Miracle-dz/UniFAR-FTUs huggingface dataset:
Endocarditis in kidney transplant recipients: a systematic review

Infective Endocarditis (IE) carries significant mortality. Bacteremia, which is a predisposing factor for IE, occurs more frequently in immunocompromised individuals. Interestingly, IE in kidney transplant recipients has not been adequately described. The aim of this study was to systematically review all published cases of IE in kidney transplant recipients and describe their epidemiology, microbiology, clinical characteristics, treatment and outcomes. A systematic review of PubMed (through 13th December 2019) for studies providing epidemiological, clinical, microbiological as well as treatment data and outcomes of IE in kidney transplant recipients was performed. A total of 60 studies, containing data of 117 patients, were included in the analysis. The most common causative pathogens were gram-positive microorganisms in 57.4%, gram-negative microorganisms in 14.8%, fungi in 20%, while in 18.9% of cases, IE was culture-negative. Aortic valve was the most commonly infected valve followed by mitral, tricuspid and the pulmonary valve. Diagnosis was set with a transthoracic ultrasound in half the cases, followed by transesophageal ultrasound and autopsy. Fever was present in most cases, while embolic phenomena were noted in two out of five cases. Aminoglycosides, cephalosporins and aminopenicillins were the most commonly used antimicrobials, and surgical management was performed in one out of three cases. Clinical cure was noted in 60.9%, while overall mortality was 45.3%. To conclude, this systematic review thoroughly describes IE in kidney transplant recipients and provides information on epidemiology, clinical presentation, treatment and outcomes. Moreover, it identifies the emerging role of Enterococci, gram-negatives and fungi in IE in this population.
What is the Impact of the Proportion of Solid Necrotic Content on the Number of Necrosectomies during EUS-Guided Drainage using Lumen-Apposing Metallic Stents of Pancreatic Walled-off Necrosis ?

BACKGROUND AND AIMS The fully-covered, lumen apposing metal stents are designed for one step placement, facilitating the direct endoscopic necrosectomy into the walled-off pancreatic necrosis. However, the prediction of the number of necrosectomy sessions in these patients is not known. This study evaluated the association between the proportion of solid necrotic material inside walled-off necrosis, as assessed during the endosonography placement of a lumen apposing metal stent, and the number of necrosectomies subsequently required. METHODS Patients from three tertiary medical centers with symptomatic walled off pancreatic necrosis (pain, infection, gastric/biliary obstruction) at more than 4 weeks after onset of acute pancreatitis were retrospectively analysed. Proportion of solid necrotic debris was estimated during endosonography procedure of lumen apposing metal stents placement. Necrosectomy was performed when obstruction or inflammation occurred subsequently. Lumen apposing metal stents were removed after clearance of necrotic content. RESULTS In 46 patients with successful lumen apposing metal stents placement, necrosectomy was performed in 39 patients (72.78%). Performance of 3 or more necrosectomies was significantly associated with more than 50% pancreatic necrosis (p=0.032), but not with walled-off pancreatic necrosis size or location. Necrotic infection during lumen apposing metal stents stenting was associated with hypoalbuminemia, but not with necrosectomy requirement. Clinical success after a median follow-up of 13.37 months was 87%. CONCLUSIONS Walled-off pancreatic necrosis with more than 50% solid necrotic content were associated with more necrosectomy procedures, requiering longer endoscopy time, intravenous sedations, and higher costs.
The Epidemiology of Plant Virus Disease: Towards a New Synthesis

