Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete Genome Sequences of Three Isolates of Xanthomonas fragariae, the Bacterium Responsible for Angular Leaf Spots on Strawberry Plants

ABSTRACT Xanthomonas fragariae is a worldwide-spread plant bacterial disease causing angular leaf spots, thus reducing the yield of production for strawberry fruits. Three isolates with various geographic and time origins were sequenced with long-read technology (PacBio) to generate finished genome sequences of virulent strains and observe the variability in their contents.
The source of fatty acids incorporated into proliferating lymphoid cells in immune-stimulated lymph nodes

To explore the hypothesis that proliferating lymphoid cells in immune-stimulated lymph nodes obtain nutrients locally from adjacent adipose tissue, adult guinea pigs were fed for 6 weeks on standard chow or on chow supplemented with 100 g suet, sunflower oil or fish oi/g. All the guinea pigs ate standard chow for the last 5 d, during which swelling of one popliteal lymph node was stimulated by repeated local injection of lipopolysaccharide. The fatty acid compositions of phospholipids in both popliteal and in several mesenteric lymph nodes, and of triacylglycerols in eleven samples of adipose tissue defined by their anatomical relations to lymph nodes, were determined by GC. The proportions of fatty acids in the phospholipids extracted from the stimulated popliteal node correlated best with those of triacylglycerols in the surrounding adipocytes, less strongly with those of adipocytes elsewhere in depots associated with lymphoid tissue, but not with those of nodeless depots. The composition of triacylglycerols in the perinodal adipose tissue changed under local immune stimulation. We conclude that proliferating lymphoid cells in activated lymph nodes obtain fatty acids mainly from the triacylglycerols in adjacent perinodal adipose tissue. Immune stimulation prompts changes in the fatty acid composition of the triacylglycerols of adipocytes in node-containing depots that equip the adipose tissue for provisioning immune responses. Such local interactions show that specialised adipocytes can act as an interface between whole-body and cellular nutrition, and may explain why mammalian adipose tissue is partitioned into a few large and many small depots.
Dynamics of confined suspensions of swimming particles

Low Reynolds number direct simulations of large populations of hydrodynamically interacting swimming particles confined between planar walls are performed. The results of simulations are compared with a theory that describes dilute suspensions of swimmers. The theory yields scalings with concentration for diffusivities and velocity fluctuations as well as a prediction of the fluid velocity spatial autocorrelation function. Even for uncorrelated swimmers, the theory predicts anticorrelations between nearby fluid elements that correspond to vortex-like swirling motions in the fluid with length scale set by the size of a swimmer and the slit height. Very similar results arise from the full simulations indicating either that correlated motion of the swimmers is not significant at the concentrations considered or that the fluid phase autocorrelation is not a sensitive measure of the correlated motion. This result is in stark contrast with results from unconfined systems, for which the fluid autocorrelation captures large-scale collective fluid structures. The additional length scale (screening length) introduced by the confinement seems to prevent these large-scale structures from forming.
Multilayer microfluidic systems with indium-tin-oxide microelectrodes for studying biological cells

Contemporary semiconductor and micromachining technologies have been exploited to develop lab-on-a-chip microsystems, which enable parallel and efficient experiments in molecular and cellular biology. In these microlab systems, microfluidics play an important role for automatic transportation or immobilization of cells and bio-molecules, as well as for separation or mixing of different chemical reagents. However, seldom microlab systems allow both morphology and electrophysiology of biological cells to be studied in situ. This kind of study is important, for example, for understanding how neuronal networks grow in response to environmental stimuli. To fulfill this application need, this paper investigates the possibility of fabricating multi-layer photoresists as microfluidic systems directly above a glass substrate with indium-tin-oxide (ITO) electrodes. The microfluidic channels are designed to guide and trap biological cells on top of ITO electrodes, through which the electrical activities of cells can be recorded or elicited. As both the microfluidic system and ITO electrodes are transparent, the cellular morphology is observable easily during electrophysiological studies. Two fabrication processes are proposed and compared. One defines the structure and curing depth of each photoresist layer simply by controlling the exposure time in lithography, while the other further utilizes a sacrificial layer to defines the structure of the bottom layer. The fabricated microfluidic system is proved bio-compatible and able to trap blood cells or neurons. Therefore, the proposed microsystem will be useful for studying cultured cells efficiently in applications such as drug-screening.
Improved Upper Bounds to the Causal Quadratic Rate-Distortion Function for Gaussian Stationary Sources

