gebhart/patrepeval huggingface dataset:
Genetically distinct pathways guide effector export through the type <scp>VI</scp> secretion system (2014)

Bacterial secretion systems often employ molecular chaperones to recognize and facilitate export of their substrates. Recent work demonstrated that a secreted component of the type VI secretion system (T6SS), haemolysin co-regulated protein (Hcp), binds directly to effectors, enhancing their stability in the bacterial cytoplasm. Herein, we describe a quantitative cellular proteomics screen for T6S substrates that exploits this chaperone-like quality of Hcp. Application of this approach to the Hcp secretion island I-encoded T6SS (H1-T6SS) of Pseudomonas aeruginosa led to the identification of a novel effector protein, termed Tse4 (type VI secretion exported 4), subsequently shown to act as a potent intra-specific H1-T6SS-delivered antibacterial toxin. Interestingly, our screen failed to identify two predicted H1-T6SS effectors, Tse5 and Tse6, which differ from Hcp-stabilized substrates by the presence of toxin-associated PAAR-repeat motifs and genetic linkage to members of the valine-glycine repeat protein G (vgrG) genes. Genetic studies further distinguished these two groups of effectors: Hcp-stabilized effectors were found to display redundancy in interbacterial competition with respect to the requirement for the two H1-T6SS-exported VgrG proteins, whereas Tse5 and Tse6 delivery strictly required a cognate VgrG. Together, we propose that interaction with either VgrG or Hcp defines distinct pathways for T6S effector export.
USING EXCESS VOLUME OF MIXING TO CORRELATE DIFFUSIVITIES IN LIQUIDS (1982)

It has been postulated in the past that diffusivities in liquids can be correlated with the excess volume or mixing. A system has been examined in which the diffusivities and excess volumes of mixing vary in a nonlinear manner with changes in concentration; however, the diffusivity is always a linear function of the excess volume of mixing.
(WIP) Towards the Automated Composition of Machine Learning Services (2018)

Automated service composition as the process of creating new software in an automated fashion has been studied in many different ways over the last decade. However, the impact of automated service composition has been rather small as its utility in real-world applications has not been demonstrated so far. This paper describes the use case of automated machine learning, a real-world scenario in which automated service composition plays an important role. It turns out that most existing service composition approaches are not able to reasonably solve this problem, because it requires to evaluate candidates by executing them during search. We briefly sketch a new service composition algorithm, MLS-PLAN, and illustrate how it can be applied to the problem of automated machine learning.
Improved synthesis and pharmacological evaluation of racemic 11 -demethylcalanolide A. (2008)

An improved and practical synthesis of racemic 11-demethylcalanolide A [(+/-)-1] was developed. This improved process involved Pechmann reaction on phloroglucinol with ethyl butyrylacetate to give 5,7,-dihydroxy4-n-propylcoumarin (3). Poly phosphoric acid (PPA) catalyzed acylation of compound (3) with crotonic acid, then intramolecular cyclization was achieved simultaneously in one step to afford the key intermediate chromanone (4). A microwave assisted synthetic method preparing chromene (6) using chromenynation of chromanone (4) with 1, 1-diethoxy-methyl-2-butene was conducted. Luche reduction of chromene (6) using NaBH4 with CeCl3 x 7H2O preferably gave (+/-)-1. The overall yield of this four step synthesis of (+/-)-1 was around 32% increasing one fold more than that of the previous method. An in vitro investigation showed that (+/-)-1 exhibited inhibitory activities against both wild-type and drug-resistant HIV-1 in HIV-1 RT and cell culture assay, and significant synergistic effects in combination with AZT, T-20, and indinavir. Its LD50 of acute toxicity in mice by intragastric administration and by intraperitoneal injection were 735.65 mg kg(-1) and 525.10 mg x kg(-1), respectively. The Cmax and AUC(0-infinity) were 0.54 microg x mL(-1) and 1.08 (microg x mL(-1) x h, respectively. The dynamics study of the inhibition of mice sera on HIV-1 RT showed that mice treated with 100 mg x kg(-1 (+/-)-1 once intraperitoneally were similar to that of 5 mg x kg(-1) of known clinical effective anti-HIV-1 drug neverapine. The results suggested that further investigation of the anti-HIV candidate (+/-)-1 was warranted.
Modified vaccinia Ankara vaccine expressing Marburg virus-like particles protects guinea pigs from lethal Marburg virus infection (2020)

