Miracle-dz/UniFAR-FTUs huggingface dataset:
Train-the-Trainer as an Effective Approach to Building Global Networks of Experts in Genomic Surveillance of Antimicrobial Resistance (AMR)

Abstract Advanced genomics and sequencing technologies are increasingly becoming critical for global health applications such as pathogen and antimicrobial resistance (AMR) surveillance. Limited resources challenge capacity development in low- and middle-income countries (LMICs), with few countries having genomics facilities and adequately trained staff. Training research and public health experts who are directly involved in the establishment of such facilities offers an effective, but limited, solution to a growing need. Instead, training them to impart their knowledge and skills to others provides a sustainable model for scaling up the much needed capacity and capability for genomic sequencing and analysis locally with global impact. We designed and developed a Train-the-Trainer course integrating pedagogical aspects with genomic and bioinformatics activities. The course was delivered to 18 participants from 12 countries in Africa, Asia, and Latin America. A combination of teaching strategies culminating in a group project created a foundation for continued development at home institutions. Upon follow-up after 6 months, at least 40% of trainees had initiated training programs and collaborations to build capacity at local, national, and regional level. This work provides a framework for implementing a training and capacity building program for the application of genomics tools and resources in AMR surveillance.
Silicon and titanium in peat profiles as indicators of human impact

A close correlation exists at four peat sites between pollen indicators of human impact, especially Plantago lanceolata and Cerealia, and the elements silicon and especially titanium as indicators of erosion. Pollen of plants with a short life cycle occur at the peak of silicon or titanium or shortly after, and a tree-pollen response follows later. Short disturbances of the vegetation or very early human impact can be detected and delimited even better by the increase of these elements than by pollen analysis. The combined use of these two elements is not so much subject to interferences of diatoms or macrofossils as the use of ash content. The method provides important environmental information additional to pollen analysis. It can be used to detect not only human impact but also natural changes in the vegetation caused by a changing climate. The determination of these two additional parameters is easy and does not require sophisticated equipment.
Simulation of storm velocity effects on flow from distributed channel networks

Programs have been designed to perform computer simulation experiments on the effects of storms traveling over drainage networks. The system of programs makes it possible to simulate the response of any channel network to storms with boundaries that are numerically specified by line segments. The excess runoff response function of discrete approximations of spatially distributed networks may be simulated for storms with any velocity and initial position. Storms are modeled as polygons surrounding areas of uniform intensity. An average flow velocity for each segment of the network can be specified independently by an input vector of transit times associated with network nodes. The computer time taken for each simulation of storm travel depends on the number of calculations performed in determining which network segments are overlapped by the storm. Results include hydrographs simulated for both actual fixed storms and for moving test storms that travel with specified speeds and directions over a binary tree model of a natural watershed with an assumed constant average internal flow rate.
Mapping Migratory Wading Bird Feeding Habitats using Satellite Imagery and Field Data, Eighty-Mile Beach, Western Australia

Abstract Eighty-Mile Beach is one of the 10 most populous sites for migratory birds in the Asian–Australasian Flyway. The birds come to Eighty-Mile Beach's tidal mudflats to feed on benthic organisms during their nonbreeding period prior to embarking on a 10,000–15,000-km migration to their breeding grounds in the Arctic. To better understand migratory birds' preferences for areas on the beach, satellite imagery was used to predict grain size and benthic invertebrate distributions. These data were statistically compared with data collected in the field to determine the accuracy of the predictions. Relationships were apparent between compared data, especially in respect to the actual benthic invertebrate distribution. Finally, feeding areas for different bird species were mapped according to where their favored foods would be found. Knowing where the birds should be feeding will help prioritize research and conservation efforts on Eighty-Mile Beach.
Increased Dietary Inflammatory Index Is Associated with Schizophrenia: Results of a Case–Control Study from Bahrain

