Showing papers by "San Diego State University published in 2008"

The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes

Abstract: Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers. A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats. The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis – the availability of high-performance computing for annotating the data. http://metagenomics.nmpdr.org

Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Abstract: Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms Recent reviews have described the range of assays that have been used for this purpose(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi) Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes This set of guidelines is 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 verify an autophagic response

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

Abstract: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

The status of the world's land and marine mammals: diversity, threat, and knowledge

Abstract: Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action.

Functional metagenomic profiling of nine biomes

Abstract: Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.

Making choices impairs subsequent self-control: A limited-resource account of decision making, self-regulation, and active initiative.

Abstract: The current research tested the hypothesis that making many choices impairs subsequent self-control. Drawing from a limited-resource model of self-regulation and executive function, the authors hypothesized that decision making depletes the same resource used for self-control and active responding. In 4 laboratory studies, some participants made choices among consumer goods or college course options, whereas others thought about the same options without making choices. Making choices led to reduced self-control (i.e., less physical stamina, reduced persistence in the face of failure, more procrastination, and less quality and quantity of arithmetic calculations). A field study then found that reduced self-control was predicted by shoppers' self-reported degree of previous active decision making. Further studies suggested that choosing is more depleting than merely deliberating and forming preferences about options and more depleting than implementing choices made by someone else and that anticipating the choice task as enjoyable can reduce the depleting effect for the first choices but not for many choices.

Egos inflating over time: a cross-temporal meta-analysis of the Narcissistic Personality Inventory.

Abstract: A cross-temporal meta-analysis found that narcissism levels have risen over the generations in 85 samples of American college students who completed the 40-item forced-choice Narcissistic Personality Inventory (NPI) between 1979 and 2006 (total n=16,475) Mean narcissism scores were significantly correlated with year of data collection when weighted by sample size (beta=53, p<001) Since 1982, NPI scores have increased 033 standard deviation Thus, almost two-thirds of recent college students are above the mean 1979-1985 narcissism score, a 30% increase The results complement previous studies finding increases in other individualistic traits such as assertiveness, agency, self-esteem, and extraversion

Baselines and Degradation of Coral Reefs in the Northern Line Islands

Abstract: Effective conservation requires rigorous baselines of pristine conditions to assess the impacts of human activities and to evaluate the efficacy of management. Most coral reefs are moderately to severely degraded by local human activities such as fishing and pollution as well as global change, hence it is difficult to separate local from global effects. To this end, we surveyed coral reefs on uninhabited atolls in the northern Line Islands to provide a baseline of reef community structure, and on increasingly populated atolls to document changes associated with human activities. We found that top predators and reef-building organisms dominated unpopulated Kingman and Palmyra, while small planktivorous fishes and fleshy algae dominated the populated atolls of Tabuaeran and Kiritimati. Sharks and other top predators overwhelmed the fish assemblages on Kingman and Palmyra so that the biomass pyramid was inverted (top-heavy). In contrast, the biomass pyramid at Tabuaeran and Kiritimati exhibited the typical bottom-heavy pattern. Reefs without people exhibited less coral disease and greater coral recruitment relative to more inhabited reefs. Thus, protection from overfishing and pollution appears to increase the resilience of reef ecosystems to the effects of global warming.

Generational differences in psychological traits and their impact on the workplace

Abstract: Purpose – The purpose of this paper is to review data from 1.4 million people who completed personality, attitude, psychopathology, or behavior scales between the 1930s and the present and to discuss how those differences may impact today's workplace.Design/methodology/approach – The data are gathered from research reports using psychological scales over the last eight decades, primarily those using college student samples.Findings – Generation Me (sometimes called Gen Y or Millennials) demonstrates higher self‐esteem, narcissism, anxiety, and depression; lower need for social approval; more external locus of control; and women with more agentic traits.Practical implications – Managers should expect to see more employees with unrealistically high expectations, a high need for praise, difficulty with criticism, an increase in creativity demands, job‐hopping, ethics scandals, casual dress, and shifting workplace norms for women. Organizations can respond to these changes with accommodations (e.g. praise pro...