Epidemiology is the science of how disease develops in populations, with applications in human, animal and plant diseases. For plant diseases, epidemiology has developed as a quantitative science with the aims of describing, understanding and predicting epidemics, and intervening to mitigate their consequences in plant populations. Although the central focus of epidemiology is at the population level, it is often necessary to recognise the system hierarchies present by scaling down to the individual plant/cellular level and scaling up to the community/landscape level. This is particularly important for diseases caused by plant viruses, which in most cases are transmitted by arthropod vectors. This leads to range of virus-plant, virus-vector and vector-plant interactions giving a distinctive character to plant virus epidemiology (whilst recognising that some fungal, oomycete and bacterial pathogens are also vector-borne). These interactions have epidemiological, ecological and evolutionary consequences with implications for agronomic practices, pest and disease management, host resistance deployment, and the health of wild plant communities. Over the last two decades, there have been attempts to bring together these differing standpoints into a new synthesis, although this is more apparent for evolutionary and ecological approaches, perhaps reflecting the greater emphasis on shorter often annual time scales in epidemiological studies. It is argued here that incorporating an epidemiological perspective, specifically quantitative, into this developing synthesis will lead to new directions in plant virus research and disease management. This synthesis can serve to further consolidate and transform epidemiology as a key element in plant virus research.
Metatalk in Advanced Spanish L2 and Heritage Learners When Solving Lexical Problems: A Multiple-case Study

Metatalk (MT) emerges in interaction when learners, working through a linguistic problem, turn their attention to features of their language (Swain, 2000; Swain & Lapkin, 2002). One factor that influences how MT develops is learners’ language proficiency. This multiple-case study explored how high-proficiency Spanish L2 and heritage learners engaged in lexical MT during a text reconstruction activity. Key findings from the analysis of learners’ lexical language-related episodes (LLREs) and commentaries from a debriefing interview revealed that (a) learners targeted mostly word meaning with few exchanges on spelling and pronunciation, (b) LLRE frequencies were comparable among dyads and learner groups, (c) learners described inferencing processes toward solving LLREs as internal and often not verbalized, thus demonstrating a transition toward self-regulation, and (d) although capable of producing MT in Spanish, learners often gravitated toward English in their metalinguistic talk. MT was materialized as dyadic collaboration when learners sought an answer together; role-taking emerged as one partner took the expert role, at least momentarily, and provided an answer to the linguistic question posed by their partner.
Why many polymers are so fragile

Many polymers exhibit extremely high fragility and deviate from most of the trends known for non-polymeric glass-forming systems. The analysis of literature data presented here demonstrates that chain rigidity might be the main reason for this peculiar behaviour. Based on this analysis a simple scenario is proposed: (i) oligomers (short polymeric chains) follow trends characteristic for non-polymeric systems; (ii) increase in molecular weight (MW) does not affect structural relaxation significantly in the case of flexible chains; (iii) however, it slows down structural relaxation in rigid chains tremendously. As a result, a strong increase of Tg with MW is observed for rigid polymers. This rise in Tg leads to extremely high ‘apparent’ fragility and failure of usual correlations between the fragility and other parameters in rigid polymers.
A Modeling and Optimization Tool for the Expandable Polystyrene Batch Process

Expandable Polystyrene (EPS), a material of the insulation productions and packages, is commonly produced in a batch process. The control of the batch process is based on predefined process recipes and process parameters such as mixing properties. The EPS production has to be able to satisfy the aims and quality requirements of the markets, which causes additional demands on the process control. In this paper we demonstrate the optimization and modeling application for the EPS-batch process. The application consists of a production optimization tool and a simulation tool for the process parameters based on the Multi-Layer Perceptron network (MLP) with retrain properties. The software can be used at the operational level as well as at the process management level. The features are programmed into standalone software built up in the Matlab environment and it is tailored for the needs of the EPS production company StyroChem Ltd. The results show that the application can offer an efficient tool to economize production and storage costs.
CD107a+ (LAMP-1) Cytotoxic CD8+ T-Cells in Lupus Nephritis Patients

