gebhart/patrepeval huggingface dataset:
A Fast, General Storage Replication Protocol for Active-Active Virtual Machine Fault Tolerance (2017)

Cloud computing enables more and more online services deployed in virtual machines (VMs), making fast VM fault tolerance particularly crucial. Unfortunately, despite much effort, achieving fast VM fault tolerance remains an open problem. A traditional way to provide VM fault tolerance is the active-passive approach, which frequently transfers tremendous updated states, including memory and storage, of a primary VM to a suspended secondary VM. The other emerging approach, namely the active-active approach, runs the secondary VM concurrently with the primary. Compared to active-passive, active-active is faster because it only performs the transfer when the externally visible states (e.g., network outputs) of the primary and secondary diverge. However, active-active aggravates the performance issue on I/O intensive workloads. In existing active-active systems, storage replication protocols hold updated storage states from both the primary and secondary on the secondary, incurring excessive I/O contention. For instance, both our evaluation and prior study show that a well-engineered active-active system, COLO, degrades the throughput of I/O intensive services by up to 61.6%. To tackle this open problem, this paper presents GANNET, a fast and general storage replication protocol for active-active VM fault tolerance systems. It greatly alleviates the I/O contention on the secondary's storage by efficiently buffering the updated disk states from both the primary and secondary VM in memory. GANNET carries a lightweight storage checkpoint algorithm to avoid consuming too much memory. GANNET is proved to be as reliable as existing storage replication protocols. We integrated GANNET into two popular active-active systems. Evaluation on six widely used services shows that GANNET incurred 15.9% overhead compared to the native executions and outperformed COLO's storage replication protocol by 1.2X~2.6X. GANNET's source code is available at github.com/hku-systems/gannet.
Protein complexes of intermediate-sized filaments: melting of cytokeratin complexes in urea reveals different polypeptide separation characteristics. (1983)

Subunit complexes of cytokeratin polypeptides from intermediate-sized filaments (IF) of various tissues and cultured cells from rat, cow, and man were solubilized in low-salt buffer containing 4 M urea and exposed to increasing concentrations of urea, followed by urea gradient electrophoresis or two-dimensional gel electrophoresis at different urea concentrations. Correspondingly, cytokeratin polypeptides dissociated in 9.5 or 10 M urea were dialyzed into lower concentrations of urea and allowed to reassociate into specific complexes. It was found that the polypeptide constituents of a given cytokeratin complex dissociate in the form of a rather sharp "melting curve" and that dissociated polypeptides reassociate in the same mode of dependence on urea concentration. The midpoint of melting in urea (Um) is a characteristic property of a given complex of cytokeratin polypeptides. Um values differ markedly between different cytokeratin complexes, ranging from 5.9 to 9.0 M urea. The results also show that cytokeratins do not form complexes with vimentin, another type of IF protein. The data suggest that certain cytokeratin polypeptides are complementary and contain sequences that direct their association into specific complexes forming IF subunits.
Podocytes Contribute to the Formation of Glomerular Crescents (2008)

The cellular composition of crescents in glomerular disease is controversial. The role of podocytes in crescent formation has been especially difficult to study because podocytes typically lose their characteristic terminally differentiated phenotype under disease conditions, making them difficult to identify. We reasoned that the intermediate filament protein nestin, a marker of progenitor cells that has recently been identified in podocytes, may allow the investigation of podocyte involvement in glomerular crescents. In a series of 35 biopsies with crescentic glomerular disease, all showed nestin-positive cells in the crescents, ranging in number from occasional to approximately 50% of crescent cells. Other podocyte markers, such as podocin and WT1, failed to identify cells in crescents, and no contribution by endothelial or myogenic cells was noted. CD68-positive cells were observed in 80% of cases but were never as numerous as the nestin-positive cells. Nestin and CD68 were not coexpressed by the same cells, providing no evidence of trans-differentiation of podocytes into a macrophage phenotype. Keratin-positive cells were found in crescents in 51% of cases, but only as occasional cells. Up to one third of crescent cells were cycling in 48% of biopsies, and double immunostaining identified these cells as a mixture of nestin-positive cells and "null" cells (negative for nestin, CD68, and keratin). In addition to our observations in human disease, we also identified nestin-positive proliferating podocytes in the crescents of 2 mouse models of crescentic glomerulonephritis. We conclude that podocytes play a role in the formation of glomerular crescents.
Supercritical CO2 Brayton Cycle Program Summary and Development Roadmap. (2011)

