bluuebunny/crossref_metadata_2025 huggingface dataset:
Small mammal assemblage composition and habitat associations across an elevational gradient in southern California
Authors: Karasov-Olson Aviv , Kelt Douglas A
Published: November 2019

Elevational gradients coincide with expansive climatic gradients and diverse plant and animal communities. We evaluated the small mammal assemblages in eight distinct vegetation types across an elevational gradient in southern California, the Deep Canyon Transect, to determine how assemblage composition changes across the gradient and to identify species with similar habitat associations. Livetrapping efforts (4,800 trap-nights) yielded 1,097 captures of 713 individuals, representing 14 heteromyid and cricetid species. Heteromyids dominated the six lower-elevation vegetation types (< 1,300 m a.s.l.), whereas cricetids dominated the upper end of the gradient. Richness and diversity exhibited bimodal responses to elevation, which do not conform to mid-domain effect null predictions. Canonical correspondence analysis revealed that 75% of the variation in small mammal abundances was explainable by habitat characteristics, and cluster analysis grouped small mammals into three ecologically distinct groups based on their habitat associations. One contained only Chaetodipus penicillatus, while the others were comprised of low- and high-elevation species, respectively. The low-elevation species exhibit unusual levels of sympatry (and syntopy) among closely related species of pocket mice (Chaetodipus). Further efforts should investigate the mechanisms of coexistence for Chaetodipus species with nearly identical associations and seasonal effects on richness and diversity. Repeated surveys of entire gradients such as the Deep Canyon Transect will help refine our understanding of temporal dynamics of community assemblage and diversity.
Strategies in Abduction: Generating and Selecting Diagnostic Hypotheses
Authors: Stanley Donald E , Nyrup Rune
Published: November 2019

We distinguish three aspects of medical diagnosis: generating new diagnostic hypotheses, selecting hypotheses for further pursuit, and evaluating their probability in light of the available evidence. Drawing on Peirce’s account of abduction, we argue that hypothesis generation is amenable to normative analysis: physicians need to make good decisions about when and how to generate new diagnostic hypothesis as well as when to stop. The intertwining relationship between the generation and selection of diagnostic hypotheses is illustrated through the analysis of a detailed clinical case study. This interaction is not adequately captured by the existing probabilistic, decision-theoretic models of the threshold approach to clinical decision-making. Instead, we propose to conceptualize medical diagnosis in terms of strategic reasoning.
Choeropsis liberiensis (Artiodactyla: Hippopotamidae)
Authors: Flacke Gabriella L , Decher Jan
Published: November 2019

Choeropsis liberiensis (Morton, 1849), commonly called the pygmy hippopotamus or pygmy hippo, is the only extant species in the genus Choeropsis. A solitary, forest-dwelling ungulate endemic to the Upper Guinean forest ecosystem in West Africa, it is classified as “Endangered” by the International Union for Conservation of Nature and Natural Resources and is a Convention on International Trade in Endangered Species of Wild Flora and Fauna (CITES) Appendix II species. The smaller of the two extant hippopotamids, it is relatively uncommon in zoological facilities and private collections worldwide.
Olivine-norite rock detected by the lunar rover Yutu-2 likely crystallized from the SPA-impact melt pool
Authors: Lin Honglei , He Zhiping , Yang Wei , Lin Yangting , Xu Rui , Zhang Chi , Zhu Meng-Hua , Chang Rui , Zhang Jinhai , Li Chunlai , Lin Hongyu , Liu Yang , Gou Sheng , Wei Yong , Hu Sen , Xue Changbin , Yang Jianfeng , Zhong Jie , Fu Xiaohui , Wan Weixing , Zou Yongliao
Published: November 2019

Chang’E-4 landed in the South Pole-Aitken (SPA) basin, providing a unique chance to probe the composition of the lunar interior. Its landing site is located on ejecta strips in Von Kármán crater that possibly originate from the neighboring Finsen crater. A surface rock and the lunar regolith at 10 sites along the rover Yutu-2 track were measured by the onboard Visible and Near-Infrared Imaging Spectrometer in the first three lunar days of mission operations. In situ spectra of the regolith have peak band positions at 1 and 2 μm, similar to the spectral data of Finsen ejecta from the Moon Mineralogy Mapper, which confirms that the regolith's composition of the landing area is mostly similar to that of Finsen ejecta. The rock spectrum shows similar band peak positions, but stronger absorptions, suggesting relatively fresh exposure. The rock may consist of 38.1 ± 5.4% low-Ca pyroxene, 13.9 ± 5.1% olivine and 48.0 ± 3.1% plagioclase, referred to as olivine-norite. The plagioclase-abundant and olivine-poor modal composition of the rock is inconsistent with the origin of the mantle, but representative of the lunar lower crust. Alternatively, the rock crystallized from the impact-derived melt pool formed by the SPA-impact event via mixing the lunar crust and mantle materials. This scenario is consistent with fast-cooling thermal conditions of a shallow melt pool, indicated by the fine to medium-sized texture (<3 mm) of the rock and the SPA-impact melting model [Icarus 2012; 220: 730–43].
Do maternal urinary iodine concentration or thyroid hormones within the normal range during pregnancy affect growth parameters at birth? A systematic review and meta-analysis
Authors: Nazeri Pantea , Shab-Bidar Sakineh , Pearce Elizabeth N , Shariat Mamak
Published: November 2019

Context

Iodine, an essential constituent of thyroid hormones, is required for proper growth and development.

