Miracle-dz/UniFAR-FTUs huggingface dataset:
The influence of fire and livestock grazing on the assemblage of non-flying small mammals in grassland-Araucaria Forest ecotones, southern Brazil

Grazing and fire, used in pasture regeneration practices, are inter-related activities in livestock management. Both activities affect habitat characteristics by changing the structure of the herbaceous and shrubby vegetation, reducing their biomass and litter cover. This study evaluated the effect of fire and livestock grazing on the assemblage of non-flying small mammals in grassland-Araucaria forest ecotones in southern Brazil. We compared four areas frequently affected by livestock management with four protected areas. Surveys were carried out in four sampling periods, one in each season of 2004. We captured a total of 325 individuals from 12 species of rodents - Akodon montensis Thomas, 1913, Akodon paranaensis Christoff, Fagundes, Sbalqueiro, Mattevi e Yonenaga-Yassuda, 2000, Akodon sp. 1, Akodon sp. 2 (2n = 34), Brucepattersonius iheringi (Thomas, 1896), Delomys dorsalis (Hensel, 1872), Oligoryzomys flavescens (Waterhouse, 1837), Oligoryzomys nigripes (Olfers, 1818), Oxymycterus nasutus (Waterhouse, 1837), Scapteromys sp. (2n = 34), Sooretamys angouya (Fischer, 1814) and Thaptomys nigrita (Lichtenstein, 1829) - and two species of marsupials - Monodelphis dimidiata (Wagner, 1847) and Philander frenatus (Olfers, 1818) -, in a total effective effort of 5254 traps.day-1. The abundance, biomass and diversity of non-flying small mammals were significantly higher in the protected areas than in those affected by fire and livestock grazing. Species strictly associated with grassland habitats were not found in the impacted area. These results indicate that the presence of herds of domestic ungulates negatively affect the assemblage of non-flying small mammals in grassland and Araucaria forest areas in southern Brazil.
Bayesian adaptive stimulus selection for dissociating models of psychophysical data

Comparing models facilitates testing different hypotheses regarding the computational basis of perception and action. Effective model comparison requires stimuli for which models make different predictions. Typically, experiments use a predetermined set of stimuli or sample stimuli randomly. Both methods have limitations; a predetermined set may not contain stimuli that dissociate the models whereas random sampling may be inefficient. To overcome these limitations, we expanded the psi-algorithm (Kontsevich & Tyler, 1999) from estimating the parameters of a psychometric curve to distinguishing models. To test our algorithm, we applied it to two distinct problems. First, we investigated dissociating sensory noise models. We simulated ideal observers with different noise models performing a 2-afc task. Stimuli were selected randomly or using our algorithm. We found using our algorithm improved the accuracy of model comparison. We also validated the algorithm in subjects by inferring which noise model underlies speed perception. Our algorithm converged quickly to the model previously proposed (Stocker & Simoncelli, 2006), whereas if stimuli were selected randomly model probabilities separated slower and sometimes supported alternative models. Second, we applied it to a different problem; comparing models of target selection under body acceleration. Previous work found target choice preference is modulated by whole body acceleration (Rincon-Gonzalez et al., 2016). However, the effect is subtle making model comparison difficult. We show that selecting stimuli adaptively could have led to stronger conclusions in model comparison. We conclude that our technique is more efficient and more reliable than current methods of stimuli selection for dissociating models. Data Availability All data and code will be posted on our institutional repository system following acceptance. In the meantime feel free to contact the authors if you would like any of the code.
Graal IR : An Extensible Declarative Intermediate Representation

We present an intermediate representation (IR) for a Java just in time (JIT) compiler written in Java. It is a graph-based IR that models both control-flow and data-flow dependencies between nodes. We show the framework in which we developed our IR. Much care has been taken to allow the programmer to focus on compiler optimization rather than IR bookkeeping. Edges between nodes are declared concisely using Java annotations, and common properties and functions on nodes are communicated to the framework by implementing interfaces. Building upon these declarations, the graph framework automatically implements a set of useful primitives that the programmer can use to implement optimizations.
Asymptotics in percolation on high‐girth expanders

