bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low Serum Angiopoietin-1, High Serum Angiopoietin-2, and High Ang-2/Ang-1 Protein Ratio are Associated with Early Onset Sepsis in Surinamese Newborns
Authors: Zonneveld Rens , Jongman Rianne , Juliana Amadu , Zijlmans Wilco , Plötz Frans , Molema Grietje , van Meurs Matijs 
Published: May 2017

ABSTRACT

Purpose:
Vascular inflammation and leakage in sepsis is mediated by Angiopoietin-1 (Ang-1) and Angiopoietin-2 (Ang-2) and their phosphorylation of the endothelial Tie-2 receptor. This study investigates levels of Ang-1 and Ang-2 in newborns to gain insight in the vascular pathophysiology of early onset sepsis (EOS) within 72 h after birth.

Methods:
A prospective cohort study was performed among 71 Surinamese newborns treated with antibiotics for suspected EOS and 20 control newborns. Newborns with suspected EOS were divided in two groups: blood culture negative and positive EOS. Ang-1 and Ang-2 levels were measured in serum obtained at the start of antibiotic treatment and at re-evaluation after 48 to 72 h.

Results:
In this cohort 8.5% of newborns had a positive blood culture. At the start of antibiotic treatment Ang-1 serum levels were lower (P < 0.01), and Ang-2 and Ang-2/Ang-1 serum protein ratios were higher (P < 0.01 and P < 0.01, respectively) in newborns with blood culture positive EOS than in controls. These levels were not dependent on timing of first blood draw after birth. After 48 to 72 h levels of Ang-1 further decreased in blood culture positive EOS, while in the other groups no change was observed.

Conclusions:
Our findings support the hypothesis that a disbalance in the Angiopoietins plays a role in the vascular pathophysiology of EOS.
Continuous lateral rotational therapy in trauma—A systematic review and meta-analysis
Authors: Schieren Mark , Piekarski Florian , Dusse Fabian , Marcus Hanke , Poels Marcel , Wappler Frank , Defosse Jérôme 
Published: May 2017

BACKGROUND
The purpose of this study was to evaluate the impact of continuous lateral rotational therapy (CLRT) on respiratory complications and mortality in patients suffering from trauma.

METHODS
The literature databases PubMed®/Medline® and the Cochrane Library® were systematically searched for prospective controlled trials comparing continuous lateral rotational therapy to conventional manual positioning in trauma patients.

RESULTS
A total of 8 publications (n= 422 patients) with comparable age and injury severity were included in the meta-analysis. A significant reduction in the incidence of nosocomial pneumonia (OR: 0.33, [95%CI: 0.17, 0.65], p=0.001) was observed in patients treated prophylactically with continuous lateral rotational therapy. When used with therapeutic intention, CLRT had no impact on the incidence of pneumonia. There were no significant differences in mortality, duration of mechanical ventilation, or ICU length of stay.

CONCLUSIONS
Analogous to studies evaluating CLRT in medical or mixed patient collectives, CLRT reduced the rates of nosocomial pneumonia in trauma patients. This, however, had no impact on overall mortality. The level of evidence of the studies included was limited by several factors. An adequately powered, well-designed multi-centre randomised controlled trial is required, to validly assess the utility of CLRT for the prevention and treatment of pulmonary complications in patients suffering from trauma.

LEVEL OF EVIDENCE
Systematic review and meta-analysis, level III.
Outcomes after traumatic injury in patients with preexisting psychiatric illness
Authors: Falsgraf Erika , Inaba Kenji , de Roulet Amory , Johnson Megan , Benjamin Elizabeth , Lam Lydia , Matsushima Kazuhide , Strumwasser Aaron , Demetriades Demetrios 
Published: May 2017

BACKGROUND
Patients with psychiatric illness have been shown to experience higher rates of traumatic injury. Injury patterns, treatment decisions, and outcomes have not been well characterized in patients with psychiatric illness after injury, in particular those who undergo acute surgical intervention. The purpose of this analysis was to determine mortality, complications, and surgical intervention rates in patients with psychiatric illness after traumatic injury.

METHODS
This is a retrospective study of trauma patients ≥18 years old admitted to LAC + USC Medical Center between January 2008 and March 2015. Patients with psychiatric diagnoses were identified using ICD-9 diagnosis codes. Multivariate logistic regression analyses taking into account demographic and injury characteristics were used to identify associations between psychiatric comorbidity, injury mechanism, surgical interventions, and outcomes in patients after injury.

