gebhart/patrepeval huggingface dataset:
Abstract 11948: A Standardized Method to Isolate and Purify Cardiomyocytes from Individual Mouse Hearts Irrespective of Postnatal Age (2021)

Rational: Primary cardiomyocytes (CMs) are invaluable for understanding postnatal heart development and elucidating disease mechanisms in genetic and pharmacological models, however, a method to obtain freshly purified CMs at any postnatal age, without the need for different age-dependent isolation procedures and cell culture, is lacking. Objective: To develop a standardized method that allows rapid isolation and purification of CMs in high yield and viability from individual neonatal, infant, and adult mice. Methods and Results: Using a novel in situ aortic cannulation procedure optimized to allow cannulation of even the very small vessel of neonates [postnatal day 0-2 (P0-2)], hearts of C57BL/6J mice were subjected to Langendorff retrograde perfusion and enzymatic digestion. After subsequent tissue disaggregation and filtration, CMs were isolated in high yield (1.55-2.2 x 10 6 CMs/heart) and viability (~78%). The larger size of infant (P10 and P13) and adult (P70), but not neonatal CMs, compared to non-myocytes, allowed their further enrichment by differential centrifugation, before purification at the bench by bead-based immunomagnetic cell separation. This involved depletion of endothelial cells (for infant and adult preparations) or non-myocytes (neonatal preparations). Together, these procedures resulted in highly purified CMs (~95%) from hearts of all ages within 1 hour. Moreover, in situ fixation immediately after tissue digestion via coronary perfusion, preserved the cytoarchitecture of isolated CMs (~94% rod-shaped CMs at all postnatal ages), allowing capture of spindle-shaped neonatal cells undergoing mitosis, as well as enabling accurate quantitation of CM area and nucleation state. RNA-sequencing of CMs purified from one P2 male and female heart per litter (n=4 litters) showed distinct clustering by litters rather than by sexes; a finding consistent with cardiac size and shape being indistinguishable between P2 male (n=6) and female (n=6) hearts as determined by micro-computed tomography (X-ray 3D imaging). Conclusion: The procedures developed here provide a universal protocol for the rapid purification of high-quality CMs from individual hearts at any postnatal age, even those of neonates.
Comparison of methods to quantify interface trap densities at dielectric/IIIV semiconductor interfaces - eScholarship (2010)

Methods to extract trap densities at high-permittivity k dielectric/III-V semiconductor interfaces and their distribution in the semiconductor band gap are compared. The conductance method, the Berglund intergral, the Castagne–Vapaille high-low frequency, and Terman methods are applied to admittance measurements from metal oxide semiconductor capacitors MOSCAPs with high-k/ In0.53Ga0.47As interfaces with different interface trap densities. The results are discussed in the context of the specifics of the In0.53Ga0.47As band structure. The influence of different conduction band approximations for determining the ideal capacitance-voltage CV characteristics and those of the MOSCAP parameters on the extracted interface trap density are investigated. The origins of discrepancies in the interface trap densities determined from the different methods are discussed. Commonly observed features in the CV characteristics of high-k/ In0.53Ga0.47As interfaces are interpreted and guidelines are developed to obtain reliable estimates for interface trap densities and the degree of Fermi level unpinning for high-k/ In0.53Ga0.47As interfaces.
Self-oscillations in an over-injected electron diode – Experiment and analysis (2019)

An experimental setup to demonstrate a recent scheme [Leopold et al., Phys. Plasmas 24, 073116 (2017)] to persistently over-inject a vacuum electron diode so that it self-oscillates in the GHz-frequency range and releases a periodic train of electron bunches is described. We present simulations in which we account for the finite rise time of the voltage accelerating electrons from a finite radius cylindrical thermionic cathode and finite grid electrode transparency, which make the experiment different from the original theoretical scheme. It was found that these experimental conditions do affect the expected results but a self-oscillating behavior is still possible. Our experimental results so far indicate the presence of the self-oscillatory behavior, but because the cathode used emits from a few hot-spots rather than uniformly, the beam current modulations are different from those obtained in the simulations.
TAK1 safeguards endothelial cells from gut microbes and inflammation (2019)

