Understanding Software in Research: Initial Results from Examining Nature and a Call for Collaboration

This lightning talk paper discusses an initial data set that has been gathered to understand the use of software in research, and is intended to spark wider interest in gathering more data. The initial data analyzes three months of articles in the journal Nature for software mentions. The wider activity that we seek is a community effort to analyze a wider set of articles, including both a longer timespan of Nature articles as well as articles in other journals. Such a collection of data could be used to understand how the role of software has changed over time and how it varies across fields.Comment: lightning talk submitted to WSSSPE5.2 (http://wssspe.researchcomputing.org.uk/wssspe5/

Meconium stained liquor in labour and mode of delivery: a time for reappraisal

Background: The objective of this study was to determine the significance of meconium staining of the amniotic fluid and find out an appropriate mode of delivery in women with MSL.Methods: A retrospective study was carried out in Lady Hardinge Medical College and Smt Sucheta Kriplani Hospital, a tertiary government hospital, New Delhi over a time period of 1 year between 2009 to 2010 on 1425 consecutive women of which 142 women were diagnosed as having meconium staining of the amniotic fluid during labour.  All cases were critically analysed and maternal and fetal outcomes were studied in these women.Results: The incidence of MSL was 10% (142/1425), 45% had thin MSL and 55% had thick MSL. In women with thick MSL, 85% had early thick MSL and 15% had late thick MSL. In women who had early thick MSL (n=66), 55 (83.3%) delivered by LSCS and 11 (16.7%) delivered vaginally. On correlating the perinatal outcome with mode of delivery irrespective of fetal heart rate abnormality in early thick MSL, it was seen that the perinatal outcome was significantly affected by mode of delivery. The rates of respiratory distress and MAS was significantly higher in babies who delivered vaginally compared to those by LSCS (18% & 100% vs 9% & 40%, p=0.012, RR- 5.2 [95% CI: 1.8-3.42]. There were no perinatal mortality in early thick MSL.Conclusions: In distinguishing between thick and thin meconium, it was noted that finding of thick meconium in the latent phase of labour (i.e. early thick MSL) is ominous and demands an urgent caesarean delivery.

Odessa's Intellectuals In the 1920s: the activities of the All-Ukrainian Committee for the Promotion of Scientists

У статті аналізуються усі сфери суспільного життя в Україні у перше десятиліття більшовицького режиму. Досліджується основні напрямків діяльності Всеукраїнського комітету сприяння вченим у 1920 рр. у великому науковому центрі України – Одесі.В статье анализируются все сферы общественной жизни в Украине в первое десятилетие большевистского режима. Исследуется основные направления деятельности Всеукраинского комитета содействия ученым в 1920 в большом научном центре Украины - Одессе.The article analyzes all spheres of public life in Ukraine in the first decade of the Bolshevik regime. The main directions of activity of the All-Ukrainian Committee for the Facilitation of Scientists in 1920 in the large scientific center of Ukraine - Odessa were investigated

Single-cell transcriptomes reveal the mechanism for a breast cancer prognostic gene panel.

The clinical benefits of the MammaPrint® signature for breast cancer is well documented; however, how these genes are related to cell cycle perturbation have not been well determined. Our single-cell transcriptome mapping (algorithm) provides details into the fine perturbation of all individual genes during a cell cycle, providing a view of the cell-cycle-phase specific landscape of any given human genes. Specifically, we identified that 38 out of the 70 (54%) MammaPrint® signature genes are perturbated to a specific phase of the cell cycle. The MammaPrint® signature panel derived its clinical prognosis power from measuring the cell cycle activity of specific breast cancer samples. Such cell cycle phase index of the MammaPrint® signature suggested that measurement of the cell cycle index from tumors could be developed into a prognosis tool for various types of cancer beyond breast cancer, potentially improving therapy through targeting a specific phase of the cell cycle of cancer cells

Synthesis, x-ray crystal structures and biological evaluation of some mono- and bi-cyclic 1,3-diazetidin-2-ones: non-natural β -lactam analogues

Mono- and bi-cyclic 1,3-diazetidin-2-ones (aza-β -lactams) are synthesised and evaluated as non-natural analogues of β -lactams. The aza-β -lactams are designed on the principle that their reaction with active site serine hydroxy will form a carbamoyl-enzyme intermediate that is sluggish to hydrolysis. The synthesis of racemic mono- and bi-cyclic aza-β -lactams is carried out starting from pyrimidinone 18 which is transformed to the densely functionalised substrate 20. The chemical reactivity of tricarbonyl 20 for selective functional group manipulation was first assessed and then it was transformed to amino alcohol 24. Cyclisation of 24 affords aza-carbapenams and its homologation followed by aldol cyclisation provides access to aza-carbacephams. The X-ray structures of aza-carbapenam 35 and aza-carbacepham 42 suggest that the structural requirements for biological activity in β -lactams are fulfilled. An unexpected ozonolysis product, phenol 52 resolves spontaneously during crystallisation and its crystal structure was also determined. The biological activity of the novel mono- and bi-cyclic aza-β -lactams was evaluated with potent gram-positive bacterial strain, Bacillus subtilis and compared with β -lactam antibiotics, ampicillin and penicillin G. Of the 19 aza-β -lactams tested, eight compounds show inhibition better than the standards while another eight are of comparable activity. This study shows that aza-β -lactams represent a novel and non-natural lead towards serine peptidase inhibitors

