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Lung diseases caused by microbial infections affect hundreds of millions of children and adults throughout the world. In Western populations, the treatment of lung infections is a primary driver of antibiotic resistance. Traditional therapeutic strategies have been based on the premise that the healthy lung is sterile and that infections grow in a pristine environment. As a consequence, rapid advances in our understanding of the composition of the microbiota of the skin and bowel have not yet been matched by studies of the respiratory tree. The recognition that the lungs are as populated with microorganisms as other mucosal surfaces provides the opportunity to reconsider the mechanisms and management of lung infections. Molecular analyses of the lung microbiota are revealing profound adverse responses to widespread antibiotic use, urbanization and globalization. This Opinion article proposes how technologies and concepts flowing from the Human Microbiome Project can transform the diagnosis and treatment of common lung diseases.

Objective: Hazardous drinking is associated with other risky behaviors and negative health-related outcomes. This study examined covariation between hazardous drinking scores and the following risky driving behaviors: Falling asleep while driving, texting (receiving and sending) while driving, and driving after consuming alcohol., Methods: The participants in this study were a sample of undergraduate students (N = 1,298) who were enrolled in an introductory health course at a large Southeastern university in spring 2016 and completed an online health survey that assessed hazardous drinking, falling asleep while driving, texting while driving, and driving after consuming alcohol. We conducted a series of 2-step regression analyses to examine covariation between hazardous drinking scores (using the Alcohol Use Disorders Identification Test-Consumption [AUDIT-C]) and the risky driving behaviors of interest., Results: We found that the majority of participants did not drink and drive (91.8%), nor did they fall asleep while driving (80.4%); however, the majority did read a text while driving (81.7%) and sent a text while driving (75.3%). In the full multivariable model, hazardous drinking score was positively associated with drinking and driving (step 2 odds ratio [OR] = 1.28, 95% confidence interval [CI], 1.18, 1.38) and sending a text message while driving (step 2 b = 0.19, P = .01). Hazardous drinking score was also positively associated with reading a text while driving (step 1 b = 0.14, P < .001) and falling asleep while driving (step 1 b = 0.02, P = .02) in the model only controlling for demographic characteristics. The analyses also indicated covariability between the following risky driving behaviors: (1) drinking and driving/reading a text message while driving, (2) drinking and driving/falling asleep and driving, (3) reading a text while driving/sending a text while driving, and (4) sending a text while driving/sleeping and driving., Conclusion: The findings of this study indicate a need for interventions discouraging both hazardous drinking and risky driving behaviors in college student populations; recommendations to reduce risky driving and hazardous drinking are discussed.

This study examined the independent and mediated associations between maternal depression symptoms (MDS), mother-child interaction, and child executive function (EF) in a prospective longitudinal sample of 1,037 children (50% boys) from predominantly low-income and rural communities. When children were 6, 15 and 24 months of age, mothers reported their level of depressive symptomatology. At 24 and 36 months of age, mother-child interactions during play were rated for warmth-sensitivity and harsh-intrusiveness, and dyadic joint attention and maternal language complexity were assessed from a book sharing activity. Children's EF (i.e., inhibitory control, working memory, and set shifting) were assessed at ages 36 and 48 months using a battery of six tasks. Results indicated that MDS at ages 15 and 24 months were negatively associated with children's EF at age 48 months. Additionally, harsh-intrusive mother-child interactions partially mediated this link. Although warmth-sensitivity, dyadic joint attention and maternal language complexity were all longitudinally related to EF, they did not serve as mediating mechanisms between MDS and EF. These results were obtained while controlling for multiple demographic factors, children's earlier cognitive abilities, maternal general distress and childcare experiences. Findings from this study identify 1 mechanism through which early exposure to MDS could be related to children's EF. (PsycINFO Database Record, ((c) 2018 APA, all rights reserved).)

Competing Interests: Competing interests: None declared.

Parent-adolescent relationship (PAR) factors such as social support and negative interactions are associated with initiation of alcohol and marijuana use during adolescence. However, few studies have examined whether the relationship between PAR, especially the paternal role, and substance use onset varies by ethnicity. This is important given that ethnic group differences have been related to alcohol and marijuana use, cultural values and parenting. This study examines whether ethnicity moderates the prospective prediction of substance use onset by PAR factors. The sample comprised 124 adolescents who self-identified as Hispanic and 795 adolescents who self-identified as non-Hispanic Whites, and was drawn from an ongoing longitudinal survey on adolescent substance use. Discrete-time survival modeling was used to prospectively predict age at onset of substance use among participants who were substance-naïve at baseline. Interactions between ethnicity and PAR factors indicated that PAR factors had a larger influence on age of alcohol and marijuana onset for Hispanics than for Caucasians. Among Hispanics, greater social support from and greater negative interactions with the father-figure were more predictive of earlier onset of alcohol, and greater social support from the mother-figure was more predictive of later alcohol onset, compared to Caucasians. Similarly, greater negative interactions with the father-figure were more predictive of earlier onset of marijuana use among Hispanics than among Caucasians. These findings suggest the influence of PAR on alcohol and marijuana use onset may be larger for Hispanics than for Caucasians. Incorporating these parenting factors in substance use prevention programs advances public health in a culturally sensitive manner that is relevant to at-risk Hispanic adolescents., (Published by Elsevier Ltd.)

Little research has examined the legacy of early maternal care for later attachment representations among low-income and ethnic minority school-aged children. Using data from a sample of 276 rural, low-income, African-American families, this study examined associations between maternal care in infancy and children's representations of attachment figures in middle childhood. Maternal care was coded from 10-min home-based observations at 6, 15, and 24 months of age. Representations of attachment figures were assessed using the Manchester Child Attachment Story Task at 6 years of age. Sensitive maternal care in infancy was not significantly related to attachment security or episodic disorganized behaviors in children's representations. However, children exposed to more harsh-intrusive parenting during infancy displayed less secure representations of attachment figures in middle childhood and more episodic disorganized behaviors, even after controlling for numerous child and family contextual covariates. Findings inform conceptualizations of attachment formation among rural, low-income, African-American parent-child dyads.

