Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis

ABSTRACT Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza H1N1/09 virus genomes from United Kingdom isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic and used their sequences, dates of isolation, and geographical locations to infer the genetic epidemiology of the epidemic in the United Kingdom. We demonstrate that the epidemic in the United Kingdom was composed of many cocirculating lineages, among which at least 13 were exclusively or predominantly United Kingdom clusters. The estimated divergence times of two of the clusters predate the detection of pandemic H1N1/09 virus in the United Kingdom, suggesting that the pandemic H1N1/09 virus was already circulating in the United Kingdom before the first clinical case. Crucially, three clusters contain isolates from the second wave of infections in the United Kingdom, two of which represent chains of transmission that appear to have persisted within the United Kingdom between the first and second waves. This demonstrates that whole-genome analysis can track in fine detail the behavior of individual influenza virus lineages during the course of a single epidemic or pandemic.
Development and Characterization of Bladder Cancer Patient-Derived Xenografts for Molecularly Guided Targeted Therapy

Background The overarching goal of this project is to establish a patient-derived bladder cancer xenograft (PDX) platform, annotated with deep sequencing and patient clinical information, to accelerate the development of new treatment options for bladder cancer patients. Herein, we describe the creation, initial characterization and use of the platform for this purpose. Methods and Findings Twenty-two PDXs with annotated clinical information were established from uncultured unselected clinical bladder cancer specimens in immunodeficient NSG mice. The morphological fidelity was maintained in PDXs. Whole exome sequencing revealed that PDXs and parental patient cancers shared 92–97% of genetic aberrations, including multiple druggable targets. For drug repurposing, an EGFR/HER2 dual inhibitor lapatinib was effective in PDX BL0440 (progression-free survival or PFS of 25.4 days versus 18.4 days in the control, p = 0.007), but not in PDX BL0269 (12 days versus 13 days in the control, p = 0.16) although both expressed HER2. To screen for the most effective MTT, we evaluated three drugs (lapatinib, ponatinib, and BEZ235) matched with aberrations in PDX BL0269; but only a PIK3CA inhibitor BEZ235 was effective (p<0.0001). To study the mechanisms of secondary resistance, a fibroblast growth factor receptor 3 inhibitor BGJ398 prolonged PFS of PDX BL0293 from 9.5 days of the control to 18.5 days (p<0.0001), and serial biopsies revealed that the MAPK/ERK and PIK3CA-AKT pathways were activated upon resistance. Inhibition of these pathways significantly prolonged PFS from 12 day of the control to 22 days (p = 0.001). To screen for effective chemotherapeutic drugs, four of the first six PDXs were sensitive to the cisplatin/gemcitabine combination, and chemoresistance to one drug could be overcome by the other drug. Conclusion The PDX models described here show good correlation with the patient at the genomic level and known patient response to treatment. This supports further evaluation of the PDXs for their ability to accurately predict a patient’s response to new targeted and combination strategies for bladder cancer.
Identifying Marine Sources of Beached Plastics Through a Bayesian Framework: Application to Southwest Netherlands

Beaches are thought to be a large reservoir for marine plastics. To protect vulnerable beaches, it is advantageous to have information on the sources of this plastic. Here, we develop a universally applicable Bayesian framework to map sources of plastic arriving on a specific beach. In this framework, we combine Lagrangian backtracking simulations of drifting particles with estimates of plastic input from coastlines, rivers and fisheries. The advantage over traditional Lagrangian simulations is that the Bayesian framework can consider information on known sources, and thus facilitates spatiotemporal source attribution for plastic arriving at the specified beach. We show that the main sources for our target beach in southwest Netherlands are the east coast of the UK, the Dutch coast, the English Channel (fisheries) and the Thames, Seine, Rhine and Trieux (rivers). We also show that floating time is a major uncertainty in source attribution using backtracking.
Earthquakes in Longmenshan and Hydrocarbon Accumulation in Western Sichuan