Abstract We introduce a new vaccine platform against Marburg virus (MARV) combining the advantages of the immunogenicity of a highly attenuated vaccine vector (Modified Vaccinia Ankara, MVA) with the authentic conformation of virus-like particles (VLPs). Our vaccine, MVA–MARV–VLP, expresses the minimal components of MARV VLPs: the envelope glycoprotein GP and the matrix protein VP40. Electron microscopy confirmed self-assembly and budding of VLPs from infected cells. Prime/boost vaccination of guinea pigs with MVA–MARV–VLP-elicited MARV-specific binding and neutralizing antibody responses. Vaccination also induced Fc-mediated innate immune effector functions including activation of NK cells and antibody-dependent phagocytosis by neutrophils and monocytes. Inoculation of vaccinated animals with guinea pig-adapted MARV demonstrated 100% protection against death and disease with no viremia. Therefore, our vaccine platform, expressing two antigens resulting in assembly of VLPs in the native conformation in vaccinated hosts, can be used as a potent vaccine against MARV.
Future Directions in Tensor-Based Computation and Modeling (2009)

High-dimensional modeling is becoming ubiquitous across the sciences and engineering because of advances in sensor technology and storage technology. Computationally-oriented\nresearchers no longer have to avoid what were once intractably large, tensor-structured data sets. The current NSF promotion of “computational thinking” is timely: we need a focused international eﬀort to oversee the transition from matrix-based to tensor-based computational\nthinking. The successful problem-solving tools provided by the numerical linear algebra community need to be broadened and generalized. However, tensor-based research is not just\nmatrix-based research with additional subscripts. Tensors are data objects in their own right and there is much to learn about their geometry and their connections to statistics and operator theory. This requires full participation of researchers from engineering, the natural sciences, and the information sciences, together with statisticians, mathematicians, numerical analysts, and software/language designers. Representatives from these disciplines participated in the Workshop. We believe that the NSF can help ensure the vitality of “big N” engineering and science by systematically supporting research in tensor-based computation and modeling.
Vasopressin and oxytocin mRNA regulation in the rat assessed by hybridization with synthetic oligonucleotides. (1983)

Vasopressin and oxytocin are nonapeptide hormones that regulate water metabolism and lactation, respectively. To study the regulation of the vasopressin and oxytocin genes at the mRNA level, we constructed a series of synthetic oligonucleotides, from 8 to 15 bases in length, for use in filter-blot hybridization assays (Northern blots) of hypothalamic mRNA levels and for primed synthesis of cDNAs from which we determined the nucleotide sequences of the 5' regions of the vasopressin and oxytocin mRNAs. A 20-fold increase occurred in the amounts of the two mRNAs present in the hypothalami of rats drinking 2% saline for three weeks. In addition, the sequence analyses of the cDNAs provided the complete amino acid sequences of the NH2-terminal signal peptides of the rat vasopressin and oxytocin precursors. Thus, synthetic oligonucleotides consisting of as few as eight nucleotides can be used to prime reverse transcription of specific cDNAs from hypothalamic RNA, and pentadecanucleotide hybridization probes readily detect changes in levels of vasopressin and oxytocin mRNAs in response to osmotic stress.
Art and Blockchain: A Primer, History, and Taxonomy of Blockchain Use Cases in the Arts (2019)

Blockchain technology, while commonly associated with cryptocurrencies, stands to bring radical structural change to the arts and creative industries.This paper presents a history, primer, and taxonomy of blockchain use cases in the arts and then explores the implications of blockchain in three regards: the blurring of the for-profit / nonprofit distinction, changes in the ownership structure of art, and potential for new structures of public and private support and related policy changes.These developments raise important questions of governance of a technology which requires expertise in cryptography, coding, and securities law for implementation.Ultimately, blockchain holds the potential to tip the role of the arts toward democratic availability through collective ownership structures or toward further commodification of cultural assets.
Swap-Aware Garbage Collection for NAND Flash Memory Based Embedded Systems (2007)

