gebhart/patrepeval huggingface dataset:
Transcription Elongation Factor SII (TFIIS) Enables RNA Polymerase II to Elongate through a Block to Transcription in a Human Gene in Vitro (1989)

Elongation and termination by RNA polymerase II are important regulatory steps for eukaryotic gene expression. We have previously studied the transcription of linear DNA templates where specific initiation of transcription by highly purified RNA polymerase II can be achieved in the absence of promoters and promoter-specific factors. Using these templates we have shown that a human histone gene, H3.3, contains sequences (intrinsic terminators) within which purified RNA polymerase II will efficiently terminate transcription (Reines, D., Wells, D., Chamberlin, M.J., and Kane, C. M. (1987) J. Mol. Biol. 196, 299-312). Curiously, these signals were found within an intron, 3'-untranslated, and protein-encoding regions of the gene suggesting that they might act to attenuate transcription of H3.3 in vivo. Here we show that intrinsic terminator sequences from an H3.3 gene intron also block in vitro transcript elongation by RNA polymerase II when the enzyme has initiated transcription from a promoter using highly purified transcription initiation factors. However, under the conditions used for promoter-specific transcription there is little transcript release. Instead the polymerase can pause at these sites for periods exceeding 60 min. We have identified and partially purified an activity from HeLa cells that causes the transcription complex to read through this block to transcription elongation. This readthrough activity fractionates with a previously characterized elongation factor (SII) over three chromatographic columns. A homogeneous preparation of calf thymus SII can also provide this activity in trans. This factor may facilitate passage of the RNA polymerase II transcription complex through such intragenic sites in cellular genes in vivo.
Nerve Growth Factor-mediated Neurite Outgrowth via Regulation of Rab5 (2007)

Nerve growth factor (NGF) induces neurite outgrowth and differentiation in a process that involves NGF binding to its receptor TrkA and endocytosis of the NGF-TrkA complex into signaling endosomes. Here, we find that biogenesis of signaling endosomes requires inactivation of Rab5 to block early endosome fusion. Expression of dominant-negative Rab5 mutants enhanced NGF-mediated neurite outgrowth, whereas a constitutively active Rab5 mutant or Rabex-5 inhibited this process. Consistently, inactivation of Rab5 sustained TrkA activation on the endosomes. Furthermore, NGF treatment rapidly decreased cellular level of active Rab5-GTP, as shown by pull-down assays. This Rab5 down-regulation was mediated by RabGAP5, which was shown to associate with TrkA by coimmunoprecipitation assays. Importantly, RNA interference of RabGAP5 as well as a RabGAP5 truncation mutant containing the TrkA-binding domain blocked NGF-mediated neurite outgrowth, indicating a requirement for RabGAP5 in this process. Thus, NGF signaling down-regulates Rab5 activity via RabGAP5 to facilitate neurite outgrowth and differentiation.
Formation of MnSb Granular Films and Their Magneto-optical Properties. (2000)

MnSb ultra-thin films with nominal thicknesses of 0.35, 0.70, 1.05, and 1.40 nm were grown on sulfur-passivated GaAs (001) substrates by molecular beam epitaxy. Atomic force microscopy analyses showed that MnSb formed nanosized dots on the substrate, and that coalescence of the clusters occurred at nominal thicknesses between 0.70 and 1.05 nm. The intensity of the polar magnetic circular dichroism of MnSb clusters and the saturation magnetization suddenly increased when the nominal thickness reached the critical value of 1.05 nm. The coalescence of the dots can be correlated with the sharp increase in the MCD intensity.
Virus infections of the gastrointestinal tract of poultry (1998)

Several different viruses have been identified as causes of gastrointestinal tract infections in poultry. These include rotaviruses, coronaviruses, enteroviruses, adenoviruses, astroviruses, and reoviruses. In addition, a number of other viruses of unknown importance have been associated with gastrointestinal diseases in poultry based on electron microscopic examination of feces and intestinal contents. Viral infections of the gastrointestinal tract of poultry are known to negatively impact poultry production, and they likely contribute to the development of other, extragastrointestinal diseases. Our current understanding of the viruses that cause gastrointestinal tract infections in poultry is reviewed, with emphasis given to those of greatest importance.
Class-D CMOS Oscillators (2013)

