bluuebunny/crossref_metadata_2025 huggingface dataset:
Anthropogenic flow intermittency shapes food‐web topology and community delineation in Mediterranean rivers
Authors: Peralta‐Maraver Ignacio , López‐Rodríguez Manuel Jesús , Robertson Anne L. , Tierno de Figueroa José Manuel
Published: April 2020

Anthropogenic flow intermittency is considered a severe disturbance for benthic macroinvertebrates with largely unknown impacts on the organization of benthic communities and their food webs. We analysed the community composition (as taxonomic composition and relative abundance of taxa) and food webs of the macroinvertebrates inhabiting the pools and riffles of two Mediterranean streams with contrasting perennial and anthropogenic intermittent flow regimes. Our analyses comprised monthly measurements in two pools and two riffles of the community composition, food‐web topology (the pattern in which specific links are arranged within the network) and food‐web complexity indexes (the number of nodes and links regardless of their identity or arrangement) over 1 year. The food webs revealed a significant annual variation in size, complexity, and diversity within pools and under perennial flow (e.g., number of nodes, number of links, link density). Multivariate analysis showed strong differences in the composition and relative abundance of taxa and food‐web topology of assemblages inhabiting pools and riffles. However, differences between communities inhabiting pools and riffles varied during the year; periods of great similarity were followed by periods in which communities were very different. This annual sequence of differences between pools and riffles was compressed under the anthropogenic flow intermittency regime. The anthropogenic intermittent flow studied here might represent a moderate stressor for Mediterranean communities well‐adapted to dry conditions. Still, the reported deviation of the community composition and food‐web topology from the reference status reflect the detrimental effect of this stressor on the benthic community.
From Microaggressions to Neural Aggressions: A Neuro‐Informed Counseling Perspective
Authors: Luke Chad , Redekop Frederick , Moralejo Jennifer
Published: April 2020

Microaggressions are explicit and implicit forms of bias committed by many well‐meaning and otherwise moral individuals, including counselors. This paradox has been explained in terms of socialized, systemic oppression of marginalized groups by those in power. In this article, the authors seek to extend this understanding by exploring the neurobiological dynamics underlying these systems. This understanding can aid counselors in increasing their multicultural counseling competence, spare clients from further injury, and model this prosocial orientation for clients and the community.

Las microagresiones son formas de prejuicio tanto explícitas como implícitas cometidas por muchas personas con buenas intenciones y normalmente éticas, incluyendo consejeros. La explicación a esta paradoja se ha dado en términos de opresión sistémica y socializada de grupos marginados por parte de las personas que ostentan el poder. En este artículo, los autores buscaron la forma de expandir esta comprensión explorando la dinámica neurobiológica subyacente en estos sistemas. Dicha comprensión puede ayudar a los consejeros a aumentar su competencia en consejería multicultural, evitar mayores daños a sus clientes y modelar esta orientación prosocial para sus clientes y la comunidad en general.
Relevance of reviewing endpoint analysis for negative results on the Xpert Xpress Flu/RSV
Authors: Matic Nancy , Ritchie Gordon , Lawson Tanya , Karakas Loretta , Romney Marc G. , Lowe Christopher F.
Published: April 2020

After the implementation of the Xpert Xpress Flu/respiratory syncytial virus (RSV) assay for rapid respiratory molecular testing, we investigated the significance of reported endpoint values for influenza A, influenza B, and RSV). This study prospectively analyzed nasopharyngeal swabs submitted to our virology laboratory in the 2018/19 influenza season. Initial testing was performed on the Xpress Flu/RSV assay. Samples were further tested on a laboratory‐developed multiplex polymerase chain reaction (laboratory‐developed multiplex respiratory test [LDT]) if the sample was reported as negative by the Xpress Flu/RSV but had an elevated endpoint value ≥5 for any respiratory virus target. There were 1040 negative results on the Xpress Flu/RSV; thirty‐one had at least one endpoint value ≥5 [influenza A (25), influenza B (1), RSV (2), influenza A/RSV (1), and influenza A/B/RSV (2)]. Five samples (5/31, 16.1%) were positive on the LDT for influenza A or RSV. In contrast, the positivity rate on the LDT for negative Xpress Flu/RSV samples with endpoint values less than 5 was 0.35% (P < .0001). A threshold for endpoint values could not reliably be established to differentiate a potential influenza A positive result from a negative result on the LDT. Routine evaluation ofendpoint values should be a consideration for laboratories implementing Xpress Flu/RSV, in addition to supplementary respiratory virus testing for clinically relevant situations.
Skin wipe test: A simple, inexpensive, and fast approach in the diagnosis of cystic fibrosis
Authors: Ďurč Pavol , Foret František , Homola Lukáš , Malá Miriam , Pokojová Eva , Vinohradská Hana , Dastych Milan , Krausová Dagmar , Nagy Dóra , Bede Olga , Dřevínek Pavel , Skalická Veronika , Kubáň Petr
Published: April 2020

Objective

To assess the performance of a newly developed skin wipe test (SWT) for the diagnosis of cystic fibrosis (CF).

