Optimizing Federated Queries Based on the Physical Design of a Data Lake

The optimization of query execution plans is known to be crucial for reducing the query execution time. In particular, query optimization has been studied thoroughly for relational databases over the past decades. Recently, the Resource Description Framework (RDF) became popular for publishing data on the Web. As a consequence, federations composed of different data models like RDF and relational databases evolved. One type of these federations are Semantic Data Lakes where every data source is kept in its original data model and semantically annotated with ontologies or controlled vocabularies. However, state-of-the-art query engines for federated query processing over Semantic Data Lakes often rely on optimization techniques tailored for RDF. In this paper, we present query optimization techniques guided by heuristics that take the physical design of a Data Lake into account. The heuristics are implemented on top of Ontario, a SPARQL query engine for Semantic Data Lakes. Using sourcespecific heuristics, the query engine is able to generate more efficient query execution plans by exploiting the knowledge about indexes and normalization in relational databases. We show that heuristics which take the physical design of the Data Lake into account are able to speed up query processing

Actinobacterial Degradation of 2-Hydroxyisobutyric Acid Proceeds via Acetone and Formyl-CoA by Employing a Thiamine-Dependent Lyase Reaction

We would like to thank C. Dilßner and M. Neytschev (UFZ) for excellent technical assistance with CoA thioester synthesis, strain cultivation and HPLC analyses. In addition, we thank Birgit Würz (UFZ) for invaluable analytical advice and help with GC mass spectrometry. We are also indebted to L. von Wintzingerode, A. Grunwald, and J. Grabengießer (UFZ) for assistance in the cultivation and enzyme assay experiments. Many thanks to K. Eismann (UFZ) as well, for help with the proteome analysis and fruitful discussions regarding different protein extraction methods.The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2020.00691/full#supplementary-materialThe tertiary branched short-chain 2-hydroxyisobutyric acid (2-HIBA) has been associated with several metabolic diseases and lysine 2-hydroxyisobutyrylation seems to be a common eukaryotic as well as prokaryotic post-translational modification in proteins. In contrast, the underlying 2-HIBA metabolism has thus far only been detected in a few microorganisms, such as the betaproteobacterium Aquincola tertiaricarbonis L108 and the Bacillus group bacterium Kyrpidia tusciae DSM 2912. In these strains, 2-HIBA can be specifically activated to the corresponding CoA thioester by the 2-HIBA-CoA ligase (HCL) and is then isomerized to 3-hydroxybutyryl-CoA in a reversible and B12-dependent mutase reaction. Here, we demonstrate that the actinobacterial strain Actinomycetospora chiangmaiensis DSM 45062 degrades 2-HIBA and also its precursor 2-methylpropane-1,2-diol via acetone and formic acid by employing a thiamine pyrophosphate-dependent lyase. The corresponding gene is located directly upstream of hcl, which has previously been found only in operonic association with the 2-hydroxyisobutyryl-CoA mutase genes in other bacteria. Heterologous expression of the lyase gene from DSM 45062 in E. coli established a 2-hydroxyisobutyryl-CoA lyase activity in the latter. In line with this, analysis of the DSM 45062 proteome reveals a strong induction of the lyase-HCL gene cluster on 2-HIBA. Acetone is likely degraded via hydroxylation to acetol catalyzed by a MimABCD-related binuclear iron monooxygenase and formic acid appears to be oxidized to CO2 by selenium-dependent dehydrogenases. The presence of the lyase-HCL gene cluster in isoprene-degrading Rhodococcus strains and Pseudonocardia associated with tropical leafcutter ant species points to a role in degradation of biogenic short-chain ketones and highly branched organic compounds.Program Topic "Chemicals in the Environment" within the Research Program "Terrestrial Environment" of the Helmholtz Association European Union (EU) 62485

Lean back and wait for the alarm? Testing an automated alarm system for nosocomial outbreaks to provide support for infection control professionals