Embedded systems use NAND flash memory as a secondary storage device because it has many attractive features such as small size, fast access speeds, shock resistance, and light weight. NAND flash memory based embedded systems exploit a "demand paging" to run applications and also use a "swapping" to extend a limited main memory space. Because the embedded systems use NAND flash memory as swap space, it should perform garbage collection, which is a time-consuming operation. Besides, the number of the erase operations allowed to each block is also limited. In this paper, we propose a new garbage collection policy for embedded systems with the swap system. The proposed garbage collection policy focuses on minimizing the garbage collection time and even wear-leveling. Trace-driven simulations show that the proposed policy performs better than existing garbage collection policies in terms of the garbage collection time and the endurance of flash memory.
Isovolumic Acceleration Measured by Tissue Doppler Echocardiography Is Preload Independent in Healthy Subjects (2007)

IVA is unchanged following significant increases in preload in healthy subjects, and thus is a potentially useful measure of global LV contractility.
Epitope Analysis of the Malaria Surface Antigen Pfs48/45 Identifies a Subdomain That Elicits Transmission Blocking Antibodies (2007)

Pfs48/45, a member of a Plasmodium-specific protein family, displays conformation-dependent epitopes and is an important target for malaria transmission-blocking (TB) immunity. To design a recombinant Pfs48/45-based TB vaccine, we analyzed the conformational TB epitopes of Pfs48/45. The Pfs48/45 protein was found to consist of a C-terminal six-cysteine module recognized by anti-epitope I antibodies, a middle four-cysteine module recognized by anti-epitopes IIb and III, and an N-terminal module recognized by anti-epitope V antibodies. Refolding assays identified that a fragment of 10 cysteines (10C), comprising the middle four-cysteine and the C-terminal six-cysteine modules, possesses superior refolding capacity. The refolded and partially purified 10C conformer elicited antibodies in mice that targeted at least two of the TB epitopes (I and III). The induced antibodies could block the fertilization of Plasmodium falciparum gametes in vivo in a concentration-dependent manner. Our results provide important insight into the structural organization of the Pfs48/45 protein and experimental support for a Pfs48/45-based subunit vaccine.
Spraying Fabrication of Durable and Transparent Coatings for Anti-Icing Application: Dynamic Water Repellency, Icing Delay, and Ice Adhesion (2018)

Anti-icing/icephobic coatings, typically applied in the form of surface functional materials, are considered to be an ideal selection to solve the icing issues faced by daily life and industrial production. However, the applications of anti-icing coatings are greatly limited by the two main challenges: bonding strength with substrates and stability of the high anti-icing performance. Here, we designed and fabricated a kind of high-performance superhydrophobic fluorinated silica (F-SiO<sub>2</sub>)@polydimethylsiloxane coatings and further emphasized the improvement of the bonding strength with substrates and the maintenance of high anti-icing performance. The resultant coatings exhibited excellent water repellency with a contact angle up to 155.3° and a very short contact time (∼10.2 ms) of impact droplets. At low temperatures, the coming droplets still rapidly rebounded off the coating surface, and the superhydrophobic coatings displayed a more than 50-fold increase of freezing time comparing with bare aluminum. The ice adhesion strength on the coatings was only 26.3 kPa, which was far less than that (821.9 kPa) of bare aluminum. Furthermore, the nanoporous structures constructed by anodic oxidation could tremendously enhance the bonding strength of the coatings with the substrate, which was evaluated through a standard method (ASTM D3359). The anti-icing properties still retained high stability under the conditions of 30 icing/deicing cycles, soaking, and scouring of acid solution (pH = 5.6). This work can effectively push the anti-icing coatings toward a real-world application.
Hyaluronic Acid Viscosupplementation and Osteoarthritis (2009)

Intra-articular hyaluronic acid viscosupplementation is gaining popularity as a treatment option in the nonoperative management of patients with osteoarthritis. Recent clinical studies have demonstrated that the anti-inflammatory, anabolic, and chondroprotective actions of hyaluronic acid reduce pain and improve patient function. With evidence mounting in support of the efficacy of this treatment modality for patients with osteoarthritis, its potential use in additional patient populations and for other pathologies affecting the knee is being investigated. The current article reviews the use of intra-articular hyaluronic acid viscosupplementation in the management of knee osteoarthritis and presents the potential for expanding its indications for other joints and alternative patient subpopulations. Additionally, future directions for the use of hyaluronic acid and areas of active research are discussed.
The late phase of ischemic preconditioning is abrogated by targeted disruption of the inducible NO synthase gene (1999)

