Miracle-dz/UniFAR-FTUs huggingface dataset:
Problems of epitypification in morphologically simple green microalgae: a case study of two widespread species of Klebsormidium (Klebsormidiophyceae, Streptophyta)

The extensive genetic cryptic diversity revealed by molecular studies in many green microalgae has caused great uncertainties in the circumscription of some species described on strictly morphological grounds. These uncertainties should be resolved by obtaining molecular data from type materials, but this procedure is not feasible in many species because the type specimens are illustrations, or too small or poorly preserved to obtain DNA sequence data. In these situations, the selection of an epitype is often a mandatory requirement to define the identity of a species and establish unambiguously its position in molecular phylogenies. In this study we investigated the identity of two widespread species of Klebsormidium (Streptophyta), K. flaccidum and K. nitens, which were recently epitypified by Mikhailyuk and colleagues. We collected several specimens of these algae from the type localities and the original habitats of these two species, for which we examined morphology in the field material and in culture, and obtained sequences of the rbcL gene. On the basis of the original descriptions, we conclude that the designation of the epitype of K. flaccidum was correct, whereas the epitype of K. nitens (which consists of material collected tens of thousands of km from the type locality) was most probably incorrect. We discuss the implications of these decisions for the classification of Klebsormidium and, more generally, the importance of the correct choice of epitype material for the taxonomy of green microalgae.
Throughput maximization for long-distance real-time data transmission over multiple UAVs

Recently, unmanned aerial vehicles (UAVs) have attracted attention as a means to observe a terrain due to their ability to fly above the place to be observed and collect information (e.g., picture, video and sensor data) easily. Moreover, UAVs can transmit data through equipped wireless transceivers. However, because the payload of UAVs is limited, the performance of the transceiver is limited as well. Therefore, UAVs need to cooperate with other UAVs for high speed and long distance data transmission. In this article, we suppose a network model for transmitting in real time observed data in a multihop relay communication; then we take into account parameters related to the observation area (e.g., area size, distance between a base station and observation area) and signal attenuation by obstacles (e.g., buildings, trees). Finally, we propose a way to maximize the network performances affected by those parameters in the network.
Structural Conservation, Variability, and Immunogenicity of the T6 Backbone Pilin of Serotype M6 Streptococcus pyogenes

ABSTRACT Group A streptococcus (GAS; Streptococcus pyogenes) is a Gram-positive human pathogen that causes a broad range of diseases ranging from acute pharyngitis to the poststreptococcal sequelae of acute rheumatic fever. GAS pili are highly diverse, long protein polymers that extend from the cell surface. They have multiple roles in infection and are promising candidates for vaccine development. This study describes the structure of the T6 backbone pilin (BP; Lancefield T-antigen) from the important M6 serotype. The structure reveals a modular arrangement of three tandem immunoglobulin-like domains, two with internal isopeptide bonds. The T6 pilin lysine, essential for polymerization, is located in a novel VAKS motif that is structurally homologous to the canonical YPKN pilin lysine in other three- and four-domain Gram-positive pilins. The T6 structure also highlights a conserved pilin core whose surface is decorated with highly variable loops and extensions. Comparison to other Gram-positive BPs shows that many of the largest variable extensions are found in conserved locations. Studies with sera from patients diagnosed with GAS-associated acute rheumatic fever showed that each of the three T6 domains, and the largest of the variable extensions (V8), are targeted by IgG during infection in vivo. Although the GAS BP show large variations in size and sequence, the modular nature of the pilus proteins revealed by the T6 structure may aid the future design of a pilus-based vaccine.
Driver's Behaviour Monitoring on Urban Roads of a Tier 2 City in India

