gebhart/patrepeval huggingface dataset:
EVALUATION OF ANTIHUMAN T LYMPHOCYTE SAPORIN IMMUNOTOXINS POTENTIALLY USEFUL IN HUMAN TRANSPLANTATION (1988)

We have synthesized 3 immunotoxins (ITs) by covalently coupling the saporin-6 hemitoxin (SAP) to OKT11, SOT3, and SOT1a murine monoclonal antibodies that recognize human T lymphocyte CD2, CD3, and CD5 surface antigens, respectively. The resulting ITs, referred to as OKT11-SAP, SOT3-SAP, and SOT1a-SAP, are equally effective in inhibiting eukaryotic protein synthesis in a cell-free system, and all 3 ITs bind to human T lymphocytes in an almost comparable manner. However, these reagents differ markedly in their ability to kill target T lymphocytes as assessed by measuring the inhibition of DNA synthesis and growth of clonable T lymphocytes in response to mitogenic and allogeneic stimuli. Whereas the anti-CD2 IT, OKT11-SAP, shows moderate cytotoxicity against T lymphocytes, the anti-CD3 IT, SOT3-SAP, and the anti-CD5 IT, SOT1a-SAP, are highly effective in eliminating the same target cells. The concentrations inhibiting 50% (IC50) of T lymphocyte DNA synthesis are 60 nM, 4.5 nM, and 1.4 nM for OKT11-SAP, SOT3-SAP, and SOT1a-SAP, respectively. Among 3 tested lysosomotropic amines, i.e., ammonium chloride, chloroquine, and amantadine, the latter only moderately potentiates the cytotoxicity of SOT1a-SAP (IC50 0.36 nM). We show that the conditions under which T lymphocyte killing is accomplished require less than 10 min exposure of T lymphocytes to the ITs, in the absence of adjuvant molecules artificially added to the incubation medium and at physiologic culture pH. These experimental characteristics of unprecedented closeness to a physiologic in-vivo model are likely to reflect the biophysical properties of the SAP moiety of the ITs. We conclude that clinical studies are warranted to define the advantage of using SAP ITs over previously described immunoconjugates.
Comparison of 7‐day and 14‐day Proton Pump Inhibitor‐Containing Triple Therapy for <i>Helicobacter pylori</i> Eradication: Neither Treatment Duration Provides Acceptable Eradication Rate in Korea (2007)

Although the 7-day PPI-containing triple anti-H. pylori therapy is not inferior to the 14-day therapy, neither treatment duration provides acceptable eradication rate reaching 90% in per-protocol analysis. New combination regimen with higher efficacy should be developed as a first-line eradication therapy for H. pylori in Korea.
Experimental and Theoretical Study of a Cadmium Coordination Polymer Based on Aminonicotinate with Second-Timescale Blue/Green Photoluminescent Emission (2017)

A new cadmium/6-aminonicotinate-based coordination polymer (CP) with an unprecedented multicolored and long-lasting emission is reported. This material shows a blue fluorescence which rapidly turns to green persistent phosphorescence with a lifetime of nearly 1 s. Time-dependent density functional theory calculations revealed that electronic transitions arising from both first excited singlet and triplet states involving ligand-centered and ligand-to-metal charge-transfer mechanisms are responsible for such behavior.
Image enhancement of whole-body oncology [18F]-FDG PET scans using deep neural networks to reduce noise (2021)

Deep learning-based image enhancement models may allow a reduction in scan time (or injected activity) by up to 50%, and can decrease reconstruction time to a third, while maintaining image quality.
2-(2-Azabicyclo[3.2.1]octa-3,6-dien-2-yl)-1,3-dimethoxyimidazolium hexafluoridophosphate (2016)