change of oil and gas well production. After Wenchuan earthquake in 2008, in Sichuan, China, the production of gas wells in Longmenshan foreland basin showed sharply change. , and at the same time, a few new emerging nature gas seepages were observed in Sichuan Basin. One of the gas seepages is far away from the epicenter zone for about 100 km. The facts indicate that huge earthquake may lead to fast hydrocarbon migration in a large range. Earthquakes occurred frequently in geological history. So, we guess that earthquakes may play key role in the secondary hydrocarbon migration and accumulation, and that may exist an "earthquake-induced” hydrocarbon migration and accumulation mechanism. The mechanism of "earthquake-induced” hydrocarbon migration may include: (1) co-seismic ruptures as fluid flow channel, (2) co-seismic ruptures as low pressure area pumping pore fluid, (3) seismic wave as additional impulse driving force. In addition, Seismogenicstress is also an important force driving pore fluid migration. Earthquake-induced oil and gas rapid migration may lead to two opposite results. If the co-seismic ruptures reach the surface, it will lead to the reservoirs destruction and the gas dissipation. If the coseismic ruptures connect the deep reservoir and the shallow high-porosity rocks, it will lead to a secondary hydrocarbon accumulation in the shallow reservoir. Under the guidance of the "earthquake-induced” hydrocarbon migration and accumulation hypothesis, we constructed a conceptual model to explain the hydrocarbon reservoir distribution in the Western Sichuan. According to the model, earthquakes in Longmenshan have result in reservoirs destruction in Longmenshan, and secondary accumulation in Longmenshan foreland basin. Lots of large oil and gas fields worldwide are adjacent to earthquake zones. "Earthquake -induced” hydrocarbon migration and accumulation may be is common worldwide. The work was supported by NSFC under grant No. 40930424
General Circulation of the Northern Adriatic Sea: Results of Long-term Measurements

Abstract Residual sea currents of the northern Adriatic were analysed in the sense of the general (global) circulation, over a period of 42 months (in one main and two control stations). At the end of the summer season and the beginning of autumn (in the so-called ‘ inversion period ’) residual surface (6 m) sea currents at the main station showed characteristic seasonal behaviour: a change of direction from the north (NW, N, NE) to the south-east (SE). The sequence with SE directions lasted about 1·5 months. After that, directions changed again to the NW (or N). The direction of bottom residual currents (37 m) in this inversion period had the same pattern as the surface ones. This behaviour of the currents can be associated with the change of the cyclonic gyre into the anticyclonic. In all other periods at the main station the surface residual sea currents have predominant north directions. Bottom residual currents mainly followed the pattern of surface currents for all stations and periods, except during the periods from January to June 1990 and 1992, when they were of opposite direction at station B.
The mass balance of the Greenland ice sheet: sensitivity to climate change as revealed by energy-balance modelling

The sensitivity of the mass balance of the Greenland ice sheet to climate change is studied with an energy-balance model of the ice/snow surface, applied at 200 m elevation intervals for four characteristic regions of the ice sheet. Solar radiation, longwave radiation, turbulent heat fluxes and refreezing of melt water in the snow pack are treated separately. The daily cycle is fully resolved. For the climatology chosen as input (mainly from work by A. Ohmura), the mean specific balance produced by the model is 0.079 m/yr (water equivalent). Comparing this with the total accumulation, 0.313 m/yr, it is obvious that the ablation is quite large. However, a 1 K decrease of the imposed annual mean temperature leads to a specific balance of 0.147 m/yr, a 1 K increase to 0.003 m/yr. Because of this large sensitivity, it appears that the present state of balance cannot be determined from climatological data. The calculations show that changes in the earth's orbit during the Holocene must have had a significant effect on the mean specific balance of the Greenland ice sheet. The balance was smaller than today during most of the last 10 000 years, probably by as much as 0.05 m/yr. Further experimentation showed that the changes in the specific balance can be related to changes in summer insolation. The difference between a typical high latitude minimum in insolation (e.g., 25 000 BP) and a high latitude maximum in insolation (e.g., 10 000 BP) is equivalent to the effect of a 2 K difference in annual mean temperature. So when considering mass balance changes for a particular glacier during the Holocene, it is important to consider the orbital and climatic effects separately, because they may work in the same or in the opposite direction, depending on the location. In a warmer world, ablation will increase, but this will be compensated to some extent by increased snowfall. For a uniform warming of 1 K, and including a precipitation rate proportional to maximum possible atmospheric water content, the model predicts a contribution to sea level rise of 0.27 mm/yr.
Photocatalytic Deoxygenation of Sulfoxides Using Visible Light: Mechanistic Investigations and Synthetic Applications

The photocatalytic deoxygenation of sulfoxides to generate sulfides facilitated by either Ir[(dF(CF3)ppy)2(dtbbpy)]PF6 or fac-Ir(ppy)3 is reported. Mechanistic studies indicate that a radical chain mechanism operates, which proceeds via a phosphoranyl radical generated from a radical/polar crossover process. Initiation of the radical chain was found to proceed via two opposing photocatalytic quenching mechanisms, offering complementary reactivity. The mild nature of the radical deoxygenation process enables the reduction of a wide range of functionalized sulfoxides, including those containing acid-sensitive groups, in typically high isolated yields.
The nature and age of the debris accumulation at Gribun, Western Mull, Inner Hebrides

