bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in Smoking Behavior Before and After Gastric Bypass
Authors: King Wendy C. , White Gretchen E. , Belle Steven H. , Yanovski Susan Z. , Pomp Alfons , Pories Walter J. , Wolfe Bruce M. , Ahmed Bestoun , Courcoulas Anita P. 
Published: February 2020

Objective:
To evaluate smoking history and change in smoking behavior, from 1 year before through 7 years after Roux-en-Y gastric bypass (RYGB) surgery, and to identify risk factors for post-surgery smoking.

Background:
Smoking behavior in the context of bariatric surgery is poorly described.

Methods:
Adults undergoing RYGB surgery entered a prospective cohort study between 2006 and 2009 and were followed up to 7 years until ≤2015. Participants (N = 1770; 80% female, median age 45 years, median body mass index 47 kg/m2) self-reported smoking history pre-surgery, and current smoking behavior annually.

Results:
Almost half of participants (45.2%) reported a pre-surgery history of smoking. Modeled prevalence of current smoking decreased in the year before surgery from 13.7% [95% confidence interval (CI) = 12.1–15.4] to 2.2% (95% CI = 1.5–2.9) at surgery, then increased to 9.6% (95% CI = 8.1–11.2) 1-year post-surgery and continued to increase to 14.0% (95% CI = 11.8–16.0) 7-years post-surgery. Among smokers, mean packs/day was 0.60 (95% CI = 0.44–0.77) at surgery, 0.70 (95% CI = 0.62–0.78) 1-year post-surgery and 0.77 (95% CI = 0.68–0.88) 7-years post-surgery. At 7-years, smoking was reported by 61.7% (95% CI = 51.9–70.8) of participants who smoked 1-year pre-surgery (n = 221), 12.3% (95% CI = 8.5–15.7) of participants who formerly smoked but quit >1 year pre-surgery (n = 507), and 3.8% (95% CI = 2.1–4.9) of participants who reported no smoking history (n = 887). Along with smoking history (ie, less time since smoked), younger age, household income <$25,000, being married or living as married, and illicit drug use were independently associated with increased risk of post-surgery smoking.

Conclusion:
Although most adults who smoked 1-year before RYGB quit pre-surgery, smoking prevalence rebounded across 7-years, primarily due to relapse.
Remote Therapy to Improve Outcomes in Lung Transplant Recipients: Design of the INSPIRE-III Randomized Clinical Trial
Authors: Blumenthal James A. , Smith Patrick J. , Sherwood Andrew , Mabe Stephanie , Snyder Laurie , Frankel Courtney , McKee Daphne C. , Hamilton Natalie , Keefe Francis J. , Shearer Sheila , Schwartz Jeanne , Palmer Scott 
Published: February 2020

Background.
Impaired functional capacity and emotional distress are associated with lower quality of life (QoL) and worse clinical outcomes in post lung transplant patients. Strategies to increase physical activity and reduce distress are needed.

Methods.
The Investigational Study of Psychological Interventions in Recipients of Lung Transplant-III study is a single site, parallel group randomized clinical trial in which 150 lung transplant recipients will be randomly assigned to 3 months of telephone-delivered coping skills training combined with aerobic exercise (CSTEX) or to a Standard of Care plus Education control group. The primary endpoints are a global measure of distress and distance walked on the 6-Minute Walk Test. Secondary outcomes include measures of transplant-specific QoL, frailty, health behaviors, and chronic lung allograft dysfunction–free survival.

Results.
Participants will be evaluated at baseline, at the conclusion of 3 months of weekly treatment, at 1-year follow-up, and followed annually thereafter for clinical events for up to 4 years (median = 2 y). We also will determine whether functional capacity, distress, and health behaviors (eg, physical activity, medication adherence, and volume of air forcefully exhaled in 1 second (FEV1), mediate the effects of the CSTEX intervention on clinical outcomes.

