gebhart/patrepeval huggingface dataset:
Mitophagy in Acute Kidney Injury and Kidney Repair (2020)

Acute kidney injury (AKI) is a major kidney disease characterized by rapid decline of renal function. Besides its acute consequence of high mortality, AKI has recently been recognized as an independent risk factor for chronic kidney disease (CKD). Maladaptive or incomplete repair of renal tubules after severe or episodic AKI leads to renal fibrosis and, eventually, CKD. Recent studies highlight a key role of mitochondrial pathology in AKI development and abnormal kidney repair after AKI. As such, timely elimination of damaged mitochondria in renal tubular cells represents an important quality control mechanism for cell homeostasis and survival during kidney injury and repair. Mitophagy is a selective form of autophagy that selectively removes redundant or damaged mitochondria. Here, we summarize our recent understanding on the molecular mechanisms of mitophagy, discuss the role of mitophagy in AKI development and kidney repair after AKI, and present future research directions and therapeutic potential.
High-resolution photoelastic pressure sensor using low-birefringence fiber (1986)

The effect of birefringence induced in a single-mode fiber by a lateral force has been applied to measure the absolute value of force or pressure with high resolution. A sensor configuration with an extended detecting surface has been investigated by means of calibrated weights. The sensor is sensitive to an incremental force of 2 x 10(-3) N, independently of the length of the fiber. The maximum force applied was 10 N/m of fiber length.
Indirect measurement of lung density and air volume from electrical impedance tomography (EIT) data (2011)

This paper describes a method for estimating lung density, air volume and changes in fluid content from a non-invasive measurement of the electrical resistivity of the lungs. Resistivity in Ω m was found by fitting measured electrical impedance tomography (EIT) data to a finite difference model of the thorax. Lung density was determined by comparing the resistivity of the lungs, measured at a relatively high frequency, with values predicted from a published model of lung structure. Lung air volume can then be calculated if total lung weight is also known. Temporal changes in lung fluid content will produce proportional changes in lung density. The method was implemented on EIT data, collected using eight electrodes placed in a single plane around the thorax, from 46 adult male subjects and 36 adult female subjects. Mean lung densities (±SD) of 246 ± 67 and 239 ± 64 kg m(-3), respectively, were obtained. In seven adult male subjects estimates of 1.68 ± 0.30, 3.42 ± 0.49 and 4.40 ± 0.53 l in residual volume, functional residual capacity and vital capacity, respectively, were obtained. Sources of error are discussed. It is concluded that absolute differences in lung density of about 30% and changes over time of less than 30% should be detected using the current technology in normal subjects. These changes would result from approximately 300 ml increase in lung fluid. The method proposed could be used for non-invasive monitoring of total lung air and fluid content in normal subjects but needs to be assessed in patients with lung disease.
GABAA receptor function in developing rat thalamic reticular neurons: whole cell recordings of GABA-mediated currents and modulation by clonazepam (1996)

