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In clinical and translational research, data science is often and fortuitously integrated with data collection. This contrasts to the typical position of data scientists in other settings, where they are isolated from data collectors. Because of this, effective use of data science techniques to resolve translational questions requires innovation in the organization and management of these data.
We propose an operational framework that respects this important difference in how research teams are organized. To maximize the accuracy and speed of the clinical and translational data science enterprise under this framework, we define a set of eight best practices for data management.
In our own work at the University of Rochester, we have strived to utilize these practices in a customized version of the open source LabKey platform for integrated data management and collaboration. We have applied this platform to cohorts that longitudinally track multidomain data from over 3000 subjects.
We argue that this has made analytical datasets more readily available and lowered the bar to interdisciplinary collaboration, enabling a team-based data science that is unique to the clinical and translational setting.
Organophosphate insecticides, which have the capacity to inhibit specific herbicide-degrading (cytochrome P450) enzymes, have been used to explore metabolic herbicide-resistance mechanisms in weeds. This study investigates the response of seven field-selected rigid ryegrass (Lolium rigidum Gaudin) populations to herbicides from three different sites of action in the presence or absence of the P450 inhibitor phorate. Phorate antagonized the thiocarbamate herbicides triallate and prosulfocarb (8-fold increase in LD50) in multiple resistant L. rigidum populations with resistance to three different site-of-action herbicides. In contrast, phorate synergized trifluralin and propyzamide in some populations, reducing the LD50 by 50%. Conversely, treatment with phorate had no significant effect on the LD50 for S-metolachlor or pyroxasulfone (inhibitors of very-long-chain fatty-acid synthesis). Phorate has diverse effects that are herbicide and population dependant in field-selected L. rigidum, suggesting P450 involvement in the metabolism of trifluralin and failure to activate thiocarbamate herbicides in these populations. This research highlights the need for implementation of diverse approaches other than herbicide alone as part of a long-term integrated strategy to reduce the likelihood of metabolism-based resistance to PPI herbicides in L. rigidum.
Diet modifies the risk of colorectal cancer (CRC), and inconclusive evidence suggests that yogurt may protect against CRC. We analysed the data collected from two separate colonoscopy-based case–control studies. The Tennessee Colorectal Polyp Study (TCPS) and Johns Hopkins Biofilm Study included 5446 and 1061 participants, respectively, diagnosed with hyperplastic polyp (HP), sessile serrated polyp, adenomatous polyp (AP) or without any polyps. Multinomial logistic regression models were used to derive OR and 95 % CI to evaluate comparisons between cases and polyp-free controls and case–case comparisons between different polyp types. We evaluated the association between frequency of yogurt intake and probiotic use with the diagnosis of colorectal polyps. In the TCPS, daily yogurt intake v. no/rare intake was associated with decreased odds of HP (OR 0·54; 95 % CI 0·31, 0·95) and weekly yogurt intake was associated with decreased odds of AP among women (OR 0·73; 95 % CI 0·55, 0·98). In the Biofilm Study, both weekly yogurt intake and probiotic use were associated with a non-significant reduction in odds of overall AP (OR 0·75; 95 % CI 0·54, 1·04) and (OR 0·72; 95 % CI 0·49, 1·06) in comparison with no use, respectively. In summary, yogurt intake may be associated with decreased odds of HP and AP and probiotic use may be associated with decreased odds of AP. Further prospective studies are needed to verify these associations.
Two field experiments were conducted during 2018 at Paskeville and Arthurton, South Australia, to identify effective herbicide options for the control of thiocarbamate-resistant rigid ryegrass in wheat. Dose–response experiments confirmed resistance in both field populations (T1 and A18) of rigid ryegrass to triallate, prosulfocarb, trifluralin, and pyroxasulfone. T1 and A18 were 17.9- and 20-fold more resistant to triallate than susceptible SLR4. The level of resistance detected in T1 to prosulfocarb (5.9-fold) and pyroxasulfone (4-fold) was lower compared to A18, which displayed 12.1- and 7.8-fold resistance to both herbicides, respectively. Despite resistance, the mixture of two different preplant-incorporated (PPI) site-of-action herbicides improved rigid ryegrass control and wheat yield compared to a single PPI herbicide only. Prosulfocarb + triallate and prosulfocarb + S-metolachlor + triallate did not reduce rigid ryegrass seed set when compared to prosulfocarb applied alone at the higher rate (2,400 g ai ha–1). Pyroxasulfone + triallate PPI followed by glyphosate (1,880 g ai ha-1) as a weed seed set control treatment reduced rigid ryegrass seed production by 93% and 95% at both sites, respectively. These herbicides also significantly improved grain yield of wheat at Paskeville (22%) and Arthurton (38%) compared to the untreated.
