Condensin and cohesin display different arm conformations with characteristic hinge angles

Structural maintenance of chromosomes (SMC) proteins play central roles in higher-order chromosome dynamics from bacteria to humans. In eukaryotes, two different SMC protein complexes, condensin and cohesin, regulate chromosome condensation and sister chromatid cohesion, respectively. Each of the complexes consists of a heterodimeric pair of SMC subunits and two or three non-SMC subunits. Previous studies have shown that a bacterial SMC homodimer has a symmetrical structure in which two long coiled-coil arms are connected by a flexible hinge. A catalytic domain with DNA- and ATP-binding activities is located at the distal end of each arm. We report here the visualization of vertebrate condensin and cohesin by electron microscopy. Both complexes display the two-armed structure characteristic of SMC proteins, but their conformations are remarkably different. The hinge of condensin is closed and the coiled-coil arms are placed close together. In contrast, the hinge of cohesin is wide open and the coiled-coils are spread apart from each other. The non-SMC subunits of both condensin and cohesin form a globular complex bound to the catalytic domains of the SMC heterodimers. We propose that the “closed” conformation of condensin and the “open” conformation of cohesin are important structural properties that contribute to their specialized biochemical and physiological functions

Compare statistical significance tests for information retrieval evaluation

Preprint of our Journal of the Association for Information Science and Technology (JASIST) paper[Abstract] Statistical significance tests can provide evidence that the observed difference in performance between two methods is not due to chance. In Information Retrieval, some studies have examined the validity and suitability of such tests for comparing search systems.We argue here that current methods for assessing the reliability of statistical tests suffer from some methodological weaknesses, and we propose a novel way to study significance tests for retrieval evaluation. Using Score Distributions, we model the output of multiple search systems, produce simulated search results from such models, and compare them using various significance tests. A key strength of this approach is that we assess statistical tests under perfect knowledge about the truth or falseness of the null hypothesis. This new method for studying the power of significance tests in Information Retrieval evaluation is formal and innovative. Following this type of analysis, we found that both the sign test and Wilcoxon signed test have more power than the permutation test and the t-test. The sign test and Wilcoxon signed test also have a good behavior in terms of type I errors. The bootstrap test shows few type I errors, but it has less power than the other methods tested.Ministerio de Econom´ıa y Competitividad; TIN2015-64282-RXunta de Galicia; GPC 2016/035Xunta de Galicia; ED431G/01Xunta de Galicia; ED431G/0

Using Machine Learning Techniques to Predict Adolescents’ Involvement in Family Conflict

[Abstract] Many cases of violence against children occur in homes and other close environments. Machine leaning is a novel approach that addresses important gaps in ways of examining this socially significant issue, illustrating innovative and emerging approaches for the use of computers from a psychological perspective. In this paper, we aim to use machine learning techniques to predict adolescents’ involvement in family conflict in a sample of adolescents living with their families(community adolescents) and adolescents living in residential care centers, who are temporarilyseparated from their families because of adverse family conditions. Participants were 251 Spanish adolescents (Mage= 15.59), of whom 167 lived in residential care and 84 lived with their families.We measured perceived interparental and family conflict, adolescents’emotional security,emotional, cognitive, and behavioral immediate responses to analog interparental conflict (IPC),and adolescents’ sociodemographic variables (i.e., age, gender). With a prediction accuracy of 65%, our results show that adolescents in residential care are not at greater risk for involvement in family conflict compared to adolescents living with their families. Age and gender are not salient predictive variables. We could identify that responses to analog IPC, adolescents’emotiona lsecurity, triangulation in IPC, and the presence of insults or blame during family disputes predict adolescents’ involvement in family conflict. These results point to variables with a potential predictive capacity, which is relevant for research and intervention.The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was partially supported by projects PLEC2021-007,662 (MCIN/AEI/10.13,039/501100011033, Ministerio de Ciencia e Innovación, Agencia Estatal de Investigación, Plan de Recuperación, Transformación y Resiliencia, Unión Europea-Next GenerationEU), RTI2018-093,336-B-C21 & RTI2018-093,336-B-C22 (Ministerio de Ciencia e Innovación, Agencia Estatal de Investigación & ERDF). The fourth and fifth authors also thank the financial support supplied by the Consellería de Educación, Universidade e Formación Profesional (accreditation 2019–2022 ED431G-2019/01 and GPC ED431 B 2019/03) and the European Regional Development Fund, which acknowledges the CITIC Research Center in ICT of the University of A Coruña as a Research Center of the Galician University System. The third author also thanks the financial support supplied by the Consellería de Educación, Universidade e Formación Profesional (accreditation 2019–2022 ED431G-2019/04, ED431 C 2018/29) and the European Regional Development Fund, which acknowledges the CiTIUS-Research Center in Intelligent Technologies of the University of Santiago de Compostela as a Research Center of the Galician University SystemXunta de Galicia; ED431G-2019/01Xunta de Galicia; ED431 B 2019/03Xunta de Galicia; ED431G-2019/04Xunta de Galicia; ED431 C 2018/2

