Hack Weeks as a model for Data Science Education and Collaboration

Across almost all scientific disciplines, the instruments that record our experimental data and the methods required for storage and data analysis are rapidly increasing in complexity. This gives rise to the need for scientific communities to adapt on shorter time scales than traditional university curricula allow for, and therefore requires new modes of knowledge transfer. The universal applicability of data science tools to a broad range of problems has generated new opportunities to foster exchange of ideas and computational workflows across disciplines. In recent years, hack weeks have emerged as an effective tool for fostering these exchanges by providing training in modern data analysis workflows. While there are variations in hack week implementation, all events consist of a common core of three components: tutorials in state-of-the-art methodology, peer-learning and project work in a collaborative environment. In this paper, we present the concept of a hack week in the larger context of scientific meetings and point out similarities and differences to traditional conferences. We motivate the need for such an event and present in detail its strengths and challenges. We find that hack weeks are successful at cultivating collaboration and the exchange of knowledge. Participants self-report that these events help them both in their day-to-day research as well as their careers. Based on our results, we conclude that hack weeks present an effective, easy-to-implement, fairly low-cost tool to positively impact data analysis literacy in academic disciplines, foster collaboration and cultivate best practices.Comment: 15 pages, 2 figures, submitted to PNAS, all relevant code available at https://github.com/uwescience/HackWeek-Writeu

Methylxanthines induce structural and functional alterations of the cardiac system in zebrafish embryos

Background: Zebrafish embryos are emerging as a model for pharmacological and toxicological studies. We used zebrafish embryos to study the general toxicity and cardiovascular effects of eight methylxanthines: aminophylline, caffeine, diprophylline, doxofylline, etophylline, 3-isobutyl-1-methylxanthine (IBMX), pentoxifylline and theophylline. Methods: Microinjections of the eight methylxanthines were performed in 1-2 cell stage zebrafish embryos and the general toxicity and cardiovascular effects were analyzed at different time points. Embryotoxicity and teratogenicity were evaluated to understand the general toxicity of these compounds. Structural and functional alterations of the heart were evaluated to assess the cardiovascular effects. Results: Our results showed different activity patterns of the methylxanthines drugs. Caffeine, IBMX, pentoxifylline and theophylline were highly embryotoxic and teratogenic; aminophylline, doxofylline and etophylline were embryotoxic and teratogenic only at higher doses, and diprophylline showed a minimal (< 10%) embryotoxicity and teratogenicity. Most of these drugs induced structural alteration of the heart in 20-40% of the injected embryos with the maximum dose. This structural alteration was fatal with the embryos ultimately dying within 120 hpf. All the drugs induced a transient increase in heart rate at 48 hpf which returned to baseline within 96 hpf. This functional effect of methylxanthines showed similarity to the studies done in humans and other vertebrates. Conclusion: Our results indicate the potential toxicity and teratogenicity of different methylxanthines in the embryos during embryonic development, the most sensitive period of life. Although interspecies differences need to be considered before drawing any conclusion, our study elucidated that a single exposure of methylxanthines at therapeutic range could induce cardiac dysfunction besides causing embryotoxicity and teratogenicity. Of all the drugs, diprophylline appeared to be safer, with lower degree of embryotoxicity, teratogenicity and cardiac toxicity as compared to other methylxanthines

Surgery of petroclival meningiomas: Recent surgical results and outcomes

Petroclival meningiomas represent only 10% of all meningiomas located in the posterior fossa, but are some of the most formidable challenges in skull base surgery. We described our recent experience (2005-September2014) regarding the surgery of these tumors. We retrospectively analyzed surgical results and outcome in 11 cases of petroclival meningiomas. Most common symptoms in our series were headache and gait disturbance, while cranial nerves palsies represented the most common presenting signs. There were 8 females and 3 males, and the mean age was 52 years. Surgical approaches chosen for petroclival meningiomas in our series were retrosigmoid (9 patients) and subtemporal transtentorial (2 patients). We achieved total tumor resection in 5 cases (45%) and subtotal resection in 6 cases (55%). Overall outcome (total/subtotal resection) was good in 6 cases, fair in 3 cases and poor in one case. One postoperative death occurred due to hemorrhagic midbrain infarction (9%). Complications were usually related to cranial nerve deficits: loss of hearing (2 patients), paresis of trochlear nerve (1 patient), trigeminal nerve (3 patients) and facial nerve (1 patient). In 4 patients these cranial nerves deficits were transient. In one case, a patient developed postoperative hydrocephalus and needed shunt placement. Despite the fact that complications can be disastrous, we considered that an appropriate approach, combined with microsurgical techniques and a better understanding of the anatomy, greatly decrease the incidence and severity of complications and make feasible a total tumor resection

Government expenditure and economic growth in the European Union countries: New evidence.

