Miracle-dz/UniFAR-FTUs huggingface dataset:
Rainfall pattern and nutrient content influences on African elephants’ debarking behaviour in Samburu and Buffalo Springs National Reserves, Kenya

The magnitude of debarking by elephants was investigated in Samburu and Buffalo Springs National Reserves. About 1617 plants were monitored for debarking intensities for 6 months spanning through dry and wet seasons. Debarking indices ranged from no debarking at all during the wet months to complete stem girding at the height of the dry season. A negative correlation was found between rainfall and debarking indices. It was hypothesized that nutrient content of the bark influenced the magnitude to which trees were debarked. Bark samples were collected from least, moderate and intensely debarked plants throughout the 6 months. These were analysed for calcium (Ca), sodium (Na), phosphorus (P), magnesium (Mg), potassium (K), nitrogen (N), iron (Fe), copper (Cu), manganese (Mn) and zinc (Zn). Significant positive correlations were found between debarking intensity and each of the nutrients N [crude protein (CP)], P, K and Zn. Bark was found to be richest in CP and Calcium. Neutral detergent fibre content was on average 67%. Monthly variations in nutrient composition were minimal. Acacia elatior, the most preferred species had significantly higher quantities of each of the four elements N, P, K and Zn than Acacia tortilis, the second most preferred woody species. Resume Nous avons etudie l’importance de l’arrachage des ecorces d’arbres par les elephants dans les Reserves Nationales de Samburu et de Buffalo Springs. Quelque 1617 plants furent ainsi suivis pendant six mois couvrant saison seche et saison des pluies. Les indices d’arrachage allaient de zero pendant les mois de pluie a une mise a nu complete du tronc au pic de la saison seche. Nous avons trouve une correlation negative entre les chutes de pluies et l’indice d’arrachage des ecorces. Nous avons emis l’hypothese que le contenu nutritionnel de l’ecorce influencait la mesure dans laquelle les arbres etaient ecorces. Nous avons recolte des echantillons d’ecorce de plants les moins touches, moderement touches et intensement touches tout au long des six mois. Ils furent analyses pour leur contenu en calcium (Ca), sodium (Na), phosphore (P), magnesium (Mg), potassium (K), azote (N), fer (Fe), cuivre (Cu), manganese (Mn) et zinc (Zn). Des correlations significativement positives furent decouvertes entre l’importance de l’ecorcage et chacun des nutriments suivants : N (proteine brute), P, K et Zn. Nous avons decouvert que l’ecorce etait surtout riche en proteine brute et en calcium. La teneur globale en elements parietaux etait en moyenne de 67%. Les variations mensuelles de la composition nutritionnelle etaient minimes. Acacia elator, l’espece preferee contenait des quantites significativement plus elevees qu’Acacia tortilis, l’espece ligneuse choisie en second lieu, pour chacun des quatre elements N, K, P et Zn.
Title Utilizing Virtual Environments to Enable Learning in Human-robot Interaction Scenarios

—This paper presents two different approaches for utilizing virtual environments to enable learning for both human and robotic students. In the first approach, we showcase a 3D interactive environment that allows a human user to learn how to interact with a virtual robot, before interaction with a physical robot. In the second approach, we present a method that utilizes a simulation environment to provide feedback to a human teacher during a training session in order to concurrently allow adaptation of the learning process for both the teacher and the robotic student. We provide details of the approaches in this paper and provide results of the learning outcomes for the two different scenarios.
Análise de algumas alternativas para obter o coeficiente angular da reta no método da altura relativa.

