bluuebunny/crossref_metadata_2025 huggingface dataset:
Circumventing Water Scarcity in the Jordan Basin
Authors: Gilmont Michael , Nassar Lara , Harper Erica , Tal Nadav , Rayner Steve
Published: January 2020

This chapter examines trends in water resources used in Jordan and Israel. Specifically it illustrates how these two economies have circumvented significant limits in their natural freshwater resource endowment to enable continued economic and population growth despite static or declining water availability. Using the concept of resource decoupling, it identifies four specific mechanisms by which economies can decouple their water needs from water availability, including economic diversification, food imports, agricultural water productivity, and nonconventional water resource development. Each of these mechanisms are illustrated for the two countries, including technical and political processes shaping their adoption. The chapter also critiques existing conceptualizations of decoupling relative to the water-specific model, highlighting the importance of understanding the unique characteristics of scarcity, flows, and substitutability of water at a global scale. Finally the chapter nests decoupling within the market modes framing this volume, before evaluating the risks and trade-offs inherent in decoupling strategies.
Managing Water for Food and Agricultural Transformation in Africa
Authors: Williams Timothy O.
Published: January 2020

This chapter examines the links between water, food and society in Africa. Agricultural transformation to promote growth, eliminate poverty and hunger and sustain ecosystems is one of the central pillars of current development agenda in Africa. Achievement of this agenda will crucially depend on sustainable water management. However, agri-food systems and water resources are under greater pressure than ever before due to demographic, economic and climatic changes. The nature and scale of these changes suggest that only a holistic and integrated management of all shades of water resources, green, blue and grey, will allow Africa to eliminate hunger and poverty. Research-based technical solutions as well as institutional and policy measures are proposed that would allow available water resources to be sustainably used to promote climate-resilient farming systems, improve agricultural productivity and food security and spur the development of viable food value chains needed for agricultural and rural transformation.
Food, Water and the Consequences of Society Not Valuing the Environment
Authors: Allan Tony
Published: January 2020

The first purpose of this chapter is to highlight the impact of the food system on environmental and human health. The delivery of secure affordable food is a political imperative. Unfortunately, the food system that delivers it is environmentally blind. Food prices do not effectively reflect the value of food and often seriously mislead on the costs and impacts of food production. For example, actual food production takes place in a failed market—the value of environmental services such as water and the supporting ecosystems are not taken into account. The second purpose is to summarize and expose the political economy of the different ‘market’ modes of the food system. It is shown that there are weak players such as underrewarded and undervalued farmers who support society by producing food and stewarding our unvalued environment. The inadequacies of accounting systems are also critiqued.
Integrating Multi-Capital Thinking into Business Decisions
Authors: Banerjee Jyoti
Published: January 2020

The global business system has had deep and problematic impacts on humankind through its focus on maximizing the short-term return on financial capital. The most severe impacts are human-induced climate change, biodiversity loss and grotesque inequality between the rich and poor. A group of companies and investors have co-created a broader model, called integrated reporting, that explores how companies create and destroy value for multiple stakeholders in the short, medium and long term. It provides a better understanding of how corporations use the other capitals, such as natural, human and social capitals, in their working. The underlying structural issues affecting the global business system—such as shareholder primacy and the responsibility of business to its stakeholders—mean that changes in reporting need to be backed up by substantive change elsewhere in the system. This article considers case studies and the development of multi-capital thinking.
The Neuroscientific Study of Music: A Burgeoning Discipline
Authors: Hodges Donald A. , Thaut Michael H.
Published: January 2020

Numerous pioneers laid the groundwork for current neuromusical research. Beginning with Franz Joseph Gall in the eighteenth century, and continuing with John Hughlings Jackson, August Knoblauch, Richard Wallaschek, and others, these early forerunners were interested in localizing musicality in the brain and learning more about how music is processed in both healthy individuals and those with dysfunctions of various kinds. Since then, research literature has mushroomed, especially in the latter part of the twentieth and early twenty-first centuries. The current volume features the work of fifty-four authors who have contributed over 350,000 words in thirty-three chapters. These chapters are organized into sections on music, the brain, and cultural contexts; music processing in the human brain; neural responses to music; musicianship and brain function; developmental issues in music and the brain; music, the brain, and health; and the future.
Music and Memory
Authors: Jäncke Lutz
Published: January 2020

Music is encoded and stored in different memory systems. These memory systems overlap with “classical” non-musical memory systems to a large extent. However, there are also some specific features that are associated with music memory. This chapter describes the memory processes and their neural underpinnings which are involved during music listening and remembering of music. One specific feature of music memory is that music encoding, storing, and retrieval are associated with neurophysiological activations controlled by a widely distributed network, indicating that lots of information is activated by the musical content. This distributed network activation could be the key to understanding the often reported and suggested beneficial influences of music on non-music memory information.
Neural Correlates of Music and Emotion
Authors: Juslin Patrik N. , Sakka Laura S.
Published: January 2020

