gebhart/patrepeval huggingface dataset:
Novel insights into pancreatic β-cell glucolipotoxicity from real-time functional analysis of mitochondrial energy metabolism in INS-1E insulinoma cells (2013)

High circulating glucose and non-esterified (free) fatty acid levels can cause pancreatic β-cell failure. The molecular mechanisms of this β-cell glucolipotoxicity are yet to be established conclusively. In the present paper we report on the involvement of mitochondrial dysfunction in fatty-acid-induced β-cell failure. We have used state-of-the-art extracellular flux technology to functionally probe mitochondrial energy metabolism in intact INS-1E insulinoma cells in real-time. We show that 24-h palmitate exposure at high glucose attenuates the glucose-sensitivity of mitochondrial respiration and lowers coupling efficiency of glucose-stimulated oxidative phosphorylation. These mitochondrial defects coincide with an increased level of ROS (reactive oxygen species), impaired GSIS (glucose-stimulated insulin secretion) and decreased cell viability. Palmitate lowers absolute glucose-stimulated respiration coupled to ATP synthesis, but does not affect mitochondrial proton leak. Palmitate is not toxic when administered at low glucose unless fatty acid β-oxidation is inhibited. Palmitoleate, on the other hand, does not affect mitochondrial respiration, ROS levels, GSIS or cell viability. Although palmitoleate protects against the palmitate-induced ROS increase and cell viability loss, it does not protect against respiratory and insulin secretory defects. We conclude that mitochondrial dysfunction contributes to fatty-acid-induced GSIS impairment, and that glucolipotoxic cell viability and GSIS phenotypes are mechanistically distinct.
Determination of the zebrafish forebrain: induction and patterning (1998)

We report an analysis of forebrain determination and patterning in the zebrafish Danio rerio. In order to study these events, we isolated zebrafish homologs of two neural markers, odd-paired-like (opl), which encodes a zinc finger protein, and fkh5, which encodes a forkhead domain protein. At mid-gastrula, expression of these genes defines a very early pattern in the presumptive neurectoderm, with opl later expressed in the telencephalon, and fkh5 in the diencephalon and more posterior neurectoderm. Using in vitro explant assays, we show that forebrain induction has occurred even earlier, by the onset of gastrulation (shield stage). Signaling from the early gastrula shield, previously shown to be an organizing center, is sufficient for activation of opl expression in vitro. In order to determine whether the organizer is required for opl regulation, we removed from late blastula stage embryos either the presumptive prechordal plate, marked by goosecoid (gsc) expression, or the entire organizer, marked by chordin (chd) expression. opl was correctly expressed after removal of the presumptive prechordal plate and consistently, opl was correctly expressed in one-eyed pinhead (oep) mutant embryos, where the prechordal plate fails to form. However, after removal of the entire organizer, no opl expression was observed, indicating that this region is crucial for forebrain induction. We further show that continued organizer function is required for forebrain induction, since beads of BMP4, which promotes ventral fates, also prevented opl expression when implanted during gastrulation. Our data show that forebrain specification begins early during gastrulation, and that a wide area of dorsal mesendoderm is required for its patterning.
Softened Elastic Response and Unzipping in Chemical Vapor Deposition Graphene Membranes (2011)

We use atomic force microscopy to image grain boundaries and ripples in graphene membranes obtained by chemical vapor deposition. Nanoindentation measurements reveal that out-of-plane ripples effectively soften graphene's in-plane stiffness. Furthermore, grain boundaries significantly decrease the breaking strength of these membranes. Molecular dynamics simulations reveal that grain boundaries are especially weakening when subnanometer voids are present in the lattice. Finally, we demonstrate that two graphene membranes brought together form membranes with higher resistance to breaking.
QoS topology control in ad hoc wireless networks (2005)

