bluuebunny/crossref_metadata_2025_split huggingface dataset:
MapGL: Inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony
Authors: Diehl Adam G , Boyle Alan P 
Published: November 2019

AbstractComparative genomics studies are growing in number partly because of their unique ability to provide insight into shared and divergent biology between species. Of particular interest is the use of phylogenetic methods to infer the evolutionary history of cis-regulatory sequence features, which contribute strongly to phenotypic divergence and are frequently gained and lost in eutherian genomes. Understanding the mechanisms by which cis-regulatory element turnover generate emergent phenotypes is crucial to our understanding of adaptive evolution. Ancestral reconstruction methods can place species-specific cis-regulatory features in their evolutionary context, thus increasing our understanding of the process of regulatory sequence turnover. However, applying these methods to gain and loss of cis-regulatory features currently requires complex workflows which represent a potential barrier to widespread adoption by a broad scientific community. MapGL simplifies phylogenetic inference of the evolutionary history of short genomic sequence features by combining the necessary steps into a single piece of software with a simple set of inputs and outputs.
Biofilm rupture by laser-induced stress waves increases with loading amplitude, independent of location
Authors: Kearns Kaitlyn L. , Boyd James D. , Grady Martha E. 
Published: November 2019

AbstractIntegral to the production of safe and biocompatible medical devices is to determine the interfacial properties that affect or control strong biofilm adhesion. The laser spallation technique has recently emerged as an advantageous method to quantify biofilm adhesion across candidate biomedical surfaces. However, there is a possibility that membrane tension is a factor that contributes to the stress required to separate biofilm and substrate. In that case, the stress amplitude, controlled by laser fluence, that initiates biofilm rupture would vary systematically with location on the biofilm. Film rupture, also known as spallation, occurs when film material is ejected during stress wave loading. In order to determine effects of membrane tension, we present a protocol that measures spall size with increasing laser fluence (variable fluence) and with respect to distance from the biofilm centroid (iso-fluence).Streptococcus mutansbiofilms on titanium substrates serves as our model system. A total of 185 biofilm loading locations are analyzed in this study. We demonstrate that biofilm spall size increases monotonically with laser fluence and apply our procedure to failure of non-biological films. In iso-fluence experiments, no correlation is found between biofilm spall size and loading location, thus providing evidence that membrane tension does not play a dominant role in biofilm adhesion measurements. We recommend our procedure as a straightforward method to determine membrane effects in the measurement of adhesion of biological films on substrate surfaces via the laser spallation technique.Graphical Abstract
“Induction of pancreatic tumor-selective ferroptosis through modulation of cystine import”
Authors: Badgley Michael A. , Kremer Daniel , Maurer H. Carlo , DelGiorno Kathleen E. , Lee Ho-Joon , Purohit Vinee , Sagalovskiy Irina , Ma Alice , Kapillian Jonathan , Firl Christina E.M. , Decker Amanda R. , Sastra Steve A. , Palermo Carmine F. , Andrade Leonardo R. , Sajjakulnukit Peter , Zhang Li , Tolstyka Zachary P. , Hirschhorn Tal , Lamb Candice , Liu Tong , Gu Wei , Seeley E. Scott , Stone Everett , Georgiou George , Manor Uri , Iuga Alina , Wahl Geoffrey M. , Stockwell Brent R. , Lyssiotis Costas A. , Olive Kenneth P. 
Published: November 2019

AbstractPancreatic ductal adenocarcinoma (PDA) is the third-leading cause of cancer mortality in the US and is highly resistant to classical, targeted, and immune therapies. We show that human PDA cells are dependent on the provision of exogenous cystine to avert a catastrophic accumulation of lipid reactive oxygen species (ROS) that, left unchecked, leads to ferroptotic cell death, bothin vitroandin vivo. Using a dual-recombinase genetically engineered model, we found that acute deletion ofSlc7a11led to tumor-selective ferroptosis, tumor stabilizations/regressions, and extended overall survival. The mechanism of ferroptosis induction in PDA cells required the concerted depletion of both glutathione and coenzyme A, highlighting a novel branch of ferroptosis-relevant metabolism. Finally, we found that cystine depletionin vivousing the pre-IND agent cyst(e)inase phenocopiedSlc7a11deletion, inducing tumor-selective ferroptosis and disease stabilizations/regressions in the well-validated KPC model of PDA.One Sentence SummaryGenetic and pharmacological targeting of cystine import induces pancreatic cancer-selective ferroptosisin vivo.
Divergent density feedback control of migratory predator recovery following sex-biased perturbations
Authors: Goto Daisuke , Hamel Martin J. , Pegg Mark A. , Hammen Jeremy J. , Rugg Matthew L. , Forbes Valery E. 
Published: November 2019

