Research Data Management: A Library Practitioner’s Perspective

Abstract Column description. The Future Voices in Public Services column is a forum for students in graduate library and information science programs to discuss key issues they see in academic library public services, to envision what they feel librarians in public service have to offer to academia, to tell us of their visions for the profession, or to tell us of research that is going on in library schools. Interested students can contact Nancy Dewald

Mirror of Atiyah flop in symplectic geometry and stability conditions

We study the mirror operation of the Atiyah flop in symplectic geometry. We formulate the operation for a symplectic manifold with a Lagrangian fibration. Furthermore we construct geometric stability conditions on the derived Fukaya category of the deformed conifold and study the action of the mirror Atiyah flop on these stability conditions.Comment: v2: 45 pages, 18 figures; revised expositio

A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300

A gene encoding a putative DNA helicase from Staphylococcus aureus USA300 was cloned and expressed in Escherichia coli. The protein was purified to over 90% purity by chromatography. The purified enzyme, SauUSI, predominantly cleaves modified DNA containing 5mC and 5-hydroxymethylcytosine. Cleavage of 5mC-modified plasmids indicated that the sites S5mCNGS (S = C or G) are preferentially digested. The endonuclease activity requires the presence of adenosine triphosphate (ATP) or dATP whereas the non-hydrolyzable γ-S-ATP does not support activity. SauUSI activity was inhibited by ethylenediaminetetraacetic acid. It is most active in Mg++ buffers. No companion methylase gene was found near the SauUSI restriction gene. The absence of a cognate methylase and cleavage of modified DNA indicate that SauUSI belongs to type IV restriction endonucleases, a group that includes EcoK McrBC and Mrr. SauUSI belongs to a family of highly similar homologs found in other sequenced S. aureus, S. epidermidis and S. carnosus genomes. More distant SauUSI orthologs can be found in over 150 sequenced bacterial/archaea genomes. Finally, we demonstrated the biological function of the type IV REase in restricting 5mC-modified plasmid DNA by transformation into clinical S. aureus strain SA564, and in restricting phage λ infection when the endonuclease is expressed in E. col

5-Phenyl-2-(4-pyrid­yl)pyrimidine

The title compound, C15H11N3, crystallizes with two independent mol­ecules in the asymmetric unit. The dihedral angles between the phenyl and pyridine rings in each mol­ecule are 53.48 (5) and 50.80 (5)°. In the crystal structure, weak inter­molecular C—H⋯N hydrogen bonds connect mol­ecules into one-dimensional chains. In addition, the crystal structure is stabilized by weak C—H⋯π(arene) inter­actions

Flood mitigation by permeable pavements in Chinese sponge city construction

It is important to evaluate the effectiveness of permeable pavements on flood mitigation at different spatial scales for their effective application, for example, sponge city construction in China. This study evaluated the effectiveness of three types of permeable pavements (i.e., permeable asphalts (PA), permeable concretes (PC), and permeable interlocking concrete pavers (PICP)) on flood mitigation at a community scale in China using a hydrological model. In addition, the effects of clogging and initial water content in permeable pavements on flood mitigation performance were assessed. The results indicated that in 12 scenarios, permeable pavements reduced total surface runoff by 1–40% and peak flow by 7–43%, respectively. The hydrological performance of permeable pavements was limited by clogging and initial water content. Clogging resulted in the effectiveness on total surface runoff reduction and peak flow reduction being decreased by 62–92% and 37–65%, respectively. By increasing initial water content at the beginning of the simulation, the effectiveness of total runoff reduction and peak flow reduction decreased by 57–85% and 37–67%, respectively. Overall, among the three types of permeable pavements, PC without clogging had the best performance in terms of flood mitigation, and PICP was the least prone to being clogged. Our findings demonstrate that both the type and the maintenance of permeable pavements have significant effects on their performance in the flood mitigation

Lung Cancer Decreased Sharply in First 5 Years After Smoking Cessation in Chinese Men

BackgroundThe rate of decline in lung cancer risk after smoking cessation among male population and the importance of the magnitude of the early decline were not sufficiently defined in the earlier studies. We evaluated the detailed duration-response relationship between years since smoking cessation and lung cancer risk across major histological types in a population-based case-referent study.MethodsWe recruited 1208 consecutive incident cases of primary lung cancer among Chinese males from the largest oncology center in Hong Kong during 2004–2006, and 1069 male community referents frequency-matched in 5-year age groups. We performed unconditional multiple logistic regression and generalized additive model incorporating smoothing spline to model the potential nonlinear effect of years since cessation on lung cancer.ResultsAll histological types of lung cancer were strongly associated with current smoking. We observed a rapidly decreasing odds ratio of lung cancer (>50%) across all major histological types of lung cancer (except for the large cell type) within the first 5 years of quitting; the odds ratio continued to decrease but at a slower rate in the subsequent years.ConclusionThe substantial benefits obtainable within a short period of 5 years' abstinence should convey an encouraging message to chronic smokers, clinicians, and public health workers