New onset and persistent symptoms of post-traumatic stress disorder self reported after deployment and combat exposures: prospective population based US military cohort study

Abstract: Objective To describe new onset and persistence of self reported post-traumatic stress disorder symptoms in a large population based military cohort, many of whom were deployed in support of the wars in Iraq and Afghanistan. Design Prospective cohort analysis. Setting and participants Survey enrolment data from the millennium cohort (July 2001 to June 2003) obtained before the wars in Iraq and Afghanistan. Follow-up (June 2004 to February 2006) data on health outcomes collected from 50 184 participants. Main outcome measures Self reported post-traumatic stress disorder as measured by the posttraumatic stress disorder checklist—civilian version using Diagnostic and Statistical Manual of Mental Disorders, fourth edition criteria. Results More than 40% of the cohort were deployed between 2001 and 2006; between baseline and follow-up, 24% deployed for the first time in support of the wars in Iraq and Afghanistan. New incidence rates of 10-13 cases of post-traumatic stress disorder per 1000 person years occurred in the millennium cohort. New onset self reported post-traumatic stress disorder symptoms or diagnosis were identified in 7.6-8.7% of deployers who reported combat exposures, 1.4-2.1% of deployers who did not report combat exposures, and 2.3-3.0% of non-deployers. Among those with self reported symptoms of post-traumatic stress disorder at baseline, deployment did not affect persistence of symptoms. Conclusions After adjustment for baseline characteristics, these prospective data indicate a threefold increase in new onset self reported post-traumatic stress disorder symptoms or diagnosis among deployed military personnel who reported combat exposures. The findings define the importance of post-traumatic stress disorder in this population and emphasise that specific combat exposures, rather than deployment itself, significantly affect the onset of symptoms of post-traumatic stress disorder after deployment.

A Systematic Review of the Relationship between Acculturation and Diet among Latinos in the United States: Implications for Future Research

Abstract: Dietary intake is an important determinant of obesity and numerous chronic health conditions. A healthful diet is an essential component of chronic disease self-management. Researchers have indicated that the healthfulness of the Latino diet deteriorates during the acculturation process. However, given the many operationalizations of acculturation, conclusive evidence regarding this relationship is still lacking. This comprehensive and systematic literature review examines the relationship between acculturation and diet by examining national, quantitative, and qualitative studies involving Latinos living in the United States. Studies of diet included those that examined dietary intake using one of several validated measures (eg, food frequency questionnaire, 24-hour dietary recall, or dietary screener) and/or dietary behaviors (eg, away-from-home-eating and fat avoidance). Articles were identified through two independent searches yielding a final sample of 34 articles. Articles were abstracted by two independent reviewers and inter-rater reliability was assessed. Analyses examined the extent to which various measures of acculturation (ie, acculturation score, years in the United States, birthplace, generational status, and language use) were associated with macronutrient intake, micronutrient intake, and dietary behaviors. Several relationships were consistent irrespective of how acculturation was measured: no relationship with intake of dietary fat and percent energy from fat; the less vs more acculturated consumed more fruit, rice, beans, and less sugar and sugar-sweetened beverages. Additional observed relationships depended on the measure of acculturation used in the study. These findings suggest a differential influence of acculturation on diet, requiring greater specificity in our dietary interventions by acculturation status.

Towards understanding the direct and indirect effects of CEOs' transformational leadership on firm innovation

Abstract: This study seeks to advance understanding of how transformational leadership by top managers (CEOs) can affect their companies' innovativeness. We propose a model that includes both direct effects and indirect effects moderated by aspects of organizational culture, structure, and the external environment. The predicted effects are tested with data collected through multiple sources on 50 Taiwanese electronics and telecommunications companies. The results support the expectation that a positive relationship exists between CEO transformational leadership and organizational innovation. They also support most of the predicted moderating effects. The implications of these findings for practice and research are delineated.

Pressure induced superconductivity in CaFe2As2.

Abstract: ${\mathrm{CaFe}}_{2}{\mathrm{As}}_{2}$ has been found to be exceptionally sensitive to the application of hydrostatic pressure and can be tuned to reveal all the salient features associated with FeAs superconductivity without introducing any disorder. The ambient pressure, 170 K, structural/magnetic, first-order phase transition is suppressed to 128 K by 3.5 kbar. At 5.5 kbar a new transition is detected at 104 K, increasing to above 300 K by 19 kbar. A low temperature, superconducting dome (${T}_{c}\ensuremath{\sim}12\text{ }\text{ }\mathrm{K}$) is centered around 5 kbar, extending down to 2.3 kbar and up to 8.6 kbar. This superconducting phase appears to exist when the low pressure transition is suppressed sufficiently, but before the high pressure transition has reduced the resistivity too dramatically.

