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Aims/hypothesis: Surviving beta cells in type 1 diabetes respond to inflammation by upregulating programmed death-ligand 1 (PD-L1) to engage immune cell programmed death protein 1 (PD-1) and limit destruction by self-reactive immune cells. Extracellular vesicles (EVs) and their cargo can serve as biomarkers of beta cell health and contribute to islet intercellular communication. We hypothesised that the inflammatory milieu of type 1 diabetes increases PD-L1 in beta cell EV cargo and that EV PD-L1 may protect beta cells against immune-mediated cell death. Methods: Beta cell lines and human islets were treated with proinflammatory cytokines to model the proinflammatory type 1 diabetes microenvironment. EVs were isolated using ultracentrifugation or size exclusion chromatography and analysed via immunoblot, flow cytometry and ELISA. EV PD-L1 binding to PD-1 was assessed using a competitive binding assay and in vitro functional assays testing the ability of EV PD-L1 to inhibit NOD CD8+ T cells. Plasma EV and soluble PD-L1 were assayed in the plasma of islet autoantibody-positive (Ab+) individuals or individuals with recent-onset type 1 diabetes and compared with levels in non-diabetic control individuals. Results: PD-L1 protein co-localised with tetraspanin-associated proteins intracellularly and was detected on the surface of beta cell EVs. Treatment with IFN-α or IFN-γ for 24 h induced a twofold increase in EV PD-L1 cargo without a corresponding increase in the number of EVs. IFN exposure predominantly increased PD-L1 expression on the surface of beta cell EVs and beta cell EV PD-L1 showed a dose-dependent capacity to bind PD-1. Functional experiments demonstrated specific effects of beta cell EV PD-L1 to suppress proliferation and cytotoxicity of murine CD8+ T cells. Plasma EV PD-L1 levels were increased in Ab+individuals, particularly in those positive for a single autoantibody. Additionally, in Ab+ individuals or those who had type 1 diabetes, but not in control individuals, plasma EV PD-L1 positively correlated with circulating C-peptide, suggesting that higher EV PD-L1 could be protective for residual beta cell function. Conclusions/interpretation: IFN exposure increases PD-L1 on the beta cell EV surface. Beta cell EV PD-L1 binds PD1 and inhibits CD8+ T cell proliferation and cytotoxicity. Circulating EV PD-L1 is higher in Ab+ individuals than in control individuals. Circulating EV PD-L1 levels correlate with residual C-peptide at different stages in type 1 diabetes progression. These findings suggest that EV PD-L1 could contribute to heterogeneity in type 1 diabetes progression and residual beta cell function and raise the possibility that EV PD-L1 could be exploited as a means to inhibit immune-mediated beta cell death. [ABSTRACT FROM AUTHOR]

The adjacency graph is a structure used to model genomes in several rearrangement distance problems. In particular, most studies use properties of a maximum cycle packing of this graph to develop bounds and algorithms for rearrangement distance problems, such as the reversal distance, the reversal and transposition distance, and the double cut and join distance. When each genome has no repeated genes, there exists only one cycle packing for the graph. However, when each genome may have repeated genes, the problem of finding a maximum cycle packing for the adjacency graph (adjacency graph packing) is NP-hard. In this work, we develop a randomized greedy heuristic and a genetic algorithm heuristic for the adjacency graph packing problem for genomes with repeated genes and unequal gene content. We also propose new algorithms with simple implementation and good practical performance for reversal distance and reversal and transposition distance in genomes without repeated genes, which we combine with the heuristics to find solutions for the problems with repeated genes. We present experimental results and compare the application of these heuristics with the application of the MSOAR framework in rearrangement distance problems. Lastly, we apply our genetic algorithm heuristic to real genomic data to validate its practical use. [ABSTRACT FROM AUTHOR]

A little less than half of the students of higher Ed institutions in the US graduate in four years, and only around 60% finish in six years. Retention rates are also less than ideal. Colleges have been experimenting with a variety of programs and policies to address this issue, especially less selective institutions whose rates are significantly lower. In this paper, we evaluate a student success and retention program called Early Alert that was implemented at a public state university in the US with a medium-to-large student body. Our dataset contains several years' worth of information on students' socio-demographic characteristics, class standing and average grades (GPAs), as well as their midterm and final grades in undergraduate courses. We employ several causal inference techniques developed for observational studies and elicit negative average treatment effects on the treated (ATT). Since it is conceivable that unobserved confounders are the real drivers of our empirical results, not the treatment, we carry out two different types of sensitivity analyses. Together with our treatment effect estimations, they lead us to the main conclusion that Early Alert does not improve student performance, at least not in the short run (as measured by course performance), and likely has a negligible impact. [ABSTRACT FROM AUTHOR]

