Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Vascular Calcification by Osteoclast Regulatory Factors RANKL and Osteoprotegerin

Vascular calcification often occurs with advancing age, atherosclerosis, various metabolic disorders such as diabetes mellitus and end-stage renal disease, or in rare genetic diseases, leading to serious clinical consequences. Such mineralization can occur at various sites (cardiac valves, arterial intima or media, capillaries), involve localized or diffuse widespread calcification, and result from numerous causes that provoke active inflammatory and osteogenic processes or disordered mineral homeostasis. Although valuable research has defined many key factors and cell types involved, surprising new insights continue to arise that deepen our understanding and suggest novel research directions or strategies for clinical intervention in calcific vasculopathies. One emerging area in vascular biology involves the RANKL/RANK/OPG system, molecules of the tumor necrosis factor-related family recently discovered to be critical regulators of immune and skeletal biology. Evidence is accumulating that such signals may be expressed, regulated, and function in vascular physiology and pathology in unique ways to promote endothelial cell survival, angiogenesis, monocyte or endothelial cell recruitment, and smooth muscle cell osteogenesis and calcification. Concerted research efforts are greatly needed to understand these potential roles, clarify whether RANKL (receptor activator of nuclear factor &kgr;B ligand) promotes and osteoprotegerin (OPG) protects against vascular calcification, define how OPG genetic polymorphisms relate to cardiovascular disease, and learn whether elevated serum OPG levels reflect endothelial dysfunction in patients. Overall, the RANKL/RANK/OPG system may mediate important and complex links between the vascular, skeletal, and immune systems. Thus, these molecules may play a central role in regulating the development of vascular calcification coincident with declines in skeletal mineralization with age, osteoporosis, or disease.
Observational constraints on Arctic Ocean clouds and radiative fluxes during the early 21st century

Arctic Ocean observations are combined to create a cloud and radiation climatology for the early 21st century (March 2000 to February 2011). Data sources include: active (CloudSat, CALIPSO) and passive (MODIS) satellite cloud observations, observed top‐of‐atmosphere (TOA) radiative fluxes (CERES‐EBAF), observationally constrained radiative flux calculations (2B‐FLXHR‐LIDAR), and observationally constrained cloud forcing calculations (CERES‐EBAF, 2B‐FLXHR‐LIDAR). Uncertainty in flux calculations is dominated by cloud uncertainty, not surface albedo uncertainty. The climatology exposes large geographic, seasonal, and interannual variability cloud forcing, but on average, Arctic Ocean clouds warm the surface (+10 W m−2, in 2B‐FLXHR‐LIDAR) and cool the TOA (−12 W m−2, in CERES‐EBAF and 2B‐FLXHR‐LIDAR). Shortwave TOA cloud cooling and longwave TOA cloud warming are stronger in 2B‐FLXHR‐LIDAR than in CERES‐EBAF, but these two differences compensate each other, yielding similar net TOA values. During the early 21st century, summer TOA albedo decreases are consistent with sea ice loss but are unrelated to summer cloud trends that are statistically insignificant. In contrast, both sea ice variability and cloud variability contribute to interannual variability in summer shortwave radiative fluxes. Summer 2007 had the largest persistent cloud, radiation, and sea ice anomalies in the climatology. During that summer, positive net shortwave radiation anomalies exceeded 20 W m−2 over much of the Arctic Ocean. This enhanced shortwave absorption resulted primarily from cloud reductions during early summer and sea ice loss during late summer. In summary, the observations show that while cloud variability influences absorbed shortwave radiation variability, there is no summer cloud trend affecting summer absorbed shortwave radiation.
Root-root interactions: extending our perspective to be more inclusive of the range of theories in ecology and agriculture using in-vivo analyses.

