Miracle-dz/UniFAR-FTUs huggingface dataset:
Bovine Leukemia Virus SU Protein Interacts with Zinc, and Mutations within Two Interacting Regions Differently Affect Viral Fusion and Infectivity In Vivo

ABSTRACT Bovine leukemia virus (BLV) and human T-cell lymphotropic virus type 1 (HTLV-1) belong to the genus of deltaretroviruses. Their entry into the host cell is supposed to be mediated by interactions of the extracellular (SU) envelope glycoproteins with cellular receptors. To gain insight into the mechanisms governing this process, we investigated the ability of SU proteins to interact with specific ligands. In particular, by affinity chromatography, we have shown that BLV SU protein specifically interacted with zinc ions. To identify the protein domains involved in binding, 16 peptides distributed along the sequence were tested. Two of them appeared to be able to interact with zinc. To unravel the role of these SU regions in the biology of the virus, mutations were introduced into the env gene of a BLV molecular clone in order to modify residues potentially interacting with zinc. The fusogenic capacity of envelope mutated within the first zinc-binding region (104 to 123) was completely abolished. Furthermore, the integrity of this domain was also required for in vivo infectivity. In contrast, mutations within the second zinc-binding region (218 to 237) did not hamper the fusogenic capacity; indeed, the syncytia were even larger. In sheep, mutations in region 218 to 237 did not alter infectivity or viral spread. Finally, we demonstrated that the envelope of the related HTLV-1 was also able to bind zinc. Interestingly, zinc ions were found to be associated with the receptor-binding domain (RBD) of Friend murine leukemia virus (Fr-MLV) SU glycoprotein, further supporting their relevance in SU structure. Based on the sequence similarities shared with the Fr-MLV RBD, whose three-dimensional structure has been experimentally determined, we located the BLV zinc-binding peptide 104-123 on the opposite side of the potential receptor-binding surface. This observation supports the hypothesis that zinc ions could mediate interactions of the SU RBD either with the C-terminal part of SU, thereby contributing to the SU structural integrity, or with a partner(s) different from the receptor.
The Geoengineering Model Intercomparison Project (GeoMIP)

To evaluate the effects of stratospheric geoengineering with sulphate aerosols, we propose standard forcing scenarios to be applied to multiple climate models to compare their results and determine the robustness of their responses. Thus far, different modeling groups have used different forcing scenarios for both global warming and geoengineering, complicating the comparison of results. We recommend four experiments to explore the extent to which geoengineering might offset climate change projected in some of the Climate Model Intercomparison Project 5 experiments. These experiments focus on stratospheric aerosols, but future experiments under this framework may focus on different means of geoengineering. Copyright © 2011 Royal Meteorological Society and Crown copyright
Increased intracellular survival of Mycobacterium smegmatis containing the Mycobacterium leprae thioredoxin-thioredoxin reductase gene

The thioredoxin (Trx) system of Mycobacterium leprae is expressed as a single hybrid protein containing thioredoxin reductase (TR) at its N terminus and Trx at its C terminus. This hybrid Trx system is unique to M. leprae, since in all other organisms studied to date, including other mycobacteria, both TR and Trx are expressed as two separate proteins. Because Trx has been shown to scavenge reactive oxygen species, we have investigated whether the TR-Trx gene product can inhibit oxygen-dependent killing of mycobacteria by human mononuclear phagocytes and as such could contribute to mycobacterial virulence. The gene encoding M. leprae TR-Trx was cloned into the apathogenic, fast-growing bacterium Mycobacterium smegmatis. Recombinant M. smegmatis containing the gene encoding TR-Trx was killed to a significantly lesser extent than M. smegmatis containing the identical vector with either no insert or a control M. leprae construct unrelated to TR-Trx. Upon phagocytosis, M. smegmatis was shown to be killed predominantly by oxygen-dependent macrophage-killing mechanisms. Coinfection of M. smegmatis expressing the gene encoding TR-Trx together with Staphylococcus aureus, which is known to be killed via oxygen-dependent microbicidal mechanisms, revealed that the TR-Trx gene product interferes with the intracellular killing of this bacterium. A similar coinfection with Streptococcus pyogenes, known to be killed by oxygen-independent mechanisms, showed that the TR-Trx gene product did not influence the oxygen-independent killing pathway. The data obtained in this study suggest that the Trx system of M. leprae can inhibit oxygen-dependent killing of intracellular bacteria and thus may represent one of the mechanisms by which M. leprae can deal with oxidative stress within human mononuclear phagocytes.
In fl uence of the Sacri fi cial Polystyrene Removal Pathway on the TiO 2 Nanocapsule Structure