Background: While the list of fusion‐driven soft tissue neoplasms is expanding rapidly, their importance among cutaneous and superficial mesenchymal and adnexal neoplasms remains poorly understood. This challenge is especially evident in cases with ambiguous histopathology that are difficult to classify based on morphology. Aims: Our goal was to investigate the benefits of next‐generation sequencing in diagnosing complex cutaneous neoplasms. Materials & Methods: Departmental archives were searched for fusion‐driven cutaneous neoplasms. Slides were retrieved and clinical information including follow‐up was obtained. Results: Fifteen cases occurred in eight female and seven male patients, with a median age of 26 years (range: 1–83) at diagnosis. Tumors involved the extremities (9), scalp (5), and head and neck (1). Predominant features included myoepithelial (5), nested spindled with clear cytoplasm (2), atypical adnexal/squamoid (2), small round blue cell (2), cellular spindled (3), and fibrohistiocytic morphology (1). Most frequently encountered fusions involved EWSR1 (6) fused to ERG (1), FLI1 (1), CREB1 (2), CREM (1), PBX3 (1), followed by PLAG1 (4) with LIFR (2), TRPS1 (1) and CHCHD7. Additional fusions encountered were YAP1::NUTM1, EML4::ALK, SS18::SSX1 (2), and a novel fusion: ACTB::ZMIZ2. Integration of histologic features and molecular findings led to final diagnoses of primary cutaneous Ewing sarcoma (2), soft tissue myoepithelioma (4), cutaneous syncytial myoepithelioma (1), cutaneous adnexal carcinoma (1), porocarcinoma (1), inflammatory myofibroblastic tumor (1), synovial sarcoma (2), clear cell sarcoma (2), and angiomatoid fibrous histiocytoma (1). Discussion and conclusion: Our results show that fusion testing can be a helpful diagnostic tool, especially in cases with unusual or uncommon morphology in superficial sites. Furthermore, it can allow for the identification of potential therapeutic targets in some instances. [ABSTRACT FROM AUTHOR]

Introduction: Adamantinoma‐like Ewing sarcoma (ALES) is a rare aggressive malignancy occasionally diagnosed in the thyroid gland. ALES shows basaloid cytomorphology, expresses keratins, p63, p40, frequently CD99, and harbours the t(11;22) EWSR1::FLI1 translocation. There is debate on whether ALES resembles more sarcoma or carcinoma. Methods: We performed RNA sequencing from two ALES cases and compared findings with skeletal Ewing's sarcomas and nonneoplastic thyroid tissue. ALES was investigated by in situ hybridization (ISH) for high‐risk human papillomavirus (HPV) DNA and immunohistochemistry for the following antigens: keratin 7, keratin 20, keratin 5, keratins (AE1/AE3 and CAM5.2), CD45, CD20, CD5, CD99, chromogranin, synaptophysin, calcitonin, thyroglobulin, PAX8, TTF1, S100, p40, p63, p16, NUT, desmin, ER, FLI1, INI1, and myogenin. Results: An uncommon EWSR1::FLI transcript with retained EWSR1 exon 8 was detected in both ALES cases. Regulators of EWSR1::FLI1 splicing (HNRNPH1, SUPT6H, SF3B1) necessary for production of a functional fusion oncoprotein, as well as 53 genes (including TNNT1, NKX2.2) activated downstream to the EWSR1::FLI1 cascade, were overexpressed. Eighty‐six genes were uniquely overexpressed in ALES, most of which were related to squamous differentiation. Immunohistochemically, ALES strongly expressed keratins 5, AE1/AE3 and CAM5.2, p63, p40, p16, and focally CD99. INI1 was retained. The remaining immunostains and HPV DNA ISH were negative. Conclusion: Comparative transcriptomic profiling reveals overlapping features of ALES with skeletal Ewing's sarcoma and an epithelial carcinoma, as evidenced by immunohistochemical expression of keratin 5, p63, p40, CD99, the transcriptome profile, and detection of EWSR1::FLI1 fusion transcript by RNA sequencing. [ABSTRACT FROM AUTHOR]

The Ocean decade (2021–2030) for sustainable development proclaimed in 2017 by the UN, seeks to promote and conserve the sustainable use of oceans, seas, and marine resources. For this, the distribution of n-alkanes, polycyclic aromatic hydrocarbons (PAHs), and biomarkers, in sediments from the Fortaleza coastal zone (Mucuripe harbor (MH) and Inner Continental shelf (ICS)) were used to assess the impacts of anthropogenic activities in the area. The concentrations of total n-alkanes (Σ16 n-alkanes) in MH and ICS sediments varied from 35.9 to 94.9 and 17.9 to 197.3 μg g−1, respectively, while the isoprenoids phytane and pristane in MH and ICS sediments ranged from 0.1 to 1.69 ug g−1 and from 0.14 and 1.20 μg g−1, respectively. Most of the sediment samples presented carbon preference index (CPI) values close to unity, indicating that the area is submitted to petroleum-related sources. The concentrations of Σ16 PAHs in MH and ICS sediments varied from 87.0 to 562.0 and 98 to 288.0 ng g−1. This work presents the first investigation of the petroleum biomarkers hopanes and steranes in the Fortaleza coastal zone, in which ΣBiomarkers varied from 0.10 to 1.79 and 0.02 to 0.24 ug g−1 in MH and ICS sediments, respectively. The presence at stations of biomarkers also indicates petrogenic input. The diagnosis of the distribution of pollutants in the investigated zones of the Fortaleza coast suggests contamination from urban areas and oil spills and vessel traffic. [ABSTRACT FROM AUTHOR]