BACKGROUND There is a large body of literature on competitive interactions among plants, but many studies have only focused on above-ground interactions and little is known about root-root dynamics between interacting plants. The perspective on possible mechanisms that explain the outcome of root-root interactions has recently been extended to include non-resource-driven mechanisms (as well as resource-driven mechanisms) of root competition and positive interactions such as facilitation. These approaches have often suffered from being static, partly due to the lack of appropriate methodologies for in-situ non-destructive root characterization. SCOPE Recent studies show that interactive effects of plant neighbourhood interactions follow non-linear and non-additive paths that are hard to explain. Common outcomes such as accumulation of roots mainly in the topsoil cannot be explained solely by competition theory but require a more inclusive theoretical, as well as an improved methodological framework. This will include the question of whether we can apply the same conceptual framework to crop versus natural species. CONCLUSIONS The development of non-invasive methods to dynamically study root-root interactions in vivo will provide the necessary tools to study a more inclusive conceptual framework for root-root interactions. By following the dynamics of root-root interactions through time in a whole range of scenarios and systems, using a wide variety of non-invasive methods, (such as fluorescent protein which now allows us to separately identify the roots of several individuals within soil), we will be much better equipped to answer some of the key questions in root physiology, ecology and agronomy.
Exploring Single-Cell Data with Deep Multitasking

4 Biomedical researchers are generating high-throughput, high-dimensional single-cell 5 data at a staggering rate. As costs of data generation decrease, experimental design is mov6 ing towards measurement of many different single-cell samples in the same dataset. These 7 samples can correspond to different patients, conditions, or treatments. While scalability of 8 methods to datasets of these sizes is a challenge on its own, dealing with large-scale exper9 imental design presents a whole new set of problems, including batch effects and sample 10
KIAA0101 Interacts with BRCA1 and Regulates Centrosome Number

To find genes and proteins that collaborate with BRCA1 or BRCA2 in the pathogenesis of breast cancer, we used an informatics approach and found a candidate BRCA interactor, KIAA0101, to function like BRCA1 in exerting a powerful control over centrosome number. The effect of KIAA0101 on centrosomes is likely direct, as its depletion does not affect the cell cycle, KIAA0101 localizes to regions coincident with the centrosomes, and KIAA0101 binds to BRCA1. We analyzed whether KIAA0101 protein is overexpressed in breast cancer tumor samples in tissue microarrays, and we found that overexpression of KIAA0101 correlated with positive Ki67 staining, a biomarker associated with increased disease severity. Furthermore, overexpression of the KIAA0101 gene in breast tumors was found to be associated with significantly decreased survival time. This study identifies KIAA0101 as a protein important for breast tumorigenesis, and as this factor has been reported as a UV repair factor, it may link the UV damage response to centrosome control. Mol Cancer Res; 9(8); 1091–9. ©2011 AACR.
The Effects of Ageing and Visual Noise on Conceptual Integration during Sentence Reading

The effortfulness hypothesis implies that difficulty in decoding the surface form, as in the case of age-related sensory limitations or background noise, consumes the attentional resources that are then unavailable for semantic integration in language comprehension. Because ageing is associated with sensory declines, degrading of the surface form by a noisy background can pose an extra challenge for older adults. In two experiments, this hypothesis was tested in a self-paced moving window paradigm in which younger and older readers’ online allocation of attentional resources to surface decoding and semantic integration was measured as they read sentences embedded in varying levels of visual noise. When visual noise was moderate (Experiment 1), resource allocation among young adults was unaffected but older adults allocated more resources to decode the surface form at the cost of resources that would otherwise be available for semantic processing; when visual noise was relatively intense (Experiment 2), both younger and older participants allocated more attention to the surface form and less attention to semantic processing. The decrease in attentional allocation to semantic integration resulted in reduced recall of core ideas in both experiments, suggesting that a less organized semantic representation was constructed in noise. The greater vulnerability of older adults at relatively low levels of noise is consistent with the effortfulness hypothesis.
Response: Barometer of Life