Colaboración entre docentes de una universidad alemana y una española para el desarrollo de seminarios prácticos acerca de la credibilidad de la información

En esta experiencia docente, presentamos una colaboración internacional entre investigadores de la Universidad de Regensburg (Baviera, Alemania) y la Universidad de Santiago de Compostela (Galicia, España), en la que el alumnado participa en dos materias de Ciencias de la Información. Se propone un enfoque en el que los estudiantes construyen su propia comprensión de las tecnologías mediante el planteamiento de un problema en el contexto de un proyecto de investigación. El área de interés en la que se propone el desafío se orienta a cómo ayudar a los usuarios finales de las tecnologías de información a establecer la credibilidad de la información. Para ello, se ha trabajado con contenidos online relacionados con la pandemia de COVID-19.In this teaching experience, we present an international collaboration between researchers from a German university and a Spanish university, in which students participate in two Information Science courses. An approach is proposed in which students build their own understanding of technologies by posing a problem in the context of a research project. The area of interest in which the challenge is proposed is oriented towards how to help end-users of information technologies to establish the credibility of information. To this end, work has been done with online content related to the COVID-19 pandemic.Este trabajo ha sido financiado por FEDER/Ministerio de Ciencia, Innovación y Universidades – Agencia Estatal de Investigación (RTI2018-093336-B-C21), y también ha recibido apoyo financiero de la Consellería de Educación, Universidade e Formación Profesional (acreditación 2019-2022 ED431G-2019/04, ED431C 2018/29, ED431C 2018/19) y de los fondos FEDER, que reconocen al CiTIUS de la USC como Centro de Investigación del Sistema Universitario de Galicia

Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements

Burkholderia mallei (Bm), the causative agent of the predominately equine disease glanders, is a genetically uniform species that is very closely related to the much more diverse species Burkholderia pseudomallei (Bp), an opportunistic human pathogen and the primary cause of melioidosis. To gain insight into the relative lack of genetic diversity within Bm, we performed whole-genome comparative analysis of seven Bm strains and contrasted these with eight Bp strains. The Bm core genome (shared by all seven strains) is smaller in size than that of Bp, but the inverse is true for the variable gene sets that are distributed across strains. Interestingly, the biological roles of the Bm variable gene sets are much more homogeneous than those of Bp. The Bm variable genes are found mostly in contiguous regions flanked by insertion sequence (IS) elements, which appear to mediate excision and subsequent elimination of groups of genes that are under reduced selection in the mammalian host. The analysis suggests that the Bm genome continues to evolve through random IS-mediated recombination events, and differences in gene content may contribute to differences in virulence observed among Bm strains. The results are consistent with the view that Bm recently evolved from a single strain of Bp upon introduction into an animal host followed by expansion of IS elements, prophage elimination, and genome rearrangements and reduction mediated by homologous recombination across IS elements

Transcriptional analysis of the HeT-A retrotransposon in mutant and wild type stocks reveals high sequence variability at Drosophila telomeres and other unusual features

<p>Abstract</p> <p>Background</p> <p>Telomere replication in Drosophila depends on the transposition of a domesticated retroelement, the <it>HeT-A </it>retrotransposon. The sequence of the <it>HeT-A </it>retrotransposon changes rapidly resulting in differentiated subfamilies. This pattern of sequence change contrasts with the essential function with which the <it>HeT-A </it>is entrusted and brings about questions concerning the extent of sequence variability, the telomere contribution of different subfamilies, and whether wild type and mutant Drosophila stocks show different <it>HeT-A </it>scenarios.</p> <p>Results</p> <p>A detailed study on the variability of <it>HeT-A </it>reveals that both the level of variability and the number of subfamilies are higher than previously reported. Comparisons between GIII, a strain with longer telomeres, and its parental strain Oregon-R indicate that both strains have the same set of <it>HeT-A </it>subfamilies. Finally, the presence of a highly conserved splicing pattern only in its antisense transcripts indicates a putative regulatory, functional or structural role for the <it>HeT-A </it>RNA. Interestingly, our results also suggest that most <it>HeT-A </it>copies are actively expressed regardless of which telomere and where in the telomere they are located.</p> <p>Conclusions</p> <p>Our study demonstrates how the <it>HeT-A </it>sequence changes much faster than previously reported resulting in at least nine different subfamilies most of which could actively contribute to telomere extension in Drosophila. Interestingly, the only significant difference observed between Oregon-R and GIII resides in the nature and proportion of the antisense transcripts, suggesting a possible mechanism that would in part explain the longer telomeres of the GIII stock.</p

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured