bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Polymyxin B Hemoperfusion on Mortality in Patients With Severe Sepsis and Septic Shock: A Systemic Review, Meta-Analysis Update, and Disease Severity Subgroup Meta-Analysis
Authors: Chang Tzu , Tu Yu-Kang , Lee Chen-Tse , Chao Anne , Huang Chi-Hsiang , Wang Ming-Jiuh , Yeh Yu-Chang
Published: April 2017

Objective:

Several studies have reported a survival benefit for polymyxin B hemoperfusion treatment in patients with severe sepsis and septic shock. However, recently, a propensity-matched analysis and a randomized controlled trial reported no survival benefit for polymyxin B hemoperfusion treatment. We performed an up-to-date meta-analysis to determine the effect of polymyxin B hemoperfusion treatment on mortality in patients with severe sepsis and septic shock.

Data Sources:

PubMed, Embase, and Cochrane Library were searched from inception to May 2016.

Study Selection:

Studies investigating the effect of polymyxin B hemoperfusion on mortality were considered eligible. We searched for terms related to severe sepsis and septic shock and terms related to polymyxin B hemoperfusion.

Data Extraction:

The following data were extracted from the original articles: the name of the first author and publication year, subjects and setting, inclusion and exclusion criteria, mean age and size of the study population, male percentage, mortality, blood pressure, Sequential Organ Failure Assessment score, pulmonary oxygenation, and levels of endotoxin and humoral cytokines.

Data Synthesis:

A total of 17 trials were included. The pooled risk ratio for overall mortality was 0.81 (95% CI, 0.70–0.95), favoring polymyxin B hemoperfusion (p = 0.007). Disease severity subgroup meta-analysis revealed a significant reduction of mortality in the intermediate- and high-risk groups (risk ratio, 0.84; 95% CI, 0.77–0.92 and risk ratio, 0.64; 95% CI, 0.52–0.78, respectively), but not in the low-risk group (risk ratio, 1.278; 95% CI, 0.888–1.839). The nonlinear meta-regression with restricted cubic spline showed an almost linear inverse association between the baseline mortality rate and reduction in the risk of mortality.

Conclusion:

The present study demonstrated that polymyxin B hemoperfusion treatment may reduce mortality in patients with severe sepsis and septic shock in specific disease severity subgroups.
Aldosterone and Vascular Mineralocorticoid Receptors in Murine Endotoxic and Human Septic Shock*
Authors: Fadel Fouad , André-Grégoire Gwennan , Gravez Basile , Bauvois Brigitte , Bouchet Sandrine , Sierra-Ramos Catalina , Polito Andrea , Mansart Arnaud , Alvarez de la Rosa Diego , Annane Djillali , Jaisser Frédéric
Published: April 2017

Objectives:

Vascular mineralocorticoid receptors play a role in vascular tone and blood pressure regulation, might participate in the pathophysiology of circulatory failure during sepsis, and represent a potential therapeutic target in this disease. We aimed to study the effects of mineralocorticoids and the involvement of vascular mineralocorticoid receptors in murine endotoxic and human septic shock.

Design:

Experimental study.

Setting:

Translational investigation including animal research and in vitro experiments using human vascular cells and plasma from septic patients.

Subjects:

Adult male C57Black 6 mice, adult patients with septic shock.

Interventions:

Mice were injected with lipopolysaccharide and/or aldosterone. Human endothelial and smooth muscle cells were treated with pro-inflammatory cytokines with or without aldosterone, nuclear factor-κB inhibitor BAY 11-7082, or plasma from septic patients.

Measurements and Main Results:

Aldosterone improved 5-day survival, invasive arterial pressure, and in vivo and ex vivo arterial response to phenylephrine at 18 hours after induction of murine endotoxic shock. Both α1-adrenoceptor and mineralocorticoid receptor expressions studied in mouse aortas were down-regulated at 6 and 18 hours in endotoxemic mice and restored in aldosterone-treated mice. Furthermore, tumor necrosis factor-α decreased both mineralocorticoid receptor and α1-adrenoceptor expressions within 5 hours in human vascular cells in a nuclear factor-κB pathway–dependent manner. Mineralocorticoid receptor expression was also blunted in human cells treated with plasma from septic patients.

Conclusion:

We found a beneficial effect of mineralocorticoids on survival, blood pressure, and vascular reactivity, associated with a restoration of α1-adrenoceptor expression in endotoxic shock. Furthermore, blunted vascular mineralocorticoid receptor expression might participate in hemodynamic failure during sepsis.
Plastic and Reconstructive Surgery in Global Health: Let’s Reconstruct Global Surgery
Authors: Chung Karen Y.
Published: April 2017