Collen and Baillie argue that expanding the IUCN Red List into a broader Barometer of Life will sometimes require making use of representative samples of sets of species ([ 1 ][1], [ 2 ][2]). We agree, and indeed the numbers we proposed assumed sampled assessments for many nonchordate taxa, for
The effect of oxidation on the Verwey transition in magnetite

At the Verwey transition (Tv≈110–120 K), magnetite transforms from monoclinic to cubic spinel structure. It has long been believed that magnetic remanence and susceptibility would change markedly at Tv in the case of coarse grains but only slightly or inappreciably in the case of fine (<1 µm) grains. We find on the contrary that remanence changes at Tv by 50–80% in both large and small crystals, if they are stoichiometric. However, minor surface oxidation suppresses the transition, and the fact that fine grains oxidize more readily leads to an apparent size dependence. Our experiments used submicron magnetite cubes with mean sizes of 0.037, 0.076, 0.10 and 0.22 µm which were initially non-stoichiometric (oxidation parameter z from 0.2–0.7). A saturation isothermal remanent magnetization (SIRM) given in a 2.5 T field at 5 K decreased steadily during zero-field warming to 300 K with little or no indication of the Verwey transition. After the oxidized surface of each crystal was reduced to stoichiometric magnetite, the SIRM decreased sharply during warming by 50–80% around 110 K. The change in SIRM for the 0.22 µm grains was almost identical to that measured for a 1.5 mm natural magnetite crystal. Thus a 1012 change in particle volume does not materially affect the remanence transition at Tv but oxidation to z=0.3 essentially suppresses the transition. The effect of the degree of oxidation on Tv provides a sensitive test for maghemitization in soils, sediments and rocks.
Globular cluster x-ray sources

Globular clusters and x-ray astronomy have a long and fruitful history. Uhuru and OSO-7 revealed highly luminous (> 1036 ergs-1) x-ray sources in globular clusters, and Einstein and ROSAT revealed a larger population of low-luminosity (< 1033 ergs-1) x-ray sources. It was realized early on that the high-luminosity sources were low-mass x-ray binaries in outburst and that they were orders of magnitude more abundant per unit mass in globular clusters than in the rest of the galaxy. However, the low-luminosity sources proved difficult to classify. Many ideas were put forth—low-mass x-ray binaries in quiescence (qLMXBs), cataclysmic variables (CVs), active main-sequence binaries (ABs), and millisecond pulsars (MSPs)—but secure identifications were scarce. In ROSAT observations of 55 clusters, about 25 low-luminosity sources were found. Chandra has now observed over 80 Galactic globular clusters, and these observations have revealed over 1,500 x-ray sources. The superb angular resolution has allowed for many counterpart identifications, providing clues to the nature of this population. It is a heterogeneous mix of qLMXBs, CVs, ABs, and MSPs, and it has been shown that the qLMXBs and CVs are both, in part, overabundant like the luminous LMXBs. The number of x-ray sources in a cluster correlates very well with its encounter frequency. This points to dynamical formation scenarios for the x-ray sources and shows them to be excellent tracers of the complicated internal dynamics. The relation between the encounter frequency and the number of x-ray sources has been used to suggest that we have misunderstood the dynamical states of globular clusters.
RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions

Prokaryotes have evolved multiple versions of an RNA-guided adaptive immune system that targets foreign nucleic acids. In each case, transcripts derived from clustered regularly interspaced short palindromic repeats (CRISPRs) are thought to selectively target invading phage and plasmids in a sequence-specific process involving a variable cassette of CRISPR-associated (cas) genes. The CRISPR locus in Pseudomonas aeruginosa (PA14) includes four cas genes that are unique to and conserved in microorganisms harboring the Csy-type (CRISPR system yersinia) immune system. Here we show that the Csy proteins (Csy1–4) assemble into a 350 kDa ribonucleoprotein complex that facilitates target recognition by enhancing sequence-specific hybridization between the CRISPR RNA and complementary target sequences. Target recognition is enthalpically driven and localized to a “seed sequence” at the 5′ end of the CRISPR RNA spacer. Structural analysis of the complex by small-angle X-ray scattering and single particle electron microscopy reveals a crescent-shaped particle that bears striking resemblance to the architecture of a large CRISPR-associated complex from Escherichia coli, termed Cascade. Although similarity between these two complexes is not evident at the sequence level, their unequal subunit stoichiometry and quaternary architecture reveal conserved structural features that may be common among diverse CRISPR-mediated defense systems.
Unravelling the Stability and Capsid Dynamics of the Three Virions of Brome Mosaic Virus Assembled Autonomously In Vivo