RESULTS
A total of 26,502 patients were analyzed. Of these, 3,040 (11.5%) had a documented psychiatric comorbidity (2.0% depressive disorder, 0.8% bipolar disorder, 1.3% schizophrenia, 0.5% anxiety disorder, 3.2% substance use disorder). Patients with psychiatric illness were significantly older (49.6 years vs. 42.0 years, p < 0.001), had a lower proportion of penetrating injuries (13.8% vs. 18.1%, p < 0.001), and had a higher incidence of self-inflicted injuries (11.6% vs. 0.72%, p < 0.001). No difference in gender distribution was observed (74.2% men vs. 74.4% men, p = 0.80). Overall mortality was similar in both groups (adjusted odds ratio [aOR], 0.73; p = 0.07). Patients with psychiatric illness were significantly less likely to undergo acute surgical intervention within 6 hours of emergency department admission (aOR, 0.64; p < 0.001). Time from ED arrival to consent for acute surgical intervention was similar in both groups (94.8 min vs. 93.0 min, p = 0.84). No significant difference in mortality after acute surgical intervention was observed (aOR, 0.26; p = 0.10). Psychiatric illness was associated with a significantly higher likelihood of developing complications (aOR, 1.90; p < 0.001) and longer hospital lengths of stay (10.6 days vs. 6.2 days, p < 0.001).

CONCLUSIONS
Trauma patients with comorbid psychiatric illness were observed to have lower rates of acute surgical interventions, higher complication rates, and longer hospital lengths of stay. Further studies are needed to better characterize the causative factors underlying these associations.

LEVEL OF EVIDENCE
Epidemiological, level III.
Animal coloration research: why it matters
Authors: Caro Tim , Stoddard Mary Caswell , Stuart-Fox Devi 
Published: May 2017

While basic research on animal coloration is the theme of this special edition, here we highlight its applied significance for industry, innovation and society. Both the nanophotonic structures producing stunning optical effects and the colour perception mechanisms in animals are extremely diverse, having been honed over millions of years of evolution for many different purposes. Consequently, there is a wealth of opportunity for biomimetic and bioinspired applications of animal coloration research, spanning colour production, perception and function. Fundamental research on the production and perception of animal coloration is contributing to breakthroughs in the design of new materials (cosmetics, textiles, paints, optical coatings, security labels) and new technologies (cameras, sensors, optical devices, robots, biomedical implants). In addition, discoveries about the function of animal colour are influencing sport, fashion, the military and conservation. Understanding and applying knowledge of animal coloration is now a multidisciplinary exercise. Our goal here is to provide a catalyst for new ideas and collaborations between biologists studying animal coloration and researchers in other disciplines.
This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.
Genomics of coloration in natural animal populations
Authors: San-Jose Luis M. , Roulin Alexandre 
Published: May 2017

Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour. In this review, we highlight aspects where genome-wide studies could be of major utility to fill in the gaps in our understanding of the biology and evolution of animal coloration. The new genomic approaches have been promptly adopted to study animal coloration although substantial work is still needed to consider a larger range of species and colour traits, such as those exhibiting continuous variation or based on reflective structures. We argue that a robust advancement in the study of animal coloration will also require large efforts to validate the functional role of the genes and variants discovered using genome-wide tools.This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.
Colour, vision and coevolution in avian brood parasitism
Authors: Stoddard Mary Caswell , Hauber Mark E. 
Published: May 2017

The coevolutionary interactions between avian brood parasites and their hosts provide a powerful system for investigating the diversity of animal coloration. Specifically, reciprocal selection pressure applied by hosts and brood parasites can give rise to novel forms and functions of animal coloration, which largely differ from those that arise when selection is imposed by predators or mates. In the study of animal colours, avian brood parasite–host dynamics therefore invite special consideration. Rapid advances across disciplines have paved the way for an integrative study of colour and vision in brood parasite–host systems. We now know that visually driven host defences and host life history have selected for a suite of phenotypic adaptations in parasites, including mimicry, crypsis and supernormal stimuli. This sometimes leads to vision-based host counter-adaptations and increased parasite trickery. Here, we review vision-based adaptations that arise in parasite–host interactions, emphasizing that these adaptations can be visual/sensory, cognitive or phenotypic in nature. We highlight recent breakthroughs in chemistry, genomics, neuroscience and computer vision, and we conclude by identifying important future directions. Moving forward, it will be essential to identify the genetic and neural bases of adaptation and to compare vision-based adaptations to those arising in other sensory modalities.This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.
The perfection of mimicry: an information approach
Authors: Sherratt Thomas N. , Peet-Paré Casey A. 
Published: May 2017