Study Design

Spontaneously formed sweat from the forearm was wiped by a cotton swab moistened with 100 µL of deionized (DI) water and extracted into 400 µL of DI water (SWT). The conventional Macroduct sweat test (ST) was performed simultaneously. SWT samples of 114 CF patients, 76 healthy carriers, and 58 controls were analyzed by capillary electrophoresis with contactless conductivity detection and Cl−/K+ and (Cl− + Na+)/K+ ion ratios were evaluated. Chloride concentrations from Macroduct ST were analyzed coulometrically.

Results

Analysis of 248 SWT samples and simultaneous Macroduct ST samples showed comparable method performance. Two ion ratios, Cl−/K+ and (Cl− + Na+)/K+, from the SWT samples and Cl− values from the ST samples were evaluated to diagnose CF. Sensitivity of the SWT method using the Cl−/K+ ratio (cutoff value 3.9) was 93.9%, compared to 99.1% when using the (Cl− + Na+)/K+ ratio (cutoff value 5.0) and 98.3% in using Macroduct Cl− (cutoff value higher or equal to 60 mmol/L). The methods' specificities were 97.8%, 94.0%, and 100.0%, respectively.

Conclusions

The developed SWT method with capillary electrophoretic analysis for CF diagnosis performs comparably to the conventional Macroduct ST. The SWT method is simple, fast, inexpensive, and completely noninvasive. Use of an ion ratio in obtained SWT samples is proposed as a new diagnostic parameter that shows significant promise in CF diagnostics.
UV sensitivity of the axion mass from instantons in partially broken gauge groups
Authors: Csáki Csaba , Ruhdorfer Maximilian , Shirman Yuri
Published: April 2020

Abstract

We examine the contribution of small instantons to the axion mass in various UV completions of QCD. We show that the reason behind the potential dominance of such contributions is the non-trivial embedding of QCD into the UV theory. The effects from instantons in the partially broken gauge group appear as “fractional instanton” corrections in the effective theory. These will exhibit unusual dependences on the various scales in the problem whenever the index of embedding is non-trivial. We present a full one-instanton calculation of the axion mass in the simplest product group models, carefully keeping track of numerical prefactors. Rather than using a ’t Hooft operator approximation we directly evaluate the contributions to the vacuum bubble, automatically capturing the effects of closing up external fermion lines with Higgs loops. This approach is manifestly finite and removes the uncertainty associated with introducing a cutoff scale for the Higgs loops. We verify that the small instantons may dominate over the QCD contribution for very high breaking scales and at least three group factors.
The Party of Reform in the Doldrums: The Convergence of Anglo-American Political Progressivism
Authors: Kim Ilnyun
Published: April 2020

In September 1955, John Kenneth Galbraith encountered British Labour Party MP Richard Crossman at a conference hall in Milan, Italy. They went there with a clear mission: to defend their parties’ achievements from expected attacks by Friedrich Hayek and other “reactionaries” at the conference. In public, they confidently boasted about the records of the Democratic and Labour governments in prosperity, full employment, and social and welfare programs during the past decades. In private talks, however, they were less confident—and more candid. “Both the American liberal and the British socialist in the 1930s,” said Galbraith to Crossman, “assumed that capitalism was not only immoral but unworkable; it was a system which must destroy itself because of its own inherent weaknesses.” But if this assumption were not true, he asked, “would that not mean the snapping of the mainspring of the Labour Party?” Crossman instantly got the point. The clothes of American liberals were “stolen by the Eisenhower Republicans, just as ours [were] by the Butlerites,” confessed the Labour MP. The task of reforming capitalism, which had been the raison d’être of the “party of reform” of both countries, lost its urgency. An era of reform had been replaced by an era of moderation. And in this new era, their parties were clearly on the losing side—and would continue to lose until they could find a new cause to fight.
The embodied teaching of complex verbal constructions with German placement verbs and spatial prepositions
Authors: Knop Sabine De
Published: April 2020

In recent years, foreign language pedagogy has recognized the need to focus (i) on larger meaningful sequences of words (Nattinger & DeCarrico, 1992;Wray, 2002;Ellis & Cadierno, 2009;Gonzalez Rey, 2013) and (ii) further on communicative goals (Nunan, 1991;Widdowson, 1992;Savignon, 2000). Difficulties in the learning process of a foreign language result from the conceptual and constructional differences between expressions in the native and foreign language. Teaching materials often propose a lexical approach with an unstructured set of constructed examples.

With the postulate of meaningful schematic templates, Construction Grammar (CxG) has a number of assets for foreign language teaching (FLT) and learning (FLL), it allows among others to establish a structured inventory of abstract constructions with prototypical exemplars and inheritance links between the constructions’ instantiations. To be proficient in a foreign language also means to use new words in constructions. Learners can be asked to extend the use of new lexical units as slot-fillers into constructional patterns. This is exemplified with the use of German posture and placement verbs in the caused motion construction and the corresponding intransitive locative construction.

