bluuebunny/crossref_metadata_2025 huggingface dataset:
Gender and Trait Preferences for Banana Cultivation and Use in Sub-Saharan Africa: A Literature Review1
Authors: Marimo Pricilla , Caron Cynthia , Van den Bergh Inge , Crichton Rhiannon , Weltzien Eva , Ortiz Rodomiro , Tumuhimbise Robooni
Published: June 2020

Gender and Trait Preferences for Banana Cultivation and Use in Sub-Saharan Africa: A Literature Review

Understanding trait preferences of different actors in the banana value chain may facilitate the selection and adoption of new cultivars. We systematically reviewed the scholarly and gray literature on banana trait preferences, with specific attention to studies that document gender-differentiated traits. Of 44 publications reviewed, only four reported gender-specific trait preferences, indicating a significant gap in the literature. The review found that banana farmers, irrespective of gender, value similar characteristics that are related to production constraints, income enhancement, consumption, and cultural or ritual uses. Farmers (as producers, processors, and consumers) often prefer traditional cultivars because of their superior consumption attributes, even if new cultivars have better agronomic and host plant resistance characteristics. Potential differences between trait preferences of farmers and other actors in the value chain should be accounted for to enhance marketing potential. Gender-specific research along the banana value chain and engaging users at the initial stages of breeding can ensure that new cultivars are acceptable to users and may improve adoption. Interdisciplinary teamwork is essential for an efficient and effective breeding program.
Enabling radiation tolerant heterogeneous GPU-based onboard data processing in space
Authors: Bruhn Fredrik C. , Tsog Nandinbaatar , Kunkel Fabian , Flordal Oskar , Troxel Ian
Published: June 2020

The last decade has seen a dramatic increase in small satellite missions for commercial, public, and government intelligence applications. Given the rapid commercialization of constellation-driven services in Earth Observation, situational domain awareness, communications including machine-to-machine interface, exploration etc., small satellites represent an enabling technology for a large growth market generating truly Big Data. Examples of modern sensors that can generate very large amounts of data are optical sensing, hyperspectral, Synthetic Aperture Radar (SAR), and Infrared imaging. Traditional handling and downloading of Big Data from space requires a large onboard mass storage and high bandwidth downlink with a trend towards optical links. Many missions and applications can benefit significantly from onboard cloud computing similarly to Earth-based cloud services. Hence, enabling space systems to provide near real-time data and enable low latency distribution of critical and time sensitive information to users. In addition, the downlink capability can be more effectively utilized by applying more onboard processing to reduce the data and create high value information products. This paper discusses current implementations and roadmap for leveraging high performance computing tools and methods on small satellites with radiation tolerant hardware. This includes runtime analysis with benchmarks of convolutional neural networks and matrix multiplications using industry standard tools (e.g., TensorFlow and PlaidML). In addition, a ½ CubeSat volume unit (0.5U) (10 × 10 × 5 cm3) cloud computing solution, called SpaceCloud™ iX5100 based on AMD 28 nm APU technology is presented as an example of heterogeneous computer solution. An evaluation of the AMD 14 nm Ryzen APU is presented as a candidate for future advanced onboard processing for space vehicles.
Space weather climate impacts on railway infrastructure
Authors: Thaduri Adithya , Galar Diego , Kumar Uday
Published: June 2020

Space weather is a phenomenon in which radioactivity and atomic particles is caused by emission from the Sun and stars. It is one of the extreme climate events that could potentially has short-term and long-term impacts on infrastructure. The effects of this phenomenon are a multi-fold process that include electronic system, equipment and component failures, short-term and long-term hazards and consequences to astronauts and aircraft crews, electrostatic charge variation of satellites, disruptions in telecommunications systems, navigational systems, power transmission failures and disturbances to the rail traffic and power grids. The critical infrastructures are becoming interdependent to each other and these infrastructures are vulnerable if one of them is affected due to space weather. Railway infrastructure could be affected by the extreme space weather events and long-term evolution due to direct and indirect effects on system components, such as track circuits, electronic components in-built in signalling systems or indirectly via interdependencies on power, communications, etc. While several space weather-related studies focus on power grids, Global Navigation Satellite System (GNSS) and aviation sectors, a little attention has focused towards probability of railway infrastructure disruptions. Nevertheless, disruptions due to space weather on signalling and train control systems has documented but other systems that railway infrastructure dependent upon are not very well studied. Due to the advancements in digitalization, cloud storage, Internet of Things (IoT), etc., that are embedded with electronic equipment are also possible to prone to these effects and it is even become more susceptible to the extreme space weather events. This paper gives a review of space weather effects on railways and other transportation systems and provide some of the mitigation measures to the infrastructure and societal point of view.
The Value of Crop Production and Pollination Services in the Eastern Amazon
Authors: Borges R C , Brito R M , Imperatriz-Fonseca V L , Giannini T C
Published: June 2020