How endothelial cells (ECs) survive in inflammatory environments remains unclear. We recently showed that TAK1 protects ECs against apoptosis induced by TNFα under physiological conditions in the intestine and liver, and under inflammatory conditions in other organs. Our results document that a single gene can affect cell fate decisions in mature ECs.
Response to Letter Regarding “Catheter Ablation of Atrial Fibrillation in Patients With Left Ventricular Systolic Dysfunction: A Systematic Review and Meta-Analysis” (2015)

We thank Petretta 1 for his appreciation of our recent meta-analysis published in Circulation: Arrhythmia Electrophysiology 2 and for giving us the ability to clarify some aspects concerning the statistical analysis.
Kinoids: A Family of Immunogens for Active Anticytokine Immunotherapy Applied to Autoimmune Diseases and Cancer (2010)

The complex homeostasis of tissues is coordinated by the cytokine network and imbalances in this network may result in chronic immune disorders. Key specific cytokines, such as TNF-alpha, IFN-alpha, IL-4 or VEGF have been demonstrated to be overproduced or abnormally released in the microenvironment of pathologic tissues. These findings have opened up the way to passive immunotherapy with anticytokine monoclonal antibodies. Even though passive immunotherapy has proved to be efficient, it is hampered by specific limitations. The discovery of a family of immunogens, the kinoids, consisting of inactivated cytokine derivatives, has led some to propose them for active immunotherapy as an alternative to passive immunotherapy. This review focuses on kinoids - on their validation in experimental mouse models and ongoing clinical trials. The advantages offered by this active immune therapy in terms of efficacy, safety and patient compliance will be stressed.
[Microbial biodiversity in rhizospheric soil of Torreya grandis 'Merrillii' relative to cultivation history]. (2018)

To examine the effects of different cultivation history (5 a,10 a, and 15 a) on soil microbial communities, we used Illumina sequencing to investigate the diversity and structure of soil bacterial and fungal communities from Torreya grandis 'Merrillii' fields. The results showed that bacterial Shannon index, the richness estimators Chao1 and ACE were lower in soil in 15 year-old stand than those in other cultivation histories, while Simpson index showed no significant variation. Results from bacterial community NMDS showed that cultivation history played a vital role in driving the changes of soil bacteria communitiy structure. The bacterial communities in 5 and 10 year-old stand had the similar composition. The variations of bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi) were significantly correlated with soil organic matters, soil C/N, and total nitrogen. The fungi richness estimators of Chao1 and ACE were significantly decreased with increasing cultivation history. Shannon and Simpson indices were significantly higher in soil with 10 year-old stand than soils with other cultivation history. Fungal NMDS could be clustered in the same era. Fungal communities were comprosed of Ascomycota, Basidiomycota and Zygomycota. Changes in fungal richness/diversity and community structure were mainly controlled by the variation of soil organic matter. In conclusion, the predominant factors affecting soil microbial communities were the cultivation history, soil C/N, total nitrogen and organic matter, respectively.
GrimAge Outperforms Other Epigenetic Clocks in the Prediction of Age-Related Clinical Phenotypes and All-Cause Mortality (2020)