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

Abstract: Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (~5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide.

Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.

Abstract: Background: Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities. Methodology/Principal Findings: We present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92%) versus ribosomal RNA. Analysis of corresponding metagenomes confirms much higher levels of assembly in the metatranscriptomic samples and a far higher yield of large gene families with .100 members, ,91% of which were novel. Conclusions/Significance: This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities – if we can overcome the challenges of elucidating the functions of so many never-seen-before gene families.

The walls speak: the interplay of quality facilities, school climate, and student achievement

Abstract: Purpose – A growing body of research connecting the quality of school facilities to student performance accompanies recent efforts to improve the state of the educational infrastructure in the USA. Less is known about the mechanisms of these relationships. This paper seeks to examine the proposition that part of the explanation may be the mediating influence of school climate.Design/methodology/approach – Teachers from 80 Virginia middle schools were surveyed employing measures including the School Climate Index, a seven‐item quality of school facilities scale, as well as three resource support items. Data on student SES and achievement were also gathered. Bivariate correlational analysis was used to explore the relationships between the quality of facilities, resource support, school climate, student SES, and student achievement. In addition, multiple regression was used to test school climate as a mediating variable between the quality of facilities and student achievement.Findings – Results confirmed a...

Uses and interpretations of non‐word repetition tasks in children with and without specific language impairments (SLI)

Abstract: Background: The non-word repetition task (NRT) has gained wide acceptance in describing language acquisition in both children with normal language development (NL) and children with specific language impairments (SLI). This task has gained wide acceptance because it so closely matches the phonological component of word learning, and correlates with measures of phonological working memory, a deficit in which is hypothesized to underlie SLI. Aims/Methods & Procedures: Recent uses of the NRT seem to accept it as a measure of phonological working memory capacity in spite of the fact that researchers have consistently acknowledged that the task taps many language processes, including speech perception, phonological encoding, phonological memory, phonological assembly and articulation. This paper reviews the literature on the use of the nonword repetition task (NRT) in children with NL and children with SLI, emphasizing the component skills necessary for successful repetition. Main Contribution: For children with NL, discussion has focused on (1) the relationship between non-word repetition ability and vocabulary, and (2) lexical and sublexical influences on repetition accuracy. For children with SLI, discussion has focused on these factors as well, but has also considered other component skills that support non-word repetition. Researchers have examined speech perception and discrimination, phonological encoding, phonological memory, phonological assembly, motor planning, and articulation, and have found evidence that children with SLI exhibit impairments in each of these supporting skills. Conclusions: Because repetition accuracy depends on lexical and sublexical properties, the NRT can be used to examine the structural properties of the lexicon in both children with NL and with SLI. Further, because the task taps so many underlying skills, it is a powerful tool that can be used to identify children with language impairments.

Structure and Mechanical Properties of Selected Biological Materials

Abstract: Mineralized biological tissues offer insight into how nature has evolved these components to optimize multifunctional purposes. These mineral constituents are weak by themselves, but interact with the organic matrix to produce materials with unexpected mechanical properties. The hierarchical structure of these materials is at the crux of this enhancement. Microstructural features such as organized, layered organic/inorganic structures and the presence of porous and fibrous elements are common in many biological components. The organic and inorganic portions interact at the molecular and micro-levels synergistically to enhance the mechanical function. In this paper, we report on recent progress on studies of the abalone and Araguaia river clam shells, arthropod exoskeletons, antlers, tusks, teeth and bird beaks.