Since the inception of the Lancet Commission in 2013 and consequent prioritization of Global Surgery at the World Health Assembly, international surgical outreach efforts have increased and become more synergistic. Plastic surgeons have been involved in international outreach for decades, and there is now a demand to collaborate and address local need in an innovative way. The aim of this article was to summarize new developments in plastic and reconstructive surgery in global health, to unify our approach to international outreach. Specifically, 5 topics are explored: current models in international outreach, benefits and concerns, the value of research, the value of international surgical outreach education, and the value of technology. A “Let’s Reconstruct Global Surgery” network has been formed using Facebook as a platform to unite plastic and reconstructive surgeons worldwide who are interested in international outreach. The article concludes with actionable recommendations from each topic.
Amnion Membrane in Diabetic Foot Wounds: A Meta-analysis
Authors: Haugh Alexandra M. , Witt Jacqueline G. , Hauch Adam , Darden Michael , Parker Geoffrey , Ellsworth Warren A. , Buell Joseph F.
Published: April 2017

Background:

Amniotic membrane is tissue obtained from human placenta rich in cytokines, growth factors, and stem cells that possess the ability to inhibit infection, improve healing, and stimulate regeneration.

Methods:

A meta-analysis was performed examining randomized controlled trials comparing amniotic tissue products with standard of care in nonhealing diabetic foot ulcers including PubMed, Cochrane Central Register of Controlled Trials, and the Cochrane Database of Systematic Reviews.

Results:

A search of 3 databases identified 596 potentially relevant articles. Application of selection criteria led to the selection of 5 randomized controlled trials. The 5 selected randomized controlled trials represented a total of 311 patients. The pooled relative risk of healing with amniotic products compared with control was 2.7496 (2.05725–3.66524, P < 0.001).

Conclusions:

The current meta-analysis indicates that the treatment of diabetic foot ulcers with amniotic membrane improves healing rates in diabetic foot ulcers. Further studies are needed to determine whether these products also decrease the incidence of subsequent complications, such as amputation or death, in diabetic patients.
One-Year Clinical Outcomes of a Corneal Inlay for Presbyopia
Authors: Beer Sandra M. C. , Santos Rodrigo , Nakano Eliane M. , Hirai Flavio , Nitschke Enrico J. , Francesconi Claudia , Campos Mauro
Published: April 2017

Purpose:

To report the results of a 1-year follow-up analysis of the safety and efficacy of the Flexivue Microlens corneal inlay.

Methods:

The Flexivue Microlens corneal inlay was implanted in the nondominant eye of patients with emmetropic presbyopia (a spherical equivalent of −0.5 to 1.00 diopter) after the creation of a 300-μm deep stromal pocket, using a femtosecond laser. The patients were followed up according to a clinical protocol involving refraction, anterior segment imaging analysis (Oculyzer), and optical quality analysis (OPD-Scan).

Results:

Thirty-one patients were enrolled in this ongoing study. The mean age was 50.7 years (range 45–60 yrs), and 70% of the patients were female. The mean uncorrected near visual acuity improved to Jaeger 1 in 87.1% of the eyes treated with the inlays. All eyes improved 4 lines at all visits. The binocular uncorrected distance visual acuity was 20/20 in all patients. Ninety percent of the patients reported that their near vision was good or excellent. Some of the patients (16.1%) lost more than 3 lines of corrected distance visual acuity. At the latest follow-up, induction of a corneal spherical aberration to improve near visual acuity was statistically significant. No other intraoperative or postoperative complication was noted.

Conclusions:

The Flexivue Microlens provided patients with improved near vision, as a result of a negative spherical aberration. A significant loss of corrected distance visual acuity in the operated eyes was observed. Overall, this intracorneal inlay was an effective alternative to other procedures for the correction of presbyopia.
Increased Mortality and Length of Stay Associated With Medical Emergency Team Review in Hospitalized Pediatric Patients: A Retrospective Cohort Study*
Authors: McKelvie Brianna , McNally James Dayre , Chan Jason , Momoli Franco , Ramsay Christa , Lobos Anna-Theresa
Published: April 2017

Objective:

Rapid response systems using medical emergency teams reduce hospital wide cardiorespiratory arrest and mortality. While rapid response systems improve hospital-wide outcomes, children receiving medical emergency team review may still be at increased risk for morbidity and mortality. The study purpose was to compare the length of stay and mortality rate in children receiving a medical emergency team review with those of other hospitalized children.

Design:

Retrospective cohort study.

Setting:

Tertiary Pediatric Hospital, Children’s Hospital of Eastern Ontario, Ottawa, Canada.

Patients:

Cohort of 42,308 pediatric admissions to the general inpatient ward.

Interventions:

Data over 7 years were obtained from a prospectively maintained rapid response systems database.

Measurements and Main Results:

From the cohort, 995 (2.35%) of the admissions had one and 276 (0.65%) had multiple medical emergency team activations. When compared with patients without, children having one or multiple medical emergency team reviews had 13.34 (95% CI, 5.33–33.2) and 50.10 (95% CI, 19.86–126.39) times the odds of death, respectively. Patients experiencing a medical emergency team review stayed in hospital 1.59 times (95% CI, 1.39–1.82) longer, whereas those with multiple medical emergency team reviews stayed 2.44 times (95% CI, 1.85–3.20) longer. The associations remained significant after controlling for important confounders and excluding elective admissions from the analyses. Most repeat medical emergency team reviews occurred within a day of the initial review or involved patients with multiple comorbidities.

