Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison and utilization of different PCR-based approaches for molecular typing of Pseudomonas syringae pv. actinidiae strains from Italy

Abstract Over the last few years, a severe bacterial disease affecting kiwifruit has been reported in Italy. Its causal agent was identified as Pseudomonas syringae pv. actinidiae. For epidemiological purposes, we evaluated the discriminatory power of various PCR-based fingerprinting approaches. Profiles were generated by rep-PCR ((GTG)5-PCR), IS50-PCR and RAPD, from a wide collection of Italian, Korean and Japanese strains. The genetic relationships between strains of pv. actinidiae and strains from related pathovars were investigated. No differences between Italian strains were identified. However, some differences were identified between Italian strains and strains from Japan and Korea. The other pathovars clustered separately, and pv. theae was always more closely related to pv. actinidiae than the others. In general, the results obtained with the different methods were in good agreement, with RAPD showing the highest values of divergence between groups.
Association between intestinal microbiota composition and tail-biting in pigs

Background: Tail-biting (TB) is a serious behavioral disorder in pigs. It is defined as a pig chewing the tail of another pig. It is an important challenge in swine production as it impacts the animal welfare, its health and the economics and safety of the pork meat supply chain. Some treatments have been proposed but have not proven optimal. Nutrition, feed type and composition, appears to be an important factor in TB behavior, perhaps by modulating the intestinal microbiota (IM). In humans, IM is increasingly recognized as a modulator of behavior. Our aim was to assess an association between TB behavior and IM in pigs through comparisons of IM in groups of biter or bitten pigs to the IM in a non-biter and non-bitten negative control group, and through comparisons of IM between the biter and bitten groups. Each group, composed of 12 pigs, was formed at the beginning of the growing/finishing phase based on a target behavior analysis centered on TB behavior for the biter group and a score of damages caused to the tail for the bitten group. Fecal and blood samples were collected from each pig during a TB episode, at time 0, t0, and after a TB episode, four weeks later, at time 1, t1. Serum cortisol level was determined by ELISA and used as an indicator of stress. The pig’s fecal microbiota was analyzed from DNA extracted from freshly collected fecal matter using amplicon sequencing of the V4 hypervariable region of the 16S rRNA gene. Results: Serum cortisol levels were significantly higher in either the biter or bitten pig groups compared to the negative control group ( p =0.02 and p =0.01, respectively). Interestingly, no significant difference was revealed between the biter and bitten groups. The microbiota alpha-diversity was not significantly different between all groups, biter, bitten and negative control. Analyses of beta-diversity, however, revealed a significant difference between either the biter or the bitten group in comparison to the negative control group in terms of structure and composition of the microbiota. Lactobacillus were significantly more abundant in the negative control group compared to the two other groups ( p =0.001). No significant difference was revealed between the biter and bitten groups. Quantitative real-time PCR (qPCR) confirmed that lactobacilli were more abundant in the negative control group. Conclusions: This study demonstrates that TB behavior is associated to the IM composition in pigs.
Caffeoylglycolic acid methyl ester, a major constituent of sorghum, exhibits anti-inflammatory activity via the Nrf2/heme oxygenase-1 pathway

Sorghum contains diverse pharmacologically active phytochemicals including tannins, phenolic acids and anthocyanins. In the present study, we show that caffeoylglycolic acid methyl ester (CGME), a major constituent of the grains of Sorghum bicolor, exerted anti-inflammatory effects by inducing HO-1 expression. Treatment of RAW264.7 cells with CGME induced HO-1 protein and mRNA expression. CGME increased nuclear translocation of nuclear factor-E2-related factor 2 (Nrf2) and knockdown of Nrf2 by siRNA blocked CGME-mediated HO-1 induction. SP600125 (a JNK inhibitor) or LY294002 (a PI3K inhibitor) blocked CGME-induced HO-1 expression and nuclear translocation of Nrf2, suggesting that CGME induces HO-1 expression via activating Nrf2 through a PI3K and JNK pathway. Consistent with the notion that HO-1 has anti-inflammatory properties, CGME inhibited the production of nitric oxide (NO), prostaglandin E2 (PGE2) and interleukin-6 (IL-6) as well as the expression of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2) and IL-6 in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. CGME also protected C57BL/6 mice from LPS-induced mortality. However, inhibition of HO-1 abrogated the inhibitory effects of CGME on the production of NO, COX-2 and IL-6 in LPS-stimulated RAW264.7 cells. Taken together, these findings suggest that CGME exerts an anti-inflammatory effect through the Nrf2/HO-1 pathway, and may be a potential HO-1 inducer for preventing or treating inflammatory diseases.
A General Constant-Switching-Frequency Model-Predictive Control of Multilevel Converters With Quasi-PS-PWM/LS-PWM Output

