bluuebunny/crossref_metadata_2025 huggingface dataset:
En mangfoldig møteplass. Åpen barnehage som integreringsarena
Authors: Skjesol Bulling Ingunn
Published: June 2020

Integrering er en uttalt målsetning i norsk innvandringspolitikk. Denne artikkelen ser på integrering på det relasjonelle nivået, og diskuterer hvordan Åpen barnehage kan fremme integreringsprosesser. De åpne barnehagene i denne studien er møteplasser for barn og deres omsorgspersoner. Artikkelen bygger på deltakende observasjon, i tillegg til intervju av både foreldre og ansatte i fem åpne barnehager. Tre kategorier presenteres for å synliggjøre hovedtrekk ved settingen som kan ha betydning for integrering: Mangfoldet i gruppa, fellesskap gjennom hverdagsaktivitet og dynamisk språkmiljø. Gjennom samhandling der både barn og voksne deltar dannes det et mulighetsrom for ulike integreringsprosesser. De utvikler språkkompetanse, blir kjent med ulike kulturer og tradisjoner, forhandler identitet og bygger nettverk. De åpne barnehagene framstår som møteplasser som oppleves som attraktive både for minoritets- og majoritetsbefolkningen.
English abstract
Integration is high on the agenda of the Norwegian migration policies. This article explores integration on the relational level, and discusses how Open Kindergarten can promote integration processes. The open kindergartens in this study are meeting points for children and their caregivers. The article is based on participatory observation and interviews, with both parents and professionals, in five open kindergartens. In this article, I present three categories which highlight how the setting may promote integration processes. These are: the diversity of the group, community through everyday activities and an interactive language environment. Through their interactions, the children and adults together, create a setting that renders integration processes possible. They develop language competence, become acquainted with different cultures and traditions, negotiate identity and build social networks. The open kindergartens are seen as attractive meeting points for both the minority and the majority population.
Increased risk of new persistent opioid use in pediatric and young adult patients with kidney stones
Authors: Hosier Gregory , McGregor Thomas , Beiko Darren , Tasian Gregory E. , Booth Christopher , Whitehead Marlo , Siemens D. Robert
Published: June 2020

Introduction: Adolescents and young adults are a vulnerable patient population for development of substance use disorder. However, the long-term impact of opioid prescribing in young adult patients with renal colic is not known. Our objective was to describe rates of opioid prescription and identify risk factors for persistent opioid use in patients age 25 years or younger with renal colic from kidney stones.

Methods: Using previously validated linked administrative databases, we performed a population-based retrospective cohort study of opioid-naïve patients age 25 years or younger with renal colic between July 1, 2013 and September 30, 2017 in Ontario. All family practitioner, urgent care, and specialist visits in the province were captured. Our primary outcome was persistent opioid use defined as filling a prescription for an opioid between 91 and 180 days after initial visit. Ontario utilizes a narcotic monitoring system, which captures all opioids dispensed in the province.

Results: Of the 6962 patients identified, 56% were prescribed an opioid at presentation and 34% of those were dispensed more than 200 oral morphine equivalents. There was persistent opioid use in 313 (8.1%) patients who filled an initial opioid prescription. In adjusted analysis, those prescribed an opioid initially had a significantly higher risk of persistent opioid use (odds ratio [OR] 1.85, 95% confidence interval [CI] 1.50–2.29) and opioid overdose (OR 3.45, 1.08- 11.04). There was a dose-dependent increase in risk of persistent opioid use with escalating initial opioid dose. History of mental illness (OR 1.32, 1.02- 1.71), and need for surgery (OR 1.71, 1.24- 2.34) were also associated with persistent opioid use.

Conclusions: Among patients with kidney stones age 25 years or younger, filling an opioid prescription after presentation is associated with an increased risk of persistent opioid use 3-6 months later and a higher risk of serious long-term complications such as opioid overdose.
WHO ethics guidance on TB care and migration: challenges to the implementation process
Authors: Wild V. , Frick M. , Denholm J.
Published: June 2020

We summarise the current ethical guidance on tuberculosis (TB) care and migration, as set out in the WHO “Ethics Guidance for the Implementation of the End TB Strategy.” Among other aspects, the Ethics Guidance states that there should be firm legal principles in
place that ensure the enforcement of migration law on the one hand and the protection of human rights, including the right to health, on the other are separated from one another. As a challenge to the Ethics Guidance and its implementation, we describe two cases, each of which typifies particular
problems. Case one describes the experience of a migrant worker in the United Arab Emirates who is deported when mandatory medical exams show evidence of current or prior TB. Case two raises the issue of providing more than TB care, which may also be needed for holistic care. The paper concludes
with our suggestions for ways in which we could make progress towards ethically optimal TB care for migrants.
Ethics and benefits of systematic screening for active tuberculosis
Authors: Hermanns S. , Bhan A. , Viney K.
Published: June 2020

Systematic screening for active tuberculosis (TB) provides public health benefits and is part of the End TB Strategy. However, two of WHO's generic principles for screening for disease state that the natural history of the disease in question must be well understood and that there must
be benefits to earlier treatment. TB fulfills the first of these only in part, the other has been less well documented. This paper considers the ethical implications of uncertain individual benefits from screening and the current research gaps.
Access to experimental medicines for TB: ethical and human rights considerations
Authors: Dagron S. , Chakhaia T. , González-Angulo L. , Hermanns S. , Skrahina A. , Wallace A. E. M.
Published: June 2020