Objective

To investigate whether growth parameters at birth are associated with maternal urinary iodine concentration (UIC) or normal ranges of thyroid hormones during pregnancy.

Data Sources

Using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines, electronic databases (namely, MEDLINE, Web of Science, the Cochrane Library, Scopus, and Google Scholar) were searched between January 1988 and November 2018 to identify relevant articles.

Data Extraction

Data from the studies included were independently extracted by 2 investigators using standardized forms developed for this review.

Data Analysis

The pooled mean birth weight, length, and head circumference values, and 95% confidence intervals were estimated in newborns born to women with UIC < 150 and UIC ≥150 μg/L during pregnancy. Possible linear or nonlinear associations between maternal UIC and the aforementioned anthropometric measures were evaluated. A narrative synthesis of the data was performed for thyroid hormones with levels within the normal range.

Results

Of the 123 studies identified, 11 were eligible for inclusion in the meta-analysis. The pooled mean birth weight, length, and head circumference in newborns whose mothers had UIC < 150 μg/L vs UIC ≥150 μg/L were 2898 g vs 2900 g (P = 0.970), 49.6 cm vs 49.4 cm (P = 0.880), and 34.0 cm vs 34.1 cm (P = 0.933), respectively. Dose-response meta-analyses revealed no significant linear or nonlinear associations between maternal UIC during pregnancy and anthropometric measures at birth. Among the different thyroid function parameters evaluated, high-normal values of maternal free thyroxine and thyrotropin during pregnancy were inversely associated with neonatal birth weight.

Conclusion

This systematic review showed that birth weight may be affected by even mild variations in the normal concentrations of maternal thyroid hormones. However, in the current meta-analysis, birth anthropometric measures were not associated with maternal UIC during pregnancy.
Pareto-improving indirect tax coordination and tax diversity
Authors: Kotsogiannis Christos , Lopez-Garcia Miguel-Angel
Published: November 2019

Coordination in tax matters, in the EU and elsewhere, has been largely driven by the movement of taxes towards some common level and, therefore, towards tax uniformity. Making use of a perfectly competitive general equilibrium framework of international trade in which governments provide global public goods, it is shown that, starting from a Nash equilibrium, there exist strict Pareto-improving multilateral tax reforms that are consistent with tax diversity.
Late Antiquity: The Age of Crowds?*
Authors: de Oliveira Julio Cesar Magalhães
Published: November 2019

The objective of this article is to place the study of urban protest and violence in the period from about 300 to about 600 CE in a broader perspective and to subject the investigation of plebeian activism to the basic precepts of analysis of collective action developed by social scientists and historians studying other periods. Its main argument is that, contrary to wide held assumptions in the historiography, what characterized Late Antiquity was not simply the exacerbation of violence or its tighter control, but the crisis of aristocratic hegemony and the expansion of opportunities for popular intervention in city life. What has been perceived as the product fanaticism, irrationality and deprivation of the masses, of the manipulation of bishops and aristocrats or of the failure of the mechanisms of coercion was actually the result of a dramatic social change that, on the one hand, involved a new dynamic of power and, on the other, a shift in the way the people understood their role and power in local communities.
Modulation of the Somatosensory Blink Reflex in the Peripersonal Space Is Defective in Episodic Migraine
Authors: Ayas Selahattin , Kızıltan Meral E , Karaali-Savrun Feray , Gündüz Ayşegül
Published: November 2019

Objective

In migraine, there is an altered behavior of patients during the attack and an altered connectivity in the cortical structures modulating and encoding the sensation and pain. Thus, we hypothesized that the extent of the peripersonal space (PPS) and the responses in the PPS may change during a migraine attack. For this reason, we analyzed the modulation of somatosensory blink reflex (SBR) in the PPS during episodic migraine.

Design

Cross-sectional assessment of modulation of SBR in patients with migraine.

Setting

Headache outpatient clinic of a tertiary referral center.

Subjects

We included 22 patients with episodic migraine, of whom 13 individuals were in the interictal period and nine were experiencing a headache episode. We also included 14 healthy individuals. The three groups were similar in age and gender.

Methods

SBR was recorded when the participants were sitting with their forearm in the extrapersonal space and also when their hands were in the PPS surrounding the face. Latency, amplitude, and area under the curve (AUC) were measured and compared.

Results

The amplitude and AUC of the SBR were significantly higher in patients during the attack compared with healthy subjects. The magnitude of the SBR was increased in the PPS in healthy subjects, whereas the increase was not significant in patients during the attack or in the interictal period.

Conclusions

We think that the modulation in the PPS is defective in patients with migraine both during the acute attack and in the interictal phase, suggesting diminished top-down modulation of the SBR.
Construct Validity of the Observable Movement Quality Scale in Pediatrics: Hypothesis Testing of a Formative Measurement Model
Authors: Dekkers Lieke M A , Janssen Anjo J W M , Donders A Rogier T , Nijhuis-van der Sanden Maria W G , de Swart Bert J M
Published: November 2019

Background

The Observable Movement Quality (OMQ) Scale measures generic movement quality. Each item of the OMQ Scale focuses on a different element; together, the 15 items assess the whole construct of movement quality.

