bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low Levels of Exhaled Surfactant Protein A Associated With BOS After Lung Transplantation
Authors: Ericson Petrea A. , Mirgorodskaya Ekaterina , Hammar Oscar S. , Viklund Emilia A. , Almstrand Ann-Charlotte R. , Larsson Per J-W. , Riise Gerdt C. , Olin Anna-Carin 
Published: August 2016

Background
There is no clinically available marker for early detection or monitoring of chronic rejection in the form of bronchiolitis obliterans syndrome (BOS), the main long-term complication after lung transplantation. Sampling and analysis of particles in exhaled air is a valid, noninvasive method for monitoring surfactant protein A (SP-A) and albumin in the distal airways.

Methods
We asked whether differences in composition of exhaled particles can be detected when comparing stable lung transplant recipients (LTRs) (n = 26) with LTRs who develop BOS (n = 7). A comparison between LTRs and a matching group of healthy controls (n = 33) was also conducted. Using a system developed in-house, particles were collected from exhaled air by the principal of inertial impaction before chemical analysis by immunoassays.

Results
Surfactant protein A in exhaled particles and the SP-A/albumin ratio were lower (P = 0.002 and P = 0.0001 respectively) in the BOS group compared to the BOS-free group. LTRs exhaled higher amount of particles (P < 0.0001) and had lower albumin content (P < 0.0001) than healthy controls.

Conclusions
We conclude that low levels of SP-A in exhaled particles are associated with increased risk of BOS in LTRs. The possibility that this noninvasive method can be used to predict BOS onset deserves further study with prospective and longitudinal approaches.
Utility of Clinical Features for the Diagnosis of Seizures in the Intensive Care Unit
Authors: Schmitt Sarah E. 
Published: August 2016

Purpose:
Seizures in the intensive care unit are often subtle, and may have little or no clinical correlate. This study attempts to determine what clinical features are most strongly associated with the presence of electrographic seizures on continuous EEG (cEEG) monitoring.

Methods:
A retrospective review for all patients who underwent cEEG monitoring between January 2003 and March 2009 for either characterization of clinical events or altered mental status was performed. Clinical events were categorized as (1) limb myoclonus/tremor, (2) extremity weakness, (3) eye movement abnormalities, (4) facial/periorbital twitching, and (5) other abnormal movements. The presence of associated dyscognitive event features was also recorded.

Results:
Records from 626 patients who underwent cEEG were reviewed—154 for event characterization and 472 for altered mental status. Seizures were captured in 48 patients (31.2%) undergoing cEEG monitoring for characterization of clinical events. This was not significantly different from the incidence of seizures in patients undergoing cEEG for altered mental status (N = 133, 28.2%). Patients undergoing cEEG monitoring for facial/periorbital twitching were significantly more likely to have electrographic seizures (78.9%, P < 0.005) than patients undergoing cEEG for altered mental status or characterization of other types of events.

Conclusions:
The incidence of seizures in patients in the intensive care unit with clinical events is generally not significantly higher than the incidence of seizures in patients in the intensive care unit with altered mental status. However, the presence of facial/periorbital twitching was associated a higher incidence of electrographic seizures.
Gender disparity in computational biology research publications
Authors: Bonham Kevin S. , Stefan Melanie I. 
Published: August 2016

AbstractWhile women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender ratio in biology is more balanced than in computer science. We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology. To this end, we examined the proportion of female authors in publications from the PubMed and arXiv databases. There are fewer female authors on research papers in computational biology, as compared to biology in general. This is true across authorship position, year, and journal impact factor. A comparison with arXiv shows that quantitative biology papers have a higher ratio of female authors than computer science papers, placing computational biology in between its two parent fields in terms of gender representation. Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance.
Metazoan ribotoxin genes acquired by Horizontal Gene Transfer
Authors: Lapadula Walter J. , Marcet Paula L. , Mascotti María L. , Puerta María V. Sánchez , Ayub Maximiliano Juri 
Published: August 2016