Background: Several studies have indicated that chronic low-grade inflammation is associated with the development of schizophrenia. Given the role of diet in modulating inflammatory markers, excessive caloric intake and increased consumption of pro-inflammatory components such as calorie-dense, nutrient-sparse foods may contribute toward increased rates of schizophrenia. This study aimed to examine the association between dietary inflammation, as measured by the dietary inflammatory index (DII®), and schizophrenia. Methods: A total of 120 cases attending the out-patient department in the Psychiatric Hospital/Bahrain were recruited, along with 120 healthy controls matched on age and sex. The energy-adjusted DII (E-DII) was computed based on dietary intake assessed using a comprehensive food frequency questionnaire (FFQ). Logistic regression was used to estimate odds ratios and 95% confidence intervals, adjusting for potential confounders including age, sex, body mass index, education, employment, diabetes, hypertension, and cardiovascular disease with E-DII expressed both as a continuous variable and categorized as quartiles. Results: The mean E-DII score for the entire sample was 1.79 ± 1.52, indicating a generally pro-inflammatory diet. The cases with schizophrenia appeared to have a higher E-DII score compared to controls: 1.99 ± 1.39 vs. 1.60 ± 1.38, respectively (p = 0.009). For every one unit increase in the E-DII score, the odds of having schizophrenia increased by 62% (OR 1.62; 95% CI 1.17–2.26). Similarly, increased risk was observed when the E-DII was used as quartiles, with participants in most pro-inflammatory quartile 4 being nearly 6 times more likely to be schizophrenic than participants in the most anti-inflammatory group quartile 1 (OR 5.96; 1.74–20.38; p-trend = 0.01). Conclusions: The data suggest that a pro-inflammatory diet, as indicated by increasing E-DII score, is associated with schizophrenia. This is the first study to examine the association between the DII and schizophrenia in a Middle Eastern population. Although these results are consistent with findings from research conducted in depression, additional studies are required before generalizing the findings to other populations.
Impact of new particle formation on the concentrations of aerosols and cloud condensation nuclei around Beijing

[1] New particle formation (NPF) is one of the most important processes in controlling the concentrations of aerosols (condensation nuclei, CN) and cloud condensation nuclei (CCN) in the atmosphere. In this study, we introduce a new aerosol model representation with 20 size bins between 1 nm and 10 μm and activation-type and kinetic nucleation parameterizations into the WRF-chem model (called NPF-explicit WRF-chem). Model calculations were conducted in the Beijing region in China for the periods during the Campaign of Air Quality Research in Beijing and Surrounding Region 2006 (CARE-Beijing 2006) campaign conducted in August and September 2006. Model calculations successfully reproduced the timing of NPF and no-NPF days in the measurements (21 of 26 days). Model calculations also reproduced the subsequent rapid growth of new particles with a time scale of half a day. These results suggest that once a reasonable nucleation rate at a diameter of 1 nm is given, explicit calculations of condensation and coagulation processes can reproduce the clear contrast between NPF and no-NPF days as well as further growth up to several tens of nanometers. With this reasonable representation of the NPF process, we show that NPF contributed 20%–30% of the CN concentrations (>10 nm in diameter) in and around Beijing on average. We also show that NPF increases CCN concentrations at higher supersaturations (S > 0.2%), while it decreases them at lower supersaturations (S < 0.1%). This is likely because NPF suppresses the increases in both the size and hygroscopicity of preexisting particles through the competition of condensable gases between new particles and preexisting particles. Sensitivity calculations show that a reduction of primary aerosol emissions, such as black carbon (BC), would not necessarily decrease CCN concentrations because of an increase in NPF. Sensitivity calculations also suggest that the reduction ratio of primary aerosol and SO2 emissions will be key in enhancing or damping the BC mitigation effect.
Towards probabilistic projections of climate change impacts on global crop yields

