Structure of the hDmc1-ssDNA filament reveals the principles of its architecture

In eukaryotes, meiotic recombination is a major source of genetic diversity, but its defects in humans lead to abnormalities such as Down's, Klinefelter's and other syndromes. Human Dmc1 (hDmc1), a RecA/Rad51 homologue, is a recombinase that plays a crucial role in faithful chromosome segregation during meiosis. The initial step of homologous recombination occurs when hDmc1 forms a filament on single-stranded (ss) DNA. However the structure of this presynaptic complex filament for hDmc1 remains unknown. To compare hDmc1-ssDNA complexes to those known for the RecA/Rad51 family we have obtained electron microscopy (EM) structures of hDmc1-ssDNA nucleoprotein filaments using single particle approach. The EM maps were analysed by docking crystal structures of Dmc1, Rad51, RadA, RecA and DNA. To fully characterise hDmc1-DNA complexes we have analysed their organisation in the presence of Ca2+, Mg2+, ATP, AMP-PNP, ssDNA and dsDNA. The 3D EM structures of the hDmc1-ssDNA filaments allowed us to elucidate the principles of their internal architecture. Similar to the RecA/Rad51 family, hDmc1 forms helical filaments on ssDNA in two states: extended (active) and compressed (inactive). However, in contrast to the RecA/Rad51 family, and the recently reported structure of hDmc1-double stranded (ds) DNA nucleoprotein filaments, the extended (active) state of the hDmc1 filament formed on ssDNA has nine protomers per helical turn, instead of the conventional six, resulting in one protomer covering two nucleotides instead of three. The control reconstruction of the hDmc1-dsDNA filament revealed 6.4 protein subunits per helical turn indicating that the filament organisation varies depending on the DNA templates. Our structural analysis has also revealed that the N-terminal domain of hDmc1 accomplishes its important role in complex formation through domain swapping between adjacent protomers, thus providing a mechanistic basis for coordinated action of hDmc1 protomers during meiotic recombination

Adaptação do inventário parental “Language Use Inventory (LUI)” para crianças entre 18 e 47 meses para o português europeu : estudo piloto

Language acquisition and development takes in account the child’s interaction with the surrounding environment. Daily social interactions with people and communication with others allow the child to acquire language being pragmatics considered a system of rules that support the communicative use of language. Identification and assessment of children at risk for language disorders are crucial in order to carry out an effective early intervention. This study was carried out taking into account first, the relevance of pragmatics as a component of language, and second the lack of assessment tools in Portugal to assess these abilities. Therefore, the aim of this study consists on the translation, adaptation and validation of the inventory “Language Use Inventory” (LUI), to European Portuguese. The LUI is a standardized parent report measure designed to assess pragmatic language development in children within 18- to 47-month-old.Objetivo: A aquisição e o desenvolvimento da linguagem resultam da interação da criança com o meio ambiente. As interações sociais cotidianas com as pessoas e a comunicação com outros permitem que a criança adquira linguagem, sendo a pragmática o sistema de regras que suporta o uso comunicativo da linguagem. A identificação e a avaliação de crianças em risco de desenvolverem transtornos de linguagem são cruciais, tendo em vista a intervenção precoce eficaz. Tendo em vista a relevância da pragmática como componente da linguagem e a escassez, em Portugal, de instrumentos de avaliação da linguagem validados para idades precoces, a finalidade deste estudo consistiu na tradução, adaptação e validação do instrumento Language Use Inventory (LUI), para o português europeu. O LUI é um inventário parental que avalia o desenvolvimento da pragmática entre os 18 e os 47 meses. Métodos: Foram adotados todos os procedimentos recomendados pelas diretrizes internacionais sobre a adaptação de testes, culminando em estudo piloto com uma amostra de 120 inventários, respondidos pelos pais/cuidadores de crianças portuguesas da referida faixa etária. Resultados: Os coeficientes de consistência interna (Alfa de Cronbach) para a versão portuguesa do LUI situaram-se em 0,97 para a escala total e entre 0,71 e 0,96 para as subescalas. Conclusão: Os resultados preliminares dos estudos de adaptação e de validação do LUI-Pt para crianças portuguesas são promissores e asseguram a validade interna desta escala em termos da sua dimensionalidade e consistência interna

Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes.