Abstract not provided.
In vitro evaluation of the biofunctionality of osteoblasts cultured on DegraPol-foam (2000)

The biofunctionality of osteoblasts cultured on DegraPol-foam, a biodegradable, elastic, and highly porous polyesterurethane-foam, was determined here to examine the possible use of this structure as bone repair material. Osteoblasts from rat tibia and from the cell line (MC3T3-E1) exhibited relatively high attachment and low doubling time that result in a confluent cell multilayer on the surface of the foam. They produced high concentrations of collagen type I and osteocalcin, and expressed increasing alkaline phosphatase activity. Exposure to 1,25-dihydroxy vitamin D (Vit. D) increased dose- and time-dependent alkaline phosphatase activity and osteocalcin concentration, and decreased the level of collagen type I and cell density. Maximal effects of Vit. D on alkaline phosphatase activity (2.2 fold), osteocalcin (1.5 fold), collagen type I (50% reduction), and on cell density (35% reduction) were found at 100 ng Vit. D ml(-1). Osteoblasts cultured on DegraPol-foam in the presence of Vit. D exhibited more spreading and less spindle-like morphology than cells cultured in the absence of Vit. D. Cell ingrowth into the pores of the foam was not affected by Vit. D treatment. Taken collectively, the osteoblasts, capability of responding to Vit. D confirms the osteoblast compatibility of DegraPol-foam and the possible use of this scaffold in the bone healing process.
THE CROSSLINKAGE THEORY OF AGING (1968)

Abstract: For many decades the theory and practice of cross‐linking (bonding that ties two or more large molecules together side to side) have been developed in industry, but only since the 1940's has the theory been considered in the field of medicine as a primary reaction underlying age‐dependent changes. Crosslinking is damaging to the tissues and involves loss of elasticity, reduced swelling capacity, increased resistance to hydrolases and probably enzymes generally, and thus an increase in molecular weight and a tendency toward embrittlement. There is a growing amount of direct evidence and much indirect evidence for postulating the relationship between crosslinking and aging. Crosslinking agents present in the living organism include aldehydes, lipid oxidation products, sulfur, alkylating agents, quinones, free radicals induced by ionizing radiation, antibodies, polybasic acids, polyhalo derivatives and polyvalent metals. The latter four types of compound are slow‐acting but can also accumulate in the body to form a frozen metabolic pool. Sufficient amounts of all these potential crosslinking materials are present in the body to make the changes of aging unavoidable.
NemoAuth: A mnemonic multimodal approach to mobile user authentication (2013)

User authentication is always the first step of security services/mechanisms in computing infrastructures. However, mobile devices and clouds bring challenges and also new dimensions into this topic, such as limited computing power, migrating objects, and various embedded sensors. When a resource located either in a mobile device or in a cloud is requested, associated security policies will trigger authentication procedures for compliance enforcement. This paper proposes a new multimodal approach, called NemoAuth, to mobile device user authentication. It has unique mnemonic and other interesting benefits, and also improves both security and user experience which breaks the limit of recent user authentication technologies.
IsdA of <i>Staphylococcus aureus</i> is a broad spectrum, iron‐regulated adhesin (2004)

As an important facet of host-pathogen interaction, Staphylococcus aureus has the ability to adhere to human extracellular matrix (ECM) components via a range of surface proteins. Here we have shown that IsdA has broad-spectrum ligand-binding activity, including fibrinogen and fibronectin. Mapping studies revealed a distinct domain responsible for ligand binding. This domain is present in a number of iron-regulated proteins of S. aureus and in other Gram-positive organisms. The isdA gene is only expressed in iron-limited conditions under the control of Fur and not in standard laboratory media. Such conditions occur in serum in vitro and during infection. Whole cell binding and clumping assays revealed that when the bacteria are grown under iron-limited conditions, IsdA constitutes a physiologically relevant adhesin to both fibrinogen and fibronectin. Thus for S. aureus, iron is an important marker for the host environment, to which the bacterium responds by differential regulation of at least one element of its adhesive strategy.
Cobalt Limitation of Growth and Mercury Methylation in Sulfate-Reducing Bacteria (2007)

