bluuebunny/crossref_metadata_2025 huggingface dataset:
Smartphone Use and Interest in a Spine Surgery Recovery Mobile Application Among Patients in a US Academic Neurosurgery Practice
Authors: Nathan Jay K , Rodoni Bridger M , Joseph Jacob R , Smith Brandon W , Park Paul
Published: April 2019

BACKGROUND

Mobile applications (apps) are serving an increasingly important role in healthcare for patients and providers alike. In addition to streamlining active communication of patient-reported outcomes regarding quality of life, pain, and opioid consumption, smartphones equipped with activity tracking afford the opportunity to passively and objectively measure mobility, a key metric of recovery in spine surgery. However, app development is a resource-intensive process.

OBJECTIVE

To survey adult neurosurgery patients regarding access to and interest in this platform.

METHODS

In June and July 2017, a paper-based anonymous survey was distributed to patients in the waiting room of the adult neurosurgery clinic of a large US academic medical center. Patients’ smartphone use and interest in using a mobile app following spine surgery were the primary and secondary outcomes, respectively.

RESULTS

Of 146 included responses, 102 patients (70%) regularly used a smartphone, and this number increased to 77% among patients with a history of spine surgery (n = 66, 45% of respondents). Seventy-one percent of patients with previous spine surgery expressed an interest in using a postoperative monitoring and communication app, compared to 81% of patients without prior spine operations (n = 80, 55%).

CONCLUSION

Among neurosurgery patients, there is a high level of access to and interest in smartphone apps to aid postoperative recovery. These results are useful for other neurosurgeons considering mobile app development for this purpose.
Inequality and market concentration, when shareholding is more skewed than consumption
Authors: Gans Joshua , Leigh Andrew , Schmalz Martin , Triggs Adam
Published: April 2019

Economic theory suggests that monopoly prices hurt consumers but benefit shareholders. But in a world where individuals or households can be both consumers and shareholders, the impact of market power on inequality depends in part on the relative distribution of consumption and corporate equity ownership across individuals or households. The paper calculates this distribution for the United States, using data from the Survey of Consumer Finances and the Consumer Expenditure Survey, spanning nearly three decades from 1989 to 2016. In 2016, the top 20 per cent consumed approximately as much as the bottom 60 per cent, but had 15 times as much corporate equity. Because ownership is more skewed than consumption, increased mark-ups increase inequality. Moreover, over time, corporate equity has become even more skewed relative to consumption.
Cardiac tissue-derived extracellular matrix scaffolds for myocardial repair: advantages and challenges
Authors: KC Pawan , Hong Yi , Zhang Ge
Published: April 2019

Decellularized extracellular matrix (dECM) derived from myocardium has been widely explored as a nature scaffold for cardiac tissue engineering applications. Cardiac dECM offers many unique advantages such as preservation of organ-specific ECM microstructure and composition, demonstration of tissue-mimetic mechanical properties and retention of biochemical cues in favor of subsequent recellularization. However, current processes of dECM decellularization and recellularization still face many challenges including the need for balance between cell removal and extracellular matrix preservation, efficient recellularization of dECM for obtaining homogenous cell distribution, tailoring material properties of dECM for enhancing bioactivity and prevascularization of thick dECM. This review summarizes the recent progresses of using dECM scaffold for cardiac repair and discusses its major advantages and challenges for producing biomimetic cardiac patch.
What makes mucosal and anergic diffuse cutaneous leishmaniases so clinically and immunopathogically different? A review in Brazil
Authors: Silveira Fernando T
Published: April 2019

American cutaneous leishmaniasis (ACL) is a parasitic protozoan disease caused by different Leishmania species widely distributed throughout Latin America. Fifteen Leishmania species belonging to the subgenera Viannia, Leishmania and Mundinia are known to cause ACL. Seven of these species are found in Brazil, of which Leishmania (Viannia) braziliensis and Leishmania (Leishmania) amazonensis have the highest potential to cause mucosal (ML) and anergic diffuse cutaneous leishmaniasis (DCL), respectively, the most severe forms of ACL. The clinical and immunopathological differences between these two clinical forms are reviewed here, taking into account their different physiopathogenic mechanisms of dissemination from cutaneous lesions to mucosal tissues in the case of ML and to almost all body surfaces in the case of anergic DCL. We also discuss some immunopathogenic mechanisms of species-specific Leishmania antigens (from the subgenera Viannia and Leishmania) that are most likely associated with the clinical and immunopathological differences between ML and anergic DCL. Those discussions emphasize the pivotal importance of some surface antigens of L. (V.) braziliensis and L. (L.) amazonensis, such as lipophosphoglycan, phosphatidylserine and CD200 (an immunoregulatory molecule that inhibits macrophage activation), that have been shown to exert strong influences on the clinical and immunopathological differences between ML and anergic DCL.
High Contiguity Whole Genome Sequence and Gene Annotation Resource for Two Venturia nashicola Isolates
Authors: Prokchorchik Maxim , Won Kyungho , Lee Yoonyoung , Choi Eu Ddeum , Segonzac Cécile , Sohn Kee Hoon
Published: April 2019