Nature safeguards living organisms and the ecosystem functions and services delivered by them. Animal pollination is an important Ecosystem Service since it plays a key role for achieving the sustainable development goals by safeguarding worldwide food production. Thus, conservation of pollination services is a major priority for guaranteeing global food security in the long term. Here we evaluate the crop pollination services in Pará state (Eastern Amazon, Brazil) focusing on two questions: (1) What is the economic value of crop production and pollination service in Pará? (2) Which municipalities are most dependent on pollination services considering local economies? We found 36 crops produced in the state; 20 (55%) crops are dependent on animal pollinators. In 2016, crop production value (CPV) for Pará state was US$ 2.95 billion and total pollination service value (PSV) was US$ 983.2 million, corresponding to 33% of CPV in Pará. Highest PSV value crops were açaí palm (US$635.6 million), cocoa (US$187.6 million), soybean (US$98.4 million), and watermelon (US$26.1 million), accounting for 96% of Pará’s PSV. Two municipalities (Medicilândia and Igarapé Miri) presented more than 50% of their GDP based on pollination services. In general, we found low crop diversity in the municipalities of Pará, suggesting an economic rural vulnerability for the state, mainly supported by the high productions of soy and açaí. Pollinator conservation and ecological intensified farming practices are urgent for supporting sustainable development for the state.
Water Splitting: From Electrode to Green Energy System
Authors: Li Xiao , Zhao Lili , Yu Jiayuan , Liu Xiaoyan , Zhang Xiaoli , Liu Hong , Zhou Weijia
Published: June 2020

Hydrogen (H2) production is a latent feasibility of renewable clean energy. The industrial H2 production is obtained from reforming of natural gas, which consumes a large amount of nonrenewable energy and simultaneously produces greenhouse gas carbon dioxide. Electrochemical water splitting is a promising approach for the H2 production, which is sustainable and pollution-free. Therefore, developing efficient and economic technologies for electrochemical water splitting has been an important goal for researchers around the world. The utilization of green energy systems to reduce overall energy consumption is more important for H2 production. Harvesting and converting energy from the environment by different green energy systems for water splitting can efficiently decrease the external power consumption. A variety of green energy systems for efficient producing H2, such as two-electrode electrolysis of water, water splitting driven by photoelectrode devices, solar cells, thermoelectric devices, triboelectric nanogenerator, pyroelectric device or electrochemical water–gas shift device, have been developed recently. In this review, some notable progress made in the different green energy cells for water splitting is discussed in detail. We hoped this review can guide people to pay more attention to the development of green energy system to generate pollution-free H2 energy, which will realize the whole process of H2 production with low cost, pollution-free and energy sustainability conversion.
The Market for Reviews: Strategic Behavior of Online Product Reviewers with Monetary Incentives
Authors: Dorner Verena , Giamattei Marcus , Greiff Matthias
Published: June 2020

Customer reviews reduce search cost and uncertainty about a product’s quality. Hence, the quantity and quality of reviews has positive impacts on purchase intentions, sales, and customer satisfaction. In order to increase review quality, retailers and online platforms employ different monetary incentives. We experimentally compare two different incentive schemes: an incentive scheme in which reviewers receive a flat salary, which is independent of review quality, and a tournament incentive scheme in which the reviewer who wrote the most helpful review receives a bonus payment. Helpfulness ratings are assigned by the other reviewers. In our experiment, adverse consequences arise under the tournament incentive scheme. Strategic considerations give rise to strategic downvoting, so that reviewers assign low helpfulness ratings to others’ reviews in order to maximize their expected payoffs. Review writing behavior remains unaffected: the tournament incentive scheme does not affect review quality. However, it does destroy the signaling power of helpfulness ratings.
Distributed computation and control of robot motion dynamics on FPGAs
Authors: Bargsten Vinzenz , de Gea Fernández José
Published: June 2020

Driven by advances in miniaturized electronics, many robotic systems today consist of modular hardware components. This leads to numerous computing units that are distributed within such systems. In order to make better use of such hardware structures from a computational point of view, the implementation of classical control approaches should be reconsidered. Following this idea, a method for distributed computation of motion dynamics of robotic systems using Field Programmable Gate Arrays is discussed. In this approach, local low-level actuator controllers are regarded as interconnected nodes, which are aware of their actuated degree of freedom and the resulting motion of the attached rigid body link element. A modified recursive Newton–Euler algorithm is computed by these nodes, where each node only exchanges data with the neighboring nodes. In the computations, a linear dependency on the dynamic parameters is kept in order to simplify the direct use of dynamic parameters estimated from experimental data. Implementation details and experimental results using a robotic manipulator arm are presented. The experiments show that the method allows compliant motion control. Payloads and external forces acting on a link are considered in the distributed computation of the model by informing the node controlling the respective link of the additional forces.
Stressful life events and adolescent suicidality: An investigation of the mediating mechanisms
Authors: Yıldız Muhammed
Published: June 2020

Introduction

While a number of studies have found an association between stressful life events and adolescent suicidality, underlying mechanisms linking the two continue to be inadequately understood. Drawing upon the stress process, general strain, and support deterioration theories, this study examined the relationship between stressful life events and suicidality in U.S. adolescents, focusing on the mediating roles of depression, substance use, and perceived social support.