1. Nucleus reticularis thalami (NRT) is a nucleus composed entirely of GABAergic neurons, which functions as a pacemaker to synchronize thalamocortical oscillations. To study the functional properties of GABAergic inhibition mediated through activation of gamma-aminobuturic acid-A (GABAA) receptors in these cells, neurons were isolated acutely from NRT at various postnatal developmental stages and recorded from using whole cell patch-clamp techniques. 2. Application of GABA to NRT neurons elicited a large, bicuculline sensitive current with an average reversal potential of -60.6 +/- 1.9 mV (mean +/- SD) in postnatal day (p) 19-21 neurons and -51.2 +/- 3.1 mV in p7 neurons, presumably mediated through activation of a GABAA-mediated chloride conductance. The potency of GABA in activating GABAA receptors decreased significantly with postnatal development in NRT neurons and was best fitted with EC50s of 24.9, 33.9, and 67.2 microM, in neurons isolated from p5-9, p18-25, and p58-74 rats, respectively. The density of GABAA receptors in the membranes of NRT neurons increased significantly with postnatal development. In addition, the GABA current decay rate slowed significantly in neurons isolated from older animals relative to early postnatal rat pups. 3. Both the potency and efficacy of benzodiazepine augmentation of GABAA responses in NRT neurons increased significantly with development. The EC50 of clonazepam decreased from 26 to 6 nM in p5-9 and p58-74 NRT neurons, respectively, whereas the efficacy increased from 126 to 163% augmentation over the same developmental range. 4. The elevated efficacy of clonazepam (CNZ) in NRT neurons relative to thalamic and cortical neurons, particularly in neurons isolated from adult (> p58) rats, is consistent with the anticonvulsant profile of this drug in controlling Generalized Absence epilepsy. Augmenting inhibition within NRT would enhance NRT/ NRT inhibitory connections and thereby decrease the amplitude of NRT-mediated synchronizing inhibitory postsynaptic potentials onto thalamus (where CNZ has low efficacy), in turn making it more difficult to elicit burst firing in thalamus due to deinactivation and subsequent activation of the low-threshold Ca2+ current. 5. The present developmental profile of GABAA responses in GABAergic NRT neurons provides data important in understanding the role of GABAergic inhibition within NRT in the modulation of normal and pathological thalamocortical rhythms in the brain and is also relevant in understanding potential differences in GABAA receptor physiology and pharmacology in GABAergic interneurons relative to glutamatergic neurons.
Expression of neuropeptide-degrading enzymes in alopecia areata: an immunohistochemical study (2001)

These findings suggest that SP is endogenously released by dermal nerve fibres around hair follicles and that it may play an important part in epithelial-mesenchymal-neuroectodermal interactions in AA. This study reveals that SP and its degrading enzymes are involved in the pathogenesis of AA, which in turn might explain the pathological significance of neurogenic and psychogenic aspects in the disease process.
Event Management and Monitoring Framework for HPC Environments using ServiceNow and Prometheus (2020)

The challenge of monitoring and event response management of a high performance computing facility grows significantly as the facilities employs and orchestrates more complex and heterogeneous systems and infrastructure. As the computational components encompassing the HPC facility system increases, the computational staff experiences rise in alert fatigue due to the false alarms and noise related to the similar events generated by monitoring tools. The National Energy Research Scientific Computing Center (NERSC) at the Lawrence Berkeley National Laboratory (LBNL) has begun to address the issues of duplication of alerts and alert remediation. However, more automation and integration is needed for collecting, aggregating, correlating, analyzing, managing and visualizing the scale of events that will be generated by the emergent hybrid computing infrastructures. In this paper, we present an event management and monitoring framework that addresses the operational needs of the future pre-exascale systems at the Lawrence Berkeley National Laboratory's National Energy Research Scientific Computing Center (NERSC). The framework integrates the Operations Monitoring and Notification Infrastructure (OMNI) at NERSC with the Prometheus, Grafana and ServiceNow platforms to help identify, diagnose, and resolve incidents in real-time, as well as conduct more thorough post-incident reviews enabled by the intuitive dashboards that provides a single pane of glass console for an efficient operations management and real-time proactive monitoring.
First steps towards an integration of a Personal Learning Environment at university level (2011)

Ebner, M., Schön, S., Taraghi, B., Drachsler, H., & Tsang, P. (2011). First steps towards an integration of a Personal Learning Environment at university level. In R. Kwan et al. (Eds.), ICT 2011, CCIS 177 (pp. 22–36), Springer-Verlag Berlin: Heidelberg 2011.
A novel human odorant-binding protein gene family resulting from genomic duplicons at 9q34: differential expression in the oral and genital spheres (2000)

Lipocalins are carrier proteins for hydrophobic molecules in many biological fluids. In the oral sphere (nasal mucus, saliva, tears), they have an environmental biosensor function and are involved in the detection of odours and pheromones. Herein, we report the first identification of human lipocalins involved in odorant binding. They correspond to a gene family located on human chromosome 9q34 produced by genomic duplications: two new odorant-binding protein genes ( hOBP (IIa) and hOBP (IIb) ), the previously described tear lipocalin LCN1 gene and two new LCN1 pseudogenes. Although 95% similar in sequence, the two hOBP (II) genes were differentially expressed in secretory structures. hOBP (IIa) was strongly expressed in the nasal structures, salivary and lachrymal glands, and lung, therefore having an oral sphere profile. hOBP (IIb) was more strongly expressed in genital sphere organs such as the prostate and mammary glands. Both were expressed in the male deferent ducts and placenta. Surprisingly, alternatively spliced mRNAs resulting in proteins with different C-termini were generated from each of the two genes. The single LCN1 gene in humans generated a putative odorant-binding protein in nasal structures. Finally, based on the proposed successive genomic duplication history, we demonstrated the recruitment of exons within intronic DNA generating diversity. This is consistent with a positive selection pressure in vertebrate evolution in the intron-late hypothesis.
Accurate power estimation of CMOS sequential circuits (1996)

