Miracle-dz/UniFAR-FTUs huggingface dataset:
Crop biomass estimation using multi regression analysis and neural networks from multitemporal L-band polarimetric synthetic aperture radar data

ABSTRACT Biomass has a direct relationship with agricultural production and may help to predict crop yield. Earth observation technology can contribute significantly to monitoring given the availability of temporally frequent and high-resolution radar or optical satellite data. Polarimetric Synthetic Aperture Radar (PolSAR) has several advantages for operational monitoring given that at these longer wavelengths atmospheric and illumination conditions do not affect acquisitions and considering the sensitivity of microwaves to the structural properties of targets. Therefore, SARs are a promising source of data for crop mapping and monitoring. With increasing access to SARs the development of robust methods to monitor crop productivity is timely. In this paper, we examine the use of machine learning and artificial intelligence approaches to analyze a time series of Polarimetric parameters for crop biomass estimation. In total, 14 polarimetric parameters from a time series of Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) airborne L-band data were used for biomass estimation for an intensively cropped site in western Canada. Then, Multiple linear regression (MR) and artificial neural network (ANN) models were developed and evaluated to estimate the biomass for canola, corn, and soybeans. According to the experimental results, the ANN provided more accurate biomass estimates compared to MR. Canola biomass, in general, showed less sensibility to almost all the polarimetric parameters. Nevertheless, Freeman-Double combined with vertical-vertical backscattering (VV) delivered the correlation coefficient (r) of 0.72, and the root mean square error (RMSE) of 56.55 g m−2of canola biomass. For corn, the highest correlation was observed between a pairing of horizontal- horizontal backscattering (HH) with Entropy (H) for biomass estimation yielding an r of 0.92 and RMSE of 196.71 g m−2. Horizontal-vertical backscattering (HV) and Yamaguchi-Surface (O Y) delivered the highest sensitivity for soybeans (r of 0.82 and RMSE of 13.48 g m−2). If all crops are pooled, H combined with O Y provided the most accurate estimates of biomass (r of 0.89 and RMSE of 135.31 g m−2). These results demonstrated that models which make use of polarimetric parameters that characterize the multiple sources of scattering typical of vegetation canopies can be used to estimate crop biomass accurately. Such results bode well for agricultural monitoring considering the increasing number of satellite SAR sensors with various frequencies, imaging modes and revisit times. As such, the time series analysis and methods proposed in this study could be used to monitor crop development and productivity using SAR space technologies.
Guidelines for health and welfare monitoring of fish used in research

The aim of this paper is to provide background material necessary for the development of international guidelines for the health and welfare monitoring of fish used in research. It provides an overview of present guidelines and discusses why more detailed and species-specific guidelines are needed. A major issue within fish research is to document the situation today and point out areas where improvements are needed.
Animation of Deformable Models Using Implicit Surfaces

The paper presents a general approach for designing and animating complex deformable models with implicit surfaces. Implicit surfaces are introduced as an extra layer coating any kind of structure that moves and deforms over time. Offering a compact definition of a smooth surface around an object, they provide an efficient collision detection mechanism. The implicit layer deforms in order to generate exact contact surfaces between colliding bodies. A simple physically based model approximating elastic behavior is then used for computing collision response. The implicit formulation also eases the control of the object's volume with a new method based on local controllers. We present two different applications that illustrate the benefits of these techniques. First, the animation of simple characters made of articulated skeletons coated with implicit flesh exploits the compactness and enhanced control of the model. The second builds on the specific properties of implicit surfaces for modeling soft inelastic substances capable of separation and fusion that maintain a constant volume when animated.
Protective vaccination with a recombinant fragment of Clostridium botulinum neurotoxin serotype A expressed from a synthetic gene in Escherichia coli