Conclusions:

Our study suggests that pediatric patients reviewed by the medical emergency team are at significantly higher risk of mortality and longer length of stay than general ward inpatients. As well, patients with multiple medical emergency team reviews were at particularly high risk compared with patients with one medical emergency team review. Patients who experience medical emergency team reviews should be recognized as a high-risk group, and future studies should consider how to decrease morbidity and mortality. Based on our findings, we suggest that these patients be followed for 24–48 hours after any medical emergency team activation.
Accelerated aging in adults with knee osteoarthritis pain: consideration for frequency, intensity, time, and total pain sites
Authors: Sibille Kimberly T. , Chen Huaihou , Bartley Emily J. , Riley Joseph , Glover Toni L. , King Christopher D. , Zhang Hang , Cruz-Almeida Yenisel , Goodin Burel R. , Sotolongo Adriana , Petrov Megan E. , Herbert Matthew , Bulls Hailey W. , Edberg Jeffrey C. , Staud Roland , Redden David , Bradley Laurence A. , Fillingim Roger B.
Published: April 2017

Introduction:

Individuals with osteoarthritis (OA) show increased morbidity and mortality. Telomere length, a measure of cellular aging, predicts increased morbidity and mortality. Telomeres shorten with persisting biological and psychosocial stress. Living with chronic OA pain is stressful. Previous research exploring telomere length in people with OA has produced inconsistent results. Considering pain severity may clarify the relationship between OA and telomeres.

Objectives:

We hypothesized that individuals with high OA chronic pain severity would have shorter telomeres than those with no or low chronic pain severity.

Methods:

One hundred thirty-six adults, ages 45 to 85 years old, with and without symptomatic knee OA were included in the analysis. Peripheral blood leukocyte telomere length was measured, and demographic, clinical, and functional data were collected. Participants were categorized into 5 pain severity groups based on an additive index of frequency, intensity, time or duration, and total number of pain sites (FITT). Covariates included age, sex, race or ethnicity, study site, and knee pain status.

Results:

The no or low chronic pain severity group had significantly longer telomeres compared with the high pain severity group,P= 0.025. A significant chronic pain severity dose response emerged for telomere length,P= 0.034. The FITT chronic pain severity index was highly correlated with the clinical and functional OA pain measures. However, individual clinical and functional measures were not associated with telomere length.

Conclusion:

Results demonstrate accelerated cellular aging with high knee OA chronic pain severity and provide evidence for the potential utility of the FITT chronic pain severity index in capturing the biological burden of chronic pain.
The role of feeding morphology and competition in governing the diet breadth of sympatric stomatopod crustaceans
Authors: deVries Maya S.
Published: April 2017

Competition for food drives divergence and specialization in feeding morphology. Stomatopod crustaceans have two kinds of highly specialized feeding appendages: either elongate spear-like appendages (
spearers
) used to ambush soft-bodied evasive prey or hammer-like appendages (
smashers
) that produce extremely high forces used both to break hard-shelled prey and to capture evasive prey. To evaluate associations between appendage type and feeding ecology, the diet of two small smasher and spearer species (size range: 21–27 mm) that co-occur were compared. Stable isotope analysis and the Bayesian mixing model MixSIAR were used to estimate the proportional contributions of prey types to the diet. Both species had relatively wide diets that included hard-shelled and soft-bodied prey, albeit in different proportions; the smasher consumed a greater proportion of hard-shelled prey, and the spearer consumed mostly soft-bodied prey. Appendage kinematics in stomatopods is known to scale linearly across species. These two small species may produce similar kinematics allowing them both to capture evasive prey and hammer hard-shelled prey, thereby widening their diets. Yet, the spearer species is more highly adept at capturing evasive prey, indicating that small spearers are stronger competitors for soft-bodied prey. These findings suggest that a smasher's ability to access hard prey reduced competition for soft prey, and therefore conferred an important benefit favouring the evolution of the impressive smashing strike.
Alan Davison. 24 March 1936 — 14 November 2015
Authors: Green Malcolm L. H. , Cummins Christopher C. , Kronauge James F.
Published: April 2017

In 1958 Professor Alan Davison started his research career at an exciting time for the field of organometallic chemistry. New developments in spectroscopy, instrumentation and techniques to manipulate materials in controlled environments to avoid reaction with water or oxygen were becoming widely available. Controlling exposure of an element with highly reactive oxygen facilitated the isolation, characterization and discovery of an abundance of unknown compounds. Alan was an insightful and talented synthetic chemist and made many new and interesting organometallic compounds. He used the earliest commercial nuclear magnetic resonance instruments to characterize the then poorly understood transition metal hydrides and also to identify the earliest fluxional organometallic molecules. In 1970 he entered a collaboration with Professor Alun G. Jones, a nuclear chemist at Harvard Medical School, to characterize and develop the chemistry of technetium. They made a major discovery of technetium molecules which had the ability to selectively locate in human heart muscle, thereby vastly expanding the practice of nuclear medicine to a global community. Professor Alan Davison was also widely known for his outstanding qualities as a teacher and mentor.
Efficient use of sentinel sites: detection of invasive honeybee pests and diseases in the UK
Authors: Keeling Matt J. , Datta Samik , Franklin Daniel N. , Flatman Ivor , Wattam Andy , Brown Mike , Budge Giles E.
Published: April 2017