Objective

The aim of this study was to determine the construct validity of the OMQ Scale using 7 hypotheses defined to conform to the Consensus-Based Standards for the Selection of Health Measurement Instruments.

Design

This was an exploratory validation study.

Methods

A pediatric physical therapist assessed motor performance in 101 children using an age-specific motor test and the OMQ Scale. The direction, magnitude, and rationale for 7 hypotheses, which concerned relationships (n = 2), probability of low scores (n = 4), and difference between diagnosis subgroups (n = 1), were defined.

Results

The results confirmed 6 of the 7 hypotheses, indicating sufficient construct validity. Significant positive relationships were found between OMQ Scale total scores and the severity of motor disabilities (r = 0.72) and z scores on motor tests (r = 0.60). Probabilities for low scores on OMQ Scale items—exceeding the chi-square critical value—were confirmed for children diagnosed with spasticity, psychomotor retardation, mitochondrial diseases, and ataxia; however, probabilities for low OMQ Scale item scores on strength regulation in children with ataxia were not confirmed. OMQ Scale total scores for children who were not ambulatory because of neurological conditions were significantly different from those for children who were not ambulatory because of fatigue (r = 0.66).

Limitations

The sample of children was based on theoretical assumptions about relevant variations in clinical representations; on the basis of the results, it appears that children with low strength regulation were underrepresented.

Conclusion

The confirmation of nearly all hypotheses supported the validity of the OMQ Scale for measuring movement quality in clinical practice in addition to standardized age-adequate motor performance tests.
The pattern of comorbidity and its prevalence among drug-resistant tuberculosis patients at treatment initiation in Lagos, Nigeria
Authors: Adejumo Olusola A , Olusola-Faleye Bolanle , Adepoju Victor A , Gidado Mustapha , Onoh Moses O , Adegboye Oluwatosin , Abdur-Razzaq H , Moronfolu Olanike , Shogbamimu Yeside
Published: November 2019

Background

Multimorbidity is increasingly being recognized as a serious public health concern in the control of both drug-susceptible and drug-resistant tuberculosis (DR-TB). This study assessed the pattern of comorbidities and their prevalence in DR-TB patients at treatment initiation in Lagos, Nigeria.

Methods

A cross-sectional study was conducted. The baseline laboratory records (human immunodeficiency virus [HIV] status, fasting blood sugar, audiometry, thyroid function tests, serum electrolyte, haemoglobin level and pregnancy test) of DR-TB patients initiated on treatment in Lagos, Nigeria between 1 August 2014 and 31 March 2017 were reviewed.

Results

A total of 565 DR-TB patients’ laboratory records were reviewed, of which 397 (70.3%) had comorbidities. The proportion with one, two, three and four comorbidities was 60.2%, 29.7%, 8.1% and 2.0%, respectively. Anaemia was the most common (48.1%) comorbid condition, while anaemia and hypokalaemia (7.3%), anaemia and hypothyroidism (6.5%) and anaemia and HIV (5%) were most common among patients with more than one comorbid condition. DR-TB patients with comorbidity were significantly older (34.8±12.3 y) than those without comorbidity (32.0±12.8 y) (p=0.038). Of the 176 females in the reproductive age group, 8 (4.5%) were pregnant at baseline.

Conclusions

The prevalence of comorbidity among DR-TB patients was high. There is a need for the national TB program to expand its DR-TB council of experts and also integrate reproductive health services into DR-TB management in Nigeria.
Identification and evolution of avian endogenous foamy viruses
Authors: Chen Yicong , Wei Xiaoman , Zhang Guojie , Holmes Edward C , Cui Jie
Published: November 2019

A history of long-term co-divergence means that foamy viruses (family Retroviridae) provide an ideal framework to understanding virus-host evolution over extended time periods. Endogenous foamy viruses (EndFVs) are rare, and to date have only been described in a limited number of mammals, amphibians, reptiles and fish genomes. By screening 414 avian genomes we identified EndFVs in two bird species: the Maguari Stork (Ciconia maguari) and the Oriental Stork (Ciconia boyciana). Analyses of phylogenetic relationships, genome structures and flanking sequences revealed a single origin of EndFVs in Ciconia species. In addition, the marked incongruence between the virus and host phylogenies suggested that this integration event occurred independently in birds. In sum, by providing evidence that birds can be infected with foamy viruses, we fill the last major gap in the taxonomic distribution of foamy viruses and their animal hosts.
Strategies to modulate zebrafish collective dynamics with a closed-loop biomimetic robotic system
Authors: Chemtob Yohann , Cazenille Leo , Bonnet Frank , Gribovskiy Alexey , Mondada Francesco , Halloy José
Published: November 2019

