Miracle-dz/UniFAR-FTUs huggingface dataset:
An ex vivo cystic fibrosis model recapitulates key clinical aspects of 1 chronic Staphylococcus aureus infection. 2

Staphylococcus aureus is the most prevalent organism isolated from the airways of people 26 with cystic fibrosis (CF), predominantly early in life. Yet its role in the pathology of lung 27 disease is poorly understood. In mice, and many experiments using cell lines, the 28 bacterium invades cells or interstitium, and forms abscesses. This is at odds with the 29 limited available clinical data: interstitial bacteria are rare in CF biopsies and abscesses 30 are highly unusual. Bacteria instead appear to localise in mucus plugs in the lumens of 31 bronchioles. We show that, in an established ex vivo model of CF infection comprising 32 porcine bronchiolar tissue and synthetic mucus, S. aureus demonstrates clinically 33 significant characteristics including colonisation of the airway lumen, with preferential 34 localisation as multicellular aggregates in mucus, initiation of a small colony variant 35 phenotype and increased antibiotic tolerance of tissue-associated aggregates. Tissue 36 invasion and abscesses were not observed. Our results may inform ongoing debates 37 relating to clinical responses to S. aureus in people with CF.
Low Cardiorespiratory Fitness Is a Risk Factor for Death Exercise Intervention May Lower Mortality?*

C ardiorespiratory fitness (CRF) level has been related to various clinical characteristics, such as age, sex, heredity, body composition, properties of skeletal muscle, underlying diseases, use of medication, quantity, and quality of physical activity, cigarette smoking, and nutritional status (1,2). CRF is related to the ability to transport oxygen from the lung to the mitochondria to perform physical exercise. The level of CRF is dependent on a chain of multiple organ processes that include pulmonary ventilation (VE) and diffusion and pulmonary vascular function, right and left ventricular function, ventricular-arterial coupling, the capacity of the vasculature to accommodate and efficiently transport blood from the heart to match oxygen requirements, the ability of the muscle cells to use the oxygen and other essential nutrients delivered by the blood, and the ability of the nervous system to recruit muscle fibers. Left ventricular stroke volume, maximal heart rate, and arteriovenous oxygen difference at exercise have determined CRF level (1). In general, CRF is related to the integration of human body function under physiological stress conditions, and it quantifies the functional capacity of an individual, reflecting body function and general health. Cardiorespiratory or aerobic fitness, as measured by peak oxygen uptake (VO2peak), has been one of the most widely examined cardiopulmonary exercise
Re‑irradiation plus hyperthermia for recurrent pediatric sarcoma; a simulation study to investigate feasibility

Recurrent pediatric tumors pose a challenge since treatment options may be limited , particularly after previous irradiation. Positive results have been reported for chemotherapy and hyperthermia, but the combination of re-irradiation and hyperthermia has not been investigated thus far, although it is a proven treatment strategy in adults. The theoretical feasibility of re-irradiation plus hyperthermia was investigated for infield recurrent pediatric sarcoma in the pelvic region and the extremities. A total of 46 recurrent pediatric sarcoma cases diagnosed at the Academic Medical Center (Amsterdam, The Netherlands) between 2002 and 2017 were evaluated. Patients not previously irradiated, outfield recurrences and locations other than the pelvis and extremities were excluded, ultimately yielding four eligible patients: Two with sarcomas in the pelvis and two in an extremity. Re-irradiation and hyperthermia treatment plans were simulated for 23x2 Gy treatment schedules and weekly hyperthermia. The radiosensitizing effect of hyperthermia was quantified using biological modelling with a temperature-dependent change in the parameters of the linear-quadratic model. The possible effectiveness of re-irradiation plus hyperthermia was estimated by calculating the equivalent radiotherapy dose distribution. Treatment planning revealed that tumors located in the pelvis and the extremities can be effectively heated in children. Equivalent dose distributions indicated that hyperthermic radiosensitization can be quantified as a target-selective additional D95% of typically 10 Gy, thereby delivering a possibly curative dose of 54 Gy, without substantially increasing the equivalent dose to the organs at risk. Therefore, re-irradiation plus hyperthermia is a theoretically feasible and possibly effective treatment option for recurrent pediatric sarcoma in the pelvic region and the extremities, and its clinical feasibility is worthy of evaluation.
Volcanic sulfur emissions: Estimates of source strength and its contribution to the global sulfate distribution