There is a widely recognized need in the scientific and policy communities for probabilistic estimates of climate change impacts, beyond simple scenario analysis. Here we propose a methodology to evaluate one major climate change impact ‐ changes in global average yields of wheat, maize, and barley by 2030 ‐ by a probabilistic approach that integrates uncertainties in climate change and crop yield responses to temperature, precipitation, and carbon dioxide. The resulting probability distributions, which are conditional on assuming the SRES A1B emission scenario and no agricultural adaptation, indicate expected changes of +1.6%, −14.1%, −1.8% for wheat, maize, and barley, with 95% probability intervals of (−4.1, +6.7), (−28.0, −4.3), (−11.0, 6.2) in percent of current yields, respectively. This fully probabilistic analysis aims at quantifying the range of plausible outcomes and allows us to gauge the relative importance of different sources of uncertainty.
Antarctic sea ice variability during 1958-1999: A simulation with a global ice-ocean model

[1] A hindcast simulation is carried out with a global ice-ocean model driven by the National Centers for Environmental Prediction (NCEP)-National Center for Atmospheric Research (NCAR) reanalysis daily surface air temperatures and winds in order to document the variability of the Antarctic sea ice cover during 1958-1999. The model consists of an ocean general circulation model coupled to a thermodynamic-dynamic sea ice model with viscous-plastic rheology. Its horizontal resolution is of 1.5degrees x 1.5degrees. Both the mean state and variability of the Antarctic ice pack over the satellite observing period are reasonably well reproduced by the model. In particular, from November 1978 to September 1998, the model produces an overall increasing trend in ice area (defined as the total area of ice-covered ocean) of 11,400 +/- 2300 km(2) yr(-1), which falls within the range of current uncertainty. The model annual mean, area-averaged ice thickness displays no significant trend over 1958-1999. In contrast, a retreat of the pack is simulated during the second half of the 1970s and the beginning of the 1980s, leading to a loss of ice cover of roughly 0.5 x 10(6) km(2) between 1958-1976 and 1982-1999. The marked weakening of the Antarctic semiannual oscillation that occurred since the mid-to-late 1970s seems to be partially responsible for this behavior. Part of the modeled decline might however be spurious and due to the 1979 change in the observing systems utilized in the NCEP-NCAR reanalysis. The simulation also reveals a pronounced decadal variability (8-10 years) in both ice area and thickness. Locally, the changes in ice thickness can reach 1 m during a particular cycle.
Stochastic versus dynamical downscaling of ensemble precipitation forecasts.

Abstract The assessment of hydrometeorological risk in small basins requires the availability of skillful, high-resolution quantitative precipitation forecasts to predict the probability of occurrence of severe, localized precipitation events. Large-scale ensemble prediction systems (EPS) currently provide forecast scenarios down to a resolution of about 50 km. High-resolution, nonhydrostatic, limited-area ensemble prediction systems provide dynamically based forecasts by extending these scenarios to smaller scales, typically on the order of 10 km. This work explores an alternative approach to the use of limited-area ensemble prediction systems, by directly applying a stochastic downscaling technique to large-scale ensemble forecasts. The performances of these two different approaches for three well-predicted precipitation events in northwestern Italy during 2006 are compared. Ensemble forecasts provided by the ECMWF EPS, downscaled using the Rainfall Filtered Autoregressive Model (RainFARM) stochastic te.
Enzymatic synthesis of cyclic dinucleotide analogs by a promiscuous cyclic-AMP-GMP synthetase and analysis of cyclic dinucleotide responsive riboswitches