In smart factories, several mobile and autonomous robots are being utilized in warehouses to reduce overhead and operating costs. In this context, this paper presents a consensus-based fault-resilient intelligent mechanism called Consensual Fault-Resilient Behavior (CFRB). The proposed approach is based on three hierarchical plans: imposition, negotiation, and consensus. Fault resilience is achieved using the collective behavior of a multi-robot system that applies ternary decisions based on these plans. The difference between this paper and our previous work is on the consensual level. As it is suitable for the analysis and design of coordinated behavior between autonomous robots, the consensus plan is restructured and enhanced. The proposed approach is tested and evaluated in a virtual warehouse based on a real environment. In addition, it is compared with other current approaches, and the results are presented, demonstrating its efficiency. [ABSTRACT FROM AUTHOR]

Genome rearrangement events are widely used to estimate a minimum-size sequence of mutations capable of transforming a genome into another. The length of this sequence is called distance, and determining it is the main goal in genome rearrangement distance problems. Problems in the genome rearrangement field differ regarding the set of rearrangement events allowed and the genome representation. In this work, we consider the scenario where the genomes share the same set of genes, gene orientation is known or unknown, and intergenic regions (structures between a pair of genes and at the extremities of the genome) are taken into account. We use two models, the first model allows only conservative events (reversals and moves), and the second model includes non-conservative events (insertions and deletions) in the intergenic regions. We show that both models result in NP-hard problems no matter if gene orientation is known or unknown. When the information regarding the orientation of genes is available, we present for both models an approximation algorithm with a factor of 2. For the scenario where this information is unavailable, we propose a 4-approximation algorithm for both models. [ABSTRACT FROM AUTHOR]

Localization is a crucial skill in mobile robotics because the robot needs to make reasonable navigation decisions to complete its mission. Many approaches exist to implement localization, but artificial intelligence can be an interesting alternative to traditional localization techniques based on model calculations. This work proposes a machine learning approach to solve the localization problem in the RobotAtFactory 4.0 competition. The idea is to obtain the relative pose of an onboard camera with respect to fiducial markers (ArUcos) and then estimate the robot pose with machine learning. The approaches were validated in a simulation. Several algorithms were tested, and the best results were obtained by using Random Forest Regressor, with an error on the millimeter scale. The proposed solution presents results as high as the analytical approach for solving the localization problem in the RobotAtFactory 4.0 scenario, with the advantage of not requiring explicit knowledge of the exact positions of the fiducial markers, as in the analytical approach. [ABSTRACT FROM AUTHOR]

Sorting by Genome Rearrangements is a classic problem in Computational Biology. Several models have been considered so far, each of them defines how a genome is modeled (for example, permutations when assuming no duplicated genes, strings if duplicated genes are allowed, and/or use of signs on each element when gene orientation is known), and which rearrangements are allowed. Recently, a new problem, called Sorting by Multi-Cut Rearrangements, was proposed. It uses the k-cut rearrangement which cuts a permutation (or a string) at k ≥ 2 places and rearranges the generated blocks to obtain a new permutation (or string) of same size. This new rearrangement may model chromoanagenesis, a phenomenon consisting of massive simultaneous rearrangements. Similarly as the Double-Cut-and-Join, this new rearrangement also generalizes several genome rearrangements such as reversals, transpositions, revrevs, transreversals, and block-interchanges. In this paper, we extend a previous work based on unsigned permutations and strings to signed permutations. We show the complexity of this problem for different values of k, and that the approximation algorithm proposed for unsigned permutations with any value of k can be adapted to signed permutations. We also show a 1.5-approximation algorithm for the specific case k = 4 , as well as a generic approximation algorithm applicable for any k ≥ 5 , that always reaches constant ratio. The latter makes use of the cycle graph, a well-known structure in genome rearrangements. We implemented and tested the proposed algorithms on simulated data. [ABSTRACT FROM AUTHOR]

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In this study, the multi-marker approach was used for the first time with a highly urbanized lake located in the city of Fortaleza, Brazil, to provide a comprehensive view of temporal trends in sources of pollutants and evaluate the relation between the influence of anthropogenic activities and socioeconomic development. Total concentrations of the markers analyzed ranged from 21.0 to 103.8 ng g−1, 450.2 to 2390.2 ng g−1, and 233.8 to 9827.3 ng g−1 for ∑PAHs, ∑n-alk, and ∑sterols, respectively. Concentrations and patterns of PAH, AH, and sterol ratio distribution changed over time and may be associated with different episodes in the history of the city of Fortaleza. The marker ratio distribution in the sediment core revealed an overlap of natural and anthropogenic sources, with degraded oil, biogenic inputs, pyrogenic processes, and fecal contamination from humans and animals in the past changing to petroleum fossil inputs and high contamination from sewage in the present day. The distribution of markers and the chronological history of Fortaleza revealed two distinct periods related to human activities during the development of the city. In the first period (prior to the 1950s), the main human activities were animal breeding and the use of biomass for domestic activities, public and cargo transportation, and commercial activities, especially food production. In the second period (after the 1950s), expansion of the city occurred due to the so-called Brazilian economic miracle and the main human activities were industrialization and urbanization processes, involving deforestation, paving, sewage discharge, and petroleum combustion. [ABSTRACT FROM AUTHOR]

