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opencc-by-sa-4.0Dec 2019View details →

A controlled vocabulary defining the semantic perimeter of Sustainable Development Goals

A set of controlled terms that define the scope and breadth of <a href="https://sustainabledevelopment.un.org/">Sustainable Development Goals (SDGs) as defined by the United Nations</a>.  These terms may be used to tag and index textual records in accordance with SDGs. The vocabulary is constructed by means of the following steps: <ol> <li>An initial set of terms per SDG target is built by extracting key terms from the UN official list of Goals, Targets and Indicators</li> <li>The list is manually enriched by performing a review of the literature produced around SDGs and by compiling lists of pertinent words per Target mentioned by the reviewed documents</li> <li>A reference textual corpus is downloaded by searching for the initial set terms defined at step 1. and 2. The corpus is used to train a Word2Vec word embedding model (a machine learning model based on neural networks).</li> <li>The terms’ list is then enriched by means of automatic methods, which are run in parallel: <ul> <li>The trained Word2Vec model is used to select, among the indexed keywords of the reference corpus, all terms “semantically close” to the initial set of words. This step is carried out to select terms that might not appear in the texts themselves, but that were deemed pertinent to label the textual records.</li> <li>Further terms that are mentioned in the texts of the reference corpus and that are valued by the trained Word2Vec model as “semantically close” to the initial set of words are also retained. This step is performed to include in the controlled vocabulary a series of terms that are related to the focus of the SDGs and which are used by practitioners.</li> <li>An automated algorithm is used to retrieve, from the APIs of WikiPedia a series of terms that have some categorical relationships (i.e. those that are indexed as “a broader concept of”, or “equivalent to” in DBpedia) with the initial set of words.</li> </ul> </li> <li>The final list produced by steps 1-4 s finally manually revised</li> </ol>

Comparison of different thyroid surgical procedures and their outcomes/complications for benign disease in relation to expertise of the surgeon in a public hospital of a developing country over 2 decades

Objective: To compare the frequency of postoperative complications with thyroid surgical procedures and the expertise of the surgeon. Design: Retrospective cross-sectional study from 1999 to 2018. Setting: A public sector tertiary care teaching hospital. Participants and methods: Patients undergoing thyroid surgery (lobectomy with isthmusectomy, subtotal thyroidectomy (STT), near total thyroidectomy (NTT), or total thyroidectomy (TT)) were included. Expertise level 1, 2 and 3 (L1, L2, L3) of the surgeon was based on years of experience or number of thyroid surgeries to their credit. Primary and Secondary Outcome Measures: Postoperative complications (hypocalcemia, recurrent laryngeal nerve (RLN) damage, airway obstruction, hemorrhage and mortality) were measured against type of thyroid surgery and expertise of surgeon. Results: 833 thyroid surgeries were performed on 695 (83.43%) females and 138 (16.57%) males. 502 (60.26%) STT, 228 (27.37%) TT, 61 (7.32%) NTT, 42 (5.04%) lobectomies with isthmusectomies were performed, with LI, 2, and 3 surgeons performing 21.25%, 45.74% and 33.01%, respectively. L1, 2 and 3 surgeons caused 49.47%, 33.45% and 17.08% of adverse events respectively. The permanent hypocalcemia, RLN damage and mortality were significantly (p<0.05) more common in surgeries performed by L1 compared with L2 and L3. Transient and permanent hypocalcemia, transient and permanent RLN damage and mortality were significantly (p<0.01) more common for total thyroidectomy compared to subtotal thyroidectomy. Conclusion: Minimizing the occurrence of complications like permanent hypocalcemia, RLN damage and mortality, expertise of the surgeon and anticipated difficulty of the procedure needs to be taken into account while selecting a thyroid procedure. Keywords: Thyroid surgery, Total thyroidectomy, Subtotal thyroidectomy, near total thyroidectomy, Lobectomy with isthmusectomy, hypoparathyroidism, hypocalcemia, recurrent laryngeal nerve, postoperative complications

Roundup causes embryonic development failure, alters metabolic pathways and gut microbiota functionality in non-target species