This chapter presents a theoretical and empirical review of studies of the neural correlates of emotional responses to music. First, it outlines basic definitions and distinctions of the field of music and affect. Second, it describes an extensive theoretical framework that may serve to organize the domain. Third, the authors review seventy-eight empirical studies (e.g., PET/fMRI, EEG, lesion studies) conducted between 1982 and 2016. They distinguish different empirical approaches to music and emotion in brain research and draw some general conclusions based on the results so far. The review reveals that some brain areas have been more or less consistently reported across studies, with partly distinct patterns for perception and induction of emotions, but that we still do not know what role each brain region plays in the emotion process. This is largely due to a lack of studies that attempt to manipulate underlying psychological mechanisms in a systematic manner. The chapter concludes by discussing the implications of the results and by making methodological recommendations for future research.
Musical Expertise and Brain Structure: The Causes and Consequences of Training
Authors: Penhune Virginia B.
Published: January 2020

Brain imaging studies have demonstrated that music training can change brain structure, predominantly in the auditor-motor network that underlies music performance. The chapter argues that the observed differences in brain structure between experts and novices, and the changes that occur with training derive from at least four sources: first, pre-existing individual differences that promote certain skills; second, lengthy and consistent training which likely produces structural changes in the brain networks tapped by performance; third, practice during specific periods of development which may result in changes that do not occur at other periods of time; fourth, the rewarding nature of music itself, as well as the reward value of practice which may make music training a particularly effective driver of brain plasticity.
Neural Mechanisms of Musical Imagery
Authors: Hubbard Timothy L.
Published: January 2020

Findings regarding the neural mechanisms of musical imagery are summarized, and both auditory and motor components of musical imagery are considered. Similarities of musical imagery and music perception (involving results from studies using behavioral and psychophysical methods, clinical data from brain-damaged patients, electrophysiology, and brain imaging), examples of involuntary musical imagery (involving anticipatory musical imagery, musical hallucinations, schizophrenia, earworms, and synesthesia), and aspects of embodied aspects of musical imagery (involving spatial and force metaphors, mimicry, the inner ear/inner voice distinction, effects of mental practice and performance, dance and other motor acts, and musical affect) are considered. It is concluded that many neural mechanisms involved in musical imagery are similar to neural mechanisms involved in music perception, cognition, and production. The importance of motor activation to musical imagery is highlighted, and the importance of an embodied approach to musical imagery is discussed.
Neurologic Music Therapy in Sensorimotor Rehabilitation
Authors: Thaut Corene , Stephan Klaus Martin
Published: January 2020

Since the 1990s, a strong body of research evidence has set the foundation for the use of rhythm and music as important tools in the development, rehabilitation, and maintenance of sensorimotor function, particularly in the treatment of neurologic disorders. This chapter examines the connection between music and sensorimotor function, and the underlying neurological principles and mechanisms behind music perception, production, and cognition as they relate to motor function. The role of neurologic music therapy to facilitate functional movement is discussed with a variety of populations and movement disorders including: Parkinson’s disease, stroke, traumatic brain injury, multiple sclerosis, cerebral palsy, autism and healthy elderly. The chapter is divided into sections related to acquired movement disorders, degenerative diseases, and developmental disorders.
The role of environmental, geographical, morphometric and spatial variables on plankton communities in lakes of the arid Patagonian plateaus
Authors: Porcel Sol , Chaparro Griselda , Marinone M Cristina , Saad Juan F , Lancelotti Julio , Izaguirre Irina
Published: January 2020

Species diversity is one of the most informative community metrics and is influenced by regional and local factors. We studied the spatial patterns of taxonomic and functional phyto- and zooplankton diversity in 33 lakes from two basaltic plateaus of the arid Patagonia. The aims of our study were to evaluate α, β and γ taxonomic diversity of phyto- and zooplankton; to assess the influence of environmental, spatial, geographical and morphometric factors on phyto- and zooplankton communities and to compare the influence of these variables on the taxonomic and functional composition. β1-diversity (within plateaus) was the major component for phytoplankton, rotifers and microcrustaceans taxonomic regional diversities. Planktonic communities were mainly constrained by macrophytes, fish, conductivity, dissolved organic carbon, altitude and spatial factors. The high dispersion of small individuals within plateaus tends to homogenize these communities, as indicated by null model results and the high explanation of fine-scale spatial factors in variation partitioning. This knowledge contributes to explaining the diversity patterns of planktonic communities of these valuable environments and to develop conservation strategies, considering both environmental heterogeneity and spatial effects.
THERMAL AND FAST NEUTRON DOSE EQUIVALENT DISTRIBUTION MEASUREMENT OF 15-MV LINEAR ACCELERATOR USING A CR-39 NUCLEAR TRACK DETECTORS
Authors: Mohammadi Sara , Behmadi Marziyeh , Mohammadi Aghil , Toossi Mohammad Taghi Bahreyni
Published: January 2020