AbstractRibosome inactivating proteins (RIPs) are RNAN-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first timein silicoevidence of RIP encoding genes in metazoans, in two closely related species of insects:Aedes aegyptiandCulex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history. A detailed study was conducted, including evaluation of taxonomic distribution, phylogenetic inferences and microsynteny analyses, indicating that the culicine RIP genes derived from a single Horizontal Gene Transfer (HGT) event, probably from a Cyanobacterial donor species. Moreover, evolutionary analyses show that, after transference, these genes evolved under purifying selection, strongly suggesting that they play functional roles in these organisms. In this work we confirm the presence of RIP genes in Culicinae species, and show solid evidence supporting the hypothesis that these genes are derived from a single prokaryotic transferred gene through HGT. In addition, clear evidence of purifying selection pressure has been recorded, supporting the hypothesis that these genes are functional within this subfamily.
Fast Antibiotic Susceptibility Testing based on single cell growth rate measurements
Authors: Baltekin Özden , Boucharin Alexis , Tano Eva , Andersson Dan I. , Elf Johan 
Published: August 2016

AbstractThe emergence and spread of antibiotic resistant bacteria is a global threat to human health. The problem is aggravated by unnecessary and incorrect use of broad-spectrum antibiotics. One way to provide correct treatment and to slow down the development of antibiotic resistance is to assay the susceptibility profile of the infecting bacteria before treatment is initiated and let this information guide the choice of antibiotic. However, current methods for Antibiotics Susceptibility Testing (AST) are too slow for point of care application. Here we present a fast AST, fASTest, that rapidly captures individual bacterial cells in nanofluidics channels and monitors their response to different antibiotics based on direct imaging. By averaging the growth rate over many cells, we determined the susceptibility to several antibiotics in less than 25 min even at cell densities as low as 104 CFU/mL. The short time scale, high sensitivity and high specificity make the method practically useful for guiding antibiotic treatment in, for example, urinary tract infections.One Sentence SummaryIndividual bacterial cells can be captured and imaged in a microfluidic device to determine how their growth rate responds to antibiotic treatment in a few minutes.
Network analysis links genome-wide phenotypic and transcriptional stress responses in a bacterial pathogen with a large pan-genome
Authors: Jensen Paul A. , Zhu Zeyu , van Opijnen Tim 
Published: August 2016

ABSTRACTBackgroundBacteria modulate subcellular processes to handle stressful environments. Genome-wide profiling of gene expression (RNA-Seq) and fitness (Tn-Seq) allows two views of the same genetic network underlying these responses. However, it remains unclear how they combine, enabling a bacterium to overcome a perturbation.ResultsHere we generate RNA-Seq and Tn-Seq profiles in three strains ofS. pneumoniaein response to stress defined by different levels of nutrient depletion. These profiles show that genes that change their expression and/or become phenotypically important come from a diverse set of functional categories, and genes that are phenotypically important tend to be highly expressed. Surprisingly, we find that expression and fitness changes rarely occur on the same gene, which we confirmed by over 140 validation experiments. To rationalize these unexpected results we built the first genome-scale metabolic model ofS. pneumoniaeshowing that differential expression and phenotypic importance actually correlate between nearest neighbors, although they are distinctly partitioned into small subnetworks. Moreover, a meta-analysis of 234S. pneumoniaegene expression studies reveals that essential genes and phenotypically important subnetworks rarely change expression, indicating that they are shielded from transcriptional fluctuations and that a clear distinction exists between transcriptional and phenotypic response networks.ConclusionsWe present a genome-wide computational/experimental approach that contextualizes changes that occur on transcriptomic and phenomic levels in response to stress. Importantly, this highlights the need to connect disparate response networks, for instance in antibiotic target identification, where preferred targets are phenotypically important genes that would be overlooked by transcriptomic analyses alone.
Influence of a mono-frequency sound on bacteria can be a function of the sound-level
Authors: Kothari Vijay , Joshi Chinmayi , Patel Pooja , Mehta Milan , Dubey Shashikant , Mishra Brijesh , Sarvaiya Niral 
Published: August 2016