Rationale: Changes in the respiratory microbiome are associated with disease progression in idiopathic pulmonary fibrosis (IPF). The role of the host response to the respiratory microbiome remains unknown., Objectives: To explore the host-microbial interactions in IPF., Methods: Sixty patients diagnosed with IPF were prospectively enrolled together with 20 matched control subjects. Subjects underwent bronchoalveolar lavage (BAL), and peripheral whole blood was collected into PAXgene tubes for all subjects at baseline. For subjects with IPF, additional samples were taken at 1, 3, and 6 months and (if alive) 1 year. Gene expression profiles were generated using Affymetrix Human Gene 1.1 ST arrays., Measurements and Main Results: By network analysis of gene expression data, we identified two gene modules that strongly associated with a diagnosis of IPF, BAL bacterial burden (determined by 16S quantitative polymerase chain reaction), and specific microbial operational taxonomic units, as well as with lavage and peripheral blood neutrophilia. Genes within these modules that are involved in the host defense response include NLRC4, PGLYRP1, MMP9, and DEFA4. The modules also contain two genes encoding specific antimicrobial peptides (SLPI and CAMP). Many of these particular transcripts were associated with survival and showed longitudinal overexpression in subjects experiencing disease progression, further strengthening the relationship of the transcripts with disease., Conclusions: Integrated analysis of the host transcriptome and microbial signatures demonstrated an apparent host response to the presence of an altered or more abundant microbiome. These responses remained elevated in longitudinal follow-up, suggesting that the bacterial communities of the lower airways may act as persistent stimuli for repetitive alveolar injury in IPF.

Despite long-standing hypotheses that intimate partner violence (IPV) may undermine children's ability to form secure attachment representations, few studies have empirically investigated this association. Particularly lacking is research that examines IPV and attachment during middle childhood, a time when the way that children understand, represent, and process the behavior of others becomes particularly important. Using data from a sample of African American children living in rural, low-income communities ( n = 98), the current study sought to address this gap by examining the association between physical IPV occurring early in children's lives and their attachment security during the first grade. Results indicate that, even after controlling for child- and family-level covariates, physical IPV was associated with a greater likelihood of being rated insecurely attached. This effect was above and beyond the influence of maternal parenting behaviors, demonstrating a unique effect of physical IPV on children's attachment representations during middle childhood.

Conventional distance sampling (CDS) methods assume that animals are uniformly distributed in the vicinity of lines or points. But when animals move in response to observers before detection, or when lines or points are not located randomly, this assumption may fail. By formulating distance sampling models as survival models, we show that using time to first detection in addition to perpendicular distance (line transect surveys) or radial distance (point transect surveys) allows estimation of detection probability, and hence density, when animal distribution in the vicinity of lines or points is not uniform and is unknown. We also show that times to detection can provide information about failure of the CDS assumption that detection probability is 1 at distance zero. We obtain a maximum likelihood estimator of line transect survey detection probability and effective strip half-width using times to detection, and we investigate its properties by simulation in situations where animals are nonuniformly distributed and their distribution is unknown. The estimator is found to perform well when detection probability at distance zero is 1. It allows unbiased estimates of density to be obtained in this case from surveys in which there has been responsive movement prior to animals coming within detectable range. When responsive movement continues within detectable range, estimates may be biased but are likely less biased than estimates from methods that assuming no responsive movement. We illustrate by estimating primate density from a line transect survey in which animals are known to avoid the transect line, and a shipboard survey of dolphins that are attracted to it., (© 2016, The International Biometric Society.)

Consistent with the gustatory-vagal hypothesis, vagal stimulation during breastfeeding may contribute to infants' physiological regulatory development independent of caregiving effects. This study examined whether breastfeeding predicted 6-month-old infants' (N = 151) and their mothers' vagal regulation during the face-to-face still-face (FFSF). Although breastfed and nonbreastfed infants showed expected vagal withdrawal during the Still-Face episode, only breastfed infants showed continued withdrawal during the reunion episode, suggesting greater physiological mobilization to repair the interaction. Breastfeeding mothers showed higher vagal tone than nonbreastfeeding mothers at baseline, suggesting greater capacity for regulation, and throughout the FFSF, suggesting calmer states. Breastfeeding effects were independent of maternal sensitivity. Findings suggest that infants' and mothers' physiological regulation may be shaped by breastfeeding independently of associated social factors., (© 2016 The Authors. Child Development © 2016 Society for Research in Child Development, Inc.)

Kinases and transcription factors (TFs) are key modulators of important signaling pathways and their activities underlie the proper function of many basic cellular processes such as cell division, differentiation, and development. Changes in kinase and TF dosage are often associated with disease, yet a systematic assessment of the cellular phenotypes caused by the combined perturbation of kinases and TFs has not been undertaken. We used a reverse-genetics approach to study the phenotypic consequences of kinase and TF overexpression (OE) in the budding yeast, Saccharomyces cerevisiae We constructed a collection of strains expressing stably integrated inducible alleles of kinases and TFs and used a variety of assays to characterize the phenotypes caused by TF and kinase OE. We used the Synthetic Genetic Array (SGA) method to examine dosage-dependent genetic interactions (GIs) between 239 gain-of-function (OE) alleles of TFs and six loss-of-function (LOF) and seven OE kinase alleles, the former identifying Synthetic Dosage Lethal (SDL) interactions and the latter testing a GI we call Double Dosage Lethality (DDL). We identified and confirmed 94 GIs between 65 OE alleles of TFs and 9 kinase alleles. Follow-up experiments validated regulatory relationships between genetically interacting pairs (Cdc28-Stb1 and Pho85-Pdr1), suggesting that GI studies involving OE alleles of regulatory proteins will be a rich source of new functional information., (Copyright © 2017 Youn et al.)