There are significant differences in individual driving patterns of drivers due to each one's varying social behaviours. A driver's incorrect perception and misinterpretation of true traffic scenario owing to his social behavioural approach causes significant problem for road traffic safety as it leads to degraded performance of driving pattern. Hence there is an urgent need to take measures and develop modules which work for the reduction of road traffic accidents. This paper proposes an approach which will try to analyze the factors which affect the social behavior of a driver. An observational study was carried out in the city of Nagpur with the help of Nagpur Traffic Police Dept. and N. K. P. Salve Institute of Medical Sciences & Research Centre, India in January 2015. Also live observations were undertaken during daylight hours by installing CCTV cameras to monitor traffic. The observations mainly tried to focus on whether drivers were engaged in any visible type of secondary activity while driving or involved in any type of traffic violation because of aggressive pattern or casual approach. The observations were quite alarming and based on results some approaches have been proposed which help to analyze the relationship between factors causing driving errors and traffic accidents.
NeuO for Neuronal Labeling in Zebrafish

We report the application of our newly developed fluorescent probe 3-(benzylamino)-4,4-difluoro-5-(4-propyl-1H-1,2,3-triazol-1-yl)-8-(4-(2-hydroxyacetamido)phen-yl)-4-bora-3a,4a-diaza-s-indacene (NeuO) to label and image live neurons in zebrafish. Immersing zebrafish embryos in NeuO or injecting NeuO into zebrafish brain ventricles results in nontoxic in vivo neuronal labeling. We demonstrate the applicability of NeuO and envisage the potential of this compound as a rapid and simple labeling reagent for studying neuron development and degeneration.
Towards Joint Optimization Over ICT and Cooling Systems in Data Centre: A Survey

Effective management of ICT (information and communications technology) and cooling is critical in modern data centres for high energy efficiency. This survey paper gives an overview of the joint optimization between ICT and cooling management under conventional air-cooled technology in the data centre. We first review the enabling techniques of ICT and cooling management in the data centre, which provide the opportunity to dynamically control the server utilization and operate cooling equipment. We then present the coupling models between ICT and cooling management, which are the basis of the optimization approaches for green data centre. The joint optimization of ICT and cooling management is considered under a set of performance metrics, including thermal requirement, power consumption, and application delay. We summarize the workload scheduling algorithms designed from the optimization approaches. We also present some testbeds in the data centres. Finally, we discuss on the future trends of the management in the data centre.
Preventing the Airborne Spread of Staphylococcus aureus by Persons With the Common Cold: Effect of Surgical Scrubs, Gowns, and Masks

Objective. Transmission of Staphylococcus aureus via air may play an important role in healthcare settings. This study investigates the impact of barrier precautions on the spread of airborne S. aureus by volunteers with experimentally induced rhinovirus infection (ie, the common cold). Design. Prospective nonrandomized study. Setting. Wake Forest University School of Medicine (Winston-Salem, NC). Participants. A convenience sample of 10 individuals with nasal S. aureus carriage selected from 593 students screened for carriage. Intervention. Airborne S. aureus dispersal was studied in the 10 participants under the following clothing conditions: street clothes, surgical scrubs, surgical scrubs and a gown, and the latter plus a face mask. After a 4-day baseline period, volunteers were exposed to a rhinovirus, and their clinical course was followed for 12 days. Daily swabs of nasal specimens, pharynx specimens, and skin specimens were obtained for quantitative culture, and cold symptoms were documented. Data were analyzed by random-effects negative binomial models. Results. All participants developed a common cold. Incidence rate ratios (IRRs) indicated that, compared with airborne levels of S. aureus during sessions in which street clothes were worn, airborne levels decreased by 75% when surgical scrubs were worn (P<.001), by 80% when scrubs and a surgical gown were worn (P<.001), and by 82% when scrubs, a gown, and a face mask were worn (P<.001). The addition of a mask to the surgical scrubs and gown did not reduce the airborne dispersal significantly (IRR, 0.92;P>.05). Male volunteers shed twice as much S. aureus as females (incidence rate ratio, 2.04; P = .013). The cold did not alter the efficacy of the barrier precautions. Conclusions. Scrubs reduced the spread of airborne S. aureus, independent of the presence of a rhinovirus-induced cold. Airborne dispersal of S. aureus during sessions in which participants wore surgical scrubs was not significantly different from that during sessions in which gowns and gowns plus masks were also worn.
Changes in peptidergic nerves in the atrioventricular valves of streptozotocin‐induced diabetic rats: A confocal microscopy study

