Model organism databases: essential resources that need the support of both funders and users.

Modern biomedical research depends critically on access to databases that house and disseminate genetic, genomic, molecular, and cell biological knowledge. Even as the explosion of available genome sequences and associated genome-scale data continues apace, the sustainability of professionally maintained biological databases is under threat due to policy changes by major funding agencies. Here, we focus on model organism databases to demonstrate the myriad ways in which biological databases not only act as repositories but actively facilitate advances in research. We present data that show that reducing financial support to model organism databases could prove to be not just scientifically, but also economically, unsound

Two new species of torrent-breeding treefrogs (Anura: Pelodryadidae: Litoria) from hill forests on the southern edge of New Guinea’s Central Cordillera

Abstract We describe two new species of torrent-breeding Litoria Tschudi, 1838 from low-elevation hill-forest habitats on the southern fringe of Papua New Guinea’s Central Cordillera. One is currently known only from the Kikori River basin, and the other is known from the Kikori and adjacent Strickland River basins. The two new species can be distinguished from all other Litoria by aspects of morphology and advertisement call structure. Both are known only from below 500 m a.s.l. and so are considered less likely to be threatened by the devastating frog pathogen Batrachochytrium dendrobatidis Longcore, Pessier & Nichols, 1999 than torrent-breeding Melanesian pelodryadid frogs occupying higher, cooler habitats, should that pathogen be introduced to the region. One hundred and ten frog species have now been documented from the Kikori River basin, a near doubling of the total recognised when the first field guide to the region was published nearly 20 years ago, emphasising the rich anuran community of this area

A Study of the Microbial Community at the Interface between Granite Bedrock and Soil Using a Culture-Independent and Culture-Dependent Approach

The dissolution of minerals plays an important role in the formation of soils and sediments. In nutrient limiting soils, minerals constitute a major reservoir of bio-essential cations. Of particular interest is granite as it is the major rock type of the continental land mass. Although certain bacteria have been shown to enhance weathering of granite-forming minerals, little is known about the dissolution of granite, at the whole rock scale, and the microbial community involved. In this study, both culture-independent and culture-dependent approaches were used to study the bacterial community at the interface between granite bedrock and nutrient limiting soil in Dartmoor National Park, United Kingdom. High throughput sequencing demonstrated that over 70% of the bacterial population consisted of the bacterial classes Bacilli, Beta-proteobacteria and Gamma-proteobacteria. Bacteria belonging to the genera Serratia, Pseudomonas, Bacillus, Paenibacillus, Chromobacterium and Burkholderia were isolated from the sample site. All of the isolates were able to grow in a minimal growth medium, which contained glucose and ammonium chloride, with granite as the sole source of bio-essential elements. Sixty six percent of the isolates significantly enhanced basalt dissolution (p < 0.05). Dissolution of Si, K, Ca and Mg correlated with production of oxalic acid and acidification. The results of this study suggest that microorganisms in nutrient limiting soils can enhance the rate of granite dissolution, which is an important part of the biogeochemical cycle

Comparing Visual Assembly Aids for Augmented Reality Work Instructions

Increased product complexity and the focus on zero defects, especially when manufacturing complex engineered products, means new tools are required for helping workers conduct challenging assembly tasks. Augmented reality (AR) has shown considerable promise in delivering work instructions over traditional methods. Many proof-of-concept systems have demonstrated the feasibility of AR but little work has been devoted to understanding how users perceive different AR work instruction interface elements. This paper presents a between-subjects study looking at how interface elements for object depth placement in a scene impact a user’s ability to quickly and accurately assemble a mock aircraft wing in a standard work cell. For object depth placement, modes with varying degrees of 3D modeled occlusion were tested, including a control group with no occlusion, virtual occlusion, and occlusion by contours. Results for total assembly time and total errors indicated no statistically significant difference between interfaces, leading the authors to conclude a floor has been reached for optimizing the current assembly when using AR for work instruction delivery. However, looking at a handful of highly error prone steps showed the impact different types of occlusion have on helping users correctly complete an assembly task. The results of the study provide insight into how to construct an interface for delivering AR work instructions using occlusion. Based on these results, the authors recommend customizing the occlusion method based on the features of the required assembly task. The authors also identified a floor effect for the steps of the assembly process, which involved picking the necessary parts from tables and bins. The authors recommend using vibrant outlines and large textual cues (e.g., numbers on parts bins) as interface elements to guide users during these types of “picking” steps

Safer and more efficient vital signs monitoring to identify the deteriorating patient: an observational study towards deriving evidence-based protocols for patient surveillance on the general hospital ward

