bluuebunny/crossref_metadata_2025_split huggingface dataset:
The fast and the frugal: Divergent locomotory strategies drive limb lengthening in theropod dinosaurs
Authors: Dececchi T. Alexander , Mloszewska Aleksandra M. , Holtz Thomas R. , Habib Michael B. , Larsson Hans C.E. 
Published: September 2019

AbstractLimb length, cursoriality and speed have long been areas of significant interest in theropod paleobiology as locomotory capacity, especially running ability, is critical in not just in prey pursuit but also to avoid become prey oneself. One aspect that is traditionally overlooked is the impact of allometry on running ability and the limiting effect of large body size. Since several different non-avian theropod lineages have each independently evolved body sizes greater than any known terrestrial carnivorous mammal, ∼1000kg or more, the effect that such larger mass has on movement ability and energetics is an area with significant implications for Mesozoic paleoecology. Here using expansive datasets, incorporating several different metrics to estimate body size, limb length and running speed, to calculate the effects of allometry running We test both on traditional metrics used to evaluate cursoriality in non-avian theropods such as distal limb length, relative hindlimb length as well as comparing the energetic cost savings of relative hindlimb elongation between members of the Tyrannosauridae and more basal megacarnivores such as Allosauroids or Ceratosauridae. We find that once the limiting effects of body size increase is incorporated, no commonly used metric including the newly suggested distal limb index (Tibia + Metatarsus/ Femur length) shows a significant correlation to top speed. The data also shows a significant split between large and small bodied theropods in terms of maximizing running potential suggesting two distinct strategies for promoting limb elongation based on the organisms’ size. For small and medium sized theropods increased leg length seems to correlate with a desire to increase top speed while amongst larger taxa it corresponds more closely to energetic efficiency and reducing foraging costs. We also find, using 3D volumetric mass estimates, that the Tyrannosauridae show significant cost of transport savings compared to more basal clades, indicating reduced energy expenditures during foraging and likely reduced need for hunting forays. This suggests that amongst theropods while no one strategy dictated hindlimb evolution. Amongst smaller bodied taxa the competing pressures of being both a predator and a prey item dominant while larger ones, freed from predation pressure, seek to maximize foraging ability. We also discuss the implications both for interactions amongst specific clades and Mesozoic paleobiology and paleoecological reconstructions as a whole.
Evolution from total variation to nonlinear sparsifying transform for sparse-view CT image reconstruction
Authors: Dong Jian , Han Chunxiao , Qin Zhuanping , Che Yanqiu 
Published: September 2019

AbstractSparse-view CT has been widely studied as an effective strategy for reducing radiation dose to patients. However, the conventional image reconstruction algorithms, such as filtered back-projection method and classical algebraic reconstruction techniques, can no longer be competent in the image reconstruction task of sparse-view CT. A new principle, called compressed sensing (CS), has been therefore developed to provide an effective solution for the ill-posed inverse problem of sparse-view CT image reconstruction. Total variation (TV) minimization, which is most extensively studied among the existing CS techniques, has been recognized as a powerful tool for dealing with this difficult problem in image reconstruction community. However, in recent years, the drawbacks of TV are being increasingly reported, which are appearance of patchy artifacts, depict of incorrect object boundaries, and loss in image textures or smooth intensity changes. These degradations appear especially in reconstructing actual CT images with complicated intensity changes. In order to address these drawbacks, a series of advanced algorithms using nonlinear sparsifying transform (NLST) have been proposed very recently. The NLST-based CS is based on a different framework from the TV, and it achieves an improvement in image quality. Since it is a relatively newly proposed idea, within the scope of our knowledge, there exist few literatures that discusses comprehensively how the image quality improvement occurs in comparison with the conventional TV method. In this study, we investigated the image quality differences between the conventional TV minimization and the NLST-based CS, as well as image quality differences among different kinds of NLST-based CS algorithms in the sparse-view CT image reconstruction. More specifically, image reconstructions of actual CT images of different body parts were carried out to demonstrate the image quality differences.
UbiFast, a rapid and deep-scale ubiquitylation profiling approach for biology and translational research
Authors: Udeshi Namrata D. , Mani Deepak C. , Satpathy Shankha , Fereshetian Shaunt , Gasser Jessica A. , Svinkina Tanya , Ebert Benjamin L. , Mertins Philipp , Carr Steven A. 
Published: September 2019