The aging process is characterized by the presence of high interindividual variation between individuals of the same chronical age prompting a search for biomarkers that capture this heterogeneity. Epigenetic clocks measure changes in DNA methylation levels at specific CpG sites that are highly correlated with calendar age. The discrepancy resulting from the regression of DNA methylation age on calendar age is hypothesized to represent a measure of biological aging with a positive/negative residual signifying age acceleration (AA)/deceleration, respectively. The present study examines the associations of 4 epigenetic clocks-Horvath, Hannum, PhenoAge, GrimAge-with a wide range of clinical phenotypes (walking speed, grip strength, Fried frailty, polypharmacy, Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment (MOCA), Sustained Attention Reaction Time, 2-choice reaction time), and with all-cause mortality at up to 10-year follow-up, in a sample of 490 participants in the Irish Longitudinal Study on Ageing (TILDA). HorvathAA and HannumAA were not predictive of health; PhenoAgeAA was associated with 4/9 outcomes (walking speed, frailty MOCA, MMSE) in minimally adjusted models, but not when adjusted for other social and lifestyle factors. GrimAgeAA by contrast was associated with 8/9 outcomes (all except grip strength) in minimally adjusted models, and remained a significant predictor of walking speed, .polypharmacy, frailty, and mortality in fully adjusted models. Results indicate that the GrimAge clock represents a step-improvement in the predictive utility of the epigenetic clocks for identifying age-related decline in an array of clinical phenotypes promising to advance precision medicine.
Analyzing relations among software patterns based on document similarity (2005)

In software development, many kinds of knowledge are shared and reused as software patterns. However, the relation analysis among software patterns by hand is difficult on the large scale. In this paper, we propose a technique for the automatic relation analysis among the patterns. Our technique is based on a new pattern model to treat various patterns, and utilizes exiting text processing techniques to extract patterns from documents and to calculate the strength of pattern relations. As a result of experiments, the system that implements our technique has extracted appropriate relations among patterns without information on relations described in original pattern documents. Moreover, our system has the ability to suggest relations among patterns that the author has not noticed.
The First Example of Chiral Induction Using Homochiral Boronic Esters in the Petasis Reaction. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
ChemInform Abstract: Novel Application of N‐Alkoxyamides in Preparative Organic Chemistry (1994)

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.
A Neural Network Realization of Fuzzy ART (1991)

A neural network realization of the fuzzy Adaptive Resonance Theory (ART) algorithm is described. Fuzzy ART is capable of rapid stable learning of recognition categories in response to arbitrary sequences of analog or binary input patterns. Fuzzy ART incorporates computations from fuzzy set theory into the ART 1 neural network, which learns to categorize only binary input patterns, thus enabling the network to learn both analog and binary input patterns. In the neural network realization of fuzzy ART, signal transduction obeys a path capacity rule. Category choice is determined by a combination of bottom-up signals and learned category biases. Top-down signals impose upper bounds on feature node activations.
DEVELOPMENT OF A NEW AORTIC CANNULA WITH DEFORMABLE TIP (2003)

Aortic cannulae usually have rigid tips with small cross section to keep aortic incision small and to avoid the aortic lumen occlusion during weaning. However, it is the small area available for blood flow that causes large hydraulic energy dissipation, high local shear stress (with hemolysis risk increase), and a blood jet that may cause aortic wall damage or atheromatous material dislodging. In this work, we present the design of a new aortic cannula, whose tip's cross section is divergent from the insertion to the outlet section. A great part of the tip's wall is deformable, so as to allow insertion, and to let the tip collapse under the natural heart's blood flow during the weaning phase. Pediatric prototypes (15 F at the incision site) were designed and manufactured. The full-section tip shape was optimized via computational fluid dynamics (CFD). Four shapes were evaluated with CFD models, and compared basing on pressure drop (δP), shear stress, kinetic energy of flow on the outlet section, and technological feasibility. With the optimized shape, prototypes were built with stainless steel (rigid parts) and silicone rubber (deformable wall thickness 0.35 and 0.50 mm). Experimental evaluation was carried out in vitro with a blood analog, both with steady and pulsatile flow, to evaluate 1) the δP across the cannula at full pump flow 2) the δP across the model aorta, and tip wall deformation at full heart flow (weaning phase) 3) δP and wall shape with both flows, at different ratios. Results were in agreement with CFD predictions. The prototype with 0.35 mm wall thickness performed better than standard straight- and curved-tip 15 F cannulae.
Statistical Software for State Space Methods (2011)