Venturia nashicola is a fungal pathogen that causes Asian pear scab disease. This pathogen is of particular importance in Northeast Asian countries, where Asian pears are grown industrially. Scab disease in Asian pear is currently controlled by fungicide spraying and this situation calls for developing scab resistant cultivars. High-quality genome data are therefore required for in-depth comparative genome analysis of different isolates of V. nashicola and V. pyrina, a closely related species, which only infects European pear plants. Here, we report the high-contiguity whole genome assembly of two V. nashicola isolates, which is expected to enable genome comparisons for identification of the genes involved in host range determination of V. nashicola.
Sources of Inoculum and Survival of Macrophomina phaseolina in Florida Strawberry Fields
Authors: Baggio Juliana S. , Cordova Leandro G. , Peres Natalia A.
Published: April 2019

Macrophomina phaseolina, the causal agent of charcoal rot, affects strawberry crowns, inducing plant collapse. The fungus survives in the soil through the production of microsclerotia and is usually controlled by preplant fumigation of soil. However, in the 2016 to 2017 Florida strawberry season, even after soil fumigation, about 30% plant mortality still occurred in plastic-covered beds that were used for a second season and where crop residue (mainly old strawberry crowns) was disposed of between beds. Therefore, this study was conducted to determine if M. phaseolina can survive on strawberry debris over summer in Florida and if so, verify whether strawberry debris might act as a source of inoculum for new transplants. Crowns from the previous season were collected from commercial farms where charcoal rot had been reported, and M. phaseolina was recovered from all samples. In a research field, infected crowns were buried in the soil at different depths and retrieved every 2 weeks during the summer. After 8 weeks, M. phaseolina could be recovered at all depths. Moreover, inoculation of strawberry plants by drenching the soil, dipping roots, or spraying leaves with a M. phaseolina microsclerotial suspension from pure cultures or infected crowns produced symptoms with differences in incubation periods depending on cultivar susceptibility. Furthermore, infected crowns disposed of in the aisles between beds or buried next to new transplants of cultivars Strawberry Festival, Florida Beauty, and Winterstar induced charcoal rot, with the level of aggressiveness depending on the cultivar susceptibility and inoculum placement in the field.
A Statewide Curriculum Model for Teaching Simulation Education Leaders
Authors: Beroz Sabrina , Schneidereith Tonya , Farina Crystel L. , Daniels Amy , Dawson Lauren , Watties-Daniels Denyce , Sullivan Nancy
Published: April 2019

Background

The Maryland Clinical Simulation Resource Consortium (MCSRC) was funded to increase the quality and quantity of simulation used in nursing education.

Problem

Schools of nursing are substituting simulation for clinical experience without requisite knowledge of simulation pedagogy.

Approach

The MCSRC developed a statewide curriculum model for a 3-day train-the-trainer program framed in theory and grounded in evidence. The program teaches nurse educators across 3 levels: novice, competent, and expert.

Outcomes

The evaluation plan was developed using Kirkpatrick's 4 levels to measure outcomes of the program. Self-confidence, satisfaction, knowledge, and behavioral changes have been realized. Nurse educators are now using theory, standards, and guidelines when conducting simulation-based experiences.

Conclusions

The curriculum model has proved effective in increasing the quality and quantity of simulation used in educating Maryland's nurses. To date, 154 nurse educators have participated in the train-the-trainer program.
Academic Activities Abroad
Authors: Lasater Kathie
Published: April 2019

Background

Nursing students need an understanding of global health concepts in the 21st century. Patients and/or populations may come from anywhere in the world, some of whom may be seeking refuge from conflict and/or war. In addition, nurses may be employed in other countries.

Problem

Nurse educators may not have international experiences or know about global opportunities or how to navigate them.

Approach

Fulbright Scholar Awards are one way for nursing educators to experience academic opportunities in another country, working with international colleagues and/or students.

Outcomes

One nurse educator describes her experience from successful application through the postaward period.

Conclusions

Fulbright offers opportunities for academics to engage in teaching and/or research, work with international colleagues, and be immersed in other cultures. Such experiences can equip nurse educators with more comprehensive global perspectives for preparing future nurses.
Development of a New Measure to Assess Primary Palliative Care Perceived Competence
Authors: Lippe Megan , Davis Andra , Threadgill Hunter , Ricamato Allison
Published: April 2019

Background

Many nursing schools have begun to address the gap in palliative care education. Recently released entry-to-practice competencies in palliative care can guide educators as they incorporate such material into their curriculum. In an effort to evaluate learning, educators need a reliable instrument that aligns with the updated competencies.

Purpose

This article describes the development of a new instrument to evaluate perceived competence to provide primary palliative care.

Methods

The psychometric properties and performance of the new instrument in evaluating perceived competence were tested via an interprofessional palliative care simulation with medical, nursing, and social work students. Perceived competence was measured before and after the simulation.

