuse manufacturing factors to the image inputs. The comparison of prediction performance with different inputs also helps us to understand their effects on the fabrication process.
The Minimum Replication Origin of Merkel Cell Polyomavirus Has a Unique Large T-Antigen Loading Architecture and Requires Small T-Antigen Expression for Optimal Replication (2009)

Merkel cell polyomavirus (MCV) is a recently discovered human polyomavirus causing the majority of human Merkel cell carcinomas. We mapped a 71-bp minimal MCV replication core origin sufficient for initiating eukaryotic DNA replication in the presence of wild-type MCV large T protein (LT). The origin includes a poly(T)-rich tract and eight variably oriented, GAGGC-like pentanucleotide sequences (PS) that serve as LT recognition sites. Mutation analysis shows that only four of the eight PS are required for origin replication. A single point mutation in one origin PS from a naturally occurring, tumor-derived virus reduces LT assembly on the origin and eliminates viral DNA replication. Tumor-derived LT having mutations truncating either the origin-binding domain or the helicase domain also prevent LT-origin assembly. Optimal MCV replication requires coexpression of MCV small T protein (sT), together with LT. An intact DnaJ domain on the LT is required for replication but is dispensable on the sT. In contrast, PP2A targeting by sT is required for enhanced replication. The MCV origin provides a novel model for eukaryotic replication from a defined DNA element and illustrates the selective pressure within tumors to abrogate independent MCV replication.
Laparoscopic vs Open Gastric Bypass Surgery (2012)

In this population-based study, LRYGB provided greater safety than ORYGB even after adjusting for patient-level socioeconomic and comorbidity differences.
Supplementary Figure 1 from The OPCML Tumor Suppressor Functions as a Cell Surface Repressor–Adaptor, Negatively Regulating Receptor Tyrosine Kinases in Epithelial Ovarian Cancer (2023)

&lt;p&gt;PDF file - 110K&lt;/p&gt;
ChemInform Abstract: Potent Mammalian Topoisomerase II Inhibitors: 1‐Cyclopropyl‐6,8‐ difluoro‐1,4‐dihydro‐7‐(2,6‐dimethyl‐4‐pyridinyl)‐4‐substituted‐ quinolines. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Color version of Fig. 3 from Identification of a Novel Prostate Tumor Target, Mindin/RG-1, for Antibody-Based Radiotherapy of Prostate Cancer (2023)

Color version of Fig. 3 from Identification of a Novel Prostate Tumor Target, Mindin/RG-1, for Antibody-Based Radiotherapy of Prostate Cancer
Design and fabrication of a transmitter optical subassembly (TOSA) in 10-gb/s small-form-factor pluggable (XFP) transceiver (2006)

A smart and compact packaging transmitter optical subassembly (TOSA) in a 10-Gb/s small-form-factor pluggable (XFP) transceiver module has been developed with an eye towards electrical and thermal performances. In the TOSA, a bias-tee circuit and a matching resistor are monolithically integrated on an AlN submount with high thermal conductivity, and a newly proposed coplanar waveguide is drawn in a transistor outline (TO)-stem. In order to improve the electrical performance of the TOSA, the equivalent circuit model of all optoelectronic components in the TOSA is introduced and utilized. The fabricated TOSA shows the -3-dB bandwidth as high as 11 GHz and 0.36-dB penalty after a 75-km transmission at an elevated temperature of 85/spl deg/C.
Improved detection of prostate cancer using a magneto-nanosensor assay for serum circulating autoantibodies (2019)

Our results suggest that this autoantibody panel along with PSA and free PSA have potential to segregate patients without cancer from those with prostate cancer with higher sensitivity and specificity than PSA alone.
Sheet-type organic active matrix amplifier system using V<inf>th</inf>-tunable, pseudo-CMOS circuits with floating-gate structure (2011)

We fabricated a flexible strain-sensing system consisting of a two-dimensional array of organic self-bias-feedback amplifier cells with signal-gain of 400 by integrating 2-V operational organic pseudo-CMOS inverters [1]. Switching voltages of pseudo-CMOS inverters with floating gates can be controlled by a randomly-accessible active matrix for reducing variations in switching voltages.
Data Accuracy Pattern-based Transmission Period Control Algorithm for IoT networks (2023)

As various Internet of Things technologies emerges, IoT monitoring services are rapidly developed. Most IoT sensors deployed in an IoT monitoring environment should reduce the energy consumption of unnecessary data transmission. In this paper, we propose a data accuracy pattern-based transmission period control algorithm. Restoration accuracy patterns of time series data that are missing due to transmission period control are broadly extracted. These restoration accuracy vectors showing similar patterns are clustered into the same cluster. The clustered patterns are modeled based on a logistic function to form a linear weighted sum-based optimization problem that considers the trade-off relationship between the mathematically modeled energy consumption function and the restoration accuracy function. In order to solve the formulated optimization problem, the particle swarm optimization technique is leveraged. The performance evaluations verify that the proposed model simultaneously achieves the best RMSE performance and the second-best energy consumption performance compared to other transmission period control algorithms.
Correlating EUV TMOKE and ARPES measurements to understand the temporal and spatial length scales underlying ultrafast demagnetization in ferromagnets (2017)