The main purpose of this study is to measure the contribution of the thermal and fast neutron dose along the central axis of the 15 MV Elekta Precise linac in a tissue equivalent phantom. In order to achieve this purpose, different points were selected in three field sizes of 5 × 5 cm2, 10 × 10 cm2 and 15 × 15 cm2. Fast and thermal neutrons were measured using CR-39 nuclear track detectors with and without thermal neutron converter of 10B, respectively. According to the results, the fast neutron dose equivalent was decreased as the depth increased (field size 5 × 5, 10 × 10 and 15 × 15 cm2 fall from 0.35 to 0.15, 0.5 to 0.3 and 0.5 to 0.3, respectively). Thermal dose equivalent was increased as the depth increased in the tissue equivalent phantom (field size 5 × 5, 10 × 10 and 15 × 15 cm2 rise from 0.1 to 0.4, 0.4 to 0.8 and 0.4 to 0.9, respectively). In conclusion, at depth <3 cm, most existing neutrons are fast and CR-39 films are sensitive to fast neutrons; therefore, they are more appropriate than thermoluminescent dosemeters in measuring neutron dose equivalent.
Rhetorical and Organizational Typification of Domestic Violence, Sexual Assault, and Stalking as Discrete Forms of Violence
Authors: Weiss Benjamin R
Published: January 2020

Despite constructions of domestic violence, sexual assault, and stalking as discrete forms of violence, research shows that violence often co-occurs. Victims experiencing multiple forms of violence require different interventions from victims experiencing only one. Service providers’ understandings of domestic violence, sexual assault, and stalking as discrete, then, potentially undermine their goal of effective intervention. Drawing on 26 months of participant observation in an anti-gender-based violence nonprofit organization, I explore how advocates construct each form of violence as independent from the others. Results show that both organizational features, such as training curricula and organizational jurisdictions, and rhetorical strategies, such as an under-emphasis on co-occurring violence, contribute to the construction of each type of violence as discrete. This paper is of interest to researchers, practitioners, and policymakers committed to designing and implementing effective responses to gender-based violence. I also advance social problems theory, showing that organizational features, not just interactional processes, contribute to typification.
Prognostic factors associated with death from visceral leishmaniasis: a case-control study in Brazil
Authors: da Silva Thais Almeida Marques , Morais Maria Helena Franco , Lopes Helen Maria de Oliveira Ramos , Gonçalves Stefanne Aparecida , Magalhães Fernanda do Carmo , Amâncio Frederico Figueiredo , Antunes Carlos Maurício Figueiredo , Carneiro Mariângela
Published: January 2020

Background

The aim of this study was to identify the prognostic factors associated with death from visceral leishmaniasis (VL) considering the clinical evolution of patients through a case-control study.

Methods

We randomly selected 180 cases (death caused by VL) and 180 controls (cured) from Belo Horizonte's hospitals in Brazil, according to data found in the patients' medical records. Five models of multivariate logistic regression were performed following the chronological order of the variables between the onset of the symptoms and evolution of the VL cases.

Results

Considering the multivariate models and the stages of clinical evolution of VL, the prognostic factors associated with death are: age >60 y, minor hemorrhagic phenomena, increased abdominal volume, jaundice, dyspnea, malnutrition, TB, billirubin >2 mg/dL, Aspartate Aminotransferase (AST) or Alanine Aminotransferase (ALT) >100 U/L, leukocytes >7000/mm3, hemoglobin <7 g/dL, platelets <50 000/mm3 and infection without defined focus and bleeding.

Conclusions

Knowledge regarding the prognostic factors associated with death from VL in different stages of the disease in large Brazilian urban centers such as Belo Horizonte may help optimize patient management strategies and contribute to reduce the high fatality rates in these cities.
Dose-dependent effects of netarsudil, a Rho-kinase inhibitor, on the distal outflow tract
Authors: Chen Si , Waxman Susannah , Wang Chao , Atta Sarah , Loewen Ralitsa , Loewen Nils A.
Published: January 2020

Purpose

To characterize the effects of netarsudil on the aqueous humor outflow tract distal to the trabecular meshwork (TM). We hypothesized that netarsudil increases outflow facility in eyes with and without circumferential ab interno trabeculectomy (AIT) that removes the TM.

Methods

64 porcine anterior segment cultures were randomly assigned to groups with (n=32) and without circumferential AIT (n=32). Cultures were exposed to 0.1, 1, and 10 μM netarsudil (N= 8 eyes per concentration). For each concentration, IOP and vessel diameters were compared to their respective pretreatment baselines. Outflow tract vessel diameters were assessed by spectral-domain optical coherence tomography (SDOCT) and rendered in 4D (XYZ time-series).