Cytotoxic CD8+ T-cells play a pivotal role in the pathogenesis of systemic lupus erythematosus (SLE). The aim of this study was to investigate the role of CD107a (LAMP-1) on cytotoxic CD8+ T-cells in SLE-patients in particular with lupus nephritis. Peripheral blood of SLE-patients (n = 31) and healthy controls (n = 21) was analyzed for the expression of CD314 and CD107a by flow cytometry. Kidney biopsies of lupus nephritis patients were investigated for the presence of CD8+ and C107a+ cells by immunohistochemistry and immunofluorescence staining. The percentages of CD107a+ on CD8+ T-cells were significantly decreased in SLE-patients as compared to healthy controls (40.2 ± 18.5% vs. 47.9 ± 15.0%, p = 0.02). This was even more significant in SLE-patients with inactive disease. There was a significant correlation between the percentages of CD107a+CD8+ T-cells and SLEDAI. The evaluation of lupus nephritis biopsies showed a significant number of CD107a+CD8+ T-cells mainly located in the peritubular infiltrates. The intrarenal expression of CD107a+ was significantly correlated with proteinuria. These results demonstrate that CD8+ T-cells of patients with systemic lupus erythematosus have an altered expression of CD107a which seems to be associated with disease activity. The proof of intrarenal CD107a+CD8+ suggests a role in the pathogenesis of lupus nephritis.
ESTIMATING THE MAGNITUDE OF THE PSE PROBLEM IN POULTRY

The magnitude of the pale soft and exudative (PSE) problem in young turkeys, mature turkey hens, and broiler chickens processed under commercial conditions is reviewed. The potential use of a fast color evaluation method and suggestions for a classification system which consists of different cutoff points (e.g., L > 50 for PSE in young turkey breast meat) are discussed.
Losses of nitrate-nitrogen in water draining from under autumn-sown crops established by direct drilling or mouldboard ploughing

SUMMARY The leaching of nitrate-N under autumn-sown arable crops was measured using hydro-logically isolated plots, about 0.24 ha in area, from 1984–1988. Fluxes of water and nitrate moving over the soil surface (surface runoff), at the interface between topsoil and subsoil (interflow), and in the subsoil (drainflow) were monitored in plots with mole-and-pipe drain systems (drained plots); surface runoff and interflow only were monitored in ‘undrained’ plots. Half the drained and undrained plots were direct-drilled, and on the other half seedbeds were prepared by tillage to 200 mm. Tillage increased the total leaching loss of nitrate by 21 % compared with direct drilling in drained plots. About 95% or the nitrate moving from the soil was present in the water intercepted by the subsoil drains in these plots. In undrained plots less water and nitrate were collected in total; more of the nitrate was present in interflow on ploughed plots and in surface runoff in direct-drilled land. Losses of nitrate for the whole experiment from 1978-1988 were analysed. This showed that, between the harvest of one crop and the spring application of fertilizer to the next, loss of nitrate-N from ploughed land (Lp) was approximated by Lp=22+Fkg N ha−1, where F was the autumn fertilizer-N applied. After fertilizer was applied in spring, loss of nitrate-N depended on rainfall such that for 100 mm rainfall about 30% of the fertilizer-N was lost by leaching. About 18% more nitrate-N was lost from direct-drilled land than from ploughed land in spring, but the total loss was generally small compared to that over winter. The apparent net mineralization of organic-N was measured in 1988. In autumn and winter there was little effect of tillage treatment (26 and 31 kg N ha−1 on direct drilled and tilled plots respectively). However, over the year 83 kg N ha−1 were mineralized in tilled plots, and 67 kg N ha−1 in direct-drilled plots. Five factors governing the leaching of nitrate are assessed and this identified that fertilizer nitrogen application to the seedbed of winter sown crops and the mineralization of nitrogen from the residues of the previous crop are the most significant factors for nitrogen leaching in the UK.
On-sky silicon photomultiplier detector performance measurements for millisecond to sub-microsecond optical source variability studies