The existence of near-closed sets makes the power estimation of sequential circuits more complicated and time consuming. If caution is not taken, the Monte Carlo-based power estimation techniques for sequential circuits can wrongly terminate the simulation with undesired results. In this paper, we have developed a strategy for a statistical power estimation technique to take into account the possible existence of near-closed sets. We propose an algorithm that partitions states into near-closed sets, if they do exist, and a technique that reduces the computation time of the probabilities of states if state transition graph (STG) is available. If STG is not available, we propose a Monte Carlo-based technique with a warm-up period. The results show that the partitioning algorithm also serves as a detector that signifies whether there may exist near-closed sets. The computation time of state probability can be reduced up to 50% in cases when near-closed sets are present. The relative error of the estimated individual node activity by the Monte Carlo-based technique with a warm-up period is within 3% of the result of long run simulation.
Specific intercellular binding of the β-amyloid precursor protein to the presenilins induces intercellular signaling: Its significance for Alzheimer’s disease (1998)

Genetic evidence has implicated three proteins, the beta-amyloid precursor protein (beta-APP) and the two homologous presenilins (PS-1 and PS-2), in the etiology of Alzheimer's disease (AD). How these three proteins jointly contribute to AD, however, is not clear. Nor is any of their normal physiological functions known. Herein, we demonstrate, confirming a prediction made earlier, that beta-APP and either PS-1 or PS-2 act as a specific membrane-bound ligand binding intercellularly with either of its two membrane receptors. This results in a cell-cell adhesion, after which rapid transient increases in protein tyrosine kinase activity and protein tyrosine phosphorylation occur coordinately inside one or both of the two adherent cells. The spectrum of proteins modified by tyrosine phosphorylation differs depending on whether PS-1 or PS-2 is involved in the specific intercellular binding to beta-APP, which implies that PS-1 and PS-2 have distinct, rather than redundant, functions in normal physiology. The relevance of this intercellular interaction and signaling process to AD is discussed.
The Effects of High-Amplitude Impulsive Noise on Hatching Success: A reanalysis of the Sooty Tern Incident (1991)

In a widely cited article, Austin ET AL. (1970a, Proc. Int. Ornith. Cong. 15:627) attributed a mass hatching failure among 50,000 pairs of Sooty Terns (Sterna fuscata) nesting on the Dry Tortugas to damage caused by sonic booms from low-flying military aircraft. Theoretically, eggshells and embryonic tissues should withstand pressures much greater than those generated by even the most intense sonic booms, so we conducted a worst case experiment to test whether impulsive noise could cause mass hatching failures. We exposed 20 chicken (Gallus gallus) and 20 quail (Coturnix couturnix) eggs to explosions of four pest-control devices (mean peak flat sound pressure level 177.3 db re 20 upa; mean CSEL of 139; mean frequency 620 Hz). None of these eggs showed the longitudinal cracks that had been reported on Dry Tortugas. We also exposed fertile chicken (13) and quail (8) eggs to five similar impulses and compared hatch rates with those of matched controls. The chicken eggs were exposed on Day 2 of incubation, the most sensitive phase of development; the quail eggs at half-way through incubation, the time of exposure on the Dry, Tortugas. Hatch rates and weights between control and exposed embryos were not significantly different.
The 1931 I C I Standard Observer and Coordinate System for Colorimetrya,b (1933)