There has been an intense debate regarding the economic, social, and environmental sustainability of confinement versus grazing dairy systems. Our goal was to conduct a meta-analysis to compare dry matter intake, milk yield and composition, nutrient use efficiency (i.e. feed efficiency, milk N efficiency), and predicted enteric CH4 emissions using studies that simultaneously evaluated confinement and grazing. We were able to include in the meta-analysis 8 peer-reviewed articles that met the following selection criteria: (1) publication between 1991 and 2021 in English language, (2) report either SEM or SD, (3) inclusion of at least 1 confinement [total mixed ration or fresh cut herbage fed indoors (i.e. zero-grazing)] and 1 grazing treatment in the same study, and (4) use of markers (internal or external) to estimate herbage dry matter intake. Two unpublished experiments were added to the data set resulting in a total of 10 studies for comparing confinement and grazing. The magnitude of the effect (i.e. effect size) was evaluated using weighted raw mean differences between grazing and confinement systems for a random effect model. Enteric CH4 production was predicted as follows: CH4 (g/d) = 33.2 (13.54) + 13.6 (0.33) × dry matter intake + 2.43 (0.245) × neutral detergent fiber. Dry matter intake (–9.5%), milk yield (–9.3%), milk fat yield (–5.8%), milk protein yield (–10%), and energy-corrected milk (–12%) all decreased in grazing versus confined dairy cows. In contrast, concentration of milk fat and feed efficiency (energy-corrected milk/dry matter intake) were not affected by management system. Whereas milk protein concentration increased, milk nitrogen (N) efficiency (milk N/N intake) tended to decrease in grazing compared with confinement. Predicted enteric CH4 production was 6.1% lower in grazing than confined dairy cows. However, CH4 yield (g/kg of dry matter intake) and CH4 intensity (g/kg of energy-corrected milk) did not change between confinement and grazing. In conclusion, while production performance decreased in grazing dairy cows, nutrient use efficiency and predicted enteric CH4 emissions were relatively similar in both management systems. Results of our meta-analysis should be interpreted with caution due to the small number of studies that met our inclusion criteria leading to a limited number of treatment mean comparisons. [ABSTRACT FROM AUTHOR]

This article discusses the integration of robotics in STEM education and the benefits it brings to students. It highlights four articles published in the Research Topic on Educational Robotics and Competitions, which cover various aspects of robotics challenges and competitions. One article focuses on how the COVID-19 pandemic led to the development of a simulated environment for the RoboCupJunior competition, allowing it to continue despite physical restrictions. Another article introduces a new competition that simulates a fully automated industrial logistics warehouse. A third article describes a robotic challenge where legged robots must climb a volcano's escarpment and collect data in a simulated volcanic eruption scenario. The final article discusses a networked virtual robotics platform that provides an accessible solution for teaching computational thinking in classrooms. These competitions and challenges motivate students, inspire researchers, and foster problem-solving skills. [Extracted from the article]

The electronic and dielectric properties of functionalized tin monolayers (stanene) using density‐functional theory and GW approximation are investigated. Charge density analysis of organic ligands adsorbed on stanene shows that these groups are able to induce a bandgap with parabolic bands in the originally metallic stanene. Furthermore, GW calculations demonstrate that the dielectric properties of functionalized stanene show adsorption in the visible region which can render stanene suitable for optoelectronic applications. [ABSTRACT FROM AUTHOR]

Stimulated parametric down-conversion is a nonlinear optical process that can be used for phase conjugation and frequency conversion of an optical field. A precise description of the outgoing stimulated field has been developed for the case where the input pump and seed fields are coherent. However, partially coherent beams can have interesting and important characteristics that are absent in coherent beams. One example is the twist phase, a novel optical phase that can appear in partially coherent Gaussian beams and gives rise to a nonzero orbital angular momentum. Here, we consider stimulated down-conversion for partially coherent input fields. As a case study, we use twisted Gaussian Schell-Model beams as the seed and pump beams in stimulated parametric down-conversion. It is shown both theoretically and experimentally that the stimulated idler beam can be written as a twisted Gaussian Schell-Model beam, where the beam parameters are determined entirely by the seed and pump. When the pump beam is coherent, the twist phase of the idler is the conjugate of that of the seed. These results could be useful for the correction of wavefront distortion such as in atmospheric turbulence in optical communication channels, and synthesis of partially coherent beams. [ABSTRACT FROM AUTHOR]

Background: In the comparative genomics field, one of the goals is to estimate a sequence of genetic changes capable of transforming a genome into another. Genome rearrangement events are mutations that can alter the genetic content or the arrangement of elements from the genome. Reversal and transposition are two of the most studied genome rearrangement events. A reversal inverts a segment of a genome while a transposition swaps two consecutive segments. Initial studies in the area considered only the order of the genes. Recent works have incorporated other genetic information in the model. In particular, the information regarding the size of intergenic regions, which are structures between each pair of genes and in the extremities of a linear genome. Results and conclusions: In this work, we investigate the sorting by intergenic reversals and transpositions problem on genomes sharing the same set of genes, considering the cases where the orientation of genes is known and unknown. Besides, we explored a variant of the problem, which generalizes the transposition event. As a result, we present an approximation algorithm that guarantees an approximation factor of 4 for both cases considering the reversal and transposition (classic definition) events, an improvement from the 4.5-approximation previously known for the scenario where the orientation of the genes is unknown. We also present a 3-approximation algorithm by incorporating the generalized transposition event, and we propose a greedy strategy to improve the performance of the algorithms. We performed practical tests adopting simulated data which indicated that the algorithms, in both cases, tend to perform better when compared with the best-known algorithms for the problem. Lastly, we conducted experiments using real genomes to demonstrate the applicability of the algorithms. [ABSTRACT FROM AUTHOR]

