Miracle-dz/UniFAR-FTUs huggingface dataset:
Invasive plants differ from native plants in their impact on native communities

Aims Although the impacts of alien plant invasions on native communities are well documented, the mechanisms that underlie these impacts are poorly resolved. Little is yet known as to why invasive alien plants have greater impacts than native species on their neighbouring species within a community. We investigated two potential mechanisms by which invasive plants may harm neighbouring species: resource competition and novel compounds of the invaders. Locations Field removal experiment in France and Switzerland, and common garden experiment at the University of Fribourg, Switzerland. Methods We first conducted a field removal experiment to compare the response of neighbouring communities to experimental biomass removal of two alien invasive vs two dominant native plant species in two sites of each target species (thus eight sites in total). In addition, we conducted a common garden pot experiment to compare the effect of eight triplets of closely related target species (24 species in total), each consisting of an alien invasive species in Europe, a dominant native and a random native species, on the growth of a grass community under the addition or not of activated carbon (AC). Results (1) Field removal experiment: in the control plots, we found that the biomass of native species explained a substantial amount of the variation in biomass of the neighbouring communities, but the invader's biomass did not. Moreover, the neighbouring community recovered from removal of the dominant native species, showing a significant increase in biomass, but did not after removal of the invaders. (2) Common garden pot experiment: we found a larger effect of invasive species than native species on the growth rate of the grass community, but this difference disappeared when AC was added. Conclusion Both experiments suggest that the impact of some invasive species is not driven by resource competition, but by other mechanisms, most likely by novel weapons or novel plant–soil interactions.
Building Placements In Urban Modeling Using Conditional Generative Latent Optimization

Generating realistic urban environments by scattering or placing buildings on maps is a challenging problem. Unlike the existing procedural methods, we employ a data-driven approach to this problem. We combine two recent advances in machine learning techniques, Generative Latent optimization (GLO) together with adversarial training, to learn a model that can easily generate and place buildings on a given map. Such a model enables its users, particularly artists, to easily generate areas with specific styles, e.g. residential or commercial, just by providing examples. In contrast, traditional procedural methods require lengthy manual tuning of hyper-parameters. Using a more flexible method like ours allows artists to iterate over their designs of urban layouts much faster. Finally, our experiments on real-world data show that our method outperforms state-of-the-art methods in visual quality and can better match the underlying distribution of the building placements.
Resistance gene discovery and cloning by sequence capture and association genetics

Genetic resistance is the most economic and environmentally sustainable approach for crop disease protection. Disease resistance (R) genes from wild relatives are a valuable resource for breeding resistant crops. However, introgression of R genes into crops is a lengthy process often associated with co-integration of deleterious linked genes1, 2 and pathogens can rapidly evolve to overcome R genes when deployed singly3. Introducing multiple cloned R genes into crops as a stack would avoid linkage drag and delay emergence of resistance-breaking pathogen races4. However, current R gene cloning methods require segregating or mutant progenies5–10, which are difficult to generate for many wild relatives due to poor agronomic traits. We exploited natural pan-genome variation in a wild diploid wheat by combining association genetics with R gene enrichment sequencing (AgRenSeq) to clone four stem rust resistance genes in <6 months. RenSeq combined with diversity panels is therefore a major advance in isolating R genes for engineering broad-spectrum resistance in crops.
The Importance Of Skip Connections In Encoder-Decoder Architectures For Colorectal Polyp Detection

Accurate polyp detection during the colonoscopy procedure impacts colorectal cancer prevention and early detection. In this paper, we investigate the influence of skip connections as the main component of encoder-decoder based convolutional neural network (CNN) architectures for colorectal polyp detection. We conduct experiments on long and short skip connections and further extend the existing architecture by introducing dense lateral skip connections. The proposed segmentation architecture utilizes short skip connections in the contracting path, moreover it utilizes dense long and lateral skip connections in between the contracting and expanding path. Results obtained from the MICCAI 2015 Challenge dataset show progressive improvement of the segmentation result with expanded utilization of skip connections. The proposed colorectal polyp segmentation architecture achieves performance comparable to the state-of-the-art under significantly reduced number of model parameters.
Deciphering the function of obesity-associated regulatory elements within FTO

