gebhart/patrepeval huggingface dataset:
The Onset and Progression of Osteoblast Differentiation is Functionally Related to Cellular Proliferation (1989)

The relationship of proliferation to the developmental sequence associated with bone cell differentiation was examined in primary osteoblast cultures derived from fetal rat and embryonic chick calvaria. A reciprocal and functional relationship exists between the decline in proliferative activity which occurs during the initial stages of the developmental sequence and the induction of genes encoding osteoblast phenotype proteins associated with matrix maturation and mineralization. This relationship is supported by 1) a temporal sequence of events in which there is an enhanced expression of alkaline phosphatase (AP) and osteopontin (OP) genes immediately following the proliferative period and expression of osteocalcin with the onset of mineralization, and 2) increases in AP and OP when DNA synthesis is inhibited. By determining cellular mRNA levels and rates of mRNA synthesis in isolated nuclei, we found that the down-regulation of cell growth-related genes is modified at both the levels of transcription and mRNA stability. For a histone gene where down-regulation is transcriptionally mediated, we have observed that the shutdown of osteoblast proliferation is associated with the selective loss of the interaction of a promoter binding factor (HiNF-D) with a proximal regulatory element (Site II). A relationship between Site II occupancy by HiNF-D and the onset of osteoblast differentiation is supported by the persistence of Site II-HiNF-D interactions when proliferating rat osteoblasts are growth arrested under conditions that do not induce differentiation; and additionally, by the loss of Site II-HiNF-D interactions during the shut-down of proliferation when HL60 promyelocytic leukemia cells are induced to differentiate into monocytes. Our results are consistent with a requirement of proliferation for expression of genes involved with production, deposition and possibly organization of the osteoblast extracellular matrix. It is also reasonable to postulate that properties of the mineralizing matrix are related to the shut-down of proliferation.
Phase angle for prognostication of survival in patients with advanced cancer: Preliminary findings (2014)

Phase angle was found to be a novel predictor of poor survival, independent of established prognostic factors, in the advanced cancer setting. This objective and noninvasive tool may be useful for bedside prognostication.
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations (2016)

RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding RNAs. Standard RNAseq requires 30 - 100 million sequencing reads and can include multiple RNA products such as mRNA and noncoding RNAs. We demonstrate how targeted RNAseq (capture) permits a focused study on selected RNA products using a desktop sequencer. RNAseq capture can characterize unannotated, low, or transiently expressed transcripts that may otherwise be missed using traditional RNAseq methods. Here we describe the extraction of RNA from cell lines, ribosomal RNA depletion, cDNA synthesis, preparation of barcoded libraries, hybridization and capture of targeted transcripts and multiplex sequencing on a desktop sequencer. We also outline the computational analysis pipeline, which includes quality control assessment, alignment, fusion detection, gene expression quantification and identification of single nucleotide variants. This assay allows for targeted transcript sequencing to characterize gene expression, gene fusions, and mutations.
A Block-Based Linear MMSE Noise Reduction with a High Temporal Resolution Modeling of the Speech Excitation (2005)

A comprehensive linear minimum mean squared error (LMMSE) approach for parametric speech enhancement is developed. The proposed algorithms aim at joint LMMSE estimation of signal power spectra and phase spectra, as well as exploitation of correlation between spectral components. The major cause of this interfrequency correlation is shown to be the prominent temporal power localization in the excitation of voiced speech. LMMSE estimators in time domain and frequency domain are first formulated. To obtain the joint estimator, we model the spectral signal covariance matrix as a full covariance matrix instead of a diagonal covariance matrix as is the case in the Wiener filter derived under the quasi-stationarity assumption. To accomplish this, we decompose the signal covariance matrix into a synthesis filter matrix and an excitation matrix. The synthesis filter matrix is built from estimates of the all-pole model coefficients, and the excitation matrix is built from estimates of the instantaneous power of the excitation sequence. A decision-directed power spectral subtraction method and a modified multipulse linear predictive coding (MPLPC) method are used in these estimations, respectively. The spectral domain formulation of the LMMSE estimator reveals important insight in interfrequency correlations. This is exploited to significantly reduce computational complexity of the estimator. For resource-limited applications such as hearing aids, the performance-to-complexity trade-off can be conveniently adjusted by tuning the number of spectral components to be included in the estimate of each component. Experiments show that the proposed algorithm is able to reduce more noise than a number of other approaches selected from the state of the art. The proposed algorithm improves the segmental SNR of the noisy signal by 13 dB for the white noise case with an input SNR of 0 dB.
Systematic Analysis of Human Cells Lacking ATG8 Proteins Uncovers Roles for GABARAPs and the CCZ1/MON1 Regulator C18orf8/RMC1 in Macroautophagic and Selective Autophagic Flux (2017)