Classical model-predictive control (MPC) of multilevel converters experiences poor steady-state performance owing to the noninterleaved and variable-frequency switching manner. To improve the steady-state performance of MPC, this article presents a general constant-switching-frequency MPC scheme for multilevel converters that can generate quasi-phase-shifted pulsewidth modulation (PWM)/quasi-level-shifted PWM output waveforms and the dc voltage utilization that compares well to that of the space vector modulation. In the proposed MPC scheme, parts of switching pairs of the multilevel converter are determined using the finite-control-set MPC using a hexagon selection approach, while the rest of the switching pairs of the multilevel converter are determined using the multiple-vector MPC for the constant-switching-frequency operation. The deadbeat approach is employed to reduce the computation burden of finite-control-set MPC. The basic concept of the proposed MPC is evaluated in both simulation and experimental tests on a five-level active-neutral-point-clamped converter.
Pitch the niche – taking responsibility for the concepts we use in ecology and species distribution modelling

In a discussion it is often easier to staunchly reject or offer resolute support for an idea. This third paper on the niche concept aims to develop a balanced argument by exploring general principles for determining an appropriate level for pitching the niche concept that will guide better use and less abuse of niche concepts. To do this we first have to accept that niche concepts are not necessarily essential for ecology. Rather than to improve niche concepts, our aim should then be to pitch the niche in terms of ecology. This aim helps us develop an ‘ultimate goal of the niche’ by which we can evaluate the concepts we use. For species distribution modelling, there has been a focus on the niche as an equilibrium outcome that perhaps has less relevance for disequilibrium situations (e.g. climate change projections). As is the case for much of ecology, more causal explanations of species' distributions use alternative terminologies and less frequently use the word ‘niche’. We suggest that niche concepts that are better aligned with the rest of ecology could arise from taking more responsibility for our own implementations, and by explaining our models with terms other than niche. A general, holistic niche concept promotes this view and promotes practical thinking about what we are modelling and how we interpret those models, which in turn should help inspire and support innovative modelling approaches in species distribution modelling.
Task‐based parallel strategies for computational fluid dynamic application in heterogeneous CPU/GPU resources

Parallel applications executing in contemporary heterogeneous clusters are complex to code and optimize. The task‐based programming model is an alternative to handle the coding complexity. This model consists of splitting the problem domain into tasks with dependencies through a directed acyclic graph, and submit the set of tasks to a runtime scheduler that maps each task dynamically to resources. We consider that computational fluid dynamics applications are typical in scientific computing but not enough exploited by designs that employ the task‐based programming model. This article presents task‐based parallel strategies for a simple CFD application that targets heterogeneous multi‐CPU/multi‐GPU computing resources. We design, develop, evaluate, and compare the performance of three parallel strategies (naive, ghost‐cells, and arrow) of a task‐based heterogeneous (CPU and GPU) application that simulates the flow of an incompressible Newtonian fluid with constant viscosity. All implementations rely on the StarPU runtime, and we use the StarVZ toolkit to conduct comprehensive performance analysis. Results indicate that the ghost cell strategy provides the best speedup (77×) considering the simulation time when the GPU resources still have available memory. However, the arrow strategy achieves better results when the simulation data increases.
Effect of combinations of chemical fertilizers and poultry manure on the productivity of crops in the cauliflower-stem amaranth-jute pattern