Viral capsids are dynamic assemblies that undergo controlled conformational transitions to perform various biological functions. The replicated three-molecule RNA progeny of Brome mosaic virus (BMV) are packaged by a single capsid protein (CP) into three types of morphologically indistinguishable icosahedral virions with T=3 quasi-symmetry. Type 1 (B1v) and type 2 (B2v) virions respectively package genomic RNA1 or RNA2, while type 3 (B3+4v) co-packages genomic RNA3 (B3) and its sub-genomic RNA4 (B4). In this study, the application of a robust Agrobacterium-mediated transient expression system allowed us to assemble each virion type separately in planta. Physical and biochemical approaches analyzing the morphology, size, and electrophoretic mobility failed to distinguish between the virion types, so protease-based mapping experiments were used to analyze the conformational dynamics of the individual virions. The crystallographic structure of the BMV capsid shows four trypsin-cleavage sites (K65, R103, K111 and K165 on the A, B and C subunits) exposed on the exterior of the capsid. Irrespective of the digestion time, while retaining their capsid structural integrity, B1v and B2v released only two peptides involving amino acids 2-8 and 16-22 from the N-proximal arginine-rich RNA binding motif. In contrast, B3+4v capsids are unstable to trypsin, releasing several peptides in addition to the four sites predicted to be exposed on the capsid exterior. These results, demonstrating qualitatively different dynamics for the three types of BMV virions, suggest that the different RNA genes they contain may have different translational timing and efficiency and may even impart different structures to their capsids. IMPORTANCE The majority of viruses contain RNA genomes protected by a shell of capsid proteins. Although crystallographic studies show that viral capsids are static structures, accumulating evidence suggests that in solution virions are highly dynamic assemblies. The three genomic RNAs (RNAs 1, 2 and 3) and a single subgenomic RNA (RNA4) of Brome mosaic virus (BMV), an RNA virus pathogenic to plants, are distributed among three physically homogeneous virions. This study examines the capsid dynamics by MALDI-TOF analyses following trypsin digestion of the three virions assembled separately in vivo using the Agrobacterium-mediated transient expression approach. The results provide compelling evidence that virions packaging genomic RNAs1 and 2 are more stable and dynamically distinct from those co-packaging RNA3 and 4, suggesting that RNA-dependent capsid dynamics play an important biological role in the viral life cycle.
Effects of Food Price Shocks on Child Malnutrition

A propitiously timed household survey carried out in Mozambique over the period 2008-09 permits us to evaluate the short-to-medium run relationship between sudden shocks to food prices and child nutrition status. We link local price inflation with child malnutrition status. We find that the prevalence of underweight amongst children rises in response to a higher inflation rate for basic food products. Stunting and wasting malnutrition measures are mostly insensitive to the inflation rate. The very high food inflation during 2008/09 was responsible for an extra 39,000 moderately underweight and 24,000 severely underweight children.
The New Statistics Why and How