Sentinel sites, where problems can be identified early or investigated in detail, form an important part of planning for exotic disease outbreaks in humans, livestock and plants. Key questions are: how many sentinels are required, where should they be positioned and how effective are they at rapidly identifying new invasions? The sentinel apiary system for invasive honeybee pests and diseases illustrates the costs and benefits of such approaches. Here, we address these issues with two mathematical modelling approaches. The first approach is generic and uses probabilistic arguments to calculate the average number of affected sites when an outbreak is first detected, providing rapid and general insights that we have applied to a range of infectious diseases. The second approach uses a computationally intensive, stochastic, spatial model to simulate multiple outbreaks and to determine appropriate sentinel locations for UK apiaries. Both models quantify the anticipated increase in success of sentinel sites as their number increases and as non-sentinel sites become worse at detection; however, unexpectedly sentinels perform relatively better for faster growing outbreaks. Additionally, the spatial model allows us to quantify the substantial role that carefully positioned sentinels can play in the rapid detection of exotic invasions.
Deterministic versus stochastic model of reprogramming: new evidence from cellular barcoding technique
Authors: Yunusova Anastasia M. , Fishman Veniamin S. , Vasiliev Gennady V. , Battulin Nariman R.
Published: April 2017

Factor-mediated reprogramming of somatic cells towards pluripotency is a low-efficiency process during which only small subsets of cells are successfully reprogrammed. Previous analyses of the determinants of the reprogramming potential are based on average measurements across a large population of cells or on monitoring a relatively small number of single cells with live imaging. Here, we applied lentiviral genetic barcoding, a powerful tool enabling the identification of familiar relationships in thousands of cells. High-throughput sequencing of barcodes from successfully reprogrammed cells revealed a significant number of barcodes from related cells. We developed a computer model, according to which a probability of synchronous reprogramming of sister cells equals 10–30%. We conclude that the reprogramming success is pre-established in some particular cells and, being a heritable trait, can be maintained through cell division. Thus, reprogramming progresses in a deterministic manner, at least at the level of cell lineages.
Relict or reintroduction? Genetic population assignment of three Tasmanian devils (Sarcophilus harrisii) recovered on mainland Australia
Authors: White Lauren C. , Austin Jeremy J.
Published: April 2017

Today, the Tasmanian devil (Sarcophilus harrisii) is found only on the island of Tasmania, despite once being widespread across mainland Australia. While the devil is thought to have become extinct on the mainland approximately 3000 years ago, three specimens were collected in Victoria (south-eastern Australia) between 1912 and 1991, raising the possibility that a relict mainland population survived in the area. Alternatively, these devils may have escaped captivity or were deliberately released after being transported from Tasmania, a practice that has been strictly controlled since the onset of devil facial tumour disease in the early 1990s. Such quarantine regimes are important to protect disease-free, ‘insurance populations’ in zoos on the mainland. To test whether the three Victorian devils were members of a relict mainland population or had been recently transported from Tasmania we identified seven single nucleotide polymorphisms (SNPs) in the mitochondrial genome that can distinguish between Tasmanian and ancient mainland populations. The three Victorian devil specimens have the same seven SNPs diagnostic of modern Tasmanian devils, confirming that they were most likely transported from Tasmania and do not represent a remnant population of mainland devils.
The dispersal of planet-forming discs: theory confronts observations
Authors: Ercolano Barbara , Pascucci Ilaria
Published: April 2017

Discs of gas and dust around million-year-old stars are a by-product of the star formation process and provide the raw material to form planets. Hence, their evolution and dispersal directly impact what type of planets can form and affect the final architecture of planetary systems. Here, we review empirical constraints on disc evolution and dispersal with special emphasis on transition discs, a subset of discs that appear to be caught in the act of clearing out planet-forming material. Along with observations, we summarize theoretical models that build our physical understanding of how discs evolve and disperse and discuss their significance in the context of the formation and evolution of planetary systems. By confronting theoretical predictions with observations, we also identify the most promising areas for future progress.
Optimal strategies for throwing accurately
Authors: Venkadesan M. , Mahadevan L.
Published: April 2017

