gebhart/patrepeval huggingface dataset:
Differentiating Engineered Tissue Images and Experimental Factors to Classify Cardiomyocyte Content (2022)

In this study, we used machine learning (ML) to classify the cardiomyocyte (CM) content on day 10 of the differentiation of human-induced pluripotent stem cell (hiPSC)-laden microspheroids using easily acquirable nondestructive phase-contrast images taken in the middle of differentiation and tunable experimental parameters. Scale-up suspension culture, use of engineered tissues to support stem cell differentiation, and CM production for improved control over cellular microenvironment in the suspension system need nondestructive methods to track engineered tissue development. The ability to couple images that capture experimenter perceived "good" or "bad" batches based on visualization at early differentiation time points with actual experimental outcomes in an unbiased way is a step toward building these methods. In recent years, ML techniques have been successfully applied to identify critical process parameters and use this information to build models that describe process outcomes in cell production and hiPSC differentiation. Building upon these successes, here, we utilize convolutional neural networks (CNNs) to build a binary classifier model for CM content on differentiation day 10 (dd10) for hiPSC-CMs. We consider two separate data sets as potential input features for the classification models. The first set includes phase-contrast images of microspheroid tissues taken on days 3 and 5 of the differentiation batches at different experimental conditions. The second set supplements the images with tunable experimental differentiation parameters, such as cell concentration and microspheroids' size. The CM content classes were <i>sufficient</i> and <i>insufficient</i>. The accuracy of the CNN classifier using images only was 63%. The addition of experimental features increased the accuracy to 85%, indicating the importance of tunable parameters in predicting CM content. Impact statement Machine learning approaches were used to predict the final cardiomyocyte (CM) content class (sufficient vs. insufficient) of engineered cardiac tissue microspheroids produced through suspension-based cardiac differentiation of human-induced pluripotent stem cell-laden engineered tissue microspheroids. The models used specified experimental features and data collected using nondestructive inexpensive methods, specifically phase-contrast images taken during the initial days of differentiation as inputs. The best model was a convolutional neural network trained using experimental features and differentiation day 5 images. It classified the CM content with 85% accuracy and replicated and formalized experimenter's visual intuition about differentiation outcomes by incorporating images from early time points.
PREBREAKDOWN PROCESSES ASSOCIATED WITHSURFACE FLASHOVER OFSOLIDINSULATORS INVACUUM (1977)

A computersimulationof the i,nsulatorsurface charging in vacuum under the applicationof a high voltage, is presentedfor alumina (A1203)insulatorand for alumina insulatorscoated with cuprous oxide (Cu2O)and chromium oxide (Cr2O3). It is shown that the mode of surfacechargedistributionis dependenton the secondaryemission yieldof the insulatorsurface. Mleasurementsof insulatorelectrodejunctionfields,using an electronicmicroforcebalance, show the effect of surface coatingson the cathodeand anode junctionfields. High speedstreakphotographyshowingthe time developmentof an arc in the case of coated insulatorsis presented. The experimentalresults support the insulatorsurfacecharging model which is simulatedon a digitalcomputer.
P5996HDAC inhibition improves myofibrillar relaxation and metabolism in a feline model of HFpEF (2019)

