gebhart/patrepeval huggingface dataset:
Effect of leucine and metabolites of branched chain amino acids on protein turnover in heart. (1979)

Leucine, but not isoleucine or valine, inhibited protein degradation and accelerated protein synthesis in hearts perfused with buffer that contained glucose (15 mM) and normal plasma levels of other amino acids, except for the branched chain compounds. Products of leucine, isoleucine, and valine metabolism also inhibited protein degradation and stimulated protein synthesis. These compounds included the transamination and decarboxylation products, as well as acetate, acetoacetate, and propionate. In some, but not all instances, inhibition of degradation and acceleration of synthesis were accompanied by an increase in intracellular leucine. When insulin was added to the perfusate, the rate of degradation was reduced by 40%, but addition of leucine was ineffective in the presence of the hormone. Insulin, leucine (2 mM) and a mixture of branched chain amino acids at normal plasma levels increased latency of cathepsin D in hearts that were perfused with buffer containing glucose. A combination of leucine and insulin increased latency more than either substance alone. These studies indicate that leucine as well as a variety of substrates that are oxidized in the citric acid cycle are involved in regulation of protein turnover in heart muscle.
Remarkable long range effects on the diastereoface selectivity in an aldol condensation (1999)

The stereochemical results in an aldol reaction between the enolate 2 and various α-methyl aldehydes indicates a stabilizing through space interaction between C4C5 unsaturation and the formyl group. This interaction leads to a reaction conformation which favors a C7C8 (epothilone numbering) anti-relationship in the aldol products. Included is an extensive study that identifies steric and electronic effects of various α-methyl aldehydes in the aldol diastereoselection.
Novel regular-array ASIC architecture for 2-D ROS sorting (1991)

In this paper a novel regular array architecture for the 2-D running order statistics sort problem will be presented. The architecture combines a high throughput in terms of sorted windows with low hardware costs and low I/O bandwidth. It will be shown that the throughput-hardware cost ratio is substantially better than that of previously published architectures for this sorting problem under the same I/O constraints. This has been achieved by a careful design of the sorting algorithm that is tuned to match as tightly as possible the needs of real-life applications requiring this type of sorting. This design illustrates that designing algorithms with both precise applications and an architectural style in mind can greatly reduce the cost of VLSI Application Specific Integrated Circuit (ASIC) implementation. In this way it enhances the feasibility of a VLSI implementation of an algorithm.
Can Deep Learning be Applied to Model-Based Multi-Object Tracking? (2022)

Multi-object tracking (MOT) is the problem of tracking the state of an unknown and time-varying number of objects using noisy measurements, with important applications such as autonomous driving, tracking animal behavior, defense systems, and others. In recent years, deep learning (DL) has been increasingly used in MOT for improving tracking performance, but mostly in settings where the measurements are high-dimensional and there are no available models of the measurement likelihood and the object dynamics. The model-based setting instead has not attracted as much attention, and it is still unclear if DL methods can outperform traditional model-based Bayesian methods, which are the state of the art (SOTA) in this context. In this paper, we propose a Transformer-based DL tracker and evaluate its performance in the model-based setting, comparing it to SOTA model-based Bayesian methods in a variety of different tasks. Our results show that the proposed DL method can match the performance of the model-based methods in simple tasks, while outperforming them when the task gets more complicated, either due to an increase in the data association complexity, or to stronger nonlinearities of the models of the environment.
Exact inverter waveform analysis using z-transform estimation techniques (1990)

The critical limitations of Fourier transform analysis are reviewed. The frequency resolution and amplitude accuracy trade-offs implicit in techniques used to minimize the effect of these limitations are presented. The fundamental theory of exact, z-transform modeling that simultaneously offers excellent resolution and accuracy is discussed. The classical techniques used to estimate z-transform coefficients from the sampled data are presented, along with a discussion of their limitations. A new approach for z-transform estimation is developed theoretically, and experimental verification is demonstrated on a PC-AT-based signal acquisition system, using actual inverter waveforms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improving the harvestability of dry beans with gibberellic acid (1997)

