gebhart/patrepeval huggingface dataset:
Convergence of many-body wave-function expansions using a plane-wave basis: From homogeneous electron gas to solid state systems (2012)

Using the finite simulation-cell homogeneous electron gas (HEG) as a model, we investigate the convergence of the correlation energy to the complete-basis-set (CBS) limit in methods utilizing plane-wave wave-function expansions. Simple analytic and numerical results from second-order M\o{}ller-Plesset theory (MP2) suggest a $1/M$ decay of the basis-set incompleteness error where $M$ is the number of plane waves used in the calculation, allowing for straightforward extrapolation to the CBS limit. As we shall show, the choice of basis-set truncation when constructing many-electron wave functions is far from obvious, and here we propose several alternatives based on the momentum transfer vector, which greatly improve the rate of convergence. This is demonstrated for a variety of wave-function methods, from MP2 to coupled-cluster doubles theory and the random-phase approximation plus second-order screened exchange. Finite basis-set energies are presented for these methods and compared with exact benchmarks. A transformation can map the orbitals of a general solid state system onto the HEG plane-wave basis and thereby allow application of these methods to more realistic physical problems. We demonstrate this explicitly for solid and molecular lithium hydride.
Stromal cell-derived factor-1α signals via the endothelium to protect the heart against ischaemia-reperfusion injury (2019)

Administration of SDF-1α is cardioprotective when administered prior to reperfusion and may, therefore, have clinical utility. SDF-1α-CXCR4-mediated cardioprotection from ischaemia-reperfusion injury is contingent on the cellular location of CXCR4 activation. Specifically, cardioprotection is mediated by endothelial signalling, while cardiomyocyte-specific deletion of CXCR4 has an infarct-sparing effect per se.
Blockchain: A game changer for securing IoT data (2018)

Internet of Things (IoT) is now in its initial stage but very soon, it is going to influence almost every day-to-day items we use. The more it will be included in our lifestyle, more will be the threat of it being misused. There is an urgent need to make IoT devices secure from getting cracked. Very soon IoT is going to expand the area for the cyber-attacks on homes and businesses by transforming objects that were used to be offline into online systems. Existing security technologies are just not enough to deal with this problem. Blockchain has emerged as the possible solution for creating more secure IoT systems in the time to come. In this paper, first an overview of the blockchain technology and its implementation has been explained; then we have discussed the infrastructure of IoT which is based on Blockchain network and at last a model has been provided for the security of internet of things using blockchain.
Suppressing the Infrared Signatures of Marine Gas Turbines (1989)

The exhaust plumes and visible areas of the engine exhaust ducting associated with marine gas turbines are major sources of infrared (IR) radiation on ships. These high-radiance sources make excellent targets for IR-guided threats. In recent years significant efforts have been made to reduce or eliminate these high-radiance sources to increase the survivability of naval and commercial ships when sailing in high-risk areas of the world. Typical IR signature suppression (IRSS) systems incorporate film cooling of visible metal sources, optical blockage to eliminate direct line-of-sight visibility of hot exhaust system parts, and cooling air injection and mixing for plume cooling. Because the metal surfaces radiate as near black bodies, every attempt is made to reduce the temperatures of the visible surfaces to near ambient conditions. The exhaust gases radiate selectively and therefore do not have to be cooled to the same degree as the metal surfaces. The present paper briefly describes the motivation for incorporating IRSS into the exhaust systems of marine power plants. IRSS hardware developed in Canada by the Canadian Department of National Defence and Davis Engineering Limited is presented along with details of their operating principles. A typical installation is presented and discussed. Design impacts on the ship are described with reference to engine back pressure, noise, and weight and center of gravity effects.
Conversion of redundant binary into two's complementrepresentations (1995)

A static CMOS circuit that converts a redundant binary representation into a two's complement representation is presented. The structure and time delay of the resulting logic are identical to a standard carry look-ahead logic for adders. The resulting layout is very regular, has no diffusion gaps and can be expanded to any desired look-ahead length. The circuit can be used for both multiplication and division.
The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes (2016)

Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper describes electron cryo-microscopy (cryoEM) structures for the intact OmRV virion to 8.9 Å resolution and the structure of the empty virus-like-particle, that lacks RNA, to 8.3 Å resolution. The icosahedral capsid contains 120-subunits and resembles another closely related arthropod-borne totivirus-like virus, the infectious myonecrosis virus (IMNV) from shrimps. Both viruses have an elevated plateau around their icosahedral 5-fold axes, surrounded by a deep canyon. Sequence and structural analysis suggests that this plateau region is mainly composed of the extended C-terminal region of the capsid proteins. In contrast to IMNV, the infectious form of OmRV lacks extensive fibre complexes at its 5-fold axes as directly confirmed by a contrast-enhancement technique, using Zernike phase-contrast cryo-EM. Instead, these fibre complexes are replaced by a short "plug" structure at the five-fold axes of OmRV. OmRV and IMNV have acquired an extracellular phase, and the structures at the five-fold axes may be significant in adaptation to cell-to-cell transmission in metazoan hosts.
Bringing the Outside In: Creating Artificial Lighting to Improve People’s Psychological Wellbeing by Evoking Biophilic Response Through Aesthetics and the Sun’s Biological Benefits (2015)

More than 50% of the world is now living in an urban environment and 90% of those people’s time is spent indoors with artificial surroundings. There are many ways these artificial surroundings can be manipulated to mimic the countless beneficial qualities of earth’s natural environments through technology and aesthetics. This document explores how earth’s organic forms can be merged into artificial lighting that simulates the sun and moon. Each prototype was created through biomimetic implementation of the sun and moon’s colour temperature to biologically keep a person’s circadian rhythm in sync while representing the presence of a psychological biophilic response through aesthetics.
Calcium‐activated DNA fragmentation kills immature thymocytes (1989)

Glucocorticoid hormones kill immature thymocytes by activating a self-destructive process that involves extensive DNA fragmentation. It has been demonstrated that thymocyte suicide is dependent on an early, sustained increase in cytosolic Ca2+ concentration, and new protein synthesis, but the biochemical lesion that leads to cell death has not been established. To determine whether endonuclease activation or activation of another Ca2+-dependent process could mediate cell killing, we treated thymocytes with the glucocorticoid methylprednisolone in the presence of inhibitors of various Ca2+-dependent degradative enzymes. The role of poly(ADP-ribose) polymerase, an enzyme known to be activated by DNA damage, was also assessed. Glucocorticoid-induced chromatin cleavage and cell killing were blocked by the endonuclease inhibitor aurintricarboxylic acid, whereas inhibitors of other Ca2+-dependent degradative processes or of poly(ADP-ribose) polymerase did not abrogate cell death. In addition, stimulation of thymocyte DNA fragmentation by the Ca2+ ionophore A23187 resulted in cell killing that could be blocked by the endonuclease inhibitor. Together, our results suggest that thymocyte suicide is caused by extensive Ca2+-stimulated DNA fragmentation.
Formally Proved Security of Assembly Code Against Power Analysis: A Case Study on Balanced Logic (2015)

In his keynote speech at CHES 2004, Kocher advocated that side-channel attacks were an illustration that formal cryptography was not as secure as it was believed because some assumptions (e.g., no auxiliary information is available during the computation) were not modeled. This failure is caused by formal methods' focus on models rather than implementations. In this paper we present formal methods and tools for designing protected code and proving its security against power analysis. These formal methods avoid the discrepancy between the model and the implementation by working on the latter rather than on a high-level model. Indeed, our methods allow us (a) to automatically insert a power balancing countermeasure directly at the assembly level, and to prove the correctness of the induced code transformation; and (b) to prove that the obtained code is balanced with regard to a reasonable leakage model. We also show how to characterize the hardware to use the resources which maximize the relevancy of the model. The tools implementing our methods are then demonstrated in a case study on an 8-bit AVR smartcard for which we generate a provably protected present implementation that reveals to be at least 250 times more resistant to CPA attacks.
Murein and the Outer Penetration Barrier of <i>Escherichia coli</i> K-12, <i>Proteus mirabilis</i> , and <i>Pseudomonas aeruginosa</i> (1972)