This work discusses the energy efficient QoS topology control problem in ad hoc wireless networks. Given a set of nodes in a plane, end-to-end traffic demands and delay bounds between node pairs, the problem is to find a network topology that can meet the QoS requirements and the maximum transmitting power of nodes is minimized. We consider two cases of the problem: 1) the traffic demands are not splittable, and 2) the traffic demands are splittable. For the former case, the problem is formulated as an integer linear programming problem. For the latter case, the problem is formulated as a mixed integer programming problem, and an optimal algorithm has been proposed to solve the problem.
[Influence of the thymus hormone on radioleucosis in mice]. (1979)

A partially purified thymic extract has determined the development of leucosis in 10 thymectomized irradiated CC57Bl mice out of 25. The pure hormone isolated from the same extract prevented the development of leucosis in intact irradiated Mice. This seems to indicate the presence of a second active substance in the extract (enhancing the development of the leucosis).
Multi Agent reinforcement learning evolutionary game algorithm for partner selection (2009)

The formation of modern enterprise alliance solid network is changing the partner selection in great project from independent enterprises to combined enterprises. By analyzing the optimization objective of subprojects and the core competence of tender enterprises,a nonlinear integer-programming model of the combined enterprises partner selection was developed. Based on the multi Agent reinforcement learning,coordination mechanisms and evolutionary game algorithm,a multi Agnet reinforcement learning evolutionary game algorithm was designed. A case study was carried out to compare the proposed algorithm with the genetic algorithm and evolutionary game algorithm. The results suggest that the proposed method is effective in both running time and performance for the large-scale partner selection of enterprise alliance.
<title>Round-robin comparison of temperature nonuniformity during RTP due to patterned layers</title> (1991)

Temperature non-uniformity caused by patterned layers during RTP is studied experimentally in six RTP-systems from different vendors. Rapid thermal oxidation and annealing are used to indirectly measure temperature non-uniformity. A good correlation is seen with theoretical predictions. The effect of a real-live pattern with LOCOS isolation is evaluated during the growth of a thin oxide by rapid thermal oxidation. The presence of thickness variations of the grown RTO oxide in the patterned areas and at the edge of the patterned region is discussed. 1.
A Technique for In Situ Monitoring of Crystallization from Solution by Solid-State<sup>13</sup>C CPMAS NMR Spectroscopy (2008)

We report a technique for carrying out in situ solid-state NMR studies of crystallization from solution, allowing the evolution of different solid state structures (polymorphs) produced during the crystallization process to be identified. The technique exploits selectivity in NMR properties (specifically, the efficiency of cross-polarization from (1)H to (13)C) between molecules in the solid and solution states, such that the first solid particles produced during the crystallization process are observed selectively, without detecting any signal from dissolved solute (or solvent) molecules. The application of the technique is demonstrated to reveal new insights concerning an isotope effect on the polymorphic outcome of crystallization of glycine from water. As revealed by this example, the in situ solid-state NMR approach reported here creates significant new opportunities for probing and understanding details of the evolution of solid state structures produced during crystallization from solution.
Extracting and answering why and why not questions about Java program output (2010)

When software developers want to understand the reason for a program's behavior, they must translate their questions about the behavior into a series of questions about code, speculating about the causes in the process. The Whyline is a new kind of debugging tool that avoids such speculation by instead enabling developers to select a question about program output from a set of “why did and why didn't” questions extracted from the program's code and execution. The tool then finds one or more possible explanations for the output in question. These explanations are derived using a static and dynamic slicing, precise call graphs, reachability analyses, and new algorithms for determining potential sources of values. Evaluations of the tool on two debugging tasks showed that developers with the Whyline were three times more successful and twice as fast at debugging, compared to developers with traditional breakpoint debuggers. The tool has the potential to simplify debugging and program understanding in many software development contexts.
Ziconotide: A new option for refractory pain (2006)