Sulfate-reducing bacteria (SRB) have been identified as the primary organisms responsible for monomethylmercury (MeHg) production in aquatic environments, but little is known of the physiologyand biochemistry of mercury(Hg) methylation. Corrinoid compounds have been implicated in enzymatic Hg methylation, although recent experiments with a vitamin B12 inhibitor indicated that incomplete-oxidizing SRB likely do not use a corrinoid-enzyme for Hg methylation, whereas experiments with complete-oxidizing SRB were inconclusive due to overall growth limitation. Here we explore the role of corrinoid-containing methyltransferases, which contain a cobalt-reactive center, in Hg methylation. To this end, we performed cobalt-limitation experiments on two SRB strains: Desulfococcus multivorans, a complete-oxidizer that uses the acetyl-CoA pathway for major carbon metabolism, and Desulfovibrio africanus, an incomplete-oxidizer that does not contain the acetyl-CoA pathway. Cultures of D. multivorans grown with no direct addition of Co or B12 became cobalt-limited and produced 3 times less MeHg per cell than control cultures. Differences in growth rate and Hg bioavailability do not account for this large decrease in MeHg production upon Co limitation. In contrast, the growth and Hg methylation rates of D. africanus cultures remained nearly constant regardless of the inorganic cobalt and vitamin B12 concentrations in the medium. These results are consistent with mercury being methylated by different pathways in the two strains: catalyzed by a B12-containing methyltransferase in D. multivorans and a B12-independent methyltransferase in D. africanus. If complete-oxidizing SRB like D. multivorans account for the bulk of MeHg production in coastal sediments as reported, the ambient Co concentration and speciation may control the rate of Hg methylation.
Contributed Session II: Perceptual brightness scales in a White's effect stimulus are not captured by multiscale spatial filtering models of brightness perception (2022)

White's effect describes a brightness difference between two gray targets embedded in the black and white phases of a high contrast (square-wave) grating. Lacking an agreed explanation of this effect, it is often used as a target for computational models of brightness perception. Such models provide transfer functions linking input luminance to model output; if interpreting the latter as perceptual magnitude, these transfer functions are analogous to perceptual scales. However, whether the model transfer functions correspond to the perceptual scales has not yet been investigated. Here we estimate perceptual scales for White’s stimulus. On each trial, observers judged which of two targets appeared lighter. Each target varied in luminance across trials, and could appear either on the black or white phase of the grating. Using Maximum Likelihood Conjoint Measurement, perceptual scales were estimated from these judgments. Scales were compressive non-linear functions. Overall, the scale for targets on the black phase is shifted up relative to the white-phase targets (in agreement with the direction of White’s effect). This shift may be larger for intermediate luminance values than when target luminance approaches the luminance of the white phase, which has also been reported using more common matching tasks. Computational models failed to predict the shapes of the scales, suggesting that perceptual scales in addition to matching data could better constrain brightness models.
Spectral estimation of human skin color using the Kubelka-Munk theory (2003)

The present paper describes a method for modeling human skin coloring and estimating the surface-spectral reflectance by using the Kubelka-Munk theory. First, human skin is modeled as two layers of turbid materials. Second, we describe the reflectance estimation problem as the Kubelka-Munk equations with unknown six parameters. These parameters are the regular reflectance at skin surface and the five weights for spectral absorption of such different pigments as melanin, carotene, oxy-hemoglobin, deoxy-hemoglobin, and bilirubin. Moreover, the optical coefficients of spectral absorption and scattering for the two skin layers and the thickness values of these layers are used for the solution. Finally, experiments are done for estimating the skin surface-spectral reflectance on some body parts, such as the cheeks of human face, the palm, the backs of hand, the inside of arm, and the outside of arm. It is confirmed that the proposed method is more reliable in all cases.
The effect of low b‐values on the intravoxel incoherent motion derived pseudodiffusion parameter in liver (2014)