The relative height method allows the characterization of stem profile without meeding sample trees to upper diameter measurements. The analytical geometry is applied on the diameter taken on 0,3 meters and on hr = (h-2)/2, as well as dbh and total height (h), making possible the measurement of these variables, simultaneously, with others measured on the permanent sampling in forest inventory. This study evaluated some alternatives in characterizing the stem profile by using analytical geometry, comparing it to the original method according Andrade (2001). It was concluded that the use of relative diameters to dbh showed better results in regression analysis to generate straight line angular coefficient. Also, to obtain better accuracy, it is more adequate to implement the relative height method using all trees inside the inventory sample unit.
FBVA: A Flow-Based Visual Analytics Approach for Citywide Crowd Mobility

Analyzing structures of crowd mobility at city level is a challenging task due to the complex crowd mobility and dynamic changes generated by the social activities over time. These structures, defined as high-dimensional mobility structures (HMSs), contain spatiotemporal information and are simultaneously influenced by the geographical distributions and daily activities of citywide crowd. However, few work has been dedicated to depict and analyze these structures, mainly due to the lack of effective models. In this paper, we propose to model the crowd mobility as a dynamical system and characterize the irregular mobility data with a novel local coherence of sparse field (LCSF) algorithm. The proposed algorithm makes it possible to measure the separation behavior of trajectories in an irregular and sparse topology network. Detected HMS, referred as local separation measure of LCSF, divides the geographical urban areas into distinct functional regions over time. We design and implement a visual analytics system to facilitate situation-aware analysis of a huge amount of crowd mobility and their socialized behaviors. Case studies based on a real-world data set demonstrate the effectiveness of the proposed approach.
Expression of a cDNA encoding palmitoyl-acyl carrier protein desaturase from cat's claw (Doxantha unguis-cati L.) in Arabidopsis thaliana and Brassica napus leads to accumulation of unusual unsaturated fatty acids and increased stearic acid content in the seed oil

A cDNA encoding palmitoyl-acyl carrier protein (ACP)-desaturase from cat's claw (Doxantha unguis-cati L.) was expressed in Arabidopsis thaliana and Brassica napus L. with the goal of decreasing the saturated fatty acid (FA) content of the seed oil. In general, transformation of Arabidopsis resulted in a greater change in the FA composition of the seed oil than for B. napus. An increase in palmitoleic acid (16:1cisΔ 9 ) was obtained in transgenic lines, suggesting that the 16:0-ACP-desaturase cDNA was expressed in the manner originally intended. Other effects on lipid metabolism, however, were observed in the seed of transgenic plants. In Arabidopsis, there was a large increase in the proportions of cis-vaccenic acid (18:1cisΔ 11 ) and cis-13-eicosenoic acid (20:1cisΔ 13 ), possibly generated through elongation of 16:1cisΔ 9 . Elongation of 18:1cisΔ 11 to 20:1cisΔ 13 , however, was not observed in B.napus indicating that certain aspects of lipid metabolism in the model plant, Arabidopsis, may not apply to B. napus. As well, the appearance of 18:1cisΔ 11 was accompanied by a decrease in the proportion of oleic acid (18:1cisΔ 9 ). Although the introduced ACP-desaturase resulted in synthesis of some unsaturated FAs, the overall saturated FA content was maintained at similar levels to the control or was enhanced. Increased levels of saturation were mainly associated with an increase in stearic acid, which unlike 16:0, is considered non-atherogenic. The results suggest that a mechanism exists further downstream in oil biosynthesis to counteract the decrease in saturation brought about by the 16:0-ACP-desaturase action.
Persistence of Conidia of Metarhizium anisopliae in Sugarcane Fields: Effect of isolate and formulation on persistence over 3.5 years