Background: Research around the weedkiller Roundup is among the most contentious of the 21st century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests.We apply a system biology approach to the biomedical and ecological model species Daphnia to quantify the impact of Glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in Daphnia. We then apply machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes. Results: We demonstrate that chronic exposure to ecologically relevant concentrations of Glyphosate and Roundup at the approved regulatory threshold for drinking water in the US induce embryonic developmental failure, significant DNA damage (genotoxicity), and interfere with signaling. Furthermore, chronic exposure to the weedkiller alters the gut microbiota functionality and composition interfering with carbon and fat metabolism, as well as homeostasis. Using the 'Reactome', we identify conserved pathways across the Tree of Life, which are potential targets for Roundup in other species, including liver metabolism, inflammation pathways and collagen degradation, responsible for the repair of wounds and tissue remodeling. Conclusions: Our results show that chronic exposure to concentrations of Roundup and Glyphosate at the approved regulatory threshold for drinking water causes embryonic development failure, and alteration of key metabolic functions via direct effect on the host molecular processes and indirect effect on the gut microbiota. The ecological model species Daphnia occupies a central position in the food web of aquatic ecosystems, being the preferred food of small vertebrates and invertebrates as well as a grazer of algae and bacteria. The impact of the weedkiller on this keystone species has cascading effects on aquatic food webs, affecting their ability to deliver critical ecosystem services.

Data from: Development and testing of an environmental DNA (eDNA) assay for endangered Atlantic sturgeon to assess its potential as a monitoring and management tool

Significant declines in Atlantic sturgeon (Acipenser oxyrhynchus oxyrhynchus) abundances along the US east coast have spurred major research efforts and management actions over the last 50 years, yet information on spawning stock abundances and habitat use is still lacking for many river systems, including in the Chesapeake Bay, USA. Here, we developed and tested a new quantitative PCR (qPCR) assay to detect Atlantic sturgeon environmental DNA (eDNA) in water samples with the goal of providing an alternative method to monitor presence and relative abundance. We also examined Atlantic sturgeon eDNA shedding rates in laboratory experiments. A qPCR-probe assay targeting Cytochrome-B was developed and showed no amplification of other related and co-occurring fishes. Pond trials at a density of ~0.2 g/L sturgeon produced relatively strong eDNA detections (~1,000-25,000 copies/L) in all seven water samples assayed. Water samples taken from two river systems in the Chesapeake Bay produced zero eDNA detections in the summer, while fall sampling during sturgeon spawning produced positive eDNA detections in 26% of samples, though at much lower concentrations (400-1,800 copies/L) compared with the pond (mesocosm) detections. Acoustic detections of sturgeon near river sampling sites were positively associated with eDNA detections. However, the eDNA assay failed to detect the presence of sturgeon in some samples when abundances were very low or when fish were in deep water. Finally, Atlantic sturgeon eDNA shedding rates were estimated to be on the order of estimates for other fish species, which suggests that relatively weak detections in the field are not necessarily driven by low rates of eDNA shedding. Overall, eDNA analysis represents a promising new monitoring tool for Atlantic sturgeon. Applying these methods in other rivers along the US east coast is an important next step in documenting Atlantic sturgeon distribution for management and conservation purposes.

Abnormal Development of Cerebellar-Striatal Circuitry in Huntington's Disease: Supplemental Figures

Objective: To test the hypothesis that the trajectory of functional connections over time of the striatum and the cerebellum differs between pre-symptomatic patients with the HD gene expansion (GE) and patients with a family history of HD but without the gene-expansion (GNE), we evaluated function MRI data from the Kids-HD study. Methods: We utilized resting-state, functional MRI data from participants in the Kids-HD study between 6 to 18 years old. Participants were divided into the GE (CAG 36-59) and GNE (CAG <36) groups. Seed to seed correlations were calculated between four regions that provide input signals to the anterior cerebellum: 1) dorsocaudal putamen; 2) globus pallidus externa; 3) subthalamic nucleus, and 4) pontine nuclei and two regions that represented output from the cerebellum, the dentate nucleus to the: 1) ventrolateral thalamus and 2) dorsocaudal putamen. Linear mixed effects regression models evaluated differences in developmental trajectories of these connections over time between groups. Results: Four of the six striatal-cerebellum correlations showed significantly different trajectories between groups. All showed a pattern where in the early age ranges (6-12 years), there was hyperconnectivity in the GE compared to the GNE with those trajectories showing linear decline in the latter half of the age range. Conclusion: These results parallel previous findings showing striatal hypertrophy in GE children as early as age 6. These findings support the notion of developmentally higher connectivity between the striatum and cerebellum early in the life of the child with the HD gene expansion, possibly setting the stage for cerebellar compensatory mechanisms.