We consider supercritical bond percolation on a family of high‐girth d ‐regular expanders. The previous study of Alon, Benjamini and Stacey established that its critical probability for the appearance of a linear‐sized (“giant”) component is pc=1/(d−1) . Our main result recovers the sharp asymptotics of the size and degree distribution of the vertices in the giant and its 2‐core at any p>pc . It was further shown in the previous study that the second largest component, at any 0
Artificial Intelligence in Biological Data

Artificial Intelligence (AI) or Machine learning in present era serves as the primary choice for data mining and big data analysis. With effective learning and adaptation model, it provides solutions to several engineering applications. These include techniques such as Artificial Neural Network modelling, Reasoning based decision algorithms, Simulation models, DNA computing and Quantum computing among several others. With the application of AI in Biomedical research, the fuzziness and randomness in handling such type of data has significantly reduced. Rapid technological advancements have helped AI techniques evolve in manner which promotes handling such fuzzy data effectively and much more conveniently. The review presents a comprehensive view of machine learning and AI computing models, advanced data analytics and optimisation approaches used in Bioengineering such as Drug Designing and Analysis, Medical imaging, biologically inspired learning and adaption for analytics, etc.
Physicochemical features of rhodanese: A review

Rhodanese is a multifunctional, mitochondrial, sulphur transferase that catalyses the detoxification of cyanide by sulphuration in a double displacement (ping pong) mechanistic reaction. It is widely distributed occurring in varieties of plants and animals, where it activity is modulated by a number of factors including differences in species, organs, sex, age and diet. The enzyme is a single polypeptide chain of 289 amino acids with molecular weight of up to 37,000. The active site of rhodanese contains a tryptophanyl residue in close proximity with an essential sulphahydryl group. Many methods for assaying rhodanese have been reported, the most prominent being the one based on the colorimetric estimation of thiocyanate formed from the reaction of cyanide and thiosulphate, catalysed by rhodanese.
Integration of DEMATEL, ANP and DEA methods for third party logistics providers’ selection

Article history: Received October 28, 2015 Received in revised format November 28, 2015 Accepted March 22, 2016 Available online March 24, 2016 In a competitive environment many companies usually outsource their logistics functions to the Third Party Logistics (TPL) providers to focus on their core businesses. However, the selection of proper TPL provider is not an easy task because of conflicting quantitative and qualitative criteria. This study presents an integrated model based on three well-known methods Decision Making Trial and Evaluation Laboratory (DEMATEL), Analytical Network Process (ANP) and Data Envelopment Analysis (DEA) for the evaluation and selection of TPL providers. DEMATEL computes the effects between selection criteria while ANP derives the weights of each criterion related with TPL providers’ selection problem. Finally DEA presents a mathematical model for ranking TPL providers alternatives with respect to various criteria. The application of integrated model is demonstrated with a case study. The novelty of this study comes from the fact that there is no research in the literature integrating DEMATEL, ANP and DEA for the TPL selection problems. © 2016 Growing Science Ltd. All rights reserved.
Toll-like Receptor signaling in zebrafish cell lines

Toll-like receptors (TLRs) are a family of key pathogen recognition receptors which recognize microbial molecules and transduce intracellular signaling via recruitment and activation of adapter molecules e.g.TRAF6, which in turn deliver the signal to activate the transcription factor NFκB and the mitogen-activated protein kinases (MAPKs), which subsequently regulate transcription of many genes involved in inflammation and the immune response. Reverse transcription PCR revealed unique expression profiles of a set of immune-related genes in three zebrafish cell lines (ZF4, PAC2 and ZFL), including TLRs, their downstream signaling molecules, transcription factors and cytokines. The transcription factor NFkB can be activated by either TRAF6 over-expression or by stimulation with TLR ligands, in a cell-line dependent manner. Stimulation with flagellin, which is recognized by TLR5, activated NFkB in all cell lines. Microarray analysis revealed distinct transcriptome response in different cell lines upon flagellin stimulation, suggesting that zebrafish cell lines can be used to study specific signaling events involved in pathogen recognition at cellular level.
Aircraft Engineering and Aerospace Technology Foreign object debris surveillance network for runway security