Kelmscott Manor, the country home of William Morris, houses a remarkable collection of ceramics bearing a singular relationship to one of the most influential figures in Victorian cultural history. This study of Kelmscott’s collection of German stoneware reveals new interpretations of its production history and fascinating insights into its significance for the cultural context of Morris’s work. Based on a complete catalogue, the paper examines the ensemble of approximately thirty pieces of eighteenth- to nineteenth-century Westerwald stoneware, or grès de Flandres, as it was known to Morris and his contemporaries. The Kelmscott group is the largest collection of this material known from an English historic house and has a composite and well-documented provenance. Supplementary material provided as an online appendix contains a fully illustrated, descriptive catalogue.
Westerwald pottery of the seventeenth century and earlier has been extensively studied, but its ceramics of the late eighteenth to nineteenth centuries have received little attention. Most accounts stress the simplification of vessel forms and ‘degeneration’ of decorative designs during this period, leading towards mass-production c 1900. This paper re-assesses later Westerwald output, drawing attention to a vernacular pottery tradition of significant interest in its own right. This paper suggests that it was this continuing tradition of vernacular production and its naturalistic, decorative schemes that attracted the interest of Morris throughout his adult life, from the Red House experiment to the heyday of Morris & Co. Examining his writing on creativity, the minor arts and labour, the paper interprets grès de Flandres as an expression of Morris’s idealisation of the relationship between labour and craft production.
Previous studies using resting-state functional neuroimaging have revealed alterations in whole-brain images, connectome-wide functional connectivity and graph-based metrics in groups of patients with schizophrenia relative to groups of healthy controls. However, it is unclear which of these measures best captures the neural correlates of this disorder at the level of the individual patient.
Here we investigated the relative diagnostic value of these measures. A total of 295 patients with schizophrenia and 452 healthy controls were investigated using resting-state functional Magnetic Resonance Imaging at five research centres. Connectome-wide functional networks were constructed by thresholding correlation matrices of 90 brain regions, and their topological properties were analyzed using graph theory-based methods. Single-subject classification was performed using three machine learning (ML) approaches associated with varying degrees of complexity and abstraction, namely logistic regression, support vector machine and deep learning technology.
Connectome-wide functional connectivity allowed single-subject classification of patients and controls with higher accuracy (average: 81%) than both whole-brain images (average: 53%) and graph-based metrics (average: 69%). Classification based on connectome-wide functional connectivity was driven by a distributed bilateral network including the thalamus and temporal regions.
These results were replicated across the three employed ML approaches. Connectome-wide functional connectivity permits differentiation of patients with schizophrenia from healthy controls at single-subject level with greater accuracy; this pattern of results is consistent with the ‘dysconnectivity hypothesis’ of schizophrenia, which states that the neural basis of the disorder is best understood in terms of system-level functional connectivity alterations.
Sudden onset disasters exceed the capabilities of local health services. Emergency Medical Teams (EMTs), including the Australian Medical Assistance Team (AUSMAT), are a vital element of the Australian Governments capacity to respond to regional and international sudden-onset disasters. AUSMAT has the capacity to deploy an EMT Type 2 surgical field hospital and has been successfully verified by the World Health Organisation (WHO). All AUSMAT members must complete AUSMAT Team Member training. The National Critical Care and Trauma Response Centre, Darwin, Australia is responsible for all AUSMAT training.
To educate and train the Surgical Team (perioperative nurses, surgeons, and anesthetists) in preparation for AUSMAT deployments in the austere environment.
Prior to 2015, the surgical AUSMAT training was conducted via two courses: one for perioperative nurses and a separate course for surgeons and anesthetists. In 2015, the course was redesigned with the aim of collaborative training with all the Surgical Team Members. The new Surgical Team Course (STC) engages all three professions to learn alongside each other and discuss potential difficulties in techniques, the daily running of the operating room, and ethical discussions.
Since the rejuvenation of the STC, 15 surgeons, 17 anesthetists, and 18 perioperative nurses have completed the course. The attendees are familiarized with operational and clinical guidelines, the surgical field hospital, and operating room equipment including CSSD. A pivotal component of the course focuses on the essentials of medical records and Minimum Data Set reporting for EMTs as defined by WHO.
Since 2015, the NCCTRC has successfully run two courses. The revised collaborative model for AUSMAT STC has enhanced the quality of the program and subsequent learning experiences for participants.
Five populations of rigid ryegrass (Lolium rigidum Gaudin) from fields across cropping regions in southern Australia were suspected of having resistance to thiocarbamates, chloroacetamides, and sulfonylisoxazoline herbicides. Resistant (R) populations 375-14, 198-15, 16.2, EP162, RAC1, and A18 and two susceptible (S) populations (SLR4 and VLR1) were included in a dose–response study. All suspected R populations expressed resistance to one or all herbicides (thiocarbamates, chloroacetamides, and pyroxasulfone). Population 198-15 exhibited the highest LD50 to triallate (44.7-fold), prosulfocarb (45.7-fold), S-metolachlor (31.5-fold), and metazachlor (27.2-fold) compared with the S populations. Populations 198-15 and 375-14 were also resistant to pyroxasulfone (13.5- and 14.9-fold) compared with the S populations, as was population EP162. This study documents the first case of field-evolved resistance to thiocarbamate, chloroacetamide, and sulfonylisoxazoline herbicides in L. rigidum.