The revised edition of the WHO's Ethics Guidance for the Implementation of the TB Strategy has added a new chapter on compassionate use (CU) and expanded access (EA) to TB drugs. CU and EA programmes authorise access to drugs that have not yet received marketing approval outside
of clinical trials. They are aimed at allowing researchers access to investigational drugs in the absence of complete evidence of efficacy and safety to patients with multidrug-resistant (MDR) or rifampicin-resistant TB (RR-TB) when no other treatment options are available. In doing so, the
guidance acknowledged the urgent necessity to offer these patients all possible treatments in respect of considerations of justice, human rights, human dignity, autonomy of the individual and protection of the community. Regulators are in general willing to accept a higher level of uncertainty
in the risk-benefit assessment of medicines for life-threatening diseases when there is an unmet medical need. This attests to a paradigm change, which this article argues should also apply to allow for effective access to experimental TB medicines. Furthermore, in this article, we analyse
the challenges connected to the establishment of a secure and effective regime of access to experimental drugs in the context of MDR/RR-TB as well as the ethical principles and human rights arguments in favour of the development of such programmes.
People with intellectual disabilities as heirs. Part 2
Authors: Szeroczyńska Małgorzata
Published: June 2020

This text is the next part of the series devoted to inheritance by people with intellectual disabilities after the death of their loved ones. This time, the stage of obtaining legally binding certification that you are the heir after the testator will be necessary, both in statutory and testamentary inheritance. Two alternative paths were indicated: judicial to obtain a decision on the acquisition of an inheritance and notarial to prepare an act of confirmation of inheritance. In both cases, practical difficulties were emphasized that heirs with intellectual disabilities may encounter on their way to receiving these documents, and which may lead to their discrimination and even to initiate incapacitation proceedings.
Editorial Vol. 1
Authors: Barros Márcio , Diniz Morganna , Araújo Renata , Cidral Alexandre
Published: June 2020

Editorial da primeira edição da revista iSys
Analysis of Shape-Based and Texture-Based Attributes in Classification of Mammographic Findings by Machine Learning Algorithms
Authors: De Melo Matheus , Gajadhar Andy , De Oliveira Hugo , De Andrade e Silva Arnaldo , Batista Leonardo
Published: June 2020

Breast cancer is the most frequent cancer type among women. We present a method of classification of nodules (malignant or benign) found in mammograms using shape-based attributes and texture-based ones. Firstly, we built a test database, then we segmented and extracted a Gray Level Cooccurrence Matrix (GLCM) from each mammographic finding and analyzed texture-based and shape-based attributes. Finally, classification was performed through machine learning algorithms. Tests reached a maximum Correct Classification Rate (CCR) of 93.75%, when performed with the Radial Basis Function Network algorithm. The largest area under the ROC curve (AUC), 0.964, was achieved with the Multilayer Perceptron algorithm.
Metodologia para Reconstrução da Geometria da Mama usando Sensores de Profundidade
Authors: De Araújo Franciéric , Da Silva Neto Manuel , Oliveira Tércio , Conci Aura
Published: June 2020

A reconstrução 3D, aliada à termografia, é um meio de validar, ou ajudar o diagnóstico, tornando-o mais preciso. Neste artigo é proposta uma metodologia para reconstrução da geometria 3D da mama visando a realização de simulações computacionais, assim como auxiliar no planejamento de cirurgias. A abordagem consiste em três etapas: calibração de dois Kinects; registro das nuvens de pontos adquiridas; reconstrução da superfície do objeto virtual. Nas validações a média da diferença entre as áreas de superfície foi de 3,55%, 0,93 de Coeficiente de similaridade Dice, na média, e a média da diferença das distâncias entre os mamilos foi de 3,51%.
Diagnóstico de Câncer de Mama em Mamografias baseado na Análise da Diversidade de Padrões Circulares
Authors: Ramos Neto Geovane , Benevides Marcos , Marques Ricardo , Da Rocha Simara , Braz Júnior Geraldo
Published: June 2020

Este artigo tem como objetivo prover uma melhor técnica para análise de textura em imagens de mamografia, visando uma melhor taxa de diagnóstico dos casos de câncer de mama. O diagnóstico feito por especialistas depende de fatores como a experiência do profissional, a qualidade da mamografia e de características do próprio paciente. O estudo procura utilizar métodos computacionais a fim de oferecer uma segunda opinião ao especialista, utilizando-se de técnicas de representação da imagem na forma de padrões circulares quantizados através de matrizes de co-ocorrência. Após a representação, a textura é calculada através da análise de diversidade e classificada usando Máquinas de Vetores de Suporte.
Reconhecimento de Padrões em Dados de Expressão Gênica de Pacientes Portadores de Osteogênese Imperfeita
Authors: De Novais Diogo , Kaneto Carla , Ambrósio Paulo
Published: June 2020

A crescente produção de dados biomoleculares possibilitada pelos avanços das tecnologias laboratoriais tem motivado pesquisas relacionadas à análise apoiada por modelos matemáticos e computacionais. Este trabalho discute a utilização de algoritmos de agrupamento para análise de dados de expressão gênica de pacientes com Osteogênese Imperfeita, no qual pretende-se avaliar a relação entre a fundamentação dos modelos e relevância biológica dos agrupamentos obtidos por diferentes algoritmos.
Les paradoxes de l’éthique dans la société technologique. Réflexions sur l’évolution de nos espaces politiques et des imaginaires sociaux
Authors: Chardel Pierre-Antoine ,   Philosophy Documentation Center
Published: June 2020