Conclusions.
Should the CSTEX intervention result in better outcomes compared with the standard of care plus post-transplant education, the remotely delivered CSTEX intervention can be made available to all lung transplant recipients as a way of enhancing their QoL and improving clinical outcomes.
Preserving Vascular Integrity Protects Mice Against Multidrug-Resistant Gram-Negative Bacterial Infection
Authors: Gebremariam Teclegiorgis , Zhang Lina , Alkhazraji Sondus , Gu Yiyou , Youssef Eman G. , Tong Zongzhong , Kish-Trier Erik , de Araujo Claudia V. , Rich Bianca , French Samuel W. , Li Dean Y. , Mueller Alan L. , Odelberg Shannon J. , Zhu Weiquan , Ibrahim Ashraf S. 
Published: February 2020

ABSTRACTThe rise in multidrug resistant (MDR) organisms portends a serious global threat to the healthcare system with nearly untreatable infectious diseases, including pneumonia and its often fatal sequelae, acute respiratory distress syndrome (ARDS) and sepsis. Gram-negative bacteria (GNB) includingAcinetobacter baumannii, Pseudomonas aeruginosa, and carbapenemase-producingKlebsiella pneumoniae(CPKP), are among the World Health Organization and National Institutes of Health’s high priority MDR pathogens for targeted development of new therapies. Here we show that stabilizing the host’s vasculature by genetic deletion or pharmacological inhibition of the small GTPase ADP-ribosylation factor 6 (ARF6) increases survival rates of mice infected withA. baumannii,P. aeruginosa, CPKP pneumonia. We show that pharmacological inhibition of ARF6-GTP phenocopies endothelial-specificArf6disruption in enhancing survival of mice withA. baumanniipneumonia, suggesting that inhibition is on target. Finally, we show that the mechanism of protection elicited by these small molecule inhibitors is by restoration of vascular integrity disrupted by GNB lipopolysaccharide (LPS) activation of TLR4/MyD88/ARNO/ARF6 pathway. By targeting the host’s vasculature with small molecule inhibitors of ARF6 activation, we circumvent microbial drug resistance and provide a potential alternative/adjunctive treatment for emerging and re-emerging pathogens.
Physiological and cognitive consequences of a daily 26h photoperiod in a primate(M. murinus)
Authors: Hozer Clara , Pifferi Fabien 
Published: February 2020

AbstractDaily resetting of the circadian clock to the 24h natural photoperiod might induce marginal costs that would accumulate over time and forward affect fitness. It was proposed as the circadian resonance theory by Pittendrigh in 1972. For the first time, we aimed to evaluate these physiological and cognitive costs that would partially explain the mechanisms of the circadian resonance hypothesis. We evaluated the potential costs of imposing a 26h photoperiodic regimen compared to the classical 24h entrainment measuring several physiological and cognitive parameters (body temperature, energetic expenditure, oxidative stress, cognitive performances). We found significant higher resting body temperature and energy expenditure and lower cognitive performances when the photoperiodic cycle length was 26h. Together these results suggest that a great deviation of external cycles from 24h leads to daily greater synchronization costs, and lower cognitive capacities. To our knowledge, this study is the first to highlight potential mechanisms of circadian resonance theory.
Alternative splicing coupled nonsense-mediated decay shapes the temperature-dependent transcriptome
Authors: Neumann Alexander , Meinke Stefan , Goldammer Gesine , Strauch Miriam , Schubert Daniel , Timmermann Bernd , Heyd Florian , Preußner Marco 
Published: February 2020

AbstractMammalian body temperature oscillates with the time of the day and is altered in diverse pathological conditions. We recently identified a body temperature-sensitive thermometer-like kinase, which alters SR protein phosphorylation and thereby globally controls alternative splicing (AS). AS can generate mRNA variants containing premature termination codons, which are degraded by nonsense-mediated decay (NMD). Here we show extensive coupling of body temperature-controlled AS to NMD, leading to global control of temperature-dependent gene expression (GE). Temperature-controlled NMD-inducing splicing events are evolutionarily conserved and pervasively found within RNA-binding proteins, including most SR proteins. NMD-inducing exons are essential for rhythmic GE of SR proteins and have a global role in establishing temperature-dependent rhythmic GE profiles, both, in mammals under circadian body temperature cycles and in plants in response to ambient temperature changes. Together, these data identify body temperature-driven AS-NMD as an evolutionary ancient, core clock-independent mechanism to generate rhythmic GE.
Functional reorganization of sensory processing following long-term neural adaptation to optical defects
Authors: Barbot Antoine , Park Woon-Ju , Zhang Ru-Yuan , Huxlin Krystel R , Tadin Duje , Yoon Geunyoung 
Published: February 2020