The Fluvial Archives Group (FLAG) was founded in 1996 to bring together researchers looking at the development of fluvial systems over multiple timescales and global spatial scales. Fluvial archives of various types are important not just because they provide insights into past landscape dynamics, e.g., driven by climate or crustal processes, but also because they frequently contain fossil or archaeological material for which they provide stratigraphic control. Since 1996, FLAG has evolved from a research group of the British Quaternary Research Association into an organisation with around 500 members in over 20 countries. The research group held 12 biennial meetings, comprising both presentations and field excursions, as well as multiple themed sessions at international conferences. These had resulted by 2017 in 19 journal special issues, all fully detailed by Cordier et al. (2017). The goals of FLAG are: provision of a community for discussion of key issues concerning fluvial archives, including organising the aforementioned biennial discussion/field meetings, sessions at relevant international conferences, and special issues of journals; continued promotion of the value of fluvial archives by means of readily accessible published information; and coordination of activity with other research groupings with overlapping interests, e.g., by co-convening sessions and collaborating on publications.
To assess trends of mortality attributable to child and maternal undernutrition (CMU), overweight/obesity and dietary risks of non-communicable diseases (NCD) in sub-Saharan Africa (SSA) using data from the Global Burden of Disease (GBD) Study 2015.
For each risk factor, a systematic review of data was used to compute the exposure level and the effect size. A Bayesian hierarchical meta-regression analysis was used to estimate the exposure level of the risk factors by age, sex, geography and year. The burden of all-cause mortality attributable to CMU, fourteen dietary risk factors (eight diets, five nutrients and fibre intake) and overweight/obesity was estimated.
All age groups and both sexes.
In 2015, CMU, overweight/obesity and dietary risks of NCD accounted for 826204 (95 % uncertainty interval (UI) 737346, 923789), 266768 (95 % UI 189051, 353096) and 558578 (95 % UI 453433, 680197) deaths, respectively, representing 10·3 % (95 % UI 9·1, 11·6 %), 3·3 % (95 % UI 2·4, 4·4 %) and 7·0 % (95 % UI 5·8, 8·3 %) of all-cause mortality. While the age-standardized proportion of all-cause mortality accounted for by CMU decreased by 55·2 % between 1990 and 2015 in SSA, it increased by 63·3 and 17·2 % for overweight/obesity and dietary risks of NCD, respectively.
The increasing burden of diet- and obesity-related diseases and the reduction of mortality attributable to CMU indicate that SSA is undergoing a rapid nutritional transition. To tackle the impact in SSA, interventions and international development agendas should also target dietary risks associated with NCD and overweight/obesity.
Important Bird and Biodiversity Areas (IBAs) are sites identified as being globally important for the conservation of bird populations on the basis of an internationally agreed set of criteria. We present the first review of the development and spread of the IBA concept since it was launched by BirdLife International (then ICBP) in 1979 and examine some of the characteristics of the resulting inventory. Over 13,000 global and regional IBAs have so far been identified and documented in terrestrial, freshwater and marine ecosystems in almost all of the world’s countries and territories, making this the largest global network of sites of significance for biodiversity. IBAs have been identified using standardised, data-driven criteria that have been developed and applied at global and regional levels. These criteria capture multiple dimensions of a site’s significance for avian biodiversity and relate to populations of globally threatened species (68.6% of the 10,746 IBAs that meet global criteria), restricted-range species (25.4%), biome-restricted species (27.5%) and congregatory species (50.3%); many global IBAs (52.7%) trigger two or more of these criteria. IBAs range in size from < 1 km2 to over 300,000 km2 and have an approximately log-normal size distribution (median = 125.0 km2, mean = 1,202.6 km2). They cover approximately 6.7% of the terrestrial, 1.6% of the marine and 3.1% of the total surface area of the Earth. The launch in 2016 of the KBA Global Standard, which aims to identify, document and conserve sites that contribute to the global persistence of wider biodiversity, and whose criteria for site identification build on those developed for IBAs, is a logical evolution of the IBA concept. The role of IBAs in conservation planning, policy and practice is reviewed elsewhere. Future technical priorities for the IBA initiative include completion of the global inventory, particularly in the marine environment, keeping the dataset up to date, and improving the systematic monitoring of these sites.
