Whole-genome sequencing for national surveillance of Shiga toxin–producing Escherichia coli O157

Background. National surveillance of gastrointestinal pathogens, such as Shiga toxin–producing Escherichia coli O157 (STEC O157), is key to rapidly identifying linked cases in the distributed food network to facilitate public health interventions. In this study, we used whole-genome sequencing (WGS) as a tool to inform national surveillance of STEC O157 in terms of identifying linked cases and clusters and guiding epidemiological investigation. Methods. We retrospectively analyzed 334 isolates randomly sampled from 1002 strains of STEC O157 received by the Gastrointestinal Bacteria Reference Unit at Public Health England, Colindale, in 2012. The genetic distance between each isolate, as estimated by WGS, was calculated and phylogenetic methods were used to place strains in an evolutionary context. Results. Estimates of linked clusters representing STEC O157 outbreaks in England and Wales increased by 2-fold when WGS was used instead of traditional typing techniques. The previously unidentified clusters were often widely geographically distributed and small in size. Phylogenetic analysis facilitated identification of temporally distinct cases sharing common exposures and delineating those that shared epidemiological and temporal links. Comparison with multi locus variable number tandem repeat analysis (MLVA) showed that although MLVA is as sensitive as WGS, WGS provides a more timely resolution to outbreak clustering. Conclusions. WGS has come of age as a molecular typing tool to inform national surveillance of STEC O157; it can be used in real time to provide the highest strain-level resolution for outbreak investigation. WGS allows linked cases to be identified with unprecedented specificity and sensitivity that will facilitate targeted and appropriate public health investigations

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.

Large-scale deep-coverage whole-genome sequencing (WGS) is now feasible and offers potential advantages for locus discovery. We perform WGS in 16,324 participants from four ancestries at mean depth >29X and analyze genotypes with four quantitative traits-plasma total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, and triglycerides. Common variant association yields known loci except for few variants previously poorly imputed. Rare coding variant association yields known Mendelian dyslipidemia genes but rare non-coding variant association detects no signals. A high 2M-SNP LDL-C polygenic score (top 5th percentile) confers similar effect size to a monogenic mutation (~30 mg/dl higher for each); however, among those with severe hypercholesterolemia, 23% have a high polygenic score and only 2% carry a monogenic mutation. At these sample sizes and for these phenotypes, the incremental value of WGS for discovery is limited but WGS permits simultaneous assessment of monogenic and polygenic models to severe hypercholesterolemia

Dynamics of CrO3–Fe2O3 catalysts during the high-temperature water-gas shift reaction: molecular structures and reactivity

A series of supported CrO3/Fe2O3 catalysts were investigated for the high-temperature water-gas shift (WGS) and reverse-WGS reactions and extensively characterized using in situ and operando IR, Raman, and XAS spectroscopy during the high-temperature WGS/RWGS reactions. The in situ spectroscopy examinations reveal that the initial oxidized catalysts contain surface dioxo (O═)2Cr6+O2 species and a bulk Fe2O3 phase containing some Cr3+ substituted into the iron oxide bulk lattice. Operando spectroscopy studies during the high-temperature WGS/RWGS reactions show that the catalyst transforms during the reaction. The crystalline Fe2O3 bulk phase becomes Fe3O4 ,and surface dioxo (O═)2Cr6+O2 species are reduced and mostly dissolve into the iron oxide bulk lattice. Consequently, the chromium–iron oxide catalyst surface is dominated by FeOx sites, but some minor reduced surface chromia sites are also retained. The Fe3–-xCrxO4 solid solution stabilizes the iron oxide phase from reducing to metallic Fe0 and imparts an enhanced surface area to the catalyst. Isotopic exchange studies with C16O2/H2 → C18O2/H2 isotopic switch directly show that the RWGS reaction proceeds via the redox mechanism and only O* sites from the surface region of the chromium–iron oxide catalysts are involved in the RWGS reaction. The number of redox O* sites was quantitatively determined with the isotope exchange measurements under appropriate WGS conditions and demonstrated that previous methods have undercounted the number of sites by nearly 1 order of magnitude. The TOF values suggest that only the redox O* sites affiliated with iron oxide are catalytic active sites for WGS/RWGS, though a carbonate oxygen exchange mechanism was demonstrated to exist, and that chromia is only a textural promoter that increases the number of catalytic active sites without any chemical promotion effect

Mapiranje zenskih studijev in studijev spola v akademskem polju v Sloveniji

The aim of the present paper is to map the development of women’s and gender studies (WGS) in the academic field in Slovenia. Slovenia is the first of the former Yugoslav state republics in which WGS have succeeded in entering the academic field and becoming part of institutionalized university study. In this paper we will ask the following questions: How, when and why did this happen? How was this connected to women’s and feminist movements and politics regarding women’s issues and demands? What were the obstacles in this process? Who were the agents and what were the factors that supported demands for the incorporation of WGS in academia? How has the field evolved in the last few decades? What were the phases of this development? Which fields were the forerunners, which were the late-comers and which are still left aside? What are the thematic scopes taught in WGS courses? In which degrees are the courses offered and what are their modules? Who teaches them? The mapping in this paper is mainly based on primary sources of university programmes and their curricula at faculties of the University of Ljubljana, as well as on interviews with important agents in the field. (DIPF/Orig.

ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors

The Planck-LFI flight model composite waveguides

The Low Frequency Instrument on board the PLANCK satellite is designed to give the most accurate map ever of the CMB anisotropy of the whole sky over a broad frequency band spanning 27 to 77 GHz. It is made of an array of 22 pseudo-correlation radiometers, composed of 11 actively cooled (20 K) Front End Modules (FEMs), and 11 Back End Modules (BEMs) at 300K. The connection between the two parts is made with rectangular Wave Guides. Considerations of different nature (thermal, electromagnetic and mechanical), imposed stringent requirements on the WGs characteristics and drove their design. From the thermal point of view, the WG should guarantee good insulation between the FEM and the BEM sections to avoid overloading the cryocooler. On the other hand it is essential that the signals do not undergo excessive attenuation through the WG. Finally, given the different positions of the FEM modules behind the focal surface and the mechanical constraints given by the surrounding structures, different mechanical designs were necessary. A composite configuration of Stainless Steel and Copper was selected to satisfy all the requirements. Given the complex shape and the considerable length (about 1.5-2 m), manufacturing and testing the WGs was a challenge. This work deals with the development of the LFI WGs, including the choice of the final configuration and of the fabrication process. It also describes the testing procedure adopted to fully characterize these components from the electromagnetic point of view and the space qualification process they underwent. Results obtained during the test campaign are reported and compared with the stringent requirements. The performance of the LFI WGs is in line with requirements, and the WGs were successfully space qualified.Comment: this paper is part of the Prelaunch status LFI papers published on JINST: http://www.iop.org/EJ/journal/-page=extra.proc5/jins

ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries.

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors

Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing

The ability of Shiga toxin-producing Escherichia coli (STEC) to cause severe illness in humans is determined by multiple host factors and bacterial characteristics, including Shiga toxin (Stx) subtype. Given the link between Stx2a subtype and disease severity, we sought to identify the stx subtypes present in whole genome sequences (WGS) of 444 isolates of STEC O157. Difficulties in assembling the stx genes in some strains were overcome by using two complementary bioinformatics methods: mapping and de novo assembly. We compared the WGS analysis with the results obtained using a PCR approach and investigated the diversity within and between the subtypes. All strains of STEC O157 in this study had stx1a, stx2a or stx2c or a combination of these three genes. There was over 99% (442/444) concordance between PCR and WGS. When common source strains were excluded, 236/349 strains of STEC O157 had multiple copies of different Stx subtypes and 54 had multiple copies of the same Stx subtype. Of those strains harbouring multiple copies of the same Stx subtype, 33 had variants between the alleles while 21 had identical copies. Strains harbouring Stx2a only were most commonly found to have multiple alleles of the same subtype (42%). Both the PCR and WGS approach to stx subtyping provided a good level of sensitivity and specificity. In addition, the WGS data also showed there were a significant proportion of strains harbouring multiple alleles of the same Stx subtype associated with clinical disease in England

Information Literacy at the Intersection of Scholarly Communications and Social Justice

Undergraduate outreach about Open Access (OA) lies at the intersection of information literacy and Scholarly Communications. Reframing undergraduates as current and future scholars allows us to treat them as agents within the Scholarly Communications network. Students who have mastered fundamental research skills are prepared to view them through the critical lens of Scholarly Communications in order to learn both how to locate resources and how those resources are created. This educational approach highlights the various barriers scholars can face in the research process, as well as provides an awareness of information privilege. This poster will provide a model for how OA can be integrated into information literacy instruction by describing a one-shot session delivered to a 300-level Women and Gender Studies (WGS) course. For librarians looking to integrate OA into their teaching, WGS courses are a logical starting point. There is a moral imperative for WGS scholars to be aware of OA due to its corresponding values of equality, justice, and the belief in the capacity for all people to be participants in the scholarly conversation. Advanced WGS students are prepared to apply high level critical thinking to their own research practices. Situating their scholarly activity in the greater ecosystem of scholarly communications reveals how these students are agents within this system whose choices can have an impact on the larger network