Genome-wide association studies have repeatedly shown that the strongest association with obesity arises from variants in the first intron of FTO. The intronic FTO variant rs1421085 is within an adipocyte-specific enhancer and that risk allele carriers have increased IRX3 and IRX5 expression in early adipogenesis (Claussnitzer et al., 2015). Additionally, the same human risk variant was linked to decreased AKTIP, RPGRIP1L and FTO expression in iPSC-derived neurons (Stratigopoulos et al., 2016). These data point towards several likely causal transcripts and tissues at the FTO locus and essentially, several likely mechanisms. Importantly, whether any of the high-risk variants at the FTO locus has any effect on the organismal level has not been addressed so far. The aim of my DPhil project was to use novel gene manipulation strategies in vivo to mechanistically dissect the Fto regulatory circuitry in mouse to pinpoint causal transcripts their effector tissues and to unravel their physiological role in body weight regulation . Using publicly available as well as my own genomic data (ATAC-seq) revealed that the intronic FTO regulatory element in human adipocytes is conserved in mouse pre-adipocytes. Manipulation of the corresponding motif in mouse (by deleting 82 nucleotides at the mouse orthologous region around rs1421085) resulted in depot- and sex-specific alteration of target genes Irx3 and Irx5 in pre-adipocytes. In addition to recapitulating many of the human findings in mouse, my results further unravelled a new level of regulatory complexity at the FTO/Fto locus. When these mutant mice were put on a high fat diet, I found a reduction on overall fat-mass that could be linked to altered mRNA levels of Irx3 and Irx5 in pre-adipocytes. Using a number of genetic techniques, I further showed that Irx3 regulates several processes during adipocyte development, amongst which is modulation of mitochondrial function. In summary, my findings provide new insight into how variants in FTO intron 1 affect adipocyte development and more specifically how IRX3 affects early adipocyte differentiation.
Real-Time Flow Control of Blade Section Using a Hydraulic Transmission System Based on an H-Inf Controller with LMI Design

Vibration and real-time flow control of the 2D blade section of wind turbines with three degrees of freedom (3-DOF), excited by external pitch motion, are investigated based on an H-inf (H∞) controller using linear-matrix-inequality (HIC/LMI) design. The real-time flow control for the purpose of aeroelastic flutter suppression includes not only the driving process of real-time physical equipment, but also the realization of real-time control algorithm in the physical controller. The aeroelastic system combined with pitch motion is controlled by a kind of HIC/LMI algorithm. The real-time external pitch motion is driven by rack-piston cylinder (RPC) using a hydraulic transmission system (HTS). The unsteady aerodynamic loads model is simplified by the HTS system. The HTS is actuated by a proportional-flow valve (PFV) which is controlled by another HIC/LMI algorithm, a novel algorithm for waveform tracking. According to the result of waveform tracking, the input current signal of PFV is realized by the configuration of the controller hardware system and its external circuits. In two types of HIC/LMI algorithms, controller stabilities are affirmed using Lyapunov analyses, and controller values are derived and obtained by using LMI designs. Flutter suppression for divergent and instable displacements is shown, with obvious controlled effects illustrated. An online monitoring experimental platform using hardware-in-the-loop simulation, based on Siemens S7-200 programmable logic controller (PLC) hardware and Kingview detection system, is built to implement pitch motion based on HTS and configure the signal input of PFV in pitch control.
Development of a Skin Cancer Detection Classifier using Artificial Neural Network (ANN)