Different combinations of chemical fertilizers and organic manure were applied for sustainable crop productivity in the cauliflower-stem amaranth -jute cropping pattern. The experiment was conducted at farmer’s field in Multilocation Testing (MLT) site of Pakshi, Pahna over three years. There were five combinations of chemical fertilizers (CF) and poultry manure (PM) along with absolute control arranged in a randomized complete block design. The results revealed that all three crops showed significant yield for fertilizer and poultry manure use. Higher yields were obtained with 50% CF + 50% PM followed by 75% CF + 25% PM treatments where cauliflower equivalent yield was increased by 85% and 78%, respectively, over control. This indicates a positive residual effect of poultry manure on the subsequent crops. From the economic points of view, the highest marginal benefit cost ratio (MBCR) was attained in 100% chemical fertilizer due to its lower variable cost followed by 75% CF + 25% PM treated plots. However, gross margin was higher in 50% CF + 50% PM combination for its higher total yield. Key Words: Chemical fertilizer; poultry manure; productivity. DOI: 10.3329/bjar.v34i1. 5761 Bangladesh J. Agril. Res. 34(1) : 113-121, March 2009
48-HOUR ASSAY TEST FOR EQUINE GONADOTROPIN WITH RESULTS EXPRESSED IN INTERNATIONAL UNITS

OUR PREVIOUS METHODS for assaying equine gonadotropin (1, 2) involved autopsy of the test rats 120 hours after injection. The primary purpose for this long test interval was to obtain information on the qualitative ovarian response in follicular growth, luteinization, and interstitial cell development. This information was considered essential because, conceivably, the gonadotropic activity of pregnant mare serum might depend upon two or more gonadotropic hormones. We therefore wished to compare the nature of the responses obtained from sera collected at different intervals during pregnancy as well as the responses of various fractions obtained during studies on methods of purification. After comparing the qualitative and quantitative gonad response to extracts testing 4,000 to 7,000 R. U. per mg. total solids, with the response to untreated mare serum in normal and hypophysectomized male and female rats, we concluded that mare serum contains but one gonadotropic hormone (3). Three papers (4–7), give evid.
Comparative study of L 1 regularized logistic regression methods for variable selection

Abstract L 1 regularized logistic regression consists an important tool in data science and is dedicated to solve sparse generalized linear problems. The L 1 regularization is widely used in variable selection and estimation in generalized linear model analysis. This approach is intended to select the statistically important predictors. In this paper we compare the performance of some existing L 1 regularized logistic regression methods. The goal of our simulation study is directed toward the variable selection performance of regularized logistic regression in high dimensions. We consider three varying n (number of observations), p (number of predictors) settings and we support this comparison analysis by conducting various simulated experiments taking into consideration the correlation structure of the design matrix.
Determining and Improving the Localization Accuracy of AprilTag Detection

Fiducial markers like AprilTags play an important role in robotics, e.g., for the calibration of cameras or the localization of robots. One of the most important properties of an algorithm for detecting such tags is its localization accuracy.In this paper, we present the results of an extensive comparison of four freely available libraries capable of detecting AprilTags, namely AprilTag 3, AprilTags C++, ArUco as standalone libraries, and the OpenCV algorithm based on ArUco. The focus of the comparison is on localization accuracy, but the processing time is also examined. Besides working with pure tags, their extension to checkerboard corners is investigated.In addition, we present two new post-processing techniques. Firstly, a method that can filter out very inaccurate detections resulting from partial border occlusion, and secondly a new highly accurate method for edge refinement. With this we achieve a median pixel error of 0.017 px, compared to 0.17 px for standard OpenCV corner refinement.The dataset used for the evaluation, as well as the developed post-processing techniques, are made publicly available to encourage further comparison and improvement of the detection libraries.
Image Embedding into Generative Adversarial Networks

Image Embedding into Generative Adversarial Networks Rameen Abdal We propose an efficient algorithm to embed a given image into the latent space of StyleGAN. This embedding enables semantic image editing operations that can be applied to existing photographs. Taking the StyleGAN trained on the FFHQ dataset as an example, we show results for image morphing, style transfer, and expression transfer. Studying the results of the embedding algorithm provides valuable insights into the structure of the StyleGAN latent space. We propose a set of experiments to test what class of images can be embedded, how they are embedded, what latent space is suitable for embedding, and if the embedding is semantically meaningful.
Pelagic shrimps of the Sergestes edwardsii species group (Crustacea: Decapoda: Sergestidae)