How we see is fundamentally limited by the eye’s optics, which determine retinal image quality and constrain neural processing. Elucidating how long-term exposure to optical defects alters visual processing is vital for understanding the human brain’s capacity for and limits of sensory plasticity. Using adaptive optics to bypass the eye’s optical aberrations, we assessed changes in visual processing in neurotypically-developed adults with keratoconus (KC)—a corneal disease causing severe optical aberrations during adulthood that cannot be fully corrected using conventional methods. As a result, KC patients are chronically exposed to degraded retinal images in their everyday life, making them an ideal model to understand how prolonged exposure to poor optical quality alters visual processing. Here, we show that when tested under similar fully-corrected optical conditions as neurotypical observers, KC patients exhibited altered contrast sensitivity, with impaired sensitivity for fine spatial details and better sensitivity for coarse spatial details. Both gains and losses in contrast sensitivity were more pronounced in patients with poorer habitual optical quality. Moreover, using an equivalent noise paradigm and a computational model of visual processing, we show that these alterations in visual processing are mediated by changes in signal enhancement of spatial frequency selective mechanisms. The present findings uncover fundamental properties of neural compensation mechanisms in response to long-term exposure to optical defects, which alter sensory processing and limit the benefits of improved optics. The outcome is a large-scale functional reorganization favoring the processing of sensory information less affected by the eye’s optics.Significance statementThe eye’s optics represent an intrinsic limit to human visual perception, determining the quality of retinal images. Neural adaptation optimizes the brain’s limited sensory processing capacity to the structure of the degraded retinal inputs, providing an exceptional quality of vision given these optical limitations. Here, we show that prolonged exposure to poor optical quality results in a functional reorganization of visual processing that favors sensory information less affected by the eye’s optics. The present study helps elucidate how optical factors shape the way the brain processes visual information. Notably, the resulting adaptive neural plasticity limits the immediate perceptual benefits of optical interventions, a factor that must be taken into consideration when treating the increasing human population affected by optical defects.
The limits to parapatric speciation 3: Evolution of strong reproductive isolation in presence of gene flow despite limited ecological differentiation
Authors: Blanckaert Alexandre , Bank Claudia , Hermisson Joachim 
Published: February 2020

AbstractGene flow tends to impede the accumulation of genetic divergence. Here, we determine the limits for the evolution of postzygotic reproductive isolation in a model of two populations that are connected by gene flow. We consider two selective mechanisms for the creation and maintenance of a genetic barrier: local adaptation leads to divergence among incipient species due to selection against migrants, and Dobzhansky-Muller incompatibilities (DMIs) reinforce the genetic barrier through selection against hybrids. In particular, we are interested in the maximum strength of the barrier under a limited amount of local adaptation, a challenge that may initially face many incipient species. We first confirm that with classical two-locus DMIs, the maximum amount of local adaptation is indeed a limit to the strength of a genetic barrier. However, with three or more loci and cryptic epistasis, this limit holds no longer. In particular, we identify a minimal configuration of three epistatically interacting mutations that is sufficient to confer strong reproductive isolation.
Anomalous invasion dynamics due to dispersal polymorphism and dispersal-reproduction trade-offs
Authors: Keenan Vincent A. , Cornell Stephen J. 
Published: February 2020

AbstractDispersal polymorphism and mutation play significant roles during biological invasions, potentially leading to evolution and complex behaviour such as accelerating or decelerating invasion fronts. However, life history theory predicts that reproductive fitness — another key determinant of invasion dynamics – may be lower for more dispersive strains. Here, we use a mathematical model to show that unexpected invasion dynamics emerge from the combination of heritable dispersal polymorphism, dispersal-fitness trade-offs, and mutation between strains. We show that the invasion dynamics are determined by the trade-off relationship between dispersal and population growth rates of the constituent strains. We find that invasion dynamics can be “anomalous” (i.e. faster than any of the strains in isolation), but that the ultimate invasion speed is determined by the traits of at most two strains. The model is simple but generic, so we expect the predictions to apply to a wide range of ecological, evolutionary or epidemiological invasions.
Responses of tree species traits to soil variation in the cerrado
Authors: Meira-Neto João Augusto Alves , Tolentino Glaucia Soares , Buttschardt Tillmann , Máguas Cristina 
Published: February 2020