The Effect of a Single-Session Attention Modification Program on Response to a Public-Speaking Challenge in Socially Anxious Individuals

Abstract: Research suggests that individuals with social anxiety show an attention bias for threat-relevant information However, few studies have directly manipulated attention to examine its effect on anxiety. In the current article, the authors tested the hypothesis that an attention modification program would be effective in reducing anxiety response and improving performance on a public-speaking challenge. Socially anxious participants completed a probe detection task by identifying letters (E or F) replacing one member of a pair of faces (neutral or disgust). The authors trained attention by including a contingency between the location of the neutral face and the probe in one group (Attention Modification Program; AMP). Participants in the AMP group showed significantly less attention bias to threat after training and lower levels of anxiety in response to a public-speaking challenge than did the participants in the Attention Control Condition (ACC) group. Moreover, blind raters judged the speeches of those in the AMP group as better than those in the ACC group. These results are consistent with the hypothesis that attention plays a causal role in the maintenance of social anxiety.

Relationships between the surface concentration of particulate organic carbon and optical properties in the eastern South Pacific and eastern Atlantic Oceans

Abstract: We have examined several approaches for estimating the surface concentration of particulate organic carbon, POC, from optical measurements of spectral remote-sensing reflectance, Rrs(λ), using field data collected in tropical and subtropical waters of the eastern South Pacific and eastern Atlantic Oceans These approaches include a direct empirical relationship between POC and the blue-to-green band ratio of reflectance, Rrs(λB)/Rrs(555), and two-step algorithms that consist of relationships linking reflectance to an inherent optical property IOP (beam attenuation or backscattering coefficient) and POC to the IOP We considered two-step empirical algorithms that exclusively include pairs of empirical relationships and two-step hybrid algorithms that consist of semianalytical models and empirical relationships The surface POC in our data set ranges from about 10 mg m−3 within the South Pacific Subtropical Gyre to 270 mg m−3 in the Chilean upwelling area, and ancillary data suggest a considerable variation in the characteristics of particulate assemblages in the investigated waters The POC algorithm based on the direct relationship between POC and Rrs(λB)/Rrs(555) promises reasonably good performance in the vast areas of the open ocean covering different provinces from hyperoligotrophic and oligotrophic waters within subtropical gyres to eutrophic coastal upwelling regimes characteristic of eastern ocean boundaries The best error statistics were found for power function fits to the data of POC vs Rrs(443)/Rrs(555) and POC vs Rrs(490)/Rrs(555) For our data set that includes over 50 data pairs, these relationships are characterized by the mean normalized bias of about 2% and the normalized root mean square error of about 20% We recommend that these algorithms be implemented for routine processing of ocean color satellite data to produce maps of surface POC with the status of an evaluation data product for continued work on algorithm development and refinements The two-step algorithms also deserve further attention because they can utilize various models for estimating IOPs from reflectance, offer advantages for developing an understanding of bio-optical variability underlying the algorithms, and provide flexibility for regional or seasonal parameterizations of the algorithms

Leader--member exchange, differentiation, and psychological contract fulfillment: a multilevel examination.

Abstract: Prior integrations of the leader-member exchange (LMX) and psychological contract literatures have not clarified how within-group LMX differentiation influences employees' attitudes and behaviors in the employment relationship. Therefore, using a sample of 278 members and managers of 31 intact work groups at 4 manufacturing plants, the authors examined how LMX operating at the within-group level (relative LMX, or RLMX) and the group level influenced perceptions of psychological contract fulfillment and employee-level outcomes. Controlling for individual-level perceptions of LMX quality, results indicated a positive relationship between RLMX and fulfillment, which was strengthened as group-level variability in LMX quality increased. Perceptions of fulfillment mediated the relationship between RLMX and performance and sportsmanship behaviors. The importance of conceptualizing LMX as simultaneously operating at multiple levels is highlighted.

Prefrontal Cortex Volumes in Adolescents With Alcohol Use Disorders: Unique Gender Effects