Anthropogenic emission of SO 2 and conversion into SO 4 2- is argued to be the most important factor damping and modulating the global greenhouse effect. Recent estimates of the relative strength of the three important sources of volatile sulfur (SO 2 from fossil fuel combustion ∼78 Tg S/yr, from biomass burning ∼2 Tg S/yr, and from natural sources ∼25 Tg S/yr) suggest an overwhelming effect of the anthropogenic emissions for climate forcing. However, the radiatively relevant product SO 4 2- may have different patterns due to the distribution of the sources (some very dense areas near the surface for anthropogenic SO 2 , formation of SO 2 from dimethylsulfide in the marine boundary layer, and emission of volcanic SO 2 mostly in the free atmosphere in rural areas). In this paper we study the relative contribution of volcanic SO 2 emissions to the atmospheric sulfur budget applying an atmospheric general circulation model including a full sulfur cycle and prescribed source distributions. An off-line analysis tool is applied to determine the radiative forcing of sulfate aerosols. The results show that natural S sources are at least as important as the anthropogenic ones, even though their source strength is much smaller. The reasons are different lifetimes due to different production and emission processes. Therefore, we should improve our knowledge about the volcanic volatile sources and their time-space variability.
CYTOKININ RESPONSE FACTOR2 (CRF2) and CRF3 Regulate Lateral Root Development and Response to Cold Stress in Arabidopsis

CYTOKININ RESPONSE FACTOR2 (CRF2) and CRF3 Regulate Lateral Root 1 Development in Response to Cold Stress in Arabidopsis 2 3 Jin Jeon, Chuloh Cho, Mi Rha Lee, Nguyen Van Binh, and Jungmook Kim 4 5 Department of Bioenergy Science and Technology, Chonnam National University, Buk6 Gu, Gwangju 500-757, Korea 7 Kumho Life Science Laboratory, Chonnam National University, Buk-Gu, Gwangju 8 500-757, Korea 9 10 Running Title: CRF2 and CRF3 in Lateral Root Formation and Cold 11 One-sentence summary: CRF2 and CRF3 encoding APETALA2 transcription factors 12 play an important role in lateral root initiation and root system architecture changes 13 under cold stress. 14 15 1 Address correspondence to jungmkim@jnu.ac. kr. 16 2 These authors contributed equally to this work. 17 18 The author responsible for distribution of materials integral to the findings presented in 19 this article in accordance with the policy described in the Instructions for Authors 20 (www.plantcell.org) is Jungmook Kim (jungmkim@jnu.ac.kr). 21 22 23 24 Plant Cell Advance Publication. Published on July 18, 2016, doi:10.1105/tpc.15. 00909
An evaluation of subsidence rates and sea‐level variability in the northern Gulf of Mexico

While subsidence is widely recognized as a driver of geomorphic change in the northern Gulf of Mexico (GOM), there is considerable disagreement over the rates of subsidence and the interpreted variability in these rates, which leads to controversies over the impacts of subsidence on surface land area change. Here we present a new method to calculate subsidence rates from the tide gauge record that is based on an understanding of the meteorological drivers of inter‐annual sea‐level change. In Grand Isle, LA and Galveston, TX, we explicitly show that temporal patterns of subsidence are closely linked to subsurface fluid withdrawal and coastal land loss, and suggest changes in withdrawal rates can both increase and decrease rates of subsidence and wetland loss. Our results also imply that the volume of sediment needed to rebuild GOM wetlands may currently fall within the low end of some restoration scenarios.
Field Measurements in the tidal bore of the Garonne River after a recent flood

A tidal bore is a natural phenomenon associated wit h the rising flood tide. Composed of surface waves, it may occur in estuaries and propagate up rivers. The pre sent study was conducted in the Garonne River (Fran ce) in the Arcins channel. Using an ADV unit and further recording equipments, experimental data are collected du ring a flat undular bore with a bore Froude number close t o unity. Velocity analysis and sediment characteris ation revel a slight rise in water elevation starting about 70 s prior to the front and a flow reversal about 50 s after the bore front. The turbulent transport of suspended sedimen t is presented in term of mass flux per unit area h ighlighting a negative (upriver) sediment mass transfer.
Melting history of the Patagonian Ice Sheet during Termination I inferred from marine sediments