Abstract. In our Ultra-Fast Astronomy (UFA) program, we aim to improve measurements of variability of astronomical targets on millisecond and shorter time scales. In this work, we present initial on-sky measurements of the performance of silicon photomultiplier detectors (SiPMs) for UFA. We mounted two different SiPMs at the focal plane of the 0.7-m aperture Nazarbayev University Transient Telescope at the Assy-Turgen Astrophysical Observatory, with no filter in front of the detector. The 3 mm × 3 mm SiPM single-channel detectors have a field of view of 2.2716 ′ × 2.2716 ′ . During the nights of October 28–29, 2019, we measured sky background, bright stars, and an artificial source with a 100-Hz flashing frequency. We compared detected SiPM counts with Gaia satellite G-band flux values to show that our SiPMs have a linear response. With our two SiPMs (models S14520-3050VS and S14160-3050HS), we measured a dark current of ∼130 and ∼85 kilo counts per second (kcps), and a sky background of ∼201 and ∼203 kcps, respectively. We measured an intrinsic crosstalk of 10.34% and 10.52% and derived a 5σ sensitivity of 13.9 and 14 Gaia G-band magnitude for 200-ms exposures, for the two detectors, respectively. For a 10-μs window, and allowing a false alarm rate of once per 100 nights, we derived a sensitivity of 22 detected photons, or six Gaia G-band magnitudes. For nanosecond timescales, our detection is limited by crosstalk to 12 detected photons, which corresponds to a fluence of ∼155 photons per square meter.
Scission: Performance-driven and Context-aware Cloud-Edge Distribution of Deep Neural Networks

Partitioning and distributing deep neural networks (DNNs) across end-devices, edge resources and the cloud has a potential twofold advantage: preserving privacy of the input data, and reducing the ingress bandwidth demand beyond the edge. However, for a given DNN, identifying the optimal partition configuration for distributing the DNN that maximizes performance is a significant challenge. This is because the combination of potential target hardware resources that maximizes performance and the sequence of layers of the DNN that should be distributed across the target resources needs to be determined, while accounting for user-defined objectives/constraints for partitioning. This paper presents Scission, a tool for automated benchmarking of DNNs on a given set of target device, edge and cloud resources for determining optimal partitions that maximize DNN performance. The decision-making approach is context-aware by capitalizing on hardware capabilities of the target resources, their locality, the characteristics of DNN layers, and the network condition. Experimental studies are carried out on 18 DNNs. The decisions made by Scission cannot be manually made by a human given the complexity and the number of dimensions affecting the search space. The benchmarking overheads of Scission allow for responding to operational changes periodically rather than in real-time. Scission is available for public download 1.
Kinetics of Drop Breakage in Stirred Vessels under Turbulent Conditions

The emulsification of dodecane oil was studied in a standard stirred vessel filled with distilled water. The in situ size distribution of the drops was measured at certain time intervals by using a particle size analyzer while stirring. The results showed that an increase in the stirring time and stirring rate resulted in a decrease in the mean drop size of drops and shifted the drop size distribution toward smaller sizes. The minimum droplet size in the turbulent flow was found to be proportional to amin∼(WD)−1.75. Normalization of data exhibited that the size distribution of drops is self‐preserving. The distribution of mean drop size and distribution functions of drops were determined by using models developed from the Focker‐Plank equation regarding size distribution of particles in turbulent flows. The evaluation of droplet breakage with time in isotropic turbulent flow showed that the size distribution can be represented by the summation of log‐normal distribution function in series. It was found that the experimental data could be represented well by the empirical models.
Binding of Sodium Salicylate by β-Cyclodextrin or 2,6-Di-O-methyl-β-cyclodextrin in Aqueous Solution

Abstract □ Speed of sound and conductivity experiments have been done at 298.15 K to study the encapsulation process of sodium salicylate (NaSA) by β -cyclodextrin ( β -CD) and 2,6-di-O-methyl- β -cyclodextrin (DIMEB) in aqueous solutions. Since the concentration of the salicyclic form (HSA), coming from the hydrolysis of SA − , is negligible at biological pH, the binding process studied in this work is that of the SA − species. The stoichiometries of the complexes DIMEB: SA − and β -CD:SA − have been found to be 1:1, as usually determined for most CD:drug complexes. Their association constants and their ionic molar conductivities at infinite dilution have been obtained by fitting the experimental conductivity data with a nonlinear regression method (NLR). For that purpose, a model based on that of Gelb and co-workers has been used. From the values of K β -CD:SA − = (105 ± 15) M − 1 and K DIMEB:SA − = (140 ± 20) M − 1 obtained, the bioavailability of the salicylate drug in the complexed form has been discussed.
A butterfly chromonome reveals selection dynamics during extensive and cryptic chromosomal reshuffling