Several previous studies have described the distribution of neuropeptide Y (NPY)‐like and calcitonin gene related peptide (CGRP)‐like immunoreactive nerve fibres in the atrioventricular valves of humans and various animals. It has been suggested that peptide‐containing nerve fibres might have motor or sensory roles in valvular function. Although there is evidence that diabetic changes occur in the sympathetic (preganglionic and postganglionic), parasympathetic (vagal) and peptidergic nerves of rats, the changes of peptide‐containing nerve fibres in the atrioventricular valves of the diabetic rat have not been studied. The distribution, relative density and staining intensity of NPY‐like and CGRP‐like immunoreactive nerve fibres in the mitral and tricuspid valves were studied in whole mount preparations using confocal microscopy with a computer‐assisted image analysis system. Streptozotocin‐induced diabetic and control rats were sacrificed at 12 and 24 months. The nerve staining intensity within the tricuspid valve was greater than the mitral valve in both control (P < 0.01) and diabetic (P < 0.001) rats. Nerve density in the anterior leaflet was greater than the posterior leaflet of the mitral valve. However, the anterior leaflet of the mitral and tricuspid valves showed a decreased number of nerve fibres, followed by drastic reduction in the staining intensities for both the peptides studied (P < 0.001) in the long‐term diabetic rat. The decrease in the number of nerve fibres that follow the mechanical interruption of nerves raises the possibility that cycles of degeneration may occur. It is suggested that these peptide‐containing nerve fibres in the atrioventricular valves may be involved in valvular dysfunction in the diabetic state. Anat Rec 258:277–285, 2000. © 2000 Wiley‐Liss, Inc.
Novel C-ring Analogs of Ursolic acid: Synthesis and Cytotoxic Evaluation

Ursolic acid (1), a natural pentacyclic triterpenic acid, afforded a variety of ring-C transformed products (5–11) when treated with N-bromosuccinimide under the influence of a range of protective groups and solvents. The synthesized compounds have been evaluated for cytotoxic activity against prostate PC 3, leukemia THP 1, cervical Hela and lung A-549 cancer cell lines. Among the tested analogs, compounds 5, 8, 9 and 10 showed potent activity against PC 3, THP 1 and Hela cell lines. Especially, compound 10 showed enhanced activity against the Hela cell line than the parent compound. Compounds 5, 8 and 9 showed comparable activities against PC 3 and THP 1 cell lines.
Effect of dog breed 'varieties' on population genetic structure.

Breeding for specific characteristics in purebred dogs has resulted in a wide diversity of breeds. These breeding practices probably contributed to a reduced genetic variation within breeds. The division of dogs into different breeds is mainly based on morphological appearance and/or behaviour. However, homogeneity within breeds is not always the case. Some breeds are divided into varieties or subpopulations, based on colour types and patterns, which is achieved by reproductive isolation. The reproductive isolation provided by this “breed-fragmentation” is likely to promote genetic distance between varieties or subpopulations (Mellanby et al., 2013). When a population is divided into subpopulations, there is also less heterozygosity compared to an undivided population (L acy, 1987).
Algorithmes de bandits pour la recommandation à tirages multiples

The multiple-play recommender systems (RS) are RS which recommend several items to the users. RS are based on learning models in order to choose the items to recommend. Among these models, the bandit algorithms offer the advantage to learn and exploite the learnt elements at the same time. Current approaches require running as many instances of a bandit algorithm as there are items to recommend. As opposed to that, we handle all recommendations simultaneously, by a single instance of a bandit algorithm. We show on two benchmark datasets (Movielens and Jester) that our method, MPB (Multiple Plays Bandit), obtains a learning rate about thirteen times faster while obtaining equivalent click-through rates. We also show that the choice of the bandit algorithm used impacts the level of improvement.
Word retrieval in ottoman documents

