bluuebunny/crossref_metadata_2025 huggingface dataset:
Data integration with high dimensionality
Authors: Gao Xin , Carroll Raymond J.
Published: March 2017

We consider situations where the data consist of a number of responses for each individual, which may include a mix of discrete and continuous variables. The data also include a class of predictors, where the same predictor may have different physical measurements across different experiments depending on how the predictor is measured. The goal is to select which predictors affect any of the responses, where the number of such informative predictors tends to infinity as the sample size increases. There are marginal likelihoods for each experiment; we specify a pseudolikelihood combining the marginal likelihoods, and propose a pseudolikelihood information criterion. Under regularity conditions, we establish selection consistency for this criterion with unbounded true model size. The proposed method includes a Bayesian information criterion with appropriate penalty term as a special case. Simulations indicate that data integration can dramatically improve upon using only one data source.
Morphological convergence in the recently diversified Silene gigantea complex (Caryophyllaceae) in the Balkan Peninsula and south-western Turkey, with the description of a new subspecies
Authors: Du Pasquier Pierre-Emmanuel , Jeanmonod Daniel , Naciri Yamama
Published: March 2017

The Silene gigantea complex is characterized by a high degree of morphological variability that resulted in the description of three subspecies across its distribution range from the Balkan Peninsula to South-west Asia and Cyprus. In this work, we used nuclear and plastid markers in Bayesian phylogeographic analyses to investigate the taxonomy and the evolutionary history of S. gigantea. The results from plastid DNA partly support the existing taxonomic assessments since S. gigantea subsp. rhodopea is monophyletic, whereas S. gigantea subspp. gigantea and hellenica are clearly polyphyletic. This pattern suggests that a strong morphological convergence is associated with chasmophytic conditions. The results also suggest that the populations from the Epirus region (north-western Greece) did not arise from hybridization as previously claimed, but correspond to a new evolutionary lineage that is consequently described and named S. gigantea subsp. epirota. An identification key to the four subspecies is also given. Our phylogeographic study further highlights a genetic continuity across populations from the central and eastern Greek mainland to Chios and Turkey, all of them sharing the same plastid DNA haplotype and belonging to the same nuclear cluster. In addition, at least two separate colonization events are suggested for Crete. The Bayesian phylogeographic reconstruction clearly points to a post-Messinian diversification across the Aegean area. Considering the low seed dispersal ability of S. gigantea, a continuum of ancestral populations between islands and the mainland is assumed to have occurred during the last glaciations and to have played a key role in colonization processes.
Protomagnetar and black hole formation in high-mass stars
Authors: Obergaulinger M. , Aloy M. Á.
Published: March 2017

Using axisymmetric simulations coupling special relativistic magnetohydrodynamics (MHD), an approximate post-Newtonian gravitational potential and two-moment neutrino transport, we show different paths for the formation of either protomagnetars or stellar mass black holes. The fraction of prototypical stellar cores which should result in collapsars depends on a combination of several factors, among which the structure of the progenitor star and the profile of specific angular momentum are probably the foremost. Along with the implosion of the stellar core, we also obtain supernova-like explosions driven by neutrino heating and hydrodynamic instabilities or by magneto-rotational effects in cores of high-mass stars. In the latter case, highly collimated, mildly relativistic outflows are generated. We find that after a rather long post-collapse phase (lasting ≳1 s) black holes may form in cases both of successful and failed supernova-like explosions. A basic trend is that cores with a specific angular momentum smaller than that obtained by standard, one-dimensional stellar evolution calculations form black holes (and eventually collapsars). Complementary, protomagnetars result from stellar cores with the standard distribution of specific angular momentum obtained from prototypical stellar evolution calculations including magnetic torques and moderate to large mass-loss rates.
Associations Between Khat Use and HIV Risk and Status Among Voluntary Counseling and Testing Center Clients in Addis Ababa, Ethiopia
Authors: Berhanu Della , Diener-West Marie , Ruff Andrea , Davis Wendy W. , Celentano David D. , Go Vivian F.
Published: March 2017

Objectives:

Ethiopia is 1 of 15 countries that account for nearly 75% of all people living with HIV. Khat use, a common practice in Ethiopia and sub-Saharan Africa, has gained attention as a potential risk factor for HIV. Our objective was to evaluate associations between khat use and demographic and risk-taking characteristics (alcohol use, sexual behavior), and also associations between HIV status and these characteristics among voluntary counseling and testing clients in Addis Ababa, Ethiopia.

Methods:

This cross-sectional study was conducted among Pro Pride voluntary counseling and testing center clients, aged 18 to 49 years, from November 2009 to March 2010. All clients were approached, and 98.8% of these (684) completed a self-administered questionnaire. Associations between khat use, alcohol use, multiple sexual partners, and HIV status were assessed using logistic regression models.