This paper presents class-D CMOS oscillators capable of an excellent phase noise performance from a very low power supply voltage. Starting from the recognition of the time-variant nature of the class-D LC tank, accurate expressions of the oscillation frequency, oscillation amplitude, current consumption, phase noise, and figure-of-merit (FoM) have been derived. Compared with the commonly used class-B/C architectures, the optimal class-D oscillator produces less phase noise for the same power consumption, at the expense of a higher power supply pushing. A prototype of a class-D voltage-controlled oscillator (VCO) targeted for mobile applications, implemented in a standard 65-nm CMOS process, covers a 46% tuning range between 3.0 and 4.8 GHz; drawing 10 mA from 0.4 V, the phase noise at 10-MHz offset from 4.8 GHz is -143.5 dBc/Hz, for an FoM of 191 dBc/Hz with less than 1-dB variation across the tuning range. A version of the same VCO with a resonant tail filter displays a lower 1/f <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> phase-noise corner and improves the FoM by 1 dB.
Contention-free 2D-mesh cluster allocation in hypercubes (1995)

Traditionally, each job in a hypercube multiprocessor is allocated with a subcube so that communication interference among jobs may be avoided. Although the hypercube is a powerful processor topology, the 2D mesh is a more popular application topology. This paper presents a 2D-mesh cluster allocation strategy for hypercubes. The proposed auxiliary free list processor allocation strategy can efficiently allocate 2D-mesh dusters without size constraints, can reduce average job turnaround time compared with that based on subcube allocation strategies, and can guarantee no communication interference among allocated clusters when the underlying hypercube implements deadlock-free E-cube routing. The proposed auxiliary free list strategy can be easily implemented on hypercube multicomputers to increase processor utilization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Pancreatic islet cell therapy for type I diabetes: understanding the effects of glucose stimulation on islets in order to produce better islets for transplantation (2007)

While insulin replacement remains the cornerstone treatment for type I diabetes mellitus (T1DM), the transplantation of pancreatic islets of Langerhans has the potential to become an important alternative. And yet, islet transplant therapy is limited by several factors, including far too few donor pancreases. Attempts to expand mature islets or to produce islets from stem cells are far from clinical application. The production and expansion of the insulin-producing cells within the islet (so called beta cells), or even creating cells that secrete insulin under appropriate physiological control, has proven difficult. The difficulty is explained, in part, because insulin synthesis and release is complex, unique, and not entirely characterized. Understanding beta-cell function at the molecular level will likely facilitate the development of techniques to manufacture beta-cells from stem cells. We will review islet transplantation, as well as the mechanisms underlying insulin transcription, translation and glucose stimulated insulin release.
Matrix Isolation Microsampling Procedures in Quantitative Fourier Transform Infrared Spectrometry (1979)

Techniques for microsampling in infrared spectroscopy by matrix isolation are described. In the matrix isolation of liquid or solid compounds, the sample is vaporized and then diluted with a large excess of a matrix gas; the resulting gaseous mixture is deposited on a cold surface for spectroscopic examination as a solid. Detailed descriptions of the apparatus and procedures employed in the preparation of matrix-isolated samples for qualitative and quantitative analyses by Fourier transform infrared spectrometry are presented. Systems for “microsampling” (detection limits for specific compounds ∼0.5 to 1 μg) and “ultramicrosampling” (detection limits ∼50 to 100 ng) matrix isolation spectroscopy are described. Detection limits and Beer's law behavior for polycyclic aromatic hydrocarbons microsampled by matrix isolation are discussed. The advantages of matrix isolation as a technique for qualitative and quantitative infrared analysis of microsamples are itemized.
Critical Role of Vimentin Phosphorylation at Ser-56 by p21-activated Kinase in Vimentin Cytoskeleton Signaling (2006)

