University of South Carolina

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

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Social network analysis is used widely in the social and behavioral sciences, as well as in economics, marketing, and industrial engineering. The social network perspective focuses on relationships among social entities and is an important addition to standard social and behavioral research, which is primarily concerned with attributes of the social units. Social Network Analysis: Methods and Applications reviews and discusses methods for the analysis of social networks with a focus on applications of these methods to many substantive examples. It is a reference book that can be used by those who want a comprehensive review of network methods, or by researchers who have gathered network data and want to find the most appropriate method by which to analyze it. It is also intended for use as a textbook as it is the first book to provide comprehensive coverage of the methodology and applications of the field.

AINSWORTH, B. E,., W. L. HASKELL, M. C. WHITT, M. L. IRWIN, A. M. SWARTZ, S .J. STRATH, W. L. O’BRIEN, D. R. BASSETT, JR., K. H. SCHMITZ, P. O EMPLAINCOURT, D. R. JACOBS, JR., and A. S. LEON. Compendium of physical activities: an update of activity codes and MET intensities. Med. Sci. Sports Exerc., Vol. 32, No. 9, Suppl., pp. S498–S516, 2000. We provide an updated version of the Compendium of Physical Activities, a coding scheme that classifies specific physical activity (PA) by rate of energy expenditure. It was developed to enhance the comparability of results across studies using self-reports of PA. The Compendium coding scheme links a five-digit code that describes physical activities by major headings (e.g., occupation, transportation, etc.) and specific activities within each major heading with its intensity, defined as the ratio of work metabolic rate to a standard resting metabolic rate (MET). Energy expenditure in MET-minutes, MET-hours, kcal, or kcal per kilogram body weight can be estimated for specific activities by type or MET intensity. Additions to the Compendium were obtained from studies describing daily PA patterns of adults and studies measuring the energy cost of specific physical activities in field settings. The updated version includes two new major headings of volunteer and religious activities, extends the number of specific activities from 477 to 605, and provides updated MET intensity levels for selected activities.

The many 'friendly' microbes that inhabit the human gut have been implicated in numerous health-related issues, in particular those involving digestion and susceptibility to infection. A study of the faecal microbial communities of pairs of adult female twins, selected to include 'lean' and 'obese' individuals, reveals some similarities between the human gut microbiomes among family members, but each person's gut microbial community varies in the specific bacterial lineages present. There was a wide array of shared microbial genes among individuals, comprising an identifiable 'core microbiome' at the gene, rather than at the microbial species level. This core includes many novel genes for carbohydrate metabolism, and deviations from this core are associated with the obese versus lean state. The human microbiota has been implicated in many health-related issues. In this study, the microbiota composition of monozygotic and dizygotic twins and their mothers is examined. Although a core microbiome could not be defined on a phylogenetic level, the data suggests that core functions are conserved. The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides1,2,3,4,5,6. Studies of a few unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes6,7,8, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is used and stored3,4,5. Here we characterize the faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers, to address how host genotype, environmental exposure and host adiposity influence the gut microbiome. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person’s gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable ‘core microbiome’ at the gene, rather than at the organismal lineage, level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean).

OBJECTIVE: To encourage increased participation in physical activity among Americans of all ages by issuing a public health recommendation on the types and amounts of physical activity needed for health promotion and disease prevention. PARTICIPANTS: A planning committee of five scientists was established by the Centers for Disease Control and Prevention and the American College of Sports Medicine to organize a workshop. This committee selected 15 other workshop discussants on the basis of their research expertise in issues related to the health implications of physical activity. Several relevant professional or scientific organizations and federal agencies also were represented. EVIDENCE: The panel of experts reviewed the pertinent physiological, epidemiologic, and clinical evidence, including primary research articles and recent review articles. CONSENSUS PROCESS: Major issues related to physical activity and health were outlined, and selected members of the expert panel drafted sections of the paper from this outline. A draft manuscript was prepared by the planning committee and circulated to the full panel in advance of the 2-day workshop. During the workshop, each section of the manuscript was reviewed by the expert panel. Primary attention was given to achieving group consensus concerning the recommended types and amounts of physical activity. A concise "public health message" was developed to express the recommendations of the panel. During the ensuing months, the consensus statement was further reviewed and revised and was formally endorsed by both the Centers for Disease Control and Prevention and the American College of Sports Medicine. CONCLUSION: Every US adult should accumulate 30 minutes or more of moderate-intensity physical activity on most, preferably all, days of the week.