Results

The new instrument demonstrates strong reliability and validity, represents a unidimensional construct, and captures changes in perceived competence across time and disciplines.

Conclusions

The new instrument is acceptable for assessing perceived competence to provide palliative care, particularly for nursing students.
The Cognitive Lens: a primer on conceptual tools for analysing information processing in developmental and regenerative morphogenesis
Authors: Manicka Santosh , Levin Michael
Published: April 2019

Brains exhibit plasticity, multi-scale integration of information, computation and memory, having evolved by specialization of non-neural cells that already possessed many of the same molecular components and functions. The emerging field of basal cognition provides many examples of decision-making throughout a wide range of non-neural systems. How can biological information processing across scales of size and complexity be quantitatively characterized and exploited in biomedical settings? We use pattern regulation as a context in which to introduce the Cognitive Lens—a strategy using well-established concepts from cognitive and computer science to complement mechanistic investigation in biology. To facilitate the assimilation and application of these approaches across biology, we review tools from various quantitative disciplines, including dynamical systems, information theory and least-action principles. We propose that these tools can be extended beyond neural settings to predict and control systems-level outcomes, and to understand biological patterning as a form of primitive cognition. We hypothesize that a cognitive-level information-processing view of the functions of living systems can complement reductive perspectives, improving efficient top-down control of organism-level outcomes. Exploration of the deep parallels across diverse quantitative paradigms will drive integrative advances in evolutionary biology, regenerative medicine, synthetic bioengineering, cognitive neuroscience and artificial intelligence.

This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.
Plant behaviour in response to the environment: information processing in the solid state
Authors: Duran-Nebreda Salva , Bassel George W.
Published: April 2019

Information processing and storage underpins many biological processes of vital importance to organism survival. Like animals, plants also acquire, store and process environmental information relevant to their fitness, and this is particularly evident in their decision-making. The control of plant organ growth and timing of their developmental transitions are carefully orchestrated by the collective action of many connected computing agents, the cells, in what could be addressed as distributed computation. Here, we discuss some examples of biological information processing in plants, with special interest in the connection to formal computational models drawn from theoretical frameworks. Research into biological processes with a computational perspective may yield new insights and provide a general framework for information processing across different substrates.

This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.
Homeostasis as a fundamental principle for a coherent theory of brains
Authors: Turner J. Scott
Published: April 2019

‘Brains’ may be considered to be computation engines, with neurons and synapses analogized to electronic components wired into networks that process information, learn and evolve. Alternatively, ‘brains’ are cognitive systems, which contain elements of intentionality, purposefulness and creativity that do not fit comfortably into a brain-as-computer metaphor. I address the question of how we may think most constructively about brains in their various forms—solid, liquid or fluid—and whether there is a coherent theory that unites them all. In this essay, I explore cognitive systems in the context of new understanding of life's distinctive nature, in particular the core concept of homeostasis, and how this new understanding lays a sound conceptual foundation for an expansive theory of brains.

This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information'.
How does mobility help distributed systems compute?
Authors: Vining William F. , Esponda Fernando , Moses Melanie E. , Forrest Stephanie
Published: April 2019

Brains are composed of connected neurons that compute by transmitting signals. The neurons are generally fixed in space, but the communication patterns that enable information processing change rapidly. By contrast, other biological systems, such as ant colonies, bacterial colonies, slime moulds and immune systems, process information using agents that communicate locally while moving through physical space. We refer to systems in which agents are strongly connected and immobile assolid, and to systems in which agents are not hardwired to each other and can move freely asliquid. We ask how collective computation depends on agent movement. A liquid cellular automaton (LCA) demonstrates the effect of movement and communication locality on consensus problems. A simple mathematical model predicts how these properties of the LCA affect how quickly information propagates through the system. While solid brains allow complex network structures to move information over long distances, mobility provides an alternative way for agents to transport information when long-range connectivity is expensive or infeasible. Our results show how simple mobile agents solve global information processing tasks more effectively than similar systems that are stationary.

This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.
Evolutionary aspects of reservoir computing
Authors: Seoane Luís F.
Published: April 2019

Reservoir computing (RC) is a powerful computational paradigm that allows high versatility with cheap learning. While other artificial intelligence approaches need exhaustive resources to specify their inner workings, RC is based on a reservoir with highly nonlinear dynamics that does not require a fine tuning of its parts. These dynamics project input signals into high-dimensional spaces, where training linear readouts to extract input features is vastly simplified. Thus, inexpensive learning provides very powerful tools for decision-making, controlling dynamical systems, classification, etc. RC also facilitates solving multiple tasks in parallel, resulting in a high throughput. Existing literature focuses on applications in artificial intelligence and neuroscience. We review this literature from an evolutionary perspective. RC’s versatility makes it a great candidate to solve outstanding problems in biology, which raises relevant questions. Is RC as abundant in nature as its advantages should imply? Has it evolved? Once evolved, can it be easily sustained? Under what circumstances? (In other words, is RC an evolutionarily stable computing paradigm?) To tackle these issues, we introduce a conceptual morphospace that would map computational selective pressures that could select for or against RC and other computing paradigms. This guides a speculative discussion about the questions above and allows us to propose a solid research line that brings together computation and evolution with RC as test model of the proposed hypotheses.