Ziconotide has been introduced as a new nonopioid treatment for chronic pain. Structurally, it is a peptide, the synthetic analog of the omega-conotoxin, derived from the marine snail, Conus magus. N-type voltage-sensitive calcium channels play a role in the transmission of nociceptive stimuli and also are involved in the release of neurotransmitters important in pain transmission. Ziconotide's therapeutic benefit derives from its potent and selective blockade of neuronal-type voltage-sensitive calcium channels. Blockade of the channels results in suppression of abnormal ectopic discharges from the injury site or the dorsal root ganglia, possibly resulting in decreased neuroplasticity, and decreased synaptic transmission that leads to the generation of chronic pain syndromes. The advantage of ziconotide is that tolerance does not occur, while disadvantages associated with ziconotide are the need for intrathecal administration and significant neurotoxicites associated with its use. When tested in clinical trials, ziconotide has been shown to have synergistic or additive value to the effect of morphine. Ziconotide, formerly known also as SNX- 111, represents a new class of agents, the N-type calcium channel blockers. These may represent another option for patients with refractory pain and refractory pain syndromes.
Study on electron trapping and interface states of various gate dielectric materials in 4H–SiC metal-oxide-semiconductor capacitors (2000)

The characteristics of electron trapping and interface states for various gate dielectrics formed on the 4H–SiC metal-oxide-semiconductor capacitors have been studied. Thermal gate oxides prepared by dry oxidation (in pure O2) or wet oxidation (in H2:O2=1:2), oxide-nitride-oxide (ONO) stacked films and low-temperature oxide (LTO) films formed by low-pressure chemical vapor deposition were used. Post-oxidation anneal was performed at 1200 °C for 1 h in Ar ambient. It is found that the LTO film has lower interface state density and effective oxide charge density than the other gate dielectrics. Also, the LTO film showed excellent electron trapping characteristics against the electron injection. On the contrary, the electron trapping of ONO stacked film was larger than that of the thermal oxide and LTO film.
Towards Reassigning the Rare AGG Codon in <i>Escherichia coli</i> (2014)

The rare AGG codon in Escherichia coli has been reassigned to code non-canonical amino acids (ncAAs) by using the PylRS-tRNA(Pyl)(CCU) pair. When N(ε) -alloc-lysine was used as a PylRS substrate, almost quantitative occupancy of N(ε) -alloc-lysine at an AGG codon site was achieved in minimal medium. ncAAs can be potentially incorporated at the AGG codon with varying efficiencies, depending on their activities towards corresponding enzymes. As AGG is a sense codon, the approach reported here resolves the typical low ncAA incorporation issue that has been associated with ncAA mutagenesis and therefore allows bulk preparation of proteins with site-selectively incorporated ncAAs for applications such as therapeutic protein production.
Sonic Spray Ionization and Ion Formation Processes. (1999)

Sonic spray ionization technique has been developed as an interface in LC/MS and CE/MS. In this technique, a solution from a capillary is sprayed with a sonic gas flow coaxial to the capillary, and gas-phase ions and charged droplets are formed under atmospheric pressure. The amount of the produced ions depends on the gas velocity and has a maximum at the sonic velocity. The origin of the charged species cannot be ascribed to the traditional models of friction electrification, electrical double layer formed near the capillary surface, or statistical charging. An explanation is proposed based on nonuniformity of positive and negative ion concentrations near the solution surface caused by the surface potential. Based on the explanation, we have modified our technique to regulate the nonuniformity by applying an external electric field to the solution surface. Then, the ion amount is found to be dramatically enhanced and multiply-charged ions are readily formed. The analysis of the droplets produced from a nonvolatile solution also shows that the abundance of the droplets having charge numbers close to the Layleigh limit increases as the external electric field increases. These results suggest that ions are readily formed from solutions having a very wide range of chemical properties and flow rates, since highly-charged droplets are produced from the solutions by the shear stress due to the sonic gas flow.
Microarchitecture aware gate sizing: A framework for circuit-architecture co-optimization (2010)

Modern high performance microprocessors experience substantially lower utilization in many of their structural components. To recover energy efficiency from lower utilization, system architects resort to dynamic voltage frequency scaling (DVFS). In this paper, we demonstrate that dynamic adaptations using DVFS are markedly energy inefficient than techniques that design circuits ground up for lower performance. We propose a novel microarchitecture aware gate sizing and threshold voltage assignment algorithm to mitigate this current limitation. Our technique is the first of its kind that exploits architectural slack in gate sizing, and leverages on-chip redundancy and slack. We evaluate this circuit-architectural co-optimization framework in a superscalar processor by combining standard cell based gate sizing flows with state-of-the-art architectural simulation. Our results show 17-46% improvement in the datapath energy efficiency over traditional circuit designs incorporating DVFS schemes.
Unicast-based multicast communication in wormhole-routed networks (1994)