A protection motivation theory is proposed that postulates the three crucial components of a fear appeal to be (a) the magnitude of noxiousness of a depicted event; (b) the probability of that event's occurrence; and (c) the efficacy of a protective response. Each of these communication variables initiates corresponding cognitive appraisal processes that mediate attitude change. The proposed conceptualization is a special case of a more comprehensive theoretical schema: expectancy-value theories. Several suggestions are offered for reinterpreting existing data, designing new types of empirical research, and making future studies more comparable. Finally, the principal advantages of protection motivation theory over the rival formulations of Janis and Leventhal are discussed.

SUMMARY: In 1995 the American College of Sports Medicine and the Centers for Disease Control and Prevention published national guidelines on Physical Activity and Public Health. The Committee on Exercise and Cardiac Rehabilitation of the American Heart Association endorsed and supported these recommendations. The purpose of the present report is to update and clarify the 1995 recommendations on the types and amounts of physical activity needed by healthy adults to improve and maintain health. Development of this document was by an expert panel of scientists, including physicians, epidemiologists, exercise scientists, and public health specialists. This panel reviewed advances in pertinent physiologic, epidemiologic, and clinical scientific data, including primary research articles and reviews published since the original recommendation was issued in 1995. Issues considered by the panel included new scientific evidence relating physical activity to health, physical activity recommendations by various organizations in the interim, and communications issues. Key points related to updating the physical activity recommendation were outlined and writing groups were formed. A draft manuscript was prepared and circulated for review to the expert panel as well as to outside experts. Comments were integrated into the final recommendation. PRIMARY RECOMMENDATION: To promote and maintain health, all healthy adults aged 18 to 65 yr need moderate-intensity aerobic (endurance) physical activity for a minimum of 30 min on five days each week or vigorous-intensity aerobic physical activity for a minimum of 20 min on three days each week. [I (A)] Combinations of moderate- and vigorous-intensity activity can be performed to meet this recommendation. [IIa (B)] For example, a person can meet the recommendation by walking briskly for 30 min twice during the week and then jogging for 20 min on two other days. Moderate-intensity aerobic activity, which is generally equivalent to a brisk walk and noticeably accelerates the heart rate, can be accumulated toward the 30-min minimum by performing bouts each lasting 10 or more minutes. [I (B)] Vigorous-intensity activity is exemplified by jogging, and causes rapid breathing and a substantial increase in heart rate. In addition, every adult should perform activities that maintain or increase muscular strength and endurance a minimum of two days each week. [IIa (A)] Because of the dose-response relation between physical activity and health, persons who wish to further improve their personal fitness, reduce their risk for chronic diseases and disabilities or prevent unhealthy weight gain may benefit by exceeding the minimum recommended amounts of physical activity. [I (A)]

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes.
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\nFor example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy.
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\nHere, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Objective. County‐level socioeconomic and demographic data were used to construct an index of social vulnerability to environmental hazards, called the Social Vulnerability Index (SoVI) for the United States based on 1990 data. Methods. Using a factor analytic approach, 42 variables were reduced to 11 independent factors that accounted for about 76 percent of the variance. These factors were placed in an additive model to compute a summary score—the Social Vulnerability Index. Results. There are some distinct spatial patterns in the SoVI, with the most vulnerable counties clustered in metropolitan counties in the east, south Texas, and the Mississippi Delta region. Conclusion. Those factors that contribute to the overall score often are different for each county, underscoring the interactive nature of social vulnerability—some components increase vulnerability; others moderate the effects.

