Universidade Federal de São Carlos

Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

We consider here the problem of building a never-ending language learner; that is, an intelligent computer agent that runs forever and that each day must (1) extract, or read, information from the web to populate a growing structured knowledge base, and (2) learn to perform this task better than on the previous day. In particular, we propose an approach and a set of design principles for such an agent, describe a partial implementation of such a system that has already learned to extract a knowledge base containing over 242,000 beliefs with an estimated precision of 74% after running for 67 days, and discuss lessons learned from this preliminary attempt to build a never-ending learning agent.

This article describes a prototype system for quantifying bioassays and for exchanging the results of the assays digitally with physicians located off-site. The system uses paper-based microfluidic devices for running multiple assays simultaneously, camera phones or portable scanners for digitizing the intensity of color associated with each colorimetric assay, and established communications infrastructure for transferring the digital information from the assay site to an off-site laboratory for analysis by a trained medical professional; the diagnosis then can be returned directly to the healthcare provider in the field. The microfluidic devices were fabricated in paper using photolithography and were functionalized with reagents for colorimetric assays. The results of the assays were quantified by comparing the intensities of the color developed in each assay with those of calibration curves. An example of this system quantified clinically relevant concentrations of glucose and protein in artificial urine. The combination of patterned paper, a portable method for obtaining digital images, and a method for exchanging results of the assays with off-site diagnosticians offers new opportunities for inexpensive monitoring of health, especially in situations that require physicians to travel to patients (e.g., in the developing world, in emergency management, and during field operations by the military) to obtain diagnostic information that might be obtained more effectively by less valuable personnel.

Abstract Drainage basins in many parts of the world are ungauged or poorly gauged, and in some cases existing measurement networks are declining. The problem is compounded by the impacts of human-induced changes to the land surface and climate, occurring at the local, regional and global scales. Predictions of ungauged or poorly gauged basins under these conditions are highly uncertain. The IAHS Decade on Predictions in Ungauged Basins, or PUB, is a new initiative launched by the International Association of Hydrological Sciences (IAHS), aimed at formulating and implementing appropriate science programmes to engage and energize the scientific community, in a coordinated manner, towards achieving major advances in the capacity to make predictions in ungauged basins. The PUB scientific programme focuses on the estimation of predictive uncertainty, and its subsequent reduction, as its central theme. A general hydrological prediction system contains three components: (a) a model that describes the key processes of interest, (b) a set of parameters that represent those landscape properties that govern critical processes, and (c) appropriate meteorological inputs (where needed) that drive the basin response. Each of these three components of the prediction system, is either not known at all, or at best known imperfectly, due to the inherent multi-scale space—time heterogeneity of the hydrological system, especially in ungauged basins. PUB will therefore include a set of targeted scientific programmes that attempt to make inferences about climatic inputs, parameters and model structures from available but inadequate data and process knowledge, at the basin of interest and/or from other similar basins, with robust measures of the uncertainties involved, and their impacts on predictive uncertainty. Through generation of improved understanding, and methods for the efficient quantification of the underlying multi-scale heterogeneity of the basin and its response, PUB will inexorably lead to new, innovative methods for hydrological predictions in ungauged basins in different parts of the world, combined with significant reductions of predictive uncertainty. In this way, PUB will demonstrate the value of data, as well as provide the information needed to make predictions in ungauged basins, and assist in capacity building in the use of new technologies. This paper presents a summary of the science and implementation plan of PUB, with a call to the hydrological community to participate actively in the realization of these goals.

Abstract The effect of temperature on the crystallization of α, β, and γ phases of PVDF from dimethylacetamide (DMA) solution was studied. Variation in the crystallinity content of these three phases was obtained as a function of temperature using infrared spectroscopy, differential scanning calorimetry (DSC) and x‐ray diffraction techniques. Such variation is related to the dependence of the crystallization rate of each phase with temperature, and allowed a better understanding of some results found in the literature about the crystallization and interconversion of these phases. Micrographs of samples present morphologies that corroborate with the proposed explanations. © 1994 John Wiley & Sons, Inc.

The transparency and clarity of research reports, emphasizing the data collection stage, are considered important parameters for evaluating the scientific rigor of qualitative studies. The current paper aims to analyze the use of saturation sampling as a methodological concept, frequently employed in descriptions of qualitative studies in various areas of knowledge, particularly in the field of health care. We discuss and confront the following topics: definition of sampling closure by theoretical saturation; difficulties in the acceptance and operationalization of intentional samples (with examples), adequate size of the intentional sample, the significance of valuing what is repeated or the differences contained in the sample reports, inadequate uses of expressions containing the term saturation, and finally possible metaphors for understanding the concept.