But having learned a vast number of constructional templates of a language does not automatically imply that learners can produce L2-constructions and their instantiations in a creative way. Therefore, CxG must be enriched with further insights from Cognitive Linguistics which claims that conceptual categories and their linguistic expressions are the result of embodied processes (Lakoff, 1987). This chapter makes some suggestions for interactive activities which can foster ‘embodied teaching and learning’.
Gillnet fishers’ knowledge reveals seasonality in depth and habitat use of cod (Gadus morhua) in the Western Baltic Sea
Authors: Funk Steffen , Krumme Uwe , Temming Axel , Möllmann Christian
Published: April 2020

Practical and applied knowledge of local fishers can help to improve our understanding of target species ecology and fisheries management decisions. In the Western Baltic Sea (WBS), the spatio-temporal distribution of cod is still largely unknown despite decades of research. We studied changes in cod distribution by obtaining information on temporal depth and habitat use of cod from commercial gillnet fishers using semi-directed interviews supplemented by at-sea observer data. Linear and non-linear regression analyses revealed significant relationships between depth use of cod and sea surface temperature (SST) as well as thermal stratification. Moreover, habitat use was related to SST and residence depth of cod. Areas deeper than 15 m were favoured from late December until March during low SST and a mixed water column (spawning) and also from July until August during high SST and strong thermal stratification (summer aestivation). Shallower areas were favoured during the rest of the year. The depth and habitat use displayed distinct seasonal up- and downslope movements of cod. This study highlights the importance of shallow-water and structured habitats for cod in the WBS and the value of local knowledge held by fishers for a better understanding of the distributional dynamics of important marine resource populations.
Managing Food Crises: Urban Relief Stocks in Pre-Industrial Holland*
Authors: Dijkman Jessica
Published: April 2020

One of the ways in which towns and cities in pre-industrial Europe responded to food crises was by establishing public grain stocks, intended for relief. This article shows how purchases and distribution of grain in Holland were affected by the long-term developments of commercialization and state formation. Two conclusions stand out. Firstly, both the acquisition of supplies and the distribution of relief relied heavily on the market. However, while market mechanisms were originally used to provide targeted relief through subsidies, at the end of the period under examination this was supplanted by a — largely unjustified — trust in the effects of the presence and release of stocks on food prices in general. Secondly, in keeping with a long-standing tradition of decentralized governance, urban governments and urban poor relief organizations were the main providers of the safety net that protected the food entitlements of vulnerable groups throughout the period under examination, even after the establishment of a centralized unitary state in the early nineteenth century.
A Study of Economic, Cultural, and Political Causes of Police Corruption in Pakistan
Authors: Malik Nadeem , Qureshi Tariq Abbas
Published: April 2020

There is a dearth of studies on police corruption that have analysed the correlation of economic, cultural, and political causes of police corruption in Pakistan; therefore, the existing studies fail to provide such a holistic picture of the phenomenon. This article aims to fill the gap. It is claimed that police corruption in Pakistan is a politicized, institutionalized, and a legitimized phenomenon. The police force entrenched in a kinship-based patron–client social and political culture benefits the political elite to use the police force for controlling the electorate and political opponents. The policy reforms for curbing police corruption have failed and cannot be successful without a strong political will of the political elite. This is a qualitative study using a purposive sampling method. The article will be a useful reference for readers, including police officials who are interested in understanding why corruption could not be effectively prevented and may have some broader relevance to other South Asian countries.
Food protein-induced enterocolitis syndrome epidemiology, diagnosis, and treatment
Authors: Pecora Valentina , Valluzzi Rocco , Dahdah Lamia , Fierro Vincenzo , Mennini Maurizio , Fiocchi Alessandro
Published: April 2020

Purpose of review

In the last years, the interest of the scientific community toward food protein-induced enterocolitis syndrome (FPIES) has grown exponentially. We review here the peculiar characteristics of this syndrome.

Recent findings

The recent publication of the First International Consensus Guidelines allowed a positive interaction between different research groups with the aim of improving the diagnosis and management of patients affected by FPIES.

Several fixed points have been placed on the diagnosis and management, but further studies are needed to clarify the many shadows that still surround different aspects of the syndrome, especially regarding the pathophysiology.
Dynamic methods for ongoing assessment of site-level risk in risk-based monitoring of clinical trials: a scoping review
Authors: Cragg William J , Hurley Caroline , Yorke-Edwards Victoria , Stenning Sally P
Published: April 2020

Background/Aims

It is increasingly recognised that reliance on frequent site visits for monitoring clinical trials is inefficient. Regulators and trialists have in recent years encouraged more risk-based monitoring. Risk assessment should take place before a trial begins in order to define the overarching monitoring strategy. It can also be done on an ongoing basis, in order to target sites for monitoring activity. Various methods have been proposed for such prioritisation, often using terms like ‘central statistical monitoring’, ‘triggered monitoring’ or, as in ICH Good Clinical Practice guidance, ‘targeted on-site monitoring’. We conducted a scoping review to identify such methods, to establish if any published methods were supported by adequate evidence to allow wider implementation, and to point the way to future developments in this field of research.

Methods

We used 7 publication databases, 2 sets of methodological conference abstracts and an internet search engine to look for methods for using centrally held trial data to assess site conduct during a trial. We included only reports in English, and excluded reports published before 1996 and reports not directly relevant to our research question. We used reference and citation searches to find additional relevant reports. We extracted data using a pre- defined template. We contacted authors to request additional information about included reports and to check whether reports might be eligible.