Cardinium localization during its parasitoid wasp host's development provides insights into cytoplasmic incompatibility

Arthropods harbor heritable intracellular symbionts that may manipulate host reproduction to favor symbiont transmission. In cytoplasmic incompatibility (CI), the symbiont sabotages the reproduction of infected males such that high levels of offspring mortality result when they mate with uninfected females. In crosses with infected males and infected females, however, (the "rescue" cross), normal numbers of offspring are produced. A common CI-inducing symbiont, Cardinium hertigii, causes variable levels of CI mortality in the parasitoid wasp, Encarsia suzannae. Previous work correlated CI-induced mortality with male development time in this system, although the timing of Cardinium CI-induction and the relationship between development time and CI mortality was not well understood. Here, using a combination of crosses, manipulation of development time, and fluorescence microscopy, we identify the localization and the timing of the CI-induction step in the Cardinium-E. suzannae system. Antibiotic treatment of adult Cardinium-infected males did not reduce the mortality associated with the CI phenotype, suggesting that CI-alteration occurs prior to adulthood. Our results suggest that the alteration step occurs during the pupal period, and is limited by the duration of pupal development: 1) Encarsia produces most sperm prior to adulthood, 2), FISH localization of Cardinium in testes showed an association with sperm nuclei throughout spermatogenesis but not with mature sperm and 3) two methods of prolonging the pupal period (cool temperatures and the juvenile hormone analog methoprene) both caused greater CI mortality, suggesting the degree of alteration is limited by the duration of the pupal stage. Based on these results, we compare two models for potential mechanisms of Cardinium sperm modification in the context of what is known about analogous mechanisms of Wolbachia, a more extensively studied CI-inducing symbiont.

A co-development approach to conservation leads to informed habitat design and rapid establishment of amphibian communities

1. Effective wildlife restoration is a critical requirement of many conservation actions. The outcome of conservation interventions can be optimised through knowledge of species' habitat requirements, but few studies consider the impact of using explicit evidence from dedicated local research to inform the design phase of habitat management. Furthermore, interventions administered externally from the top down, whilst simpler than those developed in discussion with multiple stakeholders including land managers (i.e. co-development), run the risk of failing to engage local people. 2. In this study, we focus on interventions in the Scottish Highlands to improve the availability and suitability of breeding ponds for local amphibian assemblages. We collected and analysed data based on 129 ecological variables across 88 reference ponds to quantify the local habitat preferences. We used the findings from these analyses to inform the construction or restoration of 25 intervention ponds co-developed in partnership with stakeholders (landowners, foresters, citizen scientists and government agencies). Following the interventions, we monitored amphibian communities at these sites over 4 years. We assessed presence and abundance of all five native amphibians (the anurans Rana temporaria and Bufo bufo, and the salamanders Lissotriton helveticus, L. vulgaris and Triturus cristatus) using egg searching, dip-netting, torching and trapping. 3. The new habitats were overall characterised by ecological conditions more favourable to amphibians than the reference ponds. We recorded a total of 51 colonisation events. Within two breeding seasons after construction or restoration, the intervention ponds hosted the full complement of species, mirroring amphibian diversity patterns found in the local reference ponds. 4. Our study shows that ecological research to quantify local habitat requirements and working with commercial land-managers to ensure equitable benefits prior to designing conservation actions can promote rapid and efficient recovery of wildlife.

Data from: Toward the development of cavitation technology for gas hydrate prevention

In offshore gas well drilling and production, methane hydrate may block the tubing, resulting in the stoppage of gas production. Conventional methods such as injection of thermal hydrate inhibitors, thermal insulating or heating, gas dehydration, and reducing pressure are time-consuming and expensive, and sometimes they are not realistic in production conditions. New methods are needed to lower the cost of gas hydrate prevention and to overcome these limitations. The thermal effect of cavitation was applied to the prevention of gas hydrate in this study. The thermal impact of cavitation, supposed to heat the fluids and prevent the formation of gas hydrate, was evaluated. Numerical simulation was performed to study the thermal performance of cavitation. Furthermore, experimental studies of the influence of initial temperature, flow rate, fluid volume, and fluid viscosity on the thermal effect of cavitation were performed, and the results were analyzed.