The technological society, with all its potentialities in terms of well-being or improvement of daily life, is a source of many paradoxes that constitute real challenges for ethical reflection. Indeed, we have never been so free to express ourselves through information and communication technologies, while simultaneously encountering increasingly acute forms of alienation. More broadly, our current world suffers from an impoverishment of social imaginaries (if we consider the generalization of the consumerist model, identity retreats, separation logics), even though their strength is essential to the fate of ethics, let alone in technological societies that are becoming more and more structurally complex.
An early edition of Andrey Bolotov’s memoirs (from the archives and manuscripts section of the State Historical Museum)
Authors: Abramova Aleksandra A.
Published: June 2020

The history of the creation of Andrei T. Bolotov’s memoirs has been little studied. In par­ticular, the stages of his work on this text are not entirely clear. This article is an attempt to shed light on one aspect of this problem. Bolotov’s personal fund (No. 349) in the Archives and manuscripts section of the State Historical Museum contain a manuscript of Bolotov’s memoirs entitled “Part 2”. It differs significantly in its essential characteristics (paper, de­sign, size, composition, title, division into sections, etc.) from most manuscripts of Bolotov’s memoirs. The study presents a textual analysis of this manuscript and compares it with the text of memoirs published by Mikhail Semevsky, — the most complete printed edition of The Life and Adventures of Andrei Bolotov. The stages of Bolotov’s work on the manuscript are considered; a comparative analysis of lexical units, stylistic preferences, and the content of the manuscript is carried out. The results obtained suggest that the undated manuscript is the earliest version of the memoirs, supposedly written in the late 1770s.
Pushkin as a personal myth of the Russian avantgarde
Authors: Tsvigun Tatyana V. , Chernyakov Aleksey N.
Published: June 2020

This article analyses strategies for cultural appropriation and the appropriation of Push­kin’s personality and oeuvre by the Russian avant-garde. The treatment of Pushkin by the avant-garde is considered as a peculiar variant of cultural apophaticism when the object of reflection is asserted through its consistent negation. The factography of the Russian avant-garde proves that, from its earliest stages the creative system has been constructing its own Pushkin myth, within which the poet has the role of both an object of cultural overcoming and the reference point for the development of a new art. Through negation, the avant-garde strives to ‘discharge’ Pushkin and to show his strangeness to classical cultural models. By making the poet its own, the avant-garde uses him to secure its position in the literary field. Another focus of the article is the place and role of the Pushkin substrate in the poetry and theoretical treatises of Aleksei Kruchyonykh. In his works Pushkin is an object of poetical overcoming and a pole of attraction-repulsion. He is a touchstone, a reference point for the conceptualisation of a new literature. In developing his theory of the shift, Kruchyonykh views Pushkin as a ‘sound-poet’. That analytical position made it possible to move from dis­missing him as ‘a deaf singer’ to the avant-gardist glorification of Pushkin as a genius who worked with the sound texture of the poem. Kruchyonykh demonstrates that for Pushkin the shift is a powerful semantic generator of poetry, a tool that makes an error ‘the rule of break­ing rules’: semantic deviations turn into neologisms, whereas the shift itself enters the realm of productive poetic techniques.
Association of Trust and Locus of Control with Postpartum Contraception Choice
Authors: Dempsey Angela , MacLennan Jenna , Nutter Anna , Stacey Rachel , Wilson Dulaney
Published: June 2020

Objective: In this study, we explored associations of trust in the healthcare system, health locus of control, and patient factors with choice of effective postpartum contraception. Methods: For this observational study, we measured trust in the healthcare system and health
locus of control using validated scales. The primary outcome was postpartum contraceptive choice. We defined effective contraception as methods with failure rate ≤ 10%. We used bivariate and multivariate analyses to determine associated variables. Results: Neither trust in the healthcare
system nor health locus of control were associated with effective contraceptive choice. Black women were more likely to report choice of effective contraception compared to white women (OR = 4.26, 95% CI 1.43, 12.68). Choice of effective contraception did not differ between women who intended
to become pregnant again in less than 2 years versus greater than 2 years although women with no desire for future pregnancy were more likely to choose effective methods (OR = 4.78, 95% CI 1.56, 14.64). Conclusions: Neither trust nor health locus of control were associated with choice
of effective postpartum contraception. The increased likelihood of effective post-partum contraception in black women suggests coercion and bias in counseling and provision.
Cessation Conversations and Quit Attempts: Differences by Ethnicity and Language Preference
Authors: Lambert Victoria C. , Davis Rachel E. , Popova Lucy , Thrasher James F.
Published: June 2020

Objectives: Conversations about pictorial cigarette health warning labels (HWLs) encourage quit attempts, and prior research suggests prevalence of these conversations varies by ethnicity. We assessed the frequency of conversations about text-only HWLs among Latino and non-Latino
white smokers and the relationship between conversations and subsequent quit attempts. Methods: Latino and non-Latino white adult smokers in the United States (N = 4403) were surveyed every 4 months over 2 years. Surveys queried smoking behaviors, recent quit attempts, HWL responses,
including HWL conversations, and socio-demographic variables. Negative binomial generalized estimating equation (GEE) models regressed the frequency of HWL conversations on study variables. Logistic GEE models regressed quit attempts at follow-up surveys on responses from the prior wave, including
frequency of HWL conversations and their interaction with ethnicity. Results: Spanish preference Latinos reported the most HWL conversations (85%), followed by English preference Latinos (59%), and non-Latino Whites (35%). More frequent HWL conversations predicted subsequent quit attempts
(AOR = 1.74, 95% CI = 1.32, 2.30), but ethnicity did not moderate this effect. Conclusions: Latinos appear to talk more frequently about HWLs than non-Latino Whites but are no more likely to quit as a result. Cessation campaigns should use messages that encourage conversations about
quitting.
PPDiffuse: A Quantitative Prediction Tool for Diffusion of Charged
Polymers in a Nanopore
Authors: Hoogerheide David P.
Published: June 2020