Results

We included 30 reports in our final dataset, of which 21 were peer-reviewed publications. 20 reports described central statistical monitoring methods (of which 7 focussed on detection of fraud or misconduct) and 9 described triggered monitoring methods. 21 reports included some assessment of their methods’ effectiveness. Most commonly this involved exploring the methods’ characteristics using real trial data with no known integrity issues. Of the 21 with some effectiveness assessment, most presented limited or no information about whether or not concerns identified through central monitoring constituted meaningful problems. Some reports commented on cost savings from reduced on-site monitoring, but none gave detailed costings for the development and maintenance of central monitoring methods themselves.

Conclusions

Our review identified various proposed methods, some of which could be combined within the same trial. The apparent emphasis on fraud detection may not be proportionate in all trial settings. Although some methods have self-justifying benefits for data cleaning activity, many have limitations that may currently prevent their routine use for targeting trial monitoring activity. The implementation costs, or uncertainty about these, may also be a barrier. We make recommendations for how the evidence-base supporting these methods could be improved.
Pre-outbreak determinants of perceived risks of corona infection and preventive measures taken. A prospective population-based study
Authors: van der Velden Peter G. , Marchand Miquelle , Cuelenaere Boukje , Das Marcel
Published: April 2020

Objectives

Assess how people perceive the risks of coronavirus infection, whether people take preventive measures, and which (pre-outbreak) factors contribute to the perceived risks and measures taken, such as (pre-outbreak) respiratory problems, heart problems, diabetes, anxiety and depression symptoms, loneliness, age, gender, marital status and education level.

Methods

Data were collected in the longitudinal LISS panel, based on a random sample of the Dutch population. The coronavirus survey started on March 2, and the data collection ended on March 17 2020. Data were linked with surveys on health and social integration conducted at the end of 2019 (Nstudy sample=3,540).

Results

About 15% perceived the risk of infection as high, and 11% the risk becoming ill when infected. Multivariate logistic regression analyses showed the following. Older age-groups perceived the risk for coronavirus infection as lower (all adjusted Odd Ratio’s [aOR] ≤ .058). In total, 43.8% had taken preventive measures, especially females (aOR=1.47, 95% CI=1.27-1.69). Those with lower education levels less often used preventive measures (aOR=0.56, 95% CI=0.46-0.69). Those with pre-outbreak respiratory problems (aOR=2.89, 95% CI=2.24-3.73), heart problems (aOR=2.17, 95% CI=1.49-3.16) and diabetes (aOR=3.10, 95% CI=2.02-4.74) perceived the risk becoming ill when infected as higher than others. However, respondents with pre-outbreak respiratory problems and diabetes did not more often take preventive measures.

Conclusions

Vulnerable patients more often recognize that they are at risk becoming ill when infected by the coronavirus, but many do not take preventive measures. Interventions to stimulate the use of preventive measures should pay additional attention to physically vulnerable patients, men and those with lower education levels.
Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein
Authors: Dinesh Dhurvas Chandrasekaran , Chalupska Dominika , Silhan Jan , Veverka Vaclav , Boura Evzen
Published: April 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the Coronavirus disease 2019 (COVID-19) which is currently negatively affecting the population and disrupting the global economy. SARS-CoV-2 belongs to the +RNA virus family that utilize single-stranded positive-sense RNA molecules as genomes. SARS-CoV-2, like other coronaviruses, has an unusually large genome for a +RNA virus that encodes four structural proteins – the matrix (M), small envelope (E), spike (S) and nucleocapsid phosphoprotein (N) - and sixteen nonstructural proteins (nsp1-16) that together ensure replication of the virus in the host cell. The nucleocapsid phosphoprotein N is essential for linking the viral genome to the viral membrane. Its N-terminal RNA binding domain (N-NTD) captures the RNA genome while the C-terminal domain anchors the ribonucleoprotein complex to the viral membrane via its interaction with the M protein. Here, we characterized the structure of the N-NTD and its interaction with RNA using NMR spectroscopy. We observed a positively charged canyon on the surface of the N-NTD lined with arginine residues suggesting a putative RNA binding site. Next, we performed an NMR titration experiment using an RNA duplex. The observed changes in positions of signals in the N-NTD NMR spectra allowed us to construct a model of the N-NTD in complex with RNA.
Optimal COVID-19 epidemic control until vaccine deployment
Authors: Djidjou-Demasse R. , Michalakis Y. , Choisy M. , Sofonea M. T. , Alizon S.
Published: April 2020

Since Dec 2019, the COVID-19 epidemic has spread over the globe creating one of the greatest pandemics ever witnessed. This epidemic wave will only begin to roll back once a critical proportion of the population is immunised, either by mounting natural immunity following infection, or by vaccination. The latter option can minimise the cost in terms of human lives but it requires to wait until a safe and efficient vaccine is developed, a period estimated to last at least 18 months. In this work, we use optimal control theory to explore the best strategy to implement while waiting for the vaccine. We seek a solution minimizing deaths and costs due to the implementation of the control strategy itself. We find that such a solution leads to an increasing level of control with a maximum reached near the 16th month of the epidemics and a steady decrease until vaccine deployment. The average containment level is approximately 50% during the 25-months period for vaccine deployment. This strategy strongly out-performs others with constant or cycling allocations of the same amount of resources to control the outbreak. This work opens new perspectives to mitigate the effects of the ongoing COVID-19 pandemics, and be used as a proof-of-concept in using mathematical modelling techniques to enlighten decision making and public health management in the early times of an outbreak.
Quantifying the demographic vulnerabilities of dry woodlands to climate and competition using range-wide monitoring data
Authors: Shriver Robert K. , Yackulic Charles B. , Bell David M. , Bradford John B.
Published: April 2020