The objective of this study is to integrate biomimetic robots into small groups of zebrafish and to modulate their collective behaviours. A possible approach is to have the robots behave like sheepdogs. In this case, the robots would behave like a different species than the fish and would present different relevant behaviours. In this study, we explore different strategies that use biomimetic zebrafish behaviours. In past work, we have shown that robots biomimicking zebrafish can be socially integrated into zebrafish groups. We have also shown that a fish-like robot can modulate the rotation choice of zebrafish groups in a circular set-up. Here, we further study the modulation capabilities of such robots in a more complex set-up. To do this, we exploit zebrafish social behaviours we identified in previous studies. We first modulate collective departure by replicating the leadership mechanisms with the robot in a set-up composed of two rooms connected by a corridor. Then, we test different behavioural strategies to drive the fish groups towards a predefined target room. To drive the biohybrid groups towards a predefined choice, they have to adopt some specific fish-like behaviours. The first strategy is based on a single robot using the initiation behaviour. In this case, the robot keeps trying to initiate a group transition towards the target room. The second strategy is based on two robots, one initiating and one staying in the target room as a social attractant. The third strategy is based on a single robot behaving like a zebrafish but staying in the target room as a social attractant. The fourth strategy uses two robots behaving like zebrafish but staying in the target room. We conclude that robots can modulate zebrafish group behaviour by adopting strategies based on existing fish behaviours. Under these conditions, robots enable the testing of hypotheses about the behaviours of fish.
Transects, quadrats, or points? What is the best combination to get a precise estimation of a coral community?
Authors: Montilla Luis M. , Miyazawa Emy , Ascanio Alfredo , López-Hernández María , Mariño-Briceño Gloria , Rebolledo Zlatka , Rivera Andreína , Mancilla Daniela S. , Verde Alejandra , Cróquer Aldo
Published: November 2019

The characteristics of coral reef sampling and monitoring are highly variable, with numbers of units and sampling effort varying from one study to another. Numerous works have been carried out to determine an appropriate effect size through statistical power, however, always from a univariate perspective. In this work, we used the pseudo multivariate dissimilarity-based standard error (MultSE) approach to assess the precision of sampling scleractinian coral assemblages in reefs of Venezuela between 2017 and 2018 when using different combinations of number of transects, quadrats and points. For this, the MultSE of 36 sites previously sampled was estimated, using four 30m-transects with 15 photo-quadrats each and 25 random points per quadrat. We obtained that the MultSE was highly variable between sites and is not correlated with the univariate standard error nor with the richness of species. Then, a subset of sites was re-annotated using 100 uniformly distributed points, which allowed the simulation of different numbers of transects per site, quadrats per transect and points per quadrat using resampling techniques. The magnitude of the MultSE stabilized by adding more transects, however, adding more quadrats or points does not improve the estimate. For this case study, the error was reduced by half when using 10 transects, 10 quadrats per transect and 25 points per quadrat. We recommend the use of MultSE in reef monitoring programs, in particular when conducting pilot surveys to optimize the estimation of the community structure.
Using Chaos for Facile High-throughput Fabrication of Ordered Multilayer Micro- and Nanostructures
Authors: Chávez-Madero Carolina , de León-Derby María Díaz , Samandari Mohamadmahdi , Ceballos-González Carlos Fernando , Bolívar-Monsalve Edna Johana , Mendoza-Buenrostro Christian Carlos , Holmberg Sunshine , Garza-Flores Norma Alicia , Almajhadi Mohammad Ali , González-Gamboa Ivonne , Yee-de León Juan Felipe , Martínez-Chapa Sergio Omar , Rodríguez Ciro A. , Wickramasinghe Hemantha Kumar , Madou Marc , Khademhosseini Ali , Zhang Yu Shrike , Álvarez Mario Moisés , Santiago Grissel Trujillo-de
Published: November 2019

This paper introduces the concept of continuous chaotic printing, i.e., the use of chaotic flows for deterministic and continuous fabrication of fibers with internal multilayered micro-or nanostructures. Two free-flowing materials are coextruded through a printhead containing a miniaturized Kenics static mixer (KSM) composed of multiple helicoidal elements. This produces a fiber with a well-defined internal multilayer microarchitecture at high speeds (>1.0 m min-1). The number of mixing elements and the printhead diameter determine the number and thickness of the internal lamellae, which are generated according to successive bifurcations that yield a vast amount of inter-material surface area (~102 cm2 cm3) and high resolution features (~10 μm). In an exciting further development, we demonstrate a scale-down of the microstructure by 3 orders of magnitude, to the nanoscale level (~10 nm), by feeding the output of a continuous chaotic 3D printhead into an electrospinner. Comparison of experimental and computational results demonstrates the robust and predictable output and performance of continuous chaotic 3D printing. The simplicity and high resolution of continuous chaotic printing strongly supports its potential use in novel applications, including—but not limited to—bioprinting of multi-scale tissue-like structures, modeling of bacterial communities, and fabrication of smart multi-material and multilayered constructs.
Bionic 3D printed corals
Authors: Wangpraseurt Daniel , You Shangting , Azam Farooq , Jacucci Gianni , Gaidarenko Olga , Hildebrand Mark , Kühl Michael , Smith Alison G. , Davey Matthew P. , Smith Alyssa , Deheyn Dimitri D. , Chen Shaochen , Vignolini Silvia
Published: November 2019

