Atomistic Modeling and Analysis of Hydride Phase Transformation in Palladium Nanoparticles

Palladium-hydrogen (Pd-H) is a prototypical system for studying solute-induced phase transformation in various energy conversion and storage applications. While the behaviors of bulk Pd-H have been studied extensively, the detailed atomic picture of hydride phase transformation within individual Pd nanoparticles is still unclear. In this work, we employ a novel atomistic computational model, referred to as Diffusive Molecular Dynamics (DMD), to characterize the H absorption dynamics in Pd nanoparticles of spherical, octahedral and cubic shapes. The DMD model couples a non-equilibrium thermodynamic model with a discrete diffusion law, which allows it to reach diffusive time scales with atomic resolution. The model is capable of capturing the propagation of an atomistically sharp hydride phase boundary. A remarkable feature of the phase boundary structure that is predicted by the calculations is the emergence of misfit dislocations distributed over the interface. These dislocations relieve the elastic residual stresses induced by the change of volume that accompanies the phase transformation. Shape effects are also investigated in this work. More specifically, in both spherical and octahedral nanoparticles, we observe stacking faults during the H absorption process while the phase boundary in the cubic nanoparticle remains coherent. The spatial distribution of the stacking faults in the spherical sample is investigated in detail using an elastic core-shell model. We also identify the mechanisms that enable the movement of the stacking faults as they track the propagation of the phase boundary. Finally, we find that the rate of H absorption is reduced by the formation and movement of the stacking faults

Atomistic Modeling and Analysis of Hydride Phase Transformation in Palladium Nanoparticles

Palladium-hydrogen (Pd-H) is a prototypical system for studying solute-induced phase transformation in various energy conversion and storage applications. While the behaviors of bulk Pd-H have been studied extensively, the detailed atomic picture of hydride phase transformation within individual Pd nanoparticles is still unclear. In this work, we employ a novel atomistic computational model, referred to as Diffusive Molecular Dynamics (DMD), to characterize the H absorption dynamics in Pd nanoparticles of spherical, octahedral and cubic shapes. The DMD model couples a non-equilibrium thermodynamic model with a discrete diffusion law, which allows it to reach diffusive time scales with atomic resolution. The model is capable of capturing the propagation of an atomistically sharp hydride phase boundary. A remarkable feature of the phase boundary structure that is predicted by the calculations is the emergence of misfit dislocations distributed over the interface. These dislocations relieve the elastic residual stresses induced by the change of volume that accompanies the phase transformation. Shape effects are also investigated in this work. More specifically, in both spherical and octahedral nanoparticles, we observe stacking faults during the H absorption process while the phase boundary in the cubic nanoparticle remains coherent. The spatial distribution of the stacking faults in the spherical sample is investigated in detail using an elastic core-shell model. We also identify the mechanisms that enable the movement of the stacking faults as they track the propagation of the phase boundary. Finally, we find that the rate of H absorption is reduced by the formation and movement of the stacking faults

Diel vertical migrants and the ocean carbon pump: is there a ladder of migration?

Active flux performed by migrant biota is still a gap in the knowledge of the biological pump in the ocean. These organisms mainly feed upon epipelagic zooplankton and transport this carbon due to their feeding at the shallower layers and their defecation, respiration, excretion and mortality at depth. The recent finding that mesopelagic fish biomass in the ocean is one order of magnitude higher indicates that the active flux should be thoroughly evaluated. Here, we show enhanced plankton biomass, ranging from bacteria to zooplankton, reaching down to 4,000 m depth below the Atlantic and Pacific equatorial upwelling systems. We also found a striking close relationship between the zooplankton backscatter enhancement in the epi-, meso- and bathypelagic zones. Backscatter increased in a similar proportion along the subtropical, tropical, and equatorial areas in the three zones. Literature, recent data in subtropical waters, and these results suggest an intense active carbon transport from the epipelagic layer to the deep sea driven by zooplankton and micronekton, enhancing the efficiency of the biological pump and promoting true carbon sequestration beyond 1000 m depth.MALASPINA (CSD2008 00077) MAFIA (CTM2012-39587-C04