This study investigated the interaction between children's parasympathetic functioning and maternal sensitive parenting behaviors during infancy and toddlerhood in the prediction of children's executive functions (EF) at the age of 5 years. Participants included 137 children and their mothers who were followed from the age of 3 months to 5 years. Children's cardiac activity was recorded at rest at multiple times from ages 3 to 36 months, and estimates of respiratory sinus arrhythmia (RSA; a measure of parasympathetic functioning) were calculated. Sensitive parenting was assessed during a mother-child play task at ages 6, 12, 24, and 36 months, and 5 years. Children completed age appropriate EF tasks at the age of 5 years. The link between sensitive parenting during toddlerhood (ages 24 and 36 months) and children's later EF was moderated by children's RSA such that this positive link was evident only among children who had low levels of baseline RSA, and not among those who had high levels of baseline RSA. These findings were obtained while controlling for concurrent sensitive parenting and maternal and child verbal abilities. Results from this study provide evidence for the significant role of biopsychosocial processes in early childhood in the development of EF., (Copyright © International Congress of Infant Studies (ICIS).)

Background: Patients with asthma and healthy controls differ in bacterial colonization of the respiratory tract. The upper airways have been shown to reflect colonization of the lower airways, the actual site of inflammation in asthma, which is hardly accessible in population studies., Objective: We sought to characterize the bacterial communities at 2 sites of the upper respiratory tract obtained from children from a rural area and to relate these to asthma., Methods: The microbiota of 327 throat and 68 nasal samples from school-age farm and nonfarm children were analyzed by 454-pyrosequencing of the bacterial 16S ribosomal RNA gene., Results: Alterations in nasal microbiota but not of throat microbiota were associated with asthma. Children with asthma had lower α- and β-diversity of the nasal microbiota as compared with healthy control children. Furthermore, asthma presence was positively associated with a specific operational taxonomic unit from the genus Moraxella in children not exposed to farming, whereas in farm children Moraxella colonization was unrelated to asthma. In nonfarm children, Moraxella colonization explained the association between bacterial diversity and asthma to a large extent., Conclusions: Asthma was mainly associated with an altered nasal microbiota characterized by lower diversity and Moraxella abundance. Children living on farms might not be susceptible to the disadvantageous effect of Moraxella. Prospective studies may clarify whether Moraxella outgrowth is a cause or a consequence of loss in diversity., (Copyright © 2016 American Academy of Allergy, Asthma & Immunology. All rights reserved.)

This systematic review examines whether negative affect symptoms (i.e., anxiety, depression, and internalizing symptoms more broadly) predict subsequent adolescent substance use after controlling for co-occurring externalizing symptoms. Following PRISMA procedures, we identified 61 studies that tested the association of interest. Findings varied depending on the type of negative affect symptom and to some extent on the substance use outcome. The most consistent associations were evident for depressive symptoms, particularly as predictors of substance use composite scores. No clear association between anxiety and substance use or between internalizing symptoms and substance use was evident, and indeed these associations were as often negative as positive. Mixed findings regarding the depression-substance use association, however, also call for greater attention to potential moderating factors that may help define who, when, and in what context depression serves as an important risk factor for later substance use above and beyond risk associated with externalizing symptoms. (PsycINFO Database Record, ((c) 2017 APA, all rights reserved).)

Background: Bronchiectasis is accompanied by chronic bronchial infection that may drive disease progression. However, the evidence base for antibiotic therapy is limited. DNA based methods offer better identification and quantification of microbial constituents of sputum than standard clinical culture and may help inform patient management strategies. Our study objective was to determine the longitudinal variability of the non-cystic fibrosis (CF) bronchiectasis microbiome in sputum with respect to clinical variables. Eighty-five patients with non-CF bronchiectasis and daily sputum production were recruited from outpatient clinics and followed for six months. Monthly sputum samples and clinical measurements were taken, together with additional samples during exacerbations. 16S rRNA gene sequencing of the sputum microbiota was successful for 381 samples from 76 patients and analysed in conjunction with clinical data., Results: Microbial communities were highly individual in composition and stability, usually with limited diversity and often containing multiple pathogens. When compared to DNA sequencing, microbial culture had restricted sensitivity in identifying common pathogens such as Pseudomonas aeruginosa, Haemophilus influenzae, Moraxella catarrhalis. With some exceptions, community characteristics showed poor correlations with clinical features including underlying disease, antibiotic use and exacerbations, with the subject showing the strongest association with community structure. When present, the pathogens mucoid Pseudomonas aeruginosa and Haemophilus influenzae may also shape the structure of the rest of the microbial community., Conclusions: The use of microbial community analysis of sputum added to information from microbial culture. A simple model of exacerbations driven by bacterial overgrowth was not supported, suggesting a need for revision of principles for antibiotic therapy. In individual patients, the management of chronic bronchial infection may be improved by therapy specific to their microbiome, taking into account pathogen load, community stability, and acute and chronic community responses to antibiotics., Competing Interests: DB received a grant from Novartis UK for sequencing costs. The funder had no involvement in study design, collection or analysis of data, or in the decision to publish. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

The global ocean's near surface can be partitioned into distinct provinces on the basis of regional primary productivity and oceanography [1]. This ecological geography provides a valuable framework for understanding spatial variability in ecosystem function but has relevance only partway into the epipelagic zone (the top 200 m). The mesopelagic (200-1,000 m) makes up approximately 20% of the global ocean volume, plays important roles in biogeochemical cycling [2], and holds potentially huge fish resources [3-5]. It is, however, hidden from satellite observation, and a lack of globally consistent data has prevented development of a global-scale understanding. Acoustic deep scattering layers (DSLs) are prominent features of the mesopelagic. These vertically narrow (tens to hundreds of m) but horizontally extensive (continuous for tens to thousands of km) layers comprise fish and zooplankton and are readily detectable using echosounders. We have compiled a database of DSL characteristics globally. We show that DSL depth and acoustic backscattering intensity (a measure of biomass) can be modeled accurately using just surface primary productivity, temperature, and wind stress. Spatial variability in these environmental factors leads to a natural partition of the mesopelagic into ten distinct classes. These classes demark a more complex biogeography than the latitudinally banded schemes proposed before [6, 7]. Knowledge of how environmental factors influence the mesopelagic enables future change to be explored: we predict that by 2100 there will be widespread homogenization of mesopelagic communities and that mesopelagic biomass could increase by approximately 17%. The biomass increase requires increased trophic efficiency, which could arise because of ocean warming and DSL shallowing., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