AbstractAimsThe Cerrado is a rich tropical savanna in plant species and to understand how key functional traits respond to soil variables can help to understand this hotspot functioning. This work aimed to answer i) whether the Cerrado tree species respond to soil by functional traits, ii) how the functional traits respond to soil variation in the Cerrado, and iii) whether the functional traits responses are interconnected.MethodsWe used an RLQ method to associate soil variables to functional traits and GLMs for additional analysis. We used the nitrogen-fixing character as categorical trait and maximum plant height, maximum stem diameter, stem elongation, leaf nitrogen, leaf carbon, leaf C/N, leaf d15N and leaf d 13C as continuous traits.ResultsThe RLQ showed that tree species responded to the soil variables with differences between nitrogen-fixing species and other species. The increase of CEC and decrease of aluminium saturation induced an increase of SLA and of stem elongation. CEC and aluminium saturation did not influence the leaf N% and C%. The increase of soil inorganic nitrogen is associated to an increase of leaf N% and of leaf C%. The C/N ratio explained negatively the δ13C and the stem elongation variation. Nitrogen fixing species presented low C/N ratios and high δ13C.ConclusionsThe relative disassociation of the variation of SLA and stem elongation (mostly driven by CEC and aluminium variation) from the variation of N% and C% (mostly associated with inorganic nitrogen variation) can be a result of enhanced water use efficiency in N-enriched plants.
Removal modelling in ecology
Authors: de Rivera Oscar Rodriguez , McCrea Rachel 
Published: February 2020

AbstractRemoval models were proposed over 80 years ago as a tool to estimate unknown population size. Although the models have evolved over time, in essence, the protocol for data collection has remained similar: at each sampling occasion attempts are made to capture and remove individuals from the study area. Within this paper we review the literature of removal modelling and highlight the methodological developments for the analysis of removal data, in order to provide a unified resource for ecologists wishing to implement these approaches. Models for removal data have developed to better accommodate important feature of the data and we discuss the shift in the required assumption for the implementation of the models. The relative simplicity of this type of data and associated models mean that the method remains attractive and we discuss the potential future role of this technique.Author summarySince the introduction of the removal in 1939, the method has being extensively used by ecologists to estimate population size. Although the models have evolved over time, in essence, the protocol for data collection has remained similar: at each sampling occasion attempts are made to capture and remove individuals from the study area. Here, we introduce the method and how it has been applied and how it has evolved over time. Our study provides a literature review of the methods and applications followed by a review of available software. We conclude with a discussion about the opportunities of this model in the future.
A New World begomovirus infecting Cotton in Argentina
Authors: Delfosse Verónica , Debat Humberto , Zavallo Diego , Moyano Sabrina , Luna Facundo , Kresic Iván Bonacic , Asurmendi Sebastian , Gomez-Talquenca Sebastian , Distéfano Ana Julia 
Published: February 2020

AbstractCotton (Gossypiumspp.) is a globally significant cash crop cultivated for its versatile fiber, widely used in the textile industry. Cotton, as other crops, is vulnerable to infectious pathogens. Several of them, including viruses, are a major threat to cotton production. Geminiviruses (familyGeminiviridae) are insect transmitted, small non-enveloped viruses, with circular single-stranded DNA genomes, which are encapsidated in quasi-icosahedral geminated virions. Here we present evidence of a novel begomovirus (genusBegomovirus) infecting cotton from Argentina. Two circular ssDNA virus sequences were assembled from high-throughput sequencing data fromGossyipium hirsutumcotton samples showing mosaic symptoms from Argentina. Structural and functional annotation indicated that the virus sequences corresponded to complete DNA components A and B of a novel New World bipartite begomovirus. Genetic distance and evolutionary analyses support that the detected sequences correspond to a new virus, a tentative prototype member of a novel species which we propose the name “Cotton mosaic virus” (CoMV).
USP29 is a novel non-canonical Hypoxia Inducible Factor-α activator
Authors: Schober Amelie S , Martín-Barros Inés , Martín-Mateos Teresa , Pérez-Andrés Encarnación , Carlevaris Onintza , Pozo Sara , Cortazar Ana R , Aransay Ana M , Carracedo Arkaitz , Mayor Ugo , Sée Violaine , Berra Edurne 
Published: February 2020

