Exclusive Sets Research Articles

Unannotated splicing regulatory elements in deep intron space.

Deep intron space harbors a diverse array of splicing regulatory elements that cooperate with better-known exon-proximal elements to enforce proper tissue-specific and development-specific pre-mRNA processing. Many deep intron elements have been highly conserved through vertebrate evolution, yet remain poorly annotated in the human genome. Recursive splicing exons (RS-exons) and intraexons promote noncanonical, multistep resplicing pathways in long introns, involving transient intermediate structures that are greatly underrepresented in RNA-seq datasets. Decoy splice sites and decoy exons act at a distance to inhibit splicing catalysis at annotated splice sites, with functional consequences such as exon skipping and intron retention. RNA:RNA bridges can juxtapose distant sequences within or across introns to activate deep intron splicing enhancers and silencers, to loop out exons to be skipped, or to select one member of a mutually exclusive set of exons. Similarly, protein bridges mediated by interactions among transcript-bound RNA binding proteins (RBPs) can modulate splicing outcomes. Experimental disruption of deep intron elements serving any of these functions can abrogate normal splicing, strongly suggesting that natural mutations of deep intron elements can do likewise to cause human disease. Understanding noncanonical splicing pathways and discovering deep intron regulatory signals, many of which map hundreds to many thousands of nucleotides from annotated splice junctions, is of great academic interest for basic scientists studying alternative splicing mechanisms. Hopefully, this knowledge coupled with increased analysis of deep intron sequences will also have important medical applications, as better interpretation of deep intron mutations may reveal new disease mechanisms and suggest new therapies. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing.

Realization of shock accelerometer sequence-to-sequence calibration based on deep learning

The sensitivity parameters or mathematical model of sensor are obtained through traditional shock accelerometer under calibration test, and then the measurement signal is restored through compensation and correction. As the shock signal with complex components is used in a harsh environment, it is very difficult to accurately restore the measured signals. In the meantime, the deconvolution process of signal recovery is an inverse problem in mathematical physics, which has ubiquitously ill-posed problems, thereby bringing great challenges to the accuracy and precision of the solution. Thus, we propose a depth calibration network based LSTM, which can be used to learn the mapping relationship between the calibrated sensor signal and the standard signal. The measured signal can be restored through a data-driven sequence-to-sequence calibration network, which is trained and verified through the exclusive open-source data set of shock signals. The test results proved the superior performance of the network in shock signal calibration.

Relevancia de la anfotericina B liposomal en el tratamiento de las infecciones fúngicas invasoras en pacientes oncohematológicos

Liposomal amphotericin B (L-AmB) has been a key cornerstone for the management of invasive fungal infections (IFI) caused by a wide array of molds and yeasts during the last three decades. Multiple studies performed over this period have generated a large body of evidence on its efficacy and safety, becoming the main antifungal agent in the management of IFI in patients with hematologic malignancies in several not mutually exclusive clinical settings. First, L-AmB is the most commonly used antifungal agent in patients undergoing intensive chemotherapy for acute leukemia and high-risk myelodysplastic syndrome, as well as in hematopoietic stem cell transplant recipients. Additionally, due to the administration of newer targeted therapies (such as monoclonal antibodies or small molecule inhibitors), opportunistic mold infections are increasingly being reported in patients with hematologic malignancies usually considered low-risk for IFI. These agents usually have a high drug-drug interaction potential, being triazoles, commonly used for antifungal prophylaxis, included. Finally, patients developing breakthrough IFI because of either subtherapeutic concentrations of antifungal prophylactic drugs in blood or selection of resistant strains, require broad spectrum antifungal therapy, usually with an antifungal of a different class. In both situations, L-AmB remains as the best option for early antifungal therapy.