In this paper, two image matching methods are adapted to retrieve words in Ottoman documents. The first method is based on Dynamic Time Warping (DTW) method proposed in [7], while the second method is based on the Shape Context descriptor [10]. Firstly, all sub-words in a given Ottoman document are extracted. In the first method, a 4-variant feature vector (upper and lower word profiles, background to ink transition, vertical projection) is calculated for each sub-word and feature vectors' distance to each other is found by DTW algorithm. In the second method, shape context descriptor is used to calculate the distances of sub-word images. The methods are tested on an Ottoman data set, which consists of 10 pages of Leyla and Mecnun Divan of Fuzuli.
Near Optimal Viterbi Decoders for Convolutional Codes in Symmetric Alpha-Stable Noise

The design of Viterbi decoders for signals in noise modeled using the symmetric α-stable distribution is considered. The traditional Viterbi decoder, which has a branch metric optimized for Gaussian noise, performs poorly in symmetric α-stable noise. Since the optimal maximum likelihood branch metric is impractically complex, many suboptimal metrics have been proposed, such as the hard decision, p-norm and absolute (1-norm) metric. A Viterbi decoder that uses the absolute branch metric has better performance and lower complexity, however, its performance degrades when α decreases. In this paper, the effects of the suboptimal metrics on the performance of the Viterbi decoder are analyzed, and a clear justification for the performance of the decoder that uses the Gaussian and absolute metrics is provided. Moreover, this analysis is used to design a low complexity suboptimal branch metric that improves the performance of the Viterbi decoder by about 0.75 to 2 dB compared to the absolute branch metric for different values of α, at almost no additional complexity.
Shape and topology optimization involving the eigenvalues of an elastic structure: A multi-phase-field approach

Abstract A cost function involving the eigenvalues of an elastic structure is optimized using a phase-field approach, which allows for topology changes and multiple materials.We show continuity and differentiability of simple eigenvalues in the phase-field context. Existence of global minimizers can be shown, for which first order necessary optimality conditions can be obtained in generic situations. Furthermore, a combined eigenvalue and compliance optimization is discussed.
User Requirements and System Requirements

In software, we often talk about user requirements and system requirements. Most people know the terms: users give you user requirements, designers work from system requirements. The terms have entered our lingua franca. However, in my experience, people - stakeholders, analysts, and designers - often fail to differentiate the roles of these two kinds of requirements. Unfortunately, treating user and system requirements as the same thing can create problems for projects. In this column I unpack some problems I've observed with user requirements and system requirements and explore what we can do about them.
Development of Image Processing Scheme for Bacterial Classification Based on Optimal Discriminant Feature

The objective of the current work is to develop an automatic tool to identify microbiological data types using computer vision and pattern recognition. Current systems rely on the subjective reading of profiles by a human expert. This process is time-consuming and prone to errors. Bacteriophage (phage) typing & Fluorescent imaging methods are used to extract representative feature profiles and identify the bacterial types. For feature selection of Bacterial identification system, the most successful method seems to be the appearance-based approach, which generally operates directly on images or appearances of bacterial objects. The image segmentation, Linear Discriminant Analysis (LDA), Direct Fractional LDA (DFLDA) and Principal Component Analysis (PCA) are the powerful tools used for feature extraction. Then the principal components are analyzed by DFLDA and simple Nearest Neighbor Classifier technique is used to identify the type of bacteria. The effectiveness of the proposed method has been verified through experimentation using fifty popular bacterial image databases.
Selection of support materials for immobilization of Burkholderia cepacia PCL3 in treatment of carbofuran-contaminated water