The goal of this study was to interrogate the role of inducible NO synthase (iNOS) in the late phase of ischemic preconditioning (PC) in vivo. A total of 321 mice were used. Wild-type mice preconditioned 24 h earlier with six cycles of 4-min coronary occlusion/4-min reperfusion exhibited a significant (P < 0.05) increase in myocardial iNOS protein content, iNOS activity (assessed as calcium-independent L-citrulline formation), and nitrite + nitrate tissue levels. In contrast, endothelial NOS protein content and calcium-dependent NOS activity remained unchanged. No immunoreactive neuronal NOS was detected. When wild-type mice were preconditioned 24 h earlier with six 4-min occlusion/4-min reperfusion cycles, the size of the infarcts produced by a 30-min coronary occlusion followed by 24 h of reperfusion was reduced markedly (by 67%; P < 0.05) compared with sham-preconditioned controls, indicating a late PC effect. In contrast, when mice homozygous for a null iNOS allele were preconditioned 24 h earlier with the same protocol, infarct size was not reduced. Disruption of the iNOS gene had no effect on early PC or on infarct size in the absence of PC. These results demonstrate that (i) the late phase of ischemic PC is associated with selective up-regulation of iNOS, and (ii) targeted disruption of the iNOS gene completely abrogates the infarct-sparing effect of late PC (but not of early PC), providing unequivocal molecular genetic evidence for an obligatory role of iNOS in the cardioprotection afforded by the late phase of ischemic PC. Thus, this study identifies a specific protein that mediates late PC in vivo.
Spatial and Temporal Association of As and Fe Species on Aquatic Plant Roots (2002)

The formation of an Fe(III) precipitate (plaque) on the surface of aquatic plant roots may provide a means of attenuation and external exclusion of metals. Presently, the mechanisms of metal(loid) sequestration at the root surface are unresolved. Accordingly, we investigated the mechanisms of Fe and As attenuation and association on the roots of two common aquatic plant species, Phalaris arundinacea (reed canarygrass) and Typha latifolia (cattail) using X-ray absorption spectroscopy and X-ray fluorescence microtomography. Iron plaque of both P. arundinacea and T. latifolia consist predominantly of hydrated iron oxides (ferrihydrite) with lesser amounts of goethite and minor levels of siderite. Typha latifolia, however, differs from P. arundinacea by having a significant contribution from lepidocrocite as well as a greater proportion of crystalline minerals. Coexistence of goethite and lepidocrocite suggests the presence of chemically diverse microenvironments at the root surface. Arsenic exists as a combination of two sorbed As species, being comprised predominantly of arsenate- (approximately 82%) with lesser amounts (approximately 18%) of As(III)-iron (hydr)oxide complexes. Furthermore, both spatial and temporal correlations between As and Fe on the root surfaces were observed. While the iron (hydr)oxide deposits form a continuous surficial rind around the root, As exists in isolated regions on the exterior and interior of the root. Root surface-associated As generally corresponds to regions of enhanced Fe levels and may therefore occur as a direct consequence of Fe phase heterogeneity and preferential As sorption reactions.
INFLUENCE OF DEMOGRAPHIC VARIABLES ON LEVEL OF AWARENESS REGARDING RETIREMENT PLANNING (2018)

Financial freedom and financial success is one of the important dreams of each and every individual. The hard-earned money is to be carefully saved for meeting the needs and expenses during the retired life.  Retirement planning is a known concept to everyone. People are aware about their responsibility to plan for a successful retirement. But the actual question is whether they are actually getting involved in retirement planning practices. Working adults prefer to have a luxurious current life rather than saving for future. They are not at all interested in acquiring information regarding how they can actually save for retirement. Those who are highly aware will normally be having a tendency to save for retirement. As retirement is a crucial life stage the need to systematically plan for it should not be ignored.  The present study is a descriptive study conducted among 50 working individuals in private sector in Kannur District. The study analyses the impact of demographic variables on level of awareness regarding retirement planning.
Relationship between Serum and Brain Carotenoids,<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:mi mathvariant="bold-italic">α</mml:mi></mml:mrow></mml:math>-Tocopherol, and Retinol Concentrations and Cognitive Performance in the Oldest Old from the Georgia Centenarian Study (2013)