Climate change is expected to alter the distribution and abundance of tree species, impacting ecosystem structure and function. Yet, anticipating where this will occur is often hampered by a lack of understanding of how demographic rates, most notably recruitment, vary in response to climate and competition across a species range. Using large-scale monitoring data on two dry woodland tree species (Pinus edulisandJuniperus osteosperma), we develop an approach to infer recruitment, survival, and growth of both species across their range. In doing so, we account for ecological and statistical dependencies inherent in large-scale monitoring data. We find that warming and drying conditions generally lead to declines in recruitment and survival, but there were some idiosyncrasy in the strength of responses across species. Climate conditions lead to vulnerable regions, such asPinus edulisin N. Arizona, where both survival and recruitment are low. Our approach provides a path forward for leveraging emerging large-scale monitoring and remotely sensed data to anticipate the impacts of global change on species distributions.
Stability and individual variability of social attachment in imprinting
Authors: Lemaire Bastien S. , Rucco Daniele , Josserand Mathilde , Vallortigara Giorgio , Versace Elisabetta
Published: April 2020

Filial imprinting has become a model for understanding memory, learning and social behaviour in neonate animals. This fast attachment mechanism allows the young of precocial bird species to learn the characteristics of conspicuous visual stimuli and display affiliative response to them. Although more prolonged exposure to an object produces a stronger preference for it afterwards, this relation is not linear. Chicks can even prefer to approach novel rather than familiar objects at some stages of imprinting. The time course and stability of imprinting has just started to be investigated. To date, little is known about how filial preferences develop across time, due to the challenges in assessing individual performance. This study aimed to investigate filial preferences for familiar and novel imprinting objects over time. We have used an automated setup to track the behaviour of chicks continuously for subsequent days. After hatching, chicks were individually placed in an arena where stimuli were displayed on two opposite screens. The duration of exposure and the type of stimuli were manipulated while the time spent at the imprinting stimulus was monitored across six days. We showed that prolonged exposure (3 days vs 1 day) to a stimulus produced robust filial imprinting preferences. Interestingly, with a shorter exposure (1 day), animals re-evaluated their filial preferences in functions of their innate preferences and past experiences. Our study suggests that predispositions influence learning when the imprinting memories are not fully consolidated, driving animal preferences toward more predisposed stimuli.
Can biomass distribution across trophic levels predict trophic cascades?
Authors: Galiana Núria , Arnoldi Jean-François , Barbier Matthieu , Acloque Amandine , de Mazancourt Claire , Loreau Michel
Published: April 2020

The biomass distribution across trophic levels (biomass pyramid), and cascading responses to perturbations (trophic cascades), are archetypal representatives of the interconnected set of static and dynamical properties of food chains. A vast literature has explored their respective ecological drivers, sometimes generating correlations between them. Here we instead reveal a fundamental connection: both pyramids and cascades reflect the dynamical sensitivity of the food chain to changes in species intrinsic rates. We deduce a direct relationship between cascades and pyramids, modulated by what we call trophic dissipation – a synthetic concept that encodes the contribution of top-down propagation of consumer losses in the biomass pyramid. Predictable across-ecosystem patterns emerge when systems are in similar regimes of trophic dissipation. Data from 31 aquatic mesocosm experiments demonstrate how our approach can reveal the causal mechanisms linking trophic cascades and biomass distributions, thus providing a road map to deduce reliable predictions from empirical patterns.
Zebrafish macrophage developmental arrest underlies depletion of microglia and reveals Csf1r-independent metaphocytes
Authors: Kuil Laura E. , Oosterhof Nynke , Ferrero Giuliano , Mikulášová Tereza , Hason Martina , Dekker Jordy , Rovira Mireia , van der Linde Herma C. , van Strien Paulina M.H. , de Pater Emma , Schaaf Gerben , Bindels Eric M.J. , Wittamer Valerie , van Ham Tjakko J.
Published: April 2020

Macrophages derive from multiple sources of hematopoietic progenitors. Most macrophages require colony-stimulating factor 1 receptor (CSF1R), but some macrophages persist in the absence of CSF1R. Here, we analyzedmpeg1:GFP–expressing macrophages incsf1r-deficient zebrafish and report that embryonic macrophages emerge followed by their developmental arrest. In larvae,mpeg1+ cell numbers then increased showing two distinct types in the skin: branched, putative Langerhans cells, and amoeboid cells. In contrast, although numbers also increased incsf1r-mutants, exclusively amoeboidmpeg1+cells were present, which we showed by genetic lineage tracing to have a non-hematopoietic origin. They expressed macrophage-associated genes, but also showed decreased phagocytic gene expression and increased epithelial-associated gene expression, characteristic of metaphocytes, recently discovered ectoderm-derived cells. We further demonstrated that juvenilecsf1r-deficient zebrafish exhibit systemic macrophage depletion. Thus, Csf1r deficiency disrupts embryonic to adult macrophage development. Csf1r-deficient zebrafish are viable and permit analyzing the consequences of macrophage loss throughout life.
Elucidation of the signatures of proteasome-catalysed peptide splicing
Authors: Paes Wayne , Leonov German , Partridge Thomas , Nicastri Annalisa , Ternette Nicola , Borrow Persephone
Published: April 2020