This study investigated the utilization of agricultural matrices as the support materials for cell immobilization to improve the technique of bioremediation. Coir, bulrush, banana stem and water hyacinth stem in both delignified and undelignified forms were used to immobilize Burkholderia cepacia PCL3 in bioremediation of carbofuran at 5 mg l−1 in synthetic wastewater. Undelignified coir was found to be the most suitable support material for cell immobilization, giving the short half-life of carbofuran of 3.40 d (2.8 times shorter than the treatments with free cells). In addition, it could be reused three times without a loss in ability to degrade carbofuran. The growth and degradation ability of free cells were completely inhibited at the initial carbofuran concentrations of 250 mg l−1, while there was no inhibitory effect of carbofuran on the immobilized cells. The results indicated a great potential for using the agricultural matrices as support material for cell immobilization to improve the overall efficiency of carbofuran bioremediation in contaminated water by B. cepacia PCL3.
Helicobacter pylori Urease Suppresses Bactericidal Activity of Peroxynitrite via Carbon Dioxide Production

ABSTRACT Helicobacter pylori can produce a persistent infection in the human stomach, where chronic and active inflammation, including the infiltration of phagocytes such as neutrophils and monocytes, is induced. H. pylori may have a defense system against the antimicrobial actions of phagocytes. We studied the defense mechanism of H. pylori against host-derived peroxynitrite (ONOO−), a bactericidal metabolite of nitric oxide, focusing on the role of H. pylori urease, which produces CO2 and NH3 from urea and is known to be an essential factor for colonization. The viability of H. pylori decreased in a time-dependent manner with continuous exposure to 1 μM ONOO−, i.e., 0.2% of the initial bacteria remained after a 5-min treatment without urea. The bactericidal action of ONOO− against H. pyloriwas significantly attenuated by the addition of 10 mM urea, the substrate for urease, whereas ONOO−-induced killing of a urease-deficient mutant of H. pylori or Campylobacter jejuni, another microaerophilic bacterium lacking urease, was not affected by the addition of urea. Such a protective effect of urea was potentiated by supplementation with exogenous urease, and it was almost completely nullified by 10 μM flurofamide, a specific inhibitor of urease. The bactericidal action of ONOO− was also suppressed by the addition of 20 mM NaHCO3 but not by the addition of 20 mM NH3. In addition, the nitration ofl-tyrosine of H. pylori after treatment with ONOO− was significantly reduced by the addition of urea or NaHCO3, as assessed by high-performance liquid chromatography with electrochemical detection. These results suggest that H. pylori-associated urease functions to produce a potent ONOO− scavenger, CO2/HCO3−, that defends the bacteria from ONOO− cytotoxicity. The protective effect of urease may thus facilitate sustained bacterial colonization in the infected gastric mucosa.
Noninvasive kinematic analysis of the walk in healthy large-breed dogs.

OBJECTIVES To use computer-assisted kinematic analysis to describe the walk in healthy dogs and to adapt Fourier transformation for analysis of the data. DESIGN Evaluation of normal walk in dogs, using kinematic and force plate analysis. SAMPLE POPULATION 15 healthy large-breed dogs. PROCEDURE Morphometric data were collected to describe the sample population. Temporal and distance variables were measured to describe the walk. Flexion and extension movements were described for the scapulohumeral, cubital, carpal, coxofemoral, femorotibial, and tarsal joints. Fourier transformation was adapted to facilitate analysis of the joint angle waveforms. RESULTS Unique and complex patterns of flexion and extension movements were observed for each joint studied. The walk had consistency of movement in the sample population in temporal and distance variables and joint movements. Variances attributable to intra- and interdog differences were similar and 1 to 2 orders of magnitude smaller than the mean Fourier coefficients from which they were calculated for all 6 joints. The number of essential Fourier coefficients required to represent the joint angle waveforms was 3 for the coxofemoral joint, 5 each for the femorotibial, scapulohumeral, cubital, and carpal joints, and 6 for the tarsal joint. CONCLUSIONS Computer-assisted kinematic gait analysis proved to be a reliable and consistent technique for assessment of movement at the walk in dogs, and Fourier transformation was shown to be an effective tool for analysis of the kinematic data. CLINICAL RELEVANCE The database derived from the normal sample population in this study can be used as a model of musculoskeletal function at the walk for future comparisons with disease and treatment.