The title salt, C 12 H 16 N 3 O 2 + ·PF 6 − , was obtained by the dipolar cycloaddition of norbornadiene to 2-azido-1,3-dimethoxyimidazolium hexafluoridophosphate. The methoxy groups attached to the imidazolium ring of the cation adopt an anti conformation [displacements of the C atoms from the ring plane = 1.386 (4) and −1.404 (3) Å]. In the crystal, weak inter-ionic C—H...F contacts are observed. The structure was refined as a two-component twin. Positional disorder of the fluorine atoms of the PF 6 anion was observed, the occupancy ratio being 0.562 (16):0.438 (16).
Investigation of the Occupational Safety and Health act by Accidents Types of Industrial Accidents : Case Study (2019)

Objective: The purpose of this study is to investigate the types of accidents on the basis of industrial accidents cases, to identify the cause of each type of accidents, and then to understand the occupational safety and health act related to the causes. BR Background: Improving and advancing the effectiveness of the occupational safety and health act is the most fundamental improvement activity for industrial accident prevention. In order to enhance the effectiveness of the occupational safety and health act, it is necessary to clearly investigate the current status and characteristics of industrial accidents in Korea and to reflect them.BR Method: This study was conducted based on the cases of domestic industrial accidents provided by the Korea Occupational Safety and Health Agency. Examples of industrial accidents were randomly selected from accidents cases occurring in 2010-2016 in machinery, electricity, chemicals, and construction.BR Results: Fall accidents accounted for about 20.0% of the total accidents, followed by explosion 14.4%, pitting 12.8%, and electric shock 11.3%. The occupational safety and health act, according to the cause, showed the highest proportion of items related to Chapter 4, hazard risk prevention action. Second, safety and health education noncompliance was high (23.5%).BR Conclusion: The purpose of this study is to investigate the occupational safety and health act which is deemed to be highly related to the cause of accident by summarizing the types of accidents, causes of accidents and causal factors. In order to revise and redefine the occupational safety and health act, it is necessary to have a database that can be used to build data on violations of the occupational safety and health act.BR Application: The results of this study can be utilized as a methodology for the revision of the occupational safety and health act.
Abstract 1652: Evaluating cell lines andorganoidsas models for metastatic cancer through integrative analysis of open genomic data (2019)

Abstract Metastasis is the most common cause of cancer-related death and, as such, there is an urgent need to discover new therapies to treat metastasized cancers. Cancer cell lines are widely-used models to study cancer biology and test drug candidates. However, it is still unknown to what extent they adequately resemble the disease in patients. The recent accumulation of large-scale genomic data in cell lines, mouse models, and patient tissue samples provides an unprecedented opportunity to evaluate the suitability of cell lines for metastatic cancer research. In this work, we used breast cancer as a case study. The comprehensive comparison of the genetic profiles of 57 breast cancer cell lines with those of metastatic breast cancer samples revealed substantial genetic differences. In addition, we identified cell lines that more closely resemble different subtypes of metastatic breast cancer. Surprisingly, a combined analysis of mutation, copy number variation and gene expression data suggested that MDA-MB-231, the most commonly used triple negative cell line for metastatic breast cancer research, had little genomic similarity with Basal-like metastatic breast cancer samples. We further compared cell lines with organoids, a new type of preclinical model which are becoming more popular in recent years. We found that organoids outperformed cell lines in resembling the transcriptome of metastatic breast cancer samples. However, additional differential expression analysis suggested that both types of models could not mimic the effects of tumor microenvironment and meanwhile had their own bias towards modeling specific biological processes. Our work provides a guide of cell line selection in metastasis-related study and sheds light on the potential of organoids in translational research. Note: This abstract was not presented at the meeting. Citation Format: Ke Liu, Patrick Newbury, Benjamin Glicksberg, William Zeng, Eran Andrechek, Bin Chen. Evaluating cell lines andorganoidsas models for metastatic cancer through integrative analysis of open genomic data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1652.
H2O2 selectively damages the binuclear iron-sulfur cluster N1b of respiratory complex I (2023)