Purpose – Foreign object debris (FOD) poses a significant hazard to aviation safety and brings huge economic losses to the aerospace industry due to aircraft damage and out-of-service delays. Different schemes and sensors have been utilized for FOD detection. This paper aims to look into a video-based FOD detection system for airport runway security and propose a scheme for FOD surveillance network establishment. Design/methodology/approach – The FOD detection algorithm for the system is analyzed in detail, including four steps of pre-processing, background subtraction, post-processing and FOD location. Findings – The overall algorithm is applied to two sets of live video images. The results show that the algorithm is effective for FOD targets of different shades under different lighting conditions. The proposed system is also evaluated by the ground-truth data collected at Nanyang Airport. Practical implications – The runway security can be greatly increased by designing an affordable video-based FOD detection system. Originality/value – The paper presents critical techniques of video-based FOD detection system. The scheme for FOD surveillance network, as a significant part of aviation risk management at airports, is applicable and extensible.
Complexity of Continuous Glucose Monitoring Data in Critically Ill Patients: CGM Devices, Sensor Locations, and DFA Methods

BACKGROUND: Critically ill patients often experience high levels of insulin resistance and stressinduced hyperglycemia, which may negatively impact outcomes. However, evidence surrounding the causes of negative outcomes remains inconclusive. Continuous glucose monitoring (CGM) devices allow researchers to investigate glucose complexity, using detrended fluctuation analysis (DFA), to determine whether it is associated with negative outcomes. AIM: The aim of this study was to investigate the effects of CGM device type/calibration and CGM sensor location on results from DFA. METHODS: This study uses CGM data from critically ill patients who were each monitored concurrently using Medtronic iPro2’s on the thigh and abdomen, and a Medtronic Guardian RealTime on the abdomen. This allowed inter-device/calibration type and inter-sensor site variation to be assessed. DFA is a technique that has previously been used to determine the complexity of CGM data in critically ill patients. Two variants of DFA, monofractal and multifractal, were used to assess the complexity of sensor glucose (SG) data, as well as the pre-calibration raw sensor current. Monofractal DFA produces a scaling exponent (H), where H is inversely related to complexity. The results of multifractal DFA are presented graphically, by the multifractal spectrum. RESULTS: From the 10 patients recruited, 26 CGM devices produced data suitable for analysis. The values of H from abdominal iPro2 data were 0.10 [0.03 – 0.20] higher than those from Guardian Real-Time data, indicating consistently lower complexities in iPro2 data. However, repeating the analysis on the raw sensor current showed little or no difference in complexity. Sensor site had little effect on the scaling exponents in this data set. Finally, multi-fractal DFA revealed no significant associations between the multifractal spectrums and CGM device type/calibration or sensor location. CONCLUSIONS: Monofractal DFA results are dependent on the device/calibration used to obtain CGM data, but sensor location has little impact. Future studies of glucose complexity should consider the findings presented here when designing their investigations. Abbreviations: BG – blood glucose CGM – continuous glucose monitoring FDA – Food and Drug Administration DFA – detrended fluctuation analysis ICU – intensive care unit STAR – Stochastic TARgeted SG – sensor glucose BGA – blood gas analyser IQR – inter-quartile range MARD – mean absolute relative dfference
Cohort effects and spatial variation in age‐specific survival of Steller sea lions from southeastern Alaska