Results:

Using khat in the past 90 days (current khat use) was significantly associated with being Muslim, being male, alcohol use, and having a greater number of sex partners in one's lifetime. The adjusted odds of current khat use was almost 7-fold higher in those having 4 or more sexual partners in their lifetime (adjusted odds ratio 6.89, 95% confidence interval 3.87, 12.25) as compared with those with 1 or none. HIV-positive status was significantly associated with age, employment, marital status, number of sex partners in one's lifetime, and khat use. Having used khat in one's lifetime, but not currently, past khat use, was associated with over a 2-fold increased adjusted odds (adjusted odds ratio 2.64, 95% confidence interval 1.13, 6.19) of being HIV-infected.

Conclusions:

Our findings highlight associations between current khat use and the modifiable factors of number of lifetime sexual partners and alcohol use. In addition, we observed the association between HIV status and past khat use after adjusting for age, marital status, and number of sex partners in one's lifetime.
Improved Head and Neck Free Flap Outcome—Effects of a Treatment Protocol Adjustment from Pre- to Postoperative Radiotherapy
Authors: Halle Martin , Eriksson Bjorn O. , Docherty Skogh Ann-Charlott , Sommar Pehr , Hammarstedt Lalle , Gahm Caroline
Published: March 2017

Background:

The impact of preoperative radiotherapy on microvascular reconstructive surgery outcome has been a subject of debate. However, data are conflicting and often dependent on local treatment protocols. We have studied the effects of radiotherapy in a unique, single-center setting where a treatment protocol change was undertaken from pre- to postoperative radiotherapy administration for microsurgical head and neck reconstructions.

Methods:

A cohort study was conducted for 200 consecutive head and neck free flap cases, where 100 were operated on before and 100 after the treatment protocol adjustment in 2006. Only direct cancer reconstructions were included. Complication rates of anastomosis-related (flap necrosis) and flap bed–related (infection, fistula, and wound dehiscence) complications were compared between irradiated and nonirradiated patients. A multivariate analysis was performed to correct for treatment period.

Results:

One hundred twenty-six patients had received radiotherapy before reconstruction due to cases of cancer recurrence. There were no significant differences in demographic data or risk factors between irradiated and nonirradiated cases. Irradiated cases had a higher rate of both flap loss (9.5% versus 1.4%; P = 0.034) and flap bed–related complications (29% versus 13%; P = 0.014). However, after multivariate analysis, there was only a significant relationship between preoperative irradiation and infection (odds ratio = 2.51; P = 0.033) and fistula formation (odds ratio = 3.13; P = 0.034).

Conclusions:

The current single-center study clearly indicates that preoperative radiotherapy is a risk factor for both infection and fistula formation, most likely related to an impaired flap bed. We suggest postoperative radiotherapy administration whenever possible for oncological reasons, otherwise proper antibiotic cover and meticulous flap insetting to prevent radiation-related infection and fistula formation.
High-Resolution Magnetic Resonance Imaging of Aging Upper Face Fat Compartments
Authors: Foissac Rémi , Camuzard Olivier , Piereschi Sébastien , Staccini Pascal , Andreani Olivier , Georgiou Charalambos , Benatar Marc
Published: March 2017

Background:

Age-related changes in fat compartments have yet to be fully characterized. Uncertainty remains in terms of volume gains/losses or shape fluctuations over time. The authors’ aim was to determine the evolution of subcutaneous fat in the aging upper face, focusing on shifts in volume and dimension.

Methods:

Over the course of 4.5 years, 100 faces of living female Caucasian patients were prospectively studied using high-resolution magnetic resonance imaging. Subjects were stratified by age as follows: group 1, 18 to 30 years; group 2, 30 to 60 years; and group 3, older than 60 years. Superficial temporal and central forehead compartments were delimited, analyzing respective volumes and dimensions by group.

Results:

In 85 patients studied, superficial temporal fat (mean volume, 5.14 cm3) increased 35.48 percent in total volume between youth and old age (p = 0.046). Overall height and magnitude of the lower one-third also increased with aging. Central forehead fat (mean volume, 2.56 cm3), studied in 83 patients, showed a 209.75 percent volume gain in group 2 (versus group 1) and a 17.59 percent volume loss in group 3 (versus group 2) (p = 0.001).