This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.
Metabolic basis of brain-like electrical signalling in bacterial communities
Authors: Martinez-Corral Rosa , Liu Jintao , Prindle Arthur , Süel Gürol M. , Garcia-Ojalvo Jordi
Published: April 2019

Information processing in the mammalian brain relies on a careful regulation of the membrane potential dynamics of its constituent neurons, which propagates across the neuronal tissue via electrical signalling. We recently reported the existence of electrical signalling in a much simpler organism, the bacterium
Bacillus subtilis
. In dense bacterial communities known as biofilms, nutrient-deprived
B. subtilis
cells in the interior of the colony use electrical communication to transmit stress signals to the periphery, which interfere with the growth of peripheral cells and reduce nutrient consumption, thereby relieving stress from the interior. Here, we explicitly address the interplay between metabolism and electrophysiology in bacterial biofilms, by introducing a spatially extended mathematical model that combines the metabolic and electrical components of the phenomenon in a discretized reaction–diffusion scheme. The model is experimentally validated by environmental and genetic perturbations, and confirms that metabolic stress is transmitted through the bacterial population via a potassium wave. Interestingly, this behaviour is reminiscent of cortical spreading depression in the brain, characterized by a wave of electrical activity mediated by potassium diffusion that has been linked to various neurological disorders, calling for future studies on the evolutionary link between the two phenomena.

This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.
Liquid brains, solid brains
Authors: Solé Ricard , Moses Melanie , Forrest Stephanie
Published: April 2019

Cognitive networks have evolved a broad range of solutions to the problem of gathering, storing and responding to information. Some of these networks are describable as static sets of neurons linked in an adaptive web of connections. These are ‘solid’ networks, with a well-defined and physically persistent architecture. Other systems are formed by sets of agents that exchange, store and process information but without persistent connections or move relative to each other in physical space. We refer to these networks that lack stable connections and static elements as ‘liquid’ brains, a category that includes ant and termite colonies, immune systems and some microbiomes and slime moulds. What are the key differences between solid and liquid brains, particularly in their cognitive potential, ability to solve particular problems and environments, and information-processing strategies? To answer this question requires a new, integrative framework.

This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.
Modeling of Yield Losses and Risk Analysis of Fungicide Profitability for Managing Fusarium Head Blight in Brazilian Spring Wheat
Authors: Rodrigues Duffeck Maíra , dos Santos Alves Kaique , Jackson Machado Franklin , David Esker Paul , Medeiros Del Ponte Emerson
Published: April 2019

Fusarium head blight (FHB), caused by theFusarium graminearumspecies complex, is a serious disease of wheat in Brazil. A review of literature on fungicide efficacy for field trials evaluated in Brazil was conducted to obtain FHB-yield data and explore their relationship. Thirty-seven studies (9 years and 11 locations) met the criteria for inclusion (FHB index ≥ 5% and max-min range ≥ 4 percent points [p.p.]). Studies were group into two production situations: low (Yl≤ 3,631 kg ha−1) or high (Yh> 3,631 kg ha−1) yield, based on the median of maximum yields across trials. Population-average intercepts, but not the slopes, from fitting a random-coefficients model, differed significantly betweenYl(2,883.6 kg ha−1) andYh(4,419.5 kg ha−1). The calculated damage coefficient was 1.05 %−1and 1.60 %−1forYhandYl, respectively. A crop model simulated attainable wheat yields for 10 planting dates within each year during a 28-year period, including prior (1980-1989) and after (1990-2007) FHB resurgence. Simulated losses using disease predictions to penalize yield were in general agreement in magnitude with literature reports, for both periods. Economic analysis for scenarios of variable fungicide costs and wheat prices, and one versus two sprays of tebuconazole, showed that the probability of not-offsetting the costs was higher (> 0.75) prior to FHB resurgence than after the 1990. Our approach may be useful for designing of longlasting, yet profitable, contingency tactics to management FHB in wheat. Currently one spray of triazole fungicide during flowering is more likely a profitable decision than applying two sprays, for which there is greater uncertainty.
Advantages of Multi-shell Diffusion for Studies of Brain Development in Youth
Authors: Pines Adam R. , Cieslak Matthew , Baum Graham L. , Cook Philip A. , Adebimpe Azeez , Dávila Diego G. , Elliott Mark A. , Jirsaraie Robert , Murtha Kristin , Oathes Desmond J. , Piiwaa Kayla , Rosen Adon F. G. , Rush Sage , Shinohara Russell T. , Bassett Danielle S. , Roalf David R. , Satterthwaite Theodore D.
Published: April 2019