It has been more than 20 years since the raids on the premises at the Geneva Freeport were linked to Giacomo Medici. The seizure of photographic records led to a major investigation of acquisitions by museums and private collectors. This was expanded following the confiscation of archives from Robin Symes and Gianfranco Becchina. Over 350 items have been returned to Italy from North American public and private collections as well as auction houses and galleries. This article reviews the returns and identifies some of the major themes. It also notes some of the unresolved cases both in North America and in Europe and Japan.
Hill (Twin Research and Human Genetics, Vol. 21, 2018, 84–88) presented a critique of our recently published paper in Cell Reports entitled ‘Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets’ (Lam et al., Cell Reports, Vol. 21, 2017, 2597–2613). Specifically, Hill offered several interrelated comments suggesting potential problems with our use of a new analytic method called Multi-Trait Analysis of GWAS (MTAG) (Turley et al., Nature Genetics, Vol. 50, 2018, 229–237). In this brief article, we respond to each of these concerns. Using empirical data, we conclude that our MTAG results do not suffer from ‘inflation in the FDR [false discovery rate]’, as suggested by Hill (Twin Research and Human Genetics, Vol. 21, 2018, 84–88), and are not ‘more relevant to the genetic contributions to education than they are to the genetic contributions to intelligence’.
A population of rigid ryegrass (Lolium rigidum Gaudin) from a field on the Eyre Peninsula, South Australia, was suspected of resistance to thiocarbamate herbicides. Dose–response studies were conducted on this population (EP162) and two susceptible populations (SLR4 and VLR1). The resistant population exhibited cross-resistance to triallate, prosulfocarb, EPTC, and thiobencarb with higher LD50 to triallate (14.9-fold), prosulfocarb (9.4-fold), EPTC (9.7-fold), and thiobencarb (13.6-fold) compared with the susceptible populations SLR4 and VLR1. The resistant population also displayed resistance to trifluralin, pyroxasulfone, and propyzamide. The LD50 of the resistant population was higher for trifluralin (13.8-fold), pyroxasulfone (8.1-fold), and propyzamide (2.7-fold) compared with the susceptible populations. This study documents the first case of field-evolved resistance to thiocarbamate herbicides in L. rigidum.
Weed control is a challenging aspect of pumpkin production. Winter rye mulches may offer growers a means to manage weeds in pumpkin; however, rye degradation leads to an immobilization of soil nitrogen. Combining winter rye with a nitrogen fixing legume such as hairy vetch is an interesting option that may solve this problem. Twelve combinations including three hairy vetch seeding rates, two termination dates and the use or not of glyphosate before rolling cover crops were studied during the 2013 and 2014 growing seasons at the Laval University Agronomic Station in Saint-Augustin-de-Desmaures, Quebec, Canada to evaluate weed control and effects on pumpkin production. Adding hairy vetch to winter rye provided no benefits because of severe winterkill of the legume. Using glyphosate was necessary to prevent rye regrowth. Pumpkin growth was better and yields were higher than in the plots were no glyphosate was used. Mulches established at flowering (Zadoks 69) provided about 2,000 kg ha−1 more aboveground dry biomass than at early heading (Zadoks 51). This high biomass was essential in glyphosate treated plots in order to maintain excellent weed control throughout the growing season. When compared with the no-mulch weed-free control, yield in Zadoks 69+glyphosate treatment was lower in 2013 but comparable in 2014.
Disclosure mandates are pervasive. Though designed to inform consumers, such mandates may lead consumers to draw false inferences – for example, that a product is harmful when it is not. When deciding to require disclosure of an ingredient in or characteristic of a product, regulators may be motivated by evidence that the ingredient or characteristic is harmful to consumers. But they may also be motivated by a belief that consumers have a right to know what they are buying or by interest-group pressure. Consumers who misperceive the regulator's true motive, or mix of motives, will draw false inferences from the mandated disclosure. If consumers think that the disclosure is motivated by evidence of harm, when in fact it is motivated by a belief in a right to know or by interest-group pressure, then they will be inefficiently deterred from purchasing the product. We analyze this general concern about disclosure mandates. We also offer survey evidence demonstrating that the risk of false inferences is serious and real.
Since the discovery of the first pulsar in 1967, over 2500 pulsars have been discovered. Pulsars enable a broad range of studies: from the study of the properties of the interstellar medium and of pulsar magnetospheres to tests of gravity in the strong-field regime and the characterisation of the cosmological gravitation wave background. These reasons are the main drive for searching for more pulsars. A blind pulsar survey, named SPAN512, was initiated with the Nançay Radio Telescope in 2012. Conducted at 1.4 GHz with a sampling time of 64μs and 500-kHz frequency channels, SPAN512 was designed to search for fast and distant pulsars in the Galactic plane. Here we describe the current status of the survey and present the latest discovery, PSR J2055+3829, a 2.08-ms pulsar in a black widow system.