This study demonstrates the significant influence of the polystyrene removal pathway on the TiO2 nanocapsules obtained from PS@TiO2 core-shell particles. In a first step, the polystyrene spheres were coated with titanium oxide via hydrolysis and condensation of the titanium precursor to form PS@TiO2 core-shell particles. Then, the creation of the empty cavity to form TiO2 nanocapsules was achieved by removing the polystyrene template by i) thermal decomposition of the polystyrene or ii) dissolution of the polystyrene using Soxhlet extractor followed by a thermal procedure. These pathways to remove the polystyrene were investigated by thermogravimetric studies, IR spectroscopy, transmission and scanning electron microscopy and powder X-ray diffraction. The final TiO2 nanocapsule structure strongly depends on the sacrificial polystyrene removal pathway. The preservation of the TiO2 nanocapsules was obtained essentially when the polystyrene was dissolved before the crystallization of the TiO2.
Calcium-alginate coated, whey protein-based microspheres: preparation, some properties and opportunities

An ‘all aqueous’ encapsulation process followed by a heat treatment was used to prepare calcium-alginate-coated, whey protein-based, water insoluble microspheres containing micronized calcium carbonate as a model core. Results obtained with this process were compared to those obtained with a similar process in which chemical cross-linking was utilized. At an initial core load of 25 or 50% (w/w), core retention ranged from 84.2–95.12% and was not significantly affected by the initial core load or by the cross-linking method. Regardless of the cross-linking method, protein retention during the process was high and ranged from 78.2–87.5%. Outer topography of the microspheres was not influenced by the cross-linking method, however, at a given composition, the inner structure of heat treated microspheres differed from that obtained with chemically-cross-linked microspheres. Swelling properties of denovo microspheres were affected by pH. Results indicated that the micronized calcium carbonate could be used as a porogenic core. Removal of the core, by an acid treatment, allowed preparing microporous delivery devices. In addition to offer opportunities for encapsulation and delivery of crystalline core, the investigated process can provide means to prepare ‘ghost’ microporous delivery systems that can, in potential, be loaded, following their preparation, with sensitive core materials at conditions that favour the stability and functionality of this core.
Prognostic value of intraductal carcinoma of the prostate in radical prostatectomy specimens

Intraductal carcinoma of the prostate (IDC‐P) is an adverse prognostic factor for radical prostatectomy (RP). The endpoint in most IDC‐P studies is increased prostate‐specific antigen (PSA) levels. The aim of this study was to evaluate whether IDC‐P in RP specimens is an adverse prognostic factor for progression‐free survival (PFS) and cancer‐specific survival (CSS).
Hieroglyphs and Archaeology at Copan