Currently beans (Phaseolus vulagris L.) are commercially harvested in several operations. Initially mature plants are cut below the soil surface by a bean puller, swaths are later windrowed, then picked up and threshed. Attempts to improve the efficiency of bean harvesting, using straight cut harvesters have been problematic due and the proximity of the pods to the ground. Yield losses during straight cut harvesting can range from 25-90%. Increasing stem length, thereby increasing the distance of pods from the ground, will permit the direct harvest of dry beans and reduce yield losses. The effects of gibberellic acid (GA) on the canopy structure and harvestability of three cuitivars (Othello, UI 906, and Aztec ( 1995 only)) were examined in the field. Trials were conducted at two locations in 1994 and 1995. Five rates of GA (0, 12.5, 25, 37.5, and 50 ppm) were applied at three growth stages ( 1 st, 2nd, and 3rd trifoliolate leaf stages). Mechanically harvested yields were compared to hand harvested yields to determine if treatments improved the percentage yield recovery with straight cut harvesters. Some cultivars were found to be more sensitive to GA treatment than others. Gibberellic acid stimulated internode elongation in all cultivars, stem length increases of 10% to 200% over control plants were recorded. One cultivar’s (Othello) harvestability was improved by very high concentrations of GA.
Smooth Transitions in Shared Control Using Constraint-Admissible Sets (2019)

This work presents a shared-control architecture that determines driver intention to switch an automotive vehicle system between autonomous and manual modes. In all modes, the driver actuates the system solely using the steering wheel. The control system determines the driver's intention by checking whether the vehicle's current state satisfies certain pre-defined transition conditions. Three modes are considered: manual, lane-keeping, and lane-change. Transitions are activated primarily using maximal-admissible set-membership conditions; in the case of transition from lane-keeping to a lane change, the system also compares whether the cost of tracking the center lane is greater than the cost of tracking a minimal-jerk lane-change trajectory. Experimental results are presented using a CarSim-based driving simulator with gaming-wheel steering. They show smooth transitions between modes and a quick transition from autonomous to manual mode.
Data from Single-Cell Analysis Reveals a Preexisting Drug-Resistant Subpopulation in the Luminal Breast Cancer Subtype (2023)

&lt;div&gt;Abstract&lt;p&gt;Drug resistance is a major obstacle in the treatment of breast cancer. Surviving cells lead to tumor recurrence and metastasis, which remains the main cause of cancer-related mortality. Breast cancer is also highly heterogeneous, which hinders the identification of individual cells with the capacity to survive anticancer treatment. To address this, we performed extensive single-cell gene-expression profiling of the luminal-type breast cancer cell line MCF7 and its derivatives, including docetaxel-resistant cells. Upregulation of epithelial-to-mesenchymal transition and stemness-related genes and downregulation of cell-cycle–related genes, which were mainly regulated by LEF1, were observed in the drug-resistant cells. Interestingly, a small number of cells in the parental population exhibited a gene-expression profile similar to that of the drug-resistant cells, indicating that the untreated parental cells already contained a rare subpopulation of stem-like cells with an inherent predisposition toward docetaxel resistance. Our data suggest that during chemotherapy, this population may be positively selected, leading to treatment failure.&lt;/p&gt;Significance:&lt;p&gt;This study highlights the role of breast cancer intratumor heterogeneity in drug resistance at a single-cell level.&lt;/p&gt;&lt;/div&gt;
Mapping and ablation of ventricular fibrillation. (2004)