Abstract Cyclic dinucleotides are second messenger molecules produced by both prokaryotes and eukaryotes in response to external stimuli. In bacteria, these molecules bind to RNA riboswitches and several protein receptors ultimately leading to phenotypic changes such as biofilm formation, ion transport and secretion of virulence factors. Some cyclic dinucleotide analogs bind differentially to biological receptors and can therefore be used to better understand cyclic dinucleotide mechanisms in vitro and in vivo. However, production of some of these analogs involves lengthy, multistep syntheses. Here, we describe a new, simple method for enzymatic synthesis of several 3′, 5′ linked cyclic dinucleotide analogs of c-di-GMP, c-di-AMP and c-AMP-GMP using the cyclic-AMP-GMP synthetase, DncV. The enzymatic reaction efficiently produced most cyclic dinucleotide analogs, such as 2′-amino sugar substitutions and phosphorothioate backbone modifications, for all three types of cyclic dinucleotides without the use of protecting groups or organic solvents. We used these novel analogs to explore differences in phosphate backbone and 2′-hydroxyl recognition between GEMM-I and GEMM-Ib riboswitches.
Sex, scarring, and stress: understanding seasonal costs in a cryptic marine mammal

This study demonstrates that fecal glucocorticoid levels are a useful measure of diverse stressors in dugongs (a vulnerable cryptic marine mammal), including cold temperature and other seasonal factors, intraspecific aggression/injury, and pregnancy. The intrinsic underlying glucocorticoid patterns of dugongs are different between sexes, across reproductive maturity states, and vary seasonally in response to reproductive patterns and environmental conditions.
Does the SST-LHF relationship reverse for satellite derived products?

Accurate retrieval of air-sea exchange parameters from satellite is highly desirable as it contributes immensely to the understanding of climate change. Due to the inherent difficulties in the direct flux measurement, indirect approaches to flux estimation have been widely adopted in spite of the large uncertainties associated with them. More recently Fairall et al (2003) have reported the final version of the bulk flux algorithm that emerged out of a carefully planned Coupled Ocean-Atmosphere Response Experiment (COARE) where more than 7216 hours of direct flux measurements were used to validate the bulk algorithm. They have succeeded in narrowing down the uncertainty from the then existing 20-30% level to 5% for wind speeds of 0-10 m/s and to 10% for 10-20 m/s wind speed.
Seasonal Changes in Whole-body Energy Content and Estimated Consumption Rates of Age 0 Walleye Pollock from Prince William Sound, Alaska

This study examined the somatic energy content and prey consumption needs of recruiting walleye pollockTheragra chalcogrammain one of Alaska's large estuaries to begin to evaluate the role of this species in the food-web. Age 0 pollock were collected from Prince William Sound in the fall and spring during 2 years. In the fall of 1995, few recruits <70 mm standard length (SL) were present and the mean whole-body energy content (WBEC) was 3·6 (±0·2) kJ g−1wet wt. In the following spring the 1995 year class survivors were ≥80 mm SL and the mean WBEC was 4·0 kJ g−1(±0·5). In the fall of 1996 the age 0 pollock had an average WBEC of 3·6 kJ g−1(±0·2), identical to 1995, but smaller 60–70 mm fish were common. In the spring of 1997 few fish <70 mm were captured and WBEC averaged 3·4 kJ g−1(±0·4). In both years, recruits were generally able to maintain or improve their WBEC over the winter. There was marked variation in WBEC for fish from different collection sites. Changes in WBEC of the 1996 year class was monitored during their first year. On 13 June recently metamorphosed pollock had a SL of 34 (±5) mm and a mean WBEC of 2·7 (±0·2) kJ g−1vs81 (±10) mm and 3·6 (±0·2) kJ g−1on 6 October. Based on these mean values, growth rates for age 0 pollock during their first 119 days were 0·4 mm day−1and 7·8 J g−1 day−1. Modeling changes in body weight, energy content and metabolic demands for both active metabolism and growth allowed prediction of food intake over their first 270 days. Predicted wet wt of fish increased from an initial 0·37 g to a high of 7·6 g. Estimated food intake ranged from 0·21 to 1·29 kJ day−1.
Fire Ecology of Pacific Northwest Forests