Abstract The study of Copan's extensive hieroglyphic texts has grown hand in hand with long-term architectural excavations. Recent progress in Maya decipherment, much of it derived from work at Copan, now allows for new and potentially rewarding opportunities to integrate epigraphy and “dirt” archaeology. Toward this end, this paper provides an overview of the current knowledge of Copan's elite history, summarizing current knowledge of the ruler sequence and attributions of monuments and architecture to individual reigns. Thematic and stylistic changes are evident in the inscriptions between the Early and Late Classic periods, including a proliferation of subordinate elite texts in the decades leading up to political collapse. Also, new information is provided on the changing relations between Copan and Quirigua throughout the Classic period. RESUMEN Este ensayo sirve como resumen del trabajo reciente sobre los textos jeroglíficos de Copan, incluyendo ue tratamiento detallado de la secuencia dinástica de este sitio durante la época clásico. La discusión se enfoca sobre varios cambios temáticos eetre las inscripciones del clásico temprano y del clásico tardío. La mayoría de los textos del clásico temprano son fragmentários y muy difíciles à leer; por eso, la historia de este época se queda largamente obscura. Sin embargo, hay mucha información esenciál sobre el clásico temprano eh los monumetos de subsiguientes épocas, como Altar Q y la escalinata jeroglífica de la Estructura 10L-26. Los datos que tenemos, aunque scan escasos, afirman que estas fuentes tardías no son exageradas en sus recuentos de la historia más antiguo. Al contrario a los otros sitios mayas, a los textos de Copan, es-pecialmente los más tempranos, les faltan la calidad narrative de la historia. Cerca del fin del clásico tardio, después de la muerte del Gobernante 13, ó Waxaklahun Ubah K'awil, los textos acercan más la forma narrativa. Los temas de esos textos se tratan de figuras como Gobernante 16 y otras personas de la nobleza. Esos cambios de tema pueden ser productos de influencias exteriores o cambios politicos poco antes del colapso ca. 850 d.C. Tratando los hechos sobre estos temas, este ensayo intenta integrar los datos arqueológicos y epigráficos para que otros puedan hacerlo mismo.
The English Year: A Month-by-Month Guide to the Nation's Customs and Festivals, from May Day to Mischief Night

often with links to radical politics. These unorthodox thinkers are a colourful collection, ranging from Stukeley through 1010 Morganwg, William Price, and George MacGregor Reid, to today's Arthur Uther Pendragon. As a result, Druids are now seen as leading counter-cultural movements, whether ecological, spiritual, political, or a blending of all these. After expertly guiding his readers through this maze, Professor Hutton ventures to forecast that both Demonic Druids and counter-cultural Spiritual Druids will retain a place in 'the British soul' well into the twenty-first century. Let us hope he is correct.
Tradeoffs in choice between risk and delay depend on monetary amounts.

In Experiments 1 and 2, 25 and 48 college students made binary choices between hypothetical money amounts. In Part A, choices were between small amounts available with certainty and larger amounts ($10 to $10,000) available with risk. Choices in Part B were between immediate small amounts and delayed larger amounts. As money amount grew, risk aversion and delay aversion both changed but in opposite ways: Risk aversion grew but delay aversion shrank. Part C of Experiment 1 pitted risky amounts against delayed amounts, and its results were consistent with those of Parts A and B. Equivalences of particular risks and delays depended on the particular monetary amounts to which they attached. In Experiment 3, 20 college students made binary choices between money amounts, knowing that they would actually receive some of the selections they made. In Part A, choices were between certain small amounts and risky larger amounts ($1 and $10). Choice problems in Part B were between immediate small amounts and delayed receipt of $1 or $10. The results were like those of Experiment 1, though weaker. These results argue against models of choice that posit an equivalence of risk and delay that is independent of monetary amount.
Multicore/Manycore Parallel Traversal of Large Forests of Regression Trees

Machine-learnt models based on additive ensembles of binary regression trees are currently considered one of the best solutions to address complex classification, regression, and ranking tasks. To evaluate these complex models over a continuous stream of data items with high throughput requirements, we need to optimize, and possibly parallelize, the traversal of thousands of trees, each including hundreds of nodes.Document ranking in Web Search is a typical example of this challenging scenario, where complex tree-based models are used to score query-document pairs and finally rank lists of document results for each incoming query (a.k.a. Learning-to-Rank). In this extended abstract, we briefly discuss some preliminary results concerning the parallelization strategies for QUICKSCORER – indeed the state-of-art scoring algorithm that exploits ensembles of decision trees – by using multicore CPUs (with SIMD coprocessors) and manycore GPUs. We show that QUICKSCORER, which transforms the traversal of thousands of decision trees in a linear access to array data structures, can be parallelized very effectively, by achieving very interesting speedups.
Mechanical resilience and cementitious processes in Imperial Roman architectural mortar