Nanopore-based sensing of charged biopolymers is a powerful single-molecule
method. In aconventional nanopore experiment, a single biological (proteinaceous) or
solid-state nanopore perforates a thin membrane that is wetted by, and electrically
isolates, two opposing reservoirs of electrolyte solution. A potential is applied across
the membrane via external electronics coupled to the electrolyte reservoirs with
electrochemical electrodes, actuating the system. The electric field set up by the
applied potential in the nanopore and its immediate environment plays two roles:
supporting an ionic current through the nanopore, which reports on the properties of the
pore and its contents; and acting on analyte molecules to attract them to, and drive
them into, the nanopore. The presence of a large biopolymer in the pore modulates the
ionic current 𝐼(𝑡). The duration of the ionic current modulation corresponds to the
length of time the polymer spends in the pore from capture to its ultimate escape,
either by retraction to the reservoir from which it was captured, or by translocation to
the opposite reservoir . The probabilities of retraction or translocation, or splitting
probabilities, and the corresponding distributions of escape times (𝑡esc), are
particularly sensitive to the size and charge of the analyte molecule and have been the
focus of much theoretical, computational, and experimental effort. An underlying
physical framework in which the distribution of escape times is modeled as a
first-passage time from a one-dimensional potential is quantitatively predictive for a
wide range of experiments. The complexity of this potential for the general case,
however, requires calculations to guide experimental design that can be tedious to
implement. PPDiffuse is intended to remove this burden from the nanopore research
community and enable convenient, rational design of nanopore experiments with complex
substrates such as polypeptides.
Verbal expression of emotions in the course of teaching foreign language
Authors: Tomicheva Irina Valentinovna , Khlybova Nataliya Aleksandrovna , Girenko Irina Viktorovna
Published: June 2020

The subject of this research is identification of emotions based on verbal expressions. The studies dedicated to verbal expression of emotions mostly provide description and classification to the lexicon that reduce studying to semantic and mental capabilities of the phenomenon. The nature and influence of emotional states upon learning a language remain insufficiently studied. Emotional response is able to change the course of cognitive processes. Feelings and mood can greatly affect learning of a foreign language. In the process of emotive-empathic interaction, teacher and student exchange emotions. Success of the process directly depends on the proper emotional mutual perception. Another goal of this research is to determine verbal traces related to negative emotions. The author uses an empirical method of research, such as scientific observation over the behavior if students and teacher, recording the results of such observations. The scientific novelty consists in determination of the influence of emotion of students upon the reception of learning material. Positive emotions are the elements of motivation, while negative are the factors of demotivation. The presented research is a first step in using emotions, emerging in the course of study, aimed at formation of metacognitive skills of the students. The obtained conclusions may be valuable for educators to predict the expression of emotions in accordance with the learning goals and resources.  
A trans-eQTL network regulates osteoclast multinucleation and bone mass
Authors: Pereira Marie , Ko Jeong-Hun , Logan John , Protheroe Hayley , Kim Kee-Beom , Tan Amelia Li Min , Croucher Peter I , Park Kwon-Sik , Rotival Maxime , Petretto Enrico , Bassett JH Duncan , Williams Graham R , Behmoaras Jacques
Published: June 2020

Functional characterisation of cell-type-specific regulatory networks is key to establish a causal link between genetic variation and phenotype. The osteoclast offers a unique model for interrogating the contribution of co-regulated genes to in vivo phenotype as its multinucleation and resorption activities determine quantifiable skeletal traits. Here we took advantage of a trans-regulated gene network (MMnet, macrophage multinucleation network) which we found to be significantly enriched for GWAS variants associated with bone-related phenotypes. We found that the network hub gene Bcat1 and seven other co-regulated MMnet genes out of 13, regulate bone function. Specifically, global (Pik3cb-/-, Atp8b2+/-, Igsf8-/-, Eml1-/-, Appl2-/-, Deptor-/-) and myeloid-specific Slc40a1 knockout mice displayed abnormal bone phenotypes. We report opposing effects of MMnet genes on bone mass in mice and osteoclast multinucleation/resorption in humans with strong correlation between the two. These results identify MMnet as a functionally conserved network that regulates osteoclast multinucleation and bone mass.
Dynamic control of adipose tissue development and adult tissue homeostasis by platelet-derived growth factor receptor alpha
Authors: Shin Sunhye , Pang Yiyu , Park Jooman , Liu Lifeng , Lukas Brandon E , Kim Seung Hyeon , Kim Ki-Wook , Xu Pingwen , Berry Daniel C , Jiang Yuwei
Published: June 2020

Adipocytes arise from distinct progenitor populations during developmental and adult stages but little is known about how developmental progenitors differ from adult progenitors. Here, we investigate the role of platelet-derived growth factor receptor alpha (PDGFRα) in the divergent regulation of the two different adipose progenitor cells (APCs). Using in vivo adipose lineage tracking and deletion mouse models, we found that developmental PDGFRα+ cells are adipogenic and differentiated into mature adipocytes, and the deletion of Pdgfra in developmental adipose lineage disrupted white adipose tissue (WAT) formation. Interestingly, adult PDGFRα+ cells do not significantly contribute to adult adipogenesis, and deleting Pdgfra in adult adipose lineage did not affect WAT homeostasis. Mechanistically, embryonic APCs require PDGFRα for fate maintenance, and without PDGFRα, they underwent fate change from adipogenic to fibrotic lineage. Collectively, our findings indicate that PDGFRα+ cells and Pdgfra gene itself are differentially required for WAT development and adult WAT homeostasis.
Beyond polyphagy and opportunism: natural prey of hunting spiders in the canopy of apple trees
Authors: Mezőfi László , Markó Gábor , Nagy Csaba , Korányi Dávid , Markó Viktor
Published: June 2020