Language development builds upon a complex network of interacting subservient systems. It therefore follows that variations in, and subclinical disruptions of, these systems may have secondary effects on emergent language. In this paper, we consider the relationship between genetic variants, hearing, auditory processing and language development. We employ whole genome sequencing in a discovery family to target association and gene x environment interaction analyses in two large population cohorts; the Avon Longitudinal Study of Parents and Children (ALSPAC) and UK10K. These investigations indicate that USH2A variants are associated with altered low-frequency sound perception which, in turn, increases the risk of developmental language disorder. We further show that Ush2a heterozygote mice have low-level hearing impairments, persistent higher-order acoustic processing deficits and altered vocalizations. These findings provide new insights into the complexity of genetic mechanisms serving language development and disorders and the relationships between developmental auditory and neural systems

Some thoughts on the monitoring and preservation of waterlogged archaeological sites in eastern England

This study reviews five hydrological monitoring projects used on archeological sites in the waterlogged landscapes of fenland East Anglia and east Yorkshire in England. The project design, recorded variables, and implications of each are discussed. In particular, the importance of understanding the landscape context is paramount, and retrieving an appropriate dataset over a sufficiently lengthy period of time to obtain reliable results and predictability. Some of the lessons learnt and outstanding problems are explored. As former wetlands are fast disappearing around the world through dewatering and a host of wider development threats such as urbanization and gravel extraction, the low intrusion suite of methods described here for measuring the degree and certainty of organic preservation is doubly important for establishing the viability of preservation in situ schemes for waterlogged archeological sites. This is crucial to get right, as wetland archeological records are an irreplaceable resource which offer extraordinarily full and diverse datasets of human lifeways which are all too often either poorly preserved or erroneously interpreted because of the skewed datasets recovered from dryland sites.English Heritage, Huntings Technical Services (for Over), ARC (Central) Ltd. (for Etton), Hanson Building Products and SLR Consulting Ltd. (for Must Farm), the Society of Antiquaries and Fenland Archaeological Trust (for Etton), Cambridge Archaeological Unit (for Over and Must Farm), the McBurney Laboratory and the McDonald Institute for Archaeological Research, University of Cambridge (for Over and Must Farm), the Department of Archaeology, University of York and the European Research Council (for Star Carr), and the Meteorological Office (for Etton and Over

Behavioral and molecular genetics of reading-related AM and FM detection thresholds

Auditory detection thresholds for certain frequencies of both amplitude modulated (AM) and frequency modulated (FM) dynamic auditory stimuli are associated with reading in typically developing and dyslexic readers. We present the first behavioral and molecular genetic characterization of these two auditory traits. Two extant extended family datasets were given reading tasks and psychoacoustic tasks to determine FM 2 Hz and AM 20 Hz sensitivity thresholds. Univariate heritabilities were significant for both AM (h2 = 0.20) and FM (h2 = 0.29). Bayesian posterior probability of linkage (PPL) analysis found loci for AM (12q, PPL = 81 %) and FM (10p, PPL = 32 %; 20q, PPL = 65 %). Bivariate heritability analyses revealed that FM is genetically correlated with reading, while AM was not. Bivariate PPL analysis indicates that FM loci (10p, 20q) are not also associated with reading

Polychlorinated Biphenyls and Biotransformation Enzymes in Three Species of Sea Turtles from the Baja California Peninsula of Mexico

Concentrations of polychlorinated biphenyls (PCBs) as well as the expression patterns of cytochrome P450 (CYP) enzymes and glutathione-S-transferase (GST) activities were measured in livers of loggerhead (Caretta caretta), green (Chelonia mydas), and olive ridley (Lepidocheyls olivacea) sea turtles from the Baja California peninsula of Mexico. The mean concentrations of total PCBs were 18.1, 10.5, and 15.2 ng/g wet weight (ww) respectively for the three species and PCB 153 was the dominant congener in all samples. Total PCB concentrations were dominated by penta- and hexa-chlorinated biphenyls. The mean estimated TEQs were 42.8, 22.9, and 10.4 pg/g (ww) for loggerhead, green, and olive ridley, respectively, and more than 70% was accounted for by non-ortho PCBs. Western blots revealed the presence of hepatic microsomal proteins that cross-reacted with anti-CYP2K1 and anti-CYP3A27 antibodies but not with anti-CYP1A antibody. There were no significant differences in GST activities between species. Grouping congeners based on structure–activity relationships for CYP isoenzymes suggested limited activity of CYP1A contribution to PCB biotransformation in sea turtles. These results suggest potential accumulation of PCBs that are CYP1A substrates and provide evidence for biotransformation capacity, which differs from known animal models, highlighting the need for further studies in reptiles, particularly those threatened with extinction

Does a child’s language ability affect the correspondence between parent and teacher ratings of ADHD symptoms?