Background The frequency at which patients should have their vital signs (e.g. blood pressure, pulse, oxygen saturation) measured on hospital wards is currently unknown. Current National Health Service monitoring protocols are based on expert opinion but supported by little empirical evidence. The challenge is finding the balance between insufficient monitoring (risking missing early signs of deterioration and delays in treatment) and over-observation of stable patients (wasting resources needed in other aspects of care). Objective Provide an evidence-based approach to creating monitoring protocols based on a patient’s risk of deterioration and link these to nursing workload and economic impact. Design Our study consisted of two parts: (1) an observational study of nursing staff to ascertain the time to perform vital sign observations; and (2) a retrospective study of historic data on patient admissions exploring the relationships between National Early Warning Score and risk of outcome over time. These were underpinned by opinions and experiences from stakeholders. Setting and participants Observational study: observed nursing staff on 16 randomly selected adult general wards at four acute National Health Service hospitals. Retrospective study: extracted, linked and analysed routinely collected data from two large National Health Service acute trusts; data from over 400,000 patient admissions and 9,000,000 vital sign observations. Results Observational study found a variety of practices, with two hospitals having registered nurses take the majority of vital sign observations and two favouring healthcare assistants or student nurses. However, whoever took the observations spent roughly the same length of time. The average was 5:01 minutes per observation over a ‘round’, including time to locate and prepare the equipment and travel to the patient area. Retrospective study created survival models predicting the risk of outcomes over time since the patient was last observed. For low-risk patients, there was little difference in risk between 4 hours and 24 hours post observation. Conclusions We explored several different scenarios with our stakeholders (clinicians and patients), based on how ‘risk’ could be managed in different ways. Vital sign observations are often done more frequently than necessary from a bald assessment of the patient’s risk, and we show that a maximum threshold of risk could theoretically be achieved with less resource. Existing resources could therefore be redeployed within a changed protocol to achieve better outcomes for some patients without compromising the safety of the rest. Our work supports the approach of the current monitoring protocol, whereby patients’ National Early Warning Score 2 guides observation frequency. Existing practice is to observe higher-risk patients more frequently and our findings have shown that this is objectively justified. It is worth noting that important nurse–patient interactions take place during vital sign monitoring and should not be eliminated under new monitoring processes. Our study contributes to the existing evidence on how vital sign observations should be scheduled. However, ultimately, it is for the relevant professionals to decide how our work should be used. Study registration This study is registered as ISRCTN10863045. Funding This award was funded by the National Institute for Health and Care Research (NIHR) Health and Social Care Delivery Research programme (NIHR award ref: 17/05/03) and is published in full in Health and Social Care Delivery Research; Vol. 12, No. 6. See the NIHR Funding and Awards website for further award information

Dynamic evolution of porosity in lower-crustal faults during the earthquake cycle

Earthquake-induced fracturing of the dry and strong lower crust can transiently increase permeability for fluids to flow and trigger metamorphic and rheological transformations. However, little is known about the porosity that facilitates these transformations. We analyzed microstructures that have recorded the mechanisms generating porosity in the lower crust from a pristine pseudotachylyte (solidified earthquake-derived frictional melt) and a mylonitized pseudotachylyte from Lofoten, Norway to understand the evolution of fluid pathways from the coseismic to the post- and interseismic stages of the earthquake cycle. Porosity is dispersed and poorly interconnected within the pseudotachylyte vein (0.14 vol%), with a noticeably increased amount along garnet grain boundaries (0.25–0.41 vol%). This porosity formed due to a net negative volume change at the grain boundary when garnet overgrows the pseudotachylyte matrix. Efficient healing of the damage zone by fluid-assisted growth of feldspar neoblasts resulted in the preservation of only a few but relatively large interconnected pores along coseismic fractures (0.03 vol% porosity). In contrast, porosity in the mylonitized pseudotachylyte is dramatically reduced (0.02 vol% overall), because of the efficient precipitation of phases (amphibole, biotite and feldspars) into transient pores during grain-size sensitive creep. Porosity reduction on the order of &gt;85% may be a contributing factor in shear zone hardening, potentially leading to the development of new pseudotachylytes overprinting the mylonites. Our results show that earthquake-induced rheological weakening of the lower crust is intermittent and occurs when a fluid can infiltrate a transiently permeable shear zone, thereby facilitating diffusive mass transfer and creep

A new species of torrent-breeding treefrog (Pelodryadidae: Litoria) from the mountains of Papua, Indonesia, with new records and observations of Litoria dorsivena (Tyler, 1968)

The mountains of New Guinea are home to species-rich but poorly understood communities of stream or torrent-breeding pelodryadid treefrogs. Here we describe a new species of moderately sized torrent-breeding Litoria from the mountains of Papua Province, Indonesia. The new species is most similar to Litoria dorsivena but differs from that species in aspects of body size, skin texture and especially the shape of the snout. Based on recent collections, we also present new data on the distribution and colour in life of L. dorsivena. Both species show marked sexual size dimorphism when compared to most other pelodryadid treefrogs, and the colour pattern of the new species may also vary between males and females. The torrent-breeding treefrogs of New Guinea remain poorly known and, given declines of ecologically similar pelodryadids in Australia, should be a priority group for taxonomic research and population monitoring