This research examined the child, parent, and family conditions under which attachment disorganization was related to both level and change in externalizing behavior during preschool among a community sample. Using the ordinary least squares regression, we found that attachment disorganization at 12 months significantly predicted children's externalizing behavior at 36 months and this prediction was not contingent on any other factors tested. For predicting changes in externalizing behavior from 36 to 60 months, we found a significant main effect of family cumulative risk and an interaction effect between attachment disorganization at 12 months and maternal sensitivity at 24 months. Specifically, high disorganization was related to a significant decrease in externalizing behavior from 36 to 60 months when maternal sensitivity at 24 months was high. Our main-effect findings replicated the significant effect of attachment disorganization and cumulative risk on externalizing behavior with preschool-aged children. Our interaction finding provided support for understanding the parenting conditions under which infant attachment disorganization may be related to change in externalizing behavior during preschool ages. Implications of the findings were discussed.

Deficits in social orienting (i.e., gazing toward caregivers) during dyadic interactions and reactivity to stressful stimuli have been identified as behavioral correlates of oppositional defiant disorder (ODD) and callous-unemotional (CU) behaviors in older children. The goal of the current study was to investigate infants' mother-directed gaze and reactivity during the face-to-face and still-face episodes of the face-to-face stillface paradigm performed at 6 months in the prediction of ODD and CU behaviors in early childhood. Using data from the Durham Child Health and Development study (n = 206), hierarchical regression analyses revealed that infants' negative reactivity during the still-face episode and mother-directed gaze during the face-to-face episode predicted fewer ODD behaviors in early childhood. Examination of interaction effects suggested that mother-directed gaze attenuated the negative relation between reactivity and ODD and CU behaviors in early childhood. The current study is one of the first to extend downward the investigation of ODD and CU behaviors into infancy.

Background: In 2004, Congress passed legislation mandating that all public school districts participating in federal school meal programs develop a school wellness policy (SWP) to direct efforts related to nutrition and physical activity. We examined the extent to which SWPs varied in comprehensiveness and strength in a representative sample of school districts in the southeastern United States, the area of the country with the highest rates of childhood obesity., Methods: Policies were assessed using an established 96-item coding tool by 2 raters to ascertain the comprehensiveness and strength of the policies as a whole, and across distinct subsections specified by federal legislation. In addition, variability in SWP comprehensiveness and strength was assessed based on district sociodemographic characteristics., Results: Overall, SWPs in the southeastern states are weakly written, fragmented, and lack requirements necessary for healthy school environments. District size, which was the only sociodemographic factor related to policy characteristics, yielded an inverse association., Conclusions: To encourage continued promotion of healthy school environments, school districts will require technical support to improve the quality of their school wellness policies., (© 2016, American School Health Association.)

This protocol describes culturing arrays of fluorescently tagged yeast strains to early log-phase in a 96-well format for imaging on a high-throughput (HTP) microscope. The method assumes the use of the synthetic genetic array (SGA) technique to create the array of marked strains. When this approach is coupled with automated image analysis, the subcellular distribution and abundance of tagged proteins can be systematically and quantitatively examined in different genetic backgrounds and/or under different growth regimes., (© 2016 Cold Spring Harbor Laboratory Press.)

Washoff of 17 pyrethroid products resulting from a 1-h, 25.4-mm rainfall occurring 24 h after application was measured in indoor studies with concrete slabs. These products included different pyrethroid active ingredients and a range of formulation types. Based on this replicated study, 5 product pairs with contrasting washoff behaviors were chosen for an outdoor study using 6 full-scale house fronts in central California. Products in 4 of these pairs were applied once to different rectangular areas on the driveway (1 product in each pair to 3 house lots and the other to the remaining 3 house lots). The products in the fifth pair were applied 3 times at 2-mo intervals to vertical stucco walls above the driveway. All house lots received natural and simulated rainfall over 7 mo. Indoor studies showed differences up to 170-fold between paired products, whereas the maximum difference between paired products in the field was only 5-fold. In the pair applied to the wall, 1 product had 91 times the washoff of the other in the indoor study, whereas in the field the same product had 15% lower washoff. These results show that, although the formulation may influence washoff under actual use conditions, its influence is complex and not always as predicted by indoor experiments. Because the formulation also affects insect control, washoff research needs to be conducted together with efficacy testing., (© 2015 The Authors. Published by Wiley Periodicals, Inc. on behalf of SETAC.)

We assessed a multidimensional model of parent alcohol socialization in which key socialization factors were considered simultaneously to identify combinations of factors that increase or decrease risk for development of adolescent alcohol misuse. Of interest was the interplay between putative risk and protective factors, such as whether the typically detrimental effects on youth drinking of parenting practices tolerant of some adolescent alcohol use are mitigated by an effective overall approach to parenting and parental modeling of modest alcohol use. The sample included 1,530 adolescents and their mothers; adolescents' mean age was 13.0 (SD = .99) at the initial assessment. Latent profile analysis was conducted of mothers' reports of their attitude toward teen drinking, alcohol-specific parenting practices, parental alcohol use and problem use, and overall approach to parenting. The profiles were used to predict trajectories of adolescent alcohol misuse from early to middle adolescence. Four profiles were identified: 2 profiles reflected conservative alcohol-specific parenting practices and 2 reflected alcohol-tolerant practices, all in the context of other attributes. Alcohol misuse accelerated more rapidly from Grade 6 through 10 in the 2 alcohol-tolerant compared with conservative profiles. Results suggest that maternal tolerance of some youth alcohol use, even in the presence of dimensions of an effective parenting style and low parental alcohol use and problem use, is not an effective strategy for reducing risky adolescent alcohol use. (PsycINFO Database Record, ((c) 2016 APA, all rights reserved).)