Abstract Background Heart failure (HF) with preserved ejection fraction (HFpEF) accounts for about 50% of all cases of HF and there are currently no effective therapies. Purpose To assess the effects of histone deacetylase (HDAC) inhibition on cardiac and mitochondrial function and the plasma metabolome in a large mammalian model of slow-progressive pressure overload with features of HFpEF. Methods Male domestic short hair cats (n=26, aged 2mo), underwent either sham (S) procedures (n=5) or aortic constriction with a customized pre-shaped band (n=21), resulting in slow progressive pressure overload during growth. 2 months post-banding, animals were treated daily with either 10mg/kg suberoylanilide hydroxamic acid (b+SAHA) (n=8), a pan-HDAC inhibitor, or vehicle (b+veh) (n=8) for 2 months. Serial in-vivo cardiopulmonary phenotyping was performed monthly, and invasive hemodynamic and gas exchange parameters were evaluated 4 months post-banding. Ex-vivo myofibril mechanical studies and blood-based metabolomic profiling were performed. Data is presented as mean±SEM. Results Echocardiography at 4-months post-banding revealed that b+SAHA animals had a significant reduction in left ventricular hypertrophy (LVH) and LA size vs. b+veh animals. Left ventricular end-diastolic pressure (LVEDP) and mean pulmonary arterial pressure (mPAP) were significantly lower in b+SAHA vs. b+veh. SAHA treatment also improved ex-vivo myofibril relaxation independent of LVH and this effect correlated with in-vivo improvements of LV relaxation. Furthermore, SAHA treatment preserved lung structure, and improved lung compliance and oxygenation, reflected by a decrease in alveolar-capillary wall thickness and intrapulmonary shunt. SAHA treatment also reduced perivascular fluid cuffs around extra-alveolar vessels, suggesting attenuated alveolar-capillary stress failure. Treatment with SAHA caused an increase in both oxygen consumption in-vivo and the percentage of type 1 skeletal muscle fibers (higher oxidative capacity). SAHA also increased mRNA levels of coactivators that regulate mitochondrial function and induced metabolic reprogramming towards mitochondrial oxidation preferentially utilizing fatty acids. SAHA treated HeLa cells showed a significant increase in oxidative phosphorylation and ATP production. Effects of SAHA Conclusion These results show that slow-progressive pressure overload mimics critical features of HFpEF. SAHA can improve cardiac, pulmonary, and metabolic derangements caused by chronic pressure overload. Therefore, HDAC inhibition may be an interesting therapeutic strategy to treat the ever growing HFpEF population. Acknowledgement/Funding NIH [HL33921 to S.R.H, HL116848, HL127240 to T.A.M]; AHA [16SFRN31400013 to T.A.M.]; Medical University of Graz [M.W.], Stadt Graz [M.W.]
A Review of: “Mechanisms of Cell-Mediated Immunity, R.T. McCluskey and S. Cohen, eds. Wiley Biomedical-Health, New York, 1974 418 pages; hard cover; $22.50” (1974)

(1974). A Review of: “Mechanisms of Cell-Mediated Immunity, R.T. McCluskey and S. Cohen, eds. Wiley Biomedical-Health, New York, 1974 418 pages; hard cover; $22.50”. Preparative Biochemistry: Vol. 4, No. 6, pp. 573-573.
High Resolution Electroelution of Polyacrylamide Gels for the Purification of Single Proteins from Mycobacterium tuberculosis Culture Filtrate (2000)

Culture filtrate from Mycobacterium tuberculosis contains protective molecules which have been used successfully in experimental vaccines against tuberculosis. Despite an increasing number of mycobacterial proteins being characterised, a major effort is still needed to get an overview of the many potentially interesting molecules in culture filtrate. In this study we describe a high throughput method for purification and biological evaluation of protein components in complex protein mixtures. The method presents a new application of the recently developed Mini Whole Gel Eluter and employs this apparatus for the high resolution electroelution of selected molecular mass fractions of protein mixtures previously separated in large polyacrylamide gels. Two novel M. tuberculosis culture filtrate proteins (CspA and TB18.6) were purified by this method, their N-terminal sequences were determined and the open reading frame encoding each of the proteins identified. The immunological recognition of the molecules were evaluated in tuberculosis infected mice and guinea pigs. Both proteins induced DTH responses in guinea pigs and IFN-gamma release from spleen lymphocytes isolated from infected mice.
Oral Selinexor–Dexamethasone for Triple-Class Refractory Multiple Myeloma (2019)

Selinexor-dexamethasone resulted in objective treatment responses in patients with myeloma refractory to currently available therapies. (Funded by Karyopharm Therapeutics; STORM ClinicalTrials.gov number, NCT02336815.).
Effect of Intermolecular Dipole−Dipole Interactions on Interfacial Supramolecular Structures of C3-Symmetric Hexa-peri-hexabenzocoronene Derivatives (2010)