Multicast communication, in which the same message is delivered from a source node to an arbitrary number of destination nodes, is being increasingly demanded in parallel computing. System supported multicast services can potentially offer improved performance, increased functionality, and simplified programming, and may in turn be used to support various higher-level operations for data movement and global process control. This paper presents efficient algorithms to implement multicast communication in wormhole-routed direct networks, in the absence of hardware multicast support, by exploiting the properties of the switching technology. Minimum-time multicast algorithms are presented for n-dimensional meshes and hypercubes that use deterministic, dimension-ordered routing of unicast messages. Both algorithms can deliver a multicast message to m-1 destinations in [log/sub 2/ m] message passing steps, while avoiding contention among the constituent unicast messages. Performance results of implementations on a 64-node nCUBE-2 hypercube and a 168-node Symult 2010 2-D mesh are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Magnetic domain wall serial-in parallel-out shift register (2006)

We demonstrate a three-terminal magnetic nanowire logic junction that combines logical NOT and signal fan-out operations. The behavior and performance of the three-terminal device are similar to those of previous two-terminal NOT gates. However, the third terminal provides an additional, noninverted output. We have demonstrated the versatility that this brings by integrating a chain of the three-terminal hybrid elements with other nanowire logic elements to create a serial-in parallel-out shift register.
Radioimmunoassays for Ig classes G, A, M, D, and E in spinal fluids: normal values of different age groups. (1975)

Radioimmunoassay procedures of sufficient sensitivity (IgG, 0.5 mug per 100 mul; IgA, 25.0 ng. per 100 mul; IgM, 10.0 ng. per 100 mul; IgD, 0.5 U. per 100 mul; and IgE, 1.0 U. per 100 mul) were developed detect and quantitate all 5 immunoglobulin classes in the cerebrospinal fluid on small aliquots (1 ml.) of unconcentrated cerebrospinal fluid. All 5 immunoglobulin classes were routinely detected in normal individuals for the first time, the levels varying with different age groups for IgG and A but not for the remaining immunoglobulin classes. Race and sex had no effect. Standardization of techniques and establishment of normal values for different age groups sets the stage for determination of immunoglobulin changes related to central nervous system disease.
North American Tree Squirrels (2004)

carnivores in witchcraft: ''To protect themselves, people in several parts of Africa were known to eat parts of lion (as I did myself, and I have never been attacked or bewitched since then)' ' (p.188).Kruuk draws the reader into his story with anecdotes and personalized references.He identifies scientists by their first names, for example, rather than just their last names, adding a personal dimension to the book.The use of anecdotes and stories also takes the book from informative to entertaining.For example, Kruuk writes, ''Years ago in the Ngorongoro Crater in Tanzania, I remember meeting up with Jane Goodall, who was taking a break from her work on chimpanzees. . . .It was difficult not to get overenthusiastic, because there were so many analogies between my hyaenas and Jane's chimps'' (p.21).Kruuk leaves few stones unturned, covering everything from definitions and phylogeny (Chapter 1) to carnivore societies (Chapter 2), diet and hunting behavior (Chapter 3), and conflict with humans.He discusses man-eaters (Chapter 4), predation on livestock and game (Chapter 5), competition and predation between humans and predators (Chapter 6), carnivores as food or furbearers (Chapter 7), pets (Chapter 8), and introduced species (Chapter 9).He addresses the response of other species (including humans) to carnivores (Chapter 10), and concludes with an overview of the cultural role of carnivores in literature, witchcraft, religion, and heraldry (Chapter 11).The last chapter forecasts a likely future for carnivores and carnivore conservation.Kruuk is optimistic, and the final sentence of this paragraph summarizes his views and calls for hope: ''One must hope that these special appeals of carnivores are strong enough to allow for the right decisions to be made on the survival of the animals'' (p.219).The presentation of this book is eye catching, and the text is well written.I noticed only 2 errors: improper spelling of Isle Royale (p.69) and a missing period (end of the 2nd paragraph on p. 178).These are minor issues, however, and this is a great book for anyone interested in carnivores and their role in our world.
An evalution of the nitrous acid – 3-methyl-2-benzothiazolinone hydrazone hydrochloride – ferric chloride assay for chitin in rust fungi and rust-infected tissue (1982)