Diffusion tensor imaging (DTI) has advanced our understanding of how brain microstructure evolves over development. However, the proliferation of multi-shell diffusion imaging sequences has coincided with notable advances in the modeling of neuronal diffusion patterns, such as Neurite Orientation Dispersion and Density Imaging (NODDI) and Laplacian-regularized Mean Apparent Propagator MRI (MAPL). The relative utility of these newer diffusion models for understanding brain maturation remains sparsely investigated. Additionally, despite evidence that motion artifact is a major confound for studies of development, the relative vulnerability of these models to in-scanner motion has not been described. Accordingly, in a sample of 123 youth (ages 12-30) we evaluated DTI, NODDI, and MAPL for associations with age and in-scanner head motion at multiple scales, including mean white matter values, voxelwise analyses, and tractography-based structural brain networks. Our results reveal that multi-shell diffusion imaging sequences can be leveraged to robustly characterize neurodevelopment, even within the framework of DTI. However, these metrics of diffusion are variably impacted by motion, highlighting the importance of modeling choices for studies of movement-prone populations. Our findings suggest that while traditional DTI is sensitive to neurodevelopmental trends, contemporary modeling techniques confer key advantages for neurodevelopmental inquiries.
Regulation of HMGB2 integrates ribosome biogenesis and innate immune responses to DNA
Authors: Bianco Christopher , Mohr Ian
Published: April 2019

Ribosomes are universally important in biology and their production is dysregulated by developmental disorders, cancer, and virus infection. Although presumed required for protein synthesis, how ribosome biogenesis impacts virus reproduction and cell-intrinsic immune responses remains untested. Surprisingly, we find that restricting ribosome biogenesis stimulated human cytomegalovirus (HCMV) replication without suppressing translation. Interfering with ribosomal RNA (rRNA) accumulation triggered nucleolar stress and repressed expression of High Mobility Group Box 2 (HMGB2), a chromatin-associated protein that facilitates cytoplasmic double-stranded (ds) DNA-sensing by cGAS. Furthermore, it reduced cytoplasmic HMGB2 abundance and impaired induction of interferon beta (IFNB1) mRNA, which encodes a critical anti-proliferative, proinflammatory cytokine, in response to HCMV or dsDNA in uninfected cells. This establishes that rRNA accumulation regulates innate immune responses to dsDNA by controlling HMGB2 abundance. Moreover, it reveals that rRNA accumulation and/or nucleolar activity unexpectedly regulate dsDNA-sensing to restrict virus reproduction and regulate inflammation.
Can immunosuppressed mice control oral infection by the opportunistic pathogenEncephalitozoon intestinalis?
Authors: da Costa Moura Maria Lucia , Alvares-Saraiva Anuska Marcelino , Pérez Elizabeth Cristina , Xavier José Guilherme , Spadacci-Morena Diva Denelle , Moysés Carla Renata Serantoni , Dell’Armelina Rocha Paulo Ricardo , Lallo Maria Anete
Published: April 2019

Intestinal mucosa (IM), or the outer surface of the intestine, serves at the primary site for the interaction of various pathogens that cause infection via the oral route. Thus, IM is crucial for developing an efficient adaptive immune response against pathogenic micro-organisms, thereby preventing their colonization and subsequent infection. In the present study, we investigated the immune response toEncephalitozoon intestinalis-caused infection in the IM and gut-associated lymphoid tissue (GALT) in C57BL/6 female mice. To mimic an immunosuppressive condition, the mice were treated with cyclophosphamide (Cy). Histopathology revealed lymphoplasmacytic enteritis at 7 and 14 days-post-infection (dpi) in all infected groups; however, inflammation diminished at 21 and 28 dpi. Cy treatment also led to a higher number ofE. intestinalisspores and lesions, which reduced at 28 dpi. In addition, flow cytometry analysis demonstrated CD4+and CD8+T cells to be predominant immune cells, with a significant increase in both Th1 and Th2 cytokines at 7 and 14 dpi, as demonstrated by histopathology. In conclusion, Cy treatment reduced GALT (Peyer’s plaques and mesenteric lymph nodes) and peritoneum populations but increased the T-cell population in the intestinal mucosa and the production of pro-inflammatory cytokines, which were able to eliminate this opportunistic fungus and reduced the infection.
Retinal and callosal activity-dependent chandelier cell elimination shapes binocularity in primary visual cortex
Authors: Wang Bor-Shuen , Bernardez Sarria Maria Sol , He Miao , Crair Michael C , Huang Z. Josh
Published: April 2019

In mammalian primary visual cortex (V1), integration of the left and right visual scene into a binocular percept derives from convergent ipsi- and contralateral geniculocortical inputs and trans-callosal projections between the two hemispheres. However, the underlying developmental mechanisms remain incompletely understood. Using genetic methods in mice we found that during the days before eye-opening, retinal and callosal activity drives massive apoptosis of GABAergic chandelier cells (ChCs) in the binocular region of V1. Blockade of ChC elimination resulted in a contralateral-dominated V1 and deficient binocular vision. As activity patterns within and between retinas prior to vision convey organization of the visual field, their regulation of ChC density through the trans-callosal pathway may prime a nascent binocular territory for subsequent experience-driven tuning during the post-vision critical period.