Information concerning mechanistic processes underlying changes in vital rates and ultimately population growth rate is required to monitor impacts of environmental change on wildlife. We estimated age-specific survival and examined factors influencing survival for a threatened population of Steller sea lions (Eumetopias jubatus) in southeastern Alaska. We used mark-recapture models and data from 1,995 individuals marked at approximately one month of age at four of five rookeries in southeastern Alaska, and resighted from Oregon to the Bering Sea. Average annual survival probability for females was 0.64 for pups and 0.77 for yearlings, and increased from 0.91 to 0.96 from age 3–7 yrs. Annual survival probability of males averaged 0.60 for pups and 0.88 by 7 yrs, resulting in probability of survival to age 7, 33% lower for males compared to females. Pups from northern southeastern Alaska (including an area of low summer population size but rapid growth) were twice as likely to survive to age 7 compared to pups from southern rookeries (including a large, historical, stable rookery). Effects of early conditions on future fitness were observed as (1) environmental conditions in the birth year equally affected first- and second-year survival, and (2) effects of body mass at approximately one month of age were still apparent at 7 yrs. Survival from 0–2 yrs varied among five cohorts by a maximum absolute difference of 0.12. We observed survival costs for long-distance dispersal for males, particularly as juveniles. However, survival was higher for non-pups that dispersed to northern southeastern Alaska, suggesting that moving to an area with greater productivity, greater safety, or lower population size may alleviate a poor start and provide a mechanism for spatial structure for sea lion populations.
Growth rates and differential investment in male and female Juan Fernández fur seal pups

Abstract Male Juan Fernández fur seals (Arctocephalus philippii) are significantly larger than females at birth and show extreme dimorphism as adults. We investigated morphological differences among male and female pups using a cross-sectional sampling design to evaluate whether pup growth rates were sex-specific during the breeding season. We characterized growth rates using mass, length, and girth and found that length was the least variable measure of body growth (based on the coefficients of variation for the 3 measures of body size). Male pups were heavier on average than female pups on any given day of sampling but did not grow faster than females. No significant differences were noted in the body conditions of male and female pups. These findings suggest that the sexual differences among pups of A. philippii originate before birth and are not accentuated while suckling during the breeding season.
Video Game Addiction: Past, Present and Future

Gaming addiction has become a topic of increasing research interest. The last decade has witnessed a significant increase in the number of empirical studies examining various aspects of problematic video game play and video game addiction. This paper begins with a brief past history of how research into video game addiction has changed over the last three decades (i.e., the 1980s, 1990s and 2000s). It then examines more thoroughly the contemporary research literature by analyzing the (i) prevalence of problematic video game use and video game addiction, (ii) negative consequences of excessive video game use, (iii) factors associated with problematic video game use and video game addiction, and (iv) the treatment of problematic video game use and video game addiction. The paper concludes by looking at the trends in the field and a somewhat theoretical examination of what the future of video game addiction might be.
A Note on the Finite Sample Properties of the CLS Method of TAR Models

In this paper we focus on the finite sample properties of the conditional least squares (CLS) method of threshold autoregressive (TAR) parameters under the following conditions: (a) non-Gaussian model innovations; (b) two types of asymmetry (i.e. deepness and steepness) captured by TAR models. It is clearly demonstrated that the finite sample properties of the CLS method of TAR parameters significantly differ depending on the type of asymmetry. The behavior of steepness-based models is very good compared to that obtained from deepness-based models. Therefore, extreme caution must be excercised to preliminary modelling steps, such as testing the type of asymmetry before estimating TAR models in practice. A mistake in this phase of modelling can, in turn, give rise to very problematic results.
A tableau-based decision procedure for a branching-time interval temporal logic