We need to make substantial changes to how we conduct research. First, in response to heightened concern that our published research literature is incomplete and untrustworthy, we need new requirements to ensure research integrity. These include prespecification of studies whenever possible, avoidance of selection and other inappropriate data- analytic practices, complete reporting, and encouragement of replication. Second, in response to renewed recognition of the severe flaws of null-hypothesis significance testing (NHST), we need to shift from reliance on NHST to estimation and other preferred techniques. The new statistics refers to recommended practices, including estimation based on effect sizes, confidence intervals, and meta-analysis. The techniques are not new, but adopting them widely would be new for many researchers, as well as highly beneficial. This article explains why the new statistics are important and offers guidance for their use. It describes an eight-step new-statistics strategy for research with integrity, which starts with formulation of research questions in estimation terms, has no place for NHST, and is aimed at building a cumulative quantitative discipline.
Caracterização e evolução geoquímica das águas subterrâneas da mina de Candiota (RS), Brasil

In order to evaluate the mining activities influences of Candiota Mine, the largest Brazilian coal reserve, over the groundwater quality, geochemical studies were carried out on water and paralic sandstones of the Rio Bonito Formation, which constitutes a granular aquifers system. Geochemical modeling indicates that for most cases, groundwater is subsatured in relation to the balance water-carbonates and supersatured in relation to the balance water-goethite and –kaolinite. The phisico-chemical results of the water samples showed little evidence of significant acidification or sulphatisation of groundwater by acid mine drainage of mining activities. A natural but limited pyrite oxidation by the restricted entrance of oxygen in the aquifer system seems to be responsible for the positive correlations between sulphate and iron. However, the iron contents is lower than the expected value from pyrite dissolution which can be explained by the precipitation of Fe-oxi-hydroxides (e.g. goethite). The dissolution of carbonates (calcite, siderite and ankerite) is an important process of the neutralization of acidity, controlling the chemical composition of the groundwater by consuming protons and releasing Ca 2+ and Mg 2+ . Relatively to the superficial waters, calcium and magnesium are more significantly depleted than sodium and potassium in the groundwater, probably related to the selective adsorption. For the calcium-bicarbonate correlation, atmospheric and soil CO 2 as well as organic matter oxidation are considered to contribute to the increase in the total content of bicarbonate.
Indirect gradient analysis of the Mangal formation of Gazi bay (Kenya)

(1) Based on vegetation releves of sample units along transects perpendicular to the coastline, the mangal ecosystem of Gazi Bay (Kenya) has been investigated. (2) An indirect gradient analysis is performed by the ordination method Detrended Correspondence Analysis. (3) The first ordination axis can be interpreted in terms of resistance of the different species to flooding. (4) A similar zonation pattern is found as described by WALTER & STEINER (1936). (5) Zonation is closely connected with morphological and ecophysiological features of the mangrove species. Therefore stomatal density has been measured. Sonneratia has by far the lowest stomatal density, Lumnitzera the highest.
Design, fabrication, and testing of an electrohydrodynamic ion-drag micropump

This paper presents the design, fabrication, and testing of a novel electrohydrodynamic (EHD) ion-drag micropump. In order to maximize the electrical field gradients that are responsible for EHD pumping, we incorporated three-dimensional (3-D) triangular bumps of solder as part of the EHD electrodes. To form these bumps, Niobium was sputter-deposited onto a ceramic substrate, coated with photoresist, optically exposed and etched using a reactive ion etcher to define the electrode pattern. The substrate was then "dipped" into a molten solder pool. Since the solder adheres only to the metallic film, bumps of solder form on the electrodes, giving the electrodes a significant 3-D character. The overall dimensions of the micropump are 19 mm /spl times/ 32 mm /spl times/ 1.05 mm. Four different designs were fabricated and tested. Static pressure tests were performed with a 3M Thermal Fluid (HFE-7100) as the working fluid and the optimum design was identified. The results with the thermal fluid were highly promising and indicated a pumping head of up to 700 Pa at an applied voltage of 300 V. The experimental results for the four different designs show that the presence of the 3-D bump structures significantly improves the pumping performance. Also, a much better pumping performance was obtained with the micropump in which the emitter had a saw-tooth shape.