Problems in the genome rearrangement field are often formulated in terms of pairwise genome comparison: given two genomes G 1 and G 2 , find the minimum number of genome rearrangements that may have occurred during the evolutionary process. This broad definition lacks at least two important considerations: the first being which features are extracted from genomes to create a useful mathematical model, and the second being which types of genome rearrangement events should be represented. Regarding the first consideration, seminal works in the genome rearrangement field solely used gene order to represent genomes as permutations of integer numbers, neglecting many important aspects like gene duplication, intergenic regions, and complex interactions between genes. Regarding the second consideration, some rearrangement events are widely studied such as reversals and transpositions. In this paper, we shed light on the first consideration and created a model that takes into account gene order and the number of nucleotides in intergenic regions. In addition, we consider events of reversals, transpositions, and indels (insertions and deletions) of genomic material. We present a 4-approximation algorithm for reversals and indels, a 4. 5 -approximation algorithm for transpositions and indels, and a 6-approximation for reversals, transpositions, and indels. [ABSTRACT FROM AUTHOR]

Nodular fasciitis is a benign myofibroblastic neoplasm that characteristically enlarges rapidly and then usually regresses spontaneously. While the vast majority of tumors are benign, there are rare reports of morphologically benign nodular fasciitis giving rise to metastases, not predictable on histologic grounds. Here, we report what we believe is an example of morphologically malignant nodular fasciitis, which occurred in the upper extremity of a 7-year-old male. The tumor was composed of short, intersecting fascicles of myofibroblastic cells in a loose myxoid matrix, with keloidal hyalinization and admixed osteoclastic giant cells, all characteristic of nodular fasciitis. However, it additionally exhibited striking nuclear pleomorphism, a feature not compatible with conventional nodular fasciitis. Fluorescence in situ hybridization demonstrated a USP6 translocation, confirmed by next-generation sequencing to be the novel CALD1-USP6 fusion. No other somatic or germline mutations were detected. This case adds to the expanding morphologic and molecular genetic spectrum of nodular fasciitis. [ABSTRACT FROM AUTHOR]

Genome Rearrangements are events that affect large stretches of genomes during evolution. Many mathematical models have been used to estimate the evolutionary distance between two genomes based on genome rearrangements. However, most of them focused on the (order of the) genes of a genome, disregarding other important elements in it. Recently, researchers have shown that considering regions between each pair of genes, called intergenic regions, can enhance distance estimation in realistic data. Two of the most studied genome rearrangements are the reversal, which inverts a sequence of genes, and the transposition, which occurs when two adjacent gene sequences swap their positions inside the genome. In this work, we study the transposition distance between two genomes, but we also consider intergenic regions, a problem we name Sorting by Intergenic Transpositions. We show that this problem is NP-hard and propose two approximation algorithms, with factors 3.5 and 2.5, considering two distinct definitions for the problem. We also investigate the signed reversal and transposition distance between two genomes considering their intergenic regions. This second problem is called Sorting by Signed Intergenic Reversals and Intergenic Transpositions. We show that this problem is NP-hard and develop two approximation algorithms, with factors 3 and 2.5. We check how these algorithms behave when assigning weights for genome rearrangements. Finally, we implemented all these algorithms and tested them on real and simulated data. [ABSTRACT FROM AUTHOR]

Genome rearrangements are mutations affecting large portions of a genome, and a reversal is one of the most studied genome rearrangements in the literature through the Sorting by Reversals (SbR) problem. SbR is solvable in polynomial time on signed permutations (i.e., the gene orientation is known), and it is NP-hard on unsigned permutations. This problem (and many others considering genome rearrangements) models genome as a list of its genes in the order they appear, ignoring all other information present in the genome. Recent works claimed that the incorporation of the size of intergenic regions, i.e., sequences of nucleotides between genes, may result in better estimators for the real distance between genomes. Here we introduce the Sorting Signed Permutations by Intergenic Reversals problem, that sorts a signed permutation using reversals both on gene order and intergenic sizes. We show that this problem is NP-hard by a reduction from the 3-partition problem. Then, we propose a 2-approximation algorithm for it. Finally, we also incorporate intergenic indels (i.e., insertions or deletions of intergenic regions) to overcome a limitation of sorting by conservative events (such as reversals) and propose two approximation algorithms. [ABSTRACT FROM AUTHOR]

The rearrangement distance is a method to compare genomes of different species. Such distance is the number of rearrangement events necessary to transform one genome into another. Two commonly studied events are the transposition, which exchanges two consecutive blocks of the genome, and the reversal, which reverts a block of the genome. When dealing with such problems, seminal works represented genomes as sequences of genes without repetition. More realistic models started to consider gene repetition or the presence of intergenic regions, sequences of nucleotides between genes and in the extremities of the genome. This work explores the transposition and reversal events applied in a genome representation considering both gene repetition and intergenic regions. We define two problems called Minimum Common Intergenic String Partition and Reverse Minimum Common Intergenic String Partition. Using a relation with these two problems, we show a Θ k -approximation for the Intergenic Transposition Distance, the Intergenic Reversal Distance, and the Intergenic Reversal and Transposition Distance problems, where k is the maximum number of copies of a gene in the genomes. Our practical experiments on simulated genomes show that the use of partitions improves the estimates for the distances. [ABSTRACT FROM AUTHOR]