A penetration barrier operating outside the periplasmic enzyme penicillinase was studied in an ampicillin-resistant mutant of Escherichia coli K-12. Growth in the presence of lysozyme and sublethal concentrations of ampicillin partially opened the barrier. This could be recorded as an increased penetration of penicillin G, sodium cholate, and rifampin to their respective targets. Brief treatments with tris(hydroxymethyl)aminomethane-ethylenediaminetetraacetic acid and sodium cholate effectively impaired the barrier against penicillin and also caused leakage of penicillinase. Wild-type E. coli K-12, Proteus mirabilis, and Pseudomonas aeruginosa also showed an increased sensitivity to cholate after treatment with penicillins. Electron micrographs showed that lysis by cholate was due to a distortion of the cytoplasmic membrane causing a leakage of protein and RNA from the cells to the medium. Physiological data indicated that the increased sensitivity to cholate induced by growth in the presence of ampicillin or lysozyme was due to effects upon the murein. This was supported by measurement of the incorporation of (3)H-diaminopimelic acid. These results indicate that the murein sacculus either is a part of the penetration barrier or is responsible for holding the structure of the outer membrane together.
An amplifiable and deletable locus of Streptomyces ambofaciens RP181110 contains a very large gene homologous to polyketide synthase genes (1996)

Streptomyces ambofaciens RP181110 produces the macrolide polyketide spiramycin. Like many other Streptomyces species, the RP181110 strain is prone to genetic instability involving genomic rearrangements (deletions and/or amplifications) in the large unstable region of the genome. It has previously been demonstrated that the amplification of a particular locus (AUD205) affects spiramycin biosynthesis and, conversely, the loss of this amplification is correlated with the restoration of antibiotic production. This report focuses on a 0.93 kb reiterated fragment specific for the AUD205 locus. Sequencing of 3596 bp including this reiteration revealed the presence of an ORF (orfPS) whose potential product was highly homologous to the EryA and Raps proteins, responsible for the biosynthesis of erythromycin in Saccharopolyspora erythraea and rapamycin in Streptomyces hygroscopicus, respectively. orfPS encodes a protein with at least four successive domains: ketoacyl synthase, acyltransferase, ketoreductase and acyl carrier protein. This organization is very similar to most eryA and rap modules. The reiterated sequence corresponds to the acyltransferase domain. orfPS was transcribed during rapid growth and stationary phase in RP181110 and overtranscribed in the amplified mutant. Both these results suggest that the gene encodes a type I polyketide synthase and its reorganization is responsible for the loss of spiramycin production in the amplified strains.
Cloud4NFV: A platform for Virtual Network Functions (2014)

The principle of Network Functions Virtualization (NFV) aims to transform network architectures by implementing Network Functions (NFs) in software that can run on commodity hardware. There are several challenges inherent to NFV, among which is the need for an orchestration and management framework. This paper presents the Cloud4NFV platform, which follows the major NFV standard guidelines. The platform is presented in detail and special attention is given to data modelling aspects. Further, insights on the current implementation of the platform are given, showing that part of its foundations lay on cloud infrastructure management and Software Defined Networking (SDN) platforms. Finally, it is presented a proof-of-concept (PoC) that illustrates how the platform can be used to deliver a novel service to end customers, focusing on Customer Premises Equipment (CPE) related functions.
Determination of capsid size by satellite bacteriophage P4. (1978)