AbstractUncertainty in risks posed by emerging stressors such as synthetic hormones impedes conservation efforts for threatened vertebrate populations. Synthetic hormones often induce sex-biased perturbations in exposed animals by disrupting gonad development and early life-history stage transitions, potentially diminishing per capita reproductive output of depleted populations and, in turn, being manifest as Allee effects. We use a spatially-explicit biophysical model to evaluate how sex-biased perturbation in life history traits of individuals (maternal investment in egg production and male-skewed sex allocation in offspring) modulates density feedback control of year class strength and recovery trajectories of a long-lived, migratory fish–shovelnose sturgeon (Scaphirhynchus platorynchus)–under spatially and temporally dynamic synthetic androgen exposure and habitat conditions. Simulations show that reduced efficiency of maternal investment in gonad development prolonged maturation time, increased the probability of skipped spawning, and, in turn, gradually shrunk spawner abundance, weakening year class strength. However, positive density feedback quickly disappeared (no Allee effect) once the exposure ceased. By contrast, responses to the demographic perturbation manifested as strong positive density feedback; an abrupt shift in year class strength and spawner abundance followed after more than two decades owing to persistent negative population growth (a strong Allee effect), reaching an alternate state without any sign of recovery. When combined with the energetic perturbation, positive density feedback of the demographic perturbation was dampened as extended maturation time reduced the frequency of producing male-biased offspring, allowing the population to maintain positive growth rate (a weak Allee effect) and gradually recover. The emergent patterns in long-term population projections illustrate that sex-biased perturbation in life history traits of individuals can interactively regulate the strength of density feedback in depleted populations such asScaphirhynchussturgeon to further diminish reproductive capacity and abundance, posing increasingly greater conservation challenges in chemically altered riverscapes.
Heat stress induces ferroptosis in a photosynthetic prokaryote
Authors: Aguilera Anabella , Berdun Federico , Bartoli Carlos , Steelheart Charlotte , Alegre Matías , Salerno Graciela , Pagnussat Gabriela , Martin María Victoria 
Published: November 2019

AbstractFerroptosis is an oxidative iron-dependent form of cell death recently described in eukaryotic organisms like animals, plants and parasites. Here we report that a similar process takes place in the cyanobacteriumSynechocystissp. PCC 6803 in response to heat stress. After a heat shock,Synechocystiscells undergo a cell death pathway that can be suppressed by canonical ferroptosis inhibitors or by external addition of calcium, glutathione or ascorbic acid. Moreover, as described for eukaryotic cells ferroptosis, this pathway is characterized by an early depletion of antioxidants, and by lipid peroxidation. As in general prokaryotes membranes contain poorly oxidizable saturated or monounsaturated lipid molecules, it was thought that they were not susceptible to ferroptosis. Interestingly, cyanobacteria contain thylakoid membranes that are enriched in polyunsaturated-fatty-acid-containing phospholipids, which might explain their sensitivity to ferroptosis. These results indicate that all of the hallmarks described for eukaryotic ferroptosis are conserved in photosynthetic prokaryotes and suggest that ferroptosis might be an ancient cell death program.SummaryAguilera et al, show that ferroptosis, an oxidative and iron-dependent form of regulated cell death, plays an important role in the cyanobacteriumSynechocystissp. PCC 6803 in response to heat stress.
Chchd10 or Chchd2 are not Required for Human Motor Neuron Differentiation In Vitro but Modify Synaptic Transcriptomes
Authors: Harjuhaahto Sandra , Rasila Tiina S , Molchanova Svetlana M , Woldegebriel Rosa , Kvist Jouni , Konovalova Svetlana , Sainio Markus T , Pennonen Jana , Ibrahim Hazem , Otonkoski Timo , Taira Tomi , Ylikallio Emil , Tyynismaa Henna 
Published: November 2019