INTRODUCTION: Outbreaks of communicable diseases in hospitals need to be quickly detected in order to enable immediate control. The increasing digitalization of hospital data processing offers potential solutions for automated outbreak detection systems (AODS). Our goal was to assess a newly developed AODS. METHODS: Our AODS was based on the diagnostic results of routine clinical microbiological examinations. The system prospectively counted detections per bacterial pathogen over time for the years 2016 and 2017. The baseline data covers data from 2013-2015. The comparative analysis was based on six different mathematical algorithms (normal/Poisson and score prediction intervals, the early aberration reporting system, negative binomial CUSUMs, and the Farrington algorithm). The clusters automatically detected were then compared with the results of our manual outbreak detection system. RESULTS: During the analysis period, 14 different hospital outbreaks were detected as a result of conventional manual outbreak detection. Based on the pathogens' overall incidence, outbreaks were divided into two categories: outbreaks with rarely detected pathogens (sporadic) and outbreaks with often detected pathogens (endemic). For outbreaks with sporadic pathogens, the detection rate of our AODS ranged from 83% to 100%. Every algorithm detected 6 of 7 outbreaks with a sporadic pathogen. The AODS identified outbreaks with an endemic pathogen were at a detection rate of 33% to 100%. For endemic pathogens, the results varied based on the epidemiological characteristics of each outbreak and pathogen. CONCLUSION: AODS for hospitals based on routine microbiological data is feasible and can provide relevant benefits for infection control teams. It offers in-time automated notification of suspected pathogen clusters especially for sporadically occurring pathogens. However, outbreaks of endemically detected pathogens need further individual pathogen-specific and setting-specific adjustments

A Outra Dor do Parto: Género, relações de poder e violência obstétrica na assistência hospitalar ao parto