Abstract: In the United States, alcohol is the most widely consumed intoxicant among adolescents, with 75% of 12th graders having drank in their lifetime. More startling is that 30% of seniors reported getting drunk in the previous month (Johnston et al., 2005). Given the prevalence of alcohol use during adolescence, its effects on neuromaturation are of great interest. In adults, the prefrontal cortex (PFC) appears to be particularly vulnerable to the neurotoxic effects of alcohol use (Desmond et al., 2003; George et al., 2004; Pfefferbaum et al., 1997, 2001; Schweinsburg et al., 2001; Sullivan et al., 2003). Postmortem studies have found reduced glial and neuronal cell densities in the PFC of adults with alcohol use disorders (AUD) (Miguel-Hidalgo et al., 2006). Morphometric studies have revealed smaller PFC total volume (Kubota et al., 2001; Liu et al., 1998), gray matter (Chanraud et al., 2007; Liu et al., 1998; Pfefferbaum et al., 1997), and white matter volume (Kril et al., 1997; Pfefferbaum et al., 1997) among adults with AUD compared with controls. The more anterior portions of the PFC appear most vulnerable to alcohol-induced neurotoxic effects (Kril et al., 1997). Gender may moderate the effects of alcohol on PFC morphometry. It appears that women with AUD may be more sensitive to the neurotoxic effects of alcohol than men (Agartz et al., 1999; Hommer et al., 2001; Mann et al., 2005; Schweinsburg et al., 2003), although some studies have pointed to relative vulnerabilities in males (Pfefferbaum et al., 2001) and others found no evidence of brain abnormalities among alcoholic females (Kroft et al., 1991; Pfefferbaum et al., 2002). Because neuromaturation continues into late adolescence (Giedd et al., 1996a; Lenroot and Giedd, 2006; Sowell et al., 2004) studies based on adults cannot necessarily generalize to adolescents with AUD, particularly findings in the PFC, a late region to undergo gray matter pruning (Gogtay et al., 2004; Lenroot and Giedd, 2006; Sowell et al., 2004). Maturation of white matter appears to continue into the twenties, with white matter volume typically increasing (Giedd et al., 1999; Jernigan and Gamst, 2005; Paus et al., 2001) and PFC white matter integrity improving (Ashtari et al., 2007; Barnea-Goraly et al., 2005; Watts et al., 2003) from childhood to adulthood, although 1 study found decreased white matter density from ages 16 to 17 (Paus et al., 1999). Gender differences in neuromaturation also exist. Females' frontal gray matter volumes peaks at age 11.0 while males' peak at age 12.1 years on average, and male brains are about 9% larger than females' (Giedd et al., 1996b). Furthermore, in contrast with most prior studies of white matter neuromaturation (e.g., Giedd et al., 1999; Reiss et al., 1996), our laboratory found that among healthy adolescent females ages 12 to 18, PFC white matter volume actually decreased from age 15 to 18, while males' PFC white matter remained relatively stable (Nagel et al., 2006). Thus, as male and female brains mature with somewhat different time courses during adolescence, neurotoxic exposures may have disparate effects. Animal models indicate that adolescence is a period of particular vulnerability to the neurotoxic effects of alcohol (Barron et al., 2005; Carpenter-Hyland and Chandler, 2007; Crews et al., 2000; Spear, 2000). Compared with adults, adolescent animals exposed to alcohol are more likely to demonstrate cognitive, social, and neuronal damage (Crews et al., 2000; Little et al., 1996; Pyapali et al., 1999; Silveri and Spear, 1998; Swartzwelder et al., 1995, 1998; Varlinskaya and Spear, 2006; White et al., 2002; Yttri et al., 2004). Despite that many of these abnormalities are subserved by frontal systems, few studies have examined the PFC morphometric consequences of heavy alcohol use during adolescence in humans. Thus far, human adolescent studies examining the neural effects of heavy drinking have suggested alcohol-related structural (De Bellis et al., 2000, 2005; Medina et al., 2007a; Nagel et al., 2005), and functional (Tapert et al., 2004) abnormalities. Specifically, despite similar performance during a spatial working memory task, adolescents with AUD showed less PFC and cerebellar activation to complete the task with controls, with a greater degree of abnormality linked to lifetime alcohol withdrawal symptoms (Tapert et al., 2004). These results may indicate that the brain compensates for subtle alcohol-induced neuronal insult by relying on other areas (e.g., parietal cortex). A follow-up study revealed that gender moderated the relationship between alcohol use and brain response to this spatial working memory task (Caldwell et al., 2005). That is, after controlling for typical blood alcohol concentrations, girls with AUD demonstrated less frontal cortex response than female controls, while the males showed the opposite pattern. Overall, females demonstrated more alcohol-related abnormalities than males. The only study to date examining PFC morphometry (defined as anterior to the genu) in adolescents with AUD compared a treatment sample of 13- to 21-year olds with AUD and other Axis I disorders (including conduct, depressive, attention deficit hyperactivity, post-traumatic stress, generalized anxiety, bipolar, and cannabis and hallucinogen use disorders) to controls without a history of AUD (De Bellis et al., 2005). Even after controlling for comorbid disorders, males and females with AUD demonstrated smaller PFC total and white matter volumes than controls, although psychiatric contributions cannot entirely be ruled out, and gender-by-group interactions were not found. Therefore, no studies to date have examined PFC volume among adolescents with AUD without comorbid psychiatric disorders. As comorbid psychiatric and other premorbid risk factors for substance use disorders (e.g., familial AUD) are also linked to neurocognitive abnormalities (Kamarajan et al., 2006; Kim et al., 2001; Kruesi et al., 2004; Meyerhoff et al., 2004; Tapert and Brown, 2000), the current study sought to examine the relationship between AUD and PFC structure among adolescents without comorbid mood, attention, or anxiety disorders. Conduct disorder, which is highly prevalent among adolescents with AUD, was statistically controlled for, and family history of substance use disorders was equivalent between the groups. A secondary goal of the study was to examine whether gender moderated the relationship between alcohol use and PFC morphometry.