Phosphorylation and spatial reorganization of the vimentin network have been implicated in mediating smooth muscle contraction, cell migration, and mitosis. In this study, stimulation of cultured smooth muscle cells with 5-hydroxytryptamine (5-HT) induced PAK1 phosphorylation at Thr-423 (an indication of p21-activated kinase (PAK) activation). Treatment with PAK led to disassembly of wild-type (but not mutant S56A) vimentin filaments as assessed by an in vitro filament assembly assay. Furthermore, stimulation with 5-HT resulted in the dissociation of Crk-associated substrate (CAS; an adapter protein associated with smooth muscle force development) from cytoskeletal vimentin. Expression of mutant S56A vimentin in cells inhibited the increase in phosphorylation at Ser-56 and in the ratios of soluble to insoluble vimentin (an index of vimentin disassembly) and the dissociation of CAS from cytoskeletal vimentin in response to 5-HT activation compared with cells expressing wild-type vimentin. Because CAS may be involved in PAK activation, PAK phosphorylation was evaluated in cells expressing the S56A mutant. Expression of mutant S56A vimentin depressed PAK phosphorylation at Thr-423 induced by 5-HT. Expression of the S56A mutant also inhibited the spatial reorientation of vimentin filaments in cells in response to 5-HT stimulation. Our results suggest that vimentin phosphorylation at Ser-56 may inversely regulate PAK activation possibly via the increase in the amount of soluble CAS upon agonist stimulation of smooth muscle cells. Additionally, vimentin phosphorylation at this position is critical for vimentin filament spatial rearrangement elicited by agonists.
Characterization of the myosin-binding subunit of smooth muscle myosin phosphatase. (1994)

A myosin phosphatase was purified from chicken gizzard smooth muscle. The holoenzyme is a trimer and consists of 130,000-, 38,000-, and 20,000-Da subunits (in agreement with the results of Alessi et al.: Alessi, D., MacDougall, L. K., Sola, M. M., Ikebe, M., and Cohen, P. (1992) Eur. J. Biochem. 210, 1023-1035). The catalytic subunit, 38,000 Da, is the type 1 delta isoform, and its derived amino acid sequence is identical to the rat isoform. The larger subunit bound to myosin and also interacted with the catalytic subunit. cDNA clones encoding the large subunit were isolated from chicken gizzard cDNA libraries. Overlapping clones indicated the presence of two isoforms, and open reading frames of 2889 and 3012 bases were obtained. These encoded proteins of 963 and 1004 amino acids, with masses of 106,700 and 111,600 Da, respectively. The insert in the larger isoform is in the center of the molecule, at residues 512-552. The N-terminal third of the molecule is composed of eight repeat sequences, similar to the cdc10/SWI6 or ankyrin repeat. Myosin binding and binding to the catalytic subunit are properties of a 58,000-Da fragment that represents the N-terminal part of the molecule.
Decoupling of High Performance Semiconductors Using Embedded Capacitor Technology (2006)

The integration of embedded DuPont ceramic capacitors and HiK polyimide based planar capacitor materials in IC packages has been investigated by a joint program between DuPont and Georgia Institute of Technology packaging research center (PRC). Test vehicles with different types of structures were designed, fabricated and tested for individual device characterization. The test vehicles included embedded ceramic-fired-on-foil capacitors with microvia interconnects and two sequential industry standard build-up layers on each side of a BT core. Feature sizes were 12 micron lines and spaces and 50 micron diameter microvias. Other test vehicles used a core layer without build-up layers, planar capacitor layers and arrays of discrete capacitors with different size, capacitance, and interconnection designs. Each capacitor variation was electrically characterized. The electrical performance data from the test vehicles was used to perform simulations to determine the designs offering the most effective power delivery and noise decoupling for a package having 2007 ITRS die and substrate features. The embedded ceramic capacitors show a significant improvement in power system noise decoupling and charge supply to the IC in the mid-frequency range due to the low inductance design.
Statistical determinants of dendritic morphology in hippocampal pyramidal neurons: A hidden Markov model (2004)