Selective autophagy and macroautophagy sequester specific organelles/substrates or bulk cytoplasm, respectively, inside autophagosomes as cargo for delivery to lysosomes. The mammalian ATG8 orthologues (MAP1LC3A/B/C and GABARAP/L1/L2) are ubiquitin (UB)-like proteins conjugated to the autophagosome membrane and are thought to facilitate cargo receptor recruitment, vesicle maturation, and lysosomal fusion. To elucidate the molecular functions of the ATG8 proteins, we engineered cells lacking genes for each subfamily as well as all six mammalian ATG8s. Loss of GABARAPs alone attenuates autophagic flux basally and in response to macroautophagic or selective autophagic stimuli, including parkin-dependent mitophagy, and cells lacking all ATG8 proteins accumulate cytoplasmic UB aggregates, which are resolved following ectopic expression of individual GABARAPs. Autophagosomes from cells lacking GABARAPs had reduced lysosomal content by quantitative proteomics, consistent with fusion defects, but accumulated regulators of late endosome (LE)/autophagosome maturation. Through interaction proteomics of proteins accumulating in GABARAP/L1/L2-deficient cells, we identified C18orf8/RMC1 as a new subunit of the CCZ1-MON1 RAB7 guanine exchange factor (GEF) that positively regulates RAB7 recruitment to LE/autophagosomes. This work defines unique roles for GABARAP and LC3 subfamilies in macroautophagy and selective autophagy and demonstrates how analysis of autophagic machinery in the absence of flux can identify new regulatory circuits.
SCIDOT-47. EFFECT OF ulRFE COGNATES EMULATING BIOACTIVE SUBSTANCES ON ANIMAL BEHAVIOR (2019)

Abstract BACKGROUND The EMulate Therapeutics Voyager system produces a magnetic field obtained from the magnetic fluctuations produced by molecules in solution. These recordings, ultra-low radio frequency energy (ulRFE®) cognates, are intended to emulate the effects of the molecule. METHODS Mice were treated with cognates for up to 120 min on the first day, then 24 h/day for the next 15 days. RESULTS All ulRFE cognates were well tolerated. Body weights remained stable. Animals exposed to signals derived from melatonin, THC (tetrahydrocannabinol), scotch, and ethanol showed signs of mild hypo-activity, while cognates derived from CBD (cannabidiol), Everclear, nicotine, and white wine showed mild signs of somnolence. Caffeine exposure initially caused mild hyperactivity, which returned to normal after the 120 minutes. The espresso cognate induced signs of mild hyperactivity during the initial 20-minute exposure. After 40 minutes, mild head convulsions and normal activity levels were noted. After 120 minutes, signs of hypoactivity were seen. Animals exposed to caffeine ulRFE showed signs of mild hyperactivity for the duration of the 15-day exposure, and animals exposed to nicotine, melatonin, THC, CBD, Everclear, scotch, and white wine cognates experienced mild hypo-activity. Animals exposed to espresso or 100% ethanol ulRFE remained normal during the 15-day exposure. CONCLUSIONS Mice displayed altered behavior when exposed to the magnetic field produced by the cognates, which, at least in part, were consistent with some effects that would be anticipated for the molecules used to create the cognates. The ulRFE technology offers potential to emulate the effects of bioactive substances across the blood:brain barrier.
High Performance, In-service Correlation OTDR (2013)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text L. Sandstrom, D. Joffe, G. Bekken, J. Brooks, K. Schneider, and R. Goodson, "High Performance, In-service Correlation OTDR," in Optical Fiber Communication Conference/National Fiber Optic Engineers Conference 2013, OSA Technical Digest (online) (Optica Publishing Group, 2013), paper OW3G.3. Export Citation BibTex Endnote (RIS) HTML Plain Text Get Video Citation alert Save article
Current Sharing in Multiphase Converters Using Temperature Equalization (2006)