Results

Netarsudil at 1 μM reduced IOP in both eyes with TM (−0.60±0.24 mmHg, p = 0.01) and in eyes without TM (−1.79±0.42 mmHg, p<0.01). At this concentration, vessels of the distal outflow tract dilated by 72%. However, at 0.1 μM netarsudil elevated IOP in eyes with TM (1.59±0.36 mmHg, p<0.001) as well as in eyes without TM (0.23±0.32 mmHg, p<0.001). Vessels of the distal outflow tract constricted by 31%. Similarly, netarsudil at a concentration of 10 μM elevated IOP both in eyes with TM (1.91±0.193, p<0.001) and in eyes without TM (3.65±0.86 mmHg, p<0.001). At this concentration, outflow tract vessels constricted by 27%.

Conclusion

In the porcine anterior segment culture, the dose-dependent IOP changes caused by netarsudil matched the diameter changes of distal outflow tract vessels. Hyper- and hypotensive properties of netarsudil persisted after TM removal.
Analysis of KSHV B lymphocyte lineage tropism in human tonsil reveals efficient infection of CD138+ plasma cells
Authors: Aalam Farizeh , Nabiee Romina , Castano Jesus Ramirez , Totonchy Jennifer E.
Published: January 2020

Despite 25 years of research, the basic virology of Kaposi Sarcoma Herpesviruses (KSHV) in B lymphocytes remains poorly understood. This study seeks to fill critical gaps in our understanding by characterizing the B lymphocyte lineage-specific tropism of KSHV. Here, we use lymphocytes derived from 40 human tonsil specimens to determine the B lymphocyte lineages targeted by KSHV early duringde novoinfection in ourex vivomodel system. We characterize the immunological diversity of our tonsil specimens and determine that overall susceptibility of tonsil lymphocytes to KSHV infection varies substantially between donors. We demonstrate that a variety of B lymphocyte subtypes are susceptible to KSHV infection and identify CD138+ plasma cells as a rare, but highly targeted cell type forde novoKSHV infection. Finally, we determine that the host immunological status influences the course ofde novoinfection in B lymphocytes. These results improve our understanding of KSHV transmission and the biology of early KSHV infection in a naïve human host, and lay a foundation for further characterization of KSHV molecular virology in B lymphocyte lineages.
Functional heterogeneity in the fermentation capabilities of the healthy human gut microbiota
Authors: Gurry Thomas , Nguyen Le Thanh Tu , Yu Xiaoqian , Alm Eric J
Published: January 2020

The human gut microbiota is known for its highly heterogeneous composition across different individuals. However, relatively little is known about functional differences in its ability to ferment complex polysaccharides. Throughex vivomeasurements from healthy human donors, we show that individuals vary markedly in their microbial metabolic phenotypes (MMPs), mirroring differences in their microbiota composition, and resulting in the production of different quantities and proportions of Short Chain Fatty Acids (SCFAs) from the same inputs. We also show that aspects of these MMPs can be predicted from composition using 16S rRNA sequencing. From experiments performed using the same dietary fibersin vivo, we demonstrate that an ingested bolus of fiber is almost entirely consumed by the microbiota upon passage. We leverage ourex vivodata to construct a model of SCFA production and absorptionin vivo, and argue that inter-individual differences in quantities of absorbed SCFA are directly related to differences in production. Taken together, these data suggest that personalized dietary fiber supplementation based on an individual’s MMP is an attractive therapeutic strategy for treating diseases associated with SCFA production.
A real-time search strategy for finding urban disease vector infestations
Authors: Rose Erica Billig , Roy Jason A. , Castillo-Neyra Ricardo , Ross Michelle E. , Condori-Pino Carlos , Peterson Jennifer K. , Naquira-Velarde Cesar , Levy Michael Z.
Published: January 2020

Containing domestic vector infestation requires the ability to swiftly locate and treat infested homes. In urban settings where vectors are heterogeneously distributed throughout a dense housing matrix, the task of locating infestations can be challenging. Here, we present a novel stochastic compartmental model developed to help locate infested homes in urban areas. We designed the model using infestation data for the Chagas disease vector speciesTriatoma infestansin Arequipa, Peru. Our approach incorporates disease vector counts at each observed house, and the vector’s complex spatial dispersal dynamics. We used a Bayesian method to augment the observed data, estimate the insect population growth and dispersal parameters, and determine posterior infestation probabilities of households. We investigated the properties of the model through simulation studies, followed by field testing in Arequipa. Simulation studies showed the model to be accurate in its estimates of two parameters of interest: the growth rate of a domestic triatomine bug colony and the probability of a triatomine bug successfully invading a new home after dispersing from an infested home. When testing the model in the field, data collection using model estimates was hindered by low household participation rates, which severely limited the algorithm and in turn, the model’s predictive power. While future optimization efforts must improve the model’s capabilities when household participation is low, our approach is nonetheless an important step toward integrating data with predictive modeling to carry out evidence-based vector surveillance in cities.
Host and infectivity prediction of Wuhan 2019 novel coronavirus using deep learning algorithm
Authors: Guo Qian , Li Mo , Wang Chunhui , Wang Peihong , Fang Zhencheng , tan Jie , Wu Shufang , Xiao Yonghong , Zhu Huaiqiu
Published: January 2020