AbstractProtein ubiquitylation is involved in a plethora of cellular processes. Defects in the ubiquitin system are at the root of many acquired and hereditary diseases. While antibodies directed at ubiquitin remnants (K-ε-GG) have improved the ability to monitor ubiquitylation using mass spectrometry, methods for highly-multiplexed measurement of ubiquitylation in tissues and primary cells using sub-milligram amounts of sample remains a challenge. Here we present a highly-sensitive, rapid and multiplexed protocol for quantifying ∼10,000 ubiquitylation sites from as little as 500 ug peptide per sample from cells or tissue in a TMT10 plex in ca. 5 hr. High-field Asymmetric Ion Mobility Spectrometry (FAIMS) is used to improve quantitative accuracy for posttranslational modification analysis. We use the approach to rediscover substrates of the E3 ligase targeting drug lenalidomide and to identify proteins modulated by ubiquitylation in models of basal and luminal human breast cancer. The sensitivity and speed of the UbiFast method makes it suitable for large-scale studies in primary tissue samples.
The RNA helicase DDX3 induces neural crest by promoting AKT activity
Authors: Perfetto Mark , Xu Xiaolu , Yousaf Natasha , Li Jiejing , Wei Shuo 
Published: September 2019

AbstractMutations in the RNA helicase DDX3 have emerged as a frequent cause of intellectual disability in humans. Because many patients carrying DDX3 mutations have additional defects in craniofacial structures and other tissues containing neural crest (NC)-derived cells, we hypothesized that DDX3 is also important for NC development. UsingXenopus tropicalisas a model, we show that DDX3 is required for normal NC induction and craniofacial morphogenesis by regulating AKT kinase activity. Depletion of DDX3 decreases AKT activity and AKT-dependent inhibitory phosphorylation of GSK3β, leading to reduced levels of β-catenin and Snai1, two GSK3β substrates that are critical for NC induction. DDX3 function in regulating these downstream signaling events during NC induction is likely mediated by RAC1, a small GTPase whose translation depends on the RNA helicase activity of DDX3. These results suggest an evolutionarily conserved role of DDX3 in NC development by promoting AKT activity, and provide a potential mechanism for the NC-related birth defects displayed by patients harboring mutations in DDX3 and its downstream effectors in this signaling cascade.
The origin of physiological local mGluR1 supralinear Ca2+ signals in cerebellar Purkinje neurons
Authors: Ouares Karima Ait , Canepari Marco 
Published: September 2019

SUMMARYIn Purkinje neurons, the climbing fibre (CF) input provides a signal to parallel fibre (PF) synapses triggering PF synaptic plasticity. This supralinear Ca2+ signal, co-localised with the PF Ca2+ influx, occurs when PF activity precedes the CF input. Using membrane potential (Vm) and Ca2+ imaging, we identified the biophysical determinants of these supralinear Ca2+ signals. The CF-associated Ca2+ influx is mediated by T-type or by P/Q-type Ca2+ channels, depending on whether the dendritic Vm is hyperpolarised or depolarised. The resulting Ca2+ elevation is locally amplified by saturation of the endogenous Ca2+ buffer produced by the PF-associated Ca2+ influx, in particular by the slow Ca2+ influx mediated by type-1 metabotropic glutamate receptors (mGluR1s). When the dendrite is hyperpolarised, mGluR1s boost neighbouring T-type channels providing a mechanism for local coincident detection of PF-CF activity. In contrast, when the dendrite is depolarised, mGluR1s increase dendritic excitability by inactivating A-type K+ channels, but this phenomenon is not restricted to the activated PF synapses. Thus, Vm is likely a crucial parameter in determining PF synaptic plasticity and the occurrence of hyperpolarisation episodes is expected to play an important role in motor learning.
Rapid and Sustained Homeostatic Control of Presynaptic Exocytosis at a Central Synapse
Authors: Delvendahl Igor , Kita Katarzyna , Müller Martin 
Published: September 2019