A completely synthetic gene encoding fragment C, a approximately 50-kDa fragment, of botulinum neurotoxin serotype A was constructed from oligonucleotides. The gene was expressed in Escherichia coli, and full-sized product was produced as judged by Western blot (immunoblot) analysis. Crude extracts of E. coli expressing the gene were used to vaccinate mice and evaluate their survival against challenge with active toxin. Mice given three subcutaneous vaccinations were protected against an intraperitoneal administration of 10(6) 50% lethal doses (ID50) of serotype A toxin. The same mice survived when challenged with 3 LD50 of botulinum toxin serotype E but died when challenged with 10 LD50 of serotype E or 3 LD50 of serotype B. Purified fragment C was compared with the botulinum toxoid vaccine in a vaccination and challenge study. Fragment C was as efficacious in protecting against challenge with active botulinum neurotoxin serotype A as the toxoid vaccine. This recombinant protein product has many properties that make it a good candidate for human use to protect against botulinum toxin.
Combining Formal and Distributional Models of Temporal and Intensional Semantics

We outline a vision for computational semantics in which formal compositional semantics is combined with a powerful, structured lexical semantics derived from distributional statistics. We consider how existing work (Lewis and Steedman, 2013) could be extended with a much richer lexical semantics using recent techniques for modelling processes (Scaria et al., 2013)—for example, learning that visiting events start with arriving and end with leaving. We show how to closely integrate this information with theories of formal semantics, allowing complex compositional inferences such as is visiting! has arrived in but will leave, which requires interpreting both the function and content words. This will allow machine reading systems to understand not just what has happened, but when.
Use of Phosphate Solubilizing Bacteria to Leach Rare Earth Elements from Monazite-Bearing Ore

Abstract: In the present study, the feasibility to use phosphate solubilizing bacteria (PSB) to develop a biological leaching process of rare earth elements (REE) from monazite-bearing ore was determined. To predict the REE leaching capacity of bacteria, the phosphate solubilizing abilities of 10 species of PSB were determined by halo zone formation on Reyes minimal agar media supplemented with bromo cresol green together with a phosphate solubilization test in Reyes minimal liquid media as the screening studies. Calcium phosphate was used as a model mineral phosphate. Among the test PSB strains, Pseudomonas fluorescens , P. putida , P. rhizosphaerae , Mesorhizobium ciceri , Bacillus megaterium , and Acetobacter aceti formed halo zones, with the zone of A. aceti being the widest. In the phosphate solubilization test in liquid media, Azospirillum lipoferum , P. rhizosphaerae , B. megaterium , and A. aceti caused the leaching of 6.4%, 6.9%, 7.5%, and 32.5% of calcium, respectively. When PSB were used to leach REE from monazite-bearing ore, ~5.7 mg/L of cerium (0.13% of leaching efficiency) and ~2.8 mg/L of lanthanum (0.11%) were leached by
Uptake and Tolerance of Chemotherapy in Elderly Patients with Small Cell Lung Cancer and Impact on Survival

The treatment of elderly cancer patients is complicated by many factors. We sought to assess the uptake and tolerance of chemotherapy among patients 75 years and older diagnosed with small cell lung cancer (SCLC) in years 2004–2008 in Alberta, Canada, and assess their survival. All patients who met the above criteria and had an oncologist-consult were included. Data were obtained from the Alberta Cancer Registry and chart review. A total of 171 patients were included in the study, 117 (68%) of whom began chemotherapy. Of those, 52% completed all cycles, 66% did not have any dose reductions, and 31% completed all cycles at the recommended dose. The risk of death for patients who did not complete all cycles of chemotherapy was 2.72 (95% CI: 1.52–4.87) and for those who completed all cycles but with a reduced dose was 1.02 (95% CI: 0.57–1.82) relative to those who completed chemotherapy at full dose after adjusting for several demographic/clinical factors. Our results suggest that a significant proportion of elderly patients are able to tolerate chemotherapy and receive a survival benefit from it while those who experience toxicity may receive a survival benefit from a reduction in chemotherapy dose as opposed to stopping treatment.
Visual Long-Term Memory Has the Same Limit on Fidelity as Visual Working Memory

Visual long-term memory can store thousands of objects with surprising visual detail, but just how detailed are these representations, and how can one quantify this fidelity? Using the property of color as a case study, we estimated the precision of visual information in long-term memory, and compared this with the precision of the same information in working memory. Observers were shown real-world objects in random colors and were asked to recall the colors after a delay. We quantified two parameters of performance: the variability of internal representations of color (fidelity) and the probability of forgetting an object’s color altogether. Surprisingly, the fidelity of color information in long-term memory was comparable to the asymptotic precision of working memory. These results suggest that long-term memory and working memory may be constrained by a common limit, such as a bound on the fidelity required to retrieve a memory representation.
Evidence, ethics, hubris and the future of second-hand smoke policy