AbstractChromobacterium violaceumwas subjected to sonic stimulation with 300 Hz sound, at five different levels of loudness in the range of 70 – 89.5 dB. Sonic stimulation was found to affect bacterial growth and quorum sensing regulated pigment (violacein) production significantly. Magnitude of this effect was found to be dependent on sound-level. The minimum critical difference required to cause any statistically significant change in bacterial response with respect to sound-level was found to be 13 dB. Growth ofC. violaceumwas affected more at lower sound intensity, whereas pigment production was affected more at higher sound intensity. Additional experiments withC. violaceumandSerratia marcescensindicated that even a silent speaker emitting no sound can alter bacterial growth and/or pigment production upto a minor extent. Size of the test tube in which bacteria are exposed to sonic stimulation, was not found to affect the results much.
Mycobacterium ulceranslow infectious dose and atypical mechanical transmission support insect bites and puncturing injuries in the spread of Buruli ulcer
Authors: Wallace John R. , Mangas Kirstie M. , Porter Jessica L. , Marcsisin Renee , Pidot Sacha J. , Howden Brian , Omansen Till F. , Zeng Weiguang , Axford Jason K. , Johnson Paul D. R. , Stinear Timothy P. 
Published: August 2016

AbstractAddressing the transmission enigma of the neglected disease Buruli ulcer (BU) is a World Health Organization priority. In Australia, we have observed an association between mosquitoes harboring the causative agent,Mycobacterium ulcerans, and BU. Here we tested a contaminated skin model of BU transmission by dipping the tails from healthy mice in cultures of the causative agent,Mycobacterium ulcerans. Tails were exposed to mosquito (Aedes notoscriptusandAedes aegypti) blood feeding or punctured with sterile needles. Two of 11 of mice withM. ulceranscontaminated tails exposed to feedingA. notoscriptusmosquitoes developed BU. Eighteen of 20 mice subjected to contaminated tail needle puncture developed BU. Mouse tails coated only in bacteria did not develop disease. We observed a low infectious dose-50 of four colony-forming units and a median incubation time of 12 weeks, consistent with data from human infections. We have uncovered a highly efficient and biologically plausible atypical transmission mode of BU via natural or anthropogenic skin punctures.Author summaryBuruli ulcer is a neglected tropical disease caused by infection withMycobacterium ulcerans. Unfortunately, how people contract this disease is not well understood. Here we show for the first time using experimental infections in mice that a very low dose ofM. ulceransdelivered beneath the skin by a minor injury caused by a blood-feeding insect (mosquito) or a needle puncture is sufficient to cause Buruli ulcer. This research provides important laboratory evidence to advance our understanding of Buruli ulcer disease transmission.
Hepatocyte nuclear factor 4-mediated lipotoxicity provokes mitochondrial damage in peroxisome-deficientpex19mutants
Authors: Bülow Margret H. , Sellin Julia , Wingen Christian , Senyilmaz Deniz , Gosejacob Dominic , Teleman Aurelio A. , Hoch Michael 
Published: August 2016