Symbiotic corals have evolved as a highly optimised photon augmentation system leading to space-efficient microalgal growth and photosynthetic quantum efficiencies that approach theoretical limits1–3. Corals are characterized by an elastic animal tissue hosting microalgae and a light scattering calcium carbonate skeleton that maximizes light delivery towards otherwise shaded algal-containing tissues4,5. Rapid light attenuation due to algal self-shading is a key limiting factor for the upscaling of microalgal cultivation6,7. Coral-inspired light management systems could overcome this limitation and facilitate scalable bioenergy and bioproduct generation8,9. Here, we developed 3D printed bionic corals capable of growing various types of microalgae with cell densities approaching 109 cells mL-1, up to 100 times greater than in liquid culture. The hybrid photosynthetic biomaterials are produced with a new 3D bioprinting platform which mimics morphological features of living coral tissue and the underlying skeleton with micron resolution, including their optical and mechanical properties. The programmable synthetic microenvironment thus allows for replicating both structural and functional traits of the coral-algal symbiosis. Our work defines a new class of bionic materials capable of interacting with living organisms, that can be exploited for the design of next generation photobioreactors7 and disruptive approaches for coral reef conservation10.
Hidden impacts of environmental stressors on freshwater: Cytoscape® correlation networks for community ecotoxicology analysis
Authors: Lozano V.L.
Published: November 2019

Freshwater systems are affected by multiple stressors. Ecotoxicological studies using communities or higher ecological levels often are focussed on abundance analysis. We suggest incorporating correlation networks to bring to light possible hidden impacts on community interactions.
Characterization of a Human Liver NIST Reference Material fit for Proteomics Applications
Authors: Davis W. Clay , Kilpatrick Lisa E. , Ellisor Debra L. , Neely Benjamin A.
Published: November 2019

The National Institute of Standards and Technology (NIST) is creating new, economical, qualitative reference materials and data for proteomics comparisons, benchmarking and harmonization. Here we describe a large dataset from shotgun proteomic analysis of RM 8461 Human Liver for Proteomics, a reference material being developed. Consensus identifications using multiple search engines and sample preparations demonstrate a homogeneous and fit-for-purpose material that can be incorporated into automated or manual sample preparation workflows, with the resulting data used to directly assess complete sample-to-data workflows and provide harmonization and benchmarking between laboratories and techniques. Data are available via PRIDE with identifier PXD013608.
Systematic mapping of genetic interactions for de novo fatty acid synthesis
Authors: Aregger Michael , Lawson Keith A. , Billmann Maximillian , Costanzo Michael , Tong Amy H. Y. , Chan Katherine , Rahman Mahfuzur , Brown Kevin R. , Ross Catherine , Usaj Matej , Nedyalkova Lucy , Sizova Olga , Habsid Andrea , Pawling Judy , Lin Zhen-Yuan , Abdouni Hala , Weiss Alexander , Mero Patricia , Dennis James W. , Gingras Anne-Claude , Myers Chad L. , Andrews Brenda J. , Boone Charles , Moffat Jason
Published: November 2019

The de novo synthesis of fatty acids has emerged as a therapeutic target for various diseases including cancer. While several translational efforts have focused on direct perturbation of de novo fatty acid synthesis, only modest responses have been associated with mono-therapies. Since cancer cells are intrinsically buffered to combat metabolic stress, cells may adapt to loss of de novo fatty acid biosynthesis. To explore cellular response to defects in fatty acid synthesis, we used pooled genome-wide CRISPR screens to systematically map genetic interactions (GIs) in human HAP1 cells carrying a loss-of-function mutation in FASN, which catalyzes the formation of long-chain fatty acids. FASN mutant cells showed a strong dependence on lipid uptake that was reflected by negative GIs with genes involved in the LDL receptor pathway, vesicle trafficking, and protein glycosylation. Further support for these functional relationships was derived from additional GI screens in query cell lines deficient for other genes involved in lipid metabolism, including LDLR, SREBF1, SREBF2, ACACA. Our GI profiles identified a potential role for a previously uncharacterized gene LUR1 (C12orf49) in exogenous lipid uptake regulation. Overall, our data highlights the genetic determinants underlying the cellular adaptation associated with loss of de novo fatty acid synthesis and demonstrate the power of systematic GI mapping for uncovering metabolic buffering mechanisms in human cells.
Non-Equilibrial Dynamics in Under-Saturated Communities
Authors: Halloway Abdel , Staňková Kateřina , Brown Joel S.
Published: November 2019

A.

The concept of the evolutionary stable strategy (ESS) has been fundamental to the development of evolutionary game theory. It represents an equilibrial evolutionary state in which no rare invader can grow in population size. With additional work, the ESS concept has been formalized and united with other stability concepts such as convergent stability, neighborhood invasion stability, and mutual invisibility. Other work on evolutionary models, however, shows the possibility of unstable and/or non-equilibrial dynamics such as limit cycles and evolutionary suicide. Such “pathologies” remain outside of a well-defined context, especially the currently defined stability concepts of evolutionary games. Ripa et al. (2009) offer a possible reconciliation between work on non-equilibrial dynamics and the ESS concept. They noticed that the systems they analyzed show non-equilibrial dynamics when under-saturated and “far” from the ESS and that getting “closer” to the ESS through the addition of more species stabilized their systems. To that end, we analyzed three models of evolution, two predator-prey models and one competition model of evolutionary suicide, to see how the degree of saturation affects the stability of the system. In the predator-prey models, stability is linked to the degree of saturation. Specifically, a fully saturated community will only show stable dynamics, and unstable dynamics occur only when the community is under-saturated. With the competition model, we demonstrate it to be permanently under-saturated, likely showing such extreme dynamics for this reason. Though not a general proof, our analysis of the models provide evidence of the link between community saturation and evolutionary dynamics. Our results offer a possible placement of these evolutionary “pathologies” into a wider framework. In addition, the results concur with previous results showing greater evolutionary response to less biodiversity and clarifies the effect of extrinsic vs. intrinsic non-equilibrial evolutionary dynamics on a community.
A universal reading network and its modulation by writing system and reading ability in French and Chinese children
Authors: Feng Xiaoxia , Altarelli Irene , Monzalvo Karla , Ding Guosheng , Ramus Franck , Shu Hua , Dehaene Stanislas , Meng Xiangzhi , Dehaene-Lambertz Ghislaine
Published: November 2019

