gebhart/patrepeval huggingface dataset:
Assessment of corneal wound repair<i>in vitro</i> (1989)

The time course for the closure of linear wounds produced in cultured cell monolayers following either mechanical debridement or excimer laser photoablation were compared. Wounds were produced in the central zone of a confluent layer of bovine corneal epithelial cells, keratocytes, or endothelial cells, and the residual area of the wound measured at regular intervals. Differences in the rate of wound closure between cell types were demonstrated. For epithelial cells the rate of resurfacing after mechanical or excimer laser damage was similar; for keratocytes there was a lag period before cell slide began after laser injury, but the subsequent rate of resurfacing was then similar to mechanical wounds; only for endothelial layers was a significantly reduced rate of closure observed after photoablation as compared to mechanical wounding. In this model of wound healing it appears that it is the mechanism of removal of the extracellular matrix formed by endothelial cells that produces the major difference in the rate of wound closure between mechanical injury or photoablation.
Junctions and Networks of SnO Nanoribbons (2002)

Junctions and networks of SnO nanoribbons could be very useful in the fabrication of semiconducting nanosensors and optoelectronic devices. How can these structures be obtained and what are their properties are two questions that are answered here. The role that the Sn particles at the end of each ribbon have in the formation of the networks is also discussed. The Figure shows a double T-junction, which is part of a 2D network of SnO nanoribbons.
Resistance to apoptosis in CTLL-2 cells overexpressing B-Myb is associated with B-Myb-dependent bcl-2 induction. (1999)

Transcriptional regulators of the Myb family play important roles in cell proliferation, differentiation, and survival. To investigate the role of Myb proteins in the regulation of apoptosis, we studied the apoptotic response of interleukin 2-dependent CTLL-2 cells stably transfected with B-Myb. B-Myb-overexpressing cells showed a diminished cytokine dependence and were resistant to apoptosis induced by doxorubicin, ceramide, and dexamethasone. Overexpression of B-Myb was associated with enhanced expression of bcl-2, which was dependent, at least in part, on increased transcription. In transient transfection assays in T-lymphoblastic cells, B-Myb was able to stimulate the promoter activity of the bcl-2 5' flanking region linked to the chloramphenicol acetyltransferase reporter gene. A segment of the bcl-2 promoter (nucleotides +34 to +58 relative to the transcription initiation site) contained a putative Myb-binding site and was shown to specifically interact with B-Myb and to confer B-Myb responsiveness to a bcl-2/chloramphenicol acetyltransferase reporter construct. These results indicate that B-Myb promotes T cells survival by enhancing the expression of bcl-2 and identify bcl-2 as a B-Myb target gene regulated in a DNA binding-dependent manner.
An Isophote-Oriented Image Interpolation Method (2008)

This paper presents an isophote-oriented image interpolation method that attempts to produce smooth reconstructions of the image¿s level curves while still maintaining image fidelity. The proposed method employs an interpolation kernel that is obtained by looking for the explicit solution of a nonlinear PDE (partial differential equation). The PDE preserve the local continuation of isophotes (curves of constant intensity). By doing so, the curvature of the interpolated isophotes is reduced, and, thus, zigzagging artifacts are largely suppressed. Moreover, the interpolation techniques can preserve edge sharpness. In addition, the proposed methods can be used irrespective of the magnification factor (MF) and easily implemented due to their simple structure. Experiments show that images interpolated using the proposed method are both visually and quantitatively improved.
How good is automated protein docking? (2013)