Dendritic structure is traditionally characterized by distributions and interrelations of morphometric parameters, such as Sholl-like plots of the number of branches versus dendritic path distance. However, how much of a given morphology is effectively captured by any statistical description is generally unknown. In this work, we assemble a small number of standard geometrical parameters measured from experimental data in a simple stochastic algorithm to describe the dendrograms of hippocampal pyramidal cells. The model, consistent with the hidden Markov framework, is feedforward, local, and causal. It relies on two "hidden" local variables: the expected number of terminal tips in a given subtree, and the current path distance from the soma. The algorithm generates dendrograms that statistically reproduce all morphological essentials of dendrites observed in real neurons, including the distributions of branching and termination points, branch lengths, membrane area, topological asymmetry, and (assuming passive membrane parameters within physiological range) electrotonic characteristics. Thus, this algorithm and the small number of its morphometric parameters constitute a remarkably complete description of the dendrograms of hippocampal pyramidal cells. Specifically, it is found that CA3 and CA1 basal dendrites and CA3 apical dendrites can each be described as homogeneous morphological classes. In contrast, the accurate generation of CA1 apical dendrites necessitates the separate sampling of two types of branches, main and oblique, suggesting their derivations from different developmental mechanisms (terminal and interstitial growth, respectively). We further offer a plausible biophysical interpretation of the model hidden variables, relating them to microtubules and other intracellular resources.
An approach to dereverberation using multi-microphone sub-band envelope estimation (1991)

An approach to recovering acoustically reverberated signals using multi-microphone subband envelope estimation (M-SBEE) is proposed. The invertibility of a subband signal depends on the zero distribution of the transfer function in the z-plane in that subband. In a multi-microphone system, the transfer functions between the sound source and the microphones have different zero distributions. This method takes advantage of the differences of the zero distributions by choosing the best invertible microphone in each subband, and reconstructing the full band signal using the best microphone in each subband. The recovered speech signals using seven microphones with 256 subbands are perfect when the reverberation time (RT) is less than 0.43 sec, and is satisfactory for even RT=1.07 sec.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Monotonicity of entropy computations in belief functions (1997)

This article addresses the issue of quantitative information measurement within the Dempster-Shafer belief function formalism. Entropy computation in Dempster-Shafer depends on the way uncertainty measures are conceptualized. However, freed of most probability constraints, uncertainty measures in Dempster-Shafer theory can lead to further advances in optimization in information theory, which in turn may have a wide impact on decision and control. This article examines one form of current development regarding the entropy measure induced from the measure of dissonance. For a significant period, the measure of dissonance has been taken as a measure of entropy. We present in this article the entropy measure as a monotonically decreasing function, symmetrical to the measure of dissonance.
Phase I and pharmacokinetics study of crotoxin (cytotoxic PLA(2), NSC-624244) in patients with advanced cancer. (2002)

A Phase I clinical trial was performed on patients with solid tumors refractory to conventional therapy. Crotoxin was administered i.m. for 30 consecutive days at doses ranging from 0.03 to 0.22 mg/m(2). Patients entered the study after providing a written informed consent. Although 26 patients were entered only 23 were evaluated. Reversible, nonlimiting neuromuscular toxicity evidenced as diplopia because of pareses of the external ocular muscles was present in 13 patients. It started at doses of 0.18 mg/m(2) and lasted from 2 to 6 h. These episodes did not require dose adjustment and disappeared in 1-3 weeks of treatment. Three patients experienced palpebral ptosis, nystagmus (grade 2), and anxiety (grade 2-3) at the dose-limiting toxicity of 0.22 mg/m(2). Also at dose-limiting toxicity, 1 patient showed nystagmus (grade 2) and anxiety (grade 3) without evidence of palpebral ptosis. Transient increases (grades 1-3) in the levels of creatinine kinase, aspartate aminotransferase, and alanine transaminase attributed to crotoxin myotoxicity were observed but returned to normal by the last week of treatment. At 0.21 mg/m(2) there was a case of grade-3 anaphylactic reaction on day 31, which required treatment. Hypersensitivity was regarded as an adverse drug-related reaction, and the patient was removed from the protocol. Two patients at different doses (0.12 mg/m(2) and 0.22 mg/m(2)) had sialorrhea. Four patients had asymptomatic transient increase in blood pressure (up to 20 mm Hg) 12 h after the first injection, which lasted 24 h. No treatment was required and toxicity did not reappear. Six patients experienced slight eosinophilia during the first 2 weeks. The maximum tolerated dose was set at 0.21 mg/m(2). Objective measurable partial responses (>50% reduction of tumor mass) were noted in 2 patients treated at 0.21 mg/m(2) and 1 at 0.12 mg/m(2). One patient (at 0.21 mg/m(2)) presented a complete response on day 110. Crotoxin pharmacokinetics showed rapid absorption from the injection site to blood (t(1/2 A) = 5.2 +/- 0.6 min). Plasma concentration reached a peak (C(max) = 0.79 +/- 0.1 ng/ml) at tau(max) = 19 +/- 3 min. The half-life of the distribution (alpha) phase is 22 +/- 2 min. Starting at 1.5 h after injection, the decrease in plasma concentration becomes slower, reaching 14 +/- 3 pg/ml 24 h after injection. The profile is dominated by the elimination (beta) phase with a half-life of 5.2 +/- 0.6 h. Consequently, 24 h after the injection ( approximately 5 half-life) 97% of the product was eliminated. The area under plasma concentration versus time curve was 0.19 +/- 0.05 microg/min/ml. Assuming availability (F) approximately 1, the clearance is C(L) = 26.3 +/- 7 ml/min, and the apparent volume of distribution is V(d) = 12 +/- 3 liter/kg. The recommended dose for a Phase II study is 0.18 mg/m(2).
Prediction-based flow control for network-on-chip traffic (2006)