Judkins, David C. Pelagic Shrimps of the Sergestes edwardsii Species Group (Crustacea: Decapoda: Sergestidae). Smithsonian Contributions to Zoology, number 256, 34 pages, 21 figures, 4 tables, 1978. —This global study of the systematics and distribution of the edwardsii species group is based upon examination of several hundred micronekton samples collected at stations scattered throughout the world ocean. Eight species, including three new ones, are recognized and described. Although the group is represented in all tropical and in certain subtropical oceanic regions, individual species have geographically restricted ranges. Conventional and numerical phyletic analyses reveal at least two, and perhaps three, closely related yet distinct lineages within the group. Species distributions tend to be allopatric or parapatric, overlap being most extensive between species of different lineages. Evidence of character divergence in reproductive structures of co-occurring species is discussed. OFFICIAL PUBLICATION DATE is handstamped in a limited number of initial copies and is recorded in the Institution's annual report, Smithsonian Year. SERIES COVER DESIGN: The coral Montastrea cavernosa Linnaeus). Library of Congress Cataloging in Publication Data Judkins, David C. Pelagic shrimps of the Sergestes edwardsii species group (Crustacea: Decapoda: Sergestidae) (Smithsonian contributions to zoology ; no. 256) Bibliography; p. 1. Sergestes. 2. Crustacea-—Classification. 3. Crustacea—Geographical distribution. I. Title. II. Series: Smithsonian Institution. Smithsonian contributions to zoology ; no. 256. QL1.S54 no. 56 [QL444.M33] 591'. 08s [595'. 3843] 77-608177
One stone, three birds: one AIEgen with three colors for fast differentiation of three pathogens

Visually identifying pathogens favors rapid diagnosis at the point-of-care testing level. Here, we developed a microenvironment-sensitive aggregation-induced emission luminogen (AIEgen), namely IQ–Cm, for achieving fast discrimination of Gram-negative bacteria, Gram-positive bacteria and fungi by the naked-eye. With a twisted donor–acceptor and multi-rotor structure, IQ–Cm shows twisted intramolecular charge transfer (TICT) and AIE properties with sensitive fluorescence color response to the microenvironment of pathogens. Driven by the intrinsic structural differences of pathogens, IQ–Cm with a cationic isoquinolinium moiety and a membrane-active coumarin unit as the targeting and interacting groups selectively locates in different sites of three pathogens and gives three naked-eye discernible emission colors. Gram-negative bacteria are weak pink, Gram-positive bacteria are orange-red and fungi are bright yellow. Therefore, based on their distinctive fluorescence response, IQ–Cm can directly discriminate the three pathogens at the cell level under a fluorescence microscope. Furthermore, we demonstrated the feasibility of IQ–Cm as a visual probe for fast diagnosis of urinary tract infections, timely monitoring of hospital-acquired infection processes and fast detection of molds in the food field. This simple visualization strategy based on one single AIEgen provides a promising platform for rapid pathogen detection and point-of-care diagnosis.
The dietary preferences of koalas, Phascolarctos cinereus, in southwest Queensland

The koala population in southwest Queensland is a large low-density population of important conservation value which is vulnerable to habitat loss, drought and climate change. The nutrient quality of Eucalyptus food trees favoured by koalas is an important factor influencing the survival of the koala on a low-nutrient-and-high-toxin diet. This study investigated the relationship between the diet of koalas, and food tree characteristics. Vegetation surveys, cuticle analysis and leaf chemical analysis were conducted in 14 study sites in southwest Queensland during the winter of 2010. Koala diet composition was different to eucalypt tree species availability, with Eucalyptus camaldulensis (56.5%) the most important tree species, E. coolabah (15.4%) and E. populnea (12.4%) of secondary preference. Leaf chemicals (moisture, total nitrogen, total phenolics, and a nutrition index = (moisture*nitrogen) / total phenolics) were significantly related to tree species, surface water availability, soil type and proximi.
PURIFICATION OF pKYM-ENCODED REPK, A PROTEIN REQUIRED FOR THE INITIATION OF PLASMID REPLICATION