Multi-phase converters offer excellent performance advantages in transient response and efficiency. A case in point is the core converter for personal computers. These advantages can only be fully achieved if we guarantee load current sharing between all the phases of the design. This paper offers a novel approach in achieving this goal while at the same time guaranteeing another very important parameter - namely, equalization of case temperature of the switching MOSFETs. The approach taken here is to measure the temperature of the switching devices in each phase and regulate the switching current per phase so as to maintain the same temperature in all phases. Since both the conduction and dynamic losses are directly proportional to the switching current, changing the phase current amplitude higher or lower will increase or decrease the phase temperature allowing the control loop to equalize the phase temperature and current among all phases
Optical properties of low vision telescopes. (1987)

Angular magnification, resolving power, astigmatism, field of view, eye relief, and light transmittance of 157 low power telescopes comprising 25 models from seven manufacturers were measured. Roof-prism Keplerian telescopes provided about one-half the resolution, 30% lower transmittance, and more objectionable image flare than Galilean designs. The roof-prism was responsible for producing overlapping doubled images that appeared astigmatic-like. The prism further compromised rotational symmetry by deviating the image in a direction along the roof edge. The Keplerian telescopes, however, had about twice the field of view of the Galilean telescopes. Notably, several Keplerian telescope models from different suppliers were found to be optically identical, although they varied 50-100% in price.
Introducing Secure Peergroups in SP2A (2005)

Service-oriented grids are aiming at new applications beyond traditional resource-oriented scientific computing. We argue that Community Support is emerging as the real killer application. Service-oriented systems provide a flexible solution for work groups which belong to university campuses, research labs, enterprises, finance environments. We are building the service-oriented P2P architecture (SP/sup 2/A), which is the result of the positive convergence between grid and peer-to-peer computing. P2P design allows to overcome the limitations of available mechanisms for publishing and discovering grid services, which are essentially based on centralized directories, thus raising robustness, scalability and performance concerns. SP/sup 2/A is constituted by distinct communities of peers organized for specific purposes. In this paper we illustrate the group security policies of SP/sup 2/A, which define the mechanisms for peer authentication, peergroup admission control, authorization and transport security. Prototype implementation details are also exposed.
Absorption and Translocation of MON 0818 Adjuvant in Field Bindweed (<i>Convolvulus arvensis</i>) (1986)

To develop an understanding of how adjuvants might enhance glyphosate [ N -(phosphonomethyl)glycine] activity, absorption and translocation of a polyethoxylated tallow amine amphoteric surfactant (MON 0818) were examined in field bindweed ( Convolvulus arvensis L. # CONAR). Scanning electron microscopy did not reveal any physical disruption of the epicuticular waxes from spray applications of MON 0818, an oxysorbic (20 POE) (polyoxyethylene sorbitan monolaurate) surfactant, or glyphosate. Radioactive MON 0818 absorption was rapid during the first 6 h. Maximum absorption (84%) occurred by 24 h after application. Less than 3% of the applied radioactivity was recovered from the epicuticular wax of treated leaves. Movement of radioactivity away from the treated area was limited predominantly to movement within the treated leaf. Altering light intensity or humidity in which the plants developed before treatment did not influence MON 0818 absorption.
Flux qubit noise spectroscopy using Rabi oscillations under strong driving conditions (2014)

We infer the high-frequency flux noise spectrum in a superconducting flux qubit by studying the decay of Rabi oscillations under strong driving conditions. The large anharmonicity of the qubit and its strong inductive coupling to a microwave line enabled high-amplitude driving without causing significant additional decoherence. Rabi frequencies up to 1.7 GHz were achieved, approaching the qubit's level splitting of 4.8 GHz, a regime where the rotating-wave approximation breaks down as a model for the driven dynamics. The spectral density of flux noise observed in the wide frequency range decreases with increasing frequency up to 300 MHz, where the spectral density is not very far from the extrapolation of the $1/f$ spectrum obtained from the free-induction-decay measurements. We discuss a possible origin of the flux noise due to surface electron spins.
A Quick Startup Technique for High- $Q$ Oscillators Using Precisely Timed Energy Injection (2017)

High-quality (Q) oscillators are notorious for being extremely slow during startup. Their long startup time increases the average power consumption in duty-cycled systems. This paper presents a novel precisely timed energy injection technique to speed up the startup behavior of high-Q oscillators. The proposed solution is also insensitive to the frequency variations of the injection signal over a wide enough range that makes it possible to employ an integrated oscillator to provide the injection signal. A theoretical analysis is carried out to calculate the optimal injection duration. As a proof-of-concept, the proposed technique is incorporated in the design of crystal oscillators and is realized in a TSMC 65-nm CMOS technology. To verify the robustness of our technique across resonator parameters and frequency variations, six crystal resonators from different manufacturers with different packagings and Q factors were tested. The implemented IC includes multiple crystal oscillators at 1.84, 10, and 50 MHz frequencies, with measured startup times of 58, 10, and 2 μs, while consuming 6.7, 45.5, and 195 μW at steady state, respectively. To the authors' best knowledge, this is the fastest, reported startup time in the literature, with >15× improvement over prior art, while requiring the smallest startup energy (~12 nJ).
Polishing of optical media by dielectric barrier discharge inert gas plasma at atmospheric pressure (2013)

In this paper, surface smoothing of optical glasses, glass ceramic and sapphire using a low-power dielectric barrier discharge inert gas plasma at atmospheric pressure is presented. For this low temperature treatment method, no vacuum devices or chemicals are required. It is shown that by such plasma treatment the micro roughness and waviness of the investigated polished surfaces were significantly decreased, resulting in a decrease in surface scattering. Further, plasma polishing of lapped fused silica is introduced. Based on simulation results, a plasma physical process is suggested to be the underlying mechanism for initialising the observed smoothing effect.
Ultrawide-band synthetic aperture radar for detection of unexploded ordnance: modeling and measurements (2000)

Electromagnetic (EM) scattering from subsurface unexploded ordnance (UXO) is investigated both theoretically and experimentally. Three EM models are considered: the multilevel fast multipole algorithm (MLFMA), the method of moments (MoM), and physical optics (PO). The relative accuracy of these models is compared for several scattering scenarios. Moreover, the model results are compared to data measured by an experimental synthetic aperture radar (SAR) system, SAR images have been generated for subsurface UXO targets, in particular 155-mm shells. We compare SAR images from the measured data with theoretical images produced by the MoM and PO simulations, using a standard back-projection imaging technique. In addition to such comparisons with measurement, we consider additional buried-UXO scattering scenarios to better understand the underlying wave phenomenology.
Distinct Region-Specific α-Synuclein Oligomers in A53T Transgenic Mice: Implications for Neurodegeneration (2010)

Aggregation of alpha-synuclein (alpha-syn), a process that generates oligomeric intermediates, is a common pathological feature of several neurodegenerative disorders. Despite the potential importance of the oligomeric alpha-syn intermediates in neuron function, their biochemical properties and pathobiological functions in vivo remain vastly unknown. Here we used two-dimensional analytical separation and an array of biochemical and cell-based assays to characterize alpha-syn oligomers that are present in the nervous system of A53T alpha-syn transgenic mice. The most prominent species identified were 53 A detergent-soluble oligomers, which preceded neurological symptom onset, and were found at equivalent amounts in regions containing alpha-syn inclusions as well as histologically unaffected regions. These oligomers were resistant to SDS, heat, and urea but were sensitive to proteinase-K digestion. Although the oligomers shared similar basic biochemical properties, those obtained from inclusion-bearing regions were prominently reactive to antibodies that recognize oxidized alpha-syn oligomers, significantly accelerated aggregation of alpha-syn in vitro, and caused primary cortical neuron degeneration. In contrast, oligomers obtained from non-inclusion-bearing regions were not toxic and delayed the in vitro formation of alpha-syn fibrils. These data indicate that specific conformations of alpha-syn oligomers are present in distinct brain regions of A53T alpha-syn transgenic mice. The contribution of these oligomers to the development of neuron dysfunction appears to be independent of their absolute quantities and basic biochemical properties but is dictated by the composition and conformation of the intermediates as well as unrecognized brain-region-specific intrinsic factors.
Activated Carbon Applications in the Food and Pharmaceutical Industries (2023)