The protein docking server ClusPro has been participating in critical assessment of prediction of interactions (CAPRI) since its introduction in 2004. This article evaluates the performance of ClusPro 2.0 for targets 46-58 in Rounds 22-27 of CAPRI. The analysis leads to a number of important observations. First, ClusPro reliably yields acceptable or medium accuracy models for targets of moderate difficulty that have also been successfully predicted by other groups, and fails only for targets that have few acceptable models submitted. Second, the quality of automated docking by ClusPro is very close to that of the best human predictor groups, including our own submissions. This is very important, because servers have to submit results within 48 h and the predictions should be reproducible, whereas human predictors have several weeks and can use any type of information. Third, while we refined the ClusPro results for manual submission by running computationally costly Monte Carlo minimization simulations, we observed significant improvement in accuracy only for two of the six complexes correctly predicted by ClusPro. Fourth, new developments, not seen in previous rounds of CAPRI, are that the top ranked model provided by ClusPro was acceptable or better quality for all these six targets, and that the top ranked model was also the highest quality for five of the six, confirming that ranking models based on cluster size can reliably identify the best near-native conformations.
Interaction of Water with N,N′−1,2-Ethanediyl-bis(6-hydroxy-hexanamide) Crystals: A Simulation Study (2008)

Recently it has been shown, using a variety of experimental techniques, that water can be hosted in N,N'-1,2-ethanediyl-bis(6-hydroxy-hexanamide) crystals. It forms stable interactions with the hydroxyl groups at the ends of the molecule, as well as with the amide groups. However, with experimental techniques one can not observe the exact hydrogen bonding geometries of the physically bound water molecules. Here a series of molecular dynamics simulations is presented that provide an atomistically detailed picture of the interactions of water with different parts of the crystals.
Self-Controllable Secure Location Sharing for Trajectory-Based Message Delivery on Cloud-Assisted VANETs (2018)

In vehicular ad hoc networks, trajectory-based message delivery is a message forwarding strategy that utilizes the vehicle’s preferred driving routes information to deliver messages to the moving vehicles with the help of roadside units. For the purpose of supporting trajectory-based message delivery to a moving vehicle, the driving locations of the vehicle need to be shared with message senders. However, from a security perspective, vehicle users do not want their driving locations to be exposed to others except their desired senders for location privacy preservation. Therefore, in this paper, we propose a secure location-sharing system to allow a vehicle user (or driver) to share his/her driving trajectory information with roadside units authorized by the user. To design the proposed system, we put a central service manager which maintains vehicle trajectory data and acts as a broker between vehicles and roadside units to share the trajectory data on the cloud. Nevertheless, we make the trajectory data be hidden from not only unauthorized entities but also the service manager by taking advantage of a proxy re-encryption scheme. Hence, a vehicle can control that only the roadside units designated by the vehicle can access the trajectory data of the vehicle.
An amino acid substitution in the human intestinal fatty acid binding protein is associated with increased fatty acid binding, increased fat oxidation, and insulin resistance. (1995)

The intestinal fatty acid binding protein locus (FABP2) was investigated as a possible genetic factor in determining insulin action in the Pima Indian population. A polymorphism at codon 54 of FABP2 was identified that results in an alanine-encoding allele (frequency 0.71) and a threonine-encoding allele (frequency 0.29). Pimas who were homozygous or heterozygous for the threonine-encoding allele were found to have a higher mean fasting plasma insulin concentration, a lower mean insulin-stimulated glucose uptake rate, a higher mean insulin response to oral glucose and a mixed meal, and a higher mean fat oxidation rate compared with Pimas who were homozygous for the alanine-encoding allele. Since the FABP2 threonine-encoding allele was found to be associated with insulin resistance and increased fat oxidation in vivo, we further analyzed the FABP2 gene products for potential functional differences. Titration microcalorimetry studies with purified recombinant protein showed that the threonine-containing protein had a twofold greater affinity for long-chain fatty acids than the alanine-containing protein. We conclude that the threonine-containing protein may increase absorption and/or processing of dietary fatty acids by the intestine and thereby increase fat oxidation, which has been shown to reduce insulin action.
Erratum to: Flavobacterium aquaticum sp. nov., a member of the Bacteroidetes isolated from a freshwater reservoir (2013)

because another new bacterial species Flavobacterium aquaticum has been accepted or publication in IJSEM.
<title>Large flat panel profiler</title> (1996)