Oxidative stress is involved in age-related cognitive decline. The dietary antioxidants, carotenoids, tocopherols, and vitamin A may play a role in the prevention or delay in cognitive decline. In this study, sera were obtained from 78 octogenarians and 220 centenarians from the Georgia Centenarian Study. Brain tissues were obtained from 47 centenarian decedents. Samples were analyzed for carotenoids, α-tocopherol, and retinol using HPLC. Analyte concentrations were compared with cognitive tests designed to evaluate global cognition, dementia, depression and cognitive domains (memory, processing speed, attention, and executive functioning). Serum lutein, zeaxanthin, and β-carotene concentrations were most consistently related to better cognition (P < 0.05) in the whole population and in the centenarians. Only serum lutein was significantly related to better cognition in the octogenarians. In brain, lutein and β-carotene were related to cognition with lutein being consistently associated with a range of measures. There were fewer significant relationships for α-tocopherol and a negative relationship between brain retinol concentrations and delayed recognition. These findings suggest that the status of certain carotenoids in the old may reflect their cognitive function. The protective effect may not be related to an antioxidant effect given that α-tocopherol was less related to cognition than these carotenoids.
Voxels on fire [computer animation] (2004)

We introduce a method for the animation of fire propagation and the burning consumption of objects represented as volumetric data sets. Our method uses a volumetric fire propagation model based on an enhanced distance field. It can simulate the spreading of multiple fire fronts over a specified isosurface without actually having to create that isosurface. The distance field is generated from a specific shell volume that rapidly creates narrow spatial bands around the virtual surface of any given isovalue. The complete distance field is then obtained by propagation from the initial bands. At each step multiple fire fronts can evolve simultaneously on the volumetric object. The flames of the fire are constructed from streams of particles whose movement is regulated by a velocity field generated with the hardware-accelerated Lattice Boltzmann Model (LBM). The LBM provides a physically-based simulation of the air flow around the burning object. The object voxels and the splats associated with the flame particles are rendered in the same pipeline so that the volume data with its external and internal structures can be displayed along with the fire.
Quantification of intra- and inter-cluster relations in nonstationary and noisy data (2008)

The interrelation between data channels of multivariate data sets may lead to cluster formation. Revealing the cluster structure can give important information about the underlying systems' properties. Here we investigate the features of a recent genuinely multivariate cluster detection algorithm that is suitable for time-resolved and unsupervised application to nonstationary and noisy time series. Using numerical test systems it is discussed under which conditions intra- and inter-cluster relations can be disentangled and quantified. In addition different types of errors occurring when channels are automatically attributed to clusters are investigated quantitatively. Finally, the algorithm is applied to nonstationary model time series and its time-dependent performance is compared to other cluster detection algorithms.
Organophosphoryl derivatives of trivacant tungstophosphates of general formula α-A-[PW9O34(RPO)2]5−: synthesis and structure determination by multinuclear magnetic resonance spectroscopy (31P, 183W) ‡ (1998)

In the presence of NBun4Br acting as phase-transfer reagent, organophosphonic acids RPO(OH)2 reacted in acetonitrile with the trivacant tungstophosphate sodium salt β-A-Na8[HPW9O34]·24H2O to give hybrid organophosphoryl polyoxotungstate derivatives α-A-[NBun4]3Na2[PW9O34(RPO)2] (R = Et 1, Bun 2, But 3, allyl 4 or Ph 5) in satisfactory yield (>65%). The structure of the hybrid anions has been inferred from spectroscopic data, especially from multinuclear (31P, 183W) NMR studies. In particular, the five-line (1∶2∶2∶2∶2) 183W spectrum indicates a lowering of the symmetry of the tungstophosphate framework from C3v to Cs. According to spectroscopic observations and chemical analyses, the hybrid anion consists of an α-A-[PW9O34] framework on which are grafted two RPO groups through P–O–W bridges. This structure displays two nucleophilic oxygen atoms at the polyoxotungstate surface and thus remains unsaturated.