Miracle-dz/UniFAR-FTUs huggingface dataset:
OzFlux data: network integration from collection to curation

Abstract. Measurement of the exchange of energy and mass between the surface and the atmospheric boundary-layer by the eddy covariance technique has undergone great change in the last 2 decades. Early studies of these exchanges were confined to brief field campaigns in carefully controlled conditions followed by months of data analysis. Current practice is to run tower-based eddy covariance systems continuously over several years due to the need for continuous monitoring as part of a global effort to develop local-, regional-, continental- and global-scale budgets of carbon, water and energy. Efficient methods of processing the increased quantities of data are needed to maximise the time available for analysis and interpretation. Standardised methods are needed to remove differences in data processing as possible contributors to observed spatial variability. Furthermore, public availability of these data sets assists with undertaking global research efforts. The OzFlux data path has been developed (i) to provide a standard set of quality control and post-processing tools across the network, thereby facilitating inter-site integration and spatial comparisons; (ii) to increase the time available to researchers for analysis and interpretation by reducing the time spent collecting and processing data; (iii) to propagate both data and metadata to the final product; and (iv) to facilitate the use of the OzFlux data by adopting a standard file format and making the data available from web-based portals. Discovery of the OzFlux data set is facilitated through incorporation in FLUXNET data syntheses and the publication of collection metadata via the RIF-CS format. This paper serves two purposes. The first is to describe the data sets, along with their quality control and post-processing, for the other papers of this Special Issue. The second is to provide an example of one solution to the data collection and curation challenges that are encountered by similar flux tower networks worldwide.
Interactions between nocturnal turbulent flux, storage and advection at an "ideal" eucalypt woodland site

Abstract. While the eddy covariance technique has become an important technique for estimating long-term ecosystem carbon balance, under certain conditions the measured turbulent flux of CO2 at a given height above an ecosystem does not represent the true surface flux. Profile systems have been deployed to measure periodic storage of CO2 below the measurement height, but have not been widely adopted. This is most likely due to the additional expense and complexity and possibly also the perception, given that net storage over intervals exceeding 24 h is generally negligible, that these measurements are not particularly important. In this study, we used a 3-year record of net ecosystem exchange of CO2 and simultaneous measurements of CO2 storage to ascertain the relative contributions of turbulent CO2 flux, storage, and advection (calculated as a residual quantity) to the nocturnal CO2 balance and to quantify the effect of neglecting storage. The conditions at the site are in relative terms highly favourable for eddy covariance measurements, yet we found a substantial contribution (∼ 40 %) of advection to nocturnal turbulent flux underestimation. The most likely mechanism for advection is cooling-induced drainage flows, the effects of which were observed in the storage measurements. The remaining ∼ 60 % of flux underestimation was due to storage of CO2. We also showed that substantial underestimation of carbon uptake (approximately 80 gC m−2 a−1, or 25 % of annual carbon uptake) arose when standard methods (u∗ filtering) of nocturnal flux correction were implemented in the absence of storage estimates. These biases were reduced to approximately 40–45 gC m−2 a−1 when the filter was applied over the entire diel period, but they were nonetheless large relative to quantifiable uncertainties in the data. Neglect of storage also distorted the relationships between the CO2 exchange processes (respiration and photosynthesis) and their key controls (light and temperature respectively). We conclude that the addition of storage measurements to eddy covariance sites with all but the lowest measurement heights should be a high priority for the flux measurement community.
Inorganic salts interact with oxalic acid in submicron particles to form material with low hygroscopicity and volatility