Synopsis In the Gribun area of western Mull, Scottish Inner Hebrides, a large debris accumulation is interpreted as a morainic complex. Although the outermost moraine ridge is located well beyond the limits of the Loch Lomond (Younger Dryas) glaciation previously proposed for the island, lithostratigraphic and biostratigraphic evidence from a deep basin enclosed within the moraine suggest that the feature formed during the Loch Lomond Stadial. At that time the regional firn line altitude in western Mull may have been as low as c. 100 m. The pollen stratigraphy of the basin sediments indicates that the site was ice free before the close of the Loch Lomond Stadial, sensu stricto, reflecting the low altitude of the glacier and its relatively small size. Evidence from Gribun supports the view that deglaciation in parts of Highland Britain may have been underway as early as 10,600 B.P.
On the Assessment of Functional Connectivity in an Immersive Brain-Computer Interface During Motor Imagery

New trends on brain-computer interface (BCI) design are aiming to combine this technology with immersive virtual reality in order to provide a sense of realism to its users. In this study, we propose an experimental BCI to control an immersive telepresence system using motor imagery (MI). The system is immersive in the sense that the users can control the movement of a NAO humanoid robot in a first person perspective (1PP), i.e., as if the movement of the robot was his/her own. We analyze functional brain connectivity between 1PP and 3PP during the control of our BCI using graph theory properties such as degree, betweenness centrality, and efficiency. Changes in these metrics are obtained for the case of the 1PP, as well as for the traditional third person perspective (3PP) in which the user can see the movement of the robot as feedback. As proof-of-concept, electroencephalography (EEG) signals were recorded from two subjects while they performed MI to control the movement of the robot. The graph theoretical analysis was applied to the binary directed networks obtained through the partial directed coherence (PDC). In our preliminary assessment we found that the efficiency in the α brain rhythm is greater in 1PP condition in comparison to the 3PP at the prefrontal cortex. Also, a stronger influence of signals measured at EEG channel C3 (primary motor cortex) to other regions was found in 1PP condition. Furthermore, our preliminary results seem to indicate that α and β brain rhythms have a high indegree at prefrontal cortex in 1PP condition, and this could be possibly related to the experience of sense of agency. Therefore, using the PDC combined with graph theory while controlling a telepresence robot in an immersive system may contribute to understand the organization and behavior of brain networks in these environments.
Distribution of Mountain Permafrost and Climate

The relationship between mountain permafrost and climate is still relatively unknown. The implications of zonation (latitude, continentality), the various climatic parameters (MAAT; freezing and thawing indices; basal snow temperature, BTS; solar radiation; and surface heat balance) and climate change are outlined for mountain permafrost. Some research priorities are suggested.
A stochastic convective approach to account for model uncertainty due to unresolved humidity variability

[1] Forecast uncertainty can result from the neglect of humidity variability on spatial scales not resolved by forecast models. To account for this, a stochastic convective scheme for the European Centre for Medium-Range Weather Forecasts (ECMWF) ensemble prediction system is presented that uses the subgrid humidity distributions provided by the cloud scheme. Each member of a forecast ensemble randomly samples this distribution to perturb the convective parcel's initial humidity and/or the humidity of the air entrained during ascent. Accounting for humidity variability with the new scheme has a smaller impact on tropical ensemble spread in the short range compared to the ECMWF operational scheme that represents uncertainty because of parameterization error. Combining the two schemes to account for both parameterization error and subgrid humidity variability simultaneously generally improves the skill of the operational system for most variables in the short to medium range in midlatitudes, while results in the tropics are mixed, with a notable deterioration in medium-range probabilistic skill for temperature and zonal wind. This deterioration is a consequence of the methodology employed. Since the convective scheme is highly nonlinear, providing zero-mean humidity perturbations to the scheme's input profiles does not lead to zero-mean perturbations to the output tendencies. For some parameters, this results in an increased bias of the ensemble mean and a deterioration in probabilistic skill. As future convective schemes are optimized to maximize deterministic forecast skill, the methodology will require modification to ensure zero-mean convective output perturbations.
A three‐dimensional simulation of the evolution of the middle latitude winter ozone in the middle stratosphere