Improved prediction of mortality by combinations of inflammatory markers and standard clinical scores in patients with acute-on-chronic liver failure and acute decompensation

BACKGROUND AND AIM: Acute-on-chronic liver failure (ACLF) as a sinister prognosis and there is a need for accurate biomarkers and scoring systems to better characterize ACLF patients and predict prognosis. Systemic inflammation and renal failure are hallmarks in ACLF disease development and progression. We hypothesized that the combination of specific inflammatory markers in combination with clinical scores are better predictors of survival than the originally developed CLIF-C acute decompensation (AD) and CLIF-C ACLF scores. METHODS: We re-evaluated all previously measured inflammatory markers in 522 patients from the CANONIC study, 342 without and 180 with ACLF. We used the Harrell's C-index to determine the best marker alone or in combination with the original scores and calculated new scores for prediction of mortality in the original CANONIC cohort. RESULTS: The best markers to predict 90-day mortality in patients without ACLF were the plasma macrophage activation markers soluble (s)CD163 and mannose receptor (sMR). Urinary neutrophil gelatinase associated lipocalin (UNGAL) and sCD163 were predictors for 28-day mortality in patients with ACLF. The new developed CLIF-C AD+sMR score in patients without ACLF improved 90-days mortality prediction compared to the original CLIF-C AD score (C-index 0.82(0.78-0.86) vs. 0.74(0.70-0.78, P=0.004). Further, the new CLIF-C ACLF+sCD163+UNGAL improved the original CLIF-C ACLF score for 28-days mortality (0.85(0.79-0.91) vs. 0.75(0.70-0.80), P=0.039). CONCLUSIONS: The capability of these inflammatory markers to improve the original prognostic scores in cirrhosis patients without and with ACLF points to a key role of macrophage activation and inflammation in the development and progression of AD and ACLF

ERCC6L2 mitigates replication stress and promotes centromere stability

Structurally complex genomic regions, such as centromeres, are inherently difficult to duplicate. The mechanism behind centromere inheritance is not well understood, and one of the key questions relates to the reassembly of centromeric chromatin following DNA replication. Here, we define ERCC6L2 as a key regulator of this process. ERCC6L2 accumulates at centromeres and promotes deposition of core centromeric factors. Interestingly, ERCC6L2−/− cells show unrestrained replication of centromeric DNA, likely caused by the erosion of centromeric chromatin. Beyond centromeres, ERCC6L2 facilitates replication at genomic repeats and non-canonical DNA structures. Notably, ERCC6L2 interacts with the DNA-clamp PCNA through an atypical peptide, presented here in a co-crystal structure. Finally, ERCC6L2 also restricts DNA end resection, acting independently of the 53BP1-REV7-Shieldin complex. We propose a mechanistic model, which reconciles seemingly distinct functions of ERCC6L2 in DNA repair and DNA replication. These findings provide a molecular context for studies linking ERCC6L2 to human disease

Late Cretaceous continental and marine vertebrate assemblages of the Laño Quarry (Basque-Cantabrian Region, Iberian Peninsula): an update