By correlating time- and angle-resolved photoemission and time-resolved transverse- magneto- optical Kerr effect measurements, both at extreme ultraviolet wavelengths, we uncover the universal nature of the ultrafast photoinduced magnetic phase transition in Ni. This allows us to explain the ultrafast magnetic response of Ni at all laser fluences - from a small reduction of the magnetization at low laser fluences, to complete quenching at high laser fluences. Both probe methods exhibit the same demagnetization and recovery timescales. We further show that the ultrafast demagnetization in Ni is indeed a magnetic phase transition that is launched within 20 fs, followed by demagnetization of the material within ~200 fs, and subsequent recovery of the magnetization on timescales ranging from 500 fs to >70 ps. We also provide evidence of two competing channels with two distinct timescales in the recovery process, that suggest the presence of coexisting phases in the material.
Assessment of MUSIC-Based Noise-Robust Sound Source Localization with Active Frequency Range Filtering (2018)

We have studied sound source localization, using a microphone array embedded on a UAV (unmanned aerial vehicle), for the purpose of detecting for people to rescue from disaster-stricken areas or other dangerous situations, and we have proposed sound source localization methods for use in outdoor environments. In these methods, noise robustness and real-time processing have a trade-off relationship, which is a problem to be solved for the practical application of the methods. Sound source localization in a disaster area requires both noise robustness and real-time processing. For this we propose a sound source localization method using an active frequency range filter based on the MUSIC (MUltiple Signal Classification) method. Our proposed method can successively create and apply a frequency range filter by simply using the four arithmetic operations, so it can ensure both noise robustness and real-time processing. As numerical simulations carried out to compare the successful localization rate and the processing delay with conventional methods have affirmed the usefulness of the proposed method, we have successfully produced a sound source localization method that has both noise robustness and real-time processing.
Prediction of adenomyosis diagnosis based on MRI (2023)

Development of a multivariate prediction model based on MRI and clinical parameters for histological adenomyosis diagnosis. This single centre retrospective cohort study took place in the gynaecological department of a referral hospital. In all, 296 women undergoing hysterectomy with preoperative pelvic MRI between 2007–2022 were included. MRI scans were retrospectively assessed for adenomyosis markers (junctional zone [JZ] parameters, high signal intensity [HSI] foci in a blinded fashion. A multivariate regression model for histopathological adenomyosis diagnosis was developed based on MRI and clinical variables from univariate analysis with p < 0.1 and factors deemed clinically relevant. 131/296 women (44.3%) had histopathological adenomyosis. Patients had comparable age at hysterectomy, BMI and clinical symptoms, p > 0.05. Adenomyosis patients more often had: undergone a curettage (22.1% vs. 8.9%, p = 0.002), a higher mean JZ thickness (9.40 vs. 8.35 mm, p < .001), maximal JZ thickness (16.00 vs. 13.40 mm, p < .001), mean JZ/myometrium ratio (0.56 vs. 0.49, p = .040), and JZ differential (8.60 vs. 8.15 mm, p = .003). Presence of HSI foci was the strongest predictor for adenomyosis (39.7% vs. 8.9%, p < .001). Based on the parameters age and BMI, history of curettage, dysmenorrhoea, abnormal uterine bleeding (AUB), mean JZ, JZ differential ≥ 5 mm, JZ/myometrium ratio > 40, and presence of HSI foci, a predictive model was created with a good area under the curve (AUC) of .776. This is the first study to create a diagnostic tool based on MRI and clinical parameters for adenomyosis diagnosis. After sufficient external validation, this model could function as a useful clinical decision-making tool in women with suspected adenomyosis.
Tandem Isotachophoresis-Zone Electrophoresis via Base-Mediated Destacking for Increased Detection Sensitivity in Microfluidic Systems (2003)

Electrophoresis in microfluidic devices is becoming a useful analytical platform for a variety of biological assays. In this report, we present a method that allows for an increased sensitivity of detection of fluorescent molecules in microfluidic electrophoresis devices. This capability is provided by the implementation of a particular buffer system that is designed to initially function in an isotachophoretic (ITP) mode and, then after a controlled amount of electric current has been applied to the system, to transition to a zone electrophoretic mode. In the initial ITP mode, analytes dissolved in a large volume of injected sample are concentrated into a single narrow zone. After application of a sufficient and adjustable amount of electric current, the system switches into a zone electrophoretic mode, where the concentrated analytes are separated according to their electrophoretic mobilities. Application of this tandem ITP-zone electrophoretic strategy to the concentration, separation, and detection of fluorescent reporter molecules in a standard microfluidic device results in an approximately 50-fold increase in detection sensitivity relative to equivalent separations that are obtained with zone electrophoresis alone. Even with very long initial sample plugs (up to 3000 microm), this strategy produces electrophoretic separations with high resolutions and peak efficiencies. This strategy can be implemented to increase detection sensitivity in any standard microfluidic electrophoresis platform and does not require any specialized hardware or microchannel configurations.
Isolation and Characterization of Fig Lysozyme (1969)