NADH:ubiquinone oxidoreductase, respiratory complex I, plays a major role in cellular energy metabolism by coupling electron transfer with proton translocation. Electron transfer is catalyzed by a flavin mononucleotide and a series of iron-sulfur (Fe/S) clusters. As a by-product of the reaction, the reduced flavin generates reactive oxygen species (ROS). It was suggested that the ROS generated by the respiratory chain in general could damage the Fe/S clusters of the complex. Here, we show that the binuclear Fe/S cluster N1b is specifically damaged by H<sub>2</sub>O<sub>2</sub>, however, only at high concentrations. But under the same conditions, the activity of the complex is hardly affected, since N1b can be easily bypassed during electron transfer.
Interspinous process device versus conventional decompression for lumbar spinal stenosis: 5-year results of a randomized controlled trial (2022)

IPD implantation is a more expensive alternative to decompressive surgery for INC but has comparable functional outcome during follow-up. The risk of reoperation due to absence of recovery is substantial in the first 2 years after IPD implantation, but if surgery is successful this positive effect remains throughout long-term follow-up. The IPD group had less back pain during long-term follow-up, but the clinical relevance of this finding is debatable.
COSMOS on Steroids (2021)

The growing prevalence of visual disinformation has become an important problem to solve nowadays. Cheapfake is a new term used for the altered media generated by non-AI techniques. In their recent COSMOS work, the authors developed a self-supervised training strategy that detected whether different captions for a given image were out-of-context, meaning that even though pointing to the same object(s) in the image, the captions implied different meanings. In this paper, we propose four methods to improve the detection accuracy of COSMOS. These methods range from differential sensing and fake-or-fact checking that detect contradicting or fake captions to object-caption matching and threshold adjustment that modify the baseline algorithm for improved accuracy.
Case 35-2019: A 66-Year-Old Man with Pancytopenia and Rash (2019)

A 66-year-old man presented to the hospital for evaluation of pancytopenia and rash. Examination was notable for a scaling, erythematous rash on the legs and the absence of lymphadenopathy. Positron-emission tomography revealed increased 18F-fluorodeoxyglucose uptake in the spleen. A diagnostic test was performed, and management decisions were made.
Photo-response compensated piezoresistive cantilever for use in fluorescence microscopy (2010)

This paper presents the design, fabrication, and the characterization of a photo-response compensated piezoresistive cantilever. The application field of the cantilever is to measure cellular mechanical properties under fluorescence microscopy. Photo-response which is caused by an excitation light of a fluorescence microscope interferes with measurement. We proposed piezoresistive cantilevers consist of a force-sensing cantilever with a reference cantilever to cancel out the photo-response. We measured the photo-response of the fabricated device, by varying wavelength, light intensity and light incidence angle. The experimental results show that the photo-response was decreased by 87%. This verified that present device has effective photo-response compensation by using the reference cantilever.
Near-Optimal Detection of Geometric Objects by Fast Multiscale Methods (2005)

We construct detectors for "geometric" objects in noisy data. Examples include a detector for presence of a line segment of unknown length, position, and orientation in two-dimensional image data with additive white Gaussian noise. We focus on the following two issues. i) The optimal detection threshold-i.e., the signal strength below which no method of detection can be successful for large dataset size n. ii) The optimal computational complexity of a near-optimal detector, i.e., the complexity required to detect signals slightly exceeding the detection threshold. We describe a general approach to such problems which covers several classes of geometrically defined signals; for example, with one-dimensional data, signals having elevated mean on an interval, and, in d-dimensional data, signals with elevated mean on a rectangle, a ball, or an ellipsoid. In all these problems, we show that a naive or straightforward approach leads to detector thresholds and algorithms which are asymptotically far away from optimal. At the same time, a multiscale geometric analysis of these classes of objects allows us to derive asymptotically optimal detection thresholds and fast algorithms for near-optimal detectors.
High-Temperature Electrical Conduction in Magnesium Ferrite (1987)