We consider why imperfect deceptive mimics can persist when it appears to be in the predator's interest to discriminate finely between mimics and their models. One theory is that a receiver will accept being duped if the model and mimic overlap in appearance and the relative costs of attacking the model are high. However, a more fundamental explanation for the difficulty of discrimination is not based on perceptual uncertainty, but simply based on a lack of information. In particular, predators in the process of learning may cease sampling imperfect mimics entirely because the immediate pay-off and future value of information is low, allowing such mimics to persist. This outcome will be particularly likely when the model is relatively costly to attack and/or the discriminative rules the predator has to learn are complex. Information limitations neatly explain why predators tend to adopt discriminative rules based on single traits (such as stripe colour), rather than on combinations of traits (such as stripe order). They also explain why predators utilize certain salient discriminative traits while ignoring equally informative ones (a phenomenon known as overshadowing), and why imperfect mimics may be more common in phenotypically diverse prey communities.
This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.
Camouflage through colour change: mechanisms, adaptive value and ecological significance
Authors: Duarte Rafael C. , Flores Augusto A. V. , Stevens Martin 
Published: May 2017

Animals from a wide range of taxonomic groups are capable of colour change, of which camouflage is one of the main functions. A considerable amount of past work on this subject has investigated species capable of extremely rapid colour change (in seconds). However, relatively slow colour change (over hours, days, weeks and months), as well as changes arising via developmental plasticity are probably more common than rapid changes, yet less studied. We discuss three key areas of colour change and camouflage. First, we review the mechanisms underpinning colour change and developmental plasticity for camouflage, including cellular processes, visual feedback, hormonal control and dietary factors. Second, we discuss the adaptive value of colour change for camouflage, including the use of different camouflage types. Third, we discuss the evolutionary–ecological implications of colour change for concealment, including what it can tell us about intraspecific colour diversity, morph-specific strategies, and matching to different environments and microhabitats. Throughout, we discuss key unresolved questions and present directions for future work, and highlight how colour change facilitates camouflage among habitats and arises when animals are faced with environmental changes occurring over a range of spatial and temporal scales.This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.
Thermal consequences of colour and near-infrared reflectance
Authors: Stuart-Fox Devi , Newton Elizabeth , Clusella-Trullas Susana 
Published: May 2017

The importance of colour for temperature regulation in animals remains controversial. Colour can affect an animal's temperature because all else being equal, dark surfaces absorb more solar energy than do light surfaces, and that energy is converted into heat. However, in reality, the relationship between colour and thermoregulation is complex and varied because it depends on environmental conditions and the physical properties, behaviour and physiology of the animal. Furthermore, the thermal effects of colour depend as much on absorptance of near-infrared ((NIR), 700–2500 nm) as visible (300–700 nm) wavelengths of direct sunlight; yet the NIR is very rarely considered or measured. The few available data on NIR reflectance in animals indicate that the visible reflectance is often a poor predictor of NIR reflectance. Adaptive variation in animal coloration (visible reflectance) reflects a compromise between multiple competing functions such as camouflage, signalling and thermoregulation. By contrast, adaptive variation in NIR reflectance should primarily reflect thermoregulatory requirements because animal visual systems are generally insensitive to NIR wavelengths. Here, we assess evidence and identify key research questions regarding the thermoregulatory function of animal coloration, and specifically consider evidence for adaptive variation in NIR reflectance.This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.
The current and future state of animal coloration research
Authors: Endler John A. , Mappes Johanna 
Published: May 2017

Animal colour patterns are a model system for understanding evolution because they are unusually accessible for study and experimental manipulation. This is possible because their functions are readily identifiable. In this final paper of the symposium we provide a diagram of the processes affecting colour patterns and use this to summarize their functions and put the other papers in a broad context. This allows us to identify significant ‘holes’ in the field that only become obvious when we see the processes affecting colour patterns, and their interactions, as a whole. We make suggestions about new directions of research that will enhance our understanding of both the evolution of colour patterns and visual signalling but also illuminate how the evolution of multiple interacting traits works.This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.
A Systems-Level Framework for Drug Discovery Identifies Csf1R As A Novel Anti-Epileptic Drug Target
Authors: Srivastava Prashant K , van Eyll Jonathan , Godard Patrice , Mazzuferi Manuela , Danis Benedicte , Vandenplas Catherine , Foerch Patrik , Leclercq Karine , Mairet-Coello Georges , Vanclef Frederic , Shkura Kirill , Laaniste Liisi , Delahaye-Duriez Andree , Kaminski Rafal M , Petretto Enrico , Johnson Michael R 
Published: May 2017