Scale development and validation are critical to much of the work in the health, social, and behavioral sciences. However, the constellation of techniques required for scale development and evaluation can be onerous, jargon-filled, unfamiliar, and resource-intensive. Further, it is often not a part of graduate training. Therefore, our goal was to concisely review the process of scale development in as straightforward a manner as possible, both to facilitate the development of new, valid, and reliable scales, and to help improve existing ones. To do this, we have created a primer for best practices for scale development in measuring complex phenomena. This is not a systematic review, but rather the amalgamation of technical literature and lessons learned from our experiences spent creating or adapting a number of scales over the past several decades. We identified three phases that span nine steps. In the first phase, items are generated and the validity of their content is assessed. In the second phase, the scale is constructed. Steps in scale construction include pre-testing the questions, administering the survey, reducing the number of items, and understanding how many factors the scale captures. In the third phase, scale evaluation, the number of dimensions is tested, reliability is tested, and validity is assessed. We have also added examples of best practices to each step. In sum, this primer will equip both scientists and practitioners to understand the ontology and methodology of scale development and validation, thereby facilitating the advancement of our understanding of a range of health, social, and behavioral outcomes.

Arc-synthesized single-walled carbon nanotubes have been purified through preparative electrophoresis in agarose gel and glass bead matrixes. Two major impurities were isolated: fluorescent carbon and short tubular carbon. Analysis of these two classes of impurities was done. The methods described may be readily extended to the separation of other water-soluble nanoparticles. The separated fluorescent carbon and short tubule carbon species promise to be interesting nanomaterials in their own right.

SUMMARY: In 1995 the American College of Sports Medicine and the Centers for Disease Control and Prevention published national guidelines on Physical Activity and Public Health. The Committee on Exercise and Cardiac Rehabilitation of the American Heart Association endorsed and supported these recommendations. The purpose of the present report is to update and clarify the 1995 recommendations on the types and amounts of physical activity needed by healthy adults to improve and maintain health. Development of this document was by an expert panel of scientists, including physicians, epidemiologists, exercise scientists, and public health specialists. This panel reviewed advances in pertinent physiologic, epidemiologic, and clinical scientific data, including primary research articles and reviews published since the original recommendation was issued in 1995. Issues considered by the panel included new scientific evidence relating physical activity to health, physical activity recommendations by various organizations in the interim, and communications issues. Key points related to updating the physical activity recommendation were outlined and writing groups were formed. A draft manuscript was prepared and circulated for review to the expert panel as well as to outside experts. Comments were integrated into the final recommendation. PRIMARY RECOMMENDATION: To promote and maintain health, all healthy adults aged 18 to 65 yr need moderate-intensity aerobic (endurance) physical activity for a minimum of 30 min on five days each week or vigorous-intensity aerobic physical activity for a minimum of 20 min on three days each week. [I (A)] Combinations of moderate- and vigorous-intensity activity can be performed to meet this recommendation. [IIa (B)] For example, a person can meet the recommendation by walking briskly for 30 min twice during the week and then jogging for 20 min on two other days. Moderate-intensity aerobic activity, which is generally equivalent to a brisk walk and noticeably accelerates the heart rate, can be accumulated toward the 30-min minimum by performing bouts each lasting 10 or more minutes. [I (B)] Vigorous-intensity activity is exemplified by jogging, and causes rapid breathing and a substantial increase in heart rate. In addition, every adult should perform activities that maintain or increase muscular strength and endurance a minimum of two days each week. [IIa (A)] Because of the dose-response relation between physical activity and health, persons who wish to further improve their personal fitness, reduce their risk for chronic diseases and disabilities or prevent unhealthy weight gain may benefit by exceeding the minimum recommended amounts of physical activity. [I (A)].