Methods

The data came from the first two waves of the National Longitudinal Study of Adolescent to Adult Health (N = 12,801; M age = 15 at Wave I; 50.2% female). Mediation analyses were performed using the Karlson‐Holm‐Breen (KHB) method developed for nonlinear probability models.

Results

Depression, substance use, and perceived social support accounted for a substantial part of the effect of stressful life events on suicidal ideation (57%) and attempts (43%). All mediating effects were statistically significant. Depression was a relatively stronger mediator for both suicidal outcomes. Significant relationships among stressful life events and suicidal outcomes persisted even after adjusting for the proposed mediators.

Conclusion

Stressful life events increase suicidality in adolescents, partly by increasing psychological distress and eroding perceived social support. Findings underscore the necessity of continued emphasis on stress management and support programs in reducing suicidality among vulnerable adolescents exposed to these types of occurrences.
The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms
Authors: Guan Jiantao , Garcia Diego F. , Zhou Yun , Appels Rudi , Li Aili , Mao Long
Published: June 2020

In the year 2018, the world witnessed the finale of the race to sequence the genome of the world’s most widely grown crop, the common wheat. Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature. A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries, taking a conventional strategy similar to that for sequencing Arabidopsis and rice, became ferocious over time as both sequencing technologies and genome assembling methodologies advanced. At different stages, multiple versions of genome sequences of the same variety (e.g., Chinese Spring) were produced by several groups with their special strategies. Finally, 16 years after the rice genome was finished and 9 years after that of maize, the wheat research community now possesses its own reference genome. Armed with these genomics tools, wheat will reestablish itself as a model for polyploid plants in studying the mechanisms of polyploidy evolution, domestication, genetic and epigenetic regulation of homoeolog expression, as well as defining its genetic diversity and breeding on the genome level. The enhanced resolution of the wheat genome should also help accelerate development of wheat cultivars that are more tolerant to biotic and/or abiotic stresses with better quality and higher yield.
Keeping a secure hold on data through modern electronic content management
Authors: Hampton Paul
Published: June 2020

Proper storage of data is a security necessity. This is because data can often contain valuable company information, which is liable to fall into the wrong hands if not properly managed. The problem is growing in tandem with increased content creation – the world is full of data. It is estimated that the aggregate amount of data, which doubles in size every two years, measures 4.4 zettabytes (trillion gigabytes) and is likely to reach a massive 44 zettabytes by 2020. 1

Companies are attempting to deal with a tidal wave of data. And a lack of integration inside a business can promote the dangerous phenomenon of content sprawl.

This occurs when different departments do not harmonise their processes and there is no plan to address outdated content or to ensure that data is stored in the right way. Companies need to gain a tight rein on their digital assets and institute a rigid content management system to keep up with the data explosion. But that can be easier said than done, explains Paul Hampton of Alfresco.
Keeping critical assets safe when teleworking is the new norm
Authors: Evangelakos Gus
Published: June 2020

The Covid-19 pandemic has upended almost every aspect of our lives – and work is no exception. With social distancing protocols in effect across the world, tele-commuting (or remote work), has suddenly become the norm for many, rather than the exception. And the flexibility offered by remote work is a major benefit.

There are many advantages to remote working. Yet our new professional reality also comes with fresh challenges. Perhaps none of these is more important than the need to safeguard critical corporate assets within an information security landscape that has been profoundly altered, almost overnight, says Gus Evangelakos of XM Cyber.
The predictive value of intake questions on informing tailored quitline services
Authors: Seltzer Ryan G. N. , Michael Stephen , York Heather P. , Yuan Nicole
Published: June 2020

The Minimal Data Set are demographic and tobacco use questions asked during enrollment at many quitlines. We tested whether these questions can be used to predict program engagement and success, and to evaluate whether findings can inform the tailoring of protocols to disparate populations. We analyzed 7,920 Arizona Smokers' Helpline treatment records to test a Structural Equation Model of the mediating effects of quitline services and short-term cessation outcomes on the relationship between intake questions and 7-month quit rate. Education (b = 0.05), gender (b = 0.03), Medicaid (b = −0.09), longest length of previous quit attempt (b = 0.05), confidence in quitting for 24 h (b = 0.04), environmental risk (b = −0.05), and life stress (b = 0.04) all significantly (P < 0.05) predicted engagement in quitline services. Program engagement had a direct effect on an in-program cessation outcomes construct (b = 0.47) and 7-month quit rate (b = 0.44). This in-program cessation outcomes construct had a significant direct effect on 7-month quit rate (b = −0.12). This model showing the relationship between program engagement and outcomes suggests that tailoring protocols can focus on engaging clients who have historically not taken full advantage of quitline services.
Historical Institutionalism Meets Practice Theory: Renewing the Selection Process of the United Nations Secretary-General
Authors: Pouliot Vincent
Published: June 2020