The accuracy of throwing in games and sports is governed by how errors in planning and initial conditions are propagated by the dynamics of the projectile. In the simplest setting, the projectile path is typically described by a deterministic parabolic trajectory which has the potential to amplify noisy launch conditions. By analysing how parabolic trajectories propagate errors, we show how to devise optimal strategies for a throwing task demanding accuracy. Our calculations explain observed speed–accuracy trade-offs, preferred throwing style of overarm versus underarm, and strategies for games such as dart throwing, despite having left out most biological complexities. As our criteria for optimal performance depend on the target location, shape and the level of uncertainty in planning, they also naturally suggest an iterative scheme to learn throwing strategies by trial and error.
Exosomes in mammals with greater habitat variability contain more proteins and RNAs
Authors: Takemoto Kazuhiro , Imoto Miku
Published: April 2017

Factors determining habitat variability are poorly understood despite possible explanations based on genome and physiology. This is because previous studies only focused on primary measures such as genome size and body size. In this study, we hypothesize that specific gene functions determine habitat variability in order to explore new factors beyond primary measures. We comprehensively evaluate the relationship between gene functions and the climate envelope while statistically controlling for potentially confounding effects by using data on the habitat range, genome, body size and metabolism of various mammals. Our analyses show that the number of proteins and RNAs contained in exosomes is predominantly associated with the climate envelope. This finding indicates the importance of exosomes to habitat range expansion of mammals and provides a new hypothesis for the relationship between the genome and habitat variability.
Design and simulation of origami structures with smooth folds
Authors: Peraza Hernandez E. A. , Hartl D. J. , Lagoudas D. C.
Published: April 2017

Origami has enabled new approaches to the fabrication and functionality of multiple structures. Current methods for origami design are restricted to the idealization of folds as creases of zeroth-order geometric continuity. Such an idealization is not proper for origami structures of non-negligible fold thickness or maximum curvature at the folds restricted by material limitations. For such structures, folds are not properly represented as creases but rather as bent regions of higher-order geometric continuity. Such fold regions of arbitrary order of continuity are termed assmooth folds. This paper presents a method for solving the following origami design problem: given a goal shape represented as a polygonal mesh (termed as thegoal mesh), find the geometry of a single planar sheet, its pattern of smooth folds, and the history of folding motion allowing the sheet to approximate the goal mesh. The parametrization of the planar sheet and the constraints that allow for a valid pattern of smooth folds are presented. The method is tested against various goal meshes having diverse geometries. The results show that every determined sheet approximates its corresponding goal mesh in a known folded configuration having fold angles obtained from the geometry of the goal mesh.
Wrinkle surface instability of an inhomogeneous elastic block with graded stiffness
Authors: Yang Shengyou , Chen Yi-chao
Published: April 2017

Surface instabilities have been studied extensively for both homogeneous materials and film/substrate structures but relatively less for materials with continuously varying properties. This paper studies wrinkle surface instability of a graded neo-Hookean block with exponentially varying modulus under plane strain by using the linear bifurcation analysis. We derive the first variation condition for minimizing the potential energy functional and solve the linearized equations of equilibrium to find the necessary conditions for surface instability. It is found that for a homogeneous block or an inhomogeneous block with increasing modulus from the surface, the critical stretch for surface instability is 0.544 (0.456 strain), which is independent of the geometry and the elastic modulus on the surface of the block. This critical stretch coincides with that reported by Biot (1963
Appl. Sci. Res.
12
, 168–182. (
doi:10.1007/BF03184638
)) 53 years ago for the onset of wrinkle instabilities in a half-space of homogeneous neo-Hookean materials. On the other hand, for an inhomogeneous block with decreasing modulus from the surface, the critical stretch for surface instability ranges from 0.544 to 1 (0–0.456 strain), depending on the modulus gradient, and the length and height of the block. This sheds light on the effects of the material inhomogeneity and structural geometry on surface instability.
Stochastic modelling of membrane filtration
Authors: Krupp A. U. , Griffiths I. M. , Please C. P.
Published: April 2017

Membrane fouling during particle filtration occurs through a variety of mechanisms, including internal pore clogging by contaminants, coverage of pore entrances and deposition on the membrane surface. In this paper, we present an efficient method for modelling the behaviour of a filter, which accounts for different retention mechanisms, particle sizes and membrane geometries. The membrane is assumed to be composed of a series of, possibly interconnected, pores. The central feature is a
conductivity function
, which describes the blockage of each individual pore as particles arrive, which is coupled with a mechanism to account for the stochastic nature of the arrival times of particles at the pore. The result is a system of ordinary differential equations based on the pore-level interactions. We demonstrate how our model can accurately describe a wide range of filtration scenarios. Specifically, we consider a case where blocking via multiple mechanisms can occur simultaneously, which have previously required the study through individual models; the filtration of a combination of small and large particles by a track-etched membrane and particle separation using interconnected pore networks. The model is significantly faster than comparable stochastic simulations for small networks, enabling its use as a tool for efficient future simulations.
Lipid consumption in coral larvae differs among sites: a consideration of environmental history in a global ocean change scenario
Authors: Rivest Emily B. , Chen Chii-Shiarng , Fan Tung-Yung , Li Hsing-Hui , Hofmann Gretchen E.
Published: April 2017