An important parameter in the production of flat panel displays is the waviness, or micro-corrugation, of the substrate surface. It describes surface deviations in the mid spatial frequency range between roughness and global shape. Typically, the waviness has to be determined to an accuracy in the 5 nm-range. A technique is presented to measure the waviness optically in a non-contact fashion along a profile 14' long. Thus large panel substrates can be measured. Special issues to consider are: (1) suppression of the light reflected from the back surface of the panel substrate, (2) large required dynamic range due to the overall shape of the panel of more than 100 micrometers , (3) the flexibility of the panel substrates requiring well designed fixturing to avoid bending and pick-up of vibrations. The described technique is based on an extension of a phase- shifting white-light Mach-Zehnder interferometer which has been used successfully in the characterization of thin glass disk substrates.
Glutamate transport and metabolism in astrocytes (1997)

Glutamate uptake and metabolism was studied in cerebral cortical astrocytes. The expression of the astrocytic glutamate transporter GLAST was found to be stimulated by extracellular glutamate through activation of kainate receptors on the astrocytes. Energy metabolism and ammonia homeostasis are two important aspects of glutamate handling in astrocytes. It is well known that glutamate transport into astrocytes and glutamine formation are energy consuming processes. Furthermore, ammonia is required for glutamine production. On the other hand, glutamate metabolism through the tricarboxylic acid cycle is an energy and ammonia producing pathway. In the present study it was shown that at an extracellular glutamate concentration of 0.5 mM, high energy phosphates were reduced, and more than 50% of the glutamate carbon skeleton entered the tricarboxylic acid cycle to yield products like lactate, aspartate, and additionally glutamate and glutamine derived from tricarboxylic acid cycle intermediates. Entry into the cycle was not affected by the transaminase inhibitor aminooxyacetic acid, indicating that deamination is the major route for 2-oxoglutarate formation from glutamate. Synthesis of glutamate from 2-oxoglutarate, however, proceeded via transamination. In an earlier study it was shown that at glutamate concentrations at and below 0.2 mM, glutamine appears to be the major product and entry of glutamate into the tricarboxylic acid cycle is decreased 70% by aminooxyacetic acid. In an attempt to unify the above mentioned results, it is suggested that availability of ammonia and energy demands are major factors determining the metabolic fate of glutamate in astrocytes.
California graphic design (1997)

California Graphic Design takes an in-depth look at the distinctive, innovative visual style that is so uniquely Californian. Featuring the work of California's newest and best designers, this title showcases California's style, taste, and enduring sophistication. Design portfolios from 27 top design firms are showcased in this electrifying work. Some are recognized giants, some are just making their reputations, all are first-rate. Each provides a statement of purpose and in eight full-color exhibit their most current design solutions. This title is certain to have wide-ranging appeal!
Spray cooling for the 3-D cube computer (2002)

The results of an experimental investigation into high performance thermal management for an advanced 3-D computer are presented. Chips are mounted on synthetic diamond substrates. The substrates are then stacked and integrated with vertical vias. Two faces of the resulting "cube" computer are reserved for clamping the structure together, two are reserved for power insertion and signal I/O, and the remaining two faces are spray cooled. The heat generated by the chips is conducted laterally out to the cube faces in the high thermal conductivity diamond substrates. The edges of the substrates protrude through a seal plate into a compact spray chamber. Miniature atomizers are used to spray a dielectric coolant onto the substrate edges where the coolant vaporizes to carry away the waste heat. The vapor is condensed in an ambient heat exchanger and the liquid is recycled in a closed-loop system. Experimental results are presented for two different spray plate configurations using a stack of copper heater plates to simulate one half of the computer. Finite element analysis is used to aid in interpretation of the results and predict the junction temperatures that would result from a given spray plate configuration, computer geometry, and chip power loading. The results indicate that very high volume density heat removal is possible (15-20 kW from a four inch cube). Thus, the 3-D computer concept may be suitable for very high performance computing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A critical reexamination of some assumptions and implications of cable theory in neurobiology (1998)

Linear cable theory lies at the core of our understanding of how an individual neuron works. Cable theory usually assumes that neurons do not interact significantly except at specific, anatomically specialized locations (synapses and gap junctions). An analysis of the extracellular electrical fields shows that spikes in one neuron could cause a depolarization of several mV in a dendrite or axon passing by its initial segment. This is somewhat larger than typical chemical synapses; such ephaptic interactions could possibly play a role in controlling action potential failure at branch points.

