Cooperative Carbon Dioxide Adsorption in Alcoholamine- and Alkoxyalkylamine-Functionalized Metal-Organic Frameworks.

A series of structurally diverse alcoholamine- and alkoxyalkylamine-functionalized variants of the metal-organic framework Mg2 (dobpdc) are shown to adsorb CO2 selectively via cooperative chain-forming mechanisms. Solid-state NMR spectra and optimized structures obtained from van der Waals-corrected density functional theory calculations indicate that the adsorption profiles can be attributed to the formation of carbamic acid or ammonium carbamate chains that are stabilized by hydrogen bonding interactions within the framework pores. These findings significantly expand the scope of chemical functionalities that can be utilized to design cooperative CO2 adsorbents, providing further means of optimizing these powerful materials for energy-efficient CO2 separations

Motivated proteins: a web application for studying small three-dimensional protein motifs

<b>BACKGROUND:</b> Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are alphabeta-motifs, asx-motifs, asx-turns, beta-bulges, beta-bulge loops, beta-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns.We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. <b>DESCRIPTION:</b> The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. <b>CONCLUSION:</b> Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schem

East African climate pulses and early human evolution

Current evidence suggests that all of the major events in hominin evolution have occurred in East Africa. Over the last two decades, there has been intensive work undertaken to understand African palaeoclimate and tectonics in order to put together a coherent picture of how the environment of East Africa has varied in the past. The landscape of East Africa has altered dramatically over the last 10 million years. It has changed from a relatively flat, homogenous region covered with mixed tropical forest, to a varied and heterogeneous environment, with mountains over 4 km high and vegetation ranging from desert to cloud forest. The progressive rifting of East Africa has also generated numerous lake basins, which are highly sensitive to changes in the local precipitation-evaporation regime. There is now evidence that the presence of precession-driven, ephemeral deep-water lakes in East Africa were concurrent with major events in hominin evolution. It seems the unusual geology and climate of East Africa created periods of highly variable local climate, which, it has been suggested could have driven hominin speciation, encephalisation and dispersal out of Africa. One example is the significant hominin speciation and brain expansion event at ∼1.8 Ma that seems to have been coeval with the occurrence of highly variable, extensive, deep-water lakes. This complex, climatically very variable setting inspired first the variability selection hypothesis, which was then the basis for the pulsed climate variability hypothesis. The newer of the two suggests that the long-term drying trend in East Africa was punctuated by episodes of short, alternating periods of extreme humidity and aridity. Both hypotheses, together with other key theories of climate-evolution linkages, are discussed in this paper. Though useful the actual evolution mechanisms, which led to early hominins are still unclear and continue to be debated. However, it is clear that an understanding of East African lakes and their palaeoclimate history is required to understand the context within which humans evolved and eventually left East Africa

Three Key considerations for biodiversity conservation in multilateral agreements

It is nearly three decades since the world recognized the need for a global multilateral treaty aiming to address accelerating biodiversity loss. However, biodiversity continues to decline at a concerning rate. Drawing on lessons from the implementation of the current strategic plan of the Convention on Biological Diversity and the 2010 Aichi Targets, we highlight three interlinked core areas, which require attention and improvement in the development of the post‐2020 Biodiversity Framework under the Convention on Biological Diversity. They are: (1) developing robust theories of change which define agreed, adaptive plans for achieving targets; (2) using models to evaluate assumptions and effectiveness of different plans and targets; and (3) identifying the common but differentiated responsibilities of different actors/states/countries within these plans. We demonstrate how future multilateral agreements must not focus only on what needs to be done but also on how it should be done, using measurable steps, which make sense at the scales at which biodiversity change happens

Artificial Neural Network Inference (ANNI): A Study on Gene-Gene Interaction for Biomarkers in Childhood Sarcomas