This paper presents a novel approach for creating virtual LiDAR scanners through the active segmentation of point clouds. The method employs top-view point cloud segmentation in virtual LiDAR sensors that can be applied to the intelligent behavior of autonomous agents. Segmentation is correlated with the visual tracking of the agent for localization in the environment and point cloud. Virtual LiDAR sensors with different characteristics and positions can then be generated. This method is referred to as the DepthLiDAR approach, and is rigorously evaluated to quantify its performance and determine its advantages and limitations. An extensive set of experiments is conducted using real and virtual LiDAR sensors to compare both approaches. The objective is to propose a novel method to incorporate spatial perception in warehouses, aiming to achieve Industry 4.0. Thus, it is tested in a low-scale warehouse to incorporate realistic features. The analysis of the experiments shows a measurement improvement of 52.24% compared to the conventional LiDAR. [ABSTRACT FROM AUTHOR]

In the field of comparative genomics, one way of comparing two genomes is through the analysis of how they distinguish themselves based on a set of mutations called rearrangement events. When considering that genomes undergo different types of rearrangements, it can be assumed that some events are more common than others. To model this assumption, one can assign different weights to different events, where common events tend to cost less than others. However, this approach, called weighted, does not guarantee that the rearrangement assumed to be the most frequent will be also the most frequently returned by proposed algorithms. To overcome this issue, we investigate a new problem where we seek the shortest sequence of rearrangement events able to transform one genome into the other, with a restriction regarding the proportion between the events returned. Here, we consider two rearrangement events: reversal, that inverts the order and the orientation of the genes inside a segment of the genome, and transposition, that moves a segment of the genome to another position. We show the complexity of this problem for any desired proportion considering scenarios where the orientation of the genes is known or unknown. We also develop an approximation algorithm with a constant approximation factor for each scenario and, in particular, we describe an improved (asymptotic) approximation algorithm for the case where the gene orientation is known. At last, we present the experimental tests comparing the proposed algorithms with others from the literature for the version of the problem without the proportion restriction. [ABSTRACT FROM AUTHOR]

This paper discusses a novel collective sensing approach using autonomous sensors specially designed to monitor gas leaks and search for gas sources. The proposed collective behavior aims to improve the gas-source search by sharing information between mobile sensors and reducing the risks associated with gas leakage. The group acts as a composite sensor that can move independently to search for an optimal sensing zone. The autonomous searching behavior is bio-inspired by colonies of bacteria that continuously seek energy sources throughout their existence. Each sensor makes its own autonomous search decision, considering the group sense, to move in the direction of a better energy source. The collective approach is based on autonomous agents sharing information to achieve a collective sense of gas perception and utilizes more intelligent searching. The method is evaluated in a cyber-physical system specially developed to safely experiment with gases and mobile sensors while reproducing the realistic dynamic behavior of the gas. Experiments are performed to clarify the collective gas-sensing contributions, and the gas search is compared through multiple mobile sensors with and without collective sensing. The proposed approach is evaluated in an unhealthy environment to elucidate its effectiveness. In addition to presenting the related differences between collective and individual sensory approaches, this work contributes with analyzes of the scalability of mobile gas sensing systems. This work also contributed as a simulated semi-physical experimental system to test algorithms’ performance before applying it to practice. [ABSTRACT FROM AUTHOR]

Despite being involved in homeostatic control and hydro-electrolyte balance, the contribution of medullary (A1 and A2) noradrenergic neurons to the hypertonic saline infusion (HSI)-induced cardiovascular response after hypotensive hemorrhage (HH) remains to be clarified. Hence, the present study sought to determine the role of noradrenergic neurons in HSI-induced hemodynamic recovery in male Wistar rats (290–320 g) with HH. Medullary catecholaminergic neurons were lesioned by nanoinjection of antidopamine-β-hydroxylase–saporin (0.105 ng·nl−1) into A1, A2, or both (LES A1; LES A2; or LES A1+A2, respectively). Sham rats received nanoinjections of free saporin in the same regions (SHAM A1; SHAM A2; or SHAM A1+A2, respectively). After 15 days, rats were anesthetized and instrumented for cardiovascular recordings. Following 10 min of stabilization, HH was performed by withdrawing arterial blood until mean arterial pressure (MAP) reaches 60 mmHg. Subsequently, HSI was performed (NaCl 3 M; 1.8 ml·kg−1, i.v.). The HH procedure caused hypotension and bradycardia and reduced renal, aortic, and hind limb blood flows (RBF, ABF, and HBF). The HSI restored MAP, heart rate (HR), and RBF to baseline values in the SHAM, LES A1, and LES A2 groups. However, concomitant A1 and A2 lesions impaired this recovery, as demonstrated by the abolishment of MAP, RBF, and ABF responses. Although lesioning of only a group of neurons (A1 or A2) was unable to prevent HSI-induced recovery of cardiovascular parameters after hemorrhage, lesions of both A1 and A2 made this response unfeasible. These findings show that together the A1 and A2 neurons are essential to HSI-induced cardiovascular recovery in hypovolemia. By implication, simultaneous A1 and A2 dysfunctions could impair the efficacy of HSI-induced recovery during hemorrhage. [ABSTRACT FROM AUTHOR]