Two-dimensional (2D) supramolecular assemblies of a series of novel C(3)-symmetric hexa-peri-hexabenzocoronene (HBC) derivatives bearing different substituents adsorbed on highly oriented pyrolytic graphite were studied by using scanning tunneling microscopy at a solid-liquid interface. It was found that the intermolecular dipole-dipole interactions play a critical role in controlling the interfacial supramolecular assembly of these C(3)-symmetric HBC derivatives at the solid-liquid interface. The HBC molecule bearing three -CF(3) groups could form 2D honeycomb structures because of antiparallel dipole-dipole interactions, whereas HBC molecules bearing three -CN or -NO(2) groups could form hexagonal superstructures because of a special trimeric arrangement induced by dipole-dipole interactions and weak hydrogen bonding interactions ([C-H···NC-] or [C-H···O(2)N-]). Molecular mechanics and dynamics simulations were performed to reveal the physics behind the 2D structures as well as detailed functional group interactions. This work provides an example of how intermolecular dipole-dipole interactions could enable fine control over the self-assembly of disklike π-conjugated molecules.
Molecular Genetic Analysis of Two Large Kindreds With Intracranial Aneurysms Demonstrates Linkage to 11q24-25 and 14q23-31 (2006)

Molecular genetic analysis of 2 large IA kindreds confirms linkage to chromosome 11q and 14q, which were suggested to contain IA susceptibility genes in a previous study of Japanese sib pairs. Independent identification of these 2 loci strongly suggests that IA susceptibility genes lie within these regions. While demonstrating the genetic heterogeneity of IA, these results are also an important step toward cloning IA genes and ultimately understanding its pathophysiology.
Extraction and Quantitative Analysis of Oil from Commercial Corn Fiber (1996)

Extraction of commercial corn fiber with hexane or supercritical CO2 yielded an oil that comprised from 0.54 to 3.68 wt % of the fiber. An HPLC method with sensitive evaporative light-scattering detection (ELSD) was developed to analyze the lipid classes in corn fiber oil. Triacylglycerols were the most abundant lipid class, but the oil also contained sterol esters, free fatty acids, phytosterols, and very low levels of tocopherols. All fiber samples contained ferulate esters, similar in structure to "oryzanol", a cholesterol-lowering substance found in rice bran and rice bran oil. Much more oil (up to 10-fold) and more ferulate esters (up to 2-fold) could be obtained from the fiber by grinding it before hexane extraction. The finer the fiber was ground, the more oil and ferulate esters were removed. Essentially all of the extractable oil and all of the ferulate esters were removed by extraction with hexane for 1 h at 25 °C. Keywords: Corn fiber; ferulate esters; ferulate-phytosterol esters; corn; Zea mays
Dynamic modeling of patient breathing effort in response to change in pressure support in mechanical ventilation (2015)

A patient-ventilator system is introduced where the input is pressure support level (PSV) from the ventilator and the output is the patient's mechanical work of breathing per minute, or power of breathing (POB). With higher level of pressure support from the ventilator, less effort is needed by the patient to attain the needed the level of ventilation. However, due to several physiological control loops regulating the level of respiration, the dynamic response of the patient due to a change in PSV level can be very complicated. In this study, this dynamic behavior is characterized using a first order system. The dynamic model of the patient-ventilator system has been obtained numerically based on data collected from five patients receiving mechanical ventilation with different levels of pressure support. The results show a wide range of response times among the patients but very limited range in steady state behavior of the system, i.e. DC Gain.
Intentional hydrogen doping of polycrystalline ZnO thin films prepared by MOCVD technique (2005)

We investigated the role of hydrogen impurities in polycrystalline ZnO incorporated via post-deposition hydrogen exposure. From the room-temperature infrared absorption spectra, photoluminescent spectra, and electrical stability measurements under air atmosphere, we concluded that hydrogen interstitials act as shallow donors and decrease oxygen and Zn vacancies.
Radiomic Immunophenotyping of GSEA-Assessed Immunophenotypes of Glioblastoma and Its Implications for Prognosis: A Feasibility Study (2020)