Metarhizium anisopliae is being used in Australia as a biopesticide for control of sugarcane whitegrubs in soil. The field persistence in sugarcane soil of two isolates of M. anisopliae each in four formulations was tested by mixing the formulation with soil which was then placed in PVC rings and buried in sugarcane fields. The two isolates used were FI-1045, M. anisopliae var. anisopliae, the active ingredient in BioCane™ currently used for greyback canegrub control, Dermolepida albohirtum (Coleoptera: Scarabaeidae: Melolonthinae), and FI-147, M. anisopliae var. lepidiotum, being tested as a biopesticide for Lepidiota spp. (Coleoptera: Scarabaeidae: Melolonthinae) and other species of canegrub. The four formulations were rice granules (as in BioCane™), a wettable powder derived from conidia screened from the rice granules, conidia off rice suspended in water and conidia produced on agar plates, dried, and then mixed with water for adding to soil. FI-1045 was tested at three different sites in north Queensland with a range of soil types and climatic conditions while FI-147 was tested at three similarly diverse sites in southern Queensland. The PVC rings were destructively sampled every 6 months for 3.5 years and the number of viable conidia remaining determined by plating onto a selective medium. The exponential decay was determined. Monthly decay rates ranged from 0.0309 to 0.0835 (mean 0.0512). A small proportion of conidia survived the 3.5 years at all sites and all formulations. Overall, isolate FI-147 persisted better than FI-1045, but was used at the more Southerly sites. Rainfall and soil type had negligible effects on persistence. The agar-produced FI-147 conidia declined most slowly, while the two rice-produced but water-formulated conidia gave similar results. Isolate FI-1045 survived best as the BioCane™ formulation and this rice granule formulation was almost as persistent as the agar conidia with FI-147. A small proportion of conidia, in some formulations and at some sites, were recovered from immediately below the rings. This movement was thought to be due to activity of earthworms or mites. The results suggest that 3 years would be the maximum period for a BioCane™ formulation to provide some level of infection in the target pest unless augmented by conidia from infected grubs. The effectiveness of these new conidia may be reduced due to their highly aggregated distribution.
CMS: A Continuous Machine-Learning and Serving Platform for Industrial Big Data

The life-long monitoring and analysis for complex industrial equipment demands a continuously evolvable machine-learning platform. The machine-learning model must be quickly regenerated and updated. This demands the careful orchestration of trainers for model generation and modelets for model serving without the interruption of normal operations. This paper proposes a container-based Continuous Machine-Learning and Serving (CMS) platform. By designing out-of-the-box common architecture for trainers and modelets, it simplifies the model training and deployment process with minimal human interference. An orchestrator is proposed to manage the trainer’s execution and enables the model updating without interrupting the online operation of model serving. CMS has been deployed in a 1000 MW thermal power plant for about five months. The system running results show that the accuracy of eight models remains at a good level even when they experience major renovations. Moreover, CMS proved to be a resource-efficient, effective resource isolation and seamless model switching with little overhead.
SOLIOT - Decentralized Data Control and Interactions for IoT

The digital revolution affects every aspect of society and economy. In particular, the manufacturing industry faces a new age of production processes and connected collaboration. The underlying ideas and concepts, often also framed as a new “Internet of Things”, transfer IT technologies to the shop floor, entailing major challenges regarding the heterogeneity of the domain. On the other hand, web technologies have already proven their value in distributed settings. SOLID (derived from “social linked data”) is a recent approach to decentralize data control and standardize interactions for social applications in the web. Extending this approach towards industrial applications has the potential to bridge the gap between the World Wide Web and local manufacturing environments. This paper proposes SOLIOT—a combination of lightweight industrial protocols with the integration and data control provided by SOLID. An in-depth requirement analysis examines the potential but also current limitations of the approach. The conceptual capabilities are outlined, compared and extended for the IoT protocols CoAP and MQTT. The feasibility of the approach is illustrated through an open-source implementation, which is evaluated in a virtual test bed and a detailed analysis of the proposed components.
Performance Analysis of a Novel TCP Protocol Algorithm Adapted to Wireless Networks

As telecommunication systems evolve towards new-generation architectures, likewise, new protocols are created in order to improve efficiency. One of these protocols is Transmission Control Protocol (TCP), which controls the transmission bit rate in function of network congestion. Nevertheless, in wireless communications, there appear problems such as noise and interference, for which TCP was not designed. Based on these problems, there exist some methods trying to mitigate congestion, such as explicit loss notifications and the use of end-to-end codification. The aim of this work was to propose a wireless TCP protocol improvement, considering a negative acknowledgment (NACK), which allows to differentiate between losses due to congestion and losses due to wireless channel issues. NACK employs a small protocol packet and produces improvement in the quality of service metrics. The experiments were carried out in in-door and out-door environments, over an online video game scenario, and over a long-distance wireless link between two islands. The average results show a 25-percent delay improvement and a 5-percent jitter improvement when compared to the original TCP Reno protocol, while for throughput a 90-percent improvement was achieved for distances between 100 and 414 m.
Transactional simulation approach for modelling performance and energy of a heterogeneous SoC memory system. (Approche de simulation transactionnelle pour la modélisation des performances et de l'énergie d'un système mémoire pour SoC hétérogènes)