The selection process leading to the appointment of Antonio Guterres as Secretary-General of the United Nations gave way to unprecedented practices in world politics, such as public hearings with candidates. A textbook case of what historical institutionalism calls “layering,” this episode of institutional development features intriguing puzzles, including its timing, form, and limits. Drawing on historical institutionalism and practice theory, I develop a “pulling” theory of agency that complements intentionalist accounts. The webs of practices that agents find themselves in afford certain actions over others, orienting the push of interests. I infer three mechanisms—relational crossover, competence transfers, and pushback—and show how a set of nine practices, available at the UN in 2015–2016 but not in earlier episodes, account for the specifics of the recent renewal of the Secretary-General's selection procedure. A full explanation of this critical case of institutional change is impossible without understanding how agents struggled with one another under the pull of the UN web of practices, affording some innovations but not others.
Identifying social cognition subgroups in euthymic patients with bipolar disorder: a cluster analytical approach
Authors: Varo C. , Solé B. , Jiménez E. , Bonnín C. M. , Torrent C. , Valls E. , Lahera G. , Martínez-Arán A. , Carvalho A. F. , Miskowiak K. W. , Vieta E. , Reinares M.
Published: June 2020

Background

Bipolar disorder (BD) is associated with social cognition (SC) impairments even during remission periods although a large heterogeneity has been described. Our aim was to explore the existence of different profiles on SC in euthymic patients with BD, and further explore the potential impact of distinct variables on SC.

Methods

Hierarchical cluster analysis was conducted using three SC domains [Theory of Mind (ToM), Emotional Intelligence (EI) and Attributional Bias (AB)]. The sample comprised of 131 individuals, 71 patients with BD and 60 healthy control subjects who were compared in terms of SC performance, demographic, clinical, and neurocognitive variables. A logistic regression model was used to estimate the effect of SC-associated risk factors.

Results

A two-cluster solution was identified with an adjusted-performance group (N = 48, 67.6%) and a low-performance group (N = 23, 32.4%) with mild deficits in ToM and AB domains and with moderate difficulties in EI. Patients with low SC performance were mostly males, showed lower estimated IQ, higher subthreshold depressive symptoms, longer illness duration, and poorer visual memory and attention. Low estimated IQ (OR 0.920, 95% CI 0.863–0.981), male gender (OR 5.661, 95% CI 1.473–21.762), and longer illness duration (OR 1.085, 95% CI 1.006–1.171) contributed the most to the patients clustering. The model explained up to 35% of the variance in SC performance.

Conclusions

Our results confirmed the existence of two discrete profiles of SC among BD. Nearly two-thirds of patients exhibited adjusted social cognitive abilities. Longer illness duration, male gender, and lower estimated IQ were associated with low SC performance.
Endosperm variability: from endoreduplication within a seed to higher ploidy across species, and its competence
Authors: Rangan Parimalan
Published: June 2020

Endosperm tissue that nourishes the embryo during seed development, upon maturity, nourishes the global population with special reference to cereal crops like maize, wheat and rice. In about 70% of the angiosperms, endosperm genome content is ‘3n’ with 2:1 (maternal:paternal) contribution, as a result of the second fertilization event. However, angiosperms evolution also documents diversity in endosperm genome content from ‘2n’ to ‘15n’, in scale with the corresponding maternal genome dosage variability (‘1n’ to ‘14n’), whereas paternal contribution is invariable. In apomicts, due to lack of fertilization, or pseudogamy (fertilization of the central cell for endosperm formation), endosperm genome dosage (m:p) has been reported to range between 1:1 and 8:3. Exceptionally, the central cell with one unreduced nucleus and fused with a reduced sperm cell, with 2:1 normal genome dosage, has been reported inPanicum. Altered genome dosage levels are reportedly correlative with eccentricities among maternal and paternal contribution to seed resource allocation. Besides endosperm ploidy variability between species of angiosperms, the present review gives an overview of the ploidy variability in endosperm cells within a seed, up to ‘690n’. In addition to genome-scale variability in the endosperm, some taxa of angiosperms exhibit chlorophyllous endosperms and some chlorophyllous embryos. Also, endosperm cell number during seed development is reported to have a strong association with grain weight at maturity. Genes underlying these traits of variability are unknown, and the present review underscores the variability and highlights the potential of the single-cell sequencing techniques towards understanding the genetic mechanisms associated with these variable traits.
Neural machine translation of low-resource languages using SMT phrase pair injection
Authors: Sen Sukanta , Hasanuzzaman Mohammed , Ekbal Asif , Bhattacharyya Pushpak , Way Andy
Published: June 2020