Networks-on-Chip (NoC) architectures provide a scalable solution to on-chip communication problem but the bandwidth offered by NoCs can be utilized efficiently only in presence of effective flow control algorithms. Unfortunately, the flow control algorithms pub-lished to date for macronetworks, either rely on local information, or suffer from large communication overhead and unpredictable delays. Hence, using them in the NoC context is problematic at best. For this reason, we propose a predictive closed-loop flow con-trol mechanism and make the following contributions: First, we develop traffic source and router models specifically targeted to NoCs. Then, we utilize these models to predict the cases of possible congestion in the network. Based on this information, the proposed scheme controls the packet injection rate at traffic sources in order to regulate the total number of packets in the network. Evaluations involving real and synthetic traffic patterns show that the proposed controller delivers a superior performance compared to the traditional switch-to-switch flow control algorithms.
Context-aware and personalized event filtering for low-overhead continuous remote health monitoring (2008)

A particularly compelling vision of long-term remote health monitoring advocates the use of a personal pervasive device (such as a cellphone) as an intermediate relay, which transports data streams from multiple body-worn sensors to a backend analytics infrastructure. Unfortunately, a pure relay-based functionality on the cellphone is inadequate in the longer term, as increasingly sophisticated medical sensors impose unnacceptably high uplink traffic and energy consumption costs on the mobile device. To address this challenge, we are building an event-processing middleware, called HARMONI, which enables the pervasive device to perform context-aware processing and event filtering on the sensor data streams and locally extract higher-level features of interest, thereby reducing the volume of transmitted data. This paper presents the design and architectural components of HARMONI, with special emphasis on its implementation of context-aware event processing. This paper then demonstrates that the mobile device can extract localized context from the incoming sensor stream with sufficient accuracy to achieve satisfactory context-aware filtering. Our results also establish the need for personalizing such context extraction, as they show that similar sensor data patterns obtained from different individuals can imply significantly different activity contexts.
Zinc absorption in experimental osmotic diarrhea: effect of long-chain fatty acids. (1993)

The effect of free fatty acids on zinc absorption was studied in a rat model of chronic osmotic diarrhea induced with magnesium citrate and phenolphthalein. In vivo rates of zinc removal from the lumen and analysis of tissue for zinc uptake and metallothionein alterations were monitored. One mmol/L stearate enhanced zinc absorption in rats with or without diarrhea, from 207 +/- 22 and 353 +/- 13 pmol/min x cm to 676 +/- 34 and 610 +/- 26 pmol/min x cm, respectively. Palmitate was only effective in normal rats. Zinc absorption inversely correlated with mucosal zinc content in the perfused intestinal segments, in both type of rats. Hepatic metallothionein was enhanced by zinc and even more by oleate plus zinc in both groups; kidney metallothionein in animals with diarrhea was normalized by either oleate or zinc. The data support previous reports on the effect of long-chain fatty acids on the enhancement of zinc absorption: saturation and a longer chain appear to be positive factors. A membrane modification role of long-chain fatty acids could have nutritional implications in the formulation of special diets.