Copyright © 2013 by The Geochemical Society of Japan. (e.g., McCulloch and Davies, 2001; Sugden et al., 2009). Knowledge of the timing of terminal deglaciation, as well as additional information from a southern site, will allow for a better understanding of the entire melting pattern for the PIS, which in turn will help constrain the overall deglacial sea level rise to up to approximately 130 m (Yokoyama et al., 2001). Therefore, to understand the timing of deglaciation in Patagonia from TI to present, we constructed a detailed radiocarbon chronology of sediment cores and performed high-resolution bulk sediment density measurements to calculate mass accumulation rates (MAR). We then estimated terrigenous input based on Al2O3 flux in sediments from the Magellanes fjord (53°S) and southern Patagonia (55°S: Drake Passage) over the past 12 and 31 kyr, respectively.
The interaction of self-leadership and psychological climate on job performance

The purpose of the present study was to examine the interactive effect of self-leadership and psychological climate on job performance and to evaluate the extent to which psychological climate facilitates or inhibits the demonstration of self-leadership on job performance. Hierarchical multiple regression analyses were conducted in a sample of 213 employees. The results clearly showed that the interaction between self-leadership and psychological climate explained an additional variance in job performance scores over and above the effects of self-leadership and psychological climate alone. Self-leadership was positively related to job performance among employees reporting high levels of psychological climate. Conversely, the relationship was nonexistent among employees reporting low levels of psychological climate. Implications for future research and practice are discussed. Key words: Self-leadership, psychological climate, job performance, Turkey.
A statistical analysis of trends for warm and cold spells in uppsala by means of counts

Abstract Statistical studies of extremes are of interest in the climatic sciences, in particular trends of periods of unusually warm or cold weather, which could be labelled warm and cold spells, respectively. We study the yearly number of spells in Uppsala, Sweden which from a data‐analytic point of view truly are counts, and employ theory and methods from the field of regression models for counts. A possible trend for the period 1840–2012 was investigated. The trend for warm spells is positive and demonstrated to be larger in magnitude compared with the one for cold spells, and is found to be statistically significant. The methodology could be extended to analyse other climate indicators.
Assessing the ecohydrological impact of incorporating perennial vegetation into an agricultural watershed in Central Iowa, USA

Iowa’s tallgrass prairies, the once dominant vegetation, were replaced by crops so that currently, only 0.1% of native prairies remain and approximately 80% of the land is dedicated to corn (Zea mays L.) and soybean (Glycine max (L.) Merr. ) production. This dramatic land use change has caused severe hydrological alterations (i.e. surface runoff, sediment and nutrient export) affecting the productivity and water quality of the region. In the last years, incorporation of prairie vegetation within agriculturally dominated watersheds has been demonstrated to have positive effects on restoring hydrologic balance by increasing soil water infiltration and nutrient stabilization. However, less attention has been given to the impact that plant water use from native perennial vegetation might also have on stabilizing hydrologic processes. This study aimed to increase our knowledge about water use patterns in native prairies and crops, at both the stand (evapotranspiration) and plant (transpiration) level, in order to enhance our understanding of the potential role of introduced prairie ecosystems on hydrologic regulation. To accomplish the objective, two field studies were conducted at the Neal Smith National Wildlife Refuge located in Central Iowa, and one study was conducted in the Forestry greenhouse at Iowa State University. Micrometeorological, thermometric and physiological techniques were used to measure plant water use rates and understand water use patterns. Overall, prairie vegetation exhibited higher evapotranspiration than crop fields early and late in the season, suggesting a higher efficacy by the former to increase the soil water storage capacity during typical wet springs, which would help to reduce runoff. At the plant level, transpiration of native prairie species higher responsiveness than crops to changes in soil water content and a significant increment in water uptake was
Investigating enhanced Aqua MODIS aerosol optical depth retrievals over the mid‐to‐high latitude Southern Oceans through intercomparison with co‐located CALIOP, MAN, and AERONET data sets