This paper provides new evidence of the impact of government spending on economic growth in the European Union countries. Governments can adjust their levels of spending in order to influence their economies, although the relationship between these variables can be positive or negative, depending on the countries included in the sample, the period of estimation and the variables which reflect the size of the public sector. The results obtained based on regression and panel techniques suggest that government expenditure is not clearly related with economic growth in the European Union countries over the period 1994-2012

Comparing the use of ERA5 reanalysis dataset and ground-based agrometeorological data under different climates and topography in Italy

Study region: The study region is represented by seven irrigation districts distributed under different climate and topography conditions in Italy. Study focus: This study explores the reliability and consistency of the global ERA5 single levels and ERA5-Land reanalysis datasets in predicting the main agrometeorological estimates commonly used for crop water requirements calculation. In particular, the reanalysis data was compared, variable-by-variable (e.g., solar radiation, R-s; air temperature, T-air; relative humidity, RH; wind speed, u(10); reference evapotranspiration, ET0), with in situ agrometeorological obser-vations obtained from 66 automatic weather stations (2008-2020). In addition, the presence of a climate-dependency on their accuracy was assessed at the different irrigation districts. New hydrological insights for the region: A general good agreement was obtained between observed and reanalysis agrometeorological variables at both daily and seasonal scales. The best perfor-mance was obtained for T-air, followed by RH, R-s, and u(10) for both reanalysis datasets, especially under temperate climate conditions. These performances were translated into slightly higher accuracy of ET0 estimates by ERA5-Land product, confirming the potential of using reanalysis datasets as an alternative data source for retrieving the ET0 and overcoming the unavailability of observed agrometeorological data

Early Science with the Large Millimeter Telescope: Detection of Dust Emission in Multiple Images of a Normal Galaxy at z \u3e 4 Lensed by a Frontier Fields Cluster

We directly detect dust emission in an optically detected, multiply imaged galaxy lensed by the Frontier Fields cluster MACSJ0717.5+3745. We detect two images of the same galaxy at 1.1 mm with the AzTEC camera on the Large Millimeter Telescope leaving no ambiguity in the counterpart identification. This galaxy, MACS0717_Az9, is at z \u3e 4 and the strong lensing model (μ=7.5) allows us to calculate an intrinsic IR luminosity of 9.7 × 1010 Le and an obscured star formation rate of 14.6 ± 4.5 Me yr−1. The unobscured star formation rate from the UV is only 4.1 ± 0.3 Me yr−1, which means the total star formation rate (18.7 ± 4.5 Me yr−1) is dominated (75%–80%) by the obscured component. With an intrinsic stellar mass of only 6.9 × 109 Me, MACS0717_Az9 is one of only a handful of z \u3e 4 galaxies at these lower masses that is detected in dust emission. This galaxy lies close to the estimated star formation sequence at this epoch. However, it does not lie on the dust obscuration relation (IRX-β) for local starburst galaxies and is instead consistent with the Small Magellanic Cloud attenuation law. This remarkable lower mass galaxy, showing signs of both low metallicity and high dust content, may challenge our picture of dust production in the early universe

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Yeast IME2 Functions Early in Meiosis Upstream of Cell Cycle-Regulated SBF and MBF Targets

BACKGROUND: In Saccharomyces cerevisiae, the G1 cyclin/cyclin-dependent kinase (CDK) complexes Cln1,-2,-3/Cdk1 promote S phase entry during the mitotic cell cycle but do not function during meiosis. It has been proposed that the meiosis-specific protein kinase Ime2, which is required for normal timing of pre-meiotic DNA replication, is equivalent to Cln1,-2/Cdk1. These two CDK complexes directly catalyze phosphorylation of the B-type cyclin/CDK inhibitor Sic1 during the cell cycle to enable its destruction. As a result, Clb5,-6/Cdk1 become activated and facilitate initiation of DNA replication. While Ime2 is required for Sic1 destruction during meiosis, evidence now suggests that Ime2 does not directly catalyze Sic1 phosphorylation to target it for destabilization as Cln1,-2/Cdk1 do during the cell cycle. METHODOLOGY/PRINCIPAL FINDINGS: We demonstrated that Sic1 is eventually degraded in meiotic cells lacking the IME2 gene (ime2Δ), supporting an indirect role of Ime2 in Sic1 destruction. We further examined global RNA expression comparing wild type and ime2Δ cells. Analysis of these expression data has provided evidence that Ime2 is required early in meiosis for normal transcription of many genes that are also periodically expressed during late G1 of the cell cycle. CONCLUSIONS/SIGNIFICANCE: Our results place Ime2 at a position in the early meiotic pathway that lies upstream of the position occupied by Cln1,-2/Cdk1 in the analogous cell cycle pathway. Thus, Ime2 may functionally resemble Cln3/Cdk1 in promoting S phase entry, or it could play a role even further upstream in the corresponding meiotic cascade