Characterization of immunophenotypes in glioblastoma (GBM) is important for therapeutic stratification and helps predict treatment response and prognosis. Radiomics can be used to predict molecular subtypes and gene expression levels. However, whether radiomics aids immunophenotyping prediction is still unknown. In this study, to classify immunophenotypes in patients with GBM, we developed machine learning-based magnetic resonance (MR) radiomic models to evaluate the enrichment levels of four immune subsets: Cytotoxic T lymphocytes (CTLs), activated dendritic cells, regulatory T cells (Tregs), and myeloid-derived suppressor cells (MDSCs). Independent testing data and the leave-one-out cross-validation method were used to evaluate model effectiveness and model performance, respectively. We identified five immunophenotypes (G1 to G5) based on the enrichment level for the four immune subsets. G2 had the worst prognosis and comprised highly enriched MDSCs and lowly enriched CTLs. G3 had the best prognosis and comprised lowly enriched MDSCs and Tregs and highly enriched CTLs. The average accuracy of T1-weighted contrasted MR radiomics models of the enrichment level for the four immune subsets reached 79% and predicted G2, G3, and the "immune-cold" phenotype (G1) according to our radiomics models. Our radiomic immunophenotyping models feasibly characterize the immunophenotypes of GBM and can predict patient prognosis.
<title>Optical tomography at the microscopic scale by means of a numerical low-coherence holographic technique</title> (1996)

We describe here a numerical application of the optical low- coherence holographic microscopy (OLCHM) technique. A low coherent source illuminates an object and the backscattered light interfere with a reference wave which optical path's length can be precisely adjusted. Holograms are recorded by a CCD camera and numerically reconstructed. With this technique optical tomography can be performed with a single scan along the optical axis. The transverse resolution of the reconstructed images mainly depends on the optics components used and approaches the diffraction limit. Using a Ti:Sapphire laser a depth resolution of about 30 micrometers has been achieved.
Optimization and Validation of a Multiplexed Luminex Assay To Quantify Antibodies to Neutralizing Epitopes on Human Papillomaviruses 6, 11, 16, and 18 (2005)

A human papillomavirus (HPV) multiplexed competitive Luminex immunoassay first described by Opalka et al. (D. Opalka, C. E. Lachman, S. A. MacMullen, K. U. Jansen, J. F. Smith, N. Chirmule, and M. T. Esser, Clin. Diagn. Lab. Immunol. 10:108--15, 2003) was optimized and validated for use in epidemiology studies and vaccine clinical trials. Optimization increased both the analytical sensitivity and the clinical specificity of the assay to more effectively discriminate the low-titer antibody response of HPV-infected persons from noninfected individuals. The characteristics of the assay that were optimized included monoclonal antibody (MAb) specificity, scaling up the conjugation of virus-like particles (VLPs) to microspheres, VLP concentration, MAb concentration, sample matrix, sample dilution, incubation time, heat inactivation of sample sera, and detergent effects on assay buffer. The assay was automated by use of a TECAN Genesis Workstation, thus improving assay throughput, reproducibility, and operator safety. Following optimization, the assay was validated using several distinct serum panels from individuals determined to be at low and high risk for HPV infection. The validated assay was then used to determine the clinical serostatus cutoff. This high-throughput assay has proven useful for performing epidemiology studies and evaluating the efficacy of prophylactic HPV vaccines.
A Deeper Look into DeepCap (2021)

Human performance capture is a highly important computer vision problem with many applications in movie production and virtual/augmented reality. Many previous performance capture approaches either required expensive multi-view setups or did not recover dense space-time coherent geometry with frame-to-frame correspondences. We propose a novel deep learning approach for monocular dense human performance capture. Our method is trained in a weakly supervised manner based on multi-view supervision completely removing the need for training data with 3D ground truth annotations. The network architecture is based on two separate networks that disentangle the task into a pose estimation and a non-rigid surface deformation step. Extensive qualitative and quantitative evaluations show that our approach outperforms the state of the art in terms of quality and robustness. This work is an extended version of DeepCap where we provide more detailed explanations, comparisons and results as well as applications.
High speed and low power silicon-based receiver front-end for optical interconnect (2016)

We demonstrate an optical receiver front-end using a CMOS TIA with a germanium-on-silicon PD. The amplifier only occupies 0.09 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> with 12 mW power consumption, and achieves a 27.5 GHz 3-dB bandwidth. The integrated silicon-based receiver shows well opened eye diagrams up to 20 Gb/s.
Adsorption-electrochemical modification of nanoporous carbon materials by nickel complexes with Schiff bases (2012)