AbstractPeroxisomes are important metabolic organelles involved in the catabolism of several lipid classes, e.g. very-long-chain fatty acids. Malfunction or absence of peroxisomes leads to accumulation of educts for peroxisomal β-oxidation and mitochondrial damage, resulting in fatal perturbation of metabolism. The impact of peroxisome deficiency on mitochondria is not elucidated yet. Here we present a model of Hepatocyte nuclear factor 4 (Hnf4)-induced lipotoxicity and accumulation of non-esterified fatty acids (NEFA) as the cause for mitochondrial damage in consequence of peroxisome loss in a Peroxin19 (pex19) mutant. Hyperactive Hnf4 signaling leads to upregulation oflipase 3and enzymes for mitochondrial β-oxidation. This results in enhanced lipolysis, elevated concentrations of NEFA, maximal β-oxidation and mitochondrial swelling. NEFA are ligands for Hnf4 and further enhance its activity. By genetic removal of Hnf4 inpex19mutants, lipotoxicity and mitochondrial swelling are reduced and their survival is rescued.Author summaryPeroxisomes are cell organelles which play a major role in lipid metabolism. They interact with mitochondria, the organelles which are responsible for cellular energy production. Loss of peroxisomes, as it occurs in the rare, inheritable human disease class of Peroxisome Biogenesis Disorders, is lethal. Over the past couple of years, a number of studies showed that peroxisome loss leads to mitochondrial damage as a secondary consequence, but the underlying mechanism has not been understood yet. In our study, we use a mutant of the fruitflyDrosophila melanogasteras a model for Peroxisome Biogenesis Disorders and find that a protein called Hepatocyte nuclear factor 4 is hyperactive upon peroxisome loss, which provokes the mobilization of storage fat and, as a consequence, the accumulation of toxic free fatty acids. These enter the mitochondria, but cannot be used for energy gain. Free fatty acids are then trapped in the mitochondria and lead to their swelling and damage, which provides an explanation for mitochondrial defects in Peroxisomal Biogenesis Disorders. Genetic reduction of Hepatocyte nuclear factor 4 activity rescues the viability of the peroxisome mutant by reducing the accumulation of free fatty acids and the subsequent mitochondrial damage, which might provide a novel target for therapy development.
Individual level predictions ofStaphylococcus aureusbacteraemia-associated mortality
Authors: Recker Mario , Laabei Maisem , Toleman Michelle S. , Reuter Sandra , Blane Beth , Török Estee , Bayliss Sion , Peacock Sharon J. , Massey Ruth C. 
Published: August 2016

AbstractThe bacteriumStaphylococcus aureusis a major human pathogen, where the emergence of antibiotic resistance is a global public-health concern. Host factors such as age and the presence of co-morbidities have been implicated in a worse outcome for patient. However, this is complicated by the highly complex and multi-faceted nature of bacterial virulence, which has so far prevented a robust mapping between genotype, phenotype and infection outcome. To investigate the role of bacterial and host factors in contributing toS. aureusbacteraemia-associated mortality we sequenced a collection of clinical isolates (of the MLST clonal complex CC22) from patients with bloodstream infections and quantified specific virulence phenotypes. A genome-wide association scan identified several novel virulence-affecting loci, which we validated using a functional genomics approach. Analysing the data comprising bacterial genotype and phenotype as well as clinical meta-data within a machine-learning framework revealed that mortality associated with CC22 bacteraemia is not only influenced by the interactions between host and bacterial factors but can also be predicted at the individual patient-level to a high degree of accuracy. This study clearly demonstrates the potential of using a combined genomics and data analytic approach to enhance our understanding of bacterial pathogenesis. Considering both host and microbial factors, including whole genome sequence and phenotype data, within a predictive framework could thus pave the way towards personalised medicine and infectious disease management.
Does diet drive the evolution of head shape and bite force in chameleons of the genus Bradypodion?
Authors: Dollion Alexis Y. , Measey G. John , Cornette Raphaël , Carne Liza , Tolley Krystal A. , da Silva Jessica M. , Boistel Renaud , Fabre Anne‐Claire , Herrel Anthony 
Published: August 2016

Summary

The head is a complex integrated system that is implicated in many vital functions. As such, its morphology is impacted by different and sometimes conflicting demands. Consequently, head shape varies greatly depending on the environment and dietary ecology of an organism. Moreover, given its role in territory defence and mating in lizards, it is also subjected to strong sexual selection in these animals.

We investigated the relationships between head shape, bite performance and diet in 14 of the 17 extant Bradypodion species to determine whether variation in diet can explain the observed diversity in bite force and head shape in this genus. We also evaluate differences between sexes in terms of the relationships between head shape, bite force and diet and predict tighter relationships in females given that the head in this sex is principally under natural selection.