The recent outbreak of pneumonia in Wuhan, China caused by the 2019 Novel Coronavirus (2019-nCoV) emphasizes the importance of detecting novel viruses and predicting their risks of infecting people. In this report, we introduced the VHP (Virus Host Prediction) to predict the potential hosts of viruses using deep learning algorithm. Our prediction suggests that 2019-nCoV has close infectivity with other human coronaviruses, especially the severe acute respiratory syndrome coronavirus (SARS-CoV), Bat SARS-like Coronaviruses and the Middle East respiratory syndrome coronavirus (MERS-CoV). Based on our prediction, compared to the Coronaviruses infecting other vertebrates, bat coronaviruses are assigned with more similar infectivity patterns with 2019-nCoVs. Furthermore, by comparing the infectivity patterns of all viruses hosted on vertebrates, we found mink viruses show a closer infectivity pattern to 2019-nCov. These consequences of infectivity pattern analysis illustrate that bat and mink may be two candidate reservoirs of 2019-nCov.These results warn us to beware of 2019-nCoV and guide us to further explore the properties and reservoir of it.

One Sentence Summary

It is of great value to identify whether a newly discovered virus has the risk of infecting human. Guoet al. proposed a virus host prediction method based on deep learning to detect what kind of host a virus can infect with DNA sequence as input. Applied to the Wuhan 2019 Novel Coronavirus, our prediction demonstrated that several vertebrate-infectious coronaviruses have strong potential to infect human. This method will be helpful in future viral analysis and early prevention and control of viral pathogens.
When honest people cheat, and cheaters are honest: Cognitive control processes override our moral default
Authors: Speer Sebastian P.H. , Smidts Ale , Boksem Maarten A.S.
Published: January 2020

Every day, we are faced with the conflict between the temptation to cheat for financial gains and maintaining a positive image of ourselves as being a ‘good person’. While it has been proposed that cognitive control is needed to mediate this conflict between reward and our moral self-image, the exact role of cognitive control in (dis)honesty remains elusive. Here, we identify this role, by investigating the neural mechanism underlying cheating. We developed a novel task which allows for inconspicuously measuring spontaneous cheating on a trial-by-trial basis in the MRI scanner. We found that activity in the Nucleus Accumbens promotes cheating, particularly for individuals who cheat a lot, while a network consisting of Posterior Cingulate Cortex, Temporoparietal Junction and Medial Prefrontal Cortex promotes honesty, particularly in individuals who are generally honest. Finally, activity in areas associated with Cognitive Control (Anterior Cingulate Cortex and Inferior Frontal Gyrus) helped dishonest participants to be honest, whereas it promoted cheating for honest participants. Thus, our results suggest that cognitive control is not needed to be honest or dishonest per se, but that it depends on an individual’s moral default.
Virion-associated spermidine transmits with Rift Valley fever virus particles to maintain infectivity
Authors: Mastrodomenico Vincent , Esin Jeremy J. , Qazi Shefah , Omoba Oreoluwa S. , Fung Brittany L. , Khomutov Maxim A. , Ivanov Alexander V. , Mukhopadhyay Suchetana , Mounce Bryan C.
Published: January 2020

Viruses require host cell metabolites to productively infect, and the mechanisms by which viruses usurp these molecules is diverse. One group of cellular metabolites important in virus infection is the polyamines, small positively-charged molecules involved in cell cycle, translation, and nucleic acid synthesis, among other cellular functions. Polyamines also support replication of diverse viruses, and they are important for processes such as transcription, translation, and viral protein enzymatic activity. Rift Valley fever virus (RVFV) is a negative-sense RNA virus that requires polyamines to produce infectious particles. In polyamine depleted conditions, noninfectious particles are produced that interfere with virus replication and stimulate immune signaling. Here, we find that RVFV relies on virion-associated polyamines to maintain infectivity. We show that RVFV replication is facilitated by any of the three biogenic polyamines; however, we specifically find spermidine associated with purified virions. Using a panel of polyamine homologs, we observe that virions can also associate with (R)-3-methylspermidine and norspermidine, though not with other less homologous molecules. Using polyamine reporter cells, we demonstrate that virion-associated polyamines transmit from one infected cell to another. Finally, we find that virions devoid of polyamines are unstable and cannot be supplemented with exogenous polyamines to regain stability or infectivity. These data highlight a unique role for polyamines, and spermidine in particular, in maintaining virus infectivity, a function not previously appreciated. Further, these studies are the first to identify polyamines associated with RVFV virions. Targeting polyamines represents a promising antiviral strategy, and this work highlights a new mechanism by which we can inhibit virus replication through FDA-approved polyamine depleting pharmaceuticals.
The effects of cannabidiol on cue- and stress-induced reinstatement of cocaine seeking behavior in mice are reverted by the CB1 receptor antagonist AM4113
Authors: Luján Miguel Ángel , Alegre-Zurano Laia , Martín-Sánchez Ana , Valverde Olga
Published: January 2020

