202 research outputs found
Compact phases of polymers with hydrogen bonding
We propose an off-lattice model for a self-avoiding homopolymer chain with
two different competing attractive interactions, mimicking the hydrophobic
effect and the hydrogen bond formation respectively. By means of Monte Carlo
simulations, we are able to trace out the complete phase diagram for different
values of the relative strength of the two competing interactions. For strong
enough hydrogen bonding, the ground state is a helical conformation, whereas
with decreasing hydrogen bonding strength, helices get eventually destabilized
at low temperature in favor of more compact conformations resembling
-sheets appearing in native structures of proteins. For weaker hydrogen
bonding helices are not thermodynamically relevant anymore.Comment: 5 pages, 3 figures; revised version published in PR
Magnetic Field Generation in Stars
Enormous progress has been made on observing stellar magnetism in stars from
the main sequence through to compact objects. Recent data have thrown into
sharper relief the vexed question of the origin of stellar magnetic fields,
which remains one of the main unanswered questions in astrophysics. In this
chapter we review recent work in this area of research. In particular, we look
at the fossil field hypothesis which links magnetism in compact stars to
magnetism in main sequence and pre-main sequence stars and we consider why its
feasibility has now been questioned particularly in the context of highly
magnetic white dwarfs. We also review the fossil versus dynamo debate in the
context of neutron stars and the roles played by key physical processes such as
buoyancy, helicity, and superfluid turbulence,in the generation and stability
of neutron star fields.
Independent information on the internal magnetic field of neutron stars will
come from future gravitational wave detections. Thus we maybe at the dawn of a
new era of exciting discoveries in compact star magnetism driven by the opening
of a new, non-electromagnetic observational window.
We also review recent advances in the theory and computation of
magnetohydrodynamic turbulence as it applies to stellar magnetism and dynamo
theory. These advances offer insight into the action of stellar dynamos as well
as processes whichcontrol the diffusive magnetic flux transport in stars.Comment: 41 pages, 7 figures. Invited review chapter on on magnetic field
generation in stars to appear in Space Science Reviews, Springe
Atmospheric effects on extensive air showers observed with the Surface Detector of the Pierre Auger Observatory
Atmospheric parameters, such as pressure (P), temperature (T) and density,
affect the development of extensive air showers initiated by energetic cosmic
rays. We have studied the impact of atmospheric variations on extensive air
showers by means of the surface detector of the Pierre Auger Observatory. The
rate of events shows a ~10% seasonal modulation and ~2% diurnal one. We find
that the observed behaviour is explained by a model including the effects
associated with the variations of pressure and density. The former affects the
longitudinal development of air showers while the latter influences the Moliere
radius and hence the lateral distribution of the shower particles. The model is
validated with full simulations of extensive air showers using atmospheric
profiles measured at the site of the Pierre Auger Observatory.Comment: 24 pages, 9 figures, accepted for publication in Astroparticle
Physic
The Fluorescence Detector of the Pierre Auger Observatory
The Pierre Auger Observatory is a hybrid detector for ultra-high energy
cosmic rays. It combines a surface array to measure secondary particles at
ground level together with a fluorescence detector to measure the development
of air showers in the atmosphere above the array. The fluorescence detector
comprises 24 large telescopes specialized for measuring the nitrogen
fluorescence caused by charged particles of cosmic ray air showers. In this
paper we describe the components of the fluorescence detector including its
optical system, the design of the camera, the electronics, and the systems for
relative and absolute calibration. We also discuss the operation and the
monitoring of the detector. Finally, we evaluate the detector performance and
precision of shower reconstructions.Comment: 53 pages. Submitted to Nuclear Instruments and Methods in Physics
Research Section
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
Mining of nickel laterites – towards more environmentally responsible operations
Primary mining of technology metal ores is needed to enable effective decarbonisation. The use of nickel in rechargeable batteries is expected to increase global demand for nickel rapidly over the coming years. Over 60% of annual global nickel production originates from nickel laterites, with Indonesia and the Philippines leading the market. Mining of nickel laterite ore can adversely affect the environment through the release of CO2 and potentially hazardous elements (PHE), such as hexavalent chromium, or asbestiform minerals. Through our better understanding of the social and environmental impacts of mining operations and the availability of technologies that can potentially mitigate adverse impact, it is paramount to aim for more responsible mining and metal recovery operations.