Smoke-free workplaces and public places—the ongoing debate The news that French bars and restaurants will be smoke free by the end of 2007 led to hundreds of headlines, impelled by a “myth turned on its head” subtext. The tedious cliche that every second French citizen’s birthright requires them to sit in cafes smoking Gauloises and sipping pastis while reading Jean-Paul Sartre is about as accurate today as the view that Ireland is a nation of potato diggers or that all Italians obey the Pope’s dictums on contraception. Smokers have long been a minority in all three of these countries. Nonetheless, an “if they can, anyone can” incredulity has made these three nations’ decisions to ban smoking in bars globally newsworthy. Californian leadership was vital, but discounted by reasoning that alluded to their reputation for having all sorts of eccentric proclivities when it comes to diet and health. If, as expected, France follows the Irish and Italian experience with only minor enforcement problems and failure of the bar economy to collapse,1,2 doomsayers in the tobacco industry and its third-party acolytes will surely have nowhere to turn in halting the global domino effect. But there are worrying signs in the euphoria of what has now become almost predictable, repeated policy success. A small minority on the fringe of tobacco control are starting to hand hostages to fortune and abandon the sacrosanct ethical3 and evidence-based principles that underpin all good public health policy. The global push for smoke-free workplaces and public spaces was built on a bedrock of research about second-hand smoke (SHS) being harmful. Door-stopper-sized review volumes4 have synthesised this evidence, which has, with rare exceptions, been gathered from studying those who have been chronically …
Predicting Restenosis of Drug-Eluting Stents Placed in Real-World Clinical Practice: Derivation and Validation of a Risk Model From the EVENT Registry

Background—Prediction of restenosis after percutaneous coronary intervention (PCI) remains challenging, and existing risk assessment algorithms were developed before the widespread adoption of drug-eluting stents (DES). Methods and Results—We used data from the EVENT registry to develop a risk model for predicting target lesion revascularization (TLR) in 8829 unselected patients undergoing DES implantation between 2004 and 2007. Using a split-sample validation technique, predictors of TLR at 1 year were identified from two thirds of the subjects (derivation cohort) using multiple logistic regression. Integer point values were created for each predictor, and the summed risk score (range, 0 to 10) was applied to the remaining sample (validation cohort). At 1 year, TLR occurred in 4.2% of patients, and after excluding stent thrombosis and early mechanical complications, the incidence of late TLR (more likely representing restenosis-related TLR) was 3.6%. Predictors of TLR were age <60, prior PCI, unprotected left main PCI, saphenous vein graft PCI, minimum stent diameter ⩽2.5 mm, and total stent length ≥40 mm. Comparison of observed versus predicted rates of TLR according to risk score demonstrated good model fit in the validation set. There was more than a 3-fold difference in TLR rates between the lowest risk category (score=0; TLR rate, 2.2%) and the highest risk category (score ≥5; TLR rate, 7.5%). Conclusions—The overall incidence of TLR remains low among unselected patients receiving DES in routine clinical practice. A simple risk model incorporating 6 readily available clinical and angiographic variables helps identify individuals at extremely low (<2%) and modestly increased (>7%) risk of TLR after DES implantation.
A study of how ICT capabilities can influence dynamic capabilities

Purpose – Prior studies have argued that small firms with dynamic capabilities can revise and reconfigure their internal resources to meet the uncertainties of their business environment. However, there is a lack of understanding of how they can develop such critical capabilities. The purpose of this paper is to propose that small firms can employ information and communication technology (ICT) capabilities as a facilitator for developing dynamic capabilities. Thus, the study builds on resource-based view (RBV) literature and information systems (IS) literature by examining the influence of ICT capabilities on the dynamic capabilities of small firms. Design/methodology/approach – Several hypotheses were tested by analysing the survey data from 291 small high-technology firms in Sweden. Findings – The results reveal that ICT capabilities influence dynamic capabilities of small firms. More specifically, the ICT use for internal efficiency positively influences adoptive capabilities, collaborative use of ICT .
Study on the Apoptosis Mechanism Induced by T-2 Toxin