The success of early life-history stages is an environmentally sensitive bottleneck for many marine invertebrates. Responses of larvae to environmental stress may vary due to differences in maternal investment of energy stores and acclimatization/adaptation of a population to local environmental conditions. In this study, we compared two populations from sites with different environmental regimes (Moorea and Taiwan). We assessed the responses of
Pocillopora damicornis
larvae to two future co-occurring environmental stressors: elevated temperature and ocean acidification. Larvae from Taiwan were more sensitive to temperature, producing fewer energy-storage lipids under high temperature. In general, planulae in Moorea and Taiwan responded similarly to
p
CO
2
. Additionally, corals in the study sites with different environments produced larvae with different initial traits, which may have shaped the different physiological responses observed. Notably, under ambient conditions, planulae in Taiwan increased their stores of wax ester and triacylglycerol in general over the first 24 h of their dispersal, whereas planulae from Moorea consumed energy-storage lipids in all cases. Comparisons of physiological responses of
P. damicornis
larvae to conditions of ocean acidification and warming between sites across the species' biogeographic range illuminates the variety of physiological responses maintained within
P. damicornis
, which may enhance the overall persistence of this species in the light of global climate change.
Polydomy enhances foraging performance in ant colonies
Authors: Stroeymeyt N. , Joye P. , Keller L.
Published: April 2017

Collective foraging confers benefits in terms of reduced predation risk and access to social information, but it heightens local competition when resources are limited. In social insects, resource limitation has been suggested as a possible cause for the typical decrease in
per capita
productivity observed with increasing colony size, a phenomenon known as Michener's paradox. Polydomy (distribution of a colony's brood and workers across multiple nests) is believed to help circumvent this paradox through its positive effect on foraging efficiency, but there is still little supporting evidence for this hypothesis. Here, we show experimentally that polydomy enhances the foraging performance of food-deprived
Temnothorax nylanderi
ant colonies via several mechanisms. First, polydomy influences task allocation within colonies, resulting in faster retrieval of protein resources. Second, communication between sister nests reduces search times for far away resources. Third, colonies move queens, brood and workers across available nest sites in response to spatial heterogeneities in protein and carbohydrate resources. This suggests that polydomy represents a flexible mechanism for space occupancy, helping ant colonies adjust to the environment.
Wind and rain are the primary climate factors driving changing phenology of an aerial insectivore
Authors: Irons Rachel D. , Harding Scurr April , Rose Alexandra P. , Hagelin Julie C. , Blake Tricia , Doak Daniel F.
Published: April 2017

While the ecological effects of climate change have been widely observed, most efforts to document these impacts in terrestrial systems have concentrated on the impacts of temperature. We used tree swallow (
Tachycineta bicolor
) nest observations from two widely separated sites in central Alaska to examine the aspects of climate affecting breeding phenology at the northern extent of this species' range. We found that two measures of breeding phenology, annual lay and hatch dates, are more strongly predicted by windiness and precipitation than by temperature. At our longest-monitored site, breeding phenology has advanced at nearly twice the rate seen in more southern populations, and these changes correspond to long-term declines in windiness. Overall, adverse spring climate conditions known to negatively impact foraging success of swallows (wet, windy weather) appear to influence breeding phenology more than variation in temperature. Separate analyses show that short windy periods significantly delay initiation of individual clutches within years. While past reviews have emphasized that increasing variability in climate conditions may create physiological and ecological challenges for natural populations, we find that long-term reductions in inclement weather corresponded to earlier reproduction in one of our study populations. To better predict climate change impacts, ecologists need to more carefully test effects of multiple climate variables, including some, like windiness, that may be of paramount importance to some species, but have rarely been considered as strong drivers of ecological responses to climate alteration.
Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone
Authors: Villa Laura , Feudi Claudia , Fortini Daniela , Brisse Sylvain , Passet Virginie , Bonura Celestino , Endimiani Andrea , Mammina Caterina , Ocampo Ana Maria , Jimenez Judy Natalia , Doumith Michel , Woodford Neil , Hopkins Katie , Carattoli Alessandra
Published: April 2017

The global spread of Klebsiella pneumoniae producing Klebsiella pneumoniae carbapenemase (KPC) has been mainly associated with the dissemination of high-risk clones. In the last decade, hospital outbreaks involving KPC-producing K. pneumoniae have been predominantly attributed to isolates belonging to clonal group (CG) 258. However, results of recent epidemiological analysis indicate that KPC-producing sequence type (ST) 307, is emerging in different parts of the world and is a candidate to become a prevalent high-risk clone in the near future. Here we show that the ST307 genome encodes genetic features that may provide an advantage in adaptation to the hospital environment and the human host. Sequence analysis revealed novel plasmid-located virulence factors, including a cluster for glycogen synthesis. Glycogen production is considered to be one of the possible adaptive responses to long-term survival and growth in environments outside the host. Chromosomally-encoded virulence traits in the clone comprised fimbriae, an integrative conjugative element carrying the yersiniabactin siderophore, and two different capsular loci. Compared with the ST258 clone, capsulated ST307 isolates showed higher resistance to complement-mediated killing. The acquired genetic features identified in the genome of this new emerging clone may contribute to increased persistence of ST307 in the hospital environment and shed light on its potential epidemiological success.
Tissue-specific downregulation ofEDTPsuppresses polyglutamine protein aggregates and extends lifespan inDrosophila
Authors: Xiao Chengfeng , Qiu Shuang , Robertson R Meldrum , Seroude Laurent
Published: April 2017