Objective: To model the potential interaction between previously identified biomarkers in children sarcomas using artificial neural network inference (ANNI). Method: To concisely demonstrate the biological interactions between correlated genes in an interaction network map, only 2 types of sarcomas in the children small round blue cell tumors (SRBCTs) dataset are discussed in this paper. A backpropagation neural network was used to model the potential interaction between genes. The prediction weights and signal directions were used to model the strengths of the interaction signals and the direction of the interaction link between genes. The ANN model was validated using Monte Carlo cross-validation to minimize the risk of over-fitting and to optimize generalization ability of the model. Results: Strong connection links on certain genes (TNNT1 and FNDC5 in rhabdomyosarcoma (RMS); FCGRT and OLFM1 in Ewing’s sarcoma (EWS)) suggested their potency as central hubs in the interconnection of genes with different functionalities. The results showed that the RMS patients in this dataset are likely to be congenital and at low risk of cardiomyopathy development. The EWS patients are likely to be complicated by EWS-FLI fusion and deficiency in various signaling pathways, including Wnt, Fas/Rho and intracellular oxygen. Conclusions: The ANN network inference approach and the examination of identified genes in the published literature within the context of the disease highlights the substantial influence of certain genes in sarcomas

Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages

There is increasing evidence that strain variation in Mycobacterium tuberculosis complex (MTBC) might influence the outcome of tuberculosis infection and disease. To assess genotype-phenotype associations, phylogenetically robust molecular markers and appropriate genotyping tools are required. Most current genotyping methods for MTBC are based on mobile or repetitive DNA elements. Because these elements are prone to convergent evolution, the corresponding genotyping techniques are suboptimal for phylogenetic studies and strain classification. By contrast, single nucleotide polymorphisms (SNP) are ideal markers for classifying MTBC into phylogenetic lineages, as they exhibit very low degrees of homoplasy. In this study, we developed two complementary SNP-based genotyping methods to classify strains into the six main human-associated lineages of MTBC, the 'Beijing' sublineage, and the clade comprising Mycobacterium bovis and Mycobacterium caprae. Phylogenetically informative SNPs were obtained from 22 MTBC whole-genome sequences. The first assay, referred to as MOL-PCR, is a ligation-dependent PCR with signal detection by fluorescent microspheres and a Luminex flow cytometer, which simultaneously interrogates eight SNPs. The second assay is based on six individual TaqMan real-time PCR assays for singleplex SNP-typing. We compared MOL-PCR and TaqMan results in two panels of clinical MTBC isolates. Both methods agreed fully when assigning 36 well-characterized strains into the main phylogenetic lineages. The sensitivity in allele-calling was 98.6% and 98.8% for MOL-PCR and TaqMan, respectively. Typing of an additional panel of 78 unknown clinical isolates revealed 99.2% and 100% sensitivity in allele-calling, respectively, and 100% agreement in lineage assignment between both methods. While MOL-PCR and TaqMan are both highly sensitive and specific, MOL-PCR is ideal for classification of isolates with no previous information, whereas TaqMan is faster for confirmation. Furthermore, both methods are rapid, flexible and comparably inexpensive