Les appareils mobiles, a chaque nouvelle version des normes et suivant les demandes continues de nouveaux services par les utilisateurs, doivent prendre en charge de plus en plus de fonctionnalites, qui deviennent egalement de plus en plus exigeantes du point de vue informatique. Par consequent, etre en mesure de repondre aux nouvelles exigences tout en fournissant des puces a faible consommation d’energie est aujourd’hui le defi le plus important pour les concepteurs de systemes pour appareils mobiles. Pour relever ce defi, de nouvelles approches de modelisation de la performance et de la puissance au niveau systeme ont ete proposees, permettant d'explorer les architectures materielles/ logicielles (HW / SW) des les toutes premieres etapes d'un flot de conception de systemes sur puce (SoC). Cependant, les solutions existantes prennent en charge de maniere limitee l'optimisation de la puissance du systeme de memoire (y compris la memoire SDRAM), qui peut occuper plus de 70% de la surface d'une puce et consommer plus de 30% de l'energie totale. Dans nos travaux, nous proposons un cadre de simulation base sur SystemC-TLM au niveau Electronic System Level (ESL), capable de prendre en charge l’exploration commune d’une architecture SoC et de sa configuration memoire. Ce nouveau cadre permet d’optimiser la consommation d’energie des SoC tout en faisant correspondre les performances requises en termes de puissance et de performances, de bande passante memoire et de temps de latence.
Palmer Amaranth (Amaranthus palmeri) Damage Niche in Illinois Soybean Is Seed Limited

Abstract Palmer amaranth, a dioecious summer annual forb, originating in Sonoran desert washes, compromises crop yields in much of the southern United States and its range is expanding northward. Appropriate tactics for managing this weed proactively in the Upper Midwest will depend on characterizing its damage niche, the geographic range in which it can reduce crop yields. We implemented a common garden study in 2011 and 2012, planting eight accessions of Palmer amaranth from the southern and midwestern United States, into soybean crops in southern, central, and northern Illinois, at a population density of 8 plants m−2 with a biocontainment protocol. Once Palmer amaranth plants initiated flowering, they were removed and burned. Weed survival, flowering, and weed biomass were measured, in addition to soybean yield and weather data. Analyses indicated that Palmer amaranth’s damage niche in Illinois soybean was independent of weed genotype or maternal environment. Despite competing only briefly, Palmer amaranth reduced soybean yields in all site–years, indicating its damage niche in Illinois, and much of the Midwest, is limited primarily by seed immigration rate. These results highlight the urgent need for weed managers to learn Palmer amaranth identification, prevent seed introduction, and maintain a policy of zero seed return. Nomenclature: Palmer amaranth, Amaranthus palmeri S. Wats. ; soybean, Glycine max (L.) Merr.
Structure and Function of Stream Ecosystems

It has been stated often that the selection of appropriate methodological strategies for ecological investigations are highly dependent upon the question being addressed. Unfortunately this awareness has not become fully operational-questions often being formulated only after data collection. Frequently, traditional ecological studies have been taxonomic inventories of biological communities-information of limited use in answering certain functionand process-oriented questions. Such inventories seem an inappropriate fabric from which to weave important ecological generalizations. As long as the species is assumed to be the basic ecological unit, ignoring for the moment problems in defining such units, the perpetually incomplete state of our taxonomic knowledge will constitute a major constraint for the development of ecological theory. This assumption, that species recognition is the fundamental prerequisite for ecological insight, has proven particularly troublesome to the study of flowing water (or lotic) ecological systems. For example, immature stages (nymphs, larvae) of stream insects usually dominate the macroinvertebrate role in energy transformations, but the adults (usually males) constitute the coin of species identification. In addition, diatoms, the dominant lotic algae, present particularly difficult taxonomic problems. However, perhaps only the lack of attention paid the microbial components-bacteria and fungi-of natural communities has allowed the taxonomic focus to endure this long. Discrepancies between morphological, physiological, and genetic species definitions of microorganisms make it apparent how untenable a taxonomic foundation for all ecological questions can be. Thus, there is a need to identify functional groups of organisms, at least partially independent of traditional taxonomic determinations, in order to address important process-oriented ecological questions. It is certainly true that we would not now be in a position to search for other units from which to
Association of gut microbiota with cerebral cortex and cerebrovascular abnormality in human mild traumatic brain injury