O parto não é um evento apenas médico. É um acontecimento com significações pessoais, familiares, sociais e culturais. O parto pode ser entendido como um rito de passagem, repleto de rituais e símbolos. A hospitalização e medicalização, ao contrário de refutar crenças e tabus arcaicos, reforça os rituais em torno deste evento fisiológico, reafirmando a perceção do corpo feminino como defeituoso e incapaz de parir naturalmente. A dor do parto não é apenas fisiológica, mas também fruto da cultura, que tem o poder de intensificá-la. O corpo feminino tem sido instrumentalizado, alvo de controlo e intervenção social, tido como um corpo frágil e defeituoso, que difere da norma (o corpo masculino). A assistência ao parto é um exemplo expressivo deste controlo. Há um excesso de medicalização e intervenção nos partos, como se não pudessem ocorrer de maneira natural e saudável sem a “ajuda” da medicina e da tecnologia. O que ocorre é que, para além do excesso de medicalização e intervenção, há recorrentes maus tratos e abusos às mulheres nos partos. Isso pode ser classificado como violência obstétrica, uma violência de género institucionalizada, naturalizada e invisibilizada. A violência obstétrica pode ser de carácter físico, psicológico e sexual e inclui também o excesso de procedimentos e intervenções bem como o desrespeito à liberdade de escolha e consentimento informado das mulheres. Neste contexto, apresentam-se os resultados de um inquérito realizado no âmbito deste trabalho, que expõe a violência obstétrica, onde se observou que as intervenções foram realizadas de maneira rotineira, com destaque para as episiotomias, executadas em 68,5% dos casos. O que se sobressai no estudo é que grande parte das intervenções foi realizada sem informar as mulheres ou mesmo diante de sua recusa a consentir com os procedimentos. Para além dos resultados quantitativos, os depoimentos recolhidos através do inquérito são muito expressivos desta violência, que se revelou através de desrespeito, ofensas, ameaças, humilhações, linguagem rude, sujeição e agressão. O parto é um momento muito significativo na vida das mulheres e o atendimento prestado a elas no parto tem forte impacto em suas experiências de parto. Apesar de, sem dúvida, haver experiências de parto muito positivas e satisfatórias, nas quais as mulheres sentem-se seguras, confiantes e apoiadas, fica evidente que há muitas experiências negativas e traumáticas – em que as mulheres sentem-se vulneráveis, assustadas e inseguras – e que podem acarretar consequências futuras em suas vidas. A violência obstétrica institucionalizada é também uma violência consentida, no sentido de que muitas mulheres se calam e não denunciam, por opressão, medo ou por parecer inadequado se opor a quem é suposto cuidar delas. Para além de responsabilizar os profissionais de assistência ao parto enquanto um grupo, é preciso direcionar o olhar para as raízes do problema, que se inserem nas relações de poder e desigualdades de género. É preciso reconhecer a singularidade de cada mulher e cada parto e restituir às mulheres o protagonismo e o poder sobre seus corpos e seus partos.Childbirth is not only a medical event. It is an event with personal, family, social and cultural meanings. Birth can be understood as a rite of passage, full of rituals and symbols. Hospitalization and medicalization, rather than refute beliefs and archaic taboos, reinforces the rituals around this physiological event, reaffirming the perception of the female body as defective and unable to give birth naturally. The pain of labour is not only physiological, but it is a product of culture, which has the power to enhance it. The female body and its processes has been instrumentalized, target of social control and intervention, perceived as a fragile and defective body, which differs from the standard (the male body). Childbirth is a significant example of this control. There is an excess of medicalization and intervention in childbirth, as if it could not occur in a natural and healthy way without the "help" of medicine and technology. What happens is that, in addition to excessive medicalization and intervention, there are recurrent mistreatment and abuse to women in childbirth. This can be classified as obstetric violence, one institutionalized gender violence, naturalized and invisible. Obstetric violence can be physical, psychological and sexual and also includes the excess of procedures and interventions as well as disrespect of freedom of choice and informed consent of women. In this context, we present the results of a survey carried out in the scope of this work, which exposes obstetric violence, and in which it was observed that the interventions were performed routinely, especially episiotomy, executed in 68.5% of all cases. What stands out in the study is that most of the interventions were performed without informing women or even in face of their refusal to consent to the procedure. In addition to the quantitative results, the statements collected by the inquiry are very expressive of this violence, which was shown through disrespect, insults, threats, humiliations, rude language, subjugation and aggression. Birth is a very significant moment in women’s life and the care provided to them has a strong impact on their birth experiences. Although there are, undoubtedly, very positive and satisfactory birth experiences, in which women feel safe, confident and supported, it is evident that there are many negative and traumatic experiences - where women feel vulnerable, frightened and insecure - and that can lead to future consequences in their lives. Institutionalized obstetric violence is also a consensual violence, in the sense that many women stay silent and do not denounce, either by oppression, fear or because it may seem inappropriate to oppose to those who are supposed to care for them. Beyond indict care professionals as a group, it is required to regard the roots of the problem, resting upon power relations and gender inequalities. It is necessary to recognize the uniqueness of each woman and each birth and reinstate to women the role and power over their bodies and their births

Impacto da vivência de rua nas amizades de crianças em idade escolar

OBJETIVO: Trata-se de um estudo para avaliar as relações de amizade em meninos de rua de 7 a 11 anos da cidade de Porto Alegre, RS, Brasil. MÉTODOS: Uma amostra de 30 meninos de rua foi comparada com outra de 51 meninos de 7 a 11 anos que viviam com suas famílias de baixa renda, utilizando-se a Entrevista Sobre Amigos e Companheiros da Cornell (Cornell Interview of Peers and Friends). RESULTADOS: Os dois grupos apresentaram escores globais na entrevista significativamente diferentes, sendo que o grupo de meninos de rua obteve o escore médio mais alto. Da mesma forma, os meninos de rua apresentaram escores de adequação do desenvolvimento, autoestima e habilidades sociais significativamente menores do que os meninos com família. CONCLUSÕES: Levando-se em conta os resultados, é enfatizada a urgência do desenvolvimento de intervenções com as crianças com vivência de rua, especialmente com os meninos de rua.OBJECTIVE: This is a study to evaluate friendships in latency street boys of Porto Alegre, RGS, Brazil. METHODS: A sample of 30 latency street boys was compared with a sample of 51 latency boys living with their low income families, using the Cornell Interview of Peers and Friends (CIPF). RESULTS: The two groups had a significantly different CIPF global scores, and the boys of the street group had the highest mean score. Also, boys of the street had significantly lower developmental appropriateness, self-esteem and social skills scores than boys living with a family. CONCLUSIONS: The urgent need for intervention street children, especially on boys of the street, is emphasized