The Role of Agriculture and Non-Farm Economy in Addressing Food Insecurity in Ethiopia: A Review

In Ethiopia, famine and extreme poverty are a result of insufficient food relief, poor macroeconomic factors, climate shocks, undiversified livelihoods based on low productivity in rain-fed agriculture, coupled with institutional incapacity. To serve as a context, this paper provides a comprehensive review of the conceptual framework of human development and capability paradigm to food security. In addition, it highlights evidence and a comparative analysis of the Asian green revolution experience, and places emphasis on sustainable and intersectoral growth through agricultural transformation and promotion of rural non-farm economy agenda to reverse the trends of protracted food crises in Ethiopia. Rapid, science-led, and employment-intensive agricultural growth, accompanied by the promotion of the rural non-farm sector, is of great importance to the rural economy. These will bring about farm sector competitiveness and enhanced productivity, environmental outcomes, acceleration of human development, new opportunities provided to the small-scale food producers, and desirable changes to the rural landscape. The study further introduces a brief analysis of the prominent role of social protection instruments in strengthening food entitlements and basic capabilities, including individual agencies. It suggests that actualizing sustainable food security and hastening human development under Ethiopia’s exclusive settings require the recognition of the rural economic heterogeneity as well as holistic and pragmatic policies, which promote sustainable and inclusive growth.

Popularity of India’s Regional Comic Strips: A Study of the Stylistics of Narayan Debnath’s works

Though celebrated amongst the western literati and the intelligentsia thereof, Comic strips, especially the Indian produce with regional flavours in them, are seemingly juxtaposed, in the acceptance of their stylistic essence, if placed next to their western counterparts. This is also the reason why they have been infamously disregarded in the Indian academia. This paper proposes to study the stylistics aspect of the comic strips from Bengal especially the ones written by Shri Narayan Debnath, and the coming into vogue of this printed visual medium. This article aims to identify the uniqueness and the formal aspects of the stylistics of Indian Comic tradition from Bengal. Additionally, it aims to leaf through the popularity markers through Debnath’s stylistics aspect of the three comic strips that have kept the imagination of his audience alive for more than five decades. He successfully addressed the first objective through a systematic literary review with inclusion and exclusion set as a benchmark. The identification of the stylistics through close reading of the texts along with their systematic review of secondary literature, formed the basics of the second objective. Particularly those stylistics were considered which were typical of their prominence and were integral across the literature and the texts. Furthermore, a matrix was also successfully designed to map the identified stylistics. A couple of implications portray that the said interpretation may help the Post-Millennials or the Generation Z to examine and consider the sublimity and allegiance of reading, and shape the imagination prowess of young minds, apply their intellectual faculty and develop a comic disposition in life. Development of creativity in any narrative style and development of conversational mechanisms are often found to be an added bonus. However, making today’s generation read this form of narrative and chisel their fertile imagination remains a challenge for the digital-natives. There is no doubt however, that this age-old art form can be tremendously advantageous as an academic endeavour and become an integral part of children’s systematic reading habit.

A Comprehensive Performance Analysis of Neurodegenerative diseases Incidence based on Epidemiological Study in the Female subjects over varied data

Neurodegenerative diseases such as Alzheimer’s disease and dementia are gradually becoming more prevalent chronic diseases, characterized by the decline in cognitive and behavioral symptoms. Machine learning is revolu-tionising almost all domains of our life, including the clinical system. The application of machine learning has the potential to enormously augment the reach of neurodegenerative care thus building it more proficient. Throughout the globe, there is a massive burden of Alzheimer’s and demen-tia cases; which denotes an exclusive set of difficulties. This provides us with an exceptional opportunity in terms of the impending convenience of data. Harnessing this data using machine learning tools and techniques, can put scientists and physicians in the lead research position in this area. The ob-jective of this study was to develop an efficient prognostic ML model with high-performance metrics to better identify female candidate subjects at risk of having Alzheimer’s disease and dementia. The study was based on two diverse datasets. The results have been discussed employing seven perfor-mance evaluation measures i.e. accuracy, precision, recall, F-measure, Re-ceiver Operating Characteristic (ROC) area, Kappa statistic, and Root Mean Squared Error (RMSE). Also, a comprehensive performance analysis has been carried out later in the study.