Conclusion:

Subcutaneous facial fat fluctuates with aging, increasing in the upper face and promoting ptosis through basal compartmental expansion.
An Update on the Anatomy of the Forehead Compartments
Authors: Cotofana Sebastian , Mian Asima , Sykes Jonathan M. , Redka-Swoboda Wolfgang , Ladinger Andrea , Pavicic Tatjana , Schenck Thilo L. , Benslimane Fahd , Ingallina Fabio , Schlattau Alexander
Published: March 2017

Background:

The forehead is one of the most frequent locations for neuromodulator and soft tissue filler applications; however, the underlying anatomy is still poorly understood. Thus far, the presence of deep forehead compartments has not been confirmed.

Methods:

Twenty Caucasian cephalic specimens, 15 fresh frozen (six female and nine male) and five with formalin-phenol embalmment (three female and two male) were investigated using contrast-enhanced computed tomographic scans, dye injections, and anatomical dissections.

Results:

Three superficial (one central and two lateral) and three deep (one central and two lateral) forehead compartments were identified. The superficial fat compartments were found within the subcutaneous fat tissue (layer 2) and measured 2.1 × 4.6 mm for the superficial central forehead compartments and the right superficial lateral forehead compartments and 2.6 × 3.2 cm for the left superficial lateral forehead compartments, with a mean volume of 2.5, 3.1, and 3.4 cc, respectively. The deep fat compartments were identified deep to the frontalis muscle but superficial to the periosteum with an extent of 6.4 × 5.9 cm for the deep central forehead compartments, 2.6 × 5.8 cm for the right deep lateral forehead compartments, and 2.7 × 5.8 cm for the left deep lateral forehead compartments, and a mean volume of 9.1, 1.6, and 1.4 cc, respectively.

Conclusions:

The results presented in this study increase the understanding of the forehead anatomy. Understanding the presence of the superficial and the deep forehead compartments allows one to change the signs of frontal aging. The deep forehead compartments are in general avascular planes and permit blunt dissection for access to the supraorbital region.
Embracing interactions in ocean acidification research: confronting multiple stressor scenarios and context dependence
Authors: Kroeker Kristy J. , Kordas Rebecca L. , Harley Christopher D. G.
Published: March 2017

Changes in the Earth's environment are now sufficiently complex that our ability to forecast the emergent ecological consequences of ocean acidification (OA) is limited. Such projections are challenging because the effects of OA may be enhanced, reduced or even reversed by other environmental stressors or interactions among species. Despite an increasing emphasis on multifactor and multispecies studies in global change biology, our ability to forecast outcomes at higher levels of organization remains low. Much of our failure lies in a poor mechanistic understanding of nonlinear responses, a lack of specificity regarding the levels of organization at which interactions can arise, and an incomplete appreciation for linkages across these levels. To move forward, we need to fully embrace interactions. Mechanistic studies on physiological processes and individual performance in response to OA must be complemented by work on population and community dynamics. We must also increase our understanding of how linkages and feedback among multiple environmental stressors and levels of organization can generate nonlinear responses to OA. This will not be a simple undertaking, but advances are of the utmost importance as we attempt to mitigate the effects of ongoing global change.
Jewelled spiders manipulate colour-lure geometry to deceive prey
Authors: White Thomas E.
Published: March 2017

Selection is expected to favour the evolution of efficacy in visual communication. This extends to deceptive systems, and predicts functional links between the structure of visual signals and their behavioural presentation. Work to date has primarily focused on colour, however, thereby understating the multicomponent nature of visual signals. Here I examined the relationship between signal structure, presentation behaviour, and efficacy in the context of colour-based prey luring. I used the polymorphic orb-web spider
Gasteracantha fornicata
, whose yellow- or white-and-black striped dorsal colours have been broadly implicated in prey attraction. In a manipulative assay, I found that spiders actively control the orientation of their conspicuous banded signals in the web, with a distinct preference for near-diagonal bearings. Further field-based study identified a predictive relationship between pattern orientation and prey interception rates, with a local maximum at the spiders' preferred orientation. There were no morph-specific effects on capture success, either singularly or via an interaction with pattern orientation. These results reveal a dynamic element in a traditionally ‘static’ signalling context, and imply differential functions for chromatic and geometric signal components across visual contexts. More broadly, they underscore how multicomponent signal designs and display behaviours may coevolve to enhance efficacy in visual deception.
Sir Harold Walter Kroto. 7 October 1939 — 30 April 2016
Authors: Legon Anthony C.
Published: March 2017