Activated carbon has proven itself as a superior adsorbent for hundreds of food, beverage, agricultural, and pharmaceutical processing applications. This book provides a comprehensive, scientific survey of activated carbon applications based on existing literature. A valuable resource for all technical personnel involved in the processes discussed.
Mechanistic Studies on the Cytochrome P450-Catalyzed Dehydrogenation of 3-Methylindole (1996)

The mechanism of 3-methyleneindolenine (3MEI) formation from 3-methylindole (3MI) in goat lung microsomes was examined using stable isotope techniques. 3MEI is highly electrophilic, and its production is a principal factor in the systemic pneumotoxicity of 3MI. Noncompetitive intermolecular isotope effects of DV = 3.3 and D(V/K) = 1.1 obtained after deuterium substitution at the 3-methyl position indicated either that hydrogen abstraction from the methyl group was not the initial rate-limiting step or that this step was rate-limiting and was masked by a high forward commitment and low reverse commitment to catalysis. An intramolecular isotope effect of 5.5 demonstrated that hydrogen atom abstraction was probably the initial oxidative and rate-limiting step of 3MI bioactivation or that deprotonation of an aminium cation radical, produced by one-electron oxidation of the indole nitrogen, was rate-limiting. However, a mechanism which requires deprotonation of the aminium cation radical is probably precluded by an unusual requirement for specific base catalysis at a site in the cytochrome P450 enzyme other than the heme iron. The pattern of 18O incorporation into indole-3-carbinol from 18O2 and H(2)18O indicated that approximately 80% of the indole-3-carbinol was formed in goat lung microsomes by hydration of 3MEI. However, the inverse reaction, dehydration of indole-3-carbinol, did not significantly contribute to the formation of 3MEI. These results show that 3MEI was formed in a cytochrome P450-catalyzed dehydrogenation reaction in which the rate-limiting step was presumably hydrogen atom abstraction from the 3-methyl position. The ratio of the amounts of 3MEI to indole-3-carbinol formed (50:1) indicated that dehydrogenation of 3MI is an unusually facile process when compared to the dehydrogenation of other substrates catalyzed by cytochrome P450 enzymes.
Amino acid composition of the milk of some mammalian species changes with stage of lactation (1994)

To determine whether the amino acid composition of milk changes during lactation, we compared the amino acid pattern (concentration of each individual amino acid relative to the total amino acid concentration) of colostrum with that of mature milk in six mammalian species. In the human, horse, pig and cow, the pattern of amino acids changed between colostrum and mature milk: glutamate, proline, methionine, isoleucine and lysine increased; cystine, glycine, serine, threonine and alanine decreased. In these four species, the total amino acid concentration also decreased 75% between colostrum and mature milk. In the baboon (Papio cynocephalus anubis and Papio cynocephalus anubis/Papio cynocephalus cynocephalus) and rhesus monkey (Macaca mulatta), however, there was little change in the pattern of amino acids between colostrum and mature milk, and total amino acid concentration decreased only about 25% between colostrum and mature milk. Mature milk rather than colostrum was the most similar among the three primates in both amino acid pattern and total amino acid concentration. We conclude, in those species in which total amino acid concentrations decline substantially between colostrum and mature milk, amino acid patterns also change. The presence of a change in amino acid pattern and total amino acid concentration during lactation appears to be unrelated to phylogenetic order.