AbstractHypoxia Inducible Factor (HIF) is the master transcriptional regulator that orchestrates cellular adaptation to low oxygen. HIF is tightly regulated via the stability of its α-subunit, which is subjected to oxygen-dependent proline hydroxylation by Prolyl-Hydroxylase Domain containing proteins (PHDs/EGLNs), and ultimately targeted for proteasomal degradation through poly-ubiquitination by von-Hippel-Lindau protein (pVHL). However, sustained HIF-α signalling is found in many tumours independently of oxygen availability pointing towards the relevance of non-canonical HIF-α regulators. In this study, we establish the Ubiquitin Specific Protease 29 (USP29) as direct post-translational activator of HIF-α in a variety of cancer cell lines. USP29 binds to HIF-α, decreases poly-ubiquitination and thus protects HIF-α from proteasomal degradation. Deubiquitinating activity of USP29 is essential to stabilise not only HIF-1α but also HIF-2α, via their C-termini in an oxygen/PHD/pVHL-independent manner. Furthermore, in prostate cancer samples the expression ofUSP29correlates with the HIF-target geneCA9(carbonic anhydrase 9) as well as disease progression and severity.
Ctdnep1 and Eps8L2 regulate dorsal actin cables for nuclear positioning during cell migration
Authors: Calero-Cuenca Francisco J. , Osorio Daniel S. , Sridhara Sreerama Chaitanya , Jiao Yue , Diaz Jheimmy , Carvalho-Marques Sofia , Cadot Bruno , Gomes Edgar R. 
Published: February 2020

SummaryCells actively position their nuclei within the cytoplasm for multiple cellular and physiological functions. Different cell types position their nuclei away from the leading edge to migrate properly. In migrating fibroblasts, nuclear positioning is driven by dorsal actin cables connected to the nuclear envelope by the LINC complex on Transmembrane Actin-associated Nuclear (TAN) lines. How dorsal actin cables are organized to form TAN lines is unknown. Here, we report a role for Ctdnep1/Dullard, a nuclear envelope phosphatase, and the actin regulator Eps8L2, on nuclear positioning. We demonstrate that Ctdnep1 and Eps8L2 directly interact to regulate the formation and thickness of dorsal actin cables required for TAN lines engagement for nuclear positioning. Our work establishes a novel mechanism to locally regulate actin at the nuclear envelope for nuclear positioning.
Phylogeny of the stink bug tribe Chlorocorini (Heteroptera, Pentatomidae) based on DNA and morphological data: the evolution of key phenotypic traits
Authors: Genevcius Bruno C. , Greve Caroline , Koehler Samantha , Simmons Rebecca B. , Rider David A. , Grazia Jocelia , Schwertner Cristiano F. 
Published: February 2020

ABSTRACTPentatomidae is the third largest family of true bugs, comprising over 40 tribes. Few tribes have been studied in a phylogenetic context, and none of them have been examined using molecular data. Moreover, little is known about the evolution of key morphological characters widely used in taxonomic and phylogenetic studies at multiple levels. Here, we conduct a phylogenetic study of the tribe Chlorocorini (Pentatominae) combining 69 morphological characters and five DNA loci. We use the inferred phylogeny to reconstruct the evolution of key morphological characters such as the spined humeral angles of the pronotum, a dorsal projection on the apices of the femora and characters of male genitalia. We provide solid evidence that the tribe as currently recognized is not monophyletic based both on DNA and morphological data. The generaArveliusSpinola andEludocorisThomas were consistently placed outside of the Chlorocorini, while the remaining genera were found to form a monophyletic group. We also show that nearly all morphological diagnostic characters for the tribe are homoplastic. The only exception is the development of the hypandrium, which, contrary to expectations for genital traits, showed the slowest evolutionary rates. In contrast, the most rapidly evolving trait is the length of the ostiolar ruga, which may be attributed to selection favoring anti-predatory behavior and other functions of its associated scent glands. Lastly, we also provide a preliminary glimpse of the main phylogenetic relationships within the Pentatomidae, which indicates that most of the included subfamilies and tribes are not monophyletic. Our results suggest that the current subfamily-level classification of Pentatomidae is not adequate to reflect its evolutionary history, and we urge for a more complete phylogeny of the family.