Key roles of the gut–brain axis in brain injury development have been suggested in various mouse models; however, little is known about its functional significance in human mild traumatic brain injury (TBI). Here, we decipher this axis by profiling the gut microbiota in 98 acute mild TBI patients and 62 matched controls, and subgroup of them also measured circulating mediators and applied neuroimaging. Mild TBI patients had increased α-diversity and different overall microbial compositions compared with controls. 25-microbial genus classifiers distinguish patients from controls with an area under the receiver operating characteristic curve (AUC) of 0.889, while adding serum mediators and neuroimaging features further improved performance even in a small sample size (AUC = 0.969). Numerous correlations existed between gut bacteria, aberrant cortical thickness and cerebrovascular injury. Co-occurrence network analysis revealed two unique gut–brain axes in patients: 1) altered intestinal Lachnospiraceae_NK4A136_group and Eubacterium_ruminantium_group-increased serum GDNF-subcallosal hypertrophy and cerebrovascular injury; 2) decreased intestinal Eubacterium_xylanophilum_group–upregulated IL-6–thinned anterior insula. Our findings provide a new integrated mechanistic understanding and diagnostic model of mild TBI.
Iterative epigenomic analyses in the same single cell

Gene expression in individual cells is epigenetically regulated by DNA modifications, histone modifications, transcription factors and other DNA-binding proteins. It has been shown that multiple histone modifications can predict gene expression and reflect future responses of bulk cells to extracellular cues. However, the predictive ability of epigenomic analysis is still limited for mechanistic research at a single cell level. To overcome this limitation, it is useful to acquire reliable signals from multiple epigenetic marks in the same single cell. Here, we propose a new approach for analysis of several components of the epigenome in the same single cell. The new method allows reanalysis of the same single cell. We found that reanalysis of the same single cell is feasible, and provides confirmation of the signals and allows application of statistical analysis to identify reliable signals using data sets generated only from the single cell. Reanalysis of the same single cell is also useful to acquire multiple-epigenetic marks from the same single cells. The method can acquire at least 4 epigenetic marks, H3K27ac, H3K27me3, mediator complex subunit 1 and a DNA modification. We predicted active signaling pathways in K562 single cells using the data. We confirmed that the prediction results showed a strong correlation with actual active signaling pathways shown by RNA-seq results. These results suggest that the new approach provides mechanistic insights for cellular phenotypes through multi-layered epigenome analysis in the same single cells.
Integrative vectors for regulated expression of SARS-CoV-2 proteins implicated in RNA metabolism

Infection with SARS-CoV-2 is expected to result in substantial reorganization of host cell RNA metabolism. We identified 14 proteins that were predicted to interact with host RNAs or RNA binding proteins, based on published data for SARS-CoV and SARS-CoV-2. Here, we describe a series of affinity-tagged and codon-optimized expression constructs for each of these 14 proteins. Each viral gene was separately tagged at the N-terminus with Flag-His8, the C-terminus with His8-Flag, or left untagged. The resulting constructs were stably integrated into the HEK293 Flp-In TREx genome. Each viral gene was expressed under the control of an inducible Tet-On promoter, allowing expression levels to be tuned to match physiological conditions during infection. Expression time courses were successfully generated for most of the fusion proteins and quantified by western blot. A few fusion proteins were poorly expressed, whereas others, including Nsp1, Nsp12, and N protein, were toxic unless care was taken to minimize background expression. All plasmids can be obtained from Addgene and cell lines are available. We anticipate that availability of these resources will facilitate a more detailed understanding of coronavirus molecular biology.