One Sentence Summary

Prior to eye opening the developing retina primes the visual cortex for binocular vision by adjusting the density of a cortical inhibitory neuron type.
Vicarious reward unblocks associative learning about novel cues in male rats
Authors: van Gurp Sander , Hoog Jochen , Kalenscher Tobias , van Wingerden Marijn
Published: April 2019

Many species, including humans, are sensitive to social signals and their valuation is important in social learning. When social cues indicate that another is experiencing reward, they could convey vicarious reward value and prompt social learning. Here, we introduce a task that investigates if vicarious reward delivery in male rats can drive reinforcement learning in a formal associative learning paradigm. Using the blocking/unblocking paradigm, we found that when actor rats have fully learned a stimulus-self reward association, adding a cue that predicted additional partner reward unblocked associative learning about this cue. In contrast, additional cues that did not predict partner reward remained blocked from acquiring associative value. Preventing social signal exchange between the partners resulted in cues signaling partner reward remaining blocked. Taken together, these results suggest that vicarious rewards can drive reinforcement learning in rats, and that the transmission of social cues is necessary for this learning to occur.
Integration of a Computational Pipeline for Dynamic Inference of Gene Regulatory Networks in Single Cells
Authors: Ko Kyung Dae , Dell’Orso Stefania , Juan Aster H. , Sartorelli Vittorio
Published: April 2019

Single-cell RNA-seq permits the characterization of the molecular expression states of individual cells. Several methods have been developed to spatially and temporally resolve individual cell populations. However, these methods are not always integrated and some of them are constrained by prior knowledge. Here, we present an integrated pipeline for inference of gene regulatory networks. The pipeline does not rely on prior knowledge, it improves inference accuracy by integrating signatures from different data dimensions and facilitates tracing variation of gene expression by visualizing gene-interacting patterns of co-expressed gene regulatory networks at distinct developmental stages.
Dynamic response in the larval geoduck clam proteome to elevated pCO2
Authors: Timmins-Schiffman Emma , Guzmán José M. , Elliott Rhonda , Vadopalas Brent , Roberts Steven B.
Published: April 2019

Pacific geoduck clams (Panopea generosa) are found along the Northeast Pacific coast where they are significant components of coastal and estuarine ecosystems and the basis of a growing and highly profitable aquaculture industry. The Pacific coastline, however, is also the sight of rapidly changing ocean habitat, including significant reductions in pH. The impacts of ocean acidification on invertebrate bivalve larvae have been widely documented and it is well established that many species experience growth and developmental deficiencies when exposed to low pH. As a native of environments that have historically lower pH than the open ocean, it is possible that geoduck larvae are less impacted by these effects than other species. Over two weeks in larval development (days 6-19 post-fertilization) geoduck larvae were reared at pH 7.5 or 7.1 in a commercial shellfish hatchery. Larvae were sampled at six time points throughout the period for a in-depth proteomics analysis of developmental molecular physiology. Larvae reared at low pH were smaller than those reared at ambient pH, especially in the prodissoconch II phase of development. Competency for settlement was also delayed in larvae from the low pH conditions. A comparison of proteomic profiles over the course of development reveal that these differing phenotypic outcomes are likely due to environmental disruptions to the timing of molecular physiological events as suites of proteins showed differing profiles of abundance between the two pH environments. Ocean acidification likely caused an energetic stress on the larvae at pH 7.1, causing a shift in physiological prioritization with resulting loss of fitness.
Neural Selectivity, Efficiency, and Dose Equivalence in Deep Brain Stimulation through Pulse Width Tuning and Segmented Electrodes
Authors: Anderson Collin J. , Anderson Daria Nesterovich , Pulst Stefan M. , Butson Christopher R. , Dorval Alan D.
Published: April 2019

Background

Achieving deep brain stimulation (DBS) dose equivalence is challenging, especially with pulse width tuning and directional contacts. Further, the precise effects of pulse width tuning are unknown.

Methods

We created multicompartment neuron models for two axon diameters and used finite element modeling to determine extracellular influence from standard and segmented electrodes. We analyzed axon activation profiles and calculated volumes of tissue activated.

Results

Long pulse widths focus the stimulation effect on small, nearby fibers, suppressing white matter tract activation (responsible for some DBS side effects) and improving battery utilization. Directional leads enable similar benefits to a greater degree. We derive equations for equivalent activation with pulse width tuning and segmented contacts.