Harry Kroto received the Nobel Prize for Chemistry in 1996 for his discovery of several new allotropes of carbon and in particular the now-famous C
60
, whose atoms are arranged in the spheroidal shape of the truncated icosahedron and which he named as buckminsterfullerene after the architect famous for his design of geodesic domes. Earlier in his career he made important discoveries concerned with the production of small, semi-stable molecules by pyrolysis methods and their characterization, mainly by means of microwave rotational spectroscopy. He was proud to have discovered by this means the compound CH
2
=PH because it contains the first known example of a carbon–phosphorus double bond. He later also made notable contributions to the field of materials chemistry, especially through his work on carbon nanotubes. Harry used his charismatic personality to very good effect in furthering the public understanding of science and was particularly good with children in this context. He also had strong views about science and religion which led him to become a campaigning atheist. He was a loyal and supportive friend and led a very happy family life with his wife Margaret and their two sons.
Automated tracking and classification of the settlement behaviour of barnacle cyprids
Authors: Alsaab Ahmad , Aldred Nick , Clare Anthony S.
Published: March 2017

A focus on the development of nontoxic coatings to control marine biofouling has led to increasing interest in the settlement behaviour of fouling organisms. Barnacles pose a significant fouling challenge and accordingly the behaviour of their settlement-stage cypris larva (cyprid) has attracted much attention, yet remains poorly understood. Tracking technologies have been developed that quantify cyprid movement, but none have successfully automated data acquisition over the prolonged periods necessary to capture and identify the full repertoire of behaviours, from alighting on a surface to permanent attachment. Here we outline a new tracking system and a novel classification system for identifying and quantifying the exploratory behaviour of cyprids. The combined system enables, for the first time, tracking of multiple larvae, simultaneously, over long periods (hours), followed by automatic classification of typical cyprid behaviours into swimming, wide search, close search and inspection events. The system has been evaluated by comparing settlement behaviour in the light and dark (infrared illumination) and tracking one of a group of 25 cyprids from the water column to settlement over the course of 5 h. Having removed a significant technical barrier to progress in the field, it is anticipated that the system will accelerate our understanding of the process of surface selection and settlement by barnacles.
Effect of hydrophobic core on the electrophoresis of a diffuse soft particle
Authors: Gopmandal Partha P. , Bhattacharyya S. , Ohshima H.
Published: March 2017

Electrophoresis of a diffuse soft particle with a charged hydrophobic core is considered under the weak field and low charge density assumptions. The hydrophobic surface of the core is coated with a diffuse polyelectrolyte layer (PEL) in which a gradual transition of the polymer segment distribution from the impenetrable core to the surrounding electrolyte medium is considered. A mathematical model is adopted to analyse the impact of the core hydrophobicity on the diffuse soft particle electrophoresis. The mobility based on the present model for the limiting cases such as bare colloids with hydrophobic core and soft particles with no-slip rigid cores are in good agreement with the existing results. The presence of PEL charges produces the impact of the core hydrophobicity on the soft particle mobility different from the corresponding bare colloid with hydrophobic surface in an electrolyte medium. The impact of the core hydrophobicity is subtle when the hydrodynamic screening length of the PEL is low. Reversal in mobility can be achieved by tuning the core hydrophobicity for an oppositely charged core and PEL.
Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities
Authors: Wepking Carl , Avera Bethany , Badgley Brian , Barrett John E. , Franklin Josh , Knowlton Katharine F. , Ray Partha P. , Smitherman Crystal , Strickland Michael S.
Published: March 2017

Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene
ampC
was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally,
ampC
abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function.
The dynamic association between ovariole loss and sterility in adult honeybee workers
Authors: Ronai Isobel , Allsopp Michael H. , Tan Ken , Dong Shihao , Liu Xiwen , Vergoz Vanina , Oldroyd Benjamin P.
Published: March 2017

In the social insects, ovary state (the presence or absence of mature oocytes) and ovary size (the number of ovarioles) are often used as proxies for the reproductive capacity of an individual worker. Ovary size is assumed to be fixed post-eclosion whereas ovary state is demonstrably plastic post-eclosion. Here, we show that in fact ovary size declines as honeybee workers age. This finding is robust across two honeybee species:
Apis mellifera
and
A. cerana
. The ovariole loss is likely to be due to the regression of particular ovarioles via programmed cell death. We also provide further support for the observation that honeybee workers with activated ovaries (mature oocytes present) most commonly have five ovarioles rather than a greater or smaller number. This result suggests that workers with more than five ovarioles are unable to physiologically support more than five activated ovarioles and that workers with fewer than five ovarioles are below a threshold necessary for ovary activation. As a worker's ovariole number declines with age, studies on worker ovariole number need to take this plasticity into account.
The melanocortin system regulates body pigmentation and social behaviour in a colour polymorphic cichlid fish
Authors: Dijkstra Peter D. , Maguire Sean M. , Harris Rayna M. , Rodriguez Agosto A. , DeAngelis Ross S. , Flores Stephanie A. , Hofmann Hans A.
Published: March 2017