ABSTRACTThe identification of mechanistically novel drug targets is highly challenging, particularly for diseases of the central nervous system. To address this problem we developed and experimentally validated a new computational approach to drug target identification that combines gene-regulatory information with a causal reasoning framework (“causal reasoning analytical framework for target discovery” – CRAFT). Starting from gene expression data, CRAFT provides a predictive functional genomics framework for identifying membrane receptors with a direction-specified influence over network expression. As proof-of-concept we applied CRAFT to epilepsy, and predicted the tyrosine kinase receptor Csf1R as a novel therapeutic target for epilepsy. The predicted therapeutic effect of Csf1R blockade was validated in two pre-clinical models of epilepsy using a small molecule inhibitor of Csf1R. These results suggest Csf1R blockade as a novel therapeutic strategy in epilepsy, and highlight CRAFT as a systems-level framework for predicting mechanistically new drugs and targets. CRAFT is applicable to disease settings other than epilepsy.
Development of RNAseq methodologies to profile thein vivotranscriptome ofBordetella pertussisduring murine lung infection
Authors: Wong Ting , Hall Jesse , Boehm Dylan , Barbier Mariette , Heath Damron F. 
Published: May 2017

AbstractBordetella pertussisis an obligate human respiratory pathogen that causes the disease whooping cough. A whole cell vaccine (DTP) was developed in the 1940s and was subsequently replaced in the 1990s with a protein-based subunit acellular vaccine (DTaP; tdap). Today, we are observing a resurgence of whooping cough due to evolution of the pathogen and waning vaccine immunity. The use of vaccines decreased the need for basic research on this pathogen. As a result, numerous questions on the basic pathogenesis ofB. pertussisremain to be answered. Microarrays and more recently, RNA sequencing (RNAseq), have allowed the field to describe thein vitrogene expression profiles of the pathogen growing in both virulent and avirulent phases; however, no published studies have described anin vivotranscriptome of the pathogen. To address this need, we have designed and evaluated workflows to characterize thein vivotranscriptome ofB. pertussisduring infection of the murine lung. During our initial studies, we observed that only 0.014% of the ~100 million 2x50bp illumina reads corresponded to the pathogen, which is insufficient for analysis. Therefore, we developed a simple protocol to filter the bacteria out of the tissue homogenates and separate bacterial cells from the host tissue. RNA is then prepared, quantified, and theB. pertussisto host RNA ratio is determined. Here, we present the protocol and discuss the uses and next directions for which this RNAseq workflow can be applied. With this strategy we plan to fully characterize theB. pertussistranscriptome when the pathogen is infecting the murine lung in order to identify expressed genes that encode potential new vaccine antigens that will facilitate the development of the next generation of pertussis vaccines.
Using large-scale mutagenesis to guide single amino acid scanning experiments
Authors: Gray Vanessa E. , Hause Ronald J. , Fowler Douglas M. 
Published: May 2017

AbstractAlanine scanning mutagenesis is a widely-used method for identifying protein positions that are important for function or ligand binding. Alanine was chosen because it is physicochemically innocuous and constitutes a deletion of the side chain at the β- carbon. Alanine is also thought to best represent the effects of other mutations; however, this assumption has not been formally tested. To determine whether alanine substitutions are always the best choice, we analyzed 34,373 mutations in fourteen proteins whose effects were measured using large-scale mutagenesis approaches. We found that several substitutions, including histidine and asparagine, are better at recapitulating the effects of other substitutions. Histidine and asparagine also correlated best with the effects of other substitutions in different structural contexts. Furthermore, we found that alanine is among the worst substitutions for detecting ligand interface positions, despite its frequent use for this purpose. Our work highlights the utility of large-scale mutagenesis data and can help to guide future single substitution mutational scans.
Undocumented potential for primary productivity in a globally-distributed bacterial photoautotroph
Authors: Graham E.D. , Heidelberg J.F. , Tully B.J. 
Published: May 2017

AbstractAerobic anoxygenic phototrophs (AAnPs) are common in the global oceans and are associated with photoheterotrophic activity. To date, AAnPs have not been identified in the surface ocean that possess the potential for carbon fixation. Using the Tara Oceans metagenomic dataset, we have reconstructed draft genomes of four bacteria that possess the genomic potential for anoxygenic phototrophy, carbon fixation via the Calvin-Benson-Bassham cycle, and the oxidation of sulfite and thiosulfate. Forming a monophyletic clade within the Alphaproteobacteria and lacking cultured representatives, the organisms compose minor constituents of local microbial communities (0.1-1.0%), but are globally distributed, present in multiple samples from the North Pacific, Mediterranean Sea, the East Africa Coastal Province, and the South Atlantic. These organisms represent a shift in our understanding of microbially-mediated photoautotrophy in the global oceans and provide a previously undiscovered route of primary productivity.Significance StatementIn examining the genomic content of organisms collected during the Tara Oceans expedition, we have identified a novel clade within the Alphaproteobacteria that has the potential for photoautotrophy. Based on genome observations, these organisms have the potential to couple inorganic sulfur compounds as electron donors to fix carbon into biomass. They are globally distributed, present in samples from the North Pacific, Mediterranean Sea, East Africa Coastal Current, and the South Atlantic. This discovery may require re-examination of the microbial communities in the global ocean to understand and constrain the impacts of this group of organisms on the global carbon cycle.