Despite evidence that individuals living in low-income and rural communities may be at heightened risk for intimate partner violence (IPV), little is known about the prevalence and nature of IPV occurring in these communities. The goal of the current study, therefore, was to characterize IPV occurring in a population-based sample of families living in communities characterized by rural poverty. Specifically, we examined the prevalence, severity, and chronicity of IPV occurring in this high-risk sample, as well as the demographic correlates thereof. Using data from multiple assessments across the first five years of their child's life, we also examined changes in the prevalence of IPV across this time. Results indicate that IPV was most prevalent around the birth of the target child and that the population-level prevalence of IPV decreased significantly over the subsequent five years. Although previous research suggests that children under the age of five are at heightened risk for IPV relative to older children, this is the first study to our knowledge to demonstrate that there are changes in the prevalence of IPV within this high-risk age period.

Q fever patients are often reported to experience a long-term impaired health status, including fatigue, which can persist for many years. During the large Q fever epidemic in The Netherlands, many patients with a laboratory-confirmed Coxiella burnetii infection were not notified as acute Q fever because they did not fulfil the clinical criteria of the acute Q fever case definition (fever, pneumonia and/or hepatitis). Our study assessed and compared the long-term health status of notified and non-notified Q fever patients at 4 years after onset of illness, using the Nijmegen Clinical Screening Instrument (NCSI). The study included 448 notified and 193 non-notified Q fever patients. The most severely affected subdomain in both patient groups was 'Fatigue' (50·5% of the notified and 54·6% of the non-notified patients had severe fatigue). Long-term health status did not differ significantly between the notified and non-notified patient groups, and patients scored worse on all subdomains compared to a healthy reference group. Our findings suggest that the magnitude of the 2007-2009 Q fever outbreak in The Netherlands was underestimated when only notified patients according to the European Union case definition are considered.

Background: Late-onset bloodstream infection (LO-BSI) is a common complication of prematurity, and lack of timely diagnosis and treatment can have life-threatening consequences. We sought to identify clinical characteristics and microbial signatures in the gastrointestinal microbiota preceding diagnosis of LO-BSI in premature infants., Method: Daily faecal samples and clinical data were collected over two years from 369 premature neonates (<32 weeks gestation). We analysed samples from 22 neonates who developed LO-BSI and 44 matched control infants. Next-generation sequencing of 16S rRNA gene regions amplified by PCR from total faecal DNA was used to characterise the microbiota of faecal samples preceding diagnosis from infants with LO-BSI and controls. Culture of selected samples was undertaken, and bacterial isolates identified using MALDI-TOF. Antibiograms from bloodstream and faecal isolates were compared to explore strain similarity., Results: From the week prior to diagnosis, infants with LO-BSI had higher proportions of faecal aerobes/facultative anaerobes compared to controls. Risk factors for LO-BSI were identified by multivariate analysis. Enterobacteriaceal sepsis was associated with antecedent multiple lines, low birth weight and a faecal microbiota with prominent Enterobacteriaceae. Staphylococcal sepsis was associated with Staphylococcus OTU faecal over-abundance, and the number of days prior to diagnosis of mechanical ventilation and of the presence of centrally-placed lines. In 12 cases, the antibiogram of the bloodstream isolate matched that of a component of the faecal microbiota in the sample collected closest to diagnosis., Conclusions: The gastrointestinal tract is an important reservoir for LO-BSI organisms, pathogens translocating across the epithelial barrier. LO-BSI is associated with an aberrant microbiota, with abundant staphylococci and Enterobacteriaceae and a failure to mature towards predominance of obligate anaerobes.

Data from a large prospective longitudinal study (n = 1,239) was used to investigate the association between observed sensitive parenting in early childhood and children's representations of family relationships as measured by the Family Drawing Paradigm (FDP) in first grade as well as the extent to which these representations partially mediate the influences of early caregiving experiences on later conduct problems and callous-unemotional behaviors. A structural equation modeling approach revealed that less sensitive parenting at 24, 36, and 58 months predicts higher levels of conduct problems (CP) and callous-unemotional (CU) behaviors in first grade controlling for earlier measures of CP and CU behaviors. Results also indicated that greater dysfunctional family representations, as assessed with the FDP, are significantly associated with higher CU behaviors in the first grade, but not CP. Finally, a test of the indirect pathway suggests that children's dysfunctional family representations may, in part, account for the association between sensitive parenting and CU behaviors., ((c) 2015 APA, all rights reserved).)

Objective: Despite knowledge that intimate partner violence (IPV) can negatively affect children's socioemotional and behavioral development, less is known about the impact of IPV on children's cognitive development, including whether it influences their executive functioning (EF). The goal of the current study was to address this gap in the literature, by examining the association between IPV that occurs early in life and EF at school entry. This study also allowed for the investigation of maternal sensitive parenting behaviors as a possible mediator of this relation., Method: Using longitudinal data from a socioeconomically and racially diverse sample of families ( n = 154), we investigated the association between IPV measured when children were 24, 30, and 36 months old and their EF when they were 60 months old. We also tested whether maternal sensitive parenting behaviors (measured when children were 24, 36, and 60 months old) mediated this association., Results: Results indicate that, even after controlling for a number of family- and child-level covariates, IPV occurring early in children's lives was negatively associated with their EF at school entry. This relation was mediated by maternal sensitive parenting behaviors, such that higher levels of IPV were associated with lower levels of sensitive parenting behaviors, which in turn were positively associated with children's EF., Conclusions: These findings add to a limited body of literature that links IPV and children's cognitive functioning, and suggest that intervention efforts aimed at improving children's EF may want to simultaneously consider IPV and maternal sensitive parenting behaviors.