Neural machine translation (NMT) has recently shown promising results on publicly available benchmark datasets and is being rapidly adopted in various production systems. However, it requires high-quality large-scale parallel corpus, and it is not always possible to have sufficiently large corpus as it requires time, money, and professionals. Hence, many existing large-scale parallel corpus are limited to the specific languages and domains. In this paper, we propose an effective approach to improve an NMT system in low-resource scenario without using any additional data. Our approach aims at augmenting the original training data by means of parallel phrases extracted from the original training data itself using a statistical machine translation (SMT) system. Our proposed approach is based on the gated recurrent unit (GRU) and transformer networks. We choose the Hindi–English, Hindi–Bengali datasets for Health, Tourism, and Judicial (only for Hindi–English) domains. We train our NMT models for 10 translation directions, each using only 5–23k parallel sentences. Experiments show the improvements in the range of 1.38–15.36 BiLingual Evaluation Understudy points over the baseline systems. Experiments show that transformer models perform better than GRU models in low-resource scenarios. In addition to that, we also find that our proposed method outperforms SMT—which is known to work better than the neural models in low-resource scenarios—for some translation directions. In order to further show the effectiveness of our proposed model, we also employ our approach to another interesting NMT task, for example, old-to-modern English translation, using a tiny parallel corpus of only 2.7K sentences. For this task, we use publicly available old-modern English text which is approximately 1000 years old. Evaluation for this task shows significant improvement over the baseline NMT.
Learning from noisy out-of-domain corpus using dataless classification
Authors: Jin Yiping , Wanvarie Dittaya , Le Phu T. V.
Published: June 2020

In real-world applications, text classification models often suffer from a lack of accurately labelled documents. The available labelled documents may also be out of domain, making the trained model not able to perform well in the target domain. In this work, we mitigate the data problem of text classification using a two-stage approach. First, we mine representative keywords from a noisy out-of-domain data set using statistical methods. We then apply a dataless classification method to learn from the automatically selected keywords and unlabelled in-domain data. The proposed approach outperformed various supervised learning and dataless classification baselines by a large margin. We evaluated different keyword selection methods intrinsically and extrinsically by measuring their impact on the dataless classification accuracy. Last but not least, we conducted an in-depth analysis of the behaviour of the classifier and explained why the proposed dataless classification method outperformed supervised learning counterparts.
Comparison of methodological quality between the 2007 and 2019 Canadian dietary guidelines
Authors: Dai Zhaoli , Kroeger Cynthia M , Lawrence Mark , Scrinis Gyorgy , Bero Lisa
Published: June 2020

Objective:

With significant shifts in the dietary recommendations between the 2007 and 2019 Canadian dietary guidelines, such as promoting plant-based food intake, reducing highly processed food intake and advocating the practice of food skills, we compared their differences in guideline development methods.

Design:

Two reviewers used twenty-five guided criteria to appraise the methods used to develop the most recent dietary guidelines against those outlined in the 2014 WHO Handbook for Guideline Development.

Setting:

Canada.

Participants:

2007 and 2019 dietary guidelines.

Results:

We found that the 2019 guidelines were more evidence-based and met 80 % (20/25) of the WHO criteria. For example, systematic reviews and health organisation authoritative reports, but not industry reports, constituted the evidence base for the dietary recommendations. However, recommendations on food sustainability and food skill practice were driven primarily by stakeholders’ interests. By contrast, less information was recorded about the process used to develop the 2007 guidelines, resulting in 24 % (6/25) consistency with the WHO standards.

Conclusions:

Our analysis suggests that a more transparent and evidence-based approach is used to develop the 2019 Canadian dietary guidelines and that method criteria should support further incorporation of nutrition priorities (food sustainability and food skills) in future dietary guideline development.
Jupiter's Equatorial Plumes and Hot Spots: Spectral Mapping from Gemini/TEXES and Juno/MWR
Authors: Fletcher L. N. , Orton G. S. , Greathouse T. K. , Rogers J. H. , Zhang Z. , Oyafuso F. A. , Eichstädt G. , Melin H. , Li C. , Levin S. M. , Bolton S. , Janssen M. , Mettig H.‐J. , Grassi D. , Mura A. , Adriani A.
Published: June 2020

We present multiwavelength measurements of the thermal, chemical, and cloud contrasts associated with the visibly dark formations (also known as 5‐μm hot spots) and intervening bright plumes on the boundary between Jupiter's Equatorial Zone (EZ) and North Equatorial Belt (NEB). Observations made by the TEXES 5‐ to 20‐μm spectrometer at the Gemini North Telescope in March 2017 reveal the upper‐tropospheric properties of 12 hot spots, which are directly compared to measurements by Juno using the microwave radiometer (MWR), JIRAM at 5 μm, and JunoCam visible images. MWR and thermal‐infrared spectroscopic results are consistent near 0.7 bar. Mid‐infrared‐derived aerosol opacity is consistent with that inferred from visible‐albedo and 5‐μm opacity maps. Aerosol contrasts, the defining characteristics of the cloudy plumes and aerosol‐depleted hot spots, are not a good proxy for microwave brightness. The hot spots are neither uniformly warmer nor ammonia‐depleted compared to their surroundings at p<1 bar. At 0.7 bar, the microwave brightness at the edges of hot spots is comparable to other features within the NEB. Conversely, hot spots are brighter at 1.5 bar, signifying either warm temperatures and/or depleted NH3 at depth. Temperatures and ammonia are spatially variable within the hot spots, so the precise location of the observations matters to their interpretation. Reflective plumes sometimes have enhanced NH3, cold temperatures, and elevated aerosol opacity, but each plume appears different. Neither plumes nor hot spots had microwave signatures in channels sensing p>10 bars, suggesting that the hot spot/plume wave is a relatively shallow feature.
Correction: Alectinib (CH5424802) antagonizes ABCB1- and ABCG2-mediated multidrug resistance in vitro, in vivo and ex vivo
Authors: Yang Ke , Chen Yifan , To Kenneth Kin Wah , Wang Fang , Li Delan , Chen Likun , Fu Liwu
Published: June 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
CREBBP and STAT6 co-mutation and 16p13 and 1p36 loss define the t(14;18)-negative diffuse variant of follicular lymphoma
Authors: Xian Rena R. , Xie Yi , Haley Lisa M. , Yonescu Raluca , Pallavajjala Aparna , Pittaluga Stefania , Jaffe Elaine S. , Duffield Amy S. , McCall Chad M. , Gheith Shereen M. F. , Gocke Christopher D.
Published: June 2020