In this paper we review the state space approach to time series analysis and establish the notation that is adopted in this special volume of the Journal of Statistical Software. We first provide some background on the history of state space methods for the analysis of time series. This is followed by a concise overview of linear Gaussian state space analysis including the modelling framework and appropriate estimation methods. We discuss the important class of unobserved component models which incorporate a trend, a seasonal, a cycle, and fixed explanatory and intervention variables for the univariate and multivariate analysis of time series. We continue the discussion by presenting methods for the computation of different estimates for the unobserved state vector: filtering, prediction, and smoothing. Estimation approaches for the other parameters in the model are also considered. Next, we discuss how the estimation procedures can be used for constructing confidence intervals, detecting outlier observations and structural breaks, and testing model assumptions of residual independence, homoscedasticity, and normality. We then show how ARIMA and ARIMA components models fit in the state space framework to time series analysis. We also provide a basic introduction for non-Gaussian state space models. Finally, we present an overview of the software tools currently available for the analysis of time series with state space methods as they are discussed in the other contributions to this special volume.
An Assessment of Thimerosal Use in Childhood Vaccines (2001)

Our review revealed no evidence of harm caused by doses of thimerosal in vaccines, except for local hypersensitivity reactions. However, some infants may be exposed to cumulative levels of mercury during the first 6 months of life that exceed EPA recommendations. Exposure of infants to mercury in vaccines can be reduced or eliminated by using products formulated without thimerosal as a preservative.
Characterization of Anaeromyxobacter dehalogenans and Related Metal-Reducing bacteria by MALDI-TOF MS (2006)

No abstract prepared.
Trimodal therapy for invasive bladder cancer (2015)

Although radical cystectomy is still the treatment of reference for most of the patients with localized MIBC, TMT represents a reasonable alternative in highly selected patients. Any firm conclusion on the equivalence or superiority of one treatment to the other is still limited by the lack of randomized controlled trials and the heterogeneity of the available literature. Future studies and multidisciplinary approach are mandatory to optimize the patient selection and regimen of TMT.
Autonomic Responses to Orthostasis after Acetylcholinesterase Inhibition in Tetraplegia (2016)

PURPOSE: We have demonstrated that acetylcholinesterase inhibition (AcHi: pyridostigmine bromide: PB) improves orthostatic blood pressure (BP) responses to head-up tilt (HUT) compared to no drug (ND) in some individuals with tetraplegia and theorize that difference between subjects with an orthostatic BP response to PB (responders [R]) and those without a BP response (non-responders [nR]) may relate to the autonomic completeness of injury. Although we cannot directly asses the degree of autonomic cardiovascular impairment, we determined differences in the autonomic response to HUT using heart rate (HR) variability (HFV) and BP variability (BPV) after administration of PB (60 mg) compared to ND in subjects with tetraplegia. METHODS: Mixed factor ANOVA was used to determine main and interaction effects for high frequency HRV (HF: vagal) and low frequency BPV (LFsbp: sympathetic) responses to HUT (0°, 15°, 25°, 35°) following PB and ND administration in the R and nR. Beat-to-beat HR and BP were assessed using a 3-lead ECG and finger photoplethysmography, respectively; data were collected at 500 Hz for 5-minutes at each angle of HUT. RESULTS: Eleven individuals with SCI participated; however, one subject was unable to tolerate the HUT maneuver during ND therefore, results are presented in 10 subjects (age: 38±10 years; duration of injury: 13±10 years; level: C4-6; AIS: A, B, C). Five individuals were R and 5 were nR (+6.9±5.5 vs. -7.1±8.1 mmHg, respectively; p=0.012); demographics did not differ between the groups. Supine HR was lower in R compared to nR (48±3 vs. 57±8 bpm, respectively; p=0.049); supine BP did not differ. Although supine HF did not differ, supine LFsbp was increased in R compared to the nR (4.11±0.12 vs.3.82±0.24 ln, respectively; p=0.041). The group (R, nR) by condition (PB, ND) by HUT interaction effect was significant for HF (3.639; p=0.044), but not for LFsbp. CONCLUSION: These data suggest that tetraplegic individuals with increased resting sympathetic nervous system activity (LFsbp) respond to AcHi with an increased BP and vagal response to HUT, indicative of improved orthostatic baroreceptor function.
ChemInform Abstract: Metathesis in Peptides and Peptidomimetics. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Completion of structurally-incomplete matrices with reweighted low-rank and sparsity priors (2016)