Applying conclusions of linear cable theory to nonlinear spiking neurons has led to incorrect ideas about neural function. For example, in linear cable theory changing the membrane conductance can be used to scale the amplitude of EPSPs. Shunting inhibition has therefore been repeatedly proposed as a mechanism for division or normalization. This mechanism does not work if the neuron is spiking, i.e., when the output is firing rate rather than EPSP amplitude. When a neuron spikes, its time-averaged voltage does not increase much even if the firing rate goes up; therefore current through a shunt resistance is independent of firing rate, and shunting inhibition acts subtractively rather than divisively.

Cable theory also predicts that EPSPs are low-pass filtered by the membrane resistance and capacitance, and investigators have therefore assumed that the membrane time constant determines how fast a neuron can respond. Again, because of the spiking mechanism, the membrane potential never reaches steady state, so the time constant is not obviously relevant. The dynamics of firing rates may be better described by currents than voltages.

Applying this principle to the dynamics of simple feedback networks shows that a key factor in the response time of a network is the adaptation current. Without adaptation, the network time constant can belong because it is the gain of the network multiplied by the synaptic time constants. Adaptation can cancel out the long tails of synaptic current, significantly speeding up response times. Recurrent inhibition has a similar effect.

Another key factor determining input current is synaptic depression and facilitation. Recurrent networks are especially sensitive to synaptic depression because of the feedback; within a very short period of time the network behaves like a feedforward network because the recurrent synapses have been depressed away. However, facilitation and depression can act together to provide a log-exponential transform, allowing subtractive inhibition at one stage to have a divisive effect at another.
Quantification of Implant Micromotion, Strain Shielding, and Bone Resorption With Porous-Coated Anatomic Medullary Locking Femoral Prostheses (1992)

Fourteen femora containing porous-coated anatomic medullary locking (AML) femoral prostheses were retrieved from 12 patients at autopsy. Clinical roentgenograms in 13 femora showed bone remodeling changes, indicating that the implants were fixed by osseointegration. Under simulated physiologic loading, micromotion between the implant and the bone was measured using electrical displacement transducers connected to the implant and to the adjacent cortex. The micromotion between the implants at the areas of porous coating and the adjacent cortex in the one case of failed bone ingrowth measured 150 microns. Maximum relative motion between the cortex and the implant in the areas of porous coating for the 13 cases showing signs of bone ingrowth was 40 microns, and this was completely elastic relative displacement. With all implants, the micromotion between the cortex and the stem was always greatest over the uncoated portion of the stem. Four of the implants were proximally porous coated. With these, the micromotion was greater over the uncoated areas than with more extensively coated stems and was always greatest at the uncoated tip of the prosthesis. The amount of micromotion was directly related to the extent of porous coating on the implant. Maximum tip motion for the proximally coated implants was 210 micra, whereas for the fully porous-coated implants, it was 40 microns. In nine of the autopsies, the contralateral normal femur was obtained in addition to the femur containing the AML (the in vivo remodeled femur). These were used for comparative studies of strain shielding and femoral remodeling. Cortical strains were measured in the in vivo remodeled femora and were compared with measurements made in the contralateral normal femora before and following implantation of a stem identical to that present on the clinically treated side. The data showed major strain reductions in all the postmortem implanted normal femora. Comparison of the strain data from the postmortem implanted normal femora with those from the in vivo remodeled femora clearly indicated that extensive bone remodeling did not result in restoration of cortical strain levels anywhere near normal. Strain shielding continued to exist in all of the remodeled specimens, even up to 7.5 years after surgery. This strain shielding was associated with bone remodeling changes that resulted in regional reductions in bone mineral content that ranged from 7% to 78%. These observations are unique, important, and valuable in defining the in vivo function and clinical behavior of this type of porous-coated femoral component.
RNA interference mortality points to noncircadian functions for the <i>clock</i> gene in the desert locust <i>Schistocerca gregaria</i> (2012)