Drosophilaegg-derived tyrosine phosphatase (EDTP, also called JUMPY) is a lipid phosphatase essential in oogenesis and muscle function in the adult stage. Although mammalian JUMPY negatively regulates autophagy, loss-of-JUMPY causes muscle dysfunction and is associated with a rare genetic disorder called centronuclear myopathy. Here we show that tissue-specific downregulation of EDTP inDrosophilanon-muscle tissues, particularly glial cells, suppresses the expression of polyglutamine (polyQ) protein aggregates in the same cells and improves survival. Additionally, tissue-specific downregulation of EDTP in glial cells or motoneurons extends lifespan. We demonstrate an approach to fine-tune the expression of a disease-associated geneEDTPfor the removal of polyQ protein aggregate and lifespan extension inDrosophila.
Assessing species biomass contributions in microbial communities via metaproteomics
Authors: Kleiner Manuel , Thorson Erin , Sharp Christine E. , Dong Xiaoli , Liu Dan , Li Carmen , Strous Marc
Published: April 2017

Assessment of microbial community composition is the cornerstone of microbial ecology. Microbial community composition can be analyzed by quantifying cell numbers or by quantifying biomass for individual populations. However, as cell volumes can differ by orders of magnitude, these two approaches yield vastly different results. Methods for quantifying cell numbers are already available (e.g. fluorescencein situhybridization, 16S rRNA gene amplicon sequencing), yet methods for assessing community composition in terms of biomass are lacking.

We developed metaproteomics based methods for assessing microbial community composition using protein abundance as a measure for biomass contributions of individual populations. We optimized the accuracy and sensitivity of the method using artificially assembled microbial communities and found that it is less prone to some of the biases found in sequencing-based methods. We applied the method using communities from two different environments, microbial mats from two alkaline soda lakes and saliva from multiple individuals.
Identification ofcis-regulatory mutations generatingde novoedges in personalized cancer gene regulatory networks
Authors: Atak Zeynep Kalender , Imrichova Hana , Svetlichnyy Dmitry , Hulselmans Gert , Christiaens Valerie , Reumers Joke , Ceulemans Hugo , Aerts Stein
Published: April 2017

The identification of functional non-coding mutations is a key challenge in the field of genomics, where whole-genome re-sequencing can swiftly generate a set of all genomic variants in a sample, such as a tumor biopsy. The size of the human regulatory landscape places a challenge on finding recurrentcis-regulatory mutations across samples of the same cancer type. Therefore, powerful computational approaches are required to sift through the tens of thousands of non-coding variants, to identify potentially functional variants that have an impact on the gene expression profile of the sample. Here we introduce an integrative analysis pipeline, calledμ- cisTarget, to filter, annotate and prioritize non-coding variants based on their putative effect on the underlying 'personal' gene regulatory network. We first validateμ-cisTarget by re-analyzing three cases of oncogenic non-coding mutations, namely theTAL1andLMO1enhancer mutations in T-ALL, and theTERTpromoter mutation in melanoma. Next, we re-sequenced the full genome of ten cancer cell lines of six different cancer types, and used matched transcriptome data and motif discovery to infer master regulators for each sample. We identified candidate functional non-coding mutations that generatede novobinding sites for these master regulators, and that result in the up-regulation of nearby oncogenic drivers. We finally validated the predictions using tertiary data including matched epigenome data. Our approach is generally applicable to re-sequenced cancer genomes, or other genomes, when a disease- or sample-specific gene signature is available for network inference.μ-cisTarget is available fromhttp://mucistarget.aertslab.org.
MCAM contributes to the establishment of cell autonomous polarity in myogenic and chondrogenic differentiation
Authors: Moreno-Fortuny Artal , Bragg Laricia , Cossu Giulio , Roostalu Urmas
Published: April 2017