Development and Evaluation of a Global Malnutrition Composite Score

Development and Evaluation of a Global Malnutrition Composite Score

Maximum likelihood parentage assignment using quantitative genotypes.

The cost of parentage assignment precludes its application in many selective breeding programmes and molecular ecology studies, and/or limits the circumstances or number of individuals to which it is applied. Pooling samples from more than one individual, and using appropriate genetic markers and algorithms to determine parental contributions to pools, is one means of reducing the cost of parentage assignment. This paper describes and validates a novel maximum likelihood (ML) parentage-assignment method, that can be used to accurately assign parentage to pooled samples of multiple individuals-previously published ML methods are applicable to samples of single individuals only-using low-density single nucleotide polymorphism (SNP) 'quantitative' (also referred to as 'continuous') genotype data. It is demonstrated with simulated data that, when applied to pools, this 'quantitative maximum likelihood' method assigns parentage with greater accuracy than established maximum likelihood parentage-assignment approaches, which rely on accurate discrete genotype calls; exclusion methods; and estimating parental contributions to pools by solving the weighted least squares problem. Quantitative maximum likelihood can be applied to pools generated using either a 'pooling-for-individual-parentage-assignment' approach, whereby each individual in a pool is tagged or traceable and from a known and mutually exclusive set of possible parents; or a 'pooling-by-phenotype' approach, whereby individuals of the same, or similar, phenotype/s are pooled. Although computationally intensive when applied to large pools, quantitative maximum likelihood has the potential to substantially reduce the cost of parentage assignment, even if applied to pools comprised of few individuals.

The different determinants of purchasing luxury goods online: An international comparison

We propose elements of explanations on the determinants of the act of online purchase by luxury customers from three countries: the United States, the United Kingdom and France. Our research questions are: (1) What weight do cultural factors occupy in the act of buying online, compared to sociodemographic factors? In other words, to what extent would a French luxury customer with the same gender, age and income level as an American customer be less inclined to buy online than in physical stores? (2) How can we characterize these cultural differences? Is this the expression of a different relationship to luxury, different expectations or shopping habits more anchored in a historical context? We explore the reasons why French luxury clients are less likely to shop online than in store, compared to British and American customers. This research can give insights to researchers and practitioners on the behaviour and expectations of different sets of luxury clients in their customer journey. Relying on an exclusive set of customer data, we carry statistical analyses on a global sample of 2036 luxury customers from three countries. Using descriptive statistics and logistic regressions models, we highlight some determinants of online shopping. The influence of the nationality of respondents is statistically established as the second most important factor after consumer’s age. Different purchasing attitudes among countries, with an emphasis put by French clients on emotional dimensions, can explain why an online journey might be less engaging for them. We highlight the necessity to interact in a differentiated way according to the different sociodemographic groups. While social networks are the most common tools used to address the age gap among luxury clients, other functionalities can help to adapt to the expectations of shoppers from different countries. Our research is at the crossroad between cross-cultural studies on luxury shoppers, which did not provide yet an analysis on online customers, and studies dedicated to the specificities of luxury e-commerce which never employed an important international dataset.

Mammary Paget's disease and radiotherapy: a systematic literature review.

Paget disease of the breast (PDB) is a rare form of cutaneous breast cancer. Up to date, no randomized studies evaluated the different management strategies. This systematic review investigates the role of radiotherapy and its best technical profile in the treatment of this disease, with great attention to doses and fractionation regimens. A systematic search was performed on PubMed, Embase and Scopus in order to detect case reports, case series and prospective as well as retrospective clinical studies describing histologically proven PDB and providing information about pertinent radiation treatments. Searching strategy followed PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines. Inclusion criteria were met by six papers, dealing with radiation treatments performed postoperatively and in exclusive settings. No evaluations were performed on preoperative radiotherapy. Actually, the standard treatment of PDB reflects oncological principles of breast carcinoma therapy, including the role of breast-preserving surgery. The traditional radiotherapic dose is 50 Gy, with daily fractionation of 2 Gy. Adjuvant radiotherapy following breast preserving surgery represents the current standard of care; prospective studies could be of help in defining the role of exclusive radiotherapy, hypofractionated schemes and smaller target volumes.