The melanocortin system is a neuroendocrine system that regulates a range of physiological and behavioural processes. We examined the extent to which the melanocortin system simultaneously regulates colour and behaviour in the cichlid fish
Astatotilapia burtoni
. We found that yellow males are more aggressive than blue males, in line with previous studies. We then found that exogenous α-melanocyte-stimulating hormone (α-MSH) increases yellowness of the body and dispersal of xanthophore pigments in both morphs. However, α-MSH had a morph-specific effect on aggression, with only blue males showing an increase in the rate of aggression. Exogenous agouti signalling peptide (ASIP), a melanocortin antagonist, did not affect coloration but reduced the rate of aggression in both colour morphs. Blue males had higher cortisol levels than yellow males. Neural gene expression of melanocortin receptors (
mcr
) and ligands was not differentially regulated between colour morphs. In the skin, however,
mc1r
and pro-opiomelanocortin (
pomc
)
β
were upregulated in blue males, while
asip 1
was upregulated in yellow males. The effects of α-MSH on behaviour and body coloration, combined with morph-specific regulation of the stress response and the melanocortin system, suggest that the melanocortin system contributes to the polymorphism in behaviour and coloration in
A. burtoni
.
Field study suggests that sex determination in sea lamprey is directly influenced by larval growth rate
Authors: Johnson Nicholas S. , Swink William D. , Brenden Travis O.
Published: March 2017

Sex determination mechanisms in fishes lie along a genetic-environmental continuum and thereby offer opportunities to understand how physiology and environment interact to determine sex. Mechanisms and ecological consequences of sex determination in fishes are primarily garnered from teleosts, with little investigation into basal fishes. We tagged and released larval sea lamprey (
Petromyzon marinus
) into unproductive lake and productive stream environments. Sex ratios produced from these environments were quantified by recapturing tagged individuals as adults. Sex ratios from unproductive and productive environments were initially similar. However, sex ratios soon diverged, with unproductive environments becoming increasingly male-skewed and productive environments becoming less male-skewed with time. We hypothesize that slower growth in unproductive environments contributed to the sex ratio differences by directly influencing sex determination. To the best of our knowledge, this is the first study suggesting that growth rate in a fish species directly influences sex determination; other studies have suggested that the environmental variables to which sex determination is sensitive (e.g. density, temperature) act as cues for favourable or unfavourable growth conditions. Understanding mechanisms of sex determination in lampreys may provide unique insight into the underlying principles of sex determination in other vertebrates and provide innovative approaches for their management where valued and invasive.
Decoding directional genetic dependencies through orthogonal CRISPR/Cas screens
Authors: Boettcher Michael , Tian Ruilin , Blau James , Markegard Evan , Wu David , Biton Anne , Zaitlen Noah , McCormick Frank , Kampmann Martin , McManus Michael T.
Published: March 2017

Genetic interaction studies are a powerful approach to identify functional interactions between genes. This approach can reveal networks of regulatory hubs and connect uncharacterised genes to well-studied pathways. However, this approach has previously been limited to simple gene inactivation studies. Here, we present an orthogonal CRISPR/Cas-mediated genetic interaction approach that allows the systematic activation of one gene while simultaneously knocking out a second gene in the same cell. We have developed this concept into a quantitative and scalable combinatorial screening platform that allows the parallel interrogation of hundreds of thousands of genetic interactions. We demonstrate that the established platform works robustly to uncover genetic interactions in human cancer cells and to interpret the direction of the flow of genetic information.
Brucella abortusinduces a Warburg shift in host metabolism that is linked to enhanced intracellular survival of the pathogen
Authors: Czyż Daniel M. , Willett Jonathan , Crosson Sean
Published: March 2017

Intracellular bacterial pathogens exploit host cell resources to replicate and survive inside the host. Targeting these host systems is one promising approach to developing novel antimicrobials to treat intracellular infections. We show that human macrophage-like cells infected withBrucella abortusundergo a metabolic shift characterized by attenuated tricarboxylic acid cycle metabolism, reduced amino acid consumption, altered mitochondrial localization, and increased lactate production. This shift to an aerobic glycolytic state resembles the Warburg effect, a change in energy production that is well-described in cancer cells, and also occurs in activated inflammatory cells.B. abortusefficiently uses lactic acid as its sole carbon and energy source and requires the ability to metabolize lactate for normal survival in human macrophage-like cells. We demonstrate that chemical inhibitors of host glycolysis and lactate production do not affectin vitrogrowth ofB. abortusin axenic culture, but decrease its survival in the intracellular niche. Our data support a model in which infection shifts host metabolism to a Warburg-like state, andB. abortususes this change in metabolism to promote intracellular survival. Pharmacological perturbation of these features of host cell metabolism may be a useful strategy to inhibit infection by intracellular pathogens.