Cocaine addiction is a brain disorder characterized by the consumption of the drug despite harmful consequences, the loss of control over drug intake and increased risk of relapse. Albeit prolonged research efforts, there is no available medication approved for the treatment of cocaine addiction. In the last decade, cannabinoid-based compounds have drawn increased interest for its potential therapeutic applications in various psychiatric conditions. Cannabidiol, a non-psychotomimetic constituent of theC. sativaplant, shows promising results in rodent models of anxiety, schizophrenia, depression and drug addiction. However, the specific effects and mechanisms of action of cannabidiol in a rodent model of extinction-based abstinence and drug seeking relapse remain unclear. Here, we administered cannabidiol (20 mg/kg) to male CD-1 mice trained to self-administer cocaine (0.75 mg/kg/inf) during extinction training (8–12 days). Then, we evaluated the reinstatement of cocaine seeking induced by cues, stress and drug priming. To ascertain the participation of CB1 receptors in these behavioral responses, we systemically administered the neutral cannabinoid antagonist AM4113 (5 mg/kg) before each reinstatement session. The results document that cannabidiol (20 mg/kg) does not modulate extinction training but attenuates ‘extinction burst’ responding after one cannabidiol injection. Furthermore, cannabidiol specifically blocked the reinstatement of cocaine seeking triggered by a cue presentation, an effect prevented by AM4113 (5 mg/kg). Unexpectedly, cannabidiol facilitated stress-induced reinstatement of cocaine seeking behavior, also by a CB1-dependent mechanism. Finally, cannabidiol did not affect cocaine-primed (10 mg/kg) precipitation of cocaine seeking. Our results reveal a series of complex changes induced by cannabidiol treatment with opposite implications for the reinstatement of cocaine seeking behavior that may limit therapeutic opportunities. The activity of CB1 receptors seems to play a crucial role in the expression of cannabidiol-induced neuroplasticity underlying both the desirable and undesirable reinstatement effects here detailed.
Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach
Authors: Gussow Ayal B. , Shmakov Sergey A. , Makarova Kira S. , Wolf Yuri I. , Bondy-Denomy Joseph , Koonin Eugene V.
Published: January 2020

Bacteria and archaea evolve under constant pressure from numerous, diverse viruses and thus have evolved multiple defense systems. The CRISPR-Cas are adaptive immunity systems that have been harnessed for the development of the new generation of genome editing and engineering tools. In the incessant host-parasite arms race, viruses evolved multiple anti-defense mechanisms including numerous, diverse anti-CRISPR proteins (Acrs) that can inhibit CRISPR-Cas and therefore have enormous potential for application as modulators of genome editing tools. Most Acrs are small, highly variable proteins which makes their prediction a formidable task. We developed a machine learning approach for comprehensive Acr prediction. The model showed high predictive power when tested against an unseen test set that included several families of recently discovered Acrs and was employed to predict 2,500 novel candidate Acr families. An examination of the top candidates confirms that they possess typical Acr features. One of the top candidates was independently tested and found to possess anti-CRISPR activity (AcrIIA12). We provide a web resource (http://acrcatalog.pythonanywhere.com/) to access the predicted Acrs sequences and annotation. The results of this analysis expand the repertoire of predicted Acrs almost by two orders of magnitude and provide a rich resource for experimental Acr discovery.
Distribution of genetic diversity reveals colonization and philopatry of the loggerhead sea turtles across geographic scales
Authors: Baltazar-Soares Miguel , Klein Juliana L. , Correia Sandra M. , Reischig Thomas , Taxonera Amoros Albert , Monteiro Roque Silvana , Dos Passos Leno , Jandira Durão , João Pina Lomba , Dinis Herculano , Cameron Sahmorie J.K. , Stiebens Victor A. , Eizaguirre Christophe
Published: January 2020

Aim

Understanding the processes that underlie the distribution of genetic diversity in endangered species is a goal of modern conservation biology. Specifically, how population structure affects genetic diversity and contributes to a species’ adaptive potential remain elusive. The loggerhead sea turtle (Caretta caretta) faces multiple conservation challenges due to its migratory nature and philopatric behaviour.

Locations

Atlantic Ocean, Cabo Verde, island of Boavista

Methods

Here, using 4207 mtDNA sequences, we analysed the colonisation patterns and distribution of genetic diversity within a major ocean basin (the Atlantic), a regional rookery (Cabo Verde Archipelago) and a local island (Island of Boavista, Cabo Verde).

Results

Hypothesis-driven population genetic models suggest the colonization of the Atlantic has occurred in two distinct waves, each corresponding to major mtDNA lineages. We propose the oldest lineage entered the basin via the isthmus of Panama and sequentially established aggregations in Brazil, Cabo Verde and in the area of USA and Mexico. The second lineage entered the Atlantic via the Cape of Good Hope, establishing colonies in the Mediterranean Sea, and from then on, re-colonized the already existing rookeries of the Atlantic. At the Cabo Verde level, we reveal an asymmetric gene flow maintaining links across nesting groups despite significant genetic structure amongst nesting groups. This structure stems from female philopatric behaviour which could further be detected by weak but significant structure amongst beaches separated by only a few kilometres on the island of Boavista.