Spiders (Araneae) form abundant and diverse assemblages in agroecosystems such as fruit orchards, and thus might have an important role as natural enemies of orchard pests. Although spiders are polyphagous and opportunistic predators in general, limited information exists on their natural prey at both species and community levels. Thus, the aim of this study was to assess the natural prey (realized trophic niche) of arboreal hunting spiders, their role in trophic webs and their biological control potential with direct observation of predation events in apple orchards. Hunting spiders with prey in their chelicerae were collected in the canopy of apple trees in organic apple orchards in Hungary during the growing seasons between 2013 and 2019 and both spiders and their prey were identified and measured. Among others, the composition of the actual (captured by spiders) and the potential (available in the canopy) prey was compared, trophic niche and food web metrics were calculated, and some morphological, dimensional data of the spider-prey pairs were analyzed. Species-specific differences in prey composition or pest control ability were also discussed. By analyzing a total of 878 prey items captured by spiders, we concluded that arboreal hunting spiders forage selectively and consume a large number of apple pests; however, spiders’ beneficial effects are greatly reduced by their high levels of intraguild predation and by a propensity to switch from pests to alternative prey. In this study, arboreal hunting spiders showed negative selectivity for pests, no selectivity for natural enemies and positive selectivity for neutral species. In the trophic web, the dominant hunting spider taxa/groups (Carrhotus xanthogramma, Philodromus cespitum, Clubiona spp., Ebrechtella tricuspidata, Xysticus spp. and ‘Other salticids’) exhibit different levels of predation on different prey groups and the trophic web’s structure changes depending on the time of year. Hunting spiders show a high functional redundancy in their predation, but contrary to their polyphagous nature, the examined spider taxa showed differences in their natural diet, exhibited a certain degree of prey specialization and selected prey by size and taxonomic identity. Guilds (such as stalkers, ambushers and foliage runners) did not consistently predict either prey composition or predation selectivity of arboreal hunting spider species. From the economic standpoint, Ph. cespitum and Clubiona spp. were found to be the most effective natural enemies of apple pests, especially of aphids. Finally, the trophic niche width of C. xanthogramma and Ph. cespitum increased during ontogeny, resulting in a shift in their predation. These results demonstrate how specific generalist predators can differ from each other in aspects of their predation ecology even within a relatively narrow taxonomic group.
Epifaunal invertebrate assemblages associated with branching Pocilloporids in Moorea, French Polynesia
Authors: Pisapia Chiara , Stella Jessica , Silbiger Nyssa J. , Carpenter Robert
Published: June 2020

Reef-building corals can harbour high abundances of diverse invertebrate epifauna. Coral characteristics and environmental conditions are important drivers of community structure of coral-associated invertebrates; however, our current understanding of drivers of epifaunal distributions is still unclear. This study tests the relative importance of the physical environment (current flow speed) and host quality (e.g., colony height, surface area, distance between branches, penetration depth among branches, and background partial mortality) in structuring epifaunal communities living within branching Pocillopora colonies on a back reef in Moorea, French Polynesia. A total of 470 individuals belonging to four phyla, 16 families and 39 genera were extracted from 36 Pocillopora spp. colonies. Decapods were the most abundant epifaunal organisms (accounting for 84% of individuals) found living in Pocillopora spp. While coral host characteristics and flow regime are very important, these parameters were not correlated with epifaunal assemblages at the time of the study. Epifaunal assemblages associated with Pocillopora spp. were consistent and minimally affected by differences in host characteristics and flow regime. The consistency in abundance and taxon richness among colonies (regardless of habitat characteristics) highlighted the importance of total habitat availability. With escalating effects of climate change and other localized disturbances, it is critical to preserve branching corals to support epifaunal communities.
Alveolar soft-part sarcoma (ASPS) resembles a mesenchymal stromal progenitor: evidence from meta-analysis of transcriptomic data
Authors: Stockwin Luke H.
Published: June 2020

