bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACTThe 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

AbstractThis 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

SummarySymbiotic 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.
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

AbstractThe 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

ABSTRACTThe 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.AbstractThe 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

AbstractAre 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

AbstractThe 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

AbstractMathematical 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.SynopsisThis 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

AbstractAnaerobic 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

AbstractBackgroundWhole-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.ResultsAt 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.ConclusionsOverall, 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

Abstract

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

AbstractOur 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.