Background: Rating scales are often used to identify children with potential Attention-Deficit/Hyperactivity Disorder (ADHD), yet there are frequently discrepancies between informants which may be moderated by child characteristics. The current study asked whether correspondence between parent and teacher ratings on the Strengths and Weakness of ADHD symptoms and Normal behaviour scale (SWAN) varied systematically with child language ability. Method: Parent and teacher SWAN questionnaires were returned for 200 children (aged 61–81 months); 106 had low language ability (LL) and 94 had typically developing language (TL). After exploring informant correspondence (using Pearson correlation) and the discrepancy between raters, we report inter-class correlation coefficients, to assess inter-rater reliability, and Cohen’s kappa, to assess agreement regarding possible ADHD caseness. Results: Correlations between informant ratings on the SWAN were moderate. Children with LL were rated as having increased inattention and hyperactivity relative to children with TL; teachers, however, rated children with LL as having more inattention than parents. Inter-rater reliability of the SWAN was good and there were no systematic differences between the LL and TL groups. Case agreement between parent and teachers was fair; this varied by language group with poorer case agreement for children with LL. Conclusion: Children’s language abilities affect the discrepancy between informant ratings of ADHD symptomatology and the agreement between parents and teachers regarding potential ADHD caseness. The assessment of children’s core language ability would be a beneficial addition to the ADHD diagnostic process.</p

Heritability of non-speech auditory processing skills

Recent insight into the genetic bases for autism spectrum disorder, dyslexia, stuttering, and language disorders suggest that neurogenetic approaches may also reveal at least one etiology of auditory processing disorder (APD). A person with an APD typically has difficulty understanding speech in background noise despite having normal pure-tone hearing sensitivity. The estimated prevalence of APD may be as high as 10% in the pediatric population, yet the causes are unknown and have not been explored by molecular or genetic approaches. The aim of our study was to determine the heritability of frequency and temporal resolution for auditory signals and speech recognition in noise in 96 identical or fraternal twin pairs, aged 6–11 years. Measures of auditory processing (AP) of non-speech sounds included backward masking (temporal resolution), notched noise masking (spectral resolution), pure-tone frequency discrimination (temporal fine structure sensitivity), and nonsense syllable recognition in noise. We provide evidence of significant heritability, ranging from 0.32 to 0.74, for individual measures of these non-speech-based AP skills that are crucial for understanding spoken language. Identification of specific heritable AP traits such as these serve as a basis to pursue the genetic underpinnings of APD by identifying genetic variants associated with common AP disorders in children and adults

Publication and related biases in health services research: a systematic review of empirical evidence

Background: Publication and related biases (including publication bias, time-lag bias, outcome reporting bias and p-hacking) have been well documented in clinical research, but relatively little is known about their presence and extent in health services research (HSR). This paper aims to systematically review evidence concerning publication and related bias in quantitative HSR. Methods: Databases including MEDLINE, EMBASE, HMIC, CINAHL, Web of Science, Health Systems Evidence, Cochrane EPOC Review Group and several websites were searched to July 2018. Information was obtained from: (1) Methodological studies that set out to investigate publication and related biases in HSR; (2) Systematic reviews of HSR topics which examined such biases as part of the review process. Relevant information was extracted from included studies by one reviewer and checked by another. Studies were appraised according to commonly accepted scientific principles due to lack of suitable checklists. Data were synthesised narratively. Results: After screening 6155 citations, four methodological studies investigating publication bias in HSR and 184 systematic reviews of HSR topics (including three comparing published with unpublished evidence) were examined. Evidence suggestive of publication bias was reported in some of the methodological studies, but evidence presented was very weak, limited in both quality and scope. Reliable data on outcome reporting bias and p-hacking were scant. HSR systematic reviews in which published literature was compared with unpublished evidence found significant differences in the estimated intervention effects or association in some but not all cases. Conclusions: Methodological research on publication and related biases in HSR is sparse. Evidence from available literature suggests that such biases may exist in HSR but their scale and impact are difficult to estimate for various reasons discussed in this paper. Systematic review registration: PROSPERO 2016 CRD42016052333

Numerical analysis of seepage–deformation in unsaturated soils

A coupled elastic–plastic finite element analysis based on simplified consolidation theory for unsaturated soils is used to investigate the coupling processes of water infiltration and deformation. By introducing a reduced suction and an elastic–plastic constitutive equation for the soil skeleton, the simplified consolidation theory for unsaturated soils is incorporated into an in-house finite element code. Using the proposed numerical method, the generation of pore water pressure and development of deformation can be simulated under evaporation or rainfall infiltration conditions. Through a parametric study and comparison with the test results, the proposed method is found to describe well the characteristics during water evaporation/infiltration into unsaturated soils. Finally, an unsaturated soil slope with water infiltration is analyzed in detail to investigate the development of the displacement and generation of pore water pressure