We improve the existing achievable rate regions for causal and for zero-delay source coding of stationary Gaussian sources under an average mean squared error distortion measure. To begin with, we find a closed-form expression for the information-theoretic causal rate-distortion function (RDF) under such distortion measure, denoted by R<sub>c</sub><sup>it</sup>(D), for first-order Gauss-Markov processes. R<sub>c</sub><sup>it</sup>(D) is a lower bound to the optimal performance theoretically attainable (OPTA) by any causal source code, namely R<sub>c</sub><sup>op</sup>(D). We show that, for Gaussian sources, the latter can also be upper bounded as R<sub>c</sub><sup>op</sup>(D) ≤ R<sub>c</sub><sup>it</sup>(D) + 0.5 log <sub>2</sub>(2πe) bits/sample. In order to analyze R<sub>c</sub><sup>it</sup>(D) for arbitrary zero-mean Gaussian stationary sources, we introduce R<sub>c</sub><sup>it̅</sup>(D), the information-theoretic causal RDF when the reconstruction error is jointly stationary with the source. Based upon R<sub>c</sub><sup>it̅</sup>(D), we derive three closed-form upper bounds to the additive rate loss defined as R<sub>c</sub><sup>it̅</sup>(D) - R(D), where R(D) denotes Shannon's RDF. Two of these bounds are strictly smaller than 0.5 bits/sample at all rates. These bounds differ from one another in their tightness and ease of evaluation; the tighter the bound, the more involved its evaluation. We then show that, for any source spectral density and any positive distortion D ≤ σ<sub>x</sub><sup>2</sup>, RU(D) can be realized by an additive white Gaussian noise channel surrounded by a unique set of causal pre-, post-, and feed- back niters. We show that finding such filters constitutes a convex optimization problem. In order to solve the latter, we propose an iterative optimization procedure that yields the optimal niters and is guaranteed to converge to R<sub>c</sub><sup>it̅</sup>(D). Finally, by establishing a connection to feedback quantization, we design a causal and a zero-delay coding scheme which, for Gaussian sources, achieves an operational rate lower than R<sub>c</sub><sup>it̅</sup>(D) +0.254 and R<sub>c</sub><sup>it̅</sup>(D) + 0.754 bits/sample, respectively. This implies that the OPTA among all zero-delay source codes, denoted by R<sub>zd</sub><sup>op</sup>(D), is upper bounded as R<sub>zd</sub><sup>op</sup>(D) <; R<sub>c</sub><sup>it̅</sup>(D) + 1-254 <; R(D) + 1.754 bits/sample.
Palliative radiation therapy for canine osteosarcoma.

Palliation for osteosarcoma O steosarcoma accounts for approximately 85% of primary bone cancers in the dog (1). It is a common cancer of large to giant breed dogs, and it occurs primarily in the appendicular skeleton (1). Osteosarcoma can appear as a lytic, productive or, most commonly, mixed lytic-productive lesion on radiographs (Figure 1) (2). Even with removal of the primary tumor before spread of the cancer is clinically detectable, metastases to lung, bone, or other sites eventually develop in almost all dogs. Palliative radiation therapy for bone pain is indicated in those dogs that do not undergo amputation or a limb-sparing surgery. The goal of palliative therapy in cancer patients is to control pain from an incurable tumor and to support overall quality of life (3). Radiation protocols that have minimal risk of acute side effects are used, so that no discomfort results from treatment. The presence of pulmonary metastases is not a contraindication to palliative radiation treatment, as long as the patient is not showing clinical signs related to their metastatic disease.
QUALITY, OBSOLESCENCE AND UNSUSTAINABLE INNOVATION

One of the negative side effects of the consumer society and the increasing number of consumer goods available to the average household is the intransparency of product quality, especially product lifetime. There are many examples on failing products and premature obsolescence. Often this phenomenon is related to companies’ profit maximization strategies (planned obsolescence) and consumer protection policy is mobilized to stop this type of exploitation. The paper applies micro-economic analysis to discuss the problem of optimal product quality (e.g. lifetime) in terms of cost-benefit-analysis and under imperfect information (based on Akerlof’s lemon problem). Given consumers’ actual willingness to pay there is an optimal quality which is lower than the technically possible. If the innovation perspective (Schumpeter’s “creative destruction”) is added to the analysis, increasing global competition and speed of product innovation are identified as core drivers for shorter product lifecycles and tend to be the actual limiting factor of product lifetime (economic vs. technical obsolescence). Even if the goals of sustainable development are included in the analysis, this does not provide an unambiguous argument for long-life products as new products tend to be more eco-efficient. A broader discussion on optimal quality (lifetime) of products is necessary, based on holistic life-cycle assessment of alternative product quality options. And finally: The tendency of increasing aftersales disappointment of consumers’ expectations and conflicts with sustainable development goals need to be addressed in a more general debate on (limits of) consumerism. Minor changes in the laws for protecting consumers (e.g. longer warranty) will not do the job. Keywords: Obsolescence, innovation, quality competition, imperfect information, sustainable development, life-cycle analysis
Stack Overflow: A code laundering platform?

Developers use Question and Answer (Q&A) websites to exchange knowledge and expertise. Stack Overflow is a popular Q&A website where developers discuss coding problems and share code examples. Although all Stack Overflow posts are free to access, code examples on Stack Overflow are governed by the Creative Commons Attribute-ShareAlike 3.0 Unported license that developers should obey when reusing code from Stack Overflow or posting code to Stack Overflow. In this paper, we conduct a case study with 399 Android apps, to investigate whether developers respect license terms when reusing code from Stack Overflow posts (and the other way around). We found 232 code snippets in 62 Android apps from our dataset that were potentially reused from Stack Overflow, and 1,226 Stack Overflow posts containing code examples that are clones of code released in 68 Android apps, suggesting that developers may have copied the code of these apps to answer Stack Overflow questions. We investigated the licenses of these pieces of code and observed 1,279 cases of potential license violations (related to code posting to Stack overflow or code reuse from Stack overflow). This paper aims to raise the awareness of the software engineering community about potential unethical code reuse activities taking place on Q&A websites like Stack Overflow.
“What Is It?” Categorization Flexibility and Consumers' Responses to Really New Products

To understand really new products, consumers face the challenge of constructing new knowledge structures rather simply changing existing ones. Recent research in categorization suggests that one strategy for creating representations for these new products is to use information already contained in familiar product categories. While knowledge from multiple existing categories may be relevant, little research has examined how (and if) consumers process information drawn from more than one domain. We use two experiments to demonstrate how consumers use cues from multiple categories to develop expectations about and preferences for new products. Our findings suggest that the first plausible category label provided to the consumer significantly influences their categorizations, expectations, and preferences. Only when advertisers place limits on the type of information to transfer from each existing category can consumers use information from multiple categories effectively.
Interactions and systems for augmenting a live dance performance

The context of this work is to develop, adapt and integrate augmented reality related tools to enhance the emotion involved in cultural performances. Part of the work was dedicated to augmenting a stage in a live performance, with dance as an application case. In this paper, we present a milestone of this work, an augmented dance show that brings together several tools and technologies that were developed over the project's lifetime. This is the result of mixing an artistic process with scientific research and development. This augmented show brings to stage issues from the research fields of Human-Machine Interaction (HMI) and Augmented Reality (AR). Virtual elements are added on stage (visual and audio) and the dancer is able to interact with them in real-time, using different interaction techniques. The originality of this work is threefold. Firstly, we propose a set of movement-based interaction techniques that can be used independently on stage or in another context. In this set, some techniques are direct, while others go through a high level of abstraction. Namely, we performed movement-based emotion recognition on the dancer, and used the recognized emotions to generate emotional music pieces and emotional poses for a humanoid robot. Secondly, those interaction techniques rely on various interconnected systems that can be reassembled. We hence propose an integrated, interactive system for augmenting a live performance, a context where system failure is not tolerated. The final system can be adapted following the artist's preferences. Finally, those systems were validated through an on field experiment - the show itself - after which we gathered and analyzed the feedback from both the audience and the choreographer.
Mental representation and temporary recovery from unilateral neglect after vestibular stimulation.

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Strategies for Implementing Screening for Critical Congenital Heart Disease

BACKGROUND: Although newborn screening for critical congenital heart disease (CCHD) was recommended by the US Health and Human Services Secretary's Advisory Committee on Heritable Disorders in Newborns and Children to promote early detection, it was deemed by the Secretary of the HHS as not ready for adoption pending an implementation plan from HHS agencies. OBJECTIVE: To develop strategies for the implementation of safe, effective, and efficient screening. METHODS: A work group was convened with members selected by the Secretary's Advisory Committee on Heritable Disorders in Newborns and Children, the American Academy of Pediatrics, the American College of Cardiology Foundation, and the American Heart Association. RESULTS: On the basis of published and unpublished data, the work group made recommendations for a standardized approach to screening and diagnostic follow-up. Key issues for future research and evaluation were identified. CONCLUSIONS: The work-group members found sufficient evidence to begin screening for low blood oxygen saturation through the use of pulse-oximetry monitoring to detect CCHD in well-infant and intermediate care nurseries. Research is needed regarding screening in special populations (eg, at high altitude) and to evaluate service infrastructure and delivery strategies (eg, telemedicine) for nurseries without on-site echocardiography. Public health agencies will have an important role in quality assurance and surveillance. Central to the effectiveness of screening will be the development of a national technical assistance center to coordinate implementation and evaluation of newborn screening for CCHD.
Analysis of Structure and Composition of Bacterial Core Communities in Mature Drinking Water Biofilms and Bulk Water of a Citywide Network in Germany

ABSTRACT The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity.
THE SMALL-SCALE PHYSICAL STRUCTURE AND FRAGMENTATION DIFFERENCE OF TWO EMBEDDED INTERMEDIATE-MASS PROTOSTARS IN ORION

Intermediate-mass (IM) protostars, the bridge between the very common solar-like protostars and the more massive, but rarer, O and B stars, can only be studied at high physical spatial resolutions in a handful of clouds. In this paper, we present and analyze the continuum results from an observing campaign at the Submillimeter Array (SMA) targeting two well-studied IM protostars in Orion, NGC 2071 and L1641 S3 MMS 1. The extended SMA (eSMA) probes structure at angular resolutions up to 0. ″2, revealing protostellar disks on scales of ∼200 AU. Continuum flux measurements on these scales indicate that a significant amount of mass, a few tens of M☉, is present. Envelope, stellar, and disk masses are derived using compact, extended, and eSMA configurations and compared against spectral energy distribution fitting models. We hypothesize that fragmentation into three components occurred within NGC 2071 at an early time, when the envelopes were less than 10% of their current masses, e.g., <0.5 M☉. No fragmentation occurred for L1641 S3 MMS 1. For NGC 2071, evidence is given that the bulk of the envelope material currently around each source was accreted after the initial fragmentation. In addition, about 30% of the total core mass is not yet associated to one of the three sources. A global accretion model is favored and a potential accretion history of NGC 2071 is presented. It is shown that the relatively low level of fragmentation in NGC 2071 was stifled compared to the expected fragmentation from a Jeans argument. Similarly, the lack of fragmentation in L1641 S3 MMS 1 is likely due to similar arguments.
A DEM Analysis of Flow Characteristics of Noncohesive Particles in Hopper

Flow characteristics of material in hoppers, silos, and bins are critical issues for operational stability as well as structural integrity of these units. In this work, flow of noncohesive particles in hopper is studied using the discrete element method (DEM) where each particle is tracked for its position, velocity, and acceleration. Material properties tend to alter during hopper flow due to compaction, expansion, and segregation. These features are difficult to model with a continuum approach. In the first part, material flow patterns are correlated with hopper angle and hopper opening, the two main design parameters. The typical shift from mass flow to funnel flow depending on the hopper angle was successfully simulated. In the second part, the discharge rate of material was quantitatively analyzed as function of hopper design parameters. Beverloo model 1 was tested on these simulated flow rates and it was shown that the simulated flow rates follow the model for this specific granular system. However, the DEM analysis was also able to demonstrate the failure of the traditional Beverloo model in the restricted flow regime. Simulated flow rates also follow the empirical correlations with hopper angle as stated in literature. DEM simulations were validated with experimental data for both material flow pattern and discharge rates.
Determinants of parasite species richness on small taxonomical and geographical scales: Lamellodiscus monogeneans of northwestern Mediterranean sparid fish

Abstract Determinants of parasite species richness have been investigated in a host–parasite system comprising fish of the family Sparidae and their monogenean gill ectoparasites of the genus Lamellodiscus. This study was carried out on a small geographical scale in the northwestern Mediterranean Sea. Host phylogenetic relationships were taken into account by phylogenetic eigenvector regression which required the reconstruction of a phylogenetic tree for the sparid fish species using mtDNA sequences. Several ecological variables potentially acting on Lamellodiscus species richness were considered. Host body size and host migratory behaviour appeared to be the main determinants of parasite species richness in this system. It is concluded that structuring of monogenean communities is controlled more by ecological than evolutionary factors.