Empirical Study of Data Sharing by Authors Publishing in PLoS Journals

Many journals now require authors share their data with other investigators, either by depositing the data in a public repository or making it freely available upon request. These policies are explicit, but remain largely untested. We sought to determine how well authors comply with such policies by requesting data from authors who had published in one of two journals with clear data sharing policies.We requested data from ten investigators who had published in either PLoS Medicine or PLoS Clinical Trials. All responses were carefully documented. In the event that we were refused data, we reminded authors of the journal's data sharing guidelines. If we did not receive a response to our initial request, a second request was made. Following the ten requests for raw data, three investigators did not respond, four authors responded and refused to share their data, two email addresses were no longer valid, and one author requested further details. A reminder of PLoS's explicit requirement that authors share data did not change the reply from the four authors who initially refused. Only one author sent an original data set.We received only one of ten raw data sets requested. This suggests that journal policies requiring data sharing do not lead to authors making their data sets available to independent investigators

A topos for algebraic quantum theory

The aim of this paper is to relate algebraic quantum mechanics to topos theory, so as to construct new foundations for quantum logic and quantum spaces. Motivated by Bohr's idea that the empirical content of quantum physics is accessible only through classical physics, we show how a C*-algebra of observables A induces a topos T(A) in which the amalgamation of all of its commutative subalgebras comprises a single commutative C*-algebra. According to the constructive Gelfand duality theorem of Banaschewski and Mulvey, the latter has an internal spectrum S(A) in T(A), which in our approach plays the role of a quantum phase space of the system. Thus we associate a locale (which is the topos-theoretical notion of a space and which intrinsically carries the intuitionistic logical structure of a Heyting algebra) to a C*-algebra (which is the noncommutative notion of a space). In this setting, states on A become probability measures (more precisely, valuations) on S(A), and self-adjoint elements of A define continuous functions (more precisely, locale maps) from S(A) to Scott's interval domain. Noting that open subsets of S(A) correspond to propositions about the system, the pairing map that assigns a (generalized) truth value to a state and a proposition assumes an extremely simple categorical form. Formulated in this way, the quantum theory defined by A is essentially turned into a classical theory, internal to the topos T(A).Comment: 52 pages, final version, to appear in Communications in Mathematical Physic

Prevention and early detection of prostate cancer

This Review was sponsored and funded by the International Society of Cancer Prevention (ISCaP), the European Association of Urology (EAU), the National Cancer Institute, USA (NCI) (grant number 1R13CA171707-01), Prostate Cancer UK, Cancer Research UK (CRUK) (grant number C569/A16477), and the Association for International Cancer Research (AICR

Quantitative analysis of calf mortality in Great Britain

National bodies in Great Britain (GB) have expressed concern over young stock health and welfare and identified calf survival as a priority; however, no national data have been available to quantify mortality rates. The aim of this study was to quantify the temporal incidence rate, distributional features, and factors affecting variation in mortality rates in calves in GB since 2011. The purpose was to provide information to national stakeholder groups to inform resource allocation both for knowledge exchange and future research. Cattle birth and death registrations from the national British Cattle Movement Service were analyzed to determine rates of both slaughter and on-farm mortality. The number of births and deaths registered between 2011 and 2018 within GB were 21.2 and 21.6 million, respectively. Of the 3.3 million on-farm deaths, 1.8 million occurred before 24 mo of age (54%) and 818,845 (25%) happened within the first 3 mo of age. The on-farm mortality rate was 3.87% by 3 mo of age, remained relatively stable over time, and was higher for male calves (4.32%) than female calves (3.45%). Dairy calves experience higher on farm mortality rates than nondairy (beef) calves in the first 3 mo of life, with 6.00 and 2.86% mortality rates, respectively. The 0- to 3-mo death rate at slaughterhouse for male dairy calves has increased from 17.40% in 2011 to 26.16% in 2018, and has remained low ( [less than] 0.5%) for female dairy calves and beef calves of both sexes. Multivariate adaptive regression spline models were able to explain a large degree of the variation in mortality rates (coefficient of determination = 96%). Mean monthly environmental temperature and month of birth appeared to play an important role in neonatal on-farm mortality rates, with increased temperatures significantly reducing mortality rates. Taking the optimal month of birth and environmental temperature as indicators of the best possible environmental conditions, maintaining these conditions throughout the year would be expected to result in a reduction in annual 0- to 3-mo mortality of 37,571 deaths per year, with an estimated economic saving of around £11.6 million (USD $15.3 million) per annum. National cattle registers have great potential for monitoring trends in calf mortality and can provide valuable insights to the cattle industry. Environmental conditions play a significant role in calf mortality rates and further research is needed to explore how to optimize conditions to reduce calf mortality rates in GB

A 'place based' approach to work and employment: the end of reciprocity, ordinary working families and 'giggers' in a place

The authors define ‘place basing’ as the study of work and employment in a particular place. They are interested in understanding the limitations of work opportunities therein and so focus on workers and jobs that are not subject to the threat of off-shoring or relocation elsewhere but which are low paid and insecure. The authors theorize three contributions to new knowledge that flow from a place-based study of work and employment by demonstrating how precarious flexible often zero hour work eschews reciprocity between employer and employees and workers. They focus their research on ordinary working families and the ‘permissive visibility’ of bad work. The research points to an idealized model of individual and family economic functioning that is able to cope with physical and mental challenges individually without burdening the state. As the findings on workers and households demonstrate, this ideal is far from the reality they experience

The coupled boundary layers and air-sea transfer experiment in low winds

Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 88 (2007): 341-356, doi:10.1175/bams-88-3-341.The Office of Naval Research's Coupled Boundary Layers and Air–Sea Transfer (CBLAST) program is being conducted to investigate the processes that couple the marine boundary layers and govern the exchange of heat, mass, and momentum across the air–sea interface. CBLAST-LOW was designed to investigate these processes at the low-wind extreme where the processes are often driven or strongly modulated by buoyant forcing. The focus was on conditions ranging from negligible wind stress, where buoyant forcing dominates, up to wind speeds where wave breaking and Langmuir circulations play a significant role in the exchange processes. The field program provided observations from a suite of platforms deployed in the coastal ocean south of Martha's Vineyard. Highlights from the measurement campaigns include direct measurement of the momentum and heat fluxes on both sides of the air–sea interface using a specially constructed Air–Sea Interaction Tower (ASIT), and quantification of regional oceanic variability over scales of O (1–104 mm) using a mesoscale mooring array, aircraft-borne remote sensors, drifters, and ship surveys. To our knowledge, the former represents the first successful attempt to directly and simultaneously measure the heat and momentum exchange on both sides of the air–sea interface. The latter provided a 3D picture of the oceanic boundary layer during the month-long main experiment. These observations have been combined with numerical models and direct numerical and large-eddy simulations to investigate the processes that couple the atmosphere and ocean under these conditions. For example, the oceanic measurements have been used in the Regional Ocean Modeling System (ROMS) to investigate the 3D evolution of regional ocean thermal stratification. The ultimate goal of these investigations is to incorporate improved parameterizations of these processes in coupled models such as the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS) to improve marine forecasts of wind, waves, and currents.This work was supported by the Office of Naval Research

Keeping an eye on noisy movements: On different approaches to perceptual-motor skill research and training

Contemporary theorising on the complementary nature of perception and action in expert performance has led to the emergence of different emphases in studying movement coordination and gaze behaviour. On the one hand, coordination research has examined the role that variability plays in movement control, evidencing that variability facilitates individualised adaptations during both learning and performance. On the other hand, and at odds with this principle, the majority of gaze behaviour studies have tended to average data over participants and trials, proposing the importance of universal 'optimal' gaze patterns in a given task, for all performers, irrespective of stage of learning. In this article, new lines of inquiry are considered with the aim of reconciling these two distinct approaches. The role that inter- and intra-individual variability may play in gaze behaviours is considered, before suggesting directions for future research

Relationship between circulating microRNA-30c with total- and LDL-cholesterol, their circulatory transportation and effect of statins

Background: Small non-coding microRNAs (miR) have important regulatory roles and are used as biomarkers of disease. We investigated the relationship between lipoproteins and circulating miR-30c, evaluated how they are transported in circulation and determined whether statins altered the circulating concentration of miR-30c. Methods: To determine the relationship between lipoproteins and circulating miR-30c, serum samples from 79 subjects recruited from a lipid clinic were evaluated. Ultracentrifugation and nanoparticle tracking analysis was used to evaluate the transportation of miR-30c in the circulation by lipoproteins and extracellular vesicles in three healthy volunteers. Using archived samples from previous studies, the effects of 40 mg rosuvastatin (n = 22) and 40 mg pravastatin (n = 24) on miR-30c expression was also examined. RNA extraction, reverse transcription-quantitative real-time polymerase chain reaction was carried out using standard procedures. Results: When stratified according to total cholesterol concentration, there was increased miR-30c expression in the highest compared to the lowest tertile (p = 0.035). There was significant positive correlation between miR- 30c and total- (r = 0.367; p = 0.002) and LDL-cholesterol (r = 0.391; p = 0.001). We found that miR-30c was transported in both exosomes and on HDL3. There was a 3.8-fold increased expression of circulating miR-30c after pravastatin treatment for 1 year (p = 0.005) but no significant change with atorvastatin after 8 weeks (p = 0.145). Conclusions: This study shows for the first-time in humans that circulating miR-30c is significantly, positively correlated with total- and LDL-cholesterol implicating regulatory functions in lipid homeostasis. We show miR-30c is transported in both exosomes and on HDL3 and pravastatin therapy significantly increased circulating miR-30c expression adding to the pleiotropic dimensions of statins