Sudden cardiac death frequently results from ventricular fibrillation (VF). While VF is frequently the eventual mode of death in patients with abnormal ventricular substrates, it has also been described in patients with structurally normally hearts. Until recently, the management of patients who have survived sudden cardiac death has focused on treating the consequences by implantation of a defibrillator. However, such therapy remains restricted in many countries, is associated with a prohibitive cost to the community, and may be a cause of significant morbidity in patients with frequent episodes or storms of arrhythmia. Evidence emerging from the study of fibrillation both in the atria and the ventricle suggests an important role for triggers arising from the Purkinje network or the right ventricular outflow tract in the initiation of VF. Initial experience in patients with idiopathic VF and even those with VF associated with abnormal repolarization syndromes (LQT or Brugada syndrome) or myocardial infarction suggests that long term suppression of recurrent VF may be feasible by the elimination of these triggers. With the development of new mapping and ablation technologies, and greater physician experience, catheter ablation of VF, with the ultimate aim of curing such patients at risks of sudden cardiac death, may not be an unrealistic goal in the future.
Non-enzymatic, Serum-free Tissue Culture of Pre-invasive Breast Lesions for Spontaneous Generation of Mammospheres (2014)

Breast ductal carcinoma in situ (DCIS), by definition, is proliferation of neoplastic epithelial cells within the confines of the breast duct, without breaching the collagenous basement membrane. While DCIS is a non-obligate precursor to invasive breast cancers, the molecular mechanisms and cell populations that permit progression to invasive cancer are not fully known. To determine if progenitor cells capable of invasion existed within the DCIS cell population, we developed a methodology for collecting and culturing sterile human breast tissue at the time of surgery, without enzymatic disruption of tissue. Sterile breast tissue containing ductal segments is harvested from surgically excised breast tissue following routine pathological examination. Tissue containing DCIS is placed in nutrient rich, antibiotic-containing, serum free medium, and transported to the tissue culture laboratory. The breast tissue is further dissected to isolate the calcified areas. Multiple breast tissue pieces (organoids) are placed in a minimal volume of serum free medium in a flask with a removable lid and cultured in a humidified CO₂ incubator. Epithelial and fibroblast cell populations emerge from the organoid after 10 - 14 days. Mammospheres spontaneously form on and around the epithelial cell monolayer. Specific cell populations can be harvested directly from the flask without disrupting neighboring cells. Our non-enzymatic tissue culture system reliably reveals cytogenetically abnormal, invasive progenitor cells from fresh human DCIS lesions.
Identification and Characterization of Vascular Endothelial Growth Factor Receptor (Flt) in Bovine Retinal Pericytes (1996)

Vascular endothelial growth factor (VEGF) plays an important role in the hypoxia-stimulated neovascularization of ischemic retinal diseases such as proliferative diabetic retinopathy. VEGF exerts its effect through two known high-affinity tyrosine kinase receptors, named kinase insert domain-containing receptor (KDR) and the fms-like tyrosine kinase (Flt). VEGF receptors are located primarily on endothelial cells, although receptors on a few other nonocular cell types also have been described. In the present study, we demonstrate the expression of Flt, but not KDR, in bovine retinal pericytes (BRPCs). Although KDR is expressed predominantly in retinal endothelial cells, Northern blot analysis demonstrated substantial expression of the Flt gene in BRPCs without detection of KDR despite using polyadenylated RNA. Hypoxia increased Flt gene expression in BRPCs (2.7-fold, P < 0.01). 125I-labeled VEGF binding analysis on BRPCs demonstrated two apparent high-affinity receptor subtypes (Kd = 14 and 215 pmol/l), with 2.9 x 10(4) and 1.4 x 10(5) receptors/cell, respectively. 125I-VEGF affinity cross-linking demonstrated VEGF-specific binding complexes at 150, 172, 187, and 200 kDa under reducing conditions. Western blot analysis using an anti-phosphotyrosine antibody demonstrated VEGF-induced tyrosine phosphorylation of several proteins. VEGF stimulation had little effect on initial BRPCs growth rates but significantly increased BRPCs number after 7 days. These results suggest that two classes of high-affinity VEGF receptors are present on BRPCs, at least one of which is analogous to Flt and is capable of intracellular protein phosphorylation. Thus, VEGF might regulate the function of both retinal endothelial cells and retinal pericytes to induce pathological angiogenesis and vascular remodeling during proliferative diabetic retinopathy and other ischemic retinal diseases.
Biomimetic Synthesis of Water Soluble Conductive Polypyrrole and Poly(3,4‐Ethylenedioxythiophene) (2003)