Toward Refined Nash Equilibria for the SET K-COVER Problem via a Memorial Mixed-Response Algorithm

Area coverage and network lifetime are two contradictory issues to the architecture development of a wireless sensor network (WSN). A satisfactory balance could be achieved by deploying abundant sensor nodes randomly and dividing them into <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula> exclusive cover sets. Toward self-organized partition with higher efficiency, we address the problem from the perspective of networked potential games and propose a memorial mixed-response algorithm (MMRA), which is implemented in a distributed and synchronous manner. Being viewed as a game player, each sensor node first updates its memory using a temporary action, which is generated by following a mixed response rule. After this, the coordination evolves into the next iteration by each player randomly drawing an action from its memory with equal probabilities. We prove that our algorithm converges with probability 1 to a convention of Nash equilibria, with the worst approximation ratio strictly larger than 0.5. Moreover, it is also found that a tradeoff between solution efficiency and computation time could be achieved via the adjustment of the amount of randomness introduced via the memory length <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$m$ </tex-math></inline-formula> as well as the probability <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$p_{m}$ </tex-math></inline-formula> , where better partition results are more likely to be generated using a larger <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$m$ </tex-math></inline-formula> and smaller <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$p_{m}$ </tex-math></inline-formula> . Comparisons with existing distributed methods demonstrate the superiority of our method in terms of solution refinement as well as convergence speed.

The Legal Status Divide among the Children of Immigrants

Abstract Over the past thirty-five years, federal immigration policy has brightened the boundaries of the category of undocumented status. For undocumented young people who move into adulthood, the predominance of immigration status to their everyday experiences and social position has been amplified. This process of trying to continue schooling, find work, and participate in public life has become synonymous with a process of learning to be “illegal.” This essay argues that despite known variations in undocumented youths by race, place, and educational history, undocumented status has become what Everett Hughes called a “master status.” The uniform set of immigration status-based exclusions overwhelms the impact of other statuses to create a socially significant divide. The rise, fall, and survival of the Deferred Action for Childhood Arrivals program, a policy offering qualified youths a temporary semilegal status, have underlined how closely access and rights hew to the contours of contemporary immigration policy.

Рок-культура как инструмент вхождения в постиндустриальную культуру

Rock-music and rock-culture, which is formed on its basis, are methods of entering into culture of post-industrial society described by D. Bell, E. Toffler, F. Fukuyama and others. The correlation between rock-culture and post-industrial culture is established in the aspects of values, rules, practices and identities. In rock culture we can see the formation of the following values: creativity, initiative and individualism. Independence of creativity becomes an ethic imperative. It is more important than techniques and professionalism, which are characteristic of industrial culture. Exaggerated prevalence of innovation over playing tradition strengthens the status and role of the author striving for the permanent re-creation of his own image and style. Another quality, which helps rock culture penetrate into postindustrial society, is assimilation of daily routine by creative activity. This factor initiates consciousness emancipation and breakdown of hierarchical social structures. Rock-culture, as well as post-industrial society, experiences decentralization, de-synchronization and de-standardization. Such social-cultural disorder correlates with marginalization of rock-culture. It forms amateurism as a normative attitude that is opposed to professionalism. Finally the above-mentioned changes entail the collapse of the existing “big” identities, which are substituted by “small group” identities in rock-culture characterized by small potential for internalization. This change of identities, their overlapping triggers the formation of mental plurality, tolerance to mutually exclusive values, normative settings, practices and symbols. Mental pluralism allows a person to change quickly life strategies, respond to external challenges. The stable boundaries between private and public, between art and everyday life are being destroyed in the rock-culture. At the same time, the author highlights the fact that within rock culture entering post-industrial culture is carried out by non-linear way, with expenses and contradictions.