One of the core genes in the circadian regulation network is clock (clk). By forming a heterodimer with CYCLE (CYC) that binds on an E-box in the promoter region, it induces the transcription of other elements in the circadian transcriptional feedback loops and different clock output genes. In contrast to other insects, a clk double-stranded RNA (dsRNA) treatment is lethal in adults and fifth instar nymphs of the desert locust, Schistocerca gregaria, in a dose-dependent manner. Clk knock down fifth instar nymphs are able to undergo their imaginal moult but, depending on the amount of dsRNA, it takes them longer than the controls to reach adulthood. As adults, clk knock down animals do not develop their fat body and ovaries like the control animals. Therefore, we tested the expression of different genes involved in energy metabolism and reproduction to see the effect of the clk RNA interference knock down. Surprisingly, the expression of the vitellogenin gene was up-regulated in the clk knock down females who did not appear to invest their energy in egg development. Taken together, our results point out that the clk gene in the desert locust has an additional function in development besides its established role in maintaining the circadian rhythms in the brain.
Opposing Effects of Human Immunodeficiency Virus Type 1 Matrix Mutations Support a Myristyl Switch Model of Gag Membrane Targeting (1999)

Targeting of the human immunodeficiency virus type 1 (HIV-1) Gag precursor Pr55(gag) to the plasma membrane, the site of virus assembly, is primarily mediated by the N-terminal matrix (MA) domain. N-myristylation of MA is essential for the stable association of Pr55(gag) with membranes and for virus assembly. We now show that single amino acid substitutions near the N terminus of MA can dramatically impair assembly without compromising myristylation. Subcellular fractionation demonstrated that Gag membrane binding was compromised to a similar extent as in the absence of the myristyl acceptor site, indicating that the myristyl group was not available for membrane insertion. Remarkably, the effects of the N-terminal modifications could be completely suppressed by second-site mutations in the globular core of MA. The compensatory mutations enhanced Gag membrane binding and increased viral particle yields above wild-type levels, consistent with an increase in the exposure of the myristyl group. Our results support a model in which the compact globular core of MA sequesters the myristyl group to prevent aberrant binding to intracellular membranes, while the N terminus is critical to allow the controlled exposure of the myristyl group for insertion into the plasma membrane.
Cure properties of self‐extinguishing epoxy resin systems with microencapsulated latent catalysts for halogen‐free semiconductor packaging materials (2009)

Abstract The cure properties of self‐extinguishing epoxy resin systems with different microencapsulated latent catalysts were investigated, which are composed of YX4000H and NC3000H as a biphenyl epoxy resin, MEH‐7800SS as a hardener, and triphenylphosphine (TPP) microencapsulated with various polymers as a latent catalyst. The cure kinetics of these systems were analyzed by differential scanning calorimetry using an isothermal approach, and the kinetic parameters of all systems were reported in generalized kinetic equations with diffusion effects. Both the epoxy resin systems with microencapsulated latent catalysts showed lower cure conversion rate and higher critical cure reaction conversion than those with TPP. These different cure conversion rates could be explained by the decrease of crystallinity of the biphenyl epoxy resin and the activation energy of these epoxy resin systems. The cure conversion rates of the epoxy resin systems with the microencapsulated latent catalyst would be dependent on the activation energy of these systems. The storage stability tests for these systems were performed, and a good shelf‐life was observed in both the epoxy resin systems with EPCAT‐PAM, a core–shell‐type latent catalyst. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009