Are the brain mechanisms of reading acquisition similar across writing systems? And do similar brain anomalies underlie reading disabilities in alphabetic and ideographic reading systems? In a cross-cultural paradigm, we measured the fMRI responses to words, faces and houses of 96 Chinese and French 10-year-old children, half of whom struggle with reading. We observed a reading circuit which was strikingly similar across languages and consisting of the left fusiform gyrus, superior temporal gyrus/sulcus, precentral and middle frontal gyri. Activations in some of these areas were modulated either by language or by reading ability, but without interaction between those factors. In various regions previously associated with dyslexia, reading difficulty affected activation similarly in Chinese and French readers, including the middle frontal gyrus, a region previously described as specifically altered in Chinese. Our analyses reveal a large degree of cross-cultural invariance in the neural correlates of reading acquisition and reading disabilities.
Evaluation of ACMG Rules for In silico Evidence Strength Using An Independent Computational Tool Absent of Circularities on ATM and CHEK2 Breast Cancer Cases and Controls
Authors: Young Colin C. , Feng Bing-Jian , Mackenzie Colin B. , Girard Elodie , Hu Donglei , Iwasaki Yusuke , Momozawa Yukihide , Lesueur Fabienne , Ziv Elad , Neuhausen Susan L. , Tavtigian Sean V.
Published: November 2019

The American College of Medical Genetics and Genomics (ACMG) guidelines for sequence variant classification include two criteria, PP3 and BP4, for combining computational data with other evidence types contributing to sequence variant classification. PP3 and BP4 assert that computational modeling can provide “Supporting” evidence for or against pathogenicity within the ACMG framework. Here, leveraging a meta-analysis of ATM and CHEK2 breast cancer case-control mutation screening data, we evaluate the strength of evidence determined from the relatively simple computational tool Align-GVGD. Importantly, application of Align-GVGD to these ATM and CHEK2 data is free of logical circularities, hidden multiple testing, and use of other ACMG evidence types. For both genes, rare missense substitutions that are assigned the most severe Align-GVGD grade exceed a “Moderate pathogenic” evidence threshold when analyzed in a Bayesian framework; accordingly, we argue that the ACMG classification rules be updated for well-calibrated computational tools. Additionally, congruent with previous analyses of ATM and CHEK2 case-control mutation screening data, we find that both genes have a considerable burden of pathogenic missense substitutions, and that severe ATM rare missense have increased odds ratios compared to truncating and splice junction variants, indicative of a potential dominant-negative effect for those missense substitutions.
Bayesian Modeling Reveals Ultrasensitivity Underlying Metabolic Compensation in the Cyanobacterial Circadian Clock
Authors: Hong Lu , Lavrentovich Danylo O , Chavan Archana , Leypunskiy Eugene , Li Eileen , Matthews Charles , LiWang Andy , Rust Michael J , Dinner Aaron R
Published: November 2019

Mathematical models can enable a predictive understanding of mechanism in cell biology by quantitatively describing complex networks of interactions, but such models are often poorly constrained by available data. Owing to its relative biochemical simplicity, the core circadian oscillator in Synechococcus elongatus has become a prototypical system for studying how collective dynamics emerge from molecular interactions. The oscillator consists of only three proteins, KaiA, KaiB, and KaiC, and near-24-h cycles of KaiC phosphorylation can be reconstituted in vitro. Here, we formulate a molecularly-detailed but mechanistically agnostic model of the KaiA-KaiC subsystem and fit it directly to experimental data within a Bayesian parameter estimation framework. Analysis of the fits consistently reveals an ultrasensitive response for KaiC phosphorylation as a function of KaiA concentration, which we confirm experimentally. This ultrasensitivity primarily results from the differential affinity of KaiA for competing nucleotide-bound states of KaiC. We argue that the ultrasensitive stimulus-response relation is critical to metabolic compensation by suppressing premature phosphorylation at nighttime.

Synopsis

This study takes a data-driven kinetic modeling approach to characterizing the interaction between KaiA and KaiC in the cyanobacterial circadian oscillator and understanding how the oscillator responds to changes in cellular metabolic conditions.

An extensive dataset of KaiC autophosphorylation measurements was gathered and fit to a detailed yet mechanistically agnostic kinetic model within a Bayesian parameter estimation framework.

KaiA concentration tunes the sensitivity of KaiC autophosphorylation and the period of the full oscillator to %ATP.

The model reveals an ultrasensitive dependence of KaiC phosphorylation on KaiA concentration as a result of differential KaiA binding affinity to ADP- vs. ATP-bound KaiC.