Sleep disturbances in fibromyalgia syndrome: Relationship to pain and depression

Abstract: Objective This study is an examination of sleep, pain, depression, and physical functioning at baseline and 1-year followup among patients with fibromyalgia syndrome (FMS). Although it is clear that these symptoms are prevalent among FMS patients and that they are related, the direction of the relationship is unclear. We sought to identify and report sleep problems in this population and to examine their relationship to pain, depression, and physical functioning. Methods Patients diagnosed with fibromyalgia were recruited from a Southern California health maintenance organization and evaluated according to American College of Rheumatology criteria in the research laboratory. Six hundred patients completed the baseline assessment and 492 completed the 1-year assessment. Measures included the Center for Epidemiologic Studies Depression Scale, the McGill Pain Questionnaire, the Pittsburgh Sleep Quality Index, and the Fibromyalgia Impact Questionnaire. Results The majority of the sample (96% at baseline and 94.7% at 1 year) scored within the range of problem sleepers. Path analyses examined the impact of baseline values on 1-year values for each of the 4 variables. No variable of interest predicted sleep, sleep predicted pain (β = 0.13), pain predicted physical functioning (β = −0.13), and physical functioning predicted depression (β = −0.10). Conclusion These findings highlight the high prevalence of sleep problems in this population and suggest that they play a critical role in exacerbating FMS symptoms. Furthermore, they support limited existing findings that sleep predicts subsequent pain in this population, but also extend the literature, suggesting that sleep may be related to depression through pain and physical functioning.

Governing by Managing Identity Boundaries: The Case of Family Businesses

Abstract: In this paper we illustrate how boundary theory can be a useful perspective to understand the dynamics of family businesses. We integrate insights from the family business literature with the work–family and identity boundary literatures to describe degrees of integration between the family and business identities in family firms and outline contingencies that influence this integration. We also develop the notion of “differential permeability” as a state of being both integrated and segmented on various aspects of identity and articulate costs and benefits to this state, as well as to high integration and high segmentation. Finally, we invoke the research on “boundary work” as a means of managing family business boundaries and conclude by outlining additional avenues of research that stem from using such a boundary theory lens.

Phylogenetic classification of short environmental DNA fragments

Abstract: Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives the opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, the phylogenetic analysis of the short reads produced represents a significant computational challenge. The phylogenetic algorithm CARMA for predicting the source organisms of environmental 454 reads is described. The algorithm searches for conserved Pfam domain and protein families in the unassembled reads of a sample. These gene fragments (environmental gene tags, EGTs), are classified into a higher-order taxonomy based on the reconstruction of a phylogenetic tree of each matching Pfam family. The method exhibits high accuracy for a wide range of taxonomic groups, and EGTs as short as 27 amino acids can be phylogenetically classified up to the rank of genus. The algorithm was applied in a comparative study of three aquatic microbial samples obtained by 454 pyrosequencing. Profound differences in the taxonomic composition of these samples could be clearly revealed.