Abstract A novel biomimetic method for the synthesis of conducting molecular complexes of polypyrrole (PPYR) and poly(3,4‐ethylenedioxythiophene) (PEDOT) in the presence of a polyelectrolyte, such as polystyrene sulfonate (SPS) is presented. A poly(ethylene glycol) modified hematin (PEG‐Hematin) was used to catalyze the polymerization of pyrrole (PYR) and 3,4‐ethylenedioxythiophene (EDOT) in the presence of SPS to form PPYR/SPS and PEDOT/SPS complexes. UV‐VIS, FT‐IR, and electrical conductivity studies for all complexes indicated the presence of a stable and electrically conductive form of these polymers. Furthermore, the presence of SPS in this complex provides a unique combination of properties such as processability and water‐solubility.
Three-dimensional printing of patient-specific computed tomography lung phantoms: a reader study (2023)

In modern clinical decision-support algorithms, heterogeneity in image characteristics due to variations in imaging systems and protocols hinders the development of reproducible quantitative measures including for feature extraction pipelines. With the help of a reader study, we investigate the ability to provide consistent ground-truth targets by using patient-specific 3D-printed lung phantoms. PixelPrint was developed for 3D-printing lifelike computed tomography (CT) lung phantoms by directly translating clinical images into printer instructions that control density on a voxel-by-voxel basis. Data sets of three COVID-19 patients served as input for 3D-printing lung phantoms. Five radiologists rated patient and phantom images for imaging characteristics and diagnostic confidence in a blinded reader study. Effect sizes of evaluating phantom as opposed to patient images were assessed using linear mixed models. Finally, PixelPrint's production reproducibility was evaluated. Images of patients and phantoms had little variation in the estimated mean (0.03-0.29, using a 1-5 scale). When comparing phantom images to patient images, effect size analysis revealed that the difference was within one-third of the inter- and intrareader variabilities. High correspondence between the four phantoms created using the same patient images was demonstrated by PixelPrint's production repeatability tests, with greater similarity scores between high-dose acquisitions of the phantoms than between clinical-dose acquisitions of a single phantom. We demonstrated PixelPrint's ability to produce lifelike CT lung phantoms reliably. These phantoms have the potential to provide ground-truth targets for validating the generalizability of inference-based decision-support algorithms between different health centers and imaging protocols and for optimizing examination protocols with realistic patient-based phantoms. <b>Classification:</b> CT lung phantoms, reader study.
Apoptosis in Burkitt lymphoma cells is prevented by promotion of cysteine uptake (1998)

Burkitt lymphoma (BL) cells are highly sensitive to suboptimal growth conditions and undergo apoptosis when seeded at reduced serum concentration or low cell density. Irradiated fibroblasts can protect BL cells from apoptosis induced by lowering the serum concentration or cell density through secretion of a survival- and proliferation-promoting activity which is soluble and labile. Murine B cells have a restricted uptake capacity for cystine and require cysteine for proliferation, which can be supplied efficiently by feeder cells. Therefore, we have studied the role of cysteine and other compounds with free thiol groups for survival and proliferation of BL cells. Cysteine, when added alone, exerted strong toxicity on BL cells. This toxicity could be counteracted by the addition of catalase, pyruvate or bathocuproine disulfonate (BCS), all of which interfere with the production of hydrogen peroxide. Inhibition of the toxicity of cysteine was necessary to unravel the survival- and growth-promoting activity of cysteine at low cell density. Alpha-thioglycerol, beta-mercaptoethanol and dithiothreitol had similar toxic activity in the absence of catalase, pyruvate and BCS and, through stimulation of cysteine uptake and glutathione synthesis, displayed a similar survival- and growth-promoting activity in the presence of the protective agents. The survival- and proliferation-inducing activity of thiol compounds in the presence of catalase, pyruvate and BCS was not associated with induction of BCL-2 or BAX. Cysteine/cystine uptake and the intra/cellular glutathione level are thus important parameters, determining the susceptibility vs. resistance of BL cells to apoptosis.
Modeling of two-dimensional photonic crystal resonant cavities incorporating elliptically shaped dielectric cylinders (2005)