IMPORTANCE

Brucellaspp. are intracellular bacterial pathogens that cause disease in a range of mammals, including livestock. Transmission from livestock to humans is common and can lead to chronic human disease. Human macrophage-like cells infected withBrucella abortusundergo a Warburg-like metabolic shift to an aerobic glycolytic state where the host cells produce lactic acid and have reduced amino acid catabolism. We provide evidence that the pathogen can exploit this change in host metabolism to support growth and survival in the intracellular niche. Drugs that inhibit this shift in host cell metabolism inhibit intracellular replication and decrease the survival ofB. abortusin anin vitroinfection model; these drugs may be broadly useful therapeutics for intracellular infections.
UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties
Authors: Conway Jake R , Lex Alexander , Gehlenborg Nils
Published: March 2017

Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. UpSetR is available athttps://cran.r-project.org/package=UpSetRand released under the MIT License. A Shiny app is available athttps://gehlenborglab.shinyapps.io/upsetr/.
Physical activity phenotyping with activity bigrams, and their association with BMI
Authors: Millard Louise AC , Tilling Kate , Lawlor Debbie A , Flach Peter A , Gaunt Tom R
Published: March 2017

Background

Analysis of physical activity usually focuses on a small number of summary statistics derived from accelerometer recordings: average counts per minute, and the proportion of time spent in moderate-vigorous physical activity or in sedentary behaviour. We show how bigrams, a concept from the field of text mining, can be used to describe how a person’s activity levels change across (brief) time points. These variables can, for instance, differentiate between two people with the same time in moderate activity, where one person often stays in moderate activity from one moment to the next and the other does not.

Methods

We use data on 4810 participants of the Avon Longitudinal Study of Parents and Children (ALSPAC). We generate a profile of bigram frequencies for each participant and test the association of each frequency with body mass index (BMI), as an exemplar.

Results

We found several associations between changes in bigram frequencies and BMI. For instance, a 1 standard deviation decrease in the number of adjacent minutes in sedentary then moderate activity (or vice versa), with a corresponding increase in the number of adjacent minutes in moderate then vigorous activity (or vice versa), was associated with a 2.36 kg/m2lower BMI [95% CI: -3.47, -1.26], after accounting for the time spent at sedentary, low, moderate and vigorous activity.

Conclusions

Activity bigrams are novel variables that capture how a person’s activity changes from one moment to the next. These variables can be used to investigate how sequential activity patterns associate with other traits.

Key Messages

Epidemiologists typically use only a small number of variables to analyse the association of physical activity with other traits, such as the average counts per minute and the proportion of time spent in moderate-vigorous physical activity or being sedentary.

We demonstrate how activity bigrams can be used as a set of interpretable variables describing how a person’s activity levels change from one moment to the next.

Testing the association of activity bigrams with exposures or outcomes can help us gain further understanding of how physical activity is associated with other traits; with further research they might provide evidence for more refined public health advice.
Revelation of a Novel Protein Translocon in Bacterial Plasma Membrane
Authors: Jin Feng , Chang Zengyi
Published: March 2017

Many proteins are translocated across biomembranes via protein translocons in targeting to their subcellular destinations. Hitherto, the SecYEG/Sec61 translocon, existing in prokaryotes and eukaryotes, represents the most intensively studied one. According to the current perception, both periplasmic and β-barrel outer membrane proteins (β-barrel OMPs) are translocated via the SecYEG translocon in bacterial cells, although direct living cell evidences remain lacking. Here, mainly viain vivoprotein photo-crosslinking analysis, we revealed that the never reported membrane-integrated SecANprotein apparently functions as the translocon for β-barrel OMPs. Additionally, SecANcontains a GXXXG motif known for mediating protein interactions in biomembranes, and processing of β-barrel OMP precursors was severely affected in cells producing an assembly-defective SecANvariant resulted from the GXXXG motif mutations. Furthermore, SecANwas demonstrated to directly interact with the Bam complex, thus likely be a part of the supercomplex that we revealed earlier to be responsible for β-barrel OMP biogenesis.
The structure of plant spatial association networks increases plant diversity in global drylands
Authors: Saiz H. , Gómez-Gardeñes J. , Borda J.P. , Maestre F.T.
Published: March 2017

Aim

Despite their widespread use and value to unveil the complex structure of the interactions within ecological communities and their value to assess the resilience of communities, network analyses have seldom been applied in plant communities. We aim to evaluate how plant-plant interaction networks vary in global drylands, and to assess whether network structure is related to plant diversity in these ecosystems.

Location

185 dryland ecosystems from all continents except Antarctica.

Methods

We built networks using the local spatial association between all the perennial plant species present in the communities studied, and used structural equation models to evaluate the effect of abiotic factors (including geography, topography, climate and soil conditions) and network structure on plant diversity.