AbstractAnimal behavior is remarkably robust despite constant changes in neural activity. Homeostatic plasticity stabilizes central nervous system (CNS) function on time scales of hours to days. If and how CNS function is stabilized on more rapid time scales remains unknown. Here we discovered that mossy fiber synapses in the mouse cerebellum homeostatically control synaptic efficacy within minutes after pharmacological glutamate receptor impairment. This rapid form of homeostatic plasticity is expressed presynaptically. We show that modulations of readily-releasable vesicle pool size and release probability normalize synaptic strength in a hierarchical fashion upon acute pharmacological and prolonged genetic receptor perturbation. Presynaptic membrane capacitance measurements directly demonstrate regulation of vesicle pool size upon receptor impairment. Moreover, presynaptic voltage-clamp analysis revealed increased calcium-current density under specific experimental conditions. Thus, homeostatic modulation of presynaptic exocytosis through specific mechanisms stabilizes synaptic transmission in a CNS circuit on time scales ranging from minutes to months. Rapid presynaptic homeostatic plasticity may ensure stable neural circuit function in light of rapid activity-dependent plasticity.
Genetic interactions derived from high-throughput phenotyping of 7,350 yeast cell cycle mutants
Authors: Gallegos Jenna E. , Adames Neil R. , Rogers Mark F. , Kraikivski Pavel , Ibele Aubrey , Nurzynski-Loth Kevin , Kudlow Eric , Murali T.M. , Tyson John J. , Peccoud Jean 
Published: September 2019

AbstractOver the last 30 years, computational biologists have developed increasingly realistic mathematical models of the regulatory networks controlling the division of eukaryotic cells. These models capture data resulting from two complementary experimental approaches: low-throughput experiments aimed at extensively characterizing the functions of small numbers of genes, and large-scale genetic interaction screens that provide a systems-level perspective on the cell division process. The former is insufficient to capture the interconnectivity of the genetic control network, while the latter is fraught with irreproducibility issues. Here, we describe a hybrid approach in which the genetic interactions between 36 cell-cycle genes are quantitatively estimated by high-throughput phenotyping with an unprecedented number of biological replicates. Using this approach, we identify a subset of high-confidence genetic interactions, which we use to refine a previously published mathematical model of the cell cycle. We also present a quantitative dataset of the growth rate of these mutants under six different media conditions in order to inform future cell cycle models.Author SummaryThe process of cell division, also called the cell cycle, is controlled by a highly complex network of interconnected genes. If this process goes awry, diseases such as cancer can result. In order to unravel the complex interactions within the cell cycle control network, computational biologists have developed mathematical models that describe how different cell cycle genes are related. These models are built using large datasets describing the effect of mutating one or more genes within the network. In this manuscript, we present a novel method for producing such datasets. Using our method, we generate 7,350 yeast mutants to explore the interactions between key cell cycle genes. We measure the effect of the mutations by monitoring the growth rate of the yeast mutants under different environmental conditions. We use our mutants to revise an existing model of the yeast cell cycle and present a dataset of ∼44,000 gene by environment combinations as a resource to the yeast genetics and modeling communities.
A PUF hub drives self-renewal inC. elegansgermline stem cells
Authors: Haupt Kimberly A. , Law Kimberley T. , Enright Amy L. , Kanzler Charlotte R. , Shin Heaji , Wickens Marvin , Kimble Judith 
Published: September 2019