MEScan: a powerful statistical framework for genome-scale mutual exclusivity analysis of cancer mutations.

Cancer somatic driver mutations associated with genes within a pathway often show a mutually exclusive pattern across a cohort of patients. This mutually exclusive mutational signal has been frequently used to distinguish driver from passenger mutations and to investigate relationships among driver mutations. Current methods for de novo discovery of mutually exclusive mutational patterns are limited because the heterogeneity in background mutation rate can confound mutational patterns, and the presence of highly mutated genes can lead to spurious patterns. In addition, most methods only focus on a limited number of pre-selected genes and are unable to perform genome-wide analysis due to computational inefficiency. We introduce a statistical framework, MEScan, for accurate and efficient mutual exclusivity analysis at the genomic scale. Our framework contains a fast and powerful statistical test for mutual exclusivity with adjustment of the background mutation rate and impact of highly mutated genes, and a multi-step procedure for genome-wide screening with the control of false discovery rate. We demonstrate that MEScan more accurately identifies mutually exclusive gene sets than existing methods and is at least two orders of magnitude faster than most methods. By applying MEScan to data from four different cancer types and pan-cancer, we have identified several biologically meaningful mutually exclusive gene sets. MEScan is available as an R package at https://github.com/MarkeyBBSRF/MEScan. Supplementary data are available at Bioinformatics online.

Overly optimistic prediction results on imbalanced data: a case study of flaws and benefits when applying over-sampling

Information extracted from electrohysterography recordings could potentially prove to be an interesting additional source of information to estimate the risk on preterm birth. Recently, a large number of studies have reported near-perfect results to distinguish between recordings of patients that will deliver term or preterm using a public resource, called the Term/Preterm Electrohysterogram database. However, we argue that these results are overly optimistic due to a methodological flaw being made. In this work, we focus on one specific type of methodological flaw: applying over-sampling before partitioning the data into mutually exclusive training and testing sets. We show how this causes the results to be biased using two artificial datasets and reproduce results of studies in which this flaw was identified. Moreover, we evaluate the actual impact of over-sampling on predictive performance, when applied prior to data partitioning, using the same methodologies of related studies, to provide a realistic view of these methodologies’ generalization capabilities. We make our research reproducible by providing all the code under an open license.

A forward selection algorithm to identify mutually exclusive alterations in cancer studies.

Mutual exclusivity analyses provide an effective tool to identify driver genes from passenger genes for cancer studies. Various algorithms have been developed for the detection of mutual exclusivity, but controlling false positive and improving accuracy remain challenging. We propose a forward selection algorithm for identification of mutually exclusive gene sets (FSME) in this paper. The method includes an initial search of seed pair of mutually exclusive (ME) genes and subsequently including more genes into the current ME set. Simulations demonstrated that, compared to recently published approaches (i.e., CoMEt, WExT, and MEGSA), FSME could provide higher precision or recall rate to identify ME gene sets, and had superior control of false positive rates. With application to TCGA real data sets for AML, BRCA, and GBM, we confirmed that FSME can be utilized to discover cancer driver genes.

Experimental investigations on machining performance of tungsten carbide (WC) by modification of wire-cut electric discharge machining work holding setup into turning process

In this study, machining performance of Tungsten carbide (WC) was investigated by modifying the Wire-cut electric discharge machining setup as turning process. The exclusive set up was fabricated for fixing the workmaterial and to facilitate rotating and linear motion constitutes a turning process. The experiment was conducted on Tungsten Carbide (WC) for 9 different trials by varying the input conditions of pulse on-time (T-on), pulse off-time (T-off), wire feed and wire tension to analyse the Material Removal Rate and Surface Roughness. The Taguchi method was used to optimise the process parameters for better Surface Finish and Maximum Material Removal Rate. The influences of process parameters on Material Removal Rate and Surface Roughness are statistically analyzed by ANOVA. The results revealed that the more important parameters are pulse on time (T-on) and pulse off time (T-on) than wire feed and wire tension. The best parameter was identified against response characteristics.