Significance A volcanic ash–lime mortar has been regarded for centuries as the principal material constituent that provides long-term durability to ancient Roman architectural concrete. A reproduction of Imperial-age mortar based on Trajan’s Markets (110 CE) wall concrete resists microcracking through cohesion of calcium–aluminum–silicate–hydrate cementing binder and in situ crystallization of platey strätlingite, a durable calcium-aluminosilicate mineral that reinforces interfacial zones and the cementitious matrix. In the 1,900-y-old mortar dense intergrowths of the platey crystals obstruct crack propagation and preserve cohesion at the micron scale. Trajanic concrete provides a proven prototype for environmentally friendly conglomeratic concretes that contain ∼88 vol % volcanic rock yet maintain their chemical resilience and structural integrity in seismically active environments at the millenial scale. The pyroclastic aggregate concrete of Trajan’s Markets (110 CE), now Museo Fori Imperiali in Rome, has absorbed energy from seismic ground shaking and long-term foundation settlement for nearly two millenia while remaining largely intact at the structural scale. The scientific basis of this exceptional service record is explored through computed tomography of fracture surfaces and synchroton X-ray microdiffraction analyses of a reproduction of the standardized hydrated lime–volcanic ash mortar that binds decimeter-sized tuff and brick aggregate in the conglomeratic concrete. The mortar reproduction gains fracture toughness over 180 d through progressive coalescence of calcium–aluminum-silicate–hydrate (C-A-S-H) cementing binder with Ca/(Si+Al) ≈ 0.8–0.9 and crystallization of strätlingite and siliceous hydrogarnet (katoite) at ≥90 d, after pozzolanic consumption of hydrated lime was complete. Platey strätlingite crystals toughen interfacial zones along scoria perimeters and impede macroscale propagation of crack segments. In the 1,900-y-old mortar, C-A-S-H has low Ca/(Si+Al) ≈ 0.45–0.75. Dense clusters of 2- to 30-µm strätlingite plates further reinforce interfacial zones, the weakest link of modern cement-based concrete, and the cementitious matrix. These crystals formed during long-term autogeneous reaction of dissolved calcite from lime and the alkali-rich scoriae groundmass, clay mineral (halloysite), and zeolite (phillipsite and chabazite) surface textures from the Pozzolane Rosse pyroclastic flow, erupted from the nearby Alban Hills volcano. The clast-supported conglomeratic fabric of the concrete presents further resistance to fracture propagation at the structural scale.
Effective Electrons Transfer Pathway of the Ternary TiO 2 / RGO / Ag Nanocomposite with Enhanced Photocatalytic Activity under Visible Light

Mesoporous TiO2/reduced graphene oxide/Ag (TiO2/RGO/Ag) ternary nanocomposite with effective electrons transfer pathway is obtained by an electrostatic self-assembly method and photo-assisted treatment. Compared with bare mesoporous TiO2 (MT) and mesoporous TiO2/RGO (MTG), the ternary mesoporous TiO2/RGO/Ag (MTGA) nanocomposite exhibited superior photocatalytic performance for the degradation of MB under visible light, and the degradation rate reached 0.017 min-1, which was 3.4 times higher than that of MTG. It is proposed that Ag nanoparticles can form the local surface plasmon resonance (LSPR) to absorb the visible light and distract the electrons into MT, and RGO can accept the electrons from MT to accelerate the separation efficiency of carriers. The establishment of MTGA ternary nanocomposite make the three components act synergistic effect to enhance the photocatalytic performance.
Dissecting the consonant duration ratio

It has been argued that the duration ratio (DR) of two consonants in C1C2 serves as a diagnostic of syllabification: if greater than 1, then C1C2 is a syllable onset; if (approximately) 1, C1C2 is a coda– onset sequence. If valid, this diagnostic would provide a straightforward way of assessing syllabic organization. We examined the validity of the DR using the Wisconsin X-Ray Microbeam corpus, which due to its size permits a robust test. We also informed our evaluation by another archive of kinematics and acoustics, with finer comparisons. These corpora extend an evaluation of the DR to word-medial clusters, in addition to initial and crossword contexts wherein the DR has been studied before. Our results indicate that duration ratio patterns previously thought to be related to syllabification derive from levels of representation or prosody which are not specifically syllabic. These patterns are conditioned by prosodic effects and manner contrasts.
Vitrification of pronuclear‐stage mouse embryos on solid surface (SSV) versus in cryotube: Comparison of the effect of equilibration time and different sugars in the vitrification solution