This study focuses on the Sta Cruz nickel laterite deposit in the Philippines. Through a multi-scale and multi-technique analytical programme and drawing on existing knowledge1,2, we appraise the deposit holistically, focusing on (i) the geochemistry and mineralogy of major commodities and trace metals, such as the platinum group elements; (ii) carbonate forming metals, e.g. magnesium and (iii) the presence and ecotoxicity of PHE and minerals. We use this understanding to assess the potential for a circular economy in mining, via complete utilisation of the ore to maximise the metal output and minimise the waste produced. This includes the removal of CO2 through the formation of carbonate minerals (mineral carbonation). We also investigate the potential of carbonates to immobilise chromium crystallographically alongside the CO2. This aspect of mineral carbonation is currently poorly understood. We have carried out laboratory synthesis of chromium-doped carbonates at ambient P-T conditions, which indicates that the most common magnesium carbonates do not readily accommodate chromium. However, other carbonate-bearing minerals, including those belonging to layered double hydroxides, present a viable alternative. The combined PHE-CO2 mineral carbonation, when implemented at different stages of metal recovery, from ore extraction to processing, could lead to a reduction of the volume and toxicity of waste, collectively contributing to the mitigation of the adverse environmental impact of nickel laterite mining.
[1] Acquino et al (2022) Minerals, 12(3)
[2] Bacuta et al (1990) Journal of Geochem.Exploration, 3
Identification of New SRF Binding Sites in Genes Modulated by SRF Over-Expression in Mouse Hearts
Background To identify in vivo new cardiac binding sites of serum response factor (SRF) in genes and to study the response of these genes to mild over-expression of SRF, we employed a cardiac-specific, transgenic mouse model, with mild over-expression of SRF (Mild-O SRF Tg). Methodology Microarray experiments were performed on hearts of Mild-O-SRF Tg at 6 months of age. We identified 207 genes that are important for cardiac function that were differentially expressed in vivo. Among them the promoter region of 192 genes had SRF binding motifs, the classic CArG or CArG-like (CArG-L) elements. Fifty-one of the 56 genes with classic SRF binding sites had not been previously reported. These SRF-modulated genes were grouped into 12 categories based on their function. It was observed that genes associated with cardiac energy metabolism shifted toward that of carbohydrate metabolism and away from that of fatty acid metabolism. The expression of genes that are involved in transcription and ion regulation were decreased, but expression of cytoskeletal genes was significantly increased. Using public databases of mouse models of hemodynamic stress (GEO database), we also found that similar altered expression of the SRF-modulated genes occurred in these hearts with cardiac ischemia or aortic constriction as well. Conclusion and significance SRF-modulated genes are actively regulated under various physiological and pathological conditions. We have discovered that a large number of cardiac genes have classic SRF binding sites and were significantly modulated in the Mild-O-SRF Tg mouse hearts. Hence, the mild elevation of SRF protein in the heart that is observed during typical adult aging may have a major impact on many SRF-modulated genes, thereby affecting Cardiac structure and performance. The results from our study could help to enhance our understanding of SRF regulation of cellular processes in the aged heart
Genetic Sharing with Cardiovascular Disease Risk Factors and Diabetes Reveals Novel Bone Mineral Density Loci.
Bone Mineral Density (BMD) is a highly heritable trait, but genome-wide association studies have identified few genetic risk factors. Epidemiological studies suggest associations between BMD and several traits and diseases, but the nature of the suggestive comorbidity is still unknown. We used a novel genetic pleiotropy-informed conditional False Discovery Rate (FDR) method to identify single nucleotide polymorphisms (SNPs) associated with BMD by leveraging cardiovascular disease (CVD) associated disorders and metabolic traits. By conditioning on SNPs associated with the CVD-related phenotypes, type 1 diabetes, type 2 diabetes, systolic blood pressure, diastolic blood pressure, high density lipoprotein, low density lipoprotein, triglycerides and waist hip ratio, we identified 65 novel independent BMD loci (26 with femoral neck BMD and 47 with lumbar spine BMD) at conditional FDR < 0.01. Many of the loci were confirmed in genetic expression studies. Genes validated at the mRNA levels were characteristic for the osteoblast/osteocyte lineage, Wnt signaling pathway and bone metabolism. The results provide new insight into genetic mechanisms of variability in BMD, and a better understanding of the genetic underpinnings of clinical comorbidity
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