ABSTRACTStem cell regulation relies on extrinsic signaling from a niche plus intrinsic factors that respond and drive self-renewal within stem cells. Apriori,loss of niche signaling and loss of the intrinsic self-renewal factors might be expected to have equivalent stem cell defects. Yet this simple prediction has not been borne out for most stem cells, includingC. elegansgermline stem cells (GSCs). The central regulators ofC. elegansGSCs include extrinsically-acting GLP-1/Notch signaling from the niche, intrinsically-acting RNA binding proteins in the PUF family, termed FBF-1 and FBF-2 (collectively FBF), and intrinsically-acting PUF partner proteins that are direct Notch targets. Abrogation of either GLP-1/Notch signaling or its targets yields an earlier and more severe GSC defect than loss of FBF-1 and FBF-2, suggesting that additional intrinsic regulators must exist. Here, we report that those missing regulators are two additional PUF proteins, PUF-3 and PUF-11. Remarkably, anfbf-1 fbf-2; puf-3 puf-11quadruple null mutant has a GSC defect virtually identical to that of aglp-1/Notch null mutant. PUF-3 and PUF-11 both affect GSC maintenance; both are expressed in GSCs; and epistasis experiments place them at the same position as FBF within the network. Therefore, action of PUF-3 and PUF-11 explains the milder GSC defect infbf-1 fbf-2mutants. We conclude that a “PUF hub”, comprising four PUF proteins and two PUF partners, constitutes the intrinsic self-renewal node of theC. elegansGSC RNA regulatory network. Discovery of this hub underscores the significance of PUF RNA-binding proteins as key regulators of stem cell maintenance.
Heterogeneous T cell motility behaviors emerge from a coupling between speed and turningin vivo
Authors: Jerison Elizabeth R. , Quake Stephen R. 
Published: September 2019

AbstractT cellsin vivomigrate primarily via undirected random walks, but it remains unresolved how these random walks generate an efficient search. Here, we use light sheet microscopy of T cells in the larval zebrafish as a model system to study motility across large populations of cells over hours in their native context. We show that cell-to-cell variability is amplified by a correlation between speed and directional persistence, generating a characteristic cell behavioral manifold that is preserved under a perturbation to cell speeds, and seen in Mouse T cells andDictyostelium. These results suggest that there is a single variable underlying ameboid cell motility that jointly controls speed and turning. This coupling explains behavioral heterogeneity in diverse systems and allows cells to access a broad range of length scales.
Exposure to predator models during the fertile period leads to higher levels of extra‐pair paternity in blue tits
Authors: Santema Peter , Valcu Mihai , Kempenaers Bart 
Published: September 2019

Abstract

The perceived risk of predation can affect breeding behaviour and reduce reproductive success in prey species. Individuals exposed to predators may also adopt different mating tactics with potential consequences for the distribution of paternity in socially monogamous species that engage in extra‐pair copulations.

We experimentally increased perceived predation risk during the fertile period in blue tits Cyanistes caeruleus. Every morning between nest completion and the onset of egg laying, we presented a model of either a predator or a non‐predator (control) near active nestboxes.

Broods from pairs exposed to predators had higher levels of extra‐pair paternity than control broods. This mainly resulted from a higher proportion of extra‐pair offspring in broods with at least one extra‐pair young.

Females exposed to predators first emerged from the nestbox later in the morning, stayed away from the nestbox for longer and were less likely to be visited at the nest by their social mate, but we detected no behavioural differences once the model was removed.