YAP and TAZ maintain PROX1 expression in the developing lymphatic and lymphovenous valves in response to VEGF-C signaling

Lymphatic vasculature is an integral part of digestive, immune and circulatory systems. The homeobox transcription factor PROX1 is necessary for the development of lymphatic vessels, lymphatic valves (LVs) and lymphovenous valves (LVVs). We and others previously reported a feedback loop between PROX1 and Vascular Endothelial Growth Factor-C (VEGF-C) signaling. PROX1 promotes the expression of the VEGF-C receptor VEGFR3 in lymphatic endothelial cells (LECs). In turn, VEGF-C signaling maintains PROX1 expression in LECs. However, the mechanisms of PROX1/VEGF-C feedback loop remain poorly understood. Whether VEGF-C signaling is necessary for LV and LVV development is also unknown. Here, we report for the first time that VEGF-C signaling is necessary for valve morphogenesis. We have also discovered that the transcriptional co-activators YAP and TAZ are required to maintain PROX1 expression in LVs and LVVs in response to VEGF-C signaling. Deletion of Yap and Taz in the lymphatic vasculature of mouse embryos did not affect the formation of LVs or LVVs, but resulted in the degeneration of these structures. Our results have identified VEGF-C/YAP/TAZ as a critical molecular pathway in valve development.

opencc-by-4.0Dec 2020View details →

Amory et al. (2021), Geoscientific Model Development : data, model outputs and source code

Data and model outputs for the replication of the analysis made in: (see the published version of this article in Geoscientific Model Development, 2021 - please cite this version if you use these data) C. Amory, C. Kittel, L. Le Toumelin, C. Agosta, A. Delhasse, V. Favier, and X. Fettweis: Performance of MAR (v3.11) in simulating the drifting-snow climate and surface mass balance of Adelie Land, East Antarctica, Geoscientific Model Development, accepted, 2021.  See README.txt for a full description of the dataset content Please contact me at amory.charles@live.fr if you need other half-hourly outputs or for more details on the dataset

What factors influence the extent of midstorey development in Mountain Ash forests?

The midstorey is a critical component of the structure of many kinds of forest globally. We constructed statistical models of the factors influencing the percentage cover of two dominant Acacia spp. (Montane Wattle [Acacia frigiscens]) and Silver Wattle [Acacia dealbata]) in the midstorey of Mountain Ash (Eucalyptus regnans) forests in mainland south-eastern Australia. We modelled the influence on the percentage cover of two these two species of Acacia of : (1) the age of the overstorey eucalypts (which corresponded to the time elapsed since the last major stand-replacing disturbance), and (2) environmental drivers (slope, aspect, elevation, and topographic wetness). Stand age was an important factor influencing the percentage cover of both Montane Wattle and Silver Wattle. We found evidence of a non-linear, humped-shaped percentage cover-stand age relationship for the percentage cover of Montane Wattle, with the highest values in stands of Mountain Ash that were 30-60 years old. There were no differences in percentage cover among other age classes. The highest values for the percentage cover of Silver Wattle were for stands regenerating after the 2009 fire with markedly lower levels of cover in other age classes. There were no differences in cover between other age classes. Although our data contained evidence of inter-specific differences between Montane Wattle and Silver Wattle in their response to stand age, both species persisted as a midstorey component in old growth Mountain Ash forest. No environmental covariates influenced the percentage cover of Montane Wattle or Silver Wattle. Both tree species occur well beyond our study region and the set of environmental conditions we modelled may therefore not be limiting the occurrence of these tree species. We suggest that disturbance is the key driver of site occurrence of the Montane Wattle and Silver Wattle in the Mountain Ash forests of the Central Highlands of Victoria.