Proteasomes catalyse the degradation of endogenous proteins into oligopeptides, but can concurrently create spliced oligopeptides through ligation of previously non-contiguous peptide fragments. Recent studies have uncovered a formerly unappreciated role for proteasome-catalysed peptide splicing (PCPS) in the generation of non-genomically templated human leukocyte antigen class I (HLA-I)-boundcis-spliced peptides that can be targeted by CD8+T cells in cancer and infection. However, the mechanisms defining PCPS reactions are poorly understood. Here, we experimentally define the biochemical constraints of proteasome-catalysedcis-splicing reactions by examination ofin vitroproteasomal digests of a panel of viral- and self-derived polypeptide substrates using a tailored mass-spectrometry-basedde novosequencing workflow. We show that forward and reverse PCPS reactions display unique splicing signatures, defined by preferential fusion of distinct amino acid residues with stringent peptide length distributions, suggesting sequence- and size-dependent accessibility of splice reactants for proteasomal substrate binding pockets. Our data provide the basis for a more informed mechanistic understanding of PCPS that will facilitate future prediction of spliced peptides from protein sequences.
Abundantly expressed class of non-coding RNAs conserved through the multicellular evolution of dictyostelid social amoebae
Authors: Kjellin Jonas , Avesson Lotta , Reimegård Johan , Liao Zhen , Eichinger Ludwig , Noegel Angelika , Glöckner Gernot , Schaap Pauline , Söderbom Fredrik
Published: April 2020

Background

Aggregative multicellularity has evolved multiple times in diverse groups of eukaryotes. One of the most well-studied examples is the development of dictyostelid social amoebae, e.g.Dictyostelium discoideum. However, it is still poorly understood why multicellularity emerged in these amoebae while the great majority of other members of Amoebozoa are unicellular. Previously a novel type of non-coding RNA, Class I RNAs, was identified inD. discoideumand demonstrated to be important for normal multicellular development. In this study we investigated Class I RNA evolution and its connection to multicellular development.

Results

New Class I RNA genes were identified by constructing a co-variance model combined with a scoring system based on conserved up-stream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis validated that our search approach can identify expressed Class I RNA genes with high accuracy and sensitivity. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share several highly conserved structure and sequence motifs. Class I RNA genes appear to be unique to dictyostelid social amoebae since they could not be identified in searches in outgroup genomes, including the closest known relatives to Dictyostelia.

Conclusion

Our results show that Class I RNA is an ancient abundant class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Taken together, our current knowledge of Class I RNAs suggests that they may have been involved in evolution of multicellularity in Dictyostelia.
Distinct responses of oomycete plant parasites according to their lifestyle in a landscape-scale metabarcoding survey
Authors: Fiore-Donno Anna Maria , Bonkowski Michael
Published: April 2020

Oomycetes are an ubiquitous protistan lineage including devastating crop parasites. Although their ecology in agrosystems has been widely studied, little is known of their distribution in natural and semi-natural ecosystems. We provide here a baseline of the diversity and distribution of soil oomycetes, classified by lifestyles (biotrophy, hemibiotrophy and saprotrophy), at the landscape scale in temperate grassland and forest. From 600 soil samples, we obtained 1,148 Operational Taxonomy Units representing ∼20 million Illumina reads (region V4, 18S rRNA gene). We found a majority of hemibiotrophic plant pathogens, which are parasites spending part of their life cycle as saprotrophs after the death of the host. Overall both grassland and forest constitute an important reservoir of plant pathogens. In forests, relative abundances of obligate biotrophs and hemibiotrophs differed between regions and showed opposite responses to edaphic conditions and human-induced management intensification, suggesting different ecological requirements for these two functional guilds.
Synchronisation of yeast cell cycle through quorum sensing coupling
Authors: Perrino Giansimone , di Bernardo Diego
Published: April 2020

The cell cycle is present in all cells of all species and it is of fundamental importance in coordinating all the steps required for cell replication, including growth, DNA replication and cell division. Budding yeast is an unicellular organism characterised by a mother cell that buds to generate a daughter cell at each cell cycle. Each cell in a population buds at a different time. Despite its importance in biological applications, such as unravelling cell-cycle machinery mechanisms and production of valuable bioproducts, at present no yeast strain is capable of budding synchronously. To overcome this problem, we used control theory to propose a strategy to modify the yeast cell to endow it with the ability to synchronise its cell cycle across the population. Our strategy relies on a quorum sensing molecule diffusing freely in and out of the cell. The quorum sensing molecule is produced only during a specific phase of the cell cycle and couples the cell-cycle across the cell population. Here we model the proposed strategy with ordinary differential equations and numerically simulate it to demonstrate the feasibility of such an approach.
Molecularly Targeted Magnetic Resonance Imaging and Spectroscopy
Authors: Xin Jia-Xiang , Li Yi , Liu Hui-Xia , Li Jianqi , Yang Guang , Zhang Huojun , Wang Jiachen , Tong Rui , Wei Da-Xiu , Yao Ye-Feng
Published: April 2020

Magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) have tremendous utility in many fields, such as clinical diagnosis, medical research and brain science. MRI provides high resolution anatomic images of tissues/organs, and MRS provides functional molecular information related to specific regions of tissues/organs. However, it is often difficult for conventional MRI/MRS to selectively image/probe a specific metabolite molecule other than water and fat. This greatly limits study of the molecular mechanisms underlying metabolism and disease. Herein, we report a novel method for obtaining an exact molecularly targeted MRI and MRS. This method uses the nuclear spin singlet state to select the signals from a specific molecule. Several endogenous molecules in living organism such as N-acetylaspartate and dopamine have been exemplarily imaged and probed as the targeted molecules in the MRI and MRS experiments, demonstrating the unique molecular selectivity of the developed method.