Main conclusion

To explore demographic processes at diverse geographic scales improves understanding the complex evolutionary history of highly migratory philopatric species. Unveiling the past facilitates the design of conservation programmes targeting the right management scale to maintain a species’ adaptive potential and putative response to human-induced selection.
Finer Metagenomic Reconstruction via Biodiversity Optimization
Authors: Foucart Simon , Koslicki David
Published: January 2020

When analyzing communities of microorganisms from their sequenced DNA, an important task is taxonomic profiling: enumerating the presence and relative abundance of all organisms, or merely of all taxa, contained in the sample. This task can be tackled via compressive-sensing-based approaches, which favor communities featuring the fewest organisms among those consistent with the observed DNA data. Despite their successes, these parsimonious approaches sometimes conflict with biological realism by overlooking organism similarities. Here, we leverage a recently developed notion of biological diversity that simultaneously accounts for organism similarities and retains the optimization strategy underlying compressive-sensing-based approaches. We demonstrate that minimizing biological diversity still produces sparse taxonomic profiles and we experimentally validate superiority to existing compressive-sensing-based approaches. Despite showing that the objective function is almost never convex and often concave, generally yielding NP-hard problems, we exhibit ways of representing organism similarities for which minimizing diversity can be performed via a sequence of linear programs guaranteed to decrease diversity. Better yet, when biological similarity is quantified byk-mer co-occurrence (a popular notion in bioinformatics), minimizing diversity actually reduces to one linear program that can utilize multiplek-mer sizes to enhance performance. In proof-of-concept experiments, we verify that the latter procedure can lead to significant gains when taxonomically profiling a metagenomic sample, both in terms of reconstruction accuracy and computational performance. Reproducible code is available athttps://github.com/dkoslicki/MinimizeBiologicalDiversity.
Heparan sulfate structure is influenced by the ER-Golgi dynamics of its modifying enzymes
Authors: Meneghetti Maria Cecília Zorél , Deboni Paula , Palomino Carlos Modesto Vera , Braga Luiz Patekoski , Cavalheiro Renan Pelluzzi , Viana Gustavo Monteiro , Yates Edwin A. , Nader Helena B. , Lima Marcelo A.
Published: January 2020

The cell surface and extracellular matrix polysaccharide, heparan sulfate (HS) conveys chemical information to control or influence crucial biological processes. Attempts to describe its structure-function relationships with HS binding proteins in a classical ‘lock and key’ type manner, however, have been unsuccessful. HS chains are synthesized in a non-template driven process in the ER and Golgi apparatus, involving a large number of enzymes capable of fine-tuning structures. Changes in the localization of HS-modifying enzymes throughout the Golgi, rather than protein expression levels, were found to correlate with changes in the structure of HS. Following brefeldin A treatment, the HS-modifying enzymes localized preferentially in COPII vesicles and at the trans-Golgi. Further, shortly after treatment with heparin, the HS-modifying enzyme moved from cis to trans-Golgi, which coincided with increased HS trisulfated disaccharide content. Finally, it was shown that COPI subunits and Sec24 gene expression changed. Collectively, these findings highlight that the ER-Golgi dynamics of HS-modifying enzymes via vesicular trafficking processes are critical prerequisite for the complete delineation of HS biosynthesis.
A metabolomics study of ascorbic acid-inducedin situfreezing tolerance in spinach (Spinacia oleraceaL.)
Authors: Min Kyungwon , Chen Keting , Arora Rajeev
Published: January 2020

Freeze-thaw stress is one of the major environmental constraints that limit plant growth and reduces productivity and quality. Plants exhibit a variety of cellular dysfunction following freeze-thaw stress, including accumulation of reactive oxygen species (ROS). This means that enhancement of antioxidant capacity by exogenous application of antioxidants could potentially be one of major strategies for improving freezing tolerance (FT) of plants. Exogenous application of ascorbic acid (AsA), as an antioxidant, has been shown to improve plant tolerance against abiotic stresses but its effect on FT has not been investigated. We evaluated the effect of AsA-feeding on FT of spinach (Spinacia oleraceaL.) at whole-plant and excised leaf level, and conducted metabolite profiling of leaves before and after AsA-treatment to explore metabolic explanation for change in FT. AsA-application did not impede leaf-growth; instead slightly promoted it. Temperature-controlled freeze-thaw tests revealed AsA-fed plants were more freezing tolerant as indicated by: 1) less visual damage/mortality; 2) lower ion-leakage; and 3) less oxidative-injury, lower abundance of free radicals (O2•−and H2O2). Comparative leaf metabolic profiling revealed clear separation of metabolic phenotypes for controlvs. AsA-fed leaves. Specifically, AsA-fed leaves had greater abundance of antioxidants (AsA, glutathione, alpha-& gamma-tocopherol) and compatible solutes (proline, galactinol, myo-inositol). AsA-fed leaves also had higher activity of antioxidant enzymes (superoxide dismutase, ascorbate peroxidase, catalase). These changes, together, may improve FT via alleviating freeze-induced oxidative stress as well as protecting membranes from freeze-desiccation. Additionally, improved FT by AsA-feeding may potentially include enhanced cell wall/lignin augmentation and bolstered secondary metabolism as indicated by diminished level of phenylalanine and increased abundance of branched amino acids, respectively.
Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities
Authors: Herren Cristina M.
Published: January 2020