Adsorption and subsequent polymerization of nickel(II) complexes with Schiff bases were studied in a porous carbon material used to manufacture electric double-layer capacitors (supercapacitors). The optimal modification conditions of the carbon material with polymeric complexes to obtain the maximum effect as regards the accumulation of electric energy in the supercapacitor were determined and substantiated. An effective and cost-efficient technique for modification of supercapacitor electrodes with electrically active polymers was suggested.
Biotin concentrations in maternal plasma and milk during prolonged lactation. (1985)

We followed a group of exclusively breast feeding mothers for 12 months after delivery. They numbered 200 at delivery, 140 at 4 months of lactation, 116 at 6, 36 at 9 and 7 at 12 months. The milk concentration of biotin was very low at delivery and subsequently the (geometric) mean value remained at around 4.5 micrograms/l. The mean plasma value was 250 ng/l at delivery and stable (around 330 ng/l) throughout the lactation. There were large intra- and interindividual variations in the concentrations in both milk (from 0 to 27 micrograms/l) and plasma (from 142 to 1090 ng/l). The variations in the milk concentrations result in a similar variation in the biotin intake of the exclusively breast-fed infants. The current recommendations for biotin intake were not met by any of those infants but no manifestations of biotin deficiency were recorded.
Lin: Unsupervised Extraction of Tasks from Textual Communication (2020)

Commitments and requests are a hallmark of collaborative communication, especially in organizational settings. Identifying specific tasks being committed to or requests from emails and chat messages can enable important downstream tasks, such as producing to-do lists, reminders, and calendar entries. State-of-the-art approaches for task identification rely on large annotated datasets, which are not always available, especially for domain-specific tasks. Accordingly, we propose Li, an unsupervised approach of identifying tasks that leverages dependency parsing and VerbNet. Our evaluations show that Li yields comparable or more accurate results than supervised models on domains with large training sets, and maintains its excellent performance on unseen domains.
Structural and magnetotransport properties of Co/Re superlattices (1994)

Structural properties of sputtered Si/Re 50 Å/(Co 20 Å/Re x Å)40 superlattices have been investigated in detail by low- and high-angle x-ray-diffraction measurements. The low-angle x-ray reflectivity data have been analyzed using an optical model and the high-angle data have been treated on the basis of a trapezoidal model. The fitted results indicate that the films with small xRe=3, 5, and 7 Å are essentially composed of pure Co layers and Re rich alloy (∼80%) interfaces about 3–5 monolayers thick. The magnetoresistance (MR) data of the antiferromagnetically coupled films have been analyzed using a semiclassical MR model of interfacial spin-dependent scattering.
METABOLIC SYNDROME AND RISK OF AGE-RELATED MACULAR DEGENERATION (2014)

Metabolic syndrome, obesity, high glucose, and high triglycerides were predictors of progression to late AMD. These data provide additional insights into the pathogenesis of AMD.
Estimation of Sheet Modulus of Elasticity Using Drive Field Signals (2012)

Online sensing of sheet modulus of elasticity in the dry-end spans of printing grade paper machines (PMs) will permit the machine operators to control the mechanical properties of the produced paper. This paper develops an integrated sensorless tension control and sheet modulus of elasticity estimation algorithm, which is tested using field-recorded signals from a production PM and using a full model of the dry-end sections of this machine. Results show the ability of the proposed estimation algorithm to predict the sheet tension (tensile force) and sheet modulus of elasticity even in the presence of rapid changes in the speed and/or in other process operating conditions. The developed algorithms offer the papermaker new insights into the papermaking process. The ability to understand how modulus changes in real time provides a pathway to optimizing the operation of the PM drive system.
Errata to “Distributed Full-Duplex Via Wireless Side-Channel” [Aug 13 4162-4173] (2015)

In this paper (J. Bai and A. Sabharwal, “Distributed Full-Duplex via Wireless Side- Channels: Bounds and Protocols,” IEEE Trans. Wireless Commun., vol. 12, no. 8, pp. 4162–4173, Aug. 2013), there are revisions to theorems and formulas that are presented.
Supplementary Table 3 from A First-in-Human Phase I Study of INVAC-1, an Optimized Human Telomerase DNA Vaccine in Patients with Advanced Solid Tumors (2023)

&lt;p&gt;Number and percentage of patients reporting studytreatment-related AEs per cycle&lt;/p&gt;