In recent times, dermatological diseases pose one of the biggest medical challenges in the 21st century resulting in high medical cost and painful diagnostic procedures (biopsy). Cancer affecting the skin is commonly referred to as Melanoma. This condition is curled from the cell that gives rise the disease known as melanocyte. The most dangerous form of skin cancer is malignant melanoma but early detection plays an essential part in its control and cure [1]. In 2018, it was estimated that about 9,320 deaths resulted from melanoma. In this work, a computer-based system to classify histopathological images of skin tissues using Artificial Neural Network (ANN) was implemented on MATLAB. Performance measures of the proposed system are encouraging and there is no evidence of over- fitting. Therefore, an extended version of this classifier system could be used to assist patients and hospital pathologists to increase efficiency in healthcare delivery. Keywords-Melanoma, Diagnostic, Biopsy, Histopathological, Artificial Neural Network, Classifier
Phytase Activity in the Digesta from Different Parts of the Digestive Tract and Ileal Digestibility of Nutrients in Broilers Fed with Buckwheat Diets

In the present study, the effects of dietary buckwheat on phytase activity in the digesta from different parts of the digestive tract, and ileal digestibility of nutrients were determined in broilers fed with buckwheat diets. Eighty male broilers (29-d-old) were divided into four groups (20 birds each), and were fed one of the following diets until they were 36-d-old: positive control (PC) diet formulated based on the NRC recommendations, negative control (NC) diet containing 0.15% lower non-phytate phosphorus (P) than that in the PC diet, and two other diets formulated by replacing corn in NC diet with either 20% non-germinated (BU) or germinated (GBU) buckwheat. At the age of 36 d, broilers were sacrificed to collect digesta from the crop, gizzard, duodenum, jejunum, ileum, and cecum. The activity of phytase was low in the PC and NC diets, which increased in the BU diet and increased further in the GBU diet. A similar trend was observed in the crop digesta; however, the phytase activity in the crop digesta of BU and GBU diets was marginally lower when compared with that in each diet. These values decreased sharply when the digesta moved to the gizzard, and then decreased gradually. The ileal digesta exhibited significantly low activity with negligible effect of dietary treatment. The result of two-way analysis of variance with germination and digestive tract parts as main factors showed that the effect of digestive tract parts and interaction between factors was significant on the phytase activity in digesta. The dietary BU and GBU did not affect the ileal crude protein digestibility; however, it increased the ileal phytate P digestibility. These results suggest that in broilers, the crop might be the primary site of phytate degradation by buckwheat phytase, and the buckwheat might have negligible adverse effect on ileal digestibility of nutrients.
Evaluation of serum nitric oxide level and its relationship with disease activity parameters in patients with rheumatoid arthritis

Aim: Nitric oxide (NO) is a molecule known to play a role in many physiological and pathological events in the body. It is thought to play an active role in inflammation. Rheumatoid arthritis (RA) is the most common chronic inflammatory autoimmune disease worldwide. In this study, we aimed to evaluate the serum NO levels of RA patients and their relation with parameters that are indicators of disease activity. Material and Method: Thirty patients with RA (7 males/ 23 females, mean age 48.80±7.88 years old) and 30 healthy control groups were included in the study. Both groups were compared with erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), rheumatoid factor (RF), anti cyclic citrullinated peptide antibody (anti CCP) and serum NO levels and clinically with Visual Analog Scale (VAS), Disease Activity Score-28 (DAS-28) and Health Assessment Questionnaire (HAQ) scales. Results: ESR, CRP and NO levels in the patient group were significantly higher than the control group (p 3.2, inactive disease DAS-28 <3.2) according to DAS-28 scores, there was no significant difference in serum NO levels between the two groups. Serum NO levels of the patient group were not correlated with clinical (VAS, DAS-28) and laboratory markers (ESR, CRP, RF, Anti CCP) of disease activity. Conclusion: In this study, we found that serum NO levels in RA patients increased significantly compared to the healthy control group. However, increased serum NO levels in RA patients were not associated with laboratory and clinical disease activity parameters.
Molecular Screening of Adhesion Proteins Genes in Staphylococcus aureus Strains Isolated from Different Clinical Infections in Baghdad City and Identification of Their Relationship with Some Virulence Factors