Global Imperative of Suicidal Ideation in 10 Countries Amid the COVID-19 Pandemic

Background: The novel coronavirus (COVID-19) has had a detrimental impact on individuals' psychological well-being; however, a multi-country comparison on the prevalence of suicidal ideation due to the virus is still lacking.Objectives: To examine the prevalence and correlates of suicidal ideation among the general population across 10 countries during the COVID-19 pandemic.Materials and methods: This was a cross-sectional study which used convenience sampling and collected data by conducting an online survey. Participants were sourced from 10 Eastern and Western countries. The Patient Health Questionnaire (PHQ-9) was used to measure the outcome variable of suicidal ideation. Ordinal regression analysis was used to identify significant predictors associated with suicidal ideation.Results: A total of 25,053 participants (22.7% male) were recruited. Results from the analysis showed that the UK and Brazil had the lowest odds of suicidal ideation compared to Macau (p p Conclusions: The findings highlight the need for joint international collaboration to formulate effective suicide prevention strategies in a timely manner and the need to implement online mental health promotion platforms. In doing so, the potential global rising death rates by suicide during the pandemic can be reduced.</p

A Recombination Hotspot in a Schizophrenia-Associated Region of GABRB2

Background: Schizophrenia is a major disorder with complex genetic mechanisms. Earlier, population genetic studies revealed the occurrence of strong positive selection in the GABRB2 gene encoding the β2 subunit of GABAA receptors, within a segment of 3,551 bp harboring twenty-nine single nucleotide polymorphisms (SNPs) and containing schizophrenia-associated SNPs and haplotypes. Methodology/Principal Findings:In the present study, the possible occurrence of recombination in this 'S1-S29' segment was assessed. The occurrence of hotspot recombination was indicated by high resolution recombination rate estimation, haplotype diversity, abundance of rare haplotypes, recurrent mutations and torsos in haplotype networks, and experimental haplotyping of somatic and sperm DNA. The sub-segment distribution of relative recombination strength, measured by the ratio of haplotype diversity (Hd) over mutation rate (θ), was indicative of a human specific Alu-Yi6 insertion serving as a central recombining sequence facilitating homologous recombination. Local anomalous DNA conformation attributable to the Alu-Yi6 element, as suggested by enhanced DNase I sensitivity and obstruction to DNA sequencing, could be a contributing factor of the increased sequence diversity. Linkage disequilibrium (LD) analysis yielded prominent low LD points that supported ongoing recombination. LD contrast revealed significant dissimilarity between control and schizophrenic cohorts. Among the large array of inferred haplotypes, H26 and H73 were identified to be protective, and H19 and H81 risk-conferring, toward the development of schizophrenia. Conclusions/Significance: The co-occurrence of hotspot recombination and positive selection in the S1-S29 segment of GABRB2 has provided a plausible contribution to the molecular genetics mechanisms for schizophrenia. The present findings therefore suggest that genome regions characterized by the co-occurrence of positive selection and hotspot recombination, two interacting factors both affecting genetic diversity, merit close scrutiny with respect to the etiology of common complex disorders. © 2010 Ng et al

Disparities of time trends and birth cohort effects on invasive breast cancer incidence in Shanghai and Hong Kong pre- and post-menopausal women

© 2017 The Author(s). Background: Breast cancer is the leading cause of cancer morbidity among Shanghai and Hong Kong women, which contributes to 20-25% of new female cancer incidents. This study aimed to describe the temporal trend of breast cancer and interpret the potential effects on the observed secular trends. Methods: Cancer incident data were obtained from the cancer registries. Age-standardized incidence rate was computed by the direct method using the World population of 2000. Average annual percentage change (AAPC) in incidence rate was estimated by the Joinpoint regression. Age, period and cohort effects were assessed by using a log-linear model with Poisson regression. Results: During 1976-2009, an increasing trend of breast cancer incidence was observed, with an AAPC of 1.73 [95% confidence interval (CI): 1.54-1.92)] for women in Hong Kong and 2.83 (95% CI, 2.26-3.40) in Shanghai. Greater upward trends were revealed in Shanghai women aged 50 years old or above (AAPC = 3.09; 95% CI, 1.48-4.73). Using age at 50 years old as cut-point, strong birth cohort effects were shown in both pre- and post-menopausal women, though a more remarkable effect was suggested in Shanghai post-menopausal women. No evidence for a period effect was indicated. Conclusions: Incidence rate of breast cancer has been more speedy in Shanghai post-menopausal women than that of the Hong Kong women over the past 30 years. Decreased birth rate and increasing environmental exposures (e.g., light-at-night) over successive generations may have constituted major impacts on the birth cohort effects, especially for the post-menopausal breast cancer; further analytic studies are warranted.Link_to_subscribed_fulltex