ABSTRACTMitochondrial intermembrane space proteins CHCHD2 and CHCHD10 have roles in diseases affecting motor neurons such as amyotrophic lateral sclerosis, spinal muscular atrophy and axonal neuropathy and in Parkinson’s disease, and form a complex of unknown function. Here we address the importance of these two proteins in human motor neurons. We show that gene edited human induced pluripotent stem cells (iPSC) lacking either CHCHD2 or CHCHD10 are viable and can be differentiated into functional motor neurons that fire spontaneous and evoked action potentials. Knockout iPSC and motor neurons sustain mitochondrial ultrastructure and show reciprocal compensatory increases in CHCHD2 or CHCHD10. Knockout motor neurons have largely overlapping transcriptome profiles compared to isogenic control line, in particular for synaptic gene expression. Our results show that absence of CHCHD2 or CHCHD10 does not disrupt functionality, but induces similar modifications in human motor neurons. Thus pathogenic mechanisms may involve loss of synaptic function.
Inferring punctuated evolution in the learned songs of African sunbirds
Authors: McEntee Jay P. , Zhelezov Gleb , Werema Chacha , Najar Nadje , Peñalba Joshua V. , Mulungu Elia , Mbilinyi Maneno , Karimi Sylvester , Chumakova Lyubov , Burleigh J. Gordon , Bowie Rauri C.K. 
Published: November 2019

AbstractSignals used in animal communication, especially those that are learned, are thought to be prone to rapid and/or regular evolution. It has been hypothesized that the evolution of song learning in birds has resulted in elevated diversification rates, as learned song may be subject to especially rapid evolution, and song is involved in mate choice. However, we know little about the evolutionary modes of learned song divergence over timescales relevant to speciation. Here we provide evidence that aspects of the territorial songs of Eastern Afromontane sky island sunbirdsCinnyrisevolve in a punctuated fashion, with periods of stasis, on the order of hundreds of thousands of years or more, broken up by strong evolutionary pulses. Stasis in learned songs is inconsistent with learned traits being subject to constant or frequent change, as would be expected if selection does not constrain song phenotypes, or if novel phenotypes are frequently advantageous. Learned song may instead follow a process resembling peak shifts on adaptive landscapes. While much research has focused on the potential for rapid evolution in bird song, our results suggest that selection can tightly constrain the evolution of learned songs over fairly long timescales. More broadly, these results demonstrate that some aspects of highly variable, plastic traits can exhibit punctuated evolution, with stasis over fairly long time periods.
Urbanization reshapes a food web
Authors: Start Denon , Barbour Matthew A. , Bonner Colin 
Published: November 2019

Abstract

Cities represent humanity's most intense impact on our planet, with more than half of all humans now residing in urban areas. Indeed, urbanization has well‐understood impacts on both individual species and general patterns of biodiversity. However, species do not exist in isolation, but are instead members of complex interaction networks that shape patterns of diversity and influence ecosystem services.

Despite the importance of species interaction for creating patterns of diversity, we do not understand how urbanization alters these interactions. Here, we investigate how an interaction network (food web) is reshaped by urbanization.

We show that, consistent with theory, cities tend to support less diverse ecological communities, and rare species that interact with few species are particularly sensitive to urbanization. As a result, remnant urban food webs tend to have more interactions per species and greater connectance, creating more integrated interaction networks.