This report makes available in convenient form the properties of the standard observer recently recommended for colorimetric purposes by the International Commission on Illumination. These data supersede the values published in the 1922 report of the committee on colorimetry known as the O.S.A. excitation data. Forms are given for computing trilinear coordinates (trichromatic coefficients), dominant wave-length, colorimetric purity, and luminous transmission (or reflectance) from spectrophotometric data. Tables of the data needed are included for the 1931 I.C.I. standard illuminants A, B and C.
Advanced Renderman: Creating CGI for Motion Pictures (1999)

From the Publisher:
Introduced by Pixar Studios over a decade ago, the RenderMan Interface Specification is the dominant standard for sending data to the leading rendering programs used by 3D artists and animators. But users are hampered by the lack of authoritative, up-to-date information on applying the standard, having long had to rely on the ten-year-old RenderMan Companion and a far-flung collection of course notes and Web sites. Advanced RenderMan: Beyond the Companion is precisely what RenderMan users are dying for. It offers thoroughly updated coverage while moving beyond the original work's scope to provide in-depth information on dozens of advanced topics. Both a reference and a tutorial, this book will be indispensable to graphics programmers, modelers, animators, technical directors, and hobbyists-it is truly the key to their ability to achieve state-of-the-art 3D effects. 
Key Features: 

Written by the world's foremost RenderMan experts-key figures at Pixar, the company that developed and first implemented the standard Offers advanced users instruction not available anywhere else while providing a leg up to relative beginners-including tips on avoiding mistakes and an appendix covering key math skills. Filled with technical illustrations and many full-color representations of effects supported by the RenderMan standard Via a companion Web site, provides comprehensive documentation of the standard's semantics and syntax, example source code, shaders and other software, and the full set of SIGGRAPH course notes on RenderMan
Modulating CD27 signaling to treat cancer (2012)

CD27 signaling can either improve T-cell function or lead to T-cell dysfunction, depending on the duration and conditions of receptor ligation. Recent studies have shown that modulating the CD70-CD27 interaction is an attractive strategy to treat solid tumors and also to directly target leukemia stem cells.
Combination of cetuximab with chemoradiation, trastuzumab or MAPK inhibitors: mechanisms of sensitisation of cervical cancer cells (2009)

Our data suggest that cetuximab combined with chemoradiation, trastuzumab or MAPK inhibitors has useful applications for CC treatment, independently of EGFR expression.
A Cascade Framework for a Real-Time Statistical Plate Recognition System (2007)

This paper describes a plate recognition system that can process images rapidly at high accuracy rates. This system is designed to meet the requirements of performance, computational speed, and adaptation for vehicle surveillance applications, such as stolen car detection systems. These requirements are satisfied by adopting a cascade framework, utilizing plate characteristics, and developing fast one-pass algorithms. Our system is composed of three main cascading modules for plate detection, character segmentation, and postprocessing. Each module is further decomposed into several cascading procedures, which are composed of successively more complex rejecters. The first module rapidly rejects a majority of nonplate regions by using low computational gradient features and a one-pass scanning algorithm followed by heavy computational statistical rejecters. The second module rejects a majority of noncharacter regions in a similar manner. A peak-valley analysis algorithm is proposed to rapidly detect all promising candidates of character regions. The third module eliminates the plate characters that do not satisfy the plate specifications. In our experiments, the system can recognize plates over 38 frames per second with a resolution of 640 times 480 pixels on a 3-GHz Intel Pentium 4 personal computer
Stability of ranitidine admixtures frozen and refrigerated in minibags (1986)

The stability of ranitidine hydrochloride stored frozen and refrigerated in polyvinyl chloride minibags was studied. Ranitidine hydrochloride was added to either 5% dextrose injection or 0.9% sodium chloride injection to yield concentrations of 0.5, 1.0, and 2.0 mg/mL. In phase 1 of the study, admixtures containing ranitidine hydrochloride 1 mg/mL were stored at 4 degrees C for 10 days. In phase 2, solutions were frozen for 30 days at -30 degrees C and were later refrigerated for 14 days. Ranitidine concentration was tested using a stability-indicating high-performance liquid chromatographic assay at time zero and at intervals during storage. Sterility tests were performed on some samples, and various admixtures were visually inspected and tested for pH. At least 90% of the initial concentration of ranitidine remained in all solutions at all storage conditions. No visual changes or changes in pH or sterility were observed. Ranitidine hydrochloride in concentrations of 0.5, 1.0, and 2.0 mg/mL in 5% dextrose injection or 0.9% sodium chloride injection may be stored in polyvinyl chloride minibags frozen for 30 days followed by refrigeration for an additional 14 days.
Synthesis of Ag@AgAu Metal Core/Alloy Shell Bimetallic Nanoparticles with Tunable Shell Compositions by a Galvanic Replacement Reaction (2008)