Ultrasensitivity in KaiC phosphorylation contributes to metabolic compensation by suppressing premature phosphorylation at nighttime.
Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo13C and 2H metabolic network mapping
Authors: Lawson Christopher E. , Nuijten Guylaine H.L. , de Graaf Rob M. , Jacobson Tyler B. , Pabst Martin , Stevenson David. M. , Jetten Mike S.M. , Noguera Daniel R. , McMahon Katherine D. , Amador-Noguez Daniel , Lücker Sebastian
Published: November 2019

Anaerobic ammonium-oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and mixotrophy beyond genome-based predictions. Here, we experimentally resolved the central carbon metabolism of the anammox bacterium Candidatus ‘Kuenenia stuttgartiensis’ using time-series 13C and 2H isotope tracing, metabolomics, and isotopically nonstationary metabolic flux analysis (INST-MFA). Our findings confirm predicted metabolic pathways used for CO2 fixation, central metabolism, and amino acid biosynthesis in K. stuttgartiensis, and reveal several instances where genomic predictions are not supported by in vivo metabolic fluxes. This includes the use of an oxidative tricarboxylic acid cycle, despite the genome not encoding a known citrate synthase. We also demonstrate that K. stuttgartiensis is able to directly assimilate extracellular formate via the Wood-Ljungdahl pathway instead of oxidizing it completely to CO2 followed by reassimilation. In contrast, our data suggests that K. stuttgartiensis is not capable of using acetate as a carbon or energy source in situ and that acetate oxidation occurred via the metabolic activity of a low-abundance microorganism in the bioreactor’s side population. Together, these findings provide a foundation for understanding the carbon metabolism of anammox bacteria at a systems-level and will inform future studies aimed at elucidating factors governing their function and niche differentiation in natural and engineered ecosystems.
Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples
Authors: Teyssier Noam B. , Chen Anna , Duarte Elias M , Sit Rene , Greenhouse Bryan , Tessema Sofonias K.
Published: November 2019

Background

Whole-genome sequencing (WGS) is becoming increasingly useful to study the biology, epidemiology, and ecology of malaria parasites. Despite ease of sampling, DNA extracted from dried blood spots (DBS) has a high ratio of human DNA compared to parasite DNA, which poses a challenge for downstream genetic analyses. We evaluated the effects of multiple methods for DNA extraction, digestion of methylated DNA, and amplification on the quality and fidelity of WGS data recovered from DBS.

Results

At 100 parasites/μL, Chelex-Tween-McrBC samples had higher coverage (5X depth = 93% genome) than QIAamp extracted samples (5X depth = 76% genome). The two evaluated sWGA primer sets showed minor differences in overall genome coverage and SNP concordance, with a newly proposed combination of 20 primers showing a modest improvement in coverage over those previously published.

Conclusions

Overall, Tween-Chelex extracted samples that were treated with McrBC digestion and are amplified using 6A10AD sWGA conditions had minimal dropout rate, higher percentages of coverage at higher depth, and more accurate SNP concordance than QiaAMP extracted samples. These findings extend the results of previously reported methods, making whole genome sequencing accessible to a larger number of low density samples that are commonly encountered in cross-sectional surveys.
Water availability and temperature induce changes in oxidative status during pregnancy in a viviparous lizard
Authors: Dupoué Andréaz , Blaimont Pauline , Rozen‐Rechels David , Richard Murielle , Meylan Sandrine , Clobert Jean , Miles Donald B. , Martin Rémi , Decencière Beatriz , Agostini Simon , Le Galliard Jean‐François
Published: November 2019

Reproduction involves considerable reorganization in an organism's physiology that incurs potential toxicity for cells (e.g., oxidative stress) and decrease in fitness. This framework has been the cornerstone of the so‐called ‘oxidative cost of reproduction’, a theory that remains controversial and relatively overlooked in non‐model ectotherms.

Here, we used two complementary approaches in natural and controlled conditions to test whether altered access to climate conditions (water and temperature resources) alters oxidative status and mediates reproductive trade‐offs in viviparous populations of the common lizard (Zootoca vivipara).

First, we examined whether access to free‐standing water and differences in ambient temperature across 12 natural populations could be related to variation in oxidative status, reproductive effort and reproductive success. Second, we determined whether an experimental restriction to water triggers higher oxidative cost of reproduction and correlates with fitness measures (reproductive success, future survival rate and probability of future reproduction).

Pregnant females exhibited higher sensitivity than males to natural or experimental limitations in temperature and water access. That is, in restricted environments, pregnant females with higher reproductive effort exhibited stronger oxidative damage despite enhanced non‐enzymatic antioxidant capacity.

Enhanced antioxidant defensive capacity in pregnant females was positively correlated with higher reproductive success, whereas elevated oxidative damage negatively correlated with offspring annual survival.

Altogether, our results revealed a context‐dependent oxidative cost of reproduction that was concomitant with a conflict in water demand from offspring. These new insights should be critical for understanding ectotherm responses to heat waves and summer droughts that are increasing in frequency and duration.