Abstract. Volatility and hygroscopicity are two key properties of organic aerosol components, and both are strongly related to chemical identity. While the hygroscopicities of pure salts, di-carboxylic acids (DCA), and DCA salts are known, the hygroscopicity of internal mixtures of these components, as they are typically found in the atmosphere, has not been fully characterized. Here we show that inorganic–organic component interactions typically not considered in atmospheric models can lead to very strongly bound metal–organic complexes and greatly affect aerosol volatility and hygroscopicity; in particular, the bi-dentate binding of DCA to soluble inorganic ions. We have studied the volatility of pure, dry organic salt particles and the hygroscopicity of internal mixtures of oxalic acid (OxA, the dominant DCA in the atmosphere) and a number of salts, both mono- and di-valent. The formation of very low volatility organic salts was confirmed, with minimal evaporation of oxalate salt particles below 75 °C. Dramatic increases in the cloud condensation nuclei (CCN) activation diameter for particles with di-valent salts (e.g., CaCl2) and relatively small particle volume fractions of OxA indicate that standard volume additivity rules for hygroscopicity do not apply. Thus small organic compounds with high O : C ratios are capable of forming low-volatility and very low hygroscopicity particles. Given current knowledge of the formation mechanisms of OxA and M–Ox salts, surface enrichment of insoluble M–Ox salts is expected. The resulting formation of an insoluble coating of metal-oxalate salts can explain low-particle hygroscopicities. The formation of particles with a hard coating could offer an alternative explanation for observations of glass-like particles without the need for a phase transition.
Atypical use of ALN inferior vena cava filters as protection devices prior to embolization of a large portosystemic shunt with Amplatzer Vascular Plugs and Glubran 2 cyanoacrylate glue.

Spontaneous portosystemic shunts usually develop as a result of portal hypertension caused by liver cirrhosis, and may subsequently lead to hepatic encephalopathy (1,2). In cases of severe portal hypertension, a part of the portal blood may reverse direction and pass through the portosystemic anastomoses into the systemic venous system.
Interactive comment on “ The pelagic microbial food web structure in Sanggou Bay , Yellow Sea : Spatial variation over four successive seasons ” by X

Problem N◦1 What is new is to address the structure of the microbial food web (MFW) as a complex system and as such, it is a systemic approach. This is different from considering separately relationships between two components independently of the others. It was natural to start from the relationship between HNF and heterotrophic prokaryotes (HP) abundances that was already well established. After establishing that a similar relationship existed between HP and 5 other components of the MFW, the common ground to these relationships was obviously HP. Indeed, HP permanently occupy the
Impacts of a decadal drainage disturbance on surface-atmosphere fluxes of carbon dioxide in a permafrost ecosystem

Abstract. Hydrologic conditions are a major controlling factor for carbon exchange processes in high-latitude ecosystems. The presence or absence of water-logged conditions can lead to significant shifts in ecosystem structure and carbon cycle processes. In this study, we compared growing season CO2 fluxes of a wet tussock tundra ecosystem from an area affected by decadal drainage to an undisturbed area on the Kolyma floodplain in northeastern Siberia. For this comparison we found the sink strength for CO2 in recent years (2013–2015) to be systematically reduced within the drained area, with a minor increase in photosynthetic uptake due to a higher abundance of shrubs outweighed by a more pronounced increase in respiration due to warmer near-surface soil layers. Still, in comparison to the strong reduction of fluxes immediately following the drainage disturbance in 2005, recent CO2 exchange with the atmosphere over this disturbed part of the tundra indicate a higher carbon turnover, and a seasonal amplitude that is comparable again to that within the control section. This indicates that the local permafrost ecosystem is capable of adapting to significantly different hydrologic conditions without losing its capacity to act as a net sink for CO2 over the growing season. The comparison of undisturbed CO2 flux rates from 2013–2015 to the period of 2002–2004 indicates that CO2 exchange with the atmosphere was intensified, with increased component fluxes (ecosystem respiration and gross primary production) over the past decade. Net changes in CO2 fluxes are dominated by a major increase in photosynthetic uptake, resulting in a stronger CO2 sink in 2013–2015. Application of a MODIS-based classification scheme to separate the growing season into four sub-seasons improved the interpretation of interannual variability by illustrating the systematic shifts in CO2 uptake patterns that have occurred in this ecosystem over the past 10 years and highlighting the important role of the late growing season for net CO2 flux budgets.
Estimates of (co)variance components and genetic parameters for growth traits in Suffolk lambs.