Proteomics has proved invaluable in generating large-scale quantitative data; however, the development of systems approaches for examining the proteome in vivo has lagged behind. To evaluate protein abundance and localization on a proteome scale, we exploited the yeast GFP-fusion collection in a pipeline combining automated genetics, high-throughput microscopy, and computational feature analysis. We developed an ensemble of binary classifiers to generate localization data from single-cell measurements and constructed maps of ∼3,000 proteins connected to 16 localization classes. To survey proteome dynamics in response to different chemical and genetic stimuli, we measure proteome-wide abundance and localization and identified changes over time. We analyzed >20 million cells to identify dynamic proteins that redistribute among multiple localizations in hydroxyurea, rapamycin, and in an rpd3Δ background. Because our localization and abundance data are quantitative, they provide the opportunity for many types of comparative studies, single cell analyses, modeling, and prediction. VIDEO ABSTRACT., (Copyright © 2015 Elsevier Inc. All rights reserved.)

The present study extends the spillover and crossover hypotheses to more carefully model the potential interdependence between parent-parent interaction quality and parent-child interaction quality in family systems. Using propensity score matching, the present study attempted to isolate family processes that are unique across African American and European American couples that are independent of other socio-demographic factors to further clarify how interparental relationships may be related to parenting in a rural, low-income sample. The Actor-Partner Interdependence Model (APIM), a statistical analysis technique that accounts for the interdependence of relationship data, was used with a sample of married and non-married cohabiting African American and European American couples ( n = 82 dyads) to evaluate whether mothers' and fathers' observed parenting behaviours are related to their behaviours and their partner's behaviours observed in a couple problem-solving interaction. Findings revealed that interparental withdrawal behaviour, but not conflict behaviour, was associated with less optimal parenting for fathers but not mothers, and specifically so for African American fathers. Our findings support the notion of interdependence across subsystems within the family and suggest that African American fathers may be specifically responsive to variations in interparental relationship quality.

This study examines associations between maternal and paternal sensitive parenting and child cognitive development across the first 3 years of life using longitudinal data from 630 families with co-residing biological mothers and fathers. Sensitive parenting was measured by observational coding of parent-child interactions and child cognitive development was assessed with the Bayley Scales of Infant Development and the Wechsler Preschool and Primary Scales of Intelligence. There were multiple direct and indirect associations between parenting and cognitive development across mothers and fathers, suggesting primary effects, carry-forward effects, spillover effects across parents, and transactional effects across parents and children. Associations between parenting and cognitive development were statistically consistent across mothers and fathers, and the cumulative effects of early parenting on later cognitive development were comparable to the effects of later parenting on later cognitive development. As interpreted through a family systems framework, findings suggest additive and interdependent effects across parents and children.

This study examined the development of baseline autonomic nervous system (ANS) and hypothalamic-pituitary-adrenal (HPA) physiological activity from 12 to 36 months as well as antecedents (poverty) and consequents (behavior problems) of individual differences in physiological development. Children (N=179; 50% poor; 56% African American; 52% male) provided saliva samples at 12, 18, 24, 30, and 36 months of age. Latent growth curve models indicated that nonlinear change was evident for both sAA and cortisol, with sAA increasing and cortisol decreasing with age. Children residing in poor households exhibited lower initial levels of sAA, but not cortisol. African-American children showed slightly smaller decreases in cortisol over time. Initial levels of sAA predicted higher levels of internalizing behaviors at 36 months and both initial levels of and total change in sAA predicted higher levels of externalizing behaviors at 36 months. There was no evidence that sAA or cortisol mediated the relationship between poverty and later behavior problems., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Background: Necrotizing enterocolitis (NEC) is a devastating inflammatory bowel disease of premature infants speculatively associated with infection. Suspected NEC can be indistinguishable from sepsis, and in established cases an infant may die within hours of diagnosis. Present treatment is supportive. A means of presymptomatic diagnosis is urgently needed. We aimed to identify microbial signatures in the gastrointestinal microbiota preceding NEC diagnosis in premature infants., Methods: Fecal samples and clinical data were collected from a 2-year cohort of 369 premature neonates. Next-generation sequencing of 16S ribosomal RNA gene regions was used to characterize the microbiota of prediagnosis fecal samples from 12 neonates with NEC, 8 with suspected NEC, and 44 controls. Logistic regression was used to determine clinical characteristics and operational taxonomic units (OTUs) discriminating cases from controls. Samples were cultured and isolates identified using matrix-assisted laser desorption/ionization-time of flight. Clostridial isolates were typed and toxin genes detected., Results: A clostridial OTU was overabundant in prediagnosis samples from infants with established NEC (P = .006). Culture confirmed the presence of Clostridium perfringens type A. Fluorescent amplified fragment-length polymorphism typing established that no isolates were identical. Prediagnosis samples from NEC infants not carrying profuse C. perfringens revealed an overabundance of a Klebsiella OTU (P = .049). Prolonged continuous positive airway pressure (CPAP) therapy with supplemental oxygen was also associated with increased NEC risk., Conclusions: Two fecal microbiota signatures (Clostridium and Klebsiella OTUs) and need for prolonged CPAP oxygen signal increased risk of NEC in presymptomatic infants. These biomarkers will assist development of a screening tool to allow very early diagnosis of NEC. Clinical Trials Registration. NCT01102738., (© The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Many pelagic species (species that live in the water column), including herring and krill, aggregate to form schools, shoals, or swarms (hereafter simply "schools," although the words are not synonyms). Schools provide benefits to individual members, including locomotory economy and protection from predators that prey on individuals, but paradoxically make schooling species energetically viable and commercially attractive targets for predators of groups and for fishers. Large schools are easier to find and yield greater prey/catch than small schools, and there is a requirement from fields as diverse as theoretical ecology and fisheries management to understand whether and how aggregation sizes change with changing population size. We collated data from vertical echosounder surveys of taxonomically diverse pelagic stocks from geographically diverse ecosystems. The data contain common significant positive linear stock-biomass to school-number relationships. They show that the numbers of schools in the stocks change with changing stock biomass and suggest that the distributions of school sizes do not change with stock biomass. New data that we collected using a multibeam sonar, which can image entire schools, contained the same stock-biomass to school-number relationship and confirm that the distribution of school sizes is not related to changing stock size: put simply, as stocks decline, individuals are distributed among fewer schools, not smaller schools. Since school characteristics affect catchability (the ease or difficulty with which fishers can capture target species) and availability of prey to predators, our findings have commercial and ecological implications, particularly within the aspirational framework of ecosystem-based management of marine systems., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Antarctic krill (Euphausia superba; herein krill) is monitored as part of an on-going fisheries observer program that collects length-frequency data. A krill feedback management programme is currently being developed, and as part of this development, the utility of data-derived indices describing population level processes is being assessed. To date, however, little work has been carried out on the selection of optimum recruitment indices and it has not been possible to assess the performance of length-based recruitment indices across a range of recruitment variability. Neither has there been an assessment of uncertainty in the relationship between an index and the actual level of recruitment. Thus, until now, it has not been possible to take into account recruitment index uncertainty in krill stock management or when investigating relationships between recruitment and environmental drivers. Using length-frequency samples from a simulated population - where recruitment is known - the performance of six potential length-based recruitment indices is assessed, by exploring the index-to-recruitment relationship under increasing levels of recruitment variability (from ±10% to ±100% around a mean annual recruitment). The annual minimum of the proportion of individuals smaller than 40 mm (F40 min, %) was selected because it had the most robust index-to-recruitment relationship across differing levels of recruitment variability. The relationship was curvilinear and best described by a power law. Model uncertainty was described using the 95% prediction intervals, which were used to calculate coverage probabilities and assess model performance. Despite being the optimum recruitment index, the performance of F40 min degraded under high (>50%) recruitment variability. Due to the persistence of cohorts in the population over several years, the inclusion of F40 min values from preceding years in the relationship used to estimate recruitment in a given year improved its accuracy (mean bias reduction of 8.3% when including three F40 min values under a recruitment variability of 60%).

