Features in extractive supervised single-document summarization: case of Persian news

Text summarization has been one of the most challenging areas of research in NLP. Much effort has been made to overcome this challenge by using either abstractive or extractive methods. Extractive methods are preferable due to their simplicity compared with the more elaborate abstractive methods. In extractive supervised single document approaches, the system will not generate sentences. Instead, via supervised learning, it learns how to score sentences within the document based on some textual features and subsequently selects those with the highest rank. Therefore, the core objective is ranking, which enormously depends on the document structure and context. These dependencies have been unnoticed by many state-of-the-art solutions. In this work, document-related features such as topic and relative length are integrated into the vectors of every sentence to enhance the quality of summaries. Our experiment results show that the system takes contextual and structural patterns into account, which will increase the precision of the learned model. Consequently, our method will produce more comprehensive and concise summaries

Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes

Structural variants are a common cause of disease and contribute to a large extent to inter-individual variability, but their detection and interpretation remain a challenge. Here, we investigate 11 individuals with complex genomic rearrangements including germline chromothripsis by combining short- and long-read genome sequencing (GS) with Hi-C. Large-scale genomic rearrangements are identified in Hi-C interaction maps, allowing for an independent assessment of breakpoint calls derived from the GS methods, resulting in >300 genomic junctions. Based on a comprehensive breakpoint detection and Hi-C, we achieve a reconstruction of whole rearranged chromosomes. Integrating information on the three-dimensional organization of chromatin, we observe that breakpoints