N epsilon-(carboxymethyl)lysine, N epsilon-(carboxymethyl)hydroxylysine, and the fluorescent cross-link pentosidine are formed by sequential glycation and oxidation reactions between reducing sugars and proteins. These compounds, termed glycoxidation products, accumulate in tissue collagen with age and at an accelerated rate in diabetes. Although glycoxidation products are present in only trace concentrations, even in diabetic collagen, studies on glycation and oxidation of model proteins in vitro suggest that these products are biomarkers of more extensive underlying glycative and oxidative damage to the protein. Possible sources of oxidative stress and damage to proteins in diabetes include free radicals generated by autoxidation reactions of sugars and sugar adducts to protein and by autoxidation of unsaturated lipids in plasma and membrane proteins. The oxidative stress may be amplified by a continuing cycle of metabolic stress, tissue damage, and cell death, leading to increased free radical production and compromised free radical inhibitory and scavenger systems, which further exacerbate the oxidative stress. Structural characterization of the cross-links and other products accumulating in collagen in diabetes is needed to gain a better understanding of the relationship between oxidative stress and the development of complications in diabetes. Such studies may lead to therapeutic approaches for limiting the damage from glycation and oxidation reactions and for complementing existing therapy for treatment of the complications of diabetes.

The authors conducted a qualitative study of the motivations and contextual factors that induce corporate ecological responsiveness. Analytic induction applied to data collected from 53 firms in the United Kingdom and Japan revealed three motivations: competitiveness, legitimation, and ecological responsibility. These motivations were influenced by three contextual conditions: field cohesion, issue salience, and individual concern. In this article, the authors also identify the conditions that likely lead to high corporate ecological responsiveness.

Molecules of benzene-1,4-dithiol were self-assembled onto the two facing gold electrodes of a mechanically controllable break junction to form a statically stable gold-sulfur-aryl-sulfur-gold system, allowing for direct observation of charge transport through the molecules. Current-voltage measurements at room temperature demonstrated a highly reproducible apparent gap at about 0.7 volt, and the conductance-voltage curve showed two steps in both bias directions. This study provides a quantative measure of the conductance of a junction containing a single molecule, which is a fundamental step in the emerging area of molecular-scale electronics.

Abstract Strategic management researchers often encounter problems obtaining objective measures of selected aspects of organizational performance that are reliable and valid. With privately‐held firms, such data are frequently unavailable. With conglomerate business units, all or parts of such data are inextricably interwoven with corporate‐wide data. This paper examines the usefulness of subjective performance measures, obtained from top management teams, when problems are encountered in obtaining accurate performance data.

The elucidation of the human genome sequence has made it possible to identify genetic alterations in cancers in unprecedented detail. To begin a systematic analysis of such alterations, we determined the sequence of well-annotated human protein-coding genes in two common tumor types. Analysis of 13,023 genes in 11 breast and 11 colorectal cancers revealed that individual tumors accumulate an average of approximately 90 mutant genes but that only a subset of these contribute to the neoplastic process. Using stringent criteria to delineate this subset, we identified 189 genes (average of 11 per tumor) that were mutated at significant frequency. The vast majority of these genes were not known to be genetically altered in tumors and are predicted to affect a wide range of cellular functions, including transcription, adhesion, and invasion. These data define the genetic landscape of two human cancer types, provide new targets for diagnostic and therapeutic intervention, and open fertile avenues for basic research in tumor biology.

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

This feature article highlights work from the authors' laboratories on the synthesis, assembly, reactivity, and optical applications of metallic nanoparticles of nonspherical shape, especially nanorods. The synthesis is a seed-mediated growth procedure, in which metal salts are reduced initially with a strong reducing agent, in water, to produce approximately 4 nm seed particles. Subsequent reduction of more metal salt with a weak reducing agent, in the presence of structure-directing additives, leads to the controlled formation of nanorods of specified aspect ratio and can also yield other shapes of nanoparticles (stars, tetrapods, blocks, cubes, etc.). Variations in reaction conditions and crystallographic analysis of gold nanorods have led to insight into the growth mechanism of these materials. Assembly of nanorods can be driven by simple evaporation from solution or by rational design with molecular-scale connectors. Short nanorods appear to be more chemically reactive than long nanorods. Finally, optical applications in sensing and imaging, which take advantage of the visible light absorption and scattering properties of the nanorods, are discussed.