Hygienic quality of dehydrated aromatic herbs marketed in Southern Portugal

Dehydrated aromatic herbs are highly valued ingredients, widely used at home level and by food processing industry, frequently added to a great number of recipes in the Mediterranean countries. Despite being considered low-moisture products and classified as GRAS, during pre and post-harvesting stages of production they are susceptible of microbial contamination. In Europe an increasing number of food recalls and disease outbreaks associated with dehydrated herbs have been reported in recent years. In this study the microbial quality of 99 samples of aromatic herbs (bay leaves, basil, coriander, oregano, parsley, Provence herbs, rosemary and thyme) collected from retails shops in the region of Algarve (Southern Portugal) was assessed. All the samples were tested by conventional methods and were assayed for the total count of aerobic mesophilic microorganisms, Salmonella spp., Escherichia coli, coagulase-positive staphylococci and filamentous fungi. Almost 50 % of the herbs did not exceed the aerobic mesophilic level of 104 CFU/g. The fungi count regarded as unacceptable (106 CFU/g) was not found in any of the tested herbs, while 84 % of the samples ranged from ≤102 to 104 CFU/g. No sample was positive for the presence of Salmonella spp., Escherichia coli and staphylococci. The results are in compliance with the European Commission criteria although they point out to the permanent need of surveillance on the good standards of handling/cooking practices as well as the importance of avoiding contamination at production, retailing and distribution. The microbiological hazards associated with the pathogenic and toxigenic microbiota of dried herbs remain as a relevant public health issue, due to the fact that they are added to foods not submitted to any following lethal procedure. Control measures should be adopted in order to ensure that all phases of their supply chain respect the food safety standards.FCT: UID/BIA/04325/2019.info:eu-repo/semantics/publishedVersio

Why alternative teenagers self-harm: exploring the link between non-suicidal self-injury, attempted suicide and adolescent identity

Background: The term ‘self-harm’ encompasses both attempted suicide and non-suicidal self-injury (NSSI). Specific adolescent subpopulations such as ethnic or sexual minorities, and more controversially, those who identify as ‘Alternative’ (Goth, Emo) have been proposed as being more likely to self-harm, while other groups such as ‘Jocks’ are linked with protective coping behaviours (for example exercise). NSSI has autonomic (it reduces negative emotions) and social (it communicates distress or facilitates group ‘bonding’) functions. This study explores the links between such aspects of self-harm, primarily NSSI, and youth subculture.<p></p> Methods: An anonymous survey was carried out of 452 15 year old German school students. Measures included: identification with different youth cultures, i.e. Alternative (Goth, Emo, Punk), Nerd (academic) or Jock (athletic); social background, e.g. socioeconomic status; and experience of victimisation. Self-harm (suicide and NSSI) was assessed using Self-harm Behavior Questionnaire and the Functional Assessment of Self-Mutilation (FASM).<p></p> Results: An “Alternative” identity was directly (r ≈ 0.3) and a “Jock” identity inversely (r ≈ -0.1) correlated with self-harm. “Alternative” teenagers self-injured more frequently (NSSI 45.5% vs. 18.8%), repeatedly self-injured, and were 4–8 times more likely to attempt suicide (even after adjusting for social background) than their non-Alternative peers. They were also more likely to self-injure for autonomic, communicative and social reasons than other adolescents.<p></p> Conclusions: About half of ‘Alternative’ adolescents’ self-injure, primarily to regulate emotions and communicate distress. However, a minority self-injure to reinforce their group identity, i.e. ‘To feel more a part of a group’

Exogenous spatial precuing reliably modulates object processing but not object substitution masking

Object substitution masking (OSM) is used in behavioral and imaging studies to investigate processes associated with the formation of a conscious percept. Reportedly, OSM occurs only when visual attention is diffusely spread over a search display or focused away from the target location. Indeed, the presumed role of spatial attention is central to theoretical accounts of OSM and of visual processing more generally (Di Lollo, Enns, & Rensink, Journal of Experimental Psychology: General 129:481–507, 2000). We report a series of five experiments in which valid spatial precuing is shown to enhance the ability of participants to accurately report a target but, in most cases, without affecting OSM. In only one experiment (Experiment 5) was a significant effect of precuing observed on masking. This is in contrast to the reliable effect shown across all five experiments in which precuing improved overall performance. The results are convergent with recent findings from Argyropoulos, Gellatly, and Pilling (Journal of Experimental Psychology: Human Perception and Performance 39:646–661, 2013), which show that OSM is independent of the number of distractor items in a display. Our results demonstrate that OSM can operate independently of focal attention. Previous claims of the strong interrelationship between OSM and spatial attention are likely to have arisen from ceiling or floor artifacts that restricted measurable performance