Thermogravimetric analysis and electrical conductivity measurement were performed for magnesium ferrite at 1000°-1300°C under the controlled oxygen partial pressure. The ferrous ion concentration in the hematite-rich magnesium ferrite increased with decreasing oxygen partial pressure (PO2) at a fixed temperature, but remained constant in the spinel stoichiometric with respect to the cation-to-anion ratio. Enthalpy of the defect-equilibrium reaction was calculated to be 24.8kcal/mol. Both electrical conductivity and ferrous ion concentration showed similar PO2 dependences. Arrhenius plot of PO2-independent conductivity gave an activation energy of 0.16-0.21eV for hopping conduction. Detailed analysis taking into account of the temperature dependence of cation distribution showed that hopping conduction among octahedral iron ions was predominant in both stoichiometric and non-stoichiometric magnesium ferrites.
ROBUST AND EFFICIENT AGGREGATION FOR DISTRIBUTED LEARNING (2022)

Distributed learning paradigms, such as federated and decentralized learning, allow for the coordination of models across a collection of agents, and without the need to exchange raw data. Instead, agents compute model updates locally based on their available data, and subsequently share the update model with a parameter server or their peers. This is followed by an aggregation step, which traditionally takes the form of a (weighted) average. Distributed learning schemes based on averaging are known to be susceptible to outliers. A single malicious agent is able to drive an averaging-based distributed learning algorithm to an arbitrarily poor model. This has motivated the development of robust aggregation schemes, which are based on variations of the median and trimmed mean. While such procedures ensure robustness to outliers and malicious behavior, they come at the cost of significantly reduced sample efficiency. This means that current robust aggregation schemes require significantly higher agent participation rates to achieve a given level of performance than their mean-based counterparts in non-contaminated settings. In this work we remedy this drawback by developing statistically efficient and robust aggregation schemes for distributed learning.
Methods for the Derivation of Human Embryonic Stem Cell Lines (2011)

Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass (ICM) of the developing embryo. They have tremendous potential for the research of early human development, differentiation processes, and teratology, as well as for industrial and clinical purposes, such as drug screening and cell-based therapy. Since hESCs were first derived by Thomson and his ­colleagues in 1998, considerable effort has been invested to improve methods of isolating new lines, in defined conditions, and to increase success rates. This chapter discusses the most commonly used methods for deriving hESC lines, including immunosurgery and the whole embryo approach.
Development of Fluorine-18 Labeled Metabolically Activated Tracers for Imaging of Drug Efflux Transporters with Positron Emission Tomography (2015)

Increased activity of efflux transporters, e.g., P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP), at the blood-brain barrier is a pathological hallmark of many neurological diseases, and the resulting multiple drug resistance represents a major clinical challenge. Noninvasive imaging of transporter activity can help to clarify the underlying mechanisms of drug resistance and facilitate diagnosis, patient stratification, and treatment monitoring. We have developed a metabolically activated radiotracer for functional imaging of P-gp/BCRP activity with positron emission tomography (PET). In preclinical studies, the tracer showed excellent initial brain uptake and clean conversion to the desired metabolite, although at a sluggish rate. Blocking with P-gp/BCRP modulators led to increased levels of brain radioactivity; however, dynamic PET did not show differential clearance rates between treatment and control groups. Our results provide proof-of-concept for development of prodrug tracers for imaging of P-gp/BCRP function in vivo but also highlight some challenges associated with this strategy.
Engineering microbes and metabolic pathways for the production of ethylene glycol (2023)

The invention relates to recombinant cells and their use in the production of ethylene glycol.
Topical application of AMA0076, a locally acting rho kinase (ROCK) inhibitor, results in a robust IOP control in Dutch Belted Rabbits (2012)