Reactive oxygen species (ROS) can attack a diverse range of targets to exert antimicrobial activity, which accounts for their versatility in mediating host defense against a broad range of pathogens. Most ROS are formed by the partial reduction in molecular oxygen. Four major ROS are recognized comprising superoxide (O2•-), hydrogen peroxide (H2O2), hydroxyl radical (•OH), and singlet oxygen ((1)O2), but they display very different kinetics and levels of activity. The effects of O2•- and H2O2 are less acute than those of •OH and (1)O2, because the former are much less reactive and can be detoxified by endogenous antioxidants (both enzymatic and nonenzymatic) that are induced by oxidative stress. In contrast, no enzyme can detoxify •OH or (1)O2, making them extremely toxic and acutely lethal. The present review will highlight the various methods of ROS formation and their mechanism of action. Antioxidant defenses against ROS in microbial cells and the use of ROS by antimicrobial host defense systems are covered. Antimicrobial approaches primarily utilizing ROS comprise both bactericidal antibiotics and nonpharmacological methods such as photodynamic therapy, titanium dioxide photocatalysis, cold plasma, and medicinal honey. A brief final section covers reactive nitrogen species and related therapeutics, such as acidified nitrite and nitric oxide-releasing nanoparticles.

Abstract The classification of the legume family proposed here addresses the long‐known non‐monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near‐complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well‐supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community‐endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or clade‐based classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

A precise measurement of the proton flux in primary cosmic rays with rigidity (momentum/charge) from 1 GV to 1.8 TV is presented based on 300 million events. Knowledge of the rigidity dependence of the proton flux is important in understanding the origin, acceleration, and propagation of cosmic rays. We present the detailed variation with rigidity of the flux spectral index for the first time. The spectral index progressively hardens at high rigidities.

Abstract Samples containing the three crystalline phases of poly(vinylidene fluoride), α, β, and γ, have been obtained under distinct crystallization conditions. Samples containing exclusively unoriented β phase have been obtained by crystallization from dimethylformamide (DMF) solution at 60°C. Oriented β phase has been obtained by uniaxial drawing, at 80°C, of an originally α phase sample. Samples containing exclusively α phase have been obtained by melting and posterior cooling at room temperature. Samples containing both α and γ phases have been obtained by melt crystallization at 164 °C for 16 and 36 h. Presence of the crystalline phases in each sample were confirmed by Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), wide‐angle X‐ray scattering (WAXD), polarized light optical microscopy (PLOM), and scanning electron microscopy (SEM). Infrared absorption bands identifying unequivocally the presence of β and γ phases in a sample are presented. It is shown that solution crystallization at T < 70°C always results in the β phase, regardless of the solvent used. Melt temperatures of the respective phases have also been determined. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 100: 3272–3279, 2006

The field of chiral inorganic nanostructures is rapidly expanding. It started from the observation of strong circular dichroism during the synthesis of individual nanoparticles (NPs) and their assemblies and expanded to sophisticated synthetic protocols involving nanostructures from metals, semiconductors, ceramics, and nanocarbons. Besides the well-established chirality transfer from bioorganic molecules, other methods to impart handedness to nanoscale matter specific to inorganic materials were discovered, including three-dimentional lithography, multiphoton chirality transfer, polarization effects in nanoscale assemblies, and others. Multiple chiral geometries were observed with characteristic scales from ångströms to microns. Uniquely high values of chiral anisotropy factors that spurred the development of the field and differentiate it from chiral structures studied before, are now well understood; they originate from strong resonances of incident electromagnetic waves with plasmonic and excitonic states typical for metals and semiconductors. At the same time, distinct similarities with chiral supramolecular and biological systems also emerged. They can be seen in the synthesis and separation methods, chemical properties of individual NPs, geometries of the nanoparticle assemblies, and interactions with biological membranes. Their analysis can help us understand in greater depth the role of chiral asymmetry in nature inclusive of both earth and space. Consideration of both differences and similarities between chiral inorganic, organic, and biological nanostructures will also accelerate the development of technologies based on chiroplasmonic and chiroexcitonic effects. This review will cover both experiment and theory of chiral nanostructures starting with the origin and multiple components of mirror asymmetry of individual NPs and their assemblies. We shall consider four different types of chirality in nanostructures and related physical, chemical, and biological effects. Synthetic methods for chiral inorganic nanostructures are systematized according to chirality types, materials, and scales. We also assess technological prospects of chiral inorganic materials with current front runners being biosensing, chiral catalysis, and chiral photonics. Prospective venues for future fundamental research are discussed in the conclusion of this review.

Graphene and its derivatives are promising candidates for important biomedical applications because of their versatility. The prospective use of graphene-based materials in a biological context requires a detailed comprehension of the toxicity of these materials. Moreover, due to the expanding applications of nanotechnology, human and environmental exposures to graphene-based nanomaterials are likely to increase in the future. Because of the potential risk factors associated with the manufacture and use of graphene-related materials, the number of nanotoxicological studies of these compounds has been increasing rapidly in the past decade. These studies have researched the effects of the nanostructural/biological interactions on different organizational levels of the living system, from biomolecules to animals. This review discusses recent results based on in vitro and in vivo cytotoxicity and genotoxicity studies of graphene-related materials and critically examines the methodologies employed to evaluate their toxicities. The environmental impact from the manipulation and application of graphene materials is also reported and discussed. Finally, this review presents mechanistic aspects of graphene toxicity in biological systems. More detailed studies aiming to investigate the toxicity of graphene-based materials and to properly associate the biological phenomenon with their chemical, structural, and morphological variations that result from several synthetic and processing possibilities are needed. Knowledge about graphene-based materials could ensure the safe application of this versatile material. Consequently, the focus of this review is to provide a source of inspiration for new nanotoxicological approaches for graphene-based materials.