The diffuse variant of follicular lymphoma (dFL) is a rare variant of FL lacking t(14;18) that was first described in 2009. In this study, we use a comprehensive approach to define unifying pathologic and genetic features through gold-standard pathologic review, FISH, SNP-microarray, and next-generation sequencing of 16 cases of dFL. We found unique morphologic features, including interstitial sclerosis, microfollicle formation, and rounded nuclear cytology, confirmed absence of t(14;18) and recurrent deletion of 1p36, and showed a novel association with deletion/CN-LOH of 16p13 (inclusive of CREBBP, CIITA, and SOCS1). Mutational profiling demonstrated near-uniform mutations in CREBBP and STAT6, with clonal dominance of CREBBP, among other mutations typical of germinal-center B-cell lymphomas. Frequent CREBBP and CIITA codeletion/mutation suggested a mechanism for immune evasion, while subclonal STAT6 activating mutations with concurrent SOCS1 loss suggested a mechanism of BCL-xL/BCL2L1 upregulation in the absence of BCL2 rearrangements. A review of the literature showed significant enrichment for 16p13 and 1p36 loss/CN-LOH, STAT6 mutation, and CREBBP and STAT6 comutation in dFL, as compared with conventional FL. With this comprehensive approach, our study demonstrates confirmatory and novel genetic associations that can aid in the diagnosis and subclassification of this rare type of lymphoma.
Delayed treatment with an autophagy inhibitor 3-MA alleviates the progression of hyperuricemic nephropathy
Authors: Shi Yingfeng , Tao Min , Ma Xiaoyan , Hu Yan , Huang Guansen , Qiu Andong , Zhuang Shougang , Liu Na
Published: June 2020

Autophagy is a cell self-renewal process that relies on the degradation of the cytoplasmic proteins or organelles of lysosomes and is associated with development of numerous diseases. However, the therapeutic effect of autophagy inhibition on hyperuricemic nephropathy (HN) and the underlying mechanisms are still unknown. Here, we investigated the effect of delayed treatment with 3-methyladenine (3-MA), a specific autophagy inhibitor, on the development of HN in a rat model. Administration of 3-MA at 21 days following after uric acid injury protected kidney from hyperuricemic-related injuries, as demonstrated by improving renal dysfunction and architecture damage, blocking Beclin-1 and LC3II/I and decreasing the number of autophagic vacuoles. Late treatment with 3-MA was also effective in attenuating renal fibrosis as evidenced by reducing ECM protein deposition, blocking epithelial-to-mesenchymal transition (EMT) and decreasing the number of renal epithelial cells arrested at the G2/M phase of cell cycle. Injury to the kidney resulted in increased expression of TGFβ receptor I, and phosphorylation of Smad3, 3-MA significantly abrogated all these responses. Moreover, inhibition of autophagy suppressed mitochondrial fission, downregulated the expression of Dynamin-related protein 1 (Drp-1), Cofilin and F-actin, and alleviated cell apoptosis. Finally, 3-MA effectively blocked STAT3 and NF-κB phosphorylation and suppressed infiltration of macrophages and lymphocytes as well as release of multiple profibrogenic cytokines/chemokines in the injured kidney. Taken together, these findings indicate that hyperuricemia-induced autophagy is critically involved in the activation of renal fibroblasts, EMT, mitochondrial fission and apoptosis of tubular epithelial cells and development of renal fibrosis. Thus, this study provides evidence for autophagy inhibitors as the treatment of HN patients.
Efficient polygenic risk scores for biobank scale data by exploiting phenotypes from inferred relatives
Authors: Truong Buu , Zhou Xuan , Shin Jisu , Li Jiuyong , van der Werf Julius H. J. , Le Thuc D. , Lee S. Hong
Published: June 2020