Endogenous-molecule-targeted MRI and MRS can be achieved by using the new pulse sequences
A Lysate Proteome Engineering Strategy for Enhancing Cell-Free Metabolite Production
Authors: Garcia David C. , Dinglasan Jaime Lorenzo N. , Shrestha Him , Abraham Paul E. , Hettich Robert L. , Doktycz Mitchel J.
Published: April 2020

Cell-free systems present a significant opportunity to harness the metabolic potential of diverse organisms. Removing the cellular context provides the ability to produce biological products without the need to maintain cell viability and enables metabolic engineers to explore novel chemical transformation systems. Crude extracts maintain much of a cell’s capabilities. However, only limited tools are available for engineering the contents of the extracts used for cell-free systems. Thus, our ability to take full advantage of the potential of crude extracts for cell-free metabolic engineering is limited. Here, we employ Multiplex Automated Genomic Engineering (MAGE) to tag proteins for selective removal from crude extracts so as to specifically direct chemical production. Specific edits to central metabolism are possible without significantly impacting cell growth. Selective removal of pyruvate degrading enzymes are demonstrated that result in engineered crude lysates that are capable of 10 to 20-fold increases of pyruvate production when compared to the non-engineered extract. The described approach melds the tools of systems and synthetic biology to develop cell-free metabolic engineering into a practical platform for both bioprototyping and bioproduction.

Highlights

A novel method of engineering crude cell lysates for enhancing specific metabolic processes is described.

Multiplex Automated Genomic Engineering (MAGE) can be used to engineer donor strains for improving cell-free metabolite production with minimal impact on cell-growth.

The described lysate engineering strategy can specifically direct metabolic flux and create metabolic states not possible in living cells.

Pooling of the central precursor pyruvate was significantly improved through use of this lysate proteome engineering strategy.
Sexual dimorphism and sex ratio bias in the dioecious willowSalix purpureaL
Authors: Gouker Fred E. , Carlson Craig H. , Zou Junzhu , Evans Luke , Crowell Chase R. , Smart Christine D. , DiFazio Stephen P. , Smart Lawrence B.
Published: April 2020

Premise

Sexual dimorphism in dioecious plant species is often not obvious or is absent. Dioecious species populations also often exhibit deviations from expected sex ratios. Previous studies on members of the Salicaceae family have shown strong, partial, and no sexual dimorphism. Some studies have shown sex-biased ratios in severalSalixspp., however,S. purpureahas never been examined for evidence of sexual dimorphism or for the presence of sex-ratio bias, and therefore a comprehensive phenotypic study is needed to fill this knowledge gap.

Methods

This study examined a suite of morphological, phenological, physiological and wood composition traits from multi-environment and multi-year replicated field trials in a diversity panel of unrelatedS. purpureaaccessions and in full-sib F1and F2families produced through controlled cross pollinations to test for sexual dimorphism and sex ratio bias.

Key Results

Significant evidence of sexual dimorphism was found in vegetative traits with greater means for many traits in male genotypes compared to females across three populations ofS. purpurea, measured across multiple years that were highly predictive of biomass yield. Male plants exhibited greater nitrogen accumulation under fertilizer amendment as measured by SPAD in the diversity panel, and males showed greater susceptibility to fungal infection byMelampsoraspp in the F2family. There were also consistent female-biased sex ratios in both the F1and F2families.

Conclusions

These results provide the first evidence of sexual dimorphism inS. purpureaand also confirm the prevalence of female-biased sex ratios previously found in otherSalixspecies.
Seqpare: a self-consistent metric of similarity between genomic interval sets
Authors: Feng Selena C. , Sheffield Nathan C. , Feng Jianglin
Published: April 2020

Searching genomic interval sets produced by sequencing methods has been widely and routinely performed; however, existing metrics for quantifying similarities among interval sets are inconsistent. Here we introduceSeqpare, a self-consistent and effective metric of similarity and tool for comparing sequences based on their interval sets. With this metric, the similarity of two interval sets is quantified by a single index, the ratio of their effective overlap over the union: an index ofzeroindicates unrelated interval sets, and an index ofonemeans that the interval sets are identical. Analysis and tests confirm the effectiveness and self-consistency of theSeqparemetric.