Background: Zika virus (ZIKV) is a mosquito-borne virus that is also transmitted sexually; however, the epidemiological relevance of ZIKV sexual transmission in endemic regions is unclear.Methods: We performed a household-based serosurvey in Northeast Brazil to evaluate the differential exposure to ZIKV and chikungunya virus (CHIKV) among households. Individuals who participated in our previous arboviral disease cohort (indexes) were recontacted and enrolled, and their household members were newly enrolled.Results: The relative risk of sexual partners being ZIKV-seropositive when living with a ZIKV-seropositive index participant was significantly higher, whereas this was not observed among nonsexual partners of the index. For CHIKV, both sexual and nonsexual partner household members living with a CHIKV-seropositive index had a significantly higher risk of being seropositive. In the nonindex-based dyadic and generalized linear mixed model analyses, the odds of sexual dyads having a concordant ZIKV plaque reduction neutralization test result was significantly higher. We have also analyzed retrospective clinical data according to the participants' exposure to ZIKV and CHIKV.Conclusions: Our data suggest that ZIKV sexual transmission may be a key factor for the high ZIKV seroprevalence among households in endemic areas and raises important questions about differential disease from the 2 modes of transmission. [ABSTRACT FROM AUTHOR]

This paper discusses a spatial sensor to identify and track objects in the environment. The sensor is composed of an RGB-D camera that provides point cloud and RGB images and an egomotion sensor able to identify its displacement in the environment. The proposed sensor also incorporates a data processing strategy developed by the authors to conferring to the sensor different skills. The adopted approach is based on four analysis steps: egomotive, lexical, syntax, and prediction analysis. As a result, the proposed sensor can identify objects in the environment, track these objects, calculate their direction, speed, and acceleration, and also predict their future positions. The on-line detector YOLO is used as a tool to identify objects, and its output is combined with the point cloud information to obtain the spatial location of each identified object. The sensor can operate with higher precision and a lower update rate, using YOLOv2, or with a higher update rate, and a smaller accuracy using YOLOv3-tiny. The object tracking, egomotion, and collision prediction skills are tested and validated using a mobile robot having a precise speed control. The presented results show that the proposed sensor (hardware + software) achieves a satisfactory accuracy and usage rate, powering its use to mobile robotic. This paper’s contribution is developing an algorithm for identifying, tracking, and predicting the future position of objects embedded in a compact hardware. Thus, the contribution of this paper is to convert raw data from traditional sensors into useful information. [ABSTRACT FROM AUTHOR]

Copyright of Boletín Criminológico is the property of Instituto Andaluz Interuniversitario de Criminologia (Seccion Malaga) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Boletín Criminológico is the property of Instituto Andaluz Interuniversitario de Criminologia (Seccion Malaga) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Lin28a/miRNA let-7b-5p pathway has emerged as a key regulators of energy homeostasis in the skeletal muscle. However, the mechanism through which this pathway is regulated in the skeletal muscle has remained unclear. We have found that 8 wk of aerobic training (Tr) markedly decreased let-7b-5p expression in murine skeletal muscle, whereas high-fat diet (Hfd) increased its expression. Conversely, Lin28a expression, a well-known inhibitor of let-7b-5p, was induced by Tr and decreased by Hfd. Similarly, in human muscle biopsies, Tr increased LIN28 expression and decreased let-7b-5p expression. Bioinformatics analysis of LIN28a DNA sequence revealed that its enrichment in peroxisome proliferator-activated receptor delta (PPARδ) binding sites, which is a well-known metabolic regulator of exercise. Treatment of primary mouse skeletal muscle cells or C2C12 cells with PPARδ activators GW501516 and AICAR increased Lin28a expression. Lin28a and let-7b-5p expression was also regulated by PPARδ coregulators. While PPARγ coactivator-1α (PGC1α) increased Lin28a expression, corepressor NCoR1 decreased its expression. Furthermore, PGC1α markedly reduced the let-7b-5p expression. PGC1α-mediated induction of Lin28a expression was blocked by the PPARδ inhibitor GSK0660. In agreement, Lin28a expression was downregulated in PPARδ knocked-down cells leading to increased let-7b-5p expression. Finally, we show that modulation of the Lin28a-let-7b-5p pathway in muscle cells leads to changes in mitochondrial metabolism in PGC1α dependent fashion. In summary, we demonstrate that Lin28a-let-7b-5p is a direct target of PPARδ in the skeletal muscle, where it impacts mitochondrial respiration. [ABSTRACT FROM AUTHOR]