In conclusion, this study showed pseudodiffusion in the liver tended to be underestimated when too few low b-values (0 < b < 50 s/mm(2)) were included in the distribution. Therefore, it is recommended to include at least two low b-values when performing liver IVIM studies.
Building Internet of Things with the Arduino (2012)

The Internet of Things (IoT) is a global network that links physical objects using Cloud computing, web applications, and network communications. It allows devices to communicate with each other, access information on the Internet, store and retrieve data, and interact with users, creating smart, pervasive and always-connected environments. Despite the Internet of Things being a relatively new concept, there are already a few open platforms available that enable remote and seamless management and visualization of sensor data: Cosm, Nimbits, and ThingSpeak are just a few examples. And Arduino works with all of them. The Arduino is an incredibly flexible micro-controller and development environment that cannot only be used to control devices, but can also be used to read data from all kinds of sensors. Its simplicity and extensibility, in addition to its great success and adoption by users, has led to the development of a variety of hardware extensions and software libraries that enable wired and wireless communication with the Internet. Arduino is the ideal open hardware platform for experimenting with the world of the Internet of Things. Make your Arduino talk to the world! This book will provide you with all the information you need to design and create your own Internet of Things (IoT) applications using the Arduino platform. More specifically, you will learn: About the Internet of Things and Cloud Computing concepts About open platforms that allow you to store your sensor data on the Cloud (like Cosm, Nimbits and many more) The basic usage of Arduino environment for creating your own embedded projects at low cost How to connect your Arduino with your Android phone and send data over the Internet How to connect your Arduino directly to the Internet and talk to the Cloud How to reprogram your Arduino microcontroller remotely through the Cloud Detailed Table of Contents can be found at: http://www.buildinginternetofthings.com Updated version (v1.1): Contains corrections, improvements and updates about IoT Platforms!
Soft x-ray transmission characteristics of hollow-core fused-quartz fibers (1985)

Transmission factors of hollow-core fused-quartz fibers were measured as a function of curvature angle (0–90°) and photon wavelength (25–75Å). They were compared with the results obtained by a simple calculation based on geometrical optics. Both the measured and calculated transmission factors decreased exponentially with increasing curvature angle and showed a slight dependence on the wavelength.
Visualization of power system data (2005)

Effective power system operation requires power system engineers and operators to analyze vast amounts of information. In systems containing thousands of buses, a key challenge is to present this data in a form such that the user can assess the state of the system in an intuitive and quick manner. This is particularly true when trying to analyze relationships between actual network power flows, the scheduled power flows, and the capacity of the transmission system. With restructuring and the move towards having a single entity, such as an independent system operator or pool, operate a much larger system, this need has become more acute. This paper presents several power system visualization techniques to help in this task. These techniques include animation of power system flow values, contouring of bus and transmission line flow values, data aggregation techniques and virtual reality data visualization.
Reduction of radiated and conducted emissions in power electronic circuits by the continuous derivative control method (CDCM) (1998)

In this paper, we show the influence of the current gradient on the high frequency current harmonics in power electronic converters and demonstrate the advantage of wave forms which have derivatives with no discontinuities. This enable us to carry out practical experiments to demonstrate the feasibility of this theoretical proposition These results will be considered in this paper.
Gelatin Implants in Scleral Buckling Procedures (1975)

In 375 scleral buckling procedures, an absorbable gelatin implant (Retina Gelfilm) was used. This series included 192 trapdoor and scleral pouch procedures, and 183 operations in which a gelatin implant was used beneath a silicone rubber implant. Two thicknesses of gelatin implants were used, 0.5 mm and 0.75 mm. Absorption time varied from 2 to 24 months, depending on the thickness of the implant and whether it was used alone or beneath a silicone rubber implant. Gelatin is an excellent absorbable implant when used alone or under a silicone rubber implant in selected patients with retinal detachment to produce a temporary elevation or posterior extension of the buckle, or both.
Solution NMR Studies of the Aβ(1−40) and Aβ(1−42) Peptides Establish that the Met35 Oxidation State Affects the Mechanism of Amyloid Formation (2004)