The study aimed to estimate the components of (co)variance and heritability for weights at birth (BW), weaning (WW) and 180 days of age (W180), as well as the average daily gains from birth to weaning (ADG1), birth to 180 days of age (ADG2) and weaning to 180 days of age (ADG3) in Suffolk sheep. Thus, three different single-trait animal models were fitted, considering the direct additive genetic effect (Model 1), the direct additive genetic and maternal permanent environmental effects (Model 2), and in Model 3, in addition to those in Model 2, the maternal additive genetic effect was included. After comparing models through the likelihood ratio test (LRT), model 3 was chosen as the most appropriate to estimate heritability for BW, WW and ADG1. Model 2 was considered as the best to estimate the coefficient of heritability for W180 and ADG2, and model 1 for ADG3. Direct heritability estimates were inflated when maternal effects were ignored. According to the most suitable models, the heritability estimates for BW, WW, W180, ADG1, ADG2 and ADG3 were 0.06, 0.08, 0.09, 0.07, 0.08 and 0.07, respectively, indicating low possibility of genetic gain through individual selection. The results show the importance of including maternal effects in the models to properly estimate genetic parameters even at post-weaning ages.
Altered Gene Expression in Prefrontal Cortex of a Fabry Disease Mouse Model

Fabry disease is an X-chromosome linked hereditary disease that is caused by loss of function mutations in the α-galactosidase A (α-Gal A) gene, resulting in defective glycolipid degradation and subsequent accumulation of globotriaosylceramide (Gb3) in different tissues, including vascular endothelial cells and neurons in the peripheral and central nervous system. We recently reported a differential gene expression profile of α-Gal A(−/0) mouse dorsal root ganglia, an established animal model of Fabry disease, thereby providing new gene targets that might underlie the neuropathic pain related symptoms. To investigate the cognitive symptoms experienced by Fabry patients, we performed one-color based hybridization microarray expression profiling of prefrontal cortex samples from adult α-Gal A(−/0) mice and age-matched wildtype controls, followed by protein-protein interaction and pathway analyses for the differentially regulated mRNAs. We found that from a total of 381 differentially expressed genes, 135 genes were significantly upregulated, whereas 246 genes were significantly downregulated between α-Gal A(−/0) mice and wildtype controls. Enrichment analysis for downregulated genes revealed mainly immune related pathways, including immune/defense responses, regulation of cytokine production, as well as signaling and transport regulation pathways. Further analysis of the regulated genes revealed a large number of genes involved in neurodegeneration. The current analysis for the first time presents a differential gene expression profile of central nervous system tissue from α-Gal A(−/0) mice, thereby providing novel knowledge on the deregulation and a possible contribution of gene expression to Fabry disease related brain pathologies.
Team dynamics during the delivery of a large-scale, engineered system

Coordinated collective action refers to the synchronized action of agents towards achieving a predefined set of goals. Such activity is at the core of a wide range of social challenges, from organizational dynamics to team performance. Focusing on the latter, a novel dataset that captures the planned efforts to deliver a large-scale, engineered system is introduced. In detail, this dataset is composed of a total of 271 unique individuals, responsible for the delivery of a total of 721 tasks spread across a period of 745 days. The focus of this analysis is on the collaboration network between individuals, captured by their co-assignment in the delivery of particular tasks, and their dynamical patterns. Results indicate that the delivery of some tasks depends on disproportionately large collaborations, making them intrinsically harder to manage compared to tasks which depend on small, or no, collaborations. Similarly, some tasks require a disproportionately diverse set of skills to be completed, further enhancing their intrinsic complexity. Shifting focus to the topology of the contribution network, an abrupt emergence, and subsequent contraction, of a single large cluster is observed. This phenomenon corresponds to the emergence of an increasingly large and cohesive team, and its subsequent decomposition. In addition, the evolution of this cluster tightly follows the number of active tasks, suggesting that large teams are a natural way to respond to increased workload. These findings provide new insight on the underlying team dynamics that govern coordinated collective activity in general, and in the context of project delivery specifically.
Point Cloud Segmentation Using Hierarchical Tree for Architectural Models