A band of enhanced aerosol optical depth (AOD) over the mid‐to‐high latitude Southern Oceans exists in some passive satellite‐based aerosol data sets, including Moderate Resolution Imaging Spectroradiometer (MODIS) products. Past studies suggest several potential causes contributing to this phenomenon, including signal uncertainty, retrieval bias, and cloud contamination. In this paper, quality‐assured Aqua MODIS aerosol products in this zonal band are investigated to assess cloud contamination as a cause. Spatially and temporally collocated cloud and aerosol products produced by the Cloud‐Aerosol Lidar with Orthogonal Polarization (CALIOP) project relative to Aqua MODIS AOD in this region are considered. Maritime Aerosol Network (MAN) and Aerosol Robotic Network (AERONET) AOD data are also collocated with Aqua MODIS retrievals for surface context. The results of this study indicate that the high Aqua MODIS AOD are not seen in the CALIOP aerosol products, cannot be screened using active profiling of collocated observations for cloud presence, and are not detected by ground‐based observations such as MAN and AERONET. Enhanced AOD values are attributable primarily to stratocumulus and low broken cumulus cloud contamination, as identified with CALIOP products. But these clouds explain only about 30–40% of the total anomaly. Cirrus cloud contamination is also a factor. However, in contrast to the rest of the globe, they contribute less overall, relative to low‐level liquid water clouds, which are considered likely the result of misidentification of relatively warm cloud tops compared with surrounding open seas.
Predicting mortality in nursing home residents with lower respiratory tract infection: The Missouri LRI Study.

CONTEXT Lower respiratory tract infection (LRI) is a leading cause of mortality and hospitalization in nursing home residents. Treatment decisions may be aided by a clinical prediction rule that identifies residents at low and high risk of mortality. OBJECTIVE To identify patient characteristics predictive of 30-day mortality in nursing home residents with an LRI. DESIGN, SETTING, AND PATIENTS Prospective cohort study of 1406 episodes of LRI in 1044 residents of 36 nursing homes in central Missouri and the St Louis, Mo, area between August 15, 1995, and September 30, 1998. MAIN OUTCOME MEASURE Thirty-day all-cause mortality. RESULTS Thirty-day mortality was 14.7% (n = 207). In a logistic analysis, using generalized estimating equations to adjust for clustering, we developed an 8-variable model to predict 30-day mortality, including serum urea nitrogen, white blood cell count, body mass index, pulse rate, activities of daily living status, absolute lymphocyte count of less than 800/microL (0.8 x 10(9)/L), male sex, and deterioration in mood over 90 days. In validation testing, the model exhibited reasonable discrimination (c =.76) and calibration (nonsignificant Hosmer-Lemeshow goodness-of-fit statistic, P =.54). A point score based on this model's variables fit to the entire data set closely matched observed mortality. Fifty-two percent of residents had low (score of 0-4) or relatively low (score of 5-6) predicted 30-day mortality, with 2.2% and 6.2% actual mortality, respectively. CONCLUSIONS Our model distinguishes nursing home residents at relatively low risk for mortality due to LRI. If independently validated, our findings could help physicians identify nursing home residents in need of different therapeutic approaches for LRI.
SPATIAL AND TEMPORAL VARIATIONS OF NUTRIENT LOADS IN OVERLAND FLOW AND SUBSURFACE DRAINAGE FROM A MARGINAL LAND SITE IN SOUTH-EAST IRELAND

Abstract:In Ireland, Food Harvest 2020 focuses on increasing productivity while enhancing environmental sustainability of agricultural land. On underutilised or marginal land, drainage systems may be installed to expand agricultural enterprises. Mixed nutrient losses are inevitable from any drainage system, but assessing processes leading to differences in nutrient speciation, fractionation and losses in grasslands between locations or flow paths is important to achieve sustainability. This study investigates these processes in overland flow and subsurface drains over three rainfall events from four non-grazed plots recently converted from marginal land in the south-east of Ireland. A shallower water table and smaller plot size resulted in greater water and nutrient losses in overland flow per unit of land area. Nutrient losses were less in subsurface drains. Dissolved organic nitrogen (DON) dominated, but dissolved inorganic nitrogen (DIN) was more abundant in the drains. Particulate phosphorus generally dominated in drains, except in plots with a shallow water table where dissolved unreactive phosphorus (DUP) was more abundant. In overland flow, a shallower water table resulted in a switch from dissolved reactive phosphorus (DRP) to DUP. Fertilisation increased phosphorus losses in overland flow, with DRP dominating. These results highlight the importance of an integrated assessment of the controls on flow and nutrient losses to design drainage systems in marginal lands.
Continental-Oceanic Crustal Transition Off Southwest Africa