Satellite bacteriophage P4 requires all morphogenic gene products provided by a helper phage, such as coliphage P2, to assemble its own capsid, which is one-third the volume of the larger helper capsid. We have isolated a satellite phage P4 sid (size determination) mutant that is unable to direct the assembly of the small wild-type-size P4 capsid. Instead, this mutant produces P4 plaque-forming units with large P2-size capsids which contain two or three copies of the P4 sid1 genome. P4 sid1 is evidently mutated in a protein that is specifically responsible for determining the precise size and symmetry of the structure into which the helper P2 gene products will assemble. In addition, we have found that the physical size of the genome does not appear to play an essential role in the proper assembly of the icosahedral capsid, since the majority of the P4 sid1 plaque-forming units do not contain a complete capsidful of DNA.
Molecular Pathways: Blockade of the PRLR Signaling Pathway as a Novel Antihormonal Approach for the Treatment of Breast and Prostate Cancer (2013)

The prolactin (PRL)-prolactin receptor (PRLR) signaling complex has been implicated in the pathology of breast and prostate carcinoma. A multitude of pro-oncogenic intracellular signaling pathways are activated by PRL in breast and prostate epithelial cells, leading to enhanced cellular proliferation, survival, and tumorigenesis in numerous model systems. Emerging evidence suggests that targeting the PRL-PRLR axis in human cancer may represent an unexploited avenue for therapeutic intervention and, given the extensive cross-talk between PRLR and other signal transduction pathways, a potential means through which other anticancer agents could be rendered more efficacious in the clinic. LFA102 is a potent anti-PRLR neutralizing antibody that efficiently abrogates the function of this receptor in vivo, mediating significant antitumor effects in preclinical models. The clean safety profile of this antibody in animals and in the clinical experiences to date suggests that blocking the PRLR signaling pathway in human tumors may have few significant toxicologic consequences and may be a promising approach to treating cancer. A phase I trial in patients with breast and prostate cancer is underway to better understand the clinical utility of LFA102 and the contribution of PRL to the maintenance and progression of human cancer.
A Method for the Correction of Garbled Words Based on the Levenshtein Metric (1976)

In this paper we propose a new method for correcting garbled words based on Levenshtein distance and weighted Levenshtein distance. We can correct not only substitution errors, but also insertion errors and deletion errors by this method. According to the results of simulation on nearly 1000 high occurrence English words, higher error correcting rates can be achieved by this method than any other method tried to date. Hardware realization of the method is possible, though it is rather complicated.
Current applications of mini G proteins to study the structure and function of G protein-coupled receptors (2018)

G protein-coupled receptors (GPCRs) regulate intracellular signalling pathways that contribute to virtually all aspects of cell function. Characterising GPCRs in each of their conformational states is key to understanding their mechanism of action, but structure determination of receptors in their active state, bound to a heterotrimeric G protein or b-arrestin, has proved challenging. A number of G protein surrogates have been developed to simplify this process, including G protein-derived peptides, nanobodies and, most recently, mini G proteins. The aim of these surrogates is to bind the receptor and stabilise its active conformation, whilst eliminating the problems inherent to native signalling proteins, namely their large size, instability and conformational dynamics. Mini G proteins are composed of a single domain from the G protein a-subunit that has been engineered to form a stable complex with GPCRs. They induce comparable pharmacological and structural changes in the receptor to those elicited by heterotrimeric G proteins, and retain their native receptor-coupling specificity. At least one member of each G protein family has been converted into a mini G protein, which means that they can be used to characterise a wide variety of GPCRs. Since their initial publication two years ago, mini G proteins have facilitated the structure determination of three different receptors in their active state and enabled the development of a methodology to thermostabilise GPCRs in their fully active conformation. They have also been used to develop a range of assays that can measure mini G protein coupling to receptors <em>in vitro</em>, and a sensitive cell-based assay that is capable of accurately reporting ligand efficacy and quantifying G protein coupling <em>in vivo</em>. This review presents an overview of the current applications of mini G proteins to study the structure and function of GPCRs.
Treatment with liposome-encapsulated clodronate as a new strategic approach in the management of immune thrombocytopenic purpura in a mouse model (2000)