Polygenic risk scores are emerging as a potentially powerful tool to predict future phenotypes of target individuals, typically using unrelated individuals, thereby devaluing information from relatives. Here, for 50 traits from the UK Biobank data, we show that a design of 5,000 individuals with first-degree relatives of target individuals can achieve a prediction accuracy similar to that of around 220,000 unrelated individuals (mean prediction accuracy = 0.26 vs. 0.24, mean fold-change = 1.06 (95% CI: 0.99-1.13), P-value = 0.08), despite a 44-fold difference in sample size. For lifestyle traits, the prediction accuracy with 5,000 individuals including first-degree relatives of target individuals is significantly higher than that with 220,000 unrelated individuals (mean prediction accuracy = 0.22 vs. 0.16, mean fold-change = 1.40 (1.17-1.62), P-value = 0.025). Our findings suggest that polygenic prediction integrating family information may help to accelerate precision health and clinical intervention.
Investigating the use of sensory information to detect and track prey by the Sunda pangolin (Manis javanica) with conservation in mind
Authors: DiPaola Joshua D. , Yindee Marnoch , Plotnik Joshua M.
Published: June 2020

Pangolins are of conservation concern as one of the most heavily poached, yet least understood mammals. The Sunda pangolin (Manis javanica) in particular is a critically endangered species. Here, we investigate the behaviour of these pangolins, for the first time, using a battery of cognitive tasks based on a manipulation of available sensory information. In an object-choice task in which only one of two containers was baited with food, the pangolins were able to find the food with olfactory information alone (N = 2), but not with visual or acoustic information alone (N = 1). The single subject tested on all three domains was further tested on how he used smell to find food by providing him with an opportunity to find it from a controlled distance or by using scent trails as a guide. The results suggest that our subject may have the capacity to exploit scent trails left by prey which can be tracked to a final source, though we found no evidence to suggest that he had the ability to initiate hunts based on distant prey odors. Despite the small sample size, this is the first controlled experiment to investigate pangolin foraging behaviour and cognition, which may have implications for the future protection of pangolin habitat based on the location of prey species.
Robustness to extinction and plasticity derived from mutualistic bipartite ecological networks
Authors: Sheykhali Somaye , Fernández-Gracia Juan , Traveset Anna , Ziegler Maren , Voolstra Christian R. , Duarte Carlos M. , Eguíluz Víctor M.
Published: June 2020

Understanding the response of ecological networks to perturbations and disruptive events is needed to anticipate the biodiversity loss and extinction cascades. Here, we study how network plasticity reshapes the topology of mutualistic networks in response to species loss. We analyze more than one hundred empirical mutualistic networks and considered random and targeted removal as mechanisms of species extinction. Network plasticity is modeled as either random rewiring, as the most parsimonious approach, or resource affinity-driven rewiring, as a proxy for encoding the phylogenetic similarity and functional redundancy among species. This redundancy should be positively correlated with the robustness of an ecosystem, as functions can be taken by other species once one of them is extinct. We show that effective modularity,i.e. the ability of an ecosystem to adapt or restructure, increases with increasing numbers of extinctions, and with decreasing the replacement probability. Importantly, modularity is mostly affected by the extinction rather than by rewiring mechanisms. These changes in community structure are reflected in the robustness and stability due to their positive correlation with modularity. Resource affinity-driven rewiring offers an increase of modularity, robustness, and stability which could be an evolutionary favored mechanism to prevent a cascade of co-extinctions.
Using eye movements to detect visual field loss: a pragmatic assessment using simulated scotoma
Authors: Asfaw Daniel S. , Jones Pete R. , Edwards Laura A. , Smith Nicholas D. , Crabb David P.
Published: June 2020

Glaucoma is a leading cause of irreversible sight-loss and has been shown to affect natural eye-movements. These changes may provide a cheap and easy-to-obtain biomarker for improving disease detection. Here, we investigated whether these changes are large enough to be clinically useful. We used a gaze-contingent simulated visual field (VF) loss paradigm, in which participants experienced a variable magnitude of simulated VF loss based on longitudinal data from a real glaucoma patient (thereby controlling for other variables, such as age and general health). Fifty-five young participants with healthy vision were asked to view two short videos and three pictures, either with: (1) no VF loss, (2) moderate VF loss, or (3) advanced VF loss. Eye-movements were recorded using a remote eye tracker. Key eye-movement parameters were computed, including saccade amplitude, the spread of saccade endpoints (bivariate contour ellipse area), location of saccade landing positions, and similarity of fixations locations among participants (quantified using kernel density estimation). The simulated VF loss caused some statistically significant effects in the eye movement parameters. Yet, these effects were not capable of consistently identifying simulated VF loss, despite it being of a magnitude likely easily detectable by standard automated perimetry.
Spatial pattern of Bois noir: case study of a delicate balance between disease progression and recovery
Authors: Murolo Sergio , Garbarino Matteo , Mancini Valeria , Romanazzi Gianfranco
Published: June 2020