Results

The structure of plant networks found at most study sites (72%) was not random and presented properties representative of robust systems, such as high link density and structural balance. Moreover, network indices linked to system robustness had a positive and significant effect on plant diversity, sometimes higher that the effect of abiotic factors.

Main conclusions

Our results constitute the first empirical evidence showing the existence of a common network architecture structuring terrestrial plant communities at the global scale, and provide novel evidence of the importance of the network of interactions for the maintenance of biodiversity. Furthermore, they highlight the importance of system-level approaches to explain the diversity and structure of interactions in plant communities, two major drivers of terrestrial ecosystem functioning and resilience against the likely impacts derived from global change.
Correcting for cell-type heterogeneity in epigenome-wide association studies: premature analyses and conclusions
Authors: Zheng Shijie C , Beck Stephan , Jaffe Andrew E. , Koestler Devin C. , Hansen Kasper D. , Houseman Andres E. , Irizarry Rafael A. , Widschwendter Martin , Teschendorff Andrew E.
Published: March 2017

Recently, a study by Rahmani et al [1] claimed that a reference-free cell-type deconvolution method, called ReFACTor, leads to improved power and improved estimates of cell-type composition compared to competing reference-free and reference-based methods in the context of Epigenome-Wide Association Studies (EWAS). However, we identified many critical flaws (both conceptual and statistical in nature), which seriously question the validity of their claims. We outlined constructive criticism in a recent correspondence letter, Zheng et al [2]. The purpose of this letter is two-fold. First, to present additional analyses, which demonstrate that our original criticism is statistically sound. Second, to highlight additional serious concerns, which Rahmani et al have not yet addressed. In summary, we find that ReFACTor has not been demonstrated to outperform state-of-the-art reference-free methods such as SVA or RefFreeEWAS, nor state-of-the-art reference-based methods. Thus, the claim by Rahmani et al (a claim reiterated in their recent response letter [3]) that ReFACT or represents an advance over the state-of-the-art is not supported by an objective and rigorous statistical analysis of the data.
Gene expression stasis and plasticity following migration into a foreign environment
Authors: Lohman Brian K. , Stutz William E. , Bolnick Daniel I.
Published: March 2017

Selection against migrants is key to maintaining genetic differences between populations linked by dispersal. Yet, migrants are not just passively weeded out by selection. Migrants may mitigate fitness costs by proactively choosing among available habitats, or by phenotypic plasticity. We previously reported that a reciprocal transplant of lake and stream stickleback (Gasterosteus aculeatus) found little support for divergent selection. We revisit that experiment to test whether phenotypic plasticity in gene expression may have helped migrants adjust to unfamiliar habitats. We measured gene expression profiles in stickleback via TagSeq and tested whether migrants between lake and stream habitats exhibited a plastic response to their new environment that allowed them to converge on the expression profile of adapted natives. We report extensive gene expression differences between genetically divergent lake and stream stickleback, despite gene flow. But for many genes, expression was highly plastic. Fish transplanted into the adjoining habitat partially converged on the expression profile typical of their new habitat. This suggests that expression plasticity may soften the impact of migration. Nonetheless, lake and stream fish differed in survival rates and parasite infection rates in our study, implying that expression plasticity is not fast or extensive enough to fully homogenize fish performance.
Quantitative evaluation of statistical errors in small-angle X-ray scattering measurements
Authors: Sedlak Steffen M. , Bruetzel Linda K. , Lipfert Jan
Published: March 2017

A new model is proposed for the measurement errors incurred in typical small-angle X-ray scattering (SAXS) experiments, which takes into account the setup geometry and physics of the measurement process. The model accurately captures the experimentally determined errors from a large range of synchrotron and in-house anode-based measurements. Its most general formulation gives for the variance of the buffer-subtracted SAXS intensity σ2(q) = [I(q) + const.]/(kq), where I(q) is the scattering intensity as a function of the momentum transfer q; k and const. are fitting parameters that are characteristic of the experimental setup. The model gives a concrete procedure for calculating realistic measurement errors for simulated SAXS profiles. In addition, the results provide guidelines for optimizing SAXS measurements, which are in line with established procedures for SAXS experiments, and enable a quantitative evaluation of measurement errors.
Synchrotron Bragg diffraction imaging characterization of synthetic diamond crystals for optical and electronic power device applications
Authors: Tran Thi Thu Nhi , Morse J. , Caliste D. , Fernandez B. , Eon D. , Härtwig J. , Barbay C. , Mer-Calfati C. , Tranchant N. , Arnault J. C. , Lafford T. A. , Baruchel J.
Published: March 2017