The growth of the bean rust and cowpea rust fungi was examined in cultivars of French bean and cowpea using light microscopy and the nitrous acid – 3-methyl-2-benzothiazolinone hydrazone hydrochloride – ferric chloride assay for chitin. Comparison of the results indicated that the chitin assay did not detect changes in vegetative growth but only detected substances present in mature and developing urediospores. Examination of urediospores indicated that the reactive component(s) was hexosamine, probably glucosamine, but not chitin. The presence of strongly reactive substances in the urediospores, and the apparent low level of chitin in vegetative mycelium compared with that in the mycelium of the commercial mushroom, suggest that this chitin assay is of little value in estimating rust fungus growth in infected plant tissue.
Cell prestress. II. Contribution of microtubules (2002)

The tensegrity model hypothesizes that cytoskeleton-based microtubules (MTs) carry compression as they balance a portion of cell contractile stress. To test this hypothesis, we used traction force microscopy to measure traction at the interface of adhering human airway smooth muscle cells and a flexible polyacrylamide gel substrate. The prediction is that if MTs balance a portion of contractile stress, then, upon their disruption, the portion of stress balanced by MTs would shift to the substrate, thereby causing an increase in traction. Measurements were done first in maximally activated cells (10 microM histamine) and then again after MTs had been disrupted (1 microM colchicine). We found that after disruption of MTs, traction increased on average by approximately 13%. Because in activated cells colchicine induced neither an increase in intracellular Ca(2+) nor an increase in myosin light chain phosphorylation as shown previously, we concluded that the observed increase in traction was a result of load shift from MTs to the substrate. In addition, energy stored in the flexible substrate was calculated as work done by traction on the deformation of the substrate. This result was then utilized in an energetic analysis. We assumed that cytoskeleton-based MTs are slender elastic rods supported laterally by intermediate filaments and that MTs buckle as the cell contracts. Using the post-buckling equilibrium theory of Euler struts, we found that energy stored during buckling of MTs was quantitatively consistent with the measured increase in substrate energy after disruption of MTs. This is further evidence supporting the idea that MTs are intracellular compression-bearing elements.
Two Cases of Successful Clipping Closure of Iatrogenic Duodenal Perforation Occurred during Endoscopic Procedure (2006)

The risk of complications associated with endoscopic procedures, including bleeding and perforation, tends to increase due to the magnification of the therapeutic endoscopic spectrum. In cases of duodenal perforation, surgical closure is the treatment of choice; however, there have been some cases in which the nonsurgical treatment of an iatrogenic duodenal perforation during an endoscopic procedure was effected via endoscopic clipping closure. Here, we report two cases of successful endoscopic clipping closure of an iatrogenic duodenal perforation occur ring during a duodenoscopy insertion for ERCP and endoscopic mucosal resection for the treatment of duodenal adenoma.
Pressure-driven transport of confined DNA polymers in fluidic channels (2006)

The pressure-driven transport of individual DNA molecules in 175-nm to 3.8-microm high silica channels was studied by fluorescence microscopy. Two distinct transport regimes were observed. The pressure-driven mobility of DNA increased with molecular length in channels higher than a few times the molecular radius of gyration, whereas DNA mobility was practically independent of molecular length in thin channels. In addition, both the Taylor dispersion and the self-diffusion of DNA molecules decreased significantly in confined channels in accordance with scaling relationships. These transport properties, which reflect the statistical nature of DNA polymer coils, may be of interest in the development of "lab-on-a-chip" technologies.