The current manuscript sets out a position stand for blood flow restriction (BFR) exercise, focusing on the methodology, application and safety of this mode of training. With the emergence of this technique and the wide variety of applications within the literature, the aim of this position stand is to set out a current research informed guide to BFR training to practitioners. This covers the use of BFR to enhance muscular strength and hypertrophy via training with resistance and aerobic exercise and preventing muscle atrophy using the technique passively. The authorship team for this article was selected from the researchers focused in BFR training research with expertise in exercise science, strength and conditioning and sports medicine.

Paper works: Paper-based indirect ELISA (see picture) has been demonstrated through the detection of rabbit IgG and the HIV-1 envelope antigen gp41. This technique combines the sensitivity and specificity of ELISA with the low cost and ease-of-use of paper-based platforms. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

To gain a better understanding of the global application of soil erosion prediction models, we comprehensively reviewed relevant peer-reviewed research literature on soil-erosion modelling published between 1994 and 2017. We aimed to identify (i) the processes and models most frequently addressed in the literature, (ii) the regions within which models are primarily applied, (iii) the regions which remain unaddressed and why, and (iv) how frequently studies are conducted to validate/evaluate model outcomes relative to measured data. To perform this task, we combined the collective knowledge of 67 soil-erosion scientists from 25 countries. The resulting database, named 'Global Applications of Soil Erosion Modelling Tracker (GASEMT)', includes 3030 individual modelling records from 126 countries, encompassing all continents (except Antarctica). Out of the 8471 articles identified as potentially relevant, we reviewed 1697 appropriate articles and systematically evaluated and transferred 42 relevant attributes into the database. This GASEMT database provides comprehensive insights into the state-of-the-art of soil- erosion models and model applications worldwide. This database intends to support the upcoming country-based United Nations global soil-erosion assessment in addition to helping to inform soil erosion research priorities by building a foundation for future targeted, in-depth analyses. GASEMT is an open-source database available to the entire user-community to develop research, rectify errors, and make future expansions.

Abstract Zinc oxide nanoparticles (ZnO NPs) are one of the most widely used nanoparticulate materials due to their antimicrobial properties, but their main mechanism of action (MOA) has not been fully elucidated. This study characterized ZnO NPs by using X-ray diffraction, FT-IR spectroscopy and scanning electron microscopy. Antimicrobial activity of ZnO NPs against the clinically relevant bacteria Escherichia coli , Staphylococcus aureus , Pseudomonas aeruginosa , and the Gram-positive model Bacillus subtilis was evaluated by performing resazurin microtiter assay (REMA) after exposure to the ZnO NPs at concentrations ranging from 0.2 to 1.4 mM. Sensitivity was observed at 0.6 mM for the Gram-negative and 1.0 mM for the Gram-positive cells. Fluorescence microscopy was used to examine the interference of ZnO NPs on the membrane and the cell division apparatus of B. subtilis ( amy ::pspac-ftsZ-gfpmut1) expressing FtsZ-GFP. The results showed that ZnO NPs did not interfere with the assembly of the divisional Z-ring. However, 70% of the cells exhibited damage in the cytoplasmic membrane after 15 min of exposure to the ZnO NPs. Electrostatic forces, production of Zn 2+ ions and the generation of reactive oxygen species were described as possible pathways of the bactericidal action of ZnO. Therefore, understanding the bactericidal MOA of ZnO NPs can potentially help in the construction of predictive models to fight bacterial resistance.

The ten principles of GSP are presented with the aim of establishing a road map toward the development of overall greener analytical methodologies. Paramount aspects for greening sample preparation and their interconnections are identified and discussed. These include the use of safe solvents/reagents and materials that are renewable, recycled and reusable, minimizing waste generation and energy demand, and enabling high sample throughput, miniaturization, procedure simplification/automation, and operator's safety. Further, the importance of applying green metrics for assessing the greenness of sample preparation methods is highlighted, next to the contribution of GSP in achieving the broader goal of sustainability. Green sample preparation is sample preparation. It is not a new subdiscipline of sample preparation but a guiding principle that promotes sustainable development through the adoption of environmentally benign sample preparation procedures.

A qualitative study's methodological transparency is considered a key factor for achieving its reliability and should be guaranteed by the researchers. Closing the sampling process by saturation is a common approach, but it is rarely made explicit in research reports. Qualitative researchers also commonly experience technical difficulties in objectively identifying saturation. This article proposes a method to organize sample closing by saturation, with a sequence of eight procedural steps for treating and analyzing data collected through open or semi-structured interviews or focus groups. The article aims to help researchers objectively explain how and when saturation occurred and to allow their readers to know how this process occurred.