Interpretations

We find agreement with classic studies and reinterpret recent articles concluding that short pulse widths focus the stimulation effect on small, nearby fibers, decrease side effects, and improve power consumption. Our field should reconsider shortened pulse widths.
Individual structural features constrain the mouse functional connectome
Authors: Melozzi Francesca , Bergmann Eyal , Harris Julie A. , Kahn Itamar , Jirsa Viktor , Bernard Christophe
Published: April 2019

Whole brain dynamics intuitively depends upon the internal wiring of the brain; but to which extent the individual structural connectome constrains the corresponding functional connectome is unknown, even though its importance is uncontested. After acquiring structural data from individual mice, we virtualized their brain networks and simulatedin silicofunctional MRI data. Theoretical results were validated against empirical awake functional MRI data obtained from the same mice. We demonstrate that individual structural connectomes predict the functional organization of individual brains. Using a virtual mouse brain derived from the Allen Mouse Brain Connectivity Atlas, we further show that the dominant predictors of individual structure-function relations are the asymmetry and the weights of the structural links. Model predictions were validated experimentally using tracer injections, identifying which missing connections (not measurable with diffusion MRI) are important for whole brain dynamics in the mouse. Individual variations thus define a specific structural fingerprint with direct impact upon the functional organization of individual brains, a key feature for personalized medicine.

SIGNIFICANCE STATEMENT

The structural connectome is a key determinant of brain function and dysfunction. The connectome-based model approach aims to understand the functional organization of the brain by modeling the brain as a dynamical system and then studying how the functional architecture rises from the underlying structural skeleton. Here, taking advantage of mice studies, we systematically investigated the informative content of different structural features in explaining the emergence of the functional ones. We demonstrate that individual variations define a specific structural fingerprint with a direct impact upon the functional organization of individual brains stressing the importance of using individualized models to understand brain function. We show how limitations of connectome reconstruction with the diffusion-MRI method restrict our comprehension of the structural-functional relation.
Conformational Heterogeneity in Human Interphase Chromosome Organization Reconciles the FISH and Hi-C Paradox
Authors: Shi Guang , Thirumalai D.
Published: April 2019

Hi-C experiments are used to infer the contact probabilities between loci separated by varying genome lengths. Contact probability should decrease as the spatial distance between two loci increases. However, studies comparing Hi-C and FISH data show that in some cases the distance between one pair of loci, with larger Hi-C readout, is paradoxically larger compared to another pair with a smaller value of the contact probability. Here, we show that the FISH-Hi-C paradox can be resolved using a theory based on a Generalized Rouse Model for Chromosomes (GRMC). The FISH-Hi-C paradox arises because the cell population is highly heterogeneous, which means that a given contact is present in only a fraction of cells. Insights from the GRMC is used to construct a theory, without any adjustable parameters, to extract the distribution of subpopulations from the FISH data, which quantitatively reproduces the Hi-C data. Our results show that heterogeneity is pervasive in genome organization at all length scales, reflecting large cell-to-cell variations.
Fusarium verticillioides SNARE protein FvSyn1 harbors two key functional motifs that play selective roles in fungal development and virulence
Authors: Zhang Huan , Yan Huijuan , Shim Won Bo
Published: April 2019

Fusarium verticillioides is one of the key fungal pathogens responsible for maize stalk rots. While stalk rot pathogens are prevalent worldwide, our understanding of stalk rot virulence mechanism in pathogenic fungi is still very limited. We previously identified F. verticillioides FvSYN1 gene, which was demonstrated to plays an important role in maize stalk rot virulence. FvSyn1 belongs to a family of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins that play critical roles in a variety of developmental processes. In this study, we further characterized the cellular features of FvSyn1 protein motifs in F. verticillioides development and virulence. We generated FvSyn1 motif-specific deletion mutants to further investigate how different motifs contribute to development and virulence. Microscopic observation showed that Δfvsyn1 mutant exhibits rough and hyper-branched hyphae when compared to the wild type progenitor. Moreover, Δfvsyn1 mutant was sensitive to cell wall stress agents resulting in vegetative growth reduction. We showed that FvSyn1::GFP protein is associated with endomembrane but this outcome did not clarify why the deletion of this protein led to stress sensitivity and aberrant hyphal development. Characterization of FvSyn1 domains indicated that both Syntaxin N-terminus (SynN) domain and SNARE C-terminus domain play distinct roles in fungal development but collectively function in virulence. We also determined that two domains in FvSyn1 is not required for fumonisin production. Interestingly, these two domains were involved in carbon nutrient utilization including pectin, starch and sorbitol. This study further characterized the role of FvSyn1 in hyphal growth, localization, cell wall stress response and virulence in F. verticillioides.

Highlights

► F. verticillioides SNARE protein FvSYN1 is important for vegetative growth and virulence.

► FvSYN1 deletion mutant performed better under cell wall stressors.

► Dissecting of two domains and investigate the roles.
Stacks 2: Analytical Methods for Paired-end Sequencing Improve RADseq-based Population Genomics
Authors: Rochette Nicolas C. , Rivera-Colón Angel G. , Catchen Julian M.
Published: April 2019