Bragg diffraction imaging enables the quality of synthetic single-crystal diamond substrates and their overgrown, mostly doped, diamond layers to be characterized. This is very important for improving diamond-based devices produced for X-ray optics and power electronics applications. The usual first step for this characterization is white-beam X-ray diffraction topography, which is a simple and fast method to identify the extended defects (dislocations, growth sectors, boundaries, stacking faults, overall curvatureetc.) within the crystal. This allows easy and quick comparison of the crystal quality of diamond plates available from various commercial suppliers. When needed, rocking curve imaging (RCI) is also employed, which is the quantitative counterpart of monochromatic Bragg diffraction imaging. RCI enables the local determination of both the effective misorientation, which results from lattice parameter variation and the local lattice tilt, and the local Bragg position. Maps derived from these parameters are used to measure the magnitude of the distortions associated with polishing damage and the depth of this damage within the volume of the crystal. For overgrown layers, these maps also reveal the distortion induced by the incorporation of impurities such as boron, or the lattice parameter variations associated with the presence of growth-incorporated nitrogen. These techniques are described, and their capabilities for studying the quality of diamond substrates and overgrown layers, and the surface damage caused by mechanical polishing, are illustrated by examples.
X-ray diffraction analysis andin vitrocharacterization of the UAM2 protein fromOryza sativa
Authors: Welner Ditte Hededam , Tsai Alex Yi-Lin , DeGiovanni Andy M. , Scheller Henrik Vibe , Adams Paul D.
Published: March 2017

The role of seemingly non-enzymatic proteins in complexes interconverting UDP-arabinopyranose and UDP-arabinofuranose (UDP-arabinosemutases; UAMs) in the plant cytosol remains unknown. To shed light on their function, crystallographic and functional studies of the seemingly non-enzymatic UAM2 protein fromOryza sativa(OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low-dose vector data acquisition. Using size-exclusion chromatography, it is shown that the protein is monomeric in solution. Finally, limited proteolysis was employed to demonstrate DTT-enhanced proteolytic digestion, indicating the existence of at least one intramolecular disulfide bridge or, alternatively, a requirement for a structural metal ion.
Work-based learning as a catalyst for sustainability: a review and prospects
Authors: Wall Tony , Hindley Ann , Hunt Tamara , Peach Jeremy , Preston Martin , Hartley Courtney , Fairbank Amy
Published: March 2017

Purpose

The purpose of this paper is to highlight the continuing dearth of scholarship about the role of work-based learning in education for sustainable development, and particularly the urgent demands of climate literacy. It is proposed that forms of work-based learning can act as catalysts for wider cultural change, towards embedding climate literacy in higher education institutions.

Design/methodology/approach

This paper draws data from action research to present a case study of a Climate Change Project conducted through a work-based learning module at a mid-sized university in the UK.

Findings

Contrary to the predominantly fragmented and disciplinary bounded approaches to sustainability and climate literacy, the case study demonstrates how a form of work-based learning can create a unifying vision for action, and do so across multiple disciplinary, professional service, and identity boundaries. In addition, the project-generated indicators of cultural change including extensive faculty-level climate change resources, creative ideas for an innovative mobile application, and new infrastructural arrangements to further develop practice and research in climate change.

Practical implications

This paper provides an illustrative example of how a pan-faculty work-based learning module can act as a catalyst for change at a higher education institution.

Originality/value

This paper is a contemporary call for action to stimulate and expedite climate literacy in higher education, and is the first to propose that certain forms of work-based learning curricula can be a route to combating highly bounded and fragmented approaches, towards a unified and boundary-crossing approach.
The impact of leadership on trust, knowledge management, and organizational performance
Authors: Koohang Alex , Paliszkiewicz Joanna , Goluchowski Jerzy
Published: March 2017

Purpose

The purpose of this paper is to build a research model that examines the impact of leadership on trust, knowledge management and organizational performance.

Design/methodology/approach

An instrument containing six constructs (leadership: leading organization; leadership: leading people; leadership: leading self, trust, knowledge management and organizational performance) was designed and administered to subjects from all levels of management in various organizations in nine regions of the USA. Collected data were analyzed using partial least squares path modeling to test the hypotheses.

Findings

The study’s findings revealed positive and significant linear connection among leadership (leading organization, leading people and leading self), trust, knowledge management and organizational performance.

Practical implications

The findings imply that effective leadership (leading organization, leading people and leading self) contributes to elevated trust among people, promotes the successful implementation of knowledge management processes, and in turn enhances organizational performance. Therefore, leadership training and development must be a top strategic priority for any organization.

Originality/value

This study enriches the literature by demonstrating that effective leadership stands as the bedrock of the elevated trust, the successful knowledge management processes and the enhanced organizational performance.