Combined intervention of working memory and arithmetic reasoning in students with ADHD

This study compared the effects of a combined intervention of working memory (WM) and arithmetic reasoning (AR) vs WM intervention alone on the arithmetic reasoning performance of students with ADHD. Third- and fourth-grade elementary school students (n = 46) completed measures for AR, mathematical calculations, and WM. Participants were randomised using a minimisation approach taking age and IQ as variables of interest and assigned to one of the two groups: Combined Intervention (CI, n = 24) and Working Memory Intervention (WMI, n = 22). The results using GEE analysis indicated a significant group × time interaction (Waldχ2 = 6.414; gl = 2; p = 0.04) in AR performance in the immediate post-test. CI students showed significantly better performance on AR than WMI students immediately after intervention (pB = 0.042). There was an effect of time on mathematical calculations in the post-test (Waldχ2 = 48.305; gl = 2; p < 0.001). Despite the fact that the results for AR were not maintained in the deferred post-test, a combined intervention of WM and AR seems to be more efficient in improving arithmetic reasoning in ADHD students than a WM intervention alone. Nevertheless, this is not the case with other mathematical issues, such as calculation, where there was no significant difference between groups, but the effects had been maintained in the deferred post-test for both

Psychological well-being of early and continuously treated phenylketonuria patients

Background Despite enormous advances in therapy, phenylketonuria (PKU) remains an incurable, inherited metabolic disease requiring life-long treatment with potential to negatively impact quality of life and psychological well-being. Therefore, the aim of this study was to screen early diagnosed and continuously treated children with PKU on psychological strengths and behavioral difficulties. Methods Evaluation of psychological strengths and behavioral difficulties in 49 patients with PKU (23f, 2-17 years) by Strengths and Difficulties Questionnaire (SDQ; self-report 11-17 years and parent-report 2-17 years). Comparison to age, sex and BMI-matched healthy controls (n = 98; 46f). Results In patients with PKU and healthy controls median SDQ Total Difficulties Score and median scores of subscales were within the normal range in parent- and self-report, irrespective of sex and age group (children 2-10 years, adolescents 11-17 years). No influence of long-term metabolic control in PKU on SDQ could be revealed. The 2- to 10-year-old boys with PKU showed significantly higher scores in Prosocial Behavior compared to their healthy peers (P = .032). Likewise, adolescent boys with PKU showed fewer Conduct Problems (parent-report, P = .006). Adolescent girls with PKU rated themselves more often as abnormal in the subscale Emotional Problems compared to their healthy peers (P = .041). This subscale was also responsible for a significantly different Total SDQ Difficulties Score between patients and their parents' report (P = .008). Discussion SDQ represents a suitable instrument within the care for patients with PKU. Specific aspects, however, require separate consideration and evaluation with respect to this chronic disease. Special attention should be paid on adolescent PKU girls who seem to be at risk to develop emotional problem

Focus on emotion as a catalyst of memory updating during reconsolidation

We share the idea of Lane et al. that successful psychotherapy exerts its effects through memory reconsolidation. To support it, we add further evidence that a behavioral interference may trigger memory update during reconsolidation. Furthermore, we propose that-in addition to replacing maladaptive emotions-new emotions experienced in the therapeutic process catalyze reconsolidation of the updated memory structur

Genotype–phenotype correlations within the Geodermatophilaceae

The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype–phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes