The Optical Model of The Nucleus. An Indexed and Abstracted Literature Review

All available literature, dealing with optical model calculations, has been reviewed to aid in assessing suitable well parameters and to indicate when the model has been successful in predicting various nuclear data. The material investigated has been indexed according to nuclide, and short abstracts have been prepared to provide a concise summary of the contents and main results. 342 references were examined

Large-scale collective action to avoid an Amazon tipping point - key actors and interventions

The destruction of the Amazon is a major global environmental issue, not only because of greenhouse gas emissions or direct impacts on biodiversity and livelihoods, but also due to the forest\u27s role as a tipping element in the Earth System. With nearly a fifth of the Amazon already lost, there are already signs of an imminent forest dieback process that risks transforming much of the rainforest into a drier ecosystem, with climatic implications across the globe. There is a large body of literature on the underlying drivers of Amazon deforestation. However, insufficient attention has been paid to the behavioral and institutional microfoundations of change. Fundamental issues concerning cooperation, as well as the mechanisms facilitating or hampering such actions, can play a much more central role in attempts to unravel and address Amazon deforestation. We thus present the issue of preventing the Amazon biome from crossing a biophysical tipping point as a large-scale collective action problem. Drawing from collective action theory, we apply a novel analytical framework on Amazon conservation, identifying six variables that synthesize relevant collective action stressors and facilitators: information, accountability, harmony of interests, horizontal trust, knowledge about consequences, and sense of responsibility. Drawing upon literature and data, we assess Amazon deforestation and conservation through our heuristic lens, showing that while growing transparency has made information availability a collective action facilitator, lack of accountability, distrust among actors, and little sense of responsibility for halting deforestation remain key stressors. We finalize by discussing interventions that can help break the gridlock

Benchmarking van der Waals Density Functionals with Experimental Data: Potential Energy Curves for H2 Molecules on Cu(111), (100), and (110) Surfaces

Detailed physisorption data from experiment for the H_2 molecule on low-index Cu surfaces challenge theory. Recently, density-functional theory (DFT) has been developed to account for nonlocal correlation effects, including van der Waals (dispersion) forces. We show that the functional vdW-DF2 gives a potential-energy curve, potential-well energy levels, and difference in lateral corrugation promisingly close to the results obtained by resonant elastic backscattering-diffraction experiments. The backscattering barrier is found selective for choice of exchange-functional approximation. Further, the DFT-D3 and TS-vdW corrections to traditional DFT formulations are also benchmarked, and deviations are analyzed.Comment: 15 pages, 9 figure

RSpred, a set of Hidden Markov Models to detect and classify the RIFIN and STEVOR proteins of Plasmodium falciparum

<p>Abstract</p> <p>Background</p> <p>Many parasites use multicopy protein families to avoid their host's immune system through a strategy called antigenic variation. RIFIN and STEVOR proteins are variable surface antigens uniquely found in the malaria parasites <it>Plasmodium falciparum </it>and <it>P. reichenowi</it>. Although these two protein families are different, they have more similarity to each other than to any other proteins described to date. As a result, they have been grouped together in one Pfam domain. However, a recent study has described the sub-division of the RIFIN protein family into several functionally distinct groups. These sub-groups require phylogenetic analysis to sort out, which is not practical for large-scale projects, such as the sequencing of patient isolates and meta-genomic analysis.</p> <p>Results</p> <p>We have manually curated the <it>rif </it>and <it>stevor </it>gene repertoires of two <it>Plasmodium falciparum </it>genomes, isolates DD2 and HB3. We have identified 25% of mis-annotated and ~30 missing <it>rif </it>and <it>stevor </it>genes. Using these data sets, as well as sequences from the well curated reference genome (isolate 3D7) and field isolate data from Uniprot, we have developed a tool named RSpred. The tool, based on a set of hidden Markov models and an evaluation program, automatically identifies STEVOR and RIFIN sequences as well as the sub-groups: A-RIFIN, B-RIFIN, B1-RIFIN and B2-RIFIN. In addition to these groups, we distinguish a small subset of STEVOR proteins that we named STEVOR-like, as they either differ remarkably from typical STEVOR proteins or are too fragmented to reach a high enough score. When compared to Pfam and TIGRFAMs, RSpred proves to be a more robust and more sensitive method. We have applied RSpred to the proteomes of several <it>P. falciparum </it>strains, <it>P. reichenowi, P. vivax</it>, <it>P. knowlesi </it>and the rodent malaria species. All groups were found in the <it>P. falciparum </it>strains, and also in the <it>P. reichenowi </it>parasite, whereas none were predicted in the other species.</p> <p>Conclusions</p> <p>We have generated a tool for the sorting of RIFIN and STEVOR proteins, large antigenic variant protein groups, into homogeneous sub-families. Assigning functions to such protein families requires their subdivision into meaningful groups such as we have shown for the RIFIN protein family. RSpred removes the need for complicated and time consuming phylogenetic analysis methods. It will benefit both research groups sequencing whole genomes as well as others working with field isolates. RSpred is freely accessible via <url>http://www.ifm.liu.se/bioinfo/</url>.</p

Model of the complex of Parathyroid hormone-2 receptor and Tuberoinfundibular peptide of 39 residues

<p>Abstract</p> <p>Background</p> <p>We aim to propose interactions between the parathyroid hormone-2 receptor (PTH2R) and its ligand the tuberoinfundibular peptide of 39 residues (TIP39) by constructing a homology model of their complex. The two related peptides parathyroid hormone (PTH) and parathyroid hormone related protein (PTHrP) are compared with the complex to examine their interactions.</p> <p>Findings</p> <p>In the model, the hydrophobic N-terminus of TIP39 is buried in a hydrophobic part of the central cavity between helices 3 and 7. Comparison of the peptide sequences indicates that the main discriminator between the agonistic peptides TIP39 and PTH and the inactive PTHrP is a tryptophan-phenylalanine replacement. The model indicates that the smaller phenylalanine in PTHrP does not completely occupy the binding site of the larger tryptophan residue in the other peptides. As only TIP39 causes internalisation of the receptor and the primary difference being an aspartic acid in position 7 of TIP39 that interacts with histidine 396 in the receptor, versus isoleucine/histidine residues in the related hormones, this might be a trigger interaction for the events that cause internalisation.</p> <p>Conclusions</p> <p>A model is constructed for the complex and a trigger interaction for full agonistic activation between aspartic acid 7 of TIP39 and histidine 396 in the receptor is proposed.</p

Factors promoting health-related quality of life in people with rheumatic diseases: a 12 month longitudinal study

<p>Abstract</p> <p>Background</p> <p>Rheumatic diseases have a significant adverse impact on the individual from physical, mental and social aspects, resulting in a low health-related quality of life (HRQL). There is a lack of longitudinal studies on HRQL in people with rheumatic diseases that focus on factors promoting HRQL instead of risk factors. The aim of this study was to investigate the associations between suggested health promoting factors at baseline and outcome in HRQL at a 12 month follow-up in people with rheumatic diseases.</p> <p>Methods</p> <p>A longitudinal cohort study was conducted in 185 individuals with rheumatic diseases with questionnaires one week and 12 months after rehabilitation in a Swedish rheumatology clinic. HRQL was assessed by SF-36 together with suggested health factors. The associations between SF-36 subscales and the health factors were analysed by multivariable logistic regressions.</p> <p>Results</p> <p>Factors predicting better outcome in HRQL in one or several SF-36 subscales were being younger or middle-aged, feeling painless, having good sleep structure, feeling rested after sleep, performing low effort of exercise more than twice per week, having strong sense of coherence (SOC), emotional support and practical assistance, higher educational level and work capacity. The most important factors were having strong SOC, feeling rested after sleep, having work capacity, being younger or middle-aged, and having good sleep structure.</p> <p>Conclusions</p> <p>This study identified several factors that promoted a good outcome in HRQL to people with rheumatic diseases. These health factors could be important to address in clinical work with rheumatic diseases in order to optimise treatment strategies.</p