Bois noir (BN) is the most important phytoplasma disease of Euro-Mediterranean area and induces severe loss of production and even the death of vines. Understanding the delicate balance between disease progression and recovery of BN infected plants over space and time is crucial to set up management tools. The data collected and analysed allowed to provide insights into dispersal pattern of the disease, caused by’Candidatus Phytoplasma solani’. Point pattern analysis (PPA) was applied to assess the spatial arrangement of symptomatic plants and the spatial correlation of disease levels in four vineyards. For spatio-temporal patterns of BN, a mark-correlation function was applied. Space-time PPA over multiple years (2011–2015) provided graphical visualisation of grapevines more severely affected by BN along the borders of the vineyards, mainly in 2011 when disease incidence was high. PPA across the symptomatic plants in the four vineyards confirmed this visual trend: an overall aggregated pattern at small (<10 m) spatial scales (2013) that were more evident later at all spatial scales (0–15 m). Application of this innovative spatial approach based on point and surface pattern analyses allowed the spread and severity of BN to be monitored, to define the dispersal routes of the pathogen. Such data will contribute to better understand the distribution of symptomatic plants over space and time and to define a model for preventive strategies to reduce future infections.
Paroxysmal eruptions tracked by variations of helium isotopes: inferences from Piton de la Fournaise (La Réunion island)
Authors: Boudoire G. , Rizzo A. L. , Arienzo I. , Di Muro A.
Published: June 2020

Helium (He) with its isotopes (3He,4He) is a key tracer enabling the Earth’s mantle and dynamics to be characterized. Enrichment in primordial helium (3He) has been detected in volcanic gases of numerous magmatic systems in different geodynamic settings. Despite past use to monitor volcano-tectonic unrest, temporal3He/4He variability in volcanic emissions is still poorly constrained. Here, we investigate noble gas chemistry of Piton de la Fournaise hotspot volcano, where temporal fluctuations of3He/4He in response to the eruptive activity have never been studied. We compare the3He/4He signature of volcanic gases and fluid inclusions and we highlight analogous evolution of the3He/4He signature in both during the last decades of eruptive activity (1990–2017), even during the same eruption. We show that the maximum enrichment in3He is found in magmatic fluids that fed the most voluminous eruptions which culminated in caldera collapse events. We argue that this enrichment in3He mostly reflects a greater contribution of magmatic fluids from a primitive component of the mantle plume. These results emphasize that He isotopes may provide warnings of increases in deep magmatic contributions that potentially herald paroxysmal eruptions, as documented here at Piton de la Fournaise (2007) and also at Kilauea (2018).
Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex
Authors: Shah Sarah , Chen Yibi , Bhattacharya Debashish , Chan Cheong Xin
Published: June 2020

Dinoflagellates of the Symbiodiniaceae family encompass diverse symbionts that are critical to corals and other species living in coral reefs. It is well known that sexual reproduction enhances adaptive evolution in changing environments. Although genes related to meiotic functions were reported in Symbiodiniaceae, cytological evidence of meiosis and fertilisation are however yet to be observed in these taxa. Using transcriptome and genome data from 21 Symbiodiniaceae isolates, we studied genes that encode proteins associated with distinct stages of meiosis and syngamy. We report the absence of genes that encode main components of the synaptonemal complex (SC), a protein structure that mediates homologous chromosomal pairing and class I crossovers. This result suggests an independent loss of canonical SCs in the alveolates, that also includes the SC-lacking ciliates. We hypothesise that this loss was due in part to permanently condensed chromosomes and repeat-rich sequences in Symbiodiniaceae (and other dinoflagellates) which favoured the SC-independent class II crossover pathway. Our results reveal novel insights into evolution of the meiotic molecular machinery in the ecologically important Symbiodiniaceae and in other eukaryotes.
Hierarchical multi-shell hollow micro–meso–macroporous silica for Cr(VI) adsorption
Authors: Soltani Roozbeh , Marjani Azam , Soltani Reza , Shirazian Saeed
Published: June 2020

The development of easier, cheaper, and more effective synthetic strategies for hierarchical multimodal porous materials and multi-shell hollow spheres remains a challenging topic to utilize them as adsorbents in environmental applications. Here, the hierarchical architecture of multi-shell hollow micro–meso–macroporous silica with pollen-like morphology (MS-HMS-PL) has been successfully synthesized via a facile soft-templating approach and characterized for the first time. MS-HMS-PL sub-microspheres showed a trimodal hierarchical pore architecture with a high surface area of 414.5 m2 g−1, surpassing most of the previously reported multishelled hollow nanomaterials. Due to its facile preparation route and good physicochemical properties, MS-HMS-PL could be a potential candidate material in water purification, catalysis, and drug delivery. To investigate the applicability of MS-HMS-PL as an adsorbent, its adsorption performance for Cr(VI) in water was evaluated. Important adsorption factors affecting the adsorption capacity of adsorbent were systematically studied and Kinetics, isotherms, and thermodynamics parameters were computed via the non-linear fitting technique. The maximum capacity of adsorption computed from the Langmuir isotherm equation for Cr(VI) on MS-HMS-PL was 257.67 mg g−1 at 293 K and optimum conditions (pH 4.0, adsorbent dosage 5.0 mg, and contact time 90 min).