The cryopreservation of pronuclear‐stage embryos has particular importance in transgenic technology and human assisted reproductive technology (ART). The objective of this study was to improve the efficiency of cryopreservation of pronuclear‐stage mouse embryos. Two vitrification methods (solid surface vitrification (SSV) vs. vitrification in cryotube) have been compared with special emphasis on the effect of the exposure of the embryos to the solutions for various times and the sugar content (trehalose, sucrose, or raffinose) of the vitrification solutions. Pronuclear‐stage embryos were either exposed to 1 M dimethyl sulfoxide (DMSO) + 1 M propylene‐glycol (PG) solution for 2, 5, 10, or 15 min or not exposed to this “equilibration” solution. The vitrification solutions consisted of 2.75 M DMSO and 2.75 M PG in M2 medium supplemented with 1 M trehalose (DPT), 1 M sucrose (DPS), or 1 M raffinose (DPR). In the cryotube method, groups of 15–25 embryos were transferred into a 1.8 ml cryotube containing 30 μl of DPT, DPS, or DPR. After 30 sec, the cryotubes were directly plunged into liquid nitrogen (LN2) and stored for 1 day to 1 month. Vitrified samples were warmed by immersing the cryotubes in a 40°C water bath and then immediately diluted with 300 μl of 0.3 M trehalose, sucrose, or raffinose in M2. In the SSV method, after equilibration 15–20 embryos were exposed to DPT, DPS, or DPR solutions for around 20 sec before being dropped in 2‐μl drops onto a pre‐cooled (−150 to −180°C) metal surface. Vitrified droplets were stored in cryovials in LN2. Warming was performed by transferring the vitrified droplets into 0.3 M solutions of trehalose, sucrose, or raffinose at 37°C, respectively. Results showed that both SSV and cryotube vitrification methods can result in high rates of in vitro blastocyst development (up to 58.3 and 68.5% with DPR, respectively), not statistically different from that of the controls (58.3 and 64.4%). Even without the equilibration step prior to vitrification, relatively high‐survival rates have been achieved, except for the DPS solution. In conclusion, vitrification of pronuclear‐stage mouse embryos can result in high rates of in vitro development to blastocyst, and the use of raffinose in the vitrification solution is advantageous to improve cryosurvival. Mol. Reprod. Dev. 67:186–192, 2004. © 2004 Wiley‐Liss, Inc.
A Mechanism of Benzoic Acid Biosynthesis in Plants and Bacteria that Mirrors Fatty Acid β‐Oxidation

The aromatic metabolite benzoic acid (1) is a biosynthetic building block of numerous benzoyl and benzyl groups that serve as important structural elements in a large number of natural products. In eukaryotes, for example, benzoate is a component of the zaragozic acids (2), paclitaxel (taxol ; 3), salicylic acid (4), and cocaine (5) (Figure 1). Although rarer in prokaryotic organisms, benzoyl-coenzyme A (benzoyl-CoA) is a starter unit for a few bacterial polyketides, such as enterocin (6) and the wailupemycins. Despite its simple structure and widespread occurrence, the biosynthesis of 1 and its thioester 1-CoA are only partially understood. In the field of plant secondary metabolism, two major routes from L-phenylalanine (7) to benzoic acid have been reported: the b-oxidation-type pathway (Scheme 1, route a) ; and the so-called nonoxidative pathway, via benzaldehyde (11) (Scheme 1, route b). 6, 7] Both routes possess common intermediates like cinnamoyl-CoA (8) and 3-hydroxy-3-phenylpropionyl-CoA (9-CoA) before branching to involve either oxidation and thiolation (route a) or retro-aldol cleavage followed by oxidation (route b). Until recently, the only known pathway from 7 to 1 in bacteria proceeded through two oxidative decarboxylation reactions involving the intermediates phenylpyruvate and phenylglyoxylate. We recently reported that the biosynthesis of 1 in the terrestrial plants Nicotiana attenuata and Cucumis sativus, and the marine actinomycete aStreptomyces maritimuso proceeds by a similar pathway involving the intermediate 3-hydroxy-3-phenylpropionate. Figure 1. Structures of some important natural products containing benzoatederived residues.