The strength of biotic interactions within an ecological community affects the susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this “critical” level of cross-feeding, successful invaders generally causing decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community.
Dugesia japonicais the best suited of three planarian species for high-throughput toxicology screening
Authors: Ireland Danielle , Bochenek Veronica , Chaiken Daniel , Rabeler Christina , Onoe Sumi , Soni Ameet , Collins Eva-Maria S.
Published: January 2020

High-throughput screening (HTS) using new approach methods is revolutionizing toxicology. Asexual freshwater planarians are a promising invertebrate model for neurotoxicity HTS because their diverse behaviors can be used as quantitative readouts of neuronal function. Currently, three planarian species are commonly used in toxicology research:Dugesia japonica,Schmidtea mediterranea, andGirardia tigrina. However, onlyD. japonicahas been demonstrated to be suitable for HTS. Here, we assess the two other species for HTS suitability by direct comparison withD. japonica. Through quantitative assessments of morphology and multiple behaviors, we assayed the effects of 4 common solvents (DMSO, ethanol, methanol, ethyl acetate) and a negative control (sorbitol) on neurodevelopment. Each chemical was screened blind at 5 concentrations at two time points over a twelve-day period. We obtained two main results: First,G. tigrinaandS. mediterraneaplanarians showed significantly reduced movement compared toD. japonicaunder HTS conditions, due to decreased health over time and lack of movement under red lighting, respectively. This made it difficult to obtain meaningful readouts from these species. Second, we observed species differences in sensitivity to the solvents, suggesting that care must be taken when extrapolating chemical effects across planarian species. Overall, our data show thatD. japonicais best suited for behavioral HTS given the limitations of the other species. Standardizing which planarian species is used in neurotoxicity screening will facilitate data comparisons across research groups and accelerate the application of this promising invertebrate system for first-tier chemical HTS, helping streamline toxicology testing.
Entropy of city street networks linked to future spatial navigation ability
Authors: Coutrot A. , Manley E. , Goodroe S. , Gahnstrom C. , Filomena G. , Yesiltepe D. , Dalton R.C. , Wiener J. M. , Hölscher C. , Hornberger M. , Spiers H. J.
Published: January 2020

Cultural and geographical properties of the environment have been shown to deeply influence cognition and mental health[1–6]. While living near green spaces has been found to be strongly beneficial [7–11], urban residence has been associated with a higher risk of some psychiatric disorders [12–14] (although see [15]). However, how the environment one grew up in impacts later cognitive abilities remains poorly understood. Here, we used a cognitive task embedded in a video game[16] to measure non-verbal spatial navigation ability in 397,162 people from 38 countries across the world. Overall, we found that people who grew up outside cities are better at navigation. More specifically, people were better at navigating in environments topologically similar to where they grew up. Growing up in cities with low Street Network Entropy (e.g. Chicago) led to better results at video game levels with a regular layout, while growing up outside cities or in cities with higher Street Network Entropy (e.g. Prague) led to better results at more entropic video game levels. This evidences the impact of the environment on human cognition on a global scale, and highlights the importance of urban design on human cognition and brain function.
An information-theoretic approach for measuring the distance of organ tissue samples using their transcriptomic signatures
Authors: Manatakis Dimitris V. , VanDevender Aaron , Manolakos Elias S.
Published: January 2020

Motivation

Recapitulating aspects of human organ functions using in-vitro (e.g., plates, transwells, etc.), in-vivo (e.g., mouse, rat, etc.), or ex-vivo (e.g., organ chips, 3D systems, etc.) organ models are of paramount importance for precision medicine and drug discovery. It will allow us to identify potential side effects and test the effectiveness of therapeutic approaches early in their design phase and will inform the development of accurate disease models. Developing mathematical methods to reliably compare the “distance/similarity” of organ models from/to the real human organ they represent is an understudied problem with important applications in biomedicine and tissue engineering.

Results

We introduce the Transctiptomic Signature Distance,TSD, an information-theoretic distance for assessing the transcriptomic similarity of two tissue samples, or two groups of tissue samples. In developingTSD, we are leveraging next-generation sequencing data and information retrieved from well-curated databases providing signature gene sets characteristic for human organs. We present the justification and mathematical development of the new distance and demonstrate its effectiveness in different scenarios of practical importance using several publicly available RNA-seq datasets.

Contact

dimitris.manatakis@emulatebio.com

Supplementary information

Supplementary data are available atbioRxiv.