The pathogenesis of Alzheimer's disease is characterized by the aggregation and fibrillation of the 40-residue A beta(1-40) and 42-residue A beta(1-42) peptides into amyloid plaques. The structural changes associated with the conversion of monomeric A beta peptide building blocks into multimeric fibrillar beta-strand aggregates remain unknown. Recently, we established that oxidation of the methionine-35 side chain to the sulfoxide (Met35(red) --> Met35(ox)) significantly impedes the rate of aggregation and fibrillation of the A beta peptide. To explore this effect at greater resolution, we carefully compared the (1)H, (15)N, and (13)C NMR chemical shifts of four A beta peptides that had the Met35 reduced or oxidized (A beta(1-40)Met35(red), A beta(1-40)Met35(ox), A beta(1-42)Met35(red), and A beta(1-42)Met35(ox)). With the use of a special disaggregation protocol, the highly aggregation prone A beta peptides could be studied at higher, millimolar concentrations (as required by NMR) in aqueous solution at neutral pH, remaining largely monomeric at 5 degrees C as determined by sedimentation equilibrium studies. The NOE, amide-NH temperature coefficients, and chemical shift indices of the (1)H alpha, (13)C alpha, and (13)C beta established that the four peptides are largely random, extended chain structures, with the Met35(ox) reducing the propensity for beta-strand structure at two hydrophobic regions (Leu17-Ala21 and Ile31-Val36), and turn- or bendlike structures at Asp7-Glu11 and Phe20-Ser26. Additional NMR studies monitoring changes that occur during aging at 37 degrees C established that, along with a gradual loss of signal/noise, the Met35(ox) significantly hindered upfield chemical shift movements of the 2H NMR signals for the His6, His13, and His14 side chains. Taken together, the present NMR studies demonstrate that the Met35(red) --> Met35(ox) conversion prevents aggregation by reducing both hydrophobic and electrostatic association and that the A beta(1-40)Met35(red), A beta(1-40)Met35(ox), A beta(1-42)Met35(red), and A beta(1-42)Met35(ox) peptides may associate differently, through specific, sharp changes in structure during the initial stages of aggregation.
Si-based sensor for virus detection (2005)

This paper describes the development of a sensor for the detection of viruses. The detection scheme uses sense and dummy capacitors and a sense amplifier circuit to compare capacitance values. The presence of sufficient biological material within the sense capacitor alters the sense amplifier output. This promising approach has the potential to more rapidly test for the presence of virus using an IC platform.
Role of VraSR in Antibiotic Resistance and Antibiotic-Induced Stress Response in <i>Staphylococcus aureus</i> (2006)

Exposure of Staphylococcus aureus to cell wall inhibitors induces massive overexpression of a number of genes, provided that the VraSR two-component sensory regulatory system is intact. Inactivation of vraS blocks this transcriptional response and also causes a drastic reduction in the levels of resistance to beta-lactam antibiotics and vancomycin. We used an experimental system in which the essential cell wall synthesis gene of S. aureus, pbpB, was put under the control of an isopropyl-beta-d-thiogalactopyranoside-inducible promoter in order to induce reversible perturbations in cell wall synthesis without the use of any cell wall-active inhibitor. Changes in the level of transcription of pbpB were rapidly followed by parallel changes in the vraSR signal, and the abundance of the pbpB transcript was precisely mirrored by the abundance of the transcripts of vraSR and some additional genes that belong to the VraSR regulon. Beta-lactam resistance in S. aureus appears to involve a complex stress response in which VraSR performs the critical role of a sentinel system capable of sensing the perturbation of cell wall synthesis and allowing mobilization of genes that are essential for the generation of a highly resistant phenotype. One of the sites in cell wall synthesis "sensed" by the VraSR system appears to be a step catalyzed by PBP 2.