Review: Fire Ecology of Pacific Northwest Forests. By James K. Agee Reviewed by James K. Peek Department of Fish and Wildlife Resources, University University of Idaho Agee, James K. Fire Ecology of Pacific Northwest Forests. Washington, D.C.: Island Press, 1993. 490 pp. US $50.00 cloth ISBN: 1-55963-229- Fire has been a major component of the forests of much of North America, including the Pacific Northwest, over the millennia. Agee has produced a well-written, comprehensive account of the ecology and management of fire in the northwestern United States, which emphasizes its importance and inevitability. Although the fire regimes in Sitka spruce, hemlock and redwood forests are much longer than in the pine forests of the interior, fire still should be expected. Agee points out that disturbance is inevitable in these forests, and returns to this theme repeatedly. While we are now better able to predict fire behavior, the effects are less predictable. This book requires knowledge of plant succession, which is aided by the glossary. Agee's definition of fire regimes using vegetative characteristics is used throughout the book. There is a good discussion of weather patterns and their influence on fire regimes and vegetation. Fire behavior models are described and an example of the use of these models is provided, although this is not a how-to-burn manual. The discussion of the history of fire management is primarily confined to Washington and Oregon. It is of interest that in recent times no use of prescribed fire has occurred in the Blue Mountains, but just across the border in Idaho, fire is commonly used in forestry. Agee concludes that fire use must be tailored to specific areas and for specific purposes, something those who plan for broad regions in the continent should take note of. There is some use of jargon that the practitioner will be familiar with, i.e. the JABOWA disturbance model. The chapter on environmental effects includes a comprehensive discussion of soils, soil chemistry, and biological properties of soils, including the use of a soil nutrient thermometer, which helps visualize effects of different temperatures on soil nutrients. A section on the effects of fire on wildlife is disappointingly
MECHANISMS OF WAVE TRANSPORT OF MEGACLASTS ON ELEVATED CLIFF-TOP PLATFORMS: EXAMPLES FROM WESTERN IRELAND RELEVANT TO THE STORM-WAVE VERSUS TSUNAMI CONTROVERSY

Abstract:The emplacement of very large clasts (megaclasts) onto cliff-tops many metres above sea-level has often been ascribed to the action of tsunami. In western Ireland, megaclasts are found on cliff-top platforms at up to 50 metres above sea-level having been emplaced by extreme storm-waves without any tsunami action, making these some of the highest such modern deposits in the world. To test the role of storm-waves in this environment, an analysis of wave impact on vertical obstacles is presented partly based on previous work on artificial sea-walls and partly on examples from the cliffs of the Aran Islands. The impact of large waves onto cliffs can lead to overtopping of either green or white water. It is suggested that such overtopping results in the downward collapse of the overtopping water mass. This may result in the formation of a landward moving high-velocity bore. It is this bore which transports megaclasts, sometimes weighing tens of tonnes, across the cliff-top platforms. The impacting orbital wave is thus converted into a unidirectional bore and analysis is presented to ascertain the properties of such bores necessary to move megaclasts in the context of the Aran Islands.
Taphonomic alteration of reef corals; effects of reef environment and coral growth form; I, The Great Barrier Reef

Taphonomic alteration in coral death assemblages showed high variability with respect to reef environment and growth form at Orpheus Island on the Great Barrier Reef Australia. A greater degree of physical and biological alteration occurred in the lower-energy leeward Pioneer Bay site relative to the higher-energy windward Iris Point site. Greater degrees of taphonomic alteration also occurred at 6-7 m than 2-3 m water depth within each site. Clear gradients in the degree of taphonomic alteration of reef corals with reef environment indicate the utility of corals as taphonomic indicators in ancient reef settings. Because greater taphonomic differences between depths occurred at the high wave-energy site relative to the lour wave-energy site, differentiation of fossil reef taphofacies might be greatest in high energy reef settings. Interpretation of ancient reef sedimentary environments may be aided by analysis of taphonomic alteration. of reef corals.