Propositional interval temporal logics are very expressive temporal logics, with simple syntax and semantics, which allow one to naturally express statements that refer to time intervals and continuous processes. Most of them feature temporal operators that only allow one to express properties of a single timeline. In this paper we develop a branching-time interval neighborhood logic that interleaves operators that quantify over possible timelines with operators that quantify over intervals belonging to a given timeline. We define its syntax and semantics, and we provide it with a doubly-exponential tableau-based decision procedure.
eview iological collections in an ever changing world : Herbaria as tools for iogeographical and environmental studies

Plant specimens stored in herbaria are being used as never before to document the impacts of global change on humans and nature. However, published statistics on the use of biological collections are rare, and ecologists lack quantitative data demonstrating the relevance to science of herbarium specimens. I found 382 studies with original data that used herbarium specimens to document biogeographical patterns or environmental changes. Most studies are less than 10 years old, and only 1.4% of the herbarium specimens worldwide have been used to answer biogeographical or environmental questions. The vast majority (82%) of papers dealt with vascular plants, but some studies also used bryophytes, lichens, seaweeds and fungi. The herbarium specimens were collected from all continents, but most of the studies used specimens from North America (40% of studies) or Europe (28%). Many types of researches (conservation, plant disease, plant invasion, pollution, etc.) can be conducted using herbarium specimens. Climate change, and especially phenological reconstructions, are clearly emerging research topics. By group, small herbaria (<100,000 specimens) are consulted as often as very large herbaria (>1,000,000 specimens) for biogeographical and environmental research, but in most cases, only large facilities provide specimens collected worldwide. The median number of specimens per study in papers using computerized collections (15,295) was much higher than for papers that did not include electronic data (226). The use of molecular analyses to investigate herbarium specimens is still relatively unexplored, at least from biogeographical and environmental points of view. Combined with recently developed procedures to correct biases, herbarium specimens might provide in the near future exciting additional spatio-temporal insights that are currently unimaginable. © 2012 Elsevier GmbH. All rights reserved.
Optimization of Indole 3-acetic acid (IAA) production by Acetobacter diazotrophicus Ll isolated from Sugarcane

Based on morphological, cultural and biochemical characteristics, a newly isolated bacterium from the stem of the Indian sugarcane variety Co 740 was identified as Acetobacter diazotrophicus and was designated as L1. Cultural and nutritional conditions were optimized for indole 3-acetic acid (IAA) production. The effect of increasing sucrose concentration and different nitrogen sources on IAA production were studied. Shaking increased the production of IAA. The isolate produced high amount of IAA (26.28 μg/ml) when basal medium (pH 6) was supplemented with sucrose (12% w/v), yeast extract (0.05 g/l), L-tryptophan (1.2 g/l) and NH4Cl (0.1% w/v) at 200 rpm. IAA production increased up to 2.6 fold over control. Inoculation with A. diazotrophicus Ll increased root and shoot biomass as well as IAA level of the fresh root tissue of maize plant. The results indicated that A. diazotrophicus Ll produced high amount of IAA than reported earlier.
Rapid Eddy-Induced Modification of Subtropical Mode Water during the Kuroshio Extension System Study

AbstractFrom 2004 to 2006 an observational array of current- and pressure-recording inverted echo sounders (CPIES) were deployed as part of the Kuroshio Extension (KEx) System Study (KESS). KESS observed a transition from a weakly meandering (“stable”) to strongly meandering (“unstable”) state (Qiu and Chen). As the KEx made this transition, potential vorticity (PV) observed within the southern recirculation gyre (SRG) rapidly increased from January to July 2005. In this study, the authors diagnose eddy PV fluxes (EPVFs) in isentropic coordinates within the subtropical mode water (STMW) layer from the CPIES data to determine the role of mesoscale eddies in this rapid increase of PV.The rapid increase in PV within the SRG coincided with enhanced cross-front EPVFs and eddy PV flux convergence upstream of a mean trough in the KEx path and adjacent to the SRG. The enhanced cross-front EPVFs were the result of the formation of a cold-core ring (CCR) and the interaction of the jet with a preexisting CCR. Eddy d.