Modeling of photonic crystal structures is an ongoing challenge. This letter is devoted to the theoretical modeling of photonic crystal resonant cavities, composed of elliptically shaped dielectric pillars. Through this rigorous study, we can examine the impact of the elliptical-shape deformations to important quantities related to the photonic crystal cavity performance, such as the quality factor and the resonance frequency.
Strategien zur Modulation von Protein‐Protein‐Wechselwirkungen mit synthetischen Substanzen (2005)

Abstract Die Entwicklung niedermolekularer Modulatoren von Protein‐Protein‐Wechselwirkungen gilt als wichtiges Forschungsziel mit großem Potenzial für die Entdeckung neuer Therapeutika. Trotz anspruchsvoller Voraussetzungen gibt es eine Reihe von Beispielen für die Inhibierung der Wechselwirkung großer Proteinbindungspartner durch einen niedermolekularen Liganden. In diesem Aufsatz geben wir einen Überblick über die Strategien zur Modulierung von Protein‐Protein‐Wechselwirkungen und präsentieren den aktuellen Forschungsstand beim rationalen Design von Mimetika, die die Strukturen und Funktionen ihrer natürlichen Zielstrukturen abbilden.
A systematic study of the structural and regulatory features of post‐translational modifications of cellular enzymes: a case study based upon information in PhosphoSitePlus™ (2009)

PhosphoSitePlus (PSP) is an open resource offering comprehensive information about site‐specific protein modification. PSP aggregates all published sites of protein post‐translational modifications, as well as thousands of newly‐discovered modification sites identified using high‐throughput methods at CST and elsewhere. Data that is manually curated includes upstream events that regulate modifications, and downstream consequences of modifications on the protein and more global cellular processes. The vast amount of information in PSP can be mined to build signaling networks to explore novel features of cellular processes. Of &gt;10,000 proteins curated into PSP, about 1,850 are cellular enzymes with &gt;15,000 known modification sites. We have analyzed information in PSP for patterns and interactions that may provide novel insights into the biology and biochemistry of enzymatic systems. These studies include: 1) pathway analysis of regulatory information in PSP; 2) potential associations between specific upstream kinases and classes of modified enzymes, protein domains shared between enzymes, or novel sequence motifs; 3) identification of sites within motifs or domains that are common to related enzymes; and 4) role of modification sites common to sets of enzymes on regulation of downstream processes. www.phosphosite.org Supported by NIH grants R43GM065768, R44AA014848, and 5R44CA126080
Confirmation Testing and Preliminary Dynamic Measurements of a Journal Bearing Test Rig (2008)

Current modeling of the static and dynamic characteristics of fluid film bearings typically employs a single impedance matrix to represent the force transfer between a bearing and journal centerlines. A numerical method has been proposed that distributes the bearing impedances around the circumference of the fluid film to allow for more accurate modeling of higher order circumferential modes. In order for this method to be used with confidence, its results must first be validated. For this purpose, an experimental test method and apparatus capable of measuring these distributed bearing impedances has been developed. This paper will present the preliminary bearing displacement and pressure measurements collected from the journal bearing test apparatus and will compare these experimental results to those calculated numerically. Discrepancies between the data sets will be discussed and future steps will be outlined.
The pesticidal Cry6Aa toxin from Bacillus thuringiensis is structurally similar to HlyE-family alpha pore-forming toxins (2016)

Cry6 proteins are members of the alpha helical pore-forming toxins - a structural class not previously recognized among the Cry toxins of B. thuringiensis and representing a new paradigm for nematocidal and insecticidal proteins. Elucidation of both the structure and the pore-forming mechanism of action of Cry6Aa now opens the way to more detailed analysis of toxin specificity and the development of new toxin variants with novel activities.