Abstract Purpose To determine the intra ocular pressure (IOP) lowering efficacy of the local ROCK inhibitor, AMA0076, in Dutch Belted rabbits. Methods Dutch Belted rabbits (5 rabbits/group) received topically a single dose of AMA0076 in one eye. A concentration range of 0.031 ‐ 0.625% AMA0076 was tested. The contralateral eye served as control and was treated with saline. IOP was measured at baseline and 30 min, 1, 2, 3, 4, 5, 6, 7, 8h post topical administration. Results Single topical administration of AMA0076 significantly lowered IOP in all groups compared to the control eye (p&lt;0.05). Mean baseline IOP during the experiments was between 20.6 and 21.5 mmHg. Thirty minutes after topical treatment, a concentration dependent reduction in IOP was demonstrated with a ΔIOP ranging from 3.9mmHg – 7mmHg compared to the control eye. Maximal IOP reduction of each concentration following single dose administration of AMA0076 was observed ±2 hours after instillation with a ΔIOP ranging from 4.6mmHg and 7.5mmHg. The IOP lowering effect with the highest concentrations of AMA0076 (0.625% and 0.125%) was sustained during the experiment. Conclusion AMA0076 was effective in rapidly lowering IOP in a dose depended and sustained manner after a single topical dose in Dutch Belted rabbits. This new class of local ROCK inhibitors has potential therapeutic value for the IOP lowering treatment of glaucoma.
$\ell_0$-based Sparse Canonical Correlation Analysis (2020)

Canonical Correlation Analysis (CCA) models are powerful for studying the associations between two sets of variables. The canonically correlated representations, termed \textit{canonical variates} are widely used in unsupervised learning to analyze unlabeled multi-modal registered datasets. Despite their success, CCA models may break (or overfit) if the number of variables in either of the modalities exceeds the number of samples. Moreover, often a significant fraction of the variables measures modality-specific information, and thus removing them is beneficial for identifying the \textit{canonically correlated variates}. Here, we propose $\ell_0$-CCA, a method for learning correlated representations based on sparse subsets of variables from two observed modalities. Sparsity is obtained by multiplying the input variables by stochastic gates, whose parameters are learned together with the CCA weights via an $\ell_0$-regularized correlation loss. We further propose $\ell_0$-Deep CCA for solving the problem of non-linear sparse CCA by modeling the correlated representations using deep nets. We demonstrate the efficacy of the method using several synthetic and real examples. Most notably, by gating nuisance input variables, our approach improves the extracted representations compared to other linear, non-linear and sparse CCA-based models.
&lt;title&gt;Hardware/software codesign of a fuzzy ART neural clusterer: the benefits of configurable computing&lt;/title&gt; (1998)

This paper analyzes the performance differences found between software and hardware/software implementations of a reformulated Fuzzy ART neural network algorithm. This reformulated algorithm is a solution for a real time radar signal clustering problem. The software implementations run on a 50 MHz TMS320C40 DSP, and the hardware/software implementation runs on the same DSP for its software part, whereas the FPGA based application specific hardware accelerator is realized on the MiroTech's X-CIM TIM40 module. This investigation of FPGA based acceleration gave excellent results for our application: acceleration factors up to 68.9 have been reached.
Task-based Generation of Optimized Projection Sets using Differentiable Ranking (2023)

We present a method for selecting valuable projections in computed tomography (CT) scans to enhance image reconstruction and diagnosis. The approach integrates two important factors, projection-based detectability and data completeness, into a single feed-forward neural network. The network evaluates the value of projections, processes them through a differentiable ranking function and makes the final selection using a straight-through estimator. Data completeness is ensured through the label provided during training. The approach eliminates the need for heuristically enforcing data completeness, which may exclude valuable projections. The method is evaluated on simulated data in a non-destructive testing scenario, where the aim is to maximize the reconstruction quality within a specified region of interest. We achieve comparable results to previous methods, laying the foundation for using reconstruction-based loss functions to learn the selection of projections.
Measuring carotid artery stenosis using CT angiography: the dilemma of artifactual lumen eccentricity. (1998)

Artifactual luminal eccentricity has significant implications for measuring percentage of stenosis revealed by CT angiography. Eccentricity increases in longer stenoses, thicker slices, and vessels oriented perpendicular to the z-axis. With CT angiography, measurement of minimum diameters in and out of a stenosis provides the most accurate assessment of percentage of stenosis.