Over the past few years, gathering massive volume of 3D data has become straightforward due to the proliferation of laser scanners and acquisition devices. Segmentation of such large data into meaningful segments, however, remains a challenge. Raw scans usually have missing data and varying density. In this work, we present a simple yet effective method to semantically decompose and reconstruct 3D models from point clouds. Using a hierarchical tree approach, we segment and reconstruct planar as well as non-planar scenes in an outdoor environment. This tree uses an exclusive energy function and a 3D convolutional neural network, HollowNets, to classify the segments. We test the efficacy of our proposed approach on a variety of complex real and synthetic data samples, obtaining an improvement of 7.9% in mean IOU over the state of the art approaches.
Reviews and syntheses: Australian vegetation phenology: new insights from satellite remote sensing and digital repeat photography

Abstract. Phenology is the study of periodic biological occurrences and can provide important insights into the influence of climatic variability and change on ecosystems. Understanding Australia's vegetation phenology is a challenge due to its diverse range of ecosystems, from savannas and tropical rainforests to temperate eucalypt woodlands, semi-arid scrublands, and alpine grasslands. These ecosystems exhibit marked differences in seasonal patterns of canopy development and plant life-cycle events, much of which deviates from the predictable seasonal phenological pulse of temperate deciduous and boreal biomes. Many Australian ecosystems are subject to irregular events (i.e. drought, flooding, cyclones, and fire) that can alter ecosystem composition, structure, and functioning just as much as seasonal change. We show how satellite remote sensing and ground-based digital repeat photography (i.e. phenocams) can be used to improve understanding of phenology in Australian ecosystems. First, we examine temporal variation in phenology on the continental scale using the enhanced vegetation index (EVI), calculated from MODerate resolution Imaging Spectroradiometer (MODIS) data. Spatial gradients are revealed, ranging from regions with pronounced seasonality in canopy development (i.e. tropical savannas) to regions where seasonal variation is minimal (i.e. tropical rainforests) or high but irregular (i.e. arid ecosystems). Next, we use time series colour information extracted from phenocam imagery to illustrate a range of phenological signals in four contrasting Australian ecosystems. These include greening and senescing events in tropical savannas and temperate eucalypt understorey, as well as strong seasonal dynamics of individual trees in a seemingly static evergreen rainforest. We also demonstrate how phenology links with ecosystem gross primary productivity (from eddy covariance) and discuss why these processes are linked in some ecosystems but not others. We conclude that phenocams have the potential to greatly improve the current understanding of Australian ecosystems. To facilitate the sharing of this information, we have formed the Australian Phenocam Network ( http://phenocam.org.au/ ).
Thermodynamic efficiency of contagions: a statistical mechanical analysis of the SIS epidemic model

We present a novel approach to the study of epidemics on networks as thermodynamic phenomena, quantifying the thermodynamic efficiency of contagions, considered as distributed computational processes. Modelling SIS dynamics on a contact network statistical-mechanically, we follow the maximum entropy (MaxEnt) principle to obtain steady-state distributions and derive, under certain assumptions, relevant thermodynamic quantities both analytically and numerically. In particular, we obtain closed-form solutions for some cases, while interpreting key epidemic variables, such as the reproductive ratio of a SIS model, in a statistical mechanical setting. On the other hand, we consider configuration and free entropy, as well as the Fisher information, in the epidemiological context. This allowed us to identify criticality and distinct phases of epidemic processes. For each of the considered thermodynamic quantities, we compare the analytical solutions informed by the MaxEnt principle with the numerical estimates for SIS epidemics simulated on Watts–Strogatz random graphs.
Intracerebral Hemorrhage Due to Intravenous Thrombolytic Treatment in Acute Ischemic Stroke