Combination antiretroviral therapy (cART) has changed Mycobacterium avium epidemiology. A significant decrease in the incidence of disseminated M. avium complex (DMAC) infection was observed between pre-cART and post-cART periods. In contrast, diagnoses of DMAC more than doubled from 1990 to 1996. During this time, DMAC prevalence in people living with AIDS (PLHA) in developed countries reached 20-23% overall and >40% in groups with CD4 cell counts <10 cells/mm3. At present, DMAC in PLHA has an incidence of two events per 1000 patient years. Recently, the centers for disease control changed the criteria for MAC primary prophylaxis, where only patients without immediate cART and CD4 cell counts <50 cells/mm3 are prescribed 1200 mg of azithromycin weekly. Treatment is discontinued when patients initiate effective cART. Diagnosing a disseminated M. avium infection is difficult due to the low accuracy of fluid cultures and a lack of diagnostic processes. However, the usefulness of newer molecular techniques such as whole-genome sequencing has not been evaluated for DMAC and HIV/AIDS. As DMAC has a high mortality rate if not properly diagnosed and treated, we performed a literature review of HIV/AIDS and DMAC epidemiology, risk factors, prophylaxis, clinical manifestation, diagnosis, prognosis, and treatment. [ABSTRACT FROM AUTHOR]

We present three heuristics-Sliding Window, Look Ahead, and Iterative Sliding Window-to improve solutions for the Sorting Signed Permutations by Reversals and Transpositions Problem. We investigate the classical version of the problem as well as versions restricted to prefix and prefix or suffix operations. To assess the heuristics based on its improvement, we implemented algorithms described in the literature to provide initial solutions. Although we have a limited number of problems, these heuristics can be applied to many others within the area of genome rearrangement. When time is a crucial factor, Sliding Window is a better choice because it runs in linear time. If the quality of the solution is a priority, Look Ahead should be preferred. Iterative Sliding Window is the most flexible heuristic and allows us to find a trade-off for specific scenarios where running time and solution quality are relevant. [ABSTRACT FROM AUTHOR]

In this paper a mechanistic model is elaborated to simulate the corrosion behavior of aluminum–zinc–magnesium coatings on steel. The model is based on the mass transport and reactions of the ions in the electrolyte (MITReM). The finite element method has been used, which allows to perform time‐dependent simulations with micrometer scale to study local corrosion effects. The formation of corrosion products and the prediction of electrolyte concentration distributions are compared for different metallic coating compositions. The spatial and temporal simulation of complex precipitates provides an additional tool to validate the model through corrosion product characterization. The simulation results are compared to experimental observations, presented in part I of this paper. The MITReM simulations are limited to the micro‐scale and therefore to small geometries. A link is made with the potential model which can be applied on macro‐scale objects. A qualitative agreement is found between the simulations at both scales and the experiments. Further quantification of this model would optimize the simulations for material design and for predictive maintenance. [ABSTRACT FROM AUTHOR]

Corrosion of AlZnMg coated steel in chloride media is a complicated process, which progress is determined not only by the electrode reactions but also by the local pH and formation of soluble and insoluble corrosion products. In order to adequately describe and predict the corrosion behavior of steel/AlZnMg cut‐edge, a multi‐ion transport, and reaction model (MITReM) is built. Such model takes into account the transport of species in the solution together with their production/consumption in electrochemical and chemical reactions. The main aim of this work is the validation of a numerical model for describing and predicting corrosion of steel/AlZnMg cut‐edge in immersed conditions. This first part describes the experimental work done to obtain model input parameters and validation measurements. The metallic coatings are characterized experimentally with respect to their composition and microstructure, global and local electrochemical behavior (polarization curves, AESEC, and SVET). Local distribution of corrosion products and local pH are also characterized. No blocking effect of the precipitated corrosion products has been observed and dedicated measurements are performed to validate this observation. Based on the experimental input from this part, numerical models of cut‐edge corrosion with different levels of details are developed in Part II. [ABSTRACT FROM AUTHOR]

Background/Aims: Tributyltin (TBT) is an organotin (OTs) and biohazard organometallic pollutant. Recently our group has shown that TBT, even in very low doses, has deleterious effects on several tissues most likely due to its role as an endocrine-disrupting molecule. Other studies have confirmed that OT exposure could be responsible for neural, endocrine, and reproductive dysfunctions via in vitro and in vivo models.  However, TBT effects on bone lack concise data despite the fact that bone turnover is regulated by endocrine molecules, such as parathormone (PTH), estrogen (E2), etc. Our group has already shown that TBT disrupts adrenal and female gonadal functions. Methods: We studied the effects of TBT on bone metabolism and structure using DXA, microCT scan, and SEM. We also determined the calcium (Ca2+) and phosphate (Pi) metabolism in TBT-treated rats as well as some biomarkers for bone formation and resorption. Results: Surprisingly, we found that TBT leads to higher bone mineral density (BMD) although lesions in spinal bone were observed by either microCT scan or SEM. Biomarkers for bone resorption, such as the urinary deoxipyridinolines (DPD) excretion ratio was increased in TBT-treated animals versus mock-treated controls. Osteocalcin (OC) and alkaline phosphatase (AP) are markers of bone formation and are also elevated suggesting that the bone matrix suffers from a higher turnover. Serum Ca2+ (total and ionized) do not changed by TBT treatment although hypercalciuria is observed. Conclusion: It is known that Sn atoms have three valence states (Sn2+, Sn3+, and Sn4+); hence, we hypothesized that Sn (more likely Sn2+) could be competing with Ca2+ and/or Mg2+ in hydroxyapatite mineral matrix to disturb bone turnover. Further work is needed to confirm this hypothesis. [ABSTRACT FROM AUTHOR]