The first step to achieve Staphylococcus aureus infections is the adhesion process that is mediated by proteins belong to the microbial surface component recognizing adhesive matrix molecules (MSCRAMMs). The distribution of these proteins is different among S. aureus isolates. In Iraq, there are no previous studies have been done in regard of distribution of these important virulence factors. Therefore, this study was designed to use PCR for screening of MSCRAMMs genes among local S. aureus isolates and determination of some virulence factors. S. aureus isolates (32) were collected from different hospitals in Baghdad and were diagnosed by conventional methods (cultural methods, colony morphology, Gram stain and biochemical tests). API Staph. System was used to confirm the diagnosis. Antimicrobial susceptibility test was performed by disc diffusion method for ten antibiotics. The ability to produce some virulence factors by bacterial isolated was detected [hemolysis activity, Deoxy ribonuclease (DNase) production and biofilm production]. The diagnosis of bacterial isolates was super-confirmed using PCR to detect the nuc gene. Uniplex and multiplex PCR were used to detect the MSCRAMMs genes (Uniplex PCR was used to detect fnbA and cna genes (each alone). multiplex PCR were used to detect bbp and ebp genes in one run and clfA, clfB, fib and fnbB genes in other run. All isolates were diagnosed as S. aureus (were negative to oxidase. Positive to catalase, slide and tube coagulase and Ferment mannitol). All isolates were recorded as S. aureus by API Staph system. A high prevalence of MRSA strains (78 %) was detected, vancomycin and imipenem were the most affected with percentage (97 %) and (94 %) respectively; results of susceptibility to other antibiotics was variant. Beta hemolysis was detected in (65.6 %) of isolates, 34.4% of isolates did not give any zone (gamma hemolysis), while no alpha hemolysis have been detected. On the other hand, all isolates (100%) produced DNase enzyme. The results of biofilm production assay shown that 40.6% of strains gave a weak positive results. The results shown that all isolates (100%) that were diagnosed as S. aureus by traditional methods harbored the nuc gene. The distribution percentage of bbp, ebp, clfA, clfB, cna, fib, fnbA and fnbB were 21.9%, 90.6%, 100%, 81.3%, 93.8%, 96.9%, 100% and 25% respectively. The distribution of adhesive genes are variant among S. aureus isolates and the infection sources. The bbp is the most specific infection associated gene with osteomyelitis. [DOI: 10.22401/JUNS.21. 1.13]
Comparison of trend detection methods in GEV models

Abstract In recent environmental studies, the examination of extreme events has great impact. The block maxima of environment-related indices can be analyzed by the tools of extreme value theory. For instance, the monthly maxima of the fire weather index at stations in British Columbia might be modeled by GEV distribution, but it is questionable whether the underlying stochastic process is stationary. This property can lead us to different approaches to determine whether there is a significant trend in the past few years’ data or not. One such approach is a likelihood ratio based procedure, which has favorable asymptotic properties, but for realistic sample sizes it might have large decision errors. In this paper, we analyze the properties of the likelihood ratio test for extremes by bootstrap simulations and present a simulation-based procedure to overcome the problem of small sample sizes. We also propose a return level calculation method. Using our theoretical results we reassess the trends of fire weather index monthly maxima in selected stations of British Columbia.
Combatting Rose Rosette Disease with Volunteer Involvement in the Monitoring Effort