Alveolar soft-part sarcoma (ASPS) is an extremely rare malignancy characterized by the unbalanced translocation der(17)t(X;17)(p11;q25). This translocation generates a fusion protein, ASPL-TFE3, that drives pathogenesis through aberrant transcriptional activity. Although considerable progress has been made in identifying ASPS therapeutic vulnerabilities (e.g., MET inhibitors), basic research efforts are hampered by the lack of appropriate in vitro reagents with which to study the disease. In this report, previously unmined microarray data for the ASPS cell line, ASPS-1, was analyzed relative to the NCI sarcoma cell line panel. These data were combined with meta-analysis of pre-existing ASPS patient microarray and RNA-seq data to derive a platform-independent ASPS transcriptome. Results demonstrated that ASPS-1, in the context of the NCI sarcoma cell panel, had some similarities to normal mesenchymal cells and connective tissue sarcomas. The cell line was characterized by high relative expression of transcripts such asCRYAB,MT1G,GCSAML,andSV2B.Notably, ASPS-1 lacked mRNA expression of myogenesis-related factorsMYF5,MYF6,MYOD1,MYOG,PAX3,andPAX7.Furthermore, ASPS-1 had a predicted mRNA surfaceome resembling an undifferentiated mesenchymal stromal cell through expression ofGPNMB,CD9(TSPAN29),CD26(DPP4),CD49C(ITGA3),CD54(ICAM1),CD63(TSPAN30),CD68(SCARD1),CD130(IL6ST),CD146(MCAM),CD147(BSG),CD151(SFA-1),CD166(ALCAM),CD222(IGF2R),CD230(PRP),CD236(GPC),CD243(ABCB1), andCD325(CDHN). Subsequent re-analysis of ASPS patient data generated a consensus expression profile with considerable overlap between studies. In common with ASPS-1, elevated expression was noted forCTSK,DPP4,GPNMB,INHBE,LOXL4,PSG9,SLC20A1,STS,SULT1C2,SV2B,andUPP1. Transcripts over-expressed only in ASPS patient samples includedABCB5,CYP17A1,HIF1A,MDK,P4HB,PRL,andPSAP.These observations are consistent with that expected for a mesenchymal progenitor cell with adipogenic, osteogenic, or chondrogenic potential. In summary, the consensus data generated in this study highlight the unique and highly conserved nature of the ASPS transcriptome. Although the ability of the ASPL-TFE3 fusion to perturb mRNA expression must be acknowledged, the prevailing ASPS transcriptome resembles that of a mesenchymal stromal progenitor.
Evaluation of the Effectiveness of Nine Brands of Toothpaste on Streptococcus mutans Isolated from the Mouth of Students in Veritas University, Abuja
Authors: Ozoude T. O. , Okolie T. C. , Effiom O. E.
Published: June 2020

Dental caries is an infectious microbiological disease of the teeth that end up in the destruction of dental hard tissues. The use of toothpaste has been used to reduce the bacterial load in the mouth because they contain antimicrobial properties such as triclosan, fluoride, and so on. The study aimed to determine the effect of nine brands of toothpaste on Streptococcus mutans isolated from the mouth of students in veritas university. Following the isolation of Streptococcus mutans from samples collected from the mouths of Veritas students’, the antimicrobial activity of different concentrations of the dentifrices was determined by modified agar well diffusion method. In this method, Muller Hinton agar plates were seeded with a loop full of 24-hour cultures of the bacterial isolate. A sterile 8 mm cork-borer was used to cut one central and five wells at equidistance in each of the plates. 0.3 ml of the dentifrice dilutions was introduced into each of the five wells while the same amount of sterile distilled water was introduced into the first well as control. The plates were incubated at 37°C for 24 hours. The antimicrobial activity was evaluated by measuring the diameter of zones of inhibition (in mm). The diameter in which the bacteria were inhibited was indicative of the toothpaste’s antibacterial potential.  The zones of inhibition on the growth of the test strain were defined by the location where visible growth had been inhibited. All the plates were made in triplicates and the experiments repeated twice. The result showed that Mentadent-P was the most effective dentifrice with an inhibition zone of 2.8 mm, Pepsodent had inhibition zone of 2.6 mm, Oral B with 2.3 mm, Close up with 2.2 mm, followed by Colgate with a diameter of 1.9 mm, Special Lucky with a diameter of 1.6 mm, Darbur Promise with a diameter of 1.6 mm, Maclean’s with a zone of inhibition of 1.5 mm, and MY- MY with the least effective toothpaste with a zone of inhibition of 1.0 mm in diameter. The results also showed that toothpaste containing fluoride as their main antimicrobial agent proved more effective against streptococcusmutans than other toothpaste not containing fluoride as their main antimicrobial agent.
Haloglycomyces
Authors: Dong Lei , Salam Nimaichand , Li Wen‐Jun
Published: June 2020

Ha.lo.gly.co.my'ces. Gr. masc. n.
hals
salt; N.L. masc. n.
Glycomyces
a bacterial genus name; N.L. masc. n.
Haloglycomyces
a salt‐(loving)
Glycomyces
‐like bacterium.

Actinobacteria / Actinobacteria / Glycomycetales / Glycomycetaceae / Haloglycomyces

The genus
Haloglycomyces
is classified within the family
Glycomycetaceae
, order
Glycomycetales,
and within the class
Actinobacteria
. Phylogenetically, the only representative strain in this genus shares 16S rRNA sequence similarities of less than 95% with other members of the family
Glycomycetaceae
and forms a distinct clade in the maximum‐likelihood phylogenetic tree. Cells are
short
or
elongated rods
that stain
Gram‐positive
. Strain YIM 92370
T
can grow well over a relative wide range of physiological conditions: 15–40°C, pH 5.0–9.0, and
3–18% (w/v) NaCl
. They are
aerobic
,
chemoorganotrophic
, and can grow in defined media on a range of substrates. Major polar lipids are phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unidentified phosphoglycolipids, and one unidentified phospholipid. Currently, the genus consists of one species:
Haloglycomyces albus
(the type species of the genus), isolated from a hypersaline soil.

DNA G + C content (mol%)
: 60.4 (WGS).

DNA G + C content (mol%)
: 60.8 (HPLC).

Type species
:
Haloglycomyces albus
Guan et al. 2009
VP
.
Caenimicrobium
Authors: Manaia Célia M. , Vaz‐Moreira Ivone , Nunes Olga C.
Published: June 2020

Caenimicrobium
[Cae.ni.mi.cro'bi.um, L. neut. n.
caenum
mud, referring to the isolation of the type strain from activated sludge; N.L. neut. n.
microbium
microbe (from Gr. adj.
mikros
small and Gr. n.
bios
life); N.L. neut. n.
Caenimicrobium
mud (‐inhabiting) microbe].