Most matrix completion methods impose a low-rank prior or its variants to well pose the problem. However, the rank minimization is problematic to handle matrices with structural missing. To remedy this, this paper introduces a new matrix completion method using double priors on the latent matrix, named Reweighted Low-rank and Sparsity Priors. In the proposed model, the matrix is regularized by a low-rank prior to exploit the inter-column (row) correlations, and its columns (rows) are regularized by a sparsity prior under a dictionary to exploit intra-column (row) correlations. Both the low-rank and sparse priors are reweighted on the fly to promote low-rankness and sparsity, respectively. Numerical algorithm to solve our model is derived via the alternating direction method under the augmented Lagrangian multiplier framework. Experimental results show that our model is quite effective in recovering matrices with highly-structural missing, complementing the classic matrix completion models that handle random missing only.
Antiviral re-treatment of IFN-Ribavirin non-responders for recurrent post-transplantation hepatitis C (2010)

Both treatment arms showed to be effective, well tolerated and lead to an improvement in histologic outcome. Because of lower rates in side effects and equal outcome, PEG-IFN monotherapy is an adequate option for antiviral re-treatment.
A Case Study - 3D Powder Deposition onto Pharmaceutical Tablets (2005)

This paper presents the case study of a project conducted by Torrey Pines Research for Phoqus Pharmaceuticals wherein the requirement was to uniformly coat pharmaceutical tablets with various proprietary dry powders. This paper discusses the technical challenges, electrostatic constraints, solution options, and the resulting system solution.
Multi-Walled Carbon Nanotubes Inhibit Breast Cancer Cell Migration (2016)

According to the American Cancer Society, breast cancer is the second leading cause of cancer death in the US. Cancerous cells may have inadequate adhesions to the extracellular matrix and adjacent cells. Previous work has suggested that restoring these contacts may negate the cancer phenotype. This work aims to restore those contacts using multi-walled carbon nanotubes (MWNTs). Varying concentrations of carboxylated MWNTs in water, with or without type I collagen, were dried to create a thin film upon which one of three breast cell lines were seeded: cancerous and metastatic MDA- MB-231 cells, cancerous but non-metastatic MCF7 cells, or non-cancerous MCF10A cells. Proliferation, adhesion, scratch and autophagy assays, western blots, and immunochemical staining were used to assess adhesion and E-cadherin expression. Breast cancer cells grown on a MWNT-collagen coated surface displayed increased adhesion and decreased migration which correlated with an increase in E-cadherin. This work suggests an alternative approach to cancer treatment by physically mediating the cells' microenvironment.
Infrastructure ENUM Requirements (2007)

This document provides requirements for infrastructure or carrier
ENUM (E.164 Number Mapping), defined as the use of RFC 3761 technology
to facilitate interconnection of networks for E.164 number addressed
services, in particular but not restricted to VoIP (Voice over IP.)
This memo provides information for the Internet community.
Effect of Herbicides on Take-All Disease (Gaeumannomyces graminis) in Winter Wheat (Triticum aestivum) (1990)

Experiments were conducted in each of two seasons to determine possible effects of diclofop, difenzoquat, dinoseb, and mecoprop on the incidence of take-all disease and grain yield of winter wheat. All of the herbicides, especially mecoprop, reduced incidence of take-all. Treatments increased grain yields the first year but not the second, compared to the inoculated weed-free control. None of the herbicides tested increased incidence or severity of take-all disease in either of the two seasons. The technique of inoculating disease-free soil was successful in obtaining uniform and reproducible incidence of disease.