T-2 toxin is known to induce apoptosis in mammalian cells. The mechanism of apoptosis induced by T-2 toxin has been proposed to be linked with oxidative stress and mitochondrial pathway. In the current study, the toxic effect of T-2 on Hela, Bel-7402, and Chang liver cells was examined in dose-dependent and time-dependent manner by MTT assay. Caspase-3 was found to be up-regulated under T-2 toxin stress, which suggested that T-2 toxin induced cell apoptosis. Endogenous GSH and MDA levels in all three cell lines were found down- and up-regulated respectively, which indicated the link between toxic effect of T-2 toxin and intracellular oxidative stress. It was also found by MTT assay that NAC, which maintained the level of GSH in cells, could protect cells from death. Western-blot result showed that the level of both activated Caspase-8 and Caspase-9 increased when cells were treated by T-2 toxin. Caspase-9 was found to be activated earlier than Caspase-8. It was also found that p53 was up-regulated under T-2 toxin stress in the study. These results implied that the effect of T-2 toxin on cells was apoptosis rather than necrosis, and it was probably induced through mitochondrial pathway. To the best of our knowledge, the present study is the first to show that JunD is down-regulated in T-2 toxin induced apoptosis. By construction of an over-expression vector for the JunD gene, we observed that the survival ratio of JunD over-expressed cells obviously increased under T-2 toxin stress. These results suggested that the mechanism of T-2 induced cell death was closely connected with oxidative stress, and that JunD plays an important role in the defensive process against T-2 toxin stress.
The Protective Mechanism of Fluorofenidone in Renal Interstitial Inflammation and Fibrosis

Background:Deregulated inflammation has been implicated in the development of renal interstitial fibrosis and progressive renal failure. Previous work has established that fluorofenidone, a pyridone agent, attenuates renal fibrosis. However, the mechanism by which fluorofenidone prevents renal fibrosis remains unclear. The aim of this study was to investigate the in vivo effects of fluorofenidone on unilateral ureteral obstruction–induced fibrosis and the involved molecular mechanism in mouse peritoneal macrophages. Methods:Renal fibrosis was induced in rat by unilateral ureteral obstruction for 3, 7 or 14 days. Ipsilateral kidneys were harvested for morphologic analysis. Leukocyte infiltration was assessed by immunohistochemistry staining. The expression of chemokines (MCP-1, RANTAS, IP-10, MIP-1&agr; and MIP-1&bgr;) and pro-inflammatory cytokines (TNF-&agr; and IL-1&bgr;) was measured by enzyme-linked immunosorbent assay and real-time polymerase chain reaction. Mouse peritoneal macrophages and HK-2 cells were incubated with necrotic MES-13 cells or TNF-&agr; in the presence or absence of fluorofenidone. The production of MCP-1 was measured by enzyme-linked immunosorbent assay, and phosphorylation of ERK1/2, p38 and JNK was quantified by Western blot. Results:Fluorofenidone treatment hampered renal pathologic change and interstitial collagen deposition. Leukocyte infiltration and the expression of chemokines (MCP-1, RANTES, IP-10, MIP-1&agr; and MIP-1&bgr;) and pro-inflammatory cytokines (IL-1&agr;) in kidney were significantly reduced by fluorofenidone treatment. Mechanistically, fluorofenidone significantly inhibited TNF-&agr; or necrotic cell–induced activation of MAP kinase pathways in vitro. Conclusions:Fluorofenidone serves as a novel anti-inflammatory agent that attenuates ureteral obstruction-induced renal interstitial inflammation and fibrosis, possibly through the inhibition of the microtubule-associated protein kinase pathways.
Design of parallel transmission radiofrequency pulses robust against respiration in cardiac MRI at 7 Tesla