Abstract A procedure is described for the isolation of fig lysozyme from dried fig latex. The pure enzyme has a molecular weight of 29,000 and consists of a single polypeptide chain with amino-terminal glycine and carboxyl-terminal isoleucine residues. With Micrococcus lysodeikticus cells as substrate, the enzyme exhibits a sharp pH optimum at pH 4.5. Fig lysozyme is considerably more active toward chitin and tetra-N-acetyl-d-glucosamine than egg-white lysozyme. The enzyme shows a strong ionic strength dependence, maximal activity being attained at an ionic strength of 0.02 to 0.03. The physical and enzymatic properties of fig lysozyme are strikingly similar to those of papaya lysozyme, although the amino acid compositions of the two enzymes show many differences. Fig lysozyme, just as papaya and egg-white lysozymes, is powerfully inhibited by histamine. A mechanism for this inhibition is suggested.
Hyperimmune bovine colostrum in the treatment of shigellosis in children: a double-blind, randomized, controlled trial (2001)

The results indicate that HBC as an adjuvant is unable to show any beneficial effect in reducing the stool frequency, duration or severity of childhood shigellosis due to S. dysenteriae type I infection.
Identification of A Prodromal Period in Crohn's Disease But Not Ulcerative Colitis (2000)

There is a significant prodromal period before the time of diagnosis of Crohn's disease that is not found in ulcerative colitis even after exclusion of subjects with IBS.
Affine scaling transformation based methods for computing low complexity sparse solutions (2002)

This paper presents affine scaling transformation based methods for finding low complexity sparse solutions to optimization problems. The methods achieve sparse solutions in a more general context, and generalize our earlier work on FOCUSS developed to deal with the underdetermined linear inverse problem. The key result is a theorem which shows a simple condition that a sequence has to satisfy for it to converge to a sparse limiting solution. Three approaches to incorporate this condition into optimization problems are presented. These consist of either imposing the condition as an additional optimization constraint, or suitably modifying the cost function, or using a combination of the two. The benefits of the methodology when applied to the linear inverse problem are twofold. Firstly, it allows for the treatment of the overdetermined problem in addition to the underdetermined problem, and secondly it enables establishing sufficient conditions under which regularized versions of FOCUSS are assured of convergence to sparse solutions.
Discovery of N-(1-Acryloylazetidin-3-yl)-2-(1H-indol-1-yl)acetamides as Covalent Inhibitors of KRASG12C (2019)

KRAS regulates many cellular processes including proliferation, survival, and differentiation. Point mutants of KRAS have long been known to be molecular drivers of cancer. <i>KRAS p.G12C</i>, which occurs in approximately 14% of lung adenocarcinomas, 3-5% of colorectal cancers, and low levels in other solid tumors, represents an attractive therapeutic target for covalent inhibitors. Herein, we disclose the discovery of a class of novel, potent, and selective covalent inhibitors of KRAS<sup>G12C</sup> identified through a custom library synthesis and screening platform called Chemotype Evolution and structure-based design. Identification of a hidden surface groove bordered by H95/Y96/Q99 side chains was key to the optimization of this class of molecules. Best-in-series exemplars exhibit a rapid covalent reaction with cysteine 12 of GDP-KRAS<sup>G12C</sup> with submicromolar inhibition of downstream signaling in a KRAS<sup>G12C</sup>-specific manner.
Vigilin interacts with signal peptide peptidase (2012)

We have identified and validated vigilin as a novel interacting partner of SPP that could play an important role in the non-proteolytic functions of SPP. This data adds further weight to the idea that intramembrane-cleaving aspartyl proteases, such as presenilin and SPPs, could have other functions besides the proteolysis of short membrane stubs.
Analysis of high-order-accurate fluctuation splitting schemes for steady advection (2010)

Abstract This article provides an analysis of high-order-accurate two-dimensional fluctuation splitting schemes for steady advection. Using Lagrangian elements, a residual distribution scheme is formulated and its properties are assessed. Distributing the residuals over the sub-triangles of each element allows one to obtain a well-posed scheme. It is also shown that the standard elemental approach is ill-posed, insofar as it produces an undetermined linear system. A steady scalar-advection problem is used to verify that the numerical schemes do obey the analysis. Keywords: residual distributionconservation lawsLagrangian elementsfluctuation splittingsteady advection