Taxonomic orders vary in their degree of chromosomal conservation with some having high rates of chromosome number turnover despite maintaining some core sets of ordered genes (e.g. Mammalia) and others exhibiting rapid rates of gene-order reshuffling without changing chromosomal count (e.g. Diptera). However few clades exhibit as much conservation as the Lepidoptera for which both chromosomal count and gene colinearity (synteny) are very high over the past 140 MY. In contrast, here we report extensive chromosomal rearrangements in the genome of the green-veined white butterfly (Pieris napi, Pieridae, Linnaeus, 1758). This unprecedented reshuffling is cryptic: microsynteny and chromosome number do not indicate the extensive rearrangement revealed by a chromosome level assembly and high-resolution linkage map. Furthermore, the rearrangement blocks themselves appear to be non-random, as they are significantly enriched for clustered groups of functionally annotated genes revealing that the evolutionary dynamics acting on Lepidopteran genome structure are more complex than previously envisioned.
Unidimensional Simulation of Drying Stress in Radiata Pine Wood

This article reports an experimental and numeric methodology for studying the development of internal stresses during drying of solid wood. For validation purposes, tests were performed for drying of radiata pine at the equivalent of constant air-drying conditions at 44°C dry-bulb and 36°C wet-bulb temperatures. The methodology involves the simulation of drying stresses caused by the development of internal moisture content gradients during drying, where the moisture content gradients are also simulated numerically based on the theory of effective diffusion coefficient. The resulting mathematical model is a second-order nonlinear set of partial differential equations with variable coefficients, which are integrated numerically through the Control Volume Finite Element Method (CVFEM). The results showed consistency between simulated values and the experimental strain and moisture content data, both in the radial and tangential directions. It was concluded that the proposed method could be a valuable tool for studying general trends in the development of stress during drying, trends which are difficult to evaluate by measuring only due to the limited amount of data points and high experimental error associated with destructive strain tests.
Metagenomic Binning through Multi-resolution Genomic Binary Patterns

Motivation High-throughput sequencing has facilitated the analysis of complex microbial communities. Consequently, an enormous number of sequences have been generated containing various regions of bacterial and viral genomes. Image processing offers a rich source of descriptors for data analysis. Here, we introduce a feature space called multi-resolution local binary patterns (MLBP) from image processing as a feature descriptor to extract local ‘texture’ changes from nucleotide sequences. We demonstrate its applicability to the alignmentfree binning of metagenomic data. Results The effectiveness of our approach is tested using both simulated and real human gut microbial communities. We compared the performance of our method with several existing techniques that are based on k-mer frequency to show it outperforms existing techniques. In addition, we provide a time-series study of the abundance pattern of each bin to help refine the formed clusters automatically and to find relations that may exist among the clusters. Although the main aim is to introduce the use of genomic signatures using an alternative feature space (MLBP), our results show its application to the analysis of contigs from a metagenomic study. Availability The source code for our Multi-resolution Genomic Binary Patterns method can be found at https://github.com/skouchaki/MrGBP
Task-related multivariate activation states during task-free rest

Much of our lives are spent in unconstrained rest states, yet cognitive brain processes are primarily investigated using task-constrained states. It may be possible to utilize the insights gained from experimental control of task processes as reference points for investigating unconstrained rest. To facilitate comparison of rest and task functional MRI (fMRI) data we focused on activation amplitude patterns, commonly used for task but not rest analyses. During rest, we identified spontaneous changes in temporally extended whole-brain activation pattern states. This revealed a hierarchical organization of rest states. The top consisted of two competing states consistent with previously identified “task-positive” and “task-negative” activation patterns. These states were composed of more specific states that repeated over time and across individuals. Contrasting with the view that rest consists of only task-negative states, task-positive states occurred 40% of the time while individuals “rested,” suggesting task-focused activity occurs during rest. Further, analysis of task data revealed a similar hierarchical structure of brain states. Together these results suggest brain activation dynamics form a general hierarchy across task and rest, with a small number of dominant general states reflecting basic functional modes and a variety of specific states likely reflecting a rich variety of cognitive processes.