Proteobacteria / Betaproteobacteria / Burkholderiales / Alcaligenaceae / Caenimicrobium

Gram‐negative‐
staining
nonmotile
short rods, forming beige colonies on nutrient medium.
Mesophilic
,
aerobic
, and catalase‐ and cytochrome
c
oxidase‐positive.
Major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified phospholipid, and major cellular fatty acids are C

16:1

ω7
c
, C

16:0

, cyclo C

17:0

,
and C

18:1

ω7
c
. Ubiquinone 8

is the major respiratory quinone. The type and unique species is
Caenimicrobium hargitense
, represented by the type strain CGII‐59m2
T
isolated from activated sludge.
Caenimicrobium hargitense
strain CGII‐59m2
T
shares 16S rRNA gene sequence similarity >97% with members of the genera
Bordetella
,
Candidimonas
,
Paracandidimonas
, and
Parapusillimonas
.

DNA G + C content (mol%)
: 62.3 (HPLC method).

Type species:
Caenimicrobium hargitense
, Felföldi et al. 2017
VP
.
Avibacterium
Authors: Blackall Patrick J.
Published: June 2020

A.vi.bac.te'ri,um. L. fem. n.
avis
a bird; N.L. neut. n.
bacterium
rod; N.L. neut. n.
Avibacterium
bacterium of birds.

Proteobacteria / Gammaproteobacteria / Pasteurellales / Pasteurellaceae / Avibacterium

Avibacterium
is a genus within the family
Pasteurellaceae
. Members of this genus are Gram‐negative, nonmotile, rod‐shaped, or pleomorphic cells typically occurring singly. Species in this genus vary in the requirement for external sources of nicotinamide adenine dinucleotide (NAD) (often termed V factor) when grown in agar or broth. Two species,
Avibacterium gallinarum
and
Avibacterium endocarditidis
, do not require NAD, while the other species (
Avibacterium avium, Avibacterium paragallinarum,
and
Avibacterium volantium
) typically require NAD. Notably, some isolates of
A. paragallinarum
do not require NAD. The requirement for NAD results in the occurrence of satellitic growth on sheep blood agar when a nurse colony is present. Growth is mesophilic, and most isolates, particularly on initial isolation, require an atmosphere of 5% CO
2
. Nitrate is reduced without gas production. The reaction in Hugh–Leifson medium with (+)‐
d
‐glucose is fermentative without gas production. All members of the genus are catalase‐ and oxidase‐positive except that
A. paragallinarum
is catalase‐negative. Disease conditions associated with this genus are all linked to chickens and include infectious coryza (
A. paragallinarum)
, valvular endocarditis and septicemia (
A. endocarditidis
), and a chronic fowl cholera‐like condition (
A. gallinarum)
.

DNA G + C content (mol%)
: 44.2–47 (
T
m
).

Type species:
Avibacterium gallinarum
Blackall et al. 2005
VP
.
Necropsobacter
Authors: Christensen Henrik , Bisgaard Magne , Kuhnert Peter
Published: June 2020

Ne.crop.so.bac'ter. Gr. masc. n.nekros, dead body, corpse; Gr. fem. n.opsis, appearance, view; N.L. masc. n.bacter, a rod, N.L. masc. n.Necropsobacter, a rod isolated from an autopsy.

Proteobacteria / Gammaproteobacteria / Pasteurellales / Pasteurellaceae / Necropsobacter

The genusNecropsobacterincludes taxa previously reported as the SP group and Stewart–Letcher (SL) group based on phenotypic characteristics. The genus includes typical members of the familyPasteurellaceaewith respect to cultural characteristics and colony morphology. Neither hemin (X‐factor) nor NAD (V‐factor) is required for growth. Hemolysis is not observed on bovine blood agar. Acid is produced from (+)‐l‐arabinose, (+)‐d‐galactose, (+)‐d‐mannose, and maltose. Gas is produced from glucose. Negative reactions are observed for urease, ornithine decarboxylase, and indole. The genus includes isolates from guinea pigs and other rodents, rabbits, a dog, and humans. The taxon formed a monophyletic group based on 16S rRNA and partialrpoBsequence analysis compared to other genera of the family. 16S rRNA gene sequence comparison showed at least 98.5% similarity between isolates of the SP group, and strain P625 (SL group) only showed a 16S rRNA similarity of 95.5% to the SP group. The genus consists of only one speciesNecropsobacter rosorum. Strain P625 of the SL group remained unclassified at species level. Ubiquinones and demethylmenaquinone are produced by the type strain ofN. rosorum.

DNA G + C content (whole‐genomic sequencing) (mol%): 48.9.

Type species:Necropsobacter rosorumChristensen et al. 2011VP.
Halalkaliarchaeum
Authors: Sorokin Dimitry Y. , Merkel Alexander , Yakimov Mikhail M. , Oren Aharon
Published: June 2020

Hal.al.ka.li.ar.chae'um. Gr. masc. n.
hals
,
halos
salt; N.L. n.
alkali
(from Arabic article
al
and the and Arabic n.
qaliy
ashes of saltwort); N.L. neut. n.
archaeum
(from Gr. masc. adj.
archaios
ancient) archaeon; N.L. neut. n.
Halalkaliarchaeum
a haloalkaliphilic archaeon.