Iterated two-phase local search for the colored traveling salesmen problem

The colored traveling salesmen problem (CTSP) is a generalization of the popular traveling salesman problem with multiple salesmen. In CTSP, the cities are divided into m exclusive city sets (m is the number of salesmen) and one shared city set. The goal of CTSP is to determine a shortest Hamiltonian circuit (also called route or tour) for each of the m salesmen satisfying that (1) each route includes all cities of an exclusive city set and some (or all) cities of the shared city set, and (2) each city of the shared city set is included in one unique route. CTSP is a relevant model for a number of practical applications and is known to be computationally challenging. We present the first iterated two-phase local search algorithm for this important problem which combines a local optima exploration phase and a local optima escaping phase. We show computational results on 65 common benchmark instances to demonstrate its effectiveness and especially report 22 improved upper bounds. We make the source code of the algorithm publicly available to facilitate its use in future research and real applications.

Primary Education Truancy and School Performance in Social Exclusion Settings: The Case of Students in Cañada Real Galiana

Academic studies show that one of the main predictors of early school dropout at secondary education is student truancy behaviour, usually beginning at primary education. This is a problem that gets worse in socially vulnerable environments. This study analyses the prevalence and types of truancy in a population of students with high social risk in Madrid city, studying the relationship between truancy and their school performance. A questionnaire was answered by mentor teachers of students at the preschool and primary stages (N = 120), who reported information from a total of 433 students from 12 different schools. Results showed a high level of prevalence in the different types of truancy (Active and Passive). Among these behaviours, 46.86% of students skipped entire days without a valid excuse and 42.51% did not usually do their homework. Overall, 60% showed underachievement and great rates of curricular gap. In 6th grade, the last year of primary school, 74.42% of students had repeated one grade and 27.91% more than one. Moreover, significant correlations were found between truancy and school performance. The detection and early action against truancy in primary education with this type of student will reduce early dropouts and make school a key actor for the development of these students.

Identification of common signatures in idiopathic pulmonary fibrosis and lung cancer using gene expression modeling

BackgroundIdiopathic pulmonary fibrosis (IPF) is associated with an increased risk for lung cancer, but the underlying mechanisms driving malignant transformation remain largely unknown. This study aimed to identify differentially expressed genes (DEGs) distinguishing IPF and lung cancer from healthy individuals and common genes driving the transformation from healthy to IPF and lung cancer.MethodsThe gene expression data for IPF and non-small cell lung cancer (NSCLC) were retrieved from the Gene Expression Omnibus (GEO) database. The DEG signatures were identified via unsupervised two-way clustering (TWC) analysis, supervised support vector machine analysis, dimensional reduction, and mutual exclusivity analysis. Gene enrichment and pathway analyses were performed to identify common signaling pathways. The most significant signature genes in common among IPF and lung cancer were further verified by immunohistochemistry.ResultsThe gene expression data from GSE24206 and GSE18842 were merged into a super array dataset comprising 86 patients with lung disorders (17 IPF and 46 NSCLC) and 51 healthy controls and measuring 23,494 unique genes. Seventy-nine signature DEGs were found among IPF and NSCLC. The peroxisome proliferator-activated receptor (PPAR) signaling pathway was the most enriched pathway associated with lung disorders, and matrix metalloproteinase-1 (MMP-1) in this pathway was mutually exclusive with several genes in IPF and NSCLC. Subsequent immunohistochemical analysis verified enhanced MMP1 expression in NSCLC associated with IPF.ConclusionsFor the first time, we defined common signature genes for IPF and NSCLC. The mutually exclusive sets of genes were potential drivers for IPF and NSCLC.