Rose rosette disease (RRD) was ﬁrst reported on the North American continent in the early 1940s. In 2011, the causal agent of this disease was identiﬁed and described—the Rose rosette virus (RRV). In the last 10 years, RRD has gained widespread notoriety because of disease symptoms appearing on many roses which are used frequently in landscape plantings, both commercial and residential. Much of the prior scientiﬁc work on this disease was carried out on the multiﬂora rose. Currently, the disease issues are on cultivated roses within which no cultivar has been conﬁrmed to be resistant. There is an information gap in our knowledge of the pathogen, vector, and the disease on cultivated roses. Our goals for this project are to seek and identify potential disease tolerance or resistance in roses and increasing public awareness and knowledge of RRD with the purpose of reducing the disease spread with best management practices. Outreach and volunteer recruitment are key activities used to provide scientiﬁcally sound information, to establish the current disease range and to actively gather observational reports of RRD to identify resistant rose sources. Elements of these activities include educational meetings, factsheets, posters, and workshops where RRD symptoms recognition is emphasized. A web-based reporting tool was developed to capture observations from volunteers while continually keeping them engaged. It is hoped that through outreach and the collective monitoring effort, researchers will
Determination of prececal nutrient digestibility of raw, protease-supplemented shrimp meal and fish meal in broilers using regression approach

This study was carried out to measure the prececal protein and ether extract digestibility of shrimp and fish meal using the regression approach. A total of 280 Cobb 500 day-old broilers (mixed sexes) were randomly allotted to 7 treatment groups (4 replicates of 10 broilers each) in a completely randomized design. Feed intake was higher in the birds that received protease-supplemented shrimp meal and fish meal compared to the 4% raw shrimp meal and basal diets (P<0.05). Average daily gain, feed conversion ratio, final body weight, relative weight of the digestive organs, length of ileum and dressing percentage were not affected by the treatments. The effect of treatments on apparent digestibility of ether extract, organic matter, and dry matter was significant. The highest ether extract apparent digestibility was observed in the group that received 4% raw shrimp meal. Prececal digestibility of protein and ether extract was not different among raw shrimp meal, protease-supplemented shrimp meal and fish meal diets.
WiMUST: A cooperative marine robotic system for autonomous geotechnical surveys

This paper presents the main results of the European H2020 WiMUST project, whose aim was the development of a system of cooperative autonomous underwater vehicles and autonomous surface vehicles for geotechnical surveying. In particular, insights on the overall robotic technologies and methodologies employed, ranging from the communications and navigation framework to the cooperative and coordinated control solutions are given. The software architecture and the lessons learnt from the preliminary field test are also discussed. Finally, field results of the final survey campaign carried out in the Atlantic Ocean are presented, demonstrating how a team of seven robots could autonomously conduct a geotechnical survey, producing seismic images without artifacts.
How many can you catch? Factors influencing the occurrence of multi-prey loading in provisioning Greater Crested Terns§

Seabirds use several methods to transport food to their chicks; most species carry food in their stomachs or crops, but some terns and auks carry prey in their bills. Terns usually only carry one prey item at a time, limiting the rate at which they can provision their chicks, and restricting their effective foraging range. However, some terns do occasionally carry multiple prey, which should offer a selective advantage, but there are very few studies investigating the factors influencing the occurrence of multi-prey loading. We investigated the occurrence of multi-prey loads in provisioning Greater Crested Terns (Swift Tern) Thalasseus bergii bergii breeding on Robben Island, South Africa. Of 24 173 loads photographed, 1.3% comprised multiple prey items. Up to 11 fish were carried at once, but most multi-prey loads contained two Anchovies Engraulis encrasicolus, the most common prey item for this population of terns. Mixed species prey were recorded for the first time in a tern. Multi-prey loads occurred more frequently during mid- and late-provisioning, presumably because large chicks can cope with multiple prey, and have higher energetic requirements than small chicks. Mean standard length of Anchovies in multi-prey prey loads was less than Anchovies in single loads, possibly suggesting terns compensate for smaller prey sizes by bringing multiple prey back to their chick. The orientation of multiple Anchovies in a tern’s bill tended to be the same, suggesting that they were captured from polarised fish schools. At least some multi-prey loads were caught in a single dive.