The vertebrate-bearing beds of the Laño quarry (Condado de Treviño) are among the most relevant sites from the Late Cretaceous of Europe. Geologically, Laño and the adjacent region are set on the southern limb of the South-Cantabrian Synclinorium (SE Basque-Cantabrian Region, northern Iberian Peninsula). The Laño sites were discovered in 1984; thousands of bones and teeth, including microfossils, have been collected during the prospection in the field and excavation campaigns. The vertebrate remains occur at two different stratigraphic horizons within a continental to shallow marine succession of Late Campanian-Maastrichtian age. The lower horizon contains the Laño 1 and Laño 2 sites, whereas the upper horizon contains the Albaina site. In the Laño sites, three fossiliferous beds (called L1A, L1B and L2) are known within an alluvial system composed mainly of fluvial sands and silts. The sedimentary structures are consistent with channel areas within an extensive braided river system. Based mainly on stratigraphic correlations, the fluvial beds of Laño are regarded as Late Campanian to Early Maastrichtian in age. These deposits have yielded a very diverse vertebrate assemblage, which consists of nearly 40 species, including actinopterygians, lissamphibians, lepidosaurs, turtles, crocodyliforms, dinosaurs, pterosaurs, and mammals. Seven genera and ten species have been erected to date in Laño. With reference to the marine vertebrate association of Albaina, it consists of at least 37 species, including sharks and rays, actinopterygians, mosasaurids, and plesiosaurs. Two genera and species of rhinobatoids (family indet.) and two new species of rhinobatids have been erected in Albaina. The fossil association indicates a Late (but not latest) Maastrichtian age. Recently, isolated turtle and dinosaur fossils have been discovered in the sublittoral beds of Albaina. The Laño quarry is one of the most noteworthy Campanian-Maastrichtian vertebrate localities of Europe by its taxonomic diversity, and provides useful information about the composition and affinities of both continental and marine vertebrate faunas from the latest Cretaceous of southwestern Europe.Los niveles con fósiles de vertebrados de la cantera de Laño (Condado de Treviño) se cuentan entre los más importantes del Cretácico Superior de Europa. Desde un punto de vista geológico, Laño y la región adyacente forman parte del flanco sur del Sinclinorio Subcantábrico (SE de la Región Vasco-Cantábrica). El descubrimiento de los niveles fosilíferos remonta a 1984; las prospecciones de campo y las campañas de excavación han proporcionado miles de huesos y dientes, incluyendo microfósiles. Los restos de vertebrados aparecen en dos horizontes estratigráficos diferentes formando parte de una sucesión continental a marina litoral de edad Campaniense superior a Maastrichtiense. El horizonte inferior contiene los yacimientos de Laño 1 y Laño 2, mientras que el superior contiene solo uno: Albaina. En los yacimientos de Laño, se reconocen tres niveles fosilíferos (llamados L1A, L1B y L2) formados en el seno de un sistema aluvial compuesto por arenas y limos fluviales. Las estructuras sedimentarias indican áreas de canal dentro de un sistema trenzado muy extendido. Según las correlaciones estratigráficas, los depósitos fluviales de Laño son de edad Campaniense superior a Maastrichtiense inferior. Estos depósitos han proporcionado una asociación muy diversa de vertebrados, que consiste en cerca de 40 especies, incluyendo actinopterigios, lisanfibios, lepidosaurios, tortugas, cocodrilos, dinosaurios, pterosaurios y mamíferos. En Laño se han definido hasta el momento siete géneros y diez especies. Por lo que respecta a la asociación de vertebrados marinos de Albaina, se han reconocido al menos 37 especies, que incluyen tiburones y rayas, actinopterigios, mosasaurios y plesiosaurios. Hasta la fecha se han definido en Albaina cuatro nuevos rinobatoideos: dos especies de rinobátidos y dos géneros y especies cuya familia es indeterminada. La asociación fósil es de edad Maastrichtiense superior no terminal. Recientemente se ha descrito el hallazgo de restos fósiles aislados de tortugas y dinosaurios en los niveles marinos de Albaina. La cantera de Laño es una de las localidades de vertebrados más destacadas del Campaniense-Maastrichtiense por su diversidad taxonómica, y proporciona información relevante sobre la composición y afinidades de las faunas de vertebrados continentales y marinos del Cretácico final del suroeste de Europa

Iron bioavailability in two commercial cultivars of wheat: a comparison between wholegrain and white flour and the effects of nicotianamine and 2'-deoxymugineic acid on iron uptake into Caco-2 cells