Observations of O3, CH4, and N2O from the Halogen Occultation Experiment (HALOE), the Cryogenic Limb Array Etalon Spectrometer (CLAES), and the Microwave Limb Sounder on the Upper Atmosphere Research Satellite are compared with fields calculated using a three-dimensional global chemistry and transport model which uses winds from a data assimilation system. Model and observations are found to be in generally good agreement for ozone at middle latitudes between 50 and 3 hPa. Much of the horizontal structure in the observed long-lived tracers N2O and CH4 is seen in the model, but the model profile shapes differ systematically from those seen by CLAES (N2O and CH4) and HALOE (CH4). To understand the influence of transport on these comparisons, attention is focused on January and February 1992, when a series of minor warmings impact the ozone and tracer distributions. The model O3 at 6.8 hPa, which agrees well with observations, is shown to be influenced by transport from the tropics toward middle and high latitudes, which increases O3, and photochemical processes, through which O3 is destroyed. However, the model N2O and CH4 mixing ratios at middle latitudes at 6.8 hPa are much greater than observations. Good comparisons between modeled and observed O3 and poor comparisons between modeled and observed N2O and CH4 are explained by differences in the horizontal transport from the subtropics. Here photochemical processes control the O3 mixing ratio, and the horizontal winds transport air with realistic ozone mixing ratios to the middle latitudes. For the longer-lived gases, the model mixing ratios in the subtropics far exceed observations, and the horizontal winds transport air with higher than observed mixing ratios to middle latitudes, leading to the poor comparisons. This analysis shows that the photochemical and transport processes that affect O3 at middle latitudes during winter are well represented in the model. However, for long-lived tracers, errors in the model subtropics are communicated to middle latitudes by the horizontal winds.
Forecasts of forest conditions

Key Findings Among the five forest management types, only planted pine is expected to increase in area. In 2010 planted pine comprised 19 percent of southern forests. By 2060, planted pine is forecasted to comprise somewhere between 24 and 36 percent of forest area. Although predicted rates of change vary, all forecasts reveal that land use changes and conversion to pine plantations will result in a continuing downward trend in naturally regenerated pine types. Changes in forest types are influenced by urbanization and timber markets: hardwood types are most strongly influenced by urbanization; softwood types are most sensitive to future timber market conditions. Reversing a 50-year trend of accumulating about 2.5 billion cubic feet per year, forest biomass is forecasted to increase slightly over the next 10 to 20 years and then decline gradually. After accounting for harvests, forest growth, land use, and climate change, the total carbon pool represented by the South’s forests is forecasted to increase slightly from 2010 to 2020/2030 and then decline. Urbanization patterns are the dominant determinates of the size of the future forest carbon pool, although stronger forest product markets can ameliorate carbon losses. Because of increases in timber supply from 1990 to 2010, removals of forest biomass (growing stock) are forecasted to increase for all Cornerstones, including those that project decreasing prices. This reflects an outward shift in timber supply associated with forest inventories between 1990 and 2010. Removals of softwood pulpwood are responsive to futures for forest planting and product prices. Under a high price future, softwood pulpwood output would increase by 56 percent, roughly equal to the expansion observed between 1950 and 2000. Although the overall loss of upland hardwood acreage is forecasted to be in the range of 8 to 14 percent, the oakhickory forest type remains essentially constant while the areas of other forest types decline at higher rates. The yellow-poplar forest type is forecasted to decline the most, with the highest losses forecasted for the Piedmont. The age and species structure of softwood forest types are most strongly influenced by forest harvesting and management tied to timber markets. This is not the case for hardwood forests. The future structure of hardwood forests is most strongly affected by urbanization-driven land use changes (increased population growth and income). Reductions of naturally regenerated pine forests are not equally distributed among age classes. Mid-age and earlyage forests decline, but old-age forests remain relatively constant. The distribution of upland and lowland hardwoods shifts, with less of these forest management types classified as early age and more classified as older age.
Experimental determination of colloid deposition rates and collision efficiencies in natural porous media

Mobile colloids in groundwater aquifers and soils can serve as carriers for strongly sorbing contaminants and thereby facilitate contaminant transport. Therefore mobile colloids may have to be considered in modeling the fate of strongly sorbing contaminants in subsurface environments. In this study we present a Chromatographic short‐pulse technique for measuring colloid deposition rate coefficients and experimental collision efficiencies in natural porous media. The method was evaluated using four different experimental systems of increasing complexity. Short pulses (equivalent to 0.002 to 0.03 pore volumes) of latex or humic‐coated hematite suspensions were injected under saturated flow conditions into laboratory columns packed with glass beads, soil, or aquifer materials. Colloid breakthrough curves were measured on‐line using fluorescence and UVVIS spectrophotometers. Deposition rate coefficients determined with the short‐pulse method were in excellent agreement with results from step‐input experiments. Experiments with different flow rates and column dimensions showed that colloid deposition generally followed a first‐order kinetic rate law. On the basis of experimental fast deposition rates, collision efficiencies for colloid deposition can be calculated. The results demonstrate that the short‐pulse method can be used very efficiently for studying the effects of solution chemistry and flow velocity on the kinetics of colloid deposition in natural porous media. The short‐pulse method has several advantages over the more traditionally used step‐input experiment and allows running several experiments on a single column without significant blocking or filter ripening effects.