A free Plain Language Summary can be found within the Supporting Information of this article.
Calcium‐sensing receptor activating ERK1/2 and PI3K‐Akt pathways to induce the proliferation of osteosarcoma cells
Authors: Zhao Wei , Zhang Zhipeng , Zheng Leyu , You Changcheng , Chi Hui , Zhang Tingxin , Xu Gongping
Published: November 2019

Our results showed that the expression of calcium‐sensing receptor (CaSR) and the concentration of intracellular calcium were enhanced in the osteosarcoma cells MG‐63 compared with in the normal osteoblasts hFOB1.19. GdCl3 (CaSR agonist) significantly increased the proliferation rate of MG‐63 cells, the expression of PCNA and Cyclin D1 and decreased the expression of p21Cip/WAF‐1. The effect of NPS2390 (CaSR antagonist) on the above indicators was opposite to GdCl3. In addition, GdCl3 up‐regulated the phosphorylation of ERK1/2, PI3K and Akt and the proliferation rate of MG‐63 cells. However, these effects of GdCl3 were cancelled by LY294002 (a PI3K inhibitor) or PD98059 (an ERK1/2 inhibitor). Our results demonstrate that activation of CaSR promotes osteosarcoma cell multiplication by up‐regulating ERK1/2 and PI3K‐Akt pathways.
Verbal Number in Lo–Toga and Hiw: The Emergence of a Lexical Paradigm
Authors: François Alexandre
Published: November 2019

Several languages around the world encode number through a regular alternation between verb roots, in a pattern sometimes called ‘verbal number suppletion’ (Veselinova 2006). Lo–Toga and Hiw, two Oceanic languages of Vanuatu (Torres Islands), thus alternate certain verbs according to their absolutive argument's number – e.g. Hiw tō ‘go:Sing’ vs. vën ‘go:Plural’. The pattern affects 17 verb pairs in Lo–Toga, 33 in Hiw. This rich system is a local innovation in the Torres Islands, not found elsewhere in Oceanic.

This structure is here analysed for the first time. Verbal number is not just agreement: its principles and categories differ from nominal number. Despite its similarity with suppletion, the structure really involves separate words, organised into a ‘lexical paradigm’ – a structured set of lexical pairs, contrasting individual vs. collective events. The comparative method helps reconstruct the system's development. A former circumfix encoding pluractionality was the source for the number alternation; yet most verbs encoded the contrast lexically, as near‐synonyms were harnessed into the emergent paradigm. Crucially, even after it was recruited into the number paradigm, each verb remained an autonomous lexeme. While nominal number belongs to the morphology, the paradigm of verbal number in the Torres languages pertains entirely to the lexicon.
Flattening of the articular eminence is associated with the loss of occlusal support: radiological study
Authors: Oruba Z , Malisz P , Sendek J , Aardal VE , Kopycińska N , Krzystyniak K , Darczuk D , Kaczmarzyk T
Published: November 2019

Background

Degenerative changes in the temporomandibular joint might be associated with ageing and/or with the loss of occlusal support.

Objective

The aim of the study was to evaluate whether the inclination of the posterior slope of the articular eminence changes in association with: (i) ageing in patients with maintained occlusal support zones (OSZs); and (ii) the loss of OSZs in elders.

Methods

In this retrospective radiological study, selected orthopantomograms were allocated into the following groups: I—age 18–35, maintained OSZs, II—age 36–60, maintained OSZs, III—age >60, at least one OSZ per side maintained, IV—age >60, loss of all OSZs. The inclination of the articular eminence was measured relative to the Frankfort plane.

Results

The mean values of the inclination of the slope of the articular eminence amounted 34.05° ± 5.17°, 36.68° ± 5.65°, 34.86° ± 6.26° and 26.31° ± 5.12° for group I, II, III and IV respectively. There were no significant differences between the groups I to III. Group IV differed significantly from each of the previous groups.

Conclusions

Flattening of the articular eminence is associated with the loss of OSZs rather than ageing.
Carbon isotope analysis shows introduced bovines have broader dietary range than the largest native herbivores in an Australian tropical savanna
Authors: Reid Angela M. , Murphy Brett P. , Vigilante Tom ,   Wunambal Gaambera Aboriginal Corporation, Barry Linda A. , Bowman David M.J.S.
Published: November 2019

Australian savannas lack native megaherbivores (>500 kg body mass), but since the commencement of European colonisation in the 19th century bovine livestock, such as cattle (Bos sp.) and water buffalo (Bubalus bubalis), have established large feral populations that continue to geographically expand. The largest extant native herbivores are marsupials in the family Macropodidae (henceforth 'macropods': common wallaroo, Osphranter robustus [c. 40 kg]; antilopine wallaroo, O. antilopinus [c. 35 kg] and agile wallaby, Notamacropus agilis [c. 20 kg]). These species occur at low densities, with evidence that some species are in decline, the cause of which remains uncertain. We tested the hypothesis that bovines and macropods compete for nutritious forage in the North Kimberley, Western Australia by using carbon isotope analysis of feral cattle and native macropod dung (as a proxy for the relative contribution of C4 grass to their diet) and nutrient analysis of standing herbaceous biomass. Grass consumption varied between macropod species and was highest in larger wallaroo species and lowest in the smaller agile wallaby reflecting its broader diet. Grass consumption by wallaroos was maximal on fertile sites. The relative abundance of grass in the diet of cattle was lowest in the middle of the dry season with an interaction between fire and substrate fertility where grass consumption was highest on fertile sites, particularly those recently burnt. Grass consumption by cattle and wallaroos was negatively correlated with fibre content of live biomass, which was lowest on fertile and burnt sites. Introduced bovines shift their diets to non‐grasses as quality of herbaceous biomass declines with increasing fibre content, and by contrast, the largest macropod herbivores do not have this dietary flexibility. We conclude a plausible mechanism for the success of bovines and the decline of large macropods in Australian savannas is competition for nutritious grass that is abundant immediately after fire.