Two‐spoke parallel transmission (pTX) radiofrequency (RF) pulses have been demonstrated in cardiac MRI at 7T. However, current pulse designs rely on a single set of B1+/B0 maps that may not be valid for subsequent scans acquired at another phase of the respiration cycle because of organ displacement. Such mismatches may yield severe excitation profile degradation.
Evaluation of Potential Reference Genes for Relative Quantification by RT-qPCR in Different Porcine Tissues Derived from Feeding Studies

Five potential reference genes for RT-qPCR application, namely histone H3, beta-actin, GAPDH, ubiquitin and 18S rRNA, were evaluated for normalization of gene expression in four selected tissues (liver, kidney, thyroid and abdominal fat). Tissues were derived from fattening pigs exposed to different amounts and type of dietary iodine. Two software applications (geNorm and NormFinder) were used to evaluate the stability of the potential reference genes. All studied genes displayed high expression stability but different stability patterns between the investigated tissues. The results suggest GAPDH and 18S rRNA as reference genes applicable in all tissues investigated. Beta-actin and histone H3 are suitable reference genes for all tissues investigated except fat. In contrast, ubiquitin should be excluded from use as a reference gene in the porcine tissues analyzed due to variations in expression levels, despite the good expression stability.
Shiga Toxin Is Transported from the Endoplasmic Reticulum following Interaction with the Luminal Chaperone HEDJ/ERdj3

ABSTRACT Shiga toxin (Stx) follows a complex intracellular pathway in order to kill susceptible cells. After binding to cell surface glycolipids, the toxin is internalized and trafficked in retrograde fashion to the endoplasmic reticulum (ER). From the ER lumen, the toxin must gain access to the cytoplasm, where it enzymatically inactivates the 28S rRNA, inhibiting protein synthesis. The host molecules involved in this pathway and the mechanisms utilized by the toxin to access the cytoplasm from the ER are largely unknown. We found that Stx is capable of energy-dependent transport across the ER lumen, as has recently been demonstrated for the cholera and ricin toxins. Genetic screening for molecules involved in Shiga toxin trafficking yielded a cDNA encoding a prematurely truncated protein. Characterization of this cDNA revealed that it encodes a novel Hsp40 chaperone, designated HEDJ or ERdj3, localized to the ER lumen, where it interacts with BiP, a molecule known to be involved in protein retrotranslocation out of the ER. We demonstrated that within the ER lumen Stx interacts with HEDJ and other chaperones known to be involved in retrotranslocation of proteins across the ER membrane. Moreover, sequential immunoprecipitation revealed that Shiga toxin was present in a complex that included HEDJ and Sec61, the translocon through which proteins are retrotranslocated to the cytoplasm. These findings suggest that HEDJ is a component of the ER quality control system and that Stx utilizes HEDJ and other ER-localized chaperones for transport from the ER lumen to the cytosol.
Symbolic Modeling of Genetic Regulatory Networks

Understanding the functioning of genetic regulatory networks supposes a modeling of biological processes in order to simulate behaviors and to reason on the model. Unfortunately, the modeling task is confronted to incomplete knowledge about the system. To deal with this problem we propose a methodology that uses the qualitative approach developed by Thomas. A symbolic transition system can represent the set of all possible models in a concise and symbolic way. We introduce a new method based on model-checking techniques and symbolic execution to extract constraints on parameters leading to dynamics coherent with known behaviors. Our method allows us to efficiently respond to two kinds of questions: is there any model coherent with a certain hypothetic behavior? Are there behaviors common to all selected models? The first question is illustrated with the example of the mucus production in Pseudomonas aeruginosa while the second one is illustrated with the example of immunity control in bacteriophage lambda.
Vision based fuzzy control autonomous landing with UAVs: From V-REP to real experiments

This paper is focused on the design of a vision based control approach for the autonomous landing task of Vertical Take-off and Landing (VTOL) Unmanned Aerial Vehicles (UAVs). Here is presented the setup of a simulated environment developed in V-REP connected to ROS, and its uses for tuning a vision based control approach. In this work, a Fuzzy control approach was proposed to command the UAV's vertical, longitudinal, lateral and orientation velocities. The UAV's pose estimation was done based on a vision algorithm and the knowledge of the landing target. Real experiments with a quadrotor landing in a moving platform are also presented.