OBJECTIVE: Acute ischemic stroke is an emergency which can be treated by intravenous thrombolytic treatment in the first 4.5 hours. The most important complication effecting prognosis of intravenous thrombolysis is the symptomatic intracerebral hemorrhage. The aim of our study is to determine the risk factors of intracerebral hemorrhage due to intravenous thrombolytic treatment. METHODS: In our study, 12 patients with intracerebral hemorrhage due to intravenous thrombolytic therapy hospitalized in Neurological Intensive Care Unit between 2009-2014 were revised retrospectively. RESULTS: Twelve patients who had intracerebral hemorrhage due to thrombolytic treatment were included. Nine of the cases (75.0%) had asymptomatic intracerebral hemorrhage, whilst 3 (% 25.0) had symptomatic intracerebral hemorrhage. CONCLUSION: There were many studies aiming to put forth the risk of intracerebral hemorrhage associated with intravenous thrombolytic therapy. Advanced age, body weight > 95 kg, the history of diabetes mellitus and hypertension, the use of antiaggregant agents, symptom-treatment interval, hyperglycemia at the time of arrival, high value of the National Institutes of Health Stroke Scale, the presence of dense artery in first cranial computerized tomography, the size of the ischemic infarct were determined as risk factors. Also, our results showed that hyperglycemia and high blood pressure was associated with parenchymal hemorrhage.
Biosensors in Antimicrobial Drug Discovery: Since Biology until ScreeningPlatforms

Antimicrobial drug resistance is a current public health problem, which is compounded by the misuse of antibiotics in medical practice and the emergence of Multidrug-Resistant (MDR) microorganisms. Therefore it is necessary to develop new anti-infective drugs and implement new methodologies able to establish the Antimicrobial Susceptibility (AST) in field and the point-of-care. In this sense biosensors is a promising technology that can detect MDR strains and small molecules in various samples, these devices have the advantages that can be miniaturized for obtain portability, rapidity, and cost-effectiveness. The aim of this work is to present the applications of biosensors technology in antimicrobial drug discovery, since cell based biosensors and cell culture on chips, considering metabolic interactions of the microbial world and the pharmacological response to be inhibited by compounds with promising activity with the end of design antimicrobial drug screening platforms robust, automatable and reproducible.
Glucosamine Enhances Tissue Regeneration In The Process Of Wound Healing In Rats As Animal Model; A Stereological Study

Introduction: Glucosamine (GA), a water soluble hexosamine made from chitin or chitosan, was showed to have stimulatory effect on matrix formation, enhancing inflammatory response, modulating hyaluronic acid synthesis which promotes extracellular matrix remodeling leading to better wound healing. GA was also shown to have antioxidant and immunomodulatory effect which play roles in wound healing process. In this study we aimed to determine the effect of topical administration of GA on wound healing process in rats as animal model. Material and methods: 36 Wistar rats were divided into 3 groups; the control group which received no treatment; the Glucosamine group that received GA gel with 2% GA concentration, and the Base group that was treated with the vehicle. A 1 cm full-thickness wound was created on the posterior of each rat’s neck. Treatments took place every 24 hours for 15 days. The wound closure rate, volume density of collagen bundles and vessels, fibroblast population, length density and mean diameter of the vessels were estimated by using unbiased stereological and histomorphometrical methods. Results: GA enhanced the wound closure rate consequently as well as fibroblast proliferation, collagen synthesis and proliferation of hair follicles in contrast with the base and the control group. Although not statistically significant, GA also improved the revascularization process in the wound site. Conclusion: Results of this study indicate that GA has the potential for being used for treatment of skin wounds; however, still further evaluations on its mechanisms of action and clinical advantages and disadvantages should be performed.