We discuss the implications of this food web reshaping for ecological stability, eco‐evolutionary dynamics, and the joining of interaction networks and conservation planning. The role of cities in reshaping interaction networks provides an interesting study of food web (dis)assembly, while also shedding light on new approaches to applied conservation issues.
Spatial disturbance synchrony alters the association of food chain length and ecosystem size
Authors: Terui Akira , Nishijima Shota 
Published: November 2019

AbstractThe origin of variation in food chain length (FCL) has long been a central topic of ecology due to its influences on trophic control, energy flow and bioaccumulation of environmental contaminants. The positive association of FCL and ecosystem size has been consistently supported in natural systems. Recent studies, however, have begun to report no effects of ecosystem size on FCL. The emerging inconsistency among previous studies implies the existence of overlooked factors that can modulate the relationship between FCL and ecosystem size. Here, we developed a mathematical model describing metacommunity dynamics to show that large ecosystems do not necessarily support long food chains in the presence of spatially correlated disturbance. Our simple model predicted that the effect of ecosystem size was strongly dependent on the spatial extent of disturbance synchrony. When the spatial correlation of disturbance was weak, the positive association between FCL and ecosystem size appeared. However, the relationship of FCL and ecosystem size became more complex, including hump‐shaped and multimodal forms, as the spatial extent of disturbance synchrony increases. This pattern emerged because larger ecosystems have wider aerial coverage, so more chances exist that an episodic disturbance hits some of the habitat patches and spreads across the landscape. Our finding highlights the important role of spatial disturbance synchrony in driving FCL, providing insights into why ecosystem size effects are variable across systems.
‘Every single minute and hour is scrutinised’: neoliberalism and Australian private mental health care
Authors: Dawson Lisa , River Jo , McCloughen Andrea , Buus Niels 
Published: November 2019

AbstractThere is little understanding of how recovery‐oriented approaches fit within contemporary mental healthcare systems, which emphasise biomedical approaches to care, increased efficiency and cost‐cutting. This article examines the established models of service delivery in a private, youth, mental health service and the impacts of the current system on staff. It explores whether the service is prepared or capable of adopting recovery‐oriented approaches to care. Qualitative interviews were undertaken with staff and thematically analysed to understand the everyday practices on the unit. Data suggest that economic efficiencies and biomedical dominance largely shaped how health care was organised and delivered, which was perceived by staff as inflexible to change. Additionally, findings suggest that market‐oriented principles associated with neoliberalism restricted the capacity of individuals to transform services in line with alternative models of care and lowered staff morale. These finding suggest that, while neoliberal ideologies and biomedical approaches remain dominant in organisations, there will be challenges to adopting alternative recovery‐oriented models of care and promoting healthcare systems that understand mental health issues in broader socio‐political contexts and can flexibly respond to the needs of service users.
Development of the FAST‐M maternal sepsis bundle for use in low‐resource settings: a modified Delphi process
Authors: Lissauer D , Cheshire J , Dunlop C , Taki F , Wilson A , Smith JM , Daniels R , Kissoon N , Malata A , Chirwa T , Lwesha VM , Mhango C , Mhango E , Makwenda C , Banda L , Munthali L , Nambiar B , Hussein J , Williams HM , Devall AJ , Gallos I , Merriel A , Bonet M , Souza JP , Coomarasamy A 
Published: November 2019

ObjectiveTo develop a sepsis care bundle for the initial management of maternal sepsis in low resource settings.DesignModified Delphi process.SettingParticipants from 34 countries.PopulationHealthcare practitioners working in low resource settings (n = 143; 34 countries), members of an expert panel (n = 11) and consultation with the World Health Organization Global Maternal and Neonatal Sepsis Initiative technical working group.MethodsWe reviewed the literature to identify all potential interventions and practices around the initial management of sepsis that could be bundled together. A modified Delphi process, using an online questionnaire and in‐person meetings, was then undertaken to gain consensus on bundle items. Participants ranked potential bundle items in terms of perceived importance and feasibility, considering their use in both hospitals and health centres. Findings from the healthcare practitioners were then triangulated with those of the experts.Main outcome measureConsensus on bundle items.ResultsConsensus was reached after three consultation rounds, with the same items deemed most important and feasible by both the healthcare practitioners and expert panel. Final bundle items selected were: (1) Fluids, (2) Antibiotics, (3) Source identification and control, (4) Transfer (to appropriate higher‐level care) and (5) Monitoring (of both mother and neonate as appropriate). The bundle was given the acronym ‘FAST‐M’.ConclusionA clinically relevant maternal sepsis bundle for low resource settings has been developed by international consensus.Tweetable abstractA maternal sepsis bundle for low resource settings has been developed by international consensus.
Deleterious effects of electron beam irradiation on development and reproduction of tomato/potato psyllids, Bactericera cockerelli
Authors: Lei Jiaxin , Meng Jia , Chen Ivy W. , Cheng Weining , Beam Andrea L. , Islam Md‐Sajedul , Bailey Woodward D. , Pillai Suresh , Zhu‐Salzman Keyan 
Published: November 2019