Development of Data Dictionary for neonatal intensive care unit: advancement towards a better critical care unit

Background: Critical care units (CCUs) with wide use of various monitoring devices generate massive data. To utilize the valuable information of these devices; data are collected and stored using systems like Clinical Information System (CIS), Laboratory Information Management System (LIMS), etc. These systems are proprietary in nature, allow limited access to their database and have vendor specific clinical implementation. In this study we focus on developing an open source web-based meta-data repository for CCU representing stay of patient with relevant details. Methods: After developing the web-based open source repository we analyzed prospective data from two sites for four months for data quality dimensions (completeness, timeliness, validity, accuracy and consistency), morbidity and clinical outcomes. We used a regression model to highlight the significance of practice variations linked with various quality indicators. Results: Data dictionary (DD) with 1447 fields (90.39% categorical and 9.6% text fields) is presented to cover clinical workflow of NICU. The overall quality of 1795 patient days data with respect to standard quality dimensions is 87%. The data exhibit 82% completeness, 97% accuracy, 91% timeliness and 94% validity in terms of representing CCU processes. The data scores only 67% in terms of consistency. Furthermore, quality indicator and practice variations are strongly correlated (p-value < 0.05). Results: Data dictionary (DD) with 1555 fields (89.6% categorical and 11.4% text fields) is presented to cover clinical workflow of a CCU. The overall quality of 1795 patient days data with respect to standard quality dimensions is 87%. The data exhibit 82% completeness, 97% accuracy, 91% timeliness and 94% validity in terms of representing CCU processes. The data scores only 67% in terms of consistency. Furthermore, quality indicators and practice variations are strongly correlated (p-value < 0.05). Conclusion: This study documents DD for standardized data collection in CCU. This provides robust data and insights for audit purposes and pathways for CCU to target practice improvements leading to specific quality improvements.

FIGURES 41–44 in Description of Cornigamasus allotritosternus sp. nov. (Mesostigmata: Parasitidae) from China, with an emphasis on the ontogenetic development of setae

FIGURES 41–44. Cornigamasus allotritosternus sp. nov., female. 41. Gnathotectum; 42. Chelicera; 43. Palpus; 44. Hypostome.

FIGURES 31–36 in Description of Cornigamasus allotritosternus sp. nov. (Mesostigmata: Parasitidae) from China, with an emphasis on the ontogenetic development of setae

FIGURES 31–36. Cornigamasus allotritosternus sp. nov., deutonymph. 31–32. Leg I; 33. Leg II; 34. Leg III; 35–36. Leg IV.

FIGURES 26–30 in Description of Cornigamasus allotritosternus sp. nov. (Mesostigmata: Parasitidae) from China, with an emphasis on the ontogenetic development of setae

FIGURES 26–30. Cornigamasus allotritosternus sp. nov., deutonymph. 26. Tritosternum; 27. Gnathotectum; 28. Chelicera; 29. Palpus; 30. Hypostome.

FIGURES 58–64 in Description of Cornigamasus allotritosternus sp. nov. (Mesostigmata: Parasitidae) from China, with an emphasis on the ontogenetic development of setae

FIGURES 58–64. Cornigamasus allotritosternus sp. nov., male. 58–59. Leg αʹ; 60. Leg βʹ; 61. Leg γʹ; 62–63. Leg δʹ; 64. Showing of spurs on the femur II.

FIGURES 19–23 in Description of Cornigamasus allotritosternus sp. nov. (Mesostigmata: Parasitidae) from China, with an emphasis on the ontogenetic development of setae

FIGURES 19–23. Cornigamasus allotritosternus sp. nov., protonymph. 19–20. Leg I; 21. Leg II; 22. Leg III; 23. Leg IV.

FIGURES 3–7 in Description of Cornigamasus allotritosternus sp. nov. (Mesostigmata: Parasitidae) from China, with an emphasis on the ontogenetic development of setae

FIGURES 3–7. Cornigamasus allotritosternus sp. nov., larva. 3. Tritosternum; 4. Gnathotectum; 5. Chelicera; 6. Palpus; 7. Hypostome.

FIGURES 53–57 in Description of Cornigamasus allotritosternus sp. nov. (Mesostigmata: Parasitidae) from China, with an emphasis on the ontogenetic development of setae

FIGURES 53–57. Cornigamasus allotritosternus sp. nov., male. 53. Tritosternum; 54. Gnathotectum; 55. Chelicera; 56. Palpus; 57. Hypostome.

FIGURES 45–50 in Description of Cornigamasus allotritosternus sp. nov. (Mesostigmata: Parasitidae) from China, with an emphasis on the ontogenetic development of setae

FIGURES 45–50. Cornigamasus allotritosternus sp. nov., female. 45–46. Leg I; 47. Leg II; 48. Leg III; 49–50. Leg IV.