Using data from a diverse sample of 620 families residing in rural, predominately low-income communities, this study examined longitudinal links between fathers' sensitive parenting in infancy and toddlerhood and children's early executive functioning, as well as the contribution of maternal sensitive parenting. After accounting for the quality of concurrent and prior parental care, children's early cognitive ability, and other child and family factors, fathers' and mothers' sensitive and supportive parenting during play at 24 months predicted children's executive functioning at 3 years of age. In contrast, paternal parenting quality during play at 7 months did not make an independent contribution above that of maternal care, but the links between maternal sensitive and supportive parenting and executive functioning seemed to operate in similar ways during infancy and toddlerhood. These findings add to prior work on early experience and children's executive functioning, suggesting that both fathers and mothers play a distinct and complementary role in the development of these self-regulatory skills.

Background: The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents., Results: In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination., Conclusions: These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. Concurrent sequencing of negative control samples is strongly advised.

Rationale: Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease of unknown cause that leads to respiratory failure and death within 5 years of diagnosis. Overt respiratory infection and immunosuppression carry a high morbidity and mortality, and polymorphisms in genes related to epithelial integrity and host defense predispose to IPF., Objectives: To investigate the role of bacteria in the pathogenesis and progression of IPF., Methods: We prospectively enrolled patients diagnosed with IPF according to international criteria together with healthy smokers, nonsmokers, and subjects with moderate chronic obstructive pulmonary disease as control subjects. Subjects underwent bronchoalveolar lavage (BAL), from which genomic DNA was isolated. The V3-V5 region of the bacterial 16S rRNA gene was amplified, allowing quantification of bacterial load and identification of communities by 16S rRNA quantitative polymerase chain reaction and pyrosequencing., Measurements and Main Results: Sixty-five patients with IPF had double the burden of bacteria in BAL fluid compared with 44 control subjects. Baseline bacterial burden predicted the rate of decline in lung volume and risk of death and associated independently with the rs35705950 polymorphism of the MUC5B mucin gene, a proven host susceptibility factor for IPF. Sequencing yielded 912,883 high-quality reads from all subjects. We identified Haemophilus, Streptococcus, Neisseria, and Veillonella spp. to be more abundant in cases than control subjects. Regression analyses indicated that these specific operational taxonomic units as well as bacterial burden associated independently with IPF., Conclusions: IPF is characterized by an increased bacterial burden in BAL that predicts decline in lung function and death. Trials of antimicrobial therapy are needed to determine if microbial burden is pathogenic in the disease.

Many small open ocean animals, such as Antarctic krill, are an important part of marine ecosystems. To discover what will happen to animals such as krill in a changing ocean, experiments are run in aquaria where conditions can be controlled to simulate water characteristics predicted to occur in the future. The response of individual animals to changing water conditions can be hard to observe, and with current observation techniques it is very difficult to follow the progress of an individual animal through its life. Optical coherence tomography (OCT) is an optical imaging technique that allows images at high resolution to be obtained from depths up to a few millimeters inside biological specimens. It is compatible with in vivo imaging and can be used repeatedly on the same specimens. In this work, we show how OCT may be applied to post mortem krill samples and how important physiological data such as shell thickness and estimates of organ volume can be obtained. Using OCT we find an average value for the thickness of krill exoskeleton to be (30±4) µm along a 1 cm length of the animal body. We also show that the technique may be used to provide detailed imagery of the internal structure of a pleopod joint and provide an estimate for the heart volume of (0.73±0.03) mm3.

Using data from a diverse sample of 581 families living in predominantly low-income, rural communities, the current study sought to investigate the longitudinal associations among father-perpetrated intimate partner violence (IPV) and child-directed physical aggression perpetrated by the mother. The unique contributions of each of these types of family violence on children's behavioral problems at school entry were also examined. Results confirm bidirectional associations between father-perpetrated IPV and maternal physical aggression directed toward the child, and indicate that both types of physical aggression contribute to child behavior problems at school entry.