AbstractThe potato/tomato psyllid Bactericera cockerelli causes serious damage to several solanaceous crops by direct feeding and vectoring Candidatus Liberibacter solanacearum, a bacterial pathogen. Electron beam (eBeam) irradiation is an environmentally friendly, chemical‐free alternative method that is increasing in use for disinfestation of insect pests. We hypothesize that this irradiation technology will have detrimental effects on potato psyllid and thus impede its disease vectoring. To this end, we explored the effects of eBeam treatment ranging from 50 to 500 Gy on survival, development and reproduction of this pest. Impact on psyllids was apparently dose‐dependent. When irradiated at 350 Gy, eggs could not hatch, 1st instar nymphs failed to emerge, and although a small portion of irradiated 5th instar nymphs survived, the emerged adults were mostly deformed. Abnormality in eclosed adults suggests harmful effects of eBeam on metamorphosis. Reproduction was seriously impaired when female psyllids were exposed to eBeam at the 5th instar nymphal or young adult stage, presumably due to inability to form oocytes. In addition, reciprocal crosses between irradiated and untreated psyllids indicated that female psyllids were more radiosensitive than males to eBeam. Taken together, these findings indicate that eBeam negatively impacted potato psyllid development and reproduction, which would inevitably compromise its disease transmission capacity. A dose of 350 Gy can be considered as a reference dose for effective control of potato psyllids.
Inferring competitive outcomes, ranks and intransitivity from empirical data: A comparison of different methods
Authors: Feng Yanhao , Soliveres Santiago , Allan Eric , Rosenbaum Benjamin , Wagg Cameron , Tabi Andrea , De Luca Enrica , Eisenhauer Nico , Schmid Bernhard , Weigelt Alexandra , Weisser Wolfgang W. , Roscher Christiane , Fischer Markus 
Published: November 2019

Abstract

The inference of pairwise competitive outcomes (PCO) and multispecies competitive ranks and intransitivity from empirical data is essential to evaluate how competition shapes plant communities. Three categories of methods, differing in theoretical background and data requirements, have been used: (a) theoretically sound coexistence theory‐based methods, (b) index‐based methods, and (c) ‘process‐from‐pattern’ methods. However, how they are related is largely unknown.

In this study, we explored the relations between the three categories by explicitly comparing three representatives of them: (a) relative fitness difference (RFD), (b) relative yield (RY), and (c) a reverse‐engineering approach (RE). Specifically, we first conducted theoretical analyses with Lotka–Volterra competition models to explore their theoretical linkages. Second, we used data from a long‐term field experiment and a short‐term greenhouse experiment with eight herbaceous perennials to validate the theoretical findings.

The theoretical analyses showed that RY or RE applied with equilibrium data indicated equivalent, or very similar, PCO respectively to RFD, but these relations became weaker or absent with data further from equilibrium. In line with this, both RY and RE converged with RFD in indicating PCO over time in the field experiment as the communities became closer to equilibrium. Moreover, the greenhouse PCO (far from equilibrium) were only similar to the field PCO of earlier rather than later years. Intransitivity was more challenging to infer because it could be reshuffled by even a small competitive shift among similar competitors. For example, the field intransitivity inferred by three methods differed greatly: no intransitivity was detected with RFD; intransitivity detected with RY and RE was poorly correlated, changed substantially over time (even after equilibrium) and failed to explain coexistence.

Our findings greatly help the comparison and generalization of studies using different methods. For future studies, if equilibrium data are available, one can infer PCO and multispecies competitive ranks with RY or RE. If not, one should apply RFD with density gradient or time‐series data. Equilibria could be evaluated with T tests or standard deviations. To reliably infer intransitivity, one needs high quality data for a given method to first accurately infer PCO, especially among similar competitors.