Immune thrombocytopenic purpura (ITP) is an autoimmune disease related to the presence of elevated levels of platelet-associated immunoglobulin, or autoantibodies. In recent years the importance of macrophage Fcγ receptors in the uptake of platelets in ITP has been confirmed. Although in patients with ITP the platelet destruction occurs in liver and spleen, in this present experimental mouse model the liver was the principal organ of sequestration of sensitized platelets. The uptake in the spleen, bone marrow, lung, and kidneys was negligible and not different from that in control animals. In addition, the trapped platelets did not return to circulation, and new cells derived from the platelet-storage pool or new thrombocytogenesis were necessary to restore the platelet count. The depletion of splenic and hepatic murine macrophages by liposome-encapsulated clodronate (lip-clod) was studied as a new strategy for ITP treatment. Lip-clod inhibits, in a dose-dependent manner, the antibody-induced thrombocytopenia. Moreover, lip-clod treatment rapidly restored (24 hours) the platelet count in thrombocytopenic animals to hematologic safe values, and despite additional antiplatelet antiserum treatment, mice were able to maintain this level of platelets at least up to 48 hours. The bleeding times in lip-clod–treated animals was not different from those in controls, demonstrating that the hemostasis was well controlled in these animals. The results presented in this study demonstrate that lip-clod treatment can be effective in the management of experimental ITP.
[Fabrication of tissue engineered vein containing valve scaffolds]. (2012)

Based on the self-made cast, the tissue engineered vein containing valve scaffolds can be fabricated by injection molding plus thermally induced phase separation. Further researches are warranted.
Cache Replacement Policies for Multicore Processors (2010)

Abstract: Almost all of the modern computers use multiple cores, and the number of cores is expected to increase as hardware prices go down, and Moore’s law fails to hold. Most of the theoretical algorithmic work so far has focused on the setting where multiple cores are performing the same task. Indeed, one is tempted to assume that when the cores are independent then the current design performs well. This work infirms this assumption by showing that even when the cores run completely independent tasks, there exist dependencies arising from running on the same chip, and using the same cache. These dependencies cause the standard caching algorithms to underperform. To address the new challenge, we revisit some aspects of the classical caching design. More specifically, we focus on the page replacement policy of the first cache shared between all the cores (usually the L2 cache). We make the simplifying assumption that since the cores are running independent tasks, they are accessing disjoint memory locations (in particular this means that maintaining coherency is not an issue). We show, that even under this simplifying assumption, the multicore case is fundamentally different then the single core case. In particular 1. LRU performs poorly, even with resource augmentation. 2. The offline version of the caching problem is NP complete.
Template‐Fabricated Gold Nanowires and Nanotubes (2003)

Abstract Gold nanowires and nanotubes are prepared via electroless deposition of Au onto the pore walls of a porous polymeric membrane. The pores in the support membrane act as a template for the nanostructures. The support is a commercially available nanoporous polycarbonate filter with cylindrical nanoscopic pores. We have shown that by controlling the Au deposition time, Au nanotubes (short deposition times) or nanowires (longer deposition times) can be prepared. The gold nanowires and nanotube membranes can be utilized for nanoelectrode ensembles, molecular filters and as chemical switches.
Real-time synchronization control in multimedia distributed systems (1992)

Two basic synchronization problems are involved in the distributed multimedia systems. One of them is the simultaneous real-time data delivery. Simultaneous Real Time Data Delivery (SRTDD) refers to delivering multimedia data in different data streams belonging to the same time interval simultaneously. In this paper, an entire SRTDD control scheme for multimedia transmission is established. We propose a layered architecture which can be mapped to the OSI model to support the SRTDD control. The segment delivery protocols for real-time multimedia data streams are addressed. A practical segmentation method is also developed for real-time voice and video.