Cell polarity has a fundamental role in shaping the morphology of cells and growing tissues. Polarity is commonly thought to be established in response to extracellular signals. Here we used a minimalin vitroassay that enabled us to monitor the determination of cell polarity in myogenic and chondrogenic differentiation in the absence of external signalling gradients. We demonstrate that the initiation of cell polarity is regulated by melanoma cell adhesion molecule (MCAM). We found highly polarized localization of MCAM, Moesin (MSN), Scribble (SCRIB) and Van-Gogh-like 2 (VANGL2) at the distal end of elongating myotubes. Knockout of MCAM or elimination of its endocytosis motif does not impair the initiation of myogenesis or myoblast fusion, but prevents myotube elongation. MSN, SCRIB and VANGL2 remain uniformly distributed in MCAM knockout cells. We show that MCAM is also required at early stages of chondrogenic differentiation. In both myogenic and chondrogenic differentiation MCAM knockout leads to transcriptional downregulation ofScriband enhanced MAP kinase activity. Our data demonstrates the importance of cell autonomous polarity in differentiation.
The histone variant H2A.Z promotes splicing of weak introns
Authors: Nissen Kelly E. , Homer Christina M. , Ryan Colm J. , Shales Michael , Krogan Nevan J. , Patrick Kristin L. , Guthrie Christine
Published: April 2017

Multiple lines of evidence implicate chromatin in the regulation of premessenger RNA (pre-mRNA) splicing. However, the influence of chromatin factors on cotranscriptional splice site usage remains unclear. Here we investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast Schizosaccharomyces pombe. Using epistatic miniarray profiles (EMAPs) to survey the genetic interaction landscape of the Swr1 nucleosome remodeling complex, which deposits H2A.Z, we uncovered evidence for functional interactions with components of the spliceosome. In support of these genetic connections, splicing-specific microarrays show that H2A.Z and the Swr1 ATPase are required during temperature stress for the efficient splicing of a subset of introns. Notably, affected introns are enriched for H2A.Z occupancy and more likely to contain nonconsensus splice sites. To test the significance of the latter correlation, we mutated the splice sites in an affected intron to consensus and found that this suppressed the requirement for H2A.Z in splicing of that intron. These data suggest that H2A.Z occupancy promotes cotranscriptional splicing of suboptimal introns that may otherwise be discarded via proofreading ATPases. Consistent with this model, we show that overexpression of splicing ATPase Prp16 suppresses both the growth and splicing defects seen in the absence of H2A.Z.
Dicer loss and recovery induce an oncogenic switch driven by transcriptional activation of the oncofetal Imp1–3 family
Authors: JnBaptiste Courtney K. , Gurtan Allan M. , Thai Kevin K. , Lu Victoria , Bhutkar Arjun , Su Mei-Ju , Rotem Asaf , Jacks Tyler , Sharp Phillip A.
Published: April 2017

MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression critical for organismal viability. Changes in miRNA activity are common in cancer, but how these changes relate to subsequent alterations in transcription and the process of tumorigenesis is not well understood. Here, we report a deep transcriptional, oncogenic network regulated by miRNAs. We present analysis of the gene expression and phenotypic changes associated with global miRNA restoration in miRNA-deficient fibroblasts. This analysis uncovers a miRNA-repressed network containing oncofetal genes Imp1, Imp2, and Imp3 (Imp1–3) that is up-regulated primarily transcriptionally >100-fold upon Dicer loss and is resistant to resilencing by complete restoration of miRNA activity. This Dicer-resistant epigenetic switch confers tumorigenicity to these cells. Let-7 targets Imp1–3 are required for this tumorigenicity and feed back to reinforce and sustain expression of the oncogenic network. Together, these Dicer-resistant genes constitute an mRNA expression signature that is present in numerous human cancers and is associated with poor survival.
Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
Authors: Han Fan , Lamichhaney Sangeet , Grant B. Rosemary , Grant Peter R. , Andersson Leif , Webster Matthew T.
Published: April 2017

Genomic comparisons of closely related species have identified “islands” of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.
The dinuclear scandium(III) cyclooctatetraenyl chloride complex di-μ-chlorido-bis[(η8-cyclooctatetraene)(tetrahydrofuran-κO)scandium(III)]
Authors: Zhou Zheng , Greenough Joshua , Wei Zheng , Petrukhina Marina A.
Published: April 2017

Only a few cyclooctatetraene dianion (COT) π-complexes of lanthanides have been crystallographically characterized. This first single-crystal X-ray diffraction characterization of a scandium(III) COT chloride complex, namely di-μ-chlorido-bis[(η8-cyclooctatetraene)(tetrahydrofuran-κO)scandium(III)], [Sc2(C8H8)2Cl2(C4H8O)2] or [Sc(COT)Cl(THF)]2 (THF is tetrahydrofuran), (1), reveals a dimeric molecular structure with symmetric chloride bridges [average Sc—Cl = 2.5972 (7) Å] and a η8-bound COT ligand. The COT ring is planar, with an average C—C bond length of 1.399 (3) Å. The Sc—C bond lengths range from 2.417 (2) to 2.438 (2) Å [average 2.427 (2) Å]. Direct comparison of (1) with the known lanthanide (Ln) analogues (La, Ce, Pr, Nd, and Sm) illustrates the effect of metal-ion (M) size on molecular structure. Overall, the M—Cl, M—O, and M—C bond lengths in (1) are the shortest in the series. In addition, only one THF molecule completes the coordination environment of the small ScIII ion, in contrast to the previously reported dinuclear Ln–COT–Cl complexes, which all have two bound THF molecules per metal atom.