More than 1,426 mi (2,300 km) of 48-trace, 12-fold seismic reflection profiles were used to examine the nature of the continent-ocean boundary off southwest Africa. South of the Orange River, faulted blocks, which we interpret as rifted continental crust, can be traced seaward to the 3 km isobath. The transition to oceanic basement occurs in a zone 19 to 25 mi (30 to 40 km) wide beneath the continental rise. Although structural details are obscured by a thick, seaward-dipping wedge of pre-AII (pre-late Early Cretaceous) overburden, oceanic crust at the presumed contact is not older than magnetic anomaly M9 (126 to 121 m.y.B.P.). North of the Orange River, a pronounced hinge in continental crust correlates with magnetic anomaly G of Rabinowitz (1976). Seaward of the hinge, a complex fault-block terrane is evident. Oceanic basement can not be traced with any certainty landward of anomaly M4. Intracontinental stretching and associated volcanism appear to have been important in the early history of the Cape Basin. Rifting and local dike intrusion may explain the presence of some lineated magnetic anomalies previously attributed to sea-floor spreading. Related extrusives form at least part of the pre-AII wedge just seaward of the hinge zone. Our interpretation of the seismic data suggests that the initiation of normal spreading in the Cape Basin postdates by 4 to 9 m.y. the Valanginian age derived from prevailing plate tectonic reconstructions of the South Atlantic.
Soil-vegetation-atmosphere interactions in the West African monsoon / Interactions entre le sol, la végétation et l'atmosphère dans la mousson ouest-africaine

The climate of West Africa is characterised by a monsoonal system that brings rainfall onto the subcontinent during an annual rainy season. From the late 60's to the mid-90's, rainfall levels significantly below average were observed, which brought severe socio-economic implications. The causes of the uncharacteristically long drought period, and indeed the mechanisms underpinning West African climate were poorly understood at the time, but have since attracted growing attention from the scientific community. Amongst the factors identified as critical is the interaction between the Earth surface and the atmosphere. To investigate these interactions over West Africa we have adopted an approach based upon regional climate modelling, an internationally recognised discipline enabling the representation of past and future climates, and the study of specific meteorological mechanisms. Using the regional climate model MAR, we have carried out simulations of the West African climate for the years 1986, 1987, and 1988. To improve the accuracy with which the model represents the biosphere, a new dataset describing the local vegetation was incorporated and a new scheme for the representation of roots implemented. A measure of the internal variability inherent to all results produced with this, and other such models, was determined. Subsequently, the influence of soil moisture anomalies on the model behaviour was investigated. The latest version of the model was validated by comparing it to observational data for selected years. Our results have prooven the ability of the improved MAR to simulate the West African climate, its monsoon and its spatial and temporal behaviour and provide strong evidence of its suitability for further investigation of the surface-atmosphere interactions over West Africa.
Resonance Energy Transfer

Resonance energy transfer, also known as Forster- or fluorescence- resonance energy transfer, or electronic energy transfer, is a photonic process whose relevance in many major areas of science is reflected both by a wide prevalence of the effect and through numerous technical applications. The process, operating through an optical near-field mechanism, effects a transport of electronic excitation between physically distinct atomic or molecular components, based on transition dipole-dipole coupling. In this chapter a comprehensive survey of the process is presented, beginning with an outline of the history and highlighting the early contributions of Perrin and Forster. A review of the photophysics behind resonance energy transfer follows, and then a discussion of some prominent applications of resonance energy transfer. Particular emphasis is given to analysis and sensing techniques used in molecular biology, ranging from the ‘spectroscopic ruler’ measurements of functional group separation, to fluorescence lifetime microscopy. The chapter ends with a description of the role of energy transfer in photosynthetic light harvesting.