Availability

https://github.com/deepstanding/seqpare

Contact

jf.xtable@gmail.com
The classroom relational environment and children’s early development in preschool
Authors: Nguyen Tutrang , Ansari Arya , Pianta Robert C. , Whittaker Jessica V. , Vitiello Virginia E. , Ruzek Erik
Published: April 2020

The present study considered the ways in which interactional quality in the classroom and teacher–child relationships independently and synergistically shaped the early academic, social‐behavioral, and executive function outcomes of 1,498 preschoolers from low‐income families from a large, culturally, and linguistically diverse county. The findings revealed that children who had closer and less conflictual relationships with their teachers demonstrated greater improvements in all domains of school readiness across the preschool year. Moreover, preschool attendees did not reap the maximum academic benefits from high quality classroom environments unless they also had high‐quality individual relationships with their teachers. Implications for policy and practice are discussed.
Murine Cross-Reactive Nonneutralizing Polyclonal IgG1 Antibodies Induced by Influenza Vaccine Inhibit the Cross-Protective Effect of IgG2 against Heterologous Virus in Mice
Authors: Shibuya Meito , Aoshi Taiki , Kuroda Etsushi , Yoshioka Yasuo
Published: April 2020

Current influenza vaccines are generally effective against highly similar virus strains by inducing neutralizing antibodies. However, these antibodies fail to neutralize antigenically mismatched (heterologous) strains and therefore provide limited protection against them. Efforts are being made to develop vaccines with cross-protective ability that would protect broadly against heterologous strains, because the mismatch between predicted and epidemic strains cannot always be avoided, resulting in low vaccine efficacy. Here, we show that nonneutralizing IgG2 antibodies induced by an optimal adjuvant play a crucial role in cross-protection against heterologous virus challenge in mice. Furthermore, nonneutralizing polyclonal IgG1 suppressed the cross-protective effects of nonneutralizing polyclonal IgG2 by competitively blocking the binding of IgG2 to its antigen. These data shed new light on the importance of IgG isotypes and the selection of appropriate adjuvants for the development of universal influenza vaccines. Furthermore, our findings are applicable to the rational design of vaccines against other pathogens.
Metabolism of Gluconeogenic Substrates by an Intracellular Fungal Pathogen Circumvents Nutritional Limitations within Macrophages
Authors: Shen Qian , Ray Stephanie C. , Evans Heather M. , Deepe George S. , Rappleye Chad A.
Published: April 2020

Histoplasmais a primary human fungal pathogen that survives and proliferates within host immune cells, particularly within the macrophage phagosome compartment. The phagosome compartment is a nutrient-limited environment, requiringHistoplasmayeasts to be able to assimilate available carbon sources within the phagosome to meet their nutritional needs. In this study, we showed thatHistoplasmayeasts do not utilize fatty acids or hexoses for growth within macrophages. Instead,Histoplasmayeasts consume gluconeogenic substrates to proliferate in macrophages. These findings reveal the phagosome composition from a nutrient standpoint and highlight essential metabolic pathways that are required for a phagosomal pathogen to proliferate in this intracellular environment.
Pedometers can help people get more active as part of an exercise programme
Authors: Cook Rob , Davidson Peter , Martin Rosie
Published: April 2020

The study

Hodkinson A, Kontopantelis E, Adeniji C, et al.
Accelerometer- and pedometer-based physical activity interventions among adults with cardiometabolic conditions: a systematic review and meta-analysis
.
JAMA Network Open
2019;2:e1912895.

This study was funded by the NIHR School for Primary Care Research (project number 390 ESWG Workstream 3).

To read the full NIHR Signal, go to:
https://discover.dc.nihr.ac.uk/content/signal-000880/pedometers-can-help-people-get-more-active-as-part-of-an-exercise-programme
The BGOOD experimental setup at ELSA
Authors: Alef S. , Bauer P. , Bayadilov D. , Beck R. , Becker M. , Bella A. , Bieling J. , Böse S. , Braghieri A. , Brinkmann K.-Th. , Cole P. L. , Di Salvo R. , Elsner D. , Fantini A. , Freyermuth O. , Frommberger F. , Gervino G. , Ghio F. , Goertz S. , Gridnev A. , Gutz E. , Hammann D. , Hannappel J. , Hillert W. , Jahn O. , Jahn R. , Johnstone J. R. , Joosten R. , Jude T. C. , Kalinowsky H. , Kleber V. , Klein F. , Kohl K. , Koop K. , Kozlenko N. , Krusche B. , Lapik A. , Sandri P. Levi , Lisin V. , Lopatin I. , Mandaglio G. , Manganaro M. , Messi F. , Messi R. , Moricciani D. , Mushkarenkov A. , Nedorezov V. , Novinskiy D. , Pedroni P. , Polonskiy A. , Reitz B.-E. , Romaniuk M. , Rostomyan T. , Scheluchin G. , Schmieden H. , Stugelev A. , Sumachev V. , Tarakanov V. , Vegna V. , Walther D. , Zaunick H.-G. , Zimmermann T.
Published: April 2020

The BGOOD experiment at the ELSA facility in Bonn has been commissioned within the framework of an international collaboration. The experiment pursues a systematic investigation of non-strange and strange meson photoproduction, in particular t-channel processes at low momentum transfer. The setup uniquely combines a central almost $$4\pi $$4π acceptance BGO crystal calorimeter with a large aperture forward magnetic spectrometer providing excellent detection of both neutral and charged particles, complementary to other setups such as Crystal Barrel, Crystal Ball, LEPS and CLAS.