Our results suggest that the higher rates of extra‐pair paternity resulted from the disruption of morning routines, which may have inhibited within‐pair copulations or increased opportunities for females to engage in extra‐pair copulations. We conclude that the perceived risk of predation can have substantial effects on levels of extra‐pair paternity.
Seeking compromise across competing goals in conservation translocations: The case of the ‘extinct’ Floreana Island Galapagos giant tortoise
Authors: Hunter Elizabeth A. , Gibbs James P. , Cayot Linda J. , Tapia Washington , Quinzin Maud C. , Miller Joshua M. , Caccone Adalgisa , Shoemaker Kevin T. 
Published: September 2019

Abstract

Conservation translocation projects must carefully balance multiple, potentially competing objectives (e.g. population viability, retention of genetic diversity, delivery of key ecological services) against conflicting stakeholder values and severe time and cost constraints. Advanced decision support tools would facilitate identifying practical solutions.

We examined how to achieve compromise across competing objectives in conservation translocations via an examination of giant tortoises in the Galapagos Islands with ancestry from the extinct Floreana Island species (Chelonoidis niger). Efforts have begun to populate Floreana Island with tortoises genetically similar to its historical inhabitants while balancing three potentially competing objectives – restoring ecosystem services (sustaining a high tortoise population size), maximizing genome representation of the extinct C. niger species and maintaining a genetically diverse population – under realistic cost constraints.

We developed a novel approach to this conservation decision problem by coupling an individual‐based simulation model with generalized additive models and global optimization. We identified several incompatibilities among programme objectives, with quasi‐optimal single‐objective solutions (sets of management actions) differing substantially in programme duration, translocation age, incubation temperature (determinant of sex ratio) and the number of individuals directly translocated from the source population.

Quasi‐optimal single‐objective solutions were able to produce outcomes (i.e. population size and measures of genetic diversity and C. niger genome representation) to within 75% of their highest simulated outcomes (e.g. highest population size achieved across all simulations) within a cost constraint of c. $2m USD, but these solutions resulted in severe declines (up to 74% reduction) in outcomes for non‐focal objectives. However, when all programme objectives were equally weighted to produce a multi‐objective solution, all objectives were met to within 90% of the highest achievable mean values across all cost constraints.

Synthesis and applications. Multi‐objective conservation translocations are likely to encounter complex trade‐offs and conflicts among programme objectives. Here, we developed a novel combination of modelling approaches to identify optimal management strategies. We found that solutions that simultaneously addressed multiple, competing objectives performed better than single‐objective solutions. Our model‐based decision support tool demonstrates that timely, cost‐effective solutions can be identified in cases where management objectives appear to be incompatible.
Shrub encroachment decreases soil inorganic carbon stocks in Mongolian grasslands
Authors: Liu Shangshi , Zhou Luhong , Li He , Zhao Xia , Yang Yuanhe , Zhu Yankun , Hu Huifeng , Chen Leiyi , Zhang Pujin , Shen Haihua , Fang Jingyun 
Published: September 2019

Abstract

Widespread shrub encroachment in global drylands may increase plant biomass and change soil organic carbon stocks of grassland ecosystems. However, the response of soil inorganic carbon (SIC), which is a major component of dryland carbon pools, to this vegetation shift remains unknown.

We conducted a systematic field survey in 75 pairs of shrub‐encroached grassland (SEG) and control plots at 25 sites in the grasslands of the Inner Mongolia Plateau to evaluate how shrub encroachment affects SIC density (SICD) in these ecosystems.

We found that shrub encroachment significantly reduced SICD in the upper 100 cm (3.85 vs. 4.74 kg C m−2, p < .05), especially in the subsurface soil (20–50 cm layer). The magnitude of SICD changes was related to the change in soil pH, shrub patch size and initial SICD, reflecting that the reduction in SICD might be attributed to the shrub encroachment‐related soil acidification. Our results also revealed that the lost SIC was mainly released into the atmosphere rather than redistributed into deeper soil layers.

Synthesis. We provide the first evidence for the soil acidification‐induced SIC loss caused by shrub encroachment. Our findings highlight the non‐negligible role of SIC dynamics in the C budget of SEG ecosystems and the need to consider these dynamics in terrestrial C cycle research.