Euryarchaeota / Halobacteria / Haloferacales / Halorubraceae / Halalkaliarchaeum

The genus
Halalkaliarchaeum
, classified within the family
Halorubraceae
, order
Haloferacales
, and within the class
Halobacteria
, consists of pleomorphic flattened rod‐shaped nonmotile cells with a thin monolayer cell wall. Colonies on agar plates incubated aerobically are red‐orange. The single described species of the genus is extremely halophilic, requiring 2.5–5 M Na
+
and growing optimally at 4 M Na
+
, and alkaliphilic, growing at pH 7.8–9.5 with an optimum at pH 8.8–9.0. The optimum temperature is 43°C. It is facultative anaerobe, growing aerobically as a chemoorganoheterotroph on pyruvate and peptone–yeast extract or anaerobically as a chemolithoheterotroph, using H
2
or formate as electron donors, elemental sulfur as electron acceptor, and yeast extract as carbon source. Sugars are not used as carbon and energy source. The respiratory quinone is MK‐8(H
2
). The major polar lipids are C
20
–C
20
and C
25
–C
20
diether dialkylglycerol ethers, with phosphatidylglycerol phosphate methyl ester (PGP‐Me) and phosphatidylglycerol (PG) as the dominant polar lipids.

DNA G + C content (mol%)
: 63.1 (genome sequence).

Type species
:
Halalkaliarchaeum desulfuricum
Sorokin et al. 2019
VP
.
Eukaryotic Molybdenum Insertases
Authors: Kruse Tobias
Published: June 2020

The pyranopterin molybdenum cofactor (Moco) is the essential active site component of all Moco dependent enzymes (Mo‐enzymes) except for bacterial nitrogenase. Mo‐enzymes are vitally important for life as they catalyze various crucial two electron transfer reactions. Moco is synthesized by an evolutionary highly conserved multi‐step biosynthesis pathway. Here, initially GTP is converted to the first pathway intermediate, i.e. cyclic pyranopterin monophosphate (cPMP). In the second pathway step, cPMP is converted to molybdopterin (MPT) which is the substrate of the MPT adenylyltransferase. The resulting Moco biosynthesis intermediate is adenylated MPT (MPT‐AMP), which is the hitherto last known Moco precursor. Adenylation of MPT is catalyzed by the G‐domain of Mo‐insertases. The E‐domain of Mo‐insertases catalyze the molybdate insertion reaction yielding Moco. This ultimate reaction step is the last principle reaction step within the Moco biosynthesis pathway to be elucidated.
Full‐Length Human Collagen Lysyl Hydroxylases
Authors: Scietti Luigi , Forneris Federico
Published: June 2020

Procollagen lysyl hydroxylases and glycosyltransferases (LH, also known as procollagen lysyl‐2‐oxoglutarate dioxygenases (PLOD)) are essential biosynthesis enzymes present in all collagen‐containing organisms, from sponges to humans. Higher vertebrates present three separatePLODgenes encoding for distinct enzyme isoforms (LH1, LH2a/b, and LH3), sharing ∼70% amino acid sequence identity. The LH1 and LH2 isoforms exclusively display Fe2+, 2‐oxoglutarate‐dependent lysyl 5‐hydroxylase activity, whereas LH3 is a multifunctional enzyme, able to further catalyze the Mn2+‐dependent β‐(1,O)‐galactosylation and the subsequent α‐(1,2)‐glucosylation of 5‐hydroxylysines. Despite exclusive selectivity for lysine residues within collagenous polypeptides, little is known about the specificity of LH enzymes for different amino acid sequences in different collagen types: LH1 and LH3 isoforms act on collagen triple‐helical regions, whereas the LH2 isoform specifically hydroxylates collagen telopeptides, yet no consensus sequences, nor minimum sequence lengths, have been proposed as requirements for catalysis. Available crystal structures of full‐length human LH3 show an elongated homodimeric quaternary structure, with three aligned domains constituting each enzyme's polypeptide: the N‐terminal glycosyltransferase (GT) domain, a central noncatalytic accessory (AC) domain, and a C‐terminal lysyl hydroxylase (LH) domain. Dimerization occurs in the C‐terminal domain, in proximity to the LH catalytic site. Dimerization is indeed essential for LH activity, but is dispensable for the glycosyltransferase activities of LH3.
Particulate Methane Monooxygenase and thePmoDProtein
Authors: Koo Christopher W , Rosenzweig Amy C
Published: June 2020

Particulate methane monooxygenase (pMMO) is the main enzyme used by methanotrophic bacteria to metabolize methane as their sole source of carbon and energy. pMMO is a 300‐kDa copper‐dependent, membrane‐bound metalloenzyme housed in specialized intracytoplasmic membrane (ICM) structures formed under copper‐replete growth conditions. Five crystal structures of pMMO from different methanotrophic species have revealed that pMMO comprises three subunits, PmoA, PmoB, and PmoC, arranged in a (αβγ)3cylindrical‐shaped trimer. Since the last article, it has been established that pMMO contains two monocopper sites, one each in the PmoB and PmoC subunits. Both sites are likely involved in methane oxidation, but their specific roles are yet to be fully determined. The PmoD protein is unique to methanotrophs and is often encoded within the pMMO operon. PmoD consists of a single transmembrane helix and a cupredoxin‐like periplasmic domain that has been crystallographically characterized. Although its function remains unknown, disruption of the gene encoding PmoD results in a growth defect under high copper conditions, suggesting a potential role in methane oxidation. Biochemical analysis indicates that the periplasmic domain of PmoD binds copper, forming an unusual CuAsitein vitro.