OBSERVATION OF AN ISOKINETIC TEMPERATURE AND COMPENSATION EFFECT FOR HIGH TEMPERATURE CRUDE OIL FOULING

The initial fouling rates of four crude oils were determined at a nominal bulk temperature of 315 °C, an initial heated wall shear stress of 13 Pa, and initial surface temperatures between 375 and 445 °C. These initial fouling rates ranged from 1.3(10-6) to 7.8(10-5) m2 K/kJ. Corresponding Arrhenius plots were linear with the initial fouling rates passing through an isokinetic temperature of 407.5 °C. A plot of the natural logarithm of the preexponential factors (7.6(104) – 5.2(1015) m2 K/kJ) versus the apparent activation energies (128 – 269 kJ/mol) was also linear, confirming the validity of the isokinetic temperature and the presence of the compensation effect. Below the isokinetic temperature, the relative fouling rates were Crude Oil C \u3e Crude Oil A \u3e Crude Oil D \u3e Crude Oil B; above the isokinetic temperature, the relative fouling rates were reversed (Crude Oil B \u3e Crude Oil D \u3e Crude Oil A \u3e Crude Oil C). Chemical characterization of a fouling deposit suggested that the dominant fouling mechanism at these conditions was coking with significant contributions from sedimentation (iron sulfide) and corrosion (~340 μm/yr) of the 304 stainless steel test material

OBSERVATION OF AN ISOKINETIC TEMPERATURE AND COMPENSATION EFFECT FOR HIGH TEMPERATURE CRUDE OIL FOULING

The initial fouling rates of four crude oils were determined at a nominal bulk temperature of 315 °C, an initial heated wall shear stress of 13 Pa, and initial surface temperatures between 375 and 445 °C. These initial fouling rates ranged from 1.3(10-6) to 7.8(10-5) m2 K/kJ. Corresponding Arrhenius plots were linear with the initial fouling rates passing through an isokinetic temperature of 407.5 °C. A plot of the natural logarithm of the preexponential factors (7.6(104) – 5.2(1015) m2 K/kJ) versus the apparent activation energies (128 – 269 kJ/mol) was also linear, confirming the validity of the isokinetic temperature and the presence of the compensation effect. Below the isokinetic temperature, the relative fouling rates were Crude Oil C \u3e Crude Oil A \u3e Crude Oil D \u3e Crude Oil B; above the isokinetic temperature, the relative fouling rates were reversed (Crude Oil B \u3e Crude Oil D \u3e Crude Oil A \u3e Crude Oil C). Chemical characterization of a fouling deposit suggested that the dominant fouling mechanism at these conditions was coking with significant contributions from sedimentation (iron sulfide) and corrosion (~340 μm/yr) of the 304 stainless steel test material

Comparison between the for-profit human milk industry and nonprofit human milk banking: Time for regulation?

Human milk (HM) is a highly evolutionary selected, complex biofluid, which provides tailored nutrition, immune system support and developmental cues that are unique to each maternal-infant dyad. In the absence of maternal milk, the World Health Organisation recommends vulnerable infants should be fed with screened donor HM (DHM) from a HM bank (HMB) ideally embedded in local or regional lactation support services. However, demand for HM products has arisen from an increasing awareness of the developmental and health impacts of the early introduction of formula and a lack of prioritisation into government-funded and nonprofit milk banking and innovation. This survey of global nonprofit milk bank leaders aimed to outline the trends, commonalities and differences between nonprofit and for-profit HM banking, examine strategies regarding the marketing and placement of products to hospital and public customers and outline the key social, ethical and human rights concerns. The survey captured information from 59 milk bank leaders in 30 countries from every populated continent. In total, five companies are currently trading HM products with several early-stage private milk companies (PMCs). Products tended to be more expensive from PMC than HMB, milk providers were financially remunerated and lactation support for milk providers and recipients was not a core function of PMCs. Current regulatory frameworks for HM vary widely, with the majority of countries lacking any framework, and most others placing HM within food legislation, which does not include the support and care of milk donors and recipient prioritisation. Regulation as a Medical Product of Human Origin was only in place to prevent the sale of HM in four countries; export and import of HM was banned in two countries. This paper discusses the safety and ethical concerns raised by the commodification of HM and the opportunities policymakers have globally and country-level to limit the potential for exploitation and the undermining of breastfeeding

Prognostic significance of endogenous adhesion/growth-regulatory lectins in lung cancer

Objective: To determine the expression of endogenous adhesion/growth-regulatory lectins and their binding sites using labeled tissue lectins as well as the binding profile of hyaluronic acid as an approach to define new prognostic markers. Methods: Sections of paraffin-embedded histological material of 481 lungs from lung tumor patients following radical lung excision processed by a routine immunohistochemical method (avidin-biotin labeling, DAB chromogen). Specific antibodies against galectins-1 and - 3 and the heparin-binding lectin were tested. Staining by labeled galectins and hyaluronic acid was similarly visualized by a routine protocol. After semiquantitative assessment of staining, the results were compared with the pT and pN stages and the histological type. Survival was calculated by univariate and multivariate methods. Results: Binding of galectin-1 and its expression tended to increase, whereas the parameters for galectin-3 decreased in advanced pT and pN stages at a statistically significant level. The number of positive cases was considerably smaller among the cases with small cell lung cancer than in the group with non-small-cell lung cancer, among which adenocarcinomas figured prominently with the exception of galectin-1 expression. Kaplan-Meier computations revealed that the survival rate of patients with galectin-3-binding or galectin-1-expressing tumors was significantly poorer than that of the negative cases. In the multivariate calculations of survival lymph node metastases ( p < 0.0001), histological type ( p = 0.003), galectin-3-binding capacity ( p = 0.01), galectin-3 expression ( p = 0.03) and pT status ( p = 0.003) proved to be independent prognostic factors, not correlated with the pN stage. Conclusion: The expression and the capacity to bind the adhesion/growth regulatory galectin-3 is defined as an unfavorable prognostic factor not correlated with the pTN stage. Copyright (C) 2005 S. Karger AG, Basel