For half a century population genetics studies have put type II restriction endonucleases to work. Now, coupled with massively-parallel, short-read sequencing, the family of RAD protocols that wields these enzymes has generated vast genetic knowledge from the natural world. Here we describe the first software capable of using paired-end sequencing to derive short contigs from de novo RAD data natively. Stacks version 2 employs a de Bruijn graph assembler to build contigs from paired-end reads and overlap those contigs with the corresponding single-end loci. The new architecture allows all the individuals in a meta population to be considered at the same time as each RAD locus is processed. This enables a Bayesian genotype caller to provide precise SNPs, and a robust algorithm to phase those SNPs into long haplotypes – generating RAD loci that are 400-800bp in length. To prove its recall and precision, we test the software with simulated data and compare reference-aligned and de novo analyses of three empirical datasets. We show that the latest version of Stacks is highly accurate and outperforms other software in assembling and genotyping paired-end de novo datasets.
Contrasting effects of host species and phylogenetic diversity on the occurrence of HPAI H5N1 in European wild birds
Authors: Huang Zheng Y. X. , Xu Chi , van Langevelde Frank , Ma Yuying , Langendoen Tom , Mundkur Taej , Si Yali , Tian Huaiyu , Kraus Robert H. S. , Gilbert Marius , Han Guan‐Zhu , Ji Xiang , Prins Herbert H. T. , de Boer Willem F.
Published: April 2019

Studies on the highly pathogenic avian influenza (HPAI) H5N1 suggest that wild bird migration may facilitate its long‐distance spread, yet the role of wild bird community composition in its transmission risk remains poorly understood. Furthermore, most studies on the diversity–disease relationship focused on host species diversity without considering hosts’ phylogenetic relationships, which may lead to rejecting a species diversity effect when the community has host species that are only distantly related.

Here, we explored the influence of waterbird community composition for determining HPAI H5N1 occurrence in wild birds in a continental‐scale study across Europe. In particular, we tested the diversity–disease relationship using both host species diversity and host phylogenetic diversity.

Our results provide the first demonstration that host community composition—compared with previously identified environmental risk factors—can also effectively explain the spatial pattern of H5N1 occurrence in wild birds. We further show that communities with more higher risk host species and more closely related species have a higher risk of H5N1 outbreaks. Thus, both host species diversity and community phylogenetic structure, in addition to environmental factors, jointly influence H5N1 occurrence.

Our work not only extends the current theory on the diversity–disease relationship, but also has important implications for future monitoring of H5N1 and other HPAI subtypes.
Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology
Authors: Nissimov Jozef I. , Talmy David , Haramaty Liti , Fredricks Helen F. , Zelzion Ehud , Knowles Ben , Eren A. Murat , Vandzura Rebecca , Laber Christien P. , Schieler Brittany M. , Johns Christopher T. , More Kuldeep D. , Coolen Marco J. L. , Follows Michael J. , Bhattacharya Debashish , Van Mooy Benjamin A. S. , Bidle Kay D.
Published: April 2019

Coccolithoviruses (EhVs) are large, double‐stranded DNA‐containing viruses that infect the single‐celled, marine coccolithophore Emiliania huxleyi. Given the cosmopolitan nature and global importance of E. huxleyi as a bloom‐forming, calcifying, photoautotroph, E. huxleyi–EhV interactions play a key role in oceanic carbon biogeochemistry. Virally‐encoded glycosphingolipids (vGSLs) are virulence factors that are produced by the activity of virus‐encoded serine palmitoyltransferase (SPT). Here, we characterize the dynamics, diversity and catalytic production of vGSLs in an array of EhV strains in relation to their SPT sequence composition and explore the hypothesis that they are a determinant of infectivity and host demise. vGSL production and diversity was positively correlated with increased virulence, virus replication rate and lytic infection dynamics in laboratory experiments, but they do not explain the success of less‐virulent EhVs in natural EhV communities. The majority of EhV‐derived SPT amplicon sequences associated with infected cells in the North Atlantic derived from slower infecting, less virulent EhVs. Our lab‐, field‐ and mathematical model‐based data and simulations support ecological scenarios whereby slow‐infecting, less‐virulent EhVs successfully compete in North Atlantic populations of E. huxleyi, through either the preferential removal of fast‐infecting, virulent EhVs during active infection or by having access to a broader host range.
Perspectives of Central and Eastern European Countries on Research and Innovation in the New CAP
Authors: Pokrivčák Ján , Ciaian Pavel , Drabik Dušan
Published: April 2019

The Commission's proposals on the Common Agricultural Policy (CAP) post‐2020 made the Research‐Innovation‐Advice nexus a key priority with the aim of promoting sustainable growth in agricultural productivity and rural development. The proposal allocates €10 billion for this priority through the EU's Horizon Europe research programme, and it envisages strengthening the Agricultural Knowledge and Innovation Systems as well as knowledge exchange through the European Innovation Partnership. We argue that despite the evident productivity gaps between farms in the EU Member States from Central and Eastern Europe (EU‐CEE) and the EU‐15, greater support for research and innovation is not a priority for EU‐CEE countries because of structural differences in their agricultural sectors as well as a comparative disadvantage in research and innovation relative to more developed countries of the EU‐15. Other policy priorities for the future CAP – such as increasing the size of the CAP budget, which represents €365 billion in the post‐2020 financial period, external convergence, and capping of direct payments – relegate support for research and innovation to a secondary priority in the EU‐CEE. This position of the EU‐CEE might not only affect the final agreement on the CAP but also its actual implementation.