Replication of pKYM requires the plasmid-encoded RepK protein, which specifically binds to the replication origin of the plasmid. This binding was easily detected in a gel-shift assay. We have used this characteristic to purify RepK protein, to near homogeneity. The repK gene was placed under the control of the phage T7 RNA polymerase promoter on a plasmid. Upon induction of T7 RNA polymerase, Escherichia coli clones containing the recombinant plasmid overproduced the RepK protein, which was then purified in significant quantities. The molecular weight of the RepK protein under denaturing conditions is 36,000, which is consistent with the size predicted from the DNA sequence data. The N-terminal amino acid sequence determined for the purified RepK matches that deduced from the DNA sequence. RepK protein appears to bind to the replication origin as a monomer with a dissociation constant (K d ) of 2.7 × 10 −9 M
Ritmo de crecimiento diario de la producción científica sobre Covid-19. Análisis en bases de datos y repositorios en acceso abierto

La comunidad cientifica se encuentra ante uno de sus mayores retos para resolver un problema sanitario de alcance global como es la pandemia del Covid-19. Esta situacion ha generado un volumen de publicaciones sin precedentes, pero ? cual es el volumen, en terminos de publicaciones, de la investigacion sobre Covid-19? Conseguir una vision global sobre el crecimiento diario de la produccion cientifica sobre Covid-19 en diferentes fuentes de informacion (Dimensions, Web of Science Core Collection, Scopus, PubMed y ocho repositorios) es el objetivo general de este trabajo de investigacion. En relacion a los resultados obtenidos, Dimensions indexa un total de 9.435 publicaciones (69% con revision por pares y 2.677 preprints) muy por encima de Scopus (1.568) y WoS (718). Nos encontramos ante un fenomeno clasico bibliometrico de crecimiento exponencial (R2 =0,92). El ritmo de crecimiento a nivel global es de 500 publicaciones diarias en los ultimos dias y la produccion de duplica cada 15 dias. En el caso de PubMed el crecimiento semanal esta en torno a las 1.000 publicaciones, tanto en Dimensions como en LitCovid. De los ocho repositorios analizados se situan a la cabeza PubMed Central, medRxiv y SSRN, a pesar de la enorme contribucion de estos las revistas siguen siendo el nucleo de la comunicacion cientifica. Finalmente se ha establecido que tres de cada cuatro publicaciones sobre el Covid-19 estan disponibles en acceso abierto. Estas cifras exigen una respuesta de los profesionales de la informacion ante una explosion de informacion sin precedentes que nos situa en el centro de la pandemia informativa.
THE USE OF RAP-PCR IN STUDYING MYCOBACTERIUM TUBERCULOSIS INTRACELLULAR GENE DURING MACROPHAGE INFECTION.

Mycobacterium tuberculosis is the second leading cause of death from infectious agent. This study sought to detect M. tuberculosis genes, which were specifically expressed, or upregulated during intracellular infection of J774 murine macrophages; as such genes may be potential targets for novel drug action. J774 murine macrophage cell line was infected with M. tuberculosis (H37Rv strain) at 10:1 multiplicity of infection (MOI). RNA was differentially extracted from M. tuberculosis infecting J774 macrophage cell line. The control in this case was RNA from extracellular broth grown bacteria. Approximately 50 ng of RNA from intracellular derived bacteria and extracellular derived bacteria (control) were subjected to random arbitrarily primed PCR (RAP-PCR) using 50 primer combinations. Eleven differential RAP-PCR products were observed. All RAP-PCR products were cloned into pCR®2.1 and sequenced in order to determine the identity of the products. Four of the eleven products were derived from macrophage genes and another 4 products were derived from the M. tuberculosis rRNA genes (three 23S and one 16S rRNA). The 3 remaining RAP-PCR products were found to be mycobacterial genes other than ribosomal genes. The three products were genes encoding enzyme involving in a shikimate pathway, a putative carboxyphosphonoenolpyruvate phosphonomutase and a serine protease with homology to HtrA. Of the 3 mycobacterial genes other than ribosomal genes detected, none were specifically expressed during intracellular infection but competitive RT-PCR showed that aroF gene was upregulated two-fold in intracellular derived bacilli.