Truncated octahedral (TO) Ag nanoparticles are subjected to a replacement reaction with HAuCl4, where they undergo a series of morphological changes to transform into Ag@AgAu metal core/alloy shell nanoparticles (see image). In the final stage, atomic rearrangement occurrs to restore the bimetallic particles to the initial TO shape.
Phenotypic Screening in C. elegans as a Tool for the Discovery of New Geroprotective Drugs (2020)

Population aging is one of the largest challenges of the 21st century. As more people live to advanced ages, the prevalence of age-related diseases and disabilities will increase placing an ever larger burden on our healthcare system. A potential solution to this conundrum is to develop treatments that prevent, delay or reduce the severity of age-related diseases by decreasing the rate of the aging process. This ambition has been accomplished in model organisms through dietary, genetic and pharmacological interventions. The pharmacological approaches hold the greatest opportunity for successful translation to the clinic. The discovery of such pharmacological interventions in aging requires high-throughput screening strategies. However, the majority of screens performed for geroprotective drugs in <i>C. elegans</i> so far are rather low throughput. Therefore, the development of high-throughput screening strategies is of utmost importance.
Protective effect of ozone treatment on the injury associated with hepatic ischemia-reperfusion: Antioxidant-prooxidant balance (1999)

The effects of ozone treatment on the injury associated to hepatic ischemia-reperfusion (I/R) was evaluated. Ozone treatment (1 mg/kg daily during 10 days by rectal insufflation) is shown to be protective as it attenuated the increases in transaminases (AST, ALT) and lactate levels observed after I/R. I/R leads to a decrease in endogenous antioxidant (SOD and glutathione) and an increase in reactive oxygen species (H2O2) with respect to the control group. However, ozone treatment results in a preservation (glutathione) or increase (SOD) in antioxidant defense and maintains H2O2 at levels comparable to those in the control group. The present study reports a protective effect of ozone treatment on the injury associated to hepatic I/R. The effectiveness of ozone could be related to its action on endogenous antioxidants and prooxidants balance in favour of antioxidants, thus attenuating oxidative stress.
Dead space approximation for impact ionization in silicon (1996)

We demonstrate the validity of the dead space approximation for impact ionization in silicon. Monte Carlo simulations are used to obtain realistic ionization probabilities, and the corresponding avalanche gain in constant field structures is computed. We show that the hard-threshold dead space model is in good agreement with a more refined model taking into account soft-threshold effects, if an effective threshold energy of 3 eV is adopted for electrons. We also show that hole nonlocal effects do not significantly affect the result.
On the linkage between RNA processing and RNA translatability. (1994)

The immunoglobulin mu heavy chain gene of mouse hybridoma cells is expressed in two forms, microseconds and microns, differing in their use of 3' exons. As for many other mammalian genes, mutations in the mu gene which prematurely terminate translation often have the effect of reducing the amount of these mu RNAs. To test the generality of this relationship, we selected mutant hybridoma cell lines defective in IgM production and searched both for translation termination mutations which do not reduce the amount of mu RNA as well as for mutants which show the more commonly observed reduction in mu RNA. As observed previously, the amount of microseconds RNA is normal in mutants terminating in the C mu 4 exon; by contrast the amount of microns RNA is reduced in these mutants, indicating that the effect of the mutation is influenced by some feature near the 3' end of the RNA. Mutations terminating translation in other C region exons have a graded effect on RNA content, ranging from 10% the normal level for termination in the C mu 3 exon down to 1% for termination in the C mu 2 exon. By contrast, a mutant cell line terminating in the leader exon contained 25% the normal amount of mu RNA, suggesting that translation past some point might be required to fully engage the RNA degradation process.