Introduction: Heparin is safe and prevents venous thromboembolism in critical illness. We aimed to determine the guideline concordance for thromboprophylaxis in critically ill patients and its predictors, and to analyze factors associated with the use of low molecular weight heparin (LMWH), as it may be associated with a lower risk of pulmonary embolism and heparin-induced thrombocytopenia without increasing the bleeding risk., Methods: We performed a retrospective audit in 28 North American intensive care units (ICUs), including all consecutive medical-surgical patients admitted in November 2011. We documented ICU thromboprophylaxis and reasons for omission. Guideline concordance was determined by adding days in which patients without contraindications received thromboprophylaxis to days in which patients with contraindications did not receive it, divided by the total number of patient-days. We used multilevel logistic regression including time-varying, center and patient-level covariates to determine the predictors of guideline concordance and use of LMWH., Results: We enrolled 1,935 patients (62.3 ± 16.7 years, Acute Physiology and Chronic Health Evaluation [APACHE] II score 19.1 ± 8.3). Patients received thromboprophylaxis with unfractionated heparin (UFH) (54.0%) or LMWH (27.6%). Guideline concordance occurred for 95.5% patient-days and was more likely in patients who were sicker (odds ratio (OR) 1.49, 95% confidence interval (CI) 1.17, 1.75 per 10-point increase in APACHE II), heavier (OR 1.32, 95% CI 1.05, 1.65 per 10-m/kg2 increase in body mass index), had cancer (OR 3.22, 95% CI 1.81, 5.72), previous venous thromboembolism (OR 3.94, 95% CI 1.46,10.66), and received mechanical ventilation (OR 1.83, 95% CI 1.32,2.52). Reasons for not receiving thromboprophylaxis were high risk of bleeding (44.5%), current bleeding (16.3%), no reason (12.9%), recent or upcoming invasive procedure (10.2%), nighttime admission or discharge (9.7%), and life-support limitation (6.9%). LMWH was less often administered to sicker patients (OR 0.65, 95% CI 0.48, 0.89 per 10-point increase in APACHE II), surgical patients (OR 0.41, 95% CI 0.24, 0.72), those receiving vasoactive drugs (OR 0.47, 95% CI 0.35, 0.64) or renal replacement therapy (OR 0.10, 95% CI 0.05, 0.23)., Conclusions: Guideline concordance for thromboprophylaxis was high, but LMWH was less commonly used, especially in patients who were sicker, had surgery, or received vasopressors or renal replacement therapy, representing a potential quality improvement target.

Objective: To determine the level of agreement between staff and students' assessment of clinical skills in performing tasks related to cavity preparation on a traditional dental manikin., Methods: Two studies were conducted with two successive student cohorts: Study 1-138 year 1 BDS students in a 2009/10 cohort and Study 2-135 students in a 2010/11 cohort. Staff members and students rated the students' performance in preparing a cavity on a traditional dental manikin using artificial teeth: hand-held (Study 1) and located in a lower jaw (Study 2). A 5-item criterion-related scoring rubric was developed. The rubric assessed students' abilities to hold the instrument correctly, determine the angle of entry to the tooth, remove the caries, conserve healthy tissues and avoid pulp exposure., Results: Agreement between the students' self-assessment and the staff's assessment was high for three of the five criteria (i.e. removal of artificial caries on the cavity wall, removal of artificial caries from the cavity floor and avoidance of pulp exposure). Levels of agreement for the remaining two criteria were moderate. A change in task difficulty affected the levels of agreement between staff and students, such that the more difficult the task, the greater the discrepancy in ratings., Conclusions: Students tend to overrate the quality of their performance when compared with staff ratings. Task difficulty has an impact on levels of agreement., (© 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

The current study was designed to examine the relation between intimate partner violence (IPV) and children's memory and drew from a socioeconomically and racially diverse sample of children living in and around a midsized southeastern city (n = 140). Mother-reported IPV when the children were 30 months old was a significant predictor of children's short-term, working, and deliberate memory at 60 months of age, even after controlling for the children's sex and race, the families' income-to-needs ratio, the children's expressive vocabulary, and maternal harsh-intrusive parenting behaviors. These findings add to the limited extant literature that finds linkages between IPV and children's cognitive functioning and suggest that living in households in which physical violence is perpetrated among intimate partners may have a negative effect on multiple domains of children's memory development.

Objective: The rate of multiple births has increased over the last two decades. In 1982, an increased frequency of injuries among this patient population was noted, but few studies have evaluated the increased incidence of maltreatment in twins. The study aim was to evaluate the features of all multiple-birth children with substantiated physical abuse and/or neglect over a four-year period at a major children's hospital., Study Design and Methods: A Retrospective chart review was conducted of multiple-gestation children in which at least one child in the multiple set experienced child maltreatment from January 2006 to December 2009. Data regarding the child, injuries, family, and perpetrators were abstracted. We evaluated whether family and child characteristics were associated with maltreatment, and whether types of injuries were similar within multiple sets. For comparison, data from the same time period for single-birth maltreated children also were abstracted, including child age, gestational age at birth, and injury type., Results: There were 19 sets of multiple births in which at least one child had abusive injuries and/or neglect. In 10 of 19 sets (53%), all multiples were found to have a form of maltreatment, and all children in these multiple sets shared at least one injury type. Parents lived together in 63% of cases. Fathers and mothers were the alleged perpetrator in 42% of the cases. Multiple-gestation-birth maltreated children were significantly more likely than single-birth maltreated children to have abdominal trauma (13% vs. 1%, respectively; p<.01), fractures (83% vs. 39%; p<.01), and to be injured at a younger mean age (12.8 months vs. 34.8 months; p<.01)., Conclusions: Siblings of maltreated, multiple-gestation children often, but not always, were abused. In sets with two maltreated children, children usually shared the same modes of maltreatment. Multiples are significantly more likely than singletons to be younger and experience fractures and abdominal trauma. The findings support the current standard practice of evaluating all children in a multiple set when one is found to be abused or neglected., (Copyright © 2013 Elsevier Ltd. All rights reserved.)