Iron bioavailability in unleavened white and wholegrain bread made from two commercial wheat varieties was assessed by measuring ferritin production in Caco-2 cells. The breads were subjected to simulated gastrointestinal digestion and the digests applied to the Caco-2 cells. Although Riband grain contained a lower iron concentration than Rialto, iron bioavailability was higher. No iron was taken up by the cells from white bread made from Rialto flour or from wholegrain bread from either variety, but Riband white bread produced a small ferritin response. The results probably relate to differences in phytate content of the breads, although iron in soluble monoferric phytate was demonstrated to be bioavailable in the cell model. Nicotianamine, an iron chelator in plants involved in iron transport, was a more potent enhancer of iron uptake into Caco-2 cells than ascorbic acid or 2'-deoxymugineic acid, another metal chelator present in plants

Gram-negative prosthetic joint infection: outcome of a debridement, antibiotics and implant retention approach. A large multicentre study

AbstractWe aim to evaluate the epidemiology and outcome of gram-negative prosthetic joint infection (GN-PJI) treated with debridement, antibiotics and implant retention (DAIR), identify factors predictive of failure, and determine the impact of ciprofloxacin use on prognosis. We performed a retrospective, multicentre, observational study of GN-PJI diagnosed from 2003 through to 2010 in 16 Spanish hospitals. We define failure as persistence or reappearance of the inflammatory joint signs during follow-up, leading to unplanned surgery or repeat debridement >30 days from the index surgery related death, or suppressive antimicrobial therapy. Parameters predicting failure were analysed with a Cox regression model. A total of 242 patients (33% men; median age 76 years, interquartile range (IQR) 68–81) with 242 episodes of GN-PJI were studied. The implants included 150 (62%) hip, 85 (35%) knee, five (2%) shoulder and two (1%) elbow prostheses. There were 189 (78%) acute infections. Causative microorganisms were Enterobacteriaceae in 78%, Pseudomonas spp. in 20%, and other gram-negative bacilli in 2%. Overall, 19% of isolates were ciprofloxacin resistant. DAIR was used in 174 (72%) cases, with an overall success rate of 68%, which increased to 79% after a median of 25 months' follow-up in ciprofloxacin-susceptible GN-PJIs treated with ciprofloxacin. Ciprofloxacin treatment exhibited an independent protective effect (adjusted hazard ratio (aHR) 0.23; 95% CI, 0.13–0.40; p <0.001), whereas chronic renal impairment predicted failure (aHR, 2.56; 95% CI, 1.14–5.77; p 0.0232). Our results confirm a 79% success rate in ciprofloxacin-susceptible GN-PJI treated with debridement, ciprofloxacin and implant retention. New therapeutic strategies are needed for ciprofloxacin-resistant PJI

Structural and Functional Analyses of Five Conserved Positively Charged Residues in the L1 and N-Terminal DNA Binding Motifs of Archaeal RadA Protein

RecA family proteins engage in an ATP-dependent DNA strand exchange reaction that includes a ssDNA nucleoprotein helical filament and a homologous dsDNA sequence. In spite of more than 20 years of efforts, the molecular mechanism of homology pairing and strand exchange is still not fully understood. Here we report a crystal structure of Sulfolobus solfataricus RadA overwound right-handed filament with three monomers per helical pitch. This structure reveals conformational details of the first ssDNA binding disordered loop (denoted L1 motif) and the dsDNA binding N-terminal domain (NTD). L1 and NTD together form an outwardly open palm structure on the outer surface of the helical filament. Inside this palm structure, five conserved basic amino acid residues (K27, K60, R117, R223 and R229) surround a 25 Å pocket that is wide enough to accommodate anionic ssDNA, dsDNA or both. Biochemical analyses demonstrate that these five positively charged residues are essential for DNA binding and for RadA-catalyzed D-loop formation. We suggest that the overwound right-handed RadA filament represents a functional conformation in the homology search and pairing reaction. A new structural model is proposed for the homologous interactions between a RadA-ssDNA nucleoprotein filament and its dsDNA target