Our results show that there is indeed a correlation between head shape, diet and bite force, but the direction and magnitude are sex‐dependent. Whereas we observed a correlation between absolute bite force and head shape in both sexes, size‐corrected bite force was correlated with mandible and quadrate shape in females only. Despite strong correlations between bite force and prey hardness, and between prey hardness and head shape, we did not find any relationship between head shape and prey evasiveness.

These data suggest that the cranial system in chameleons of the genus Bradypodion evolves under natural selection for the ability to eat large or hard prey. Moreover, significant differences in the ecomorphological relationships between the two sexes suggest that sexual selection plays a role in driving the evolution of bite force and head shape. These data suggest that ecomorphological relationships may be sex‐dependent.
Direct interactions between invasive plants and native pollinators: evidence, impacts and approaches
Authors: Stout Jane C. , Tiedeken Erin Jo 
Published: August 2016

Summary

Invasive non‐native plants form interactions with native species and have the potential to cause direct and indirect impacts on those species, as well as the functioning of invaded ecosystems.

Many entomophilous invasive plants form interactions with resident pollinators; sometimes, these interactions are necessary for the reproductive success of the invader. However, the direct role native pollinators play in plant invasion is not well understood and varies according to invasive plant traits, including breeding system and pollination syndrome.

The majority of studies addressing impacts on plant–pollinator mutualisms have focussed on the indirect impacts of plant invasion for native plant pollination. Fewer studies have focussed on the direct effects of invasive plants on native flower visitors.

Impacts of invasive plants on native pollinators can occur at a range of scales: from the individual flower visitors (in terms of nutrition, health and fitness), to populations (size, density and growth rates), communities (richness, diversity and composition) and community‐level interactions (insect–flower interaction networks). Most research to date has focussed on community‐level impacts, with almost nothing known about the effects of invaders on native flower visitor individuals or populations.

Invasive plant traits, including reward quantity and quality, spatial and temporal availability and accessibility, modulate effects on native flower visitors, and thus, different plant species have different impacts. Similarly, flower visitors do not all respond in the same way to invasive plants. Thus, generalizations are difficult to make, but understanding impacts at the individual and population level for different visitor taxa is key to explaining community‐level impacts.

There have been varied approaches to determining impacts, with most studies attempting to compare invaded vs. non‐invaded habitats. The pros and cons of different approaches are discussed.

Since it is impractical to study every invasive plant in every ecological context in which it occurs, we recommend a better understanding of relevant individual‐level traits to predict direct interactions between invasive plants and native pollinators.

A Lay Summary is available for this article.
Dynamic changes in death cues modulate risks and rewards of corpse management in a social insect
Authors: Sun Qian , Haynes Kenneth F. , Zhou Xuguo 
Published: August 2016

Summary

In social insects, the efficiency of exploitation of resources and colony defence are mediated by chemical communication. In colonies dependent on nutritionally limited resources, corpses represent both a food resource and a risk of pathogens. Because this risk vs. reward changes with time after death, behavioural plasticity in the response to corpses would be advantageous. How social insects regulate this trade‐off remains unknown.

We conducted quantitative behavioural bioassay and chemical analysis to study corpse management in the eastern subterranean termite, Reticulitermes flavipes. We hypothesized that R. flavipes responds differently towards corpses with prolonged post‐mortem time, and this behavioural plasticity is mediated by the dynamic change in death cues.

We show that R. flavipes uses a post‐mortem signalling system that depends on an early death cue that stimulates corpse retrieval and cannibalism, and late death cues that stimulate recruitment and burial. A blend of 3‐octanone and 3‐octanol is released immediately after death, with the alcohol (possibly in conjunction with the ketone) playing a clear role as a death cue. This cue enables the colony to recycle nutrients before decomposition occurs and before risk of pathogens increases. The accumulation of late death cues, decomposition products shared by diverse arthropods, elicits a behavioural switch from cannibalism to burial.

The ability to detect and respond to the dead is vital to group‐living animals. Our study reveals a behavioural shift in corpse management triggered by the interplay of an early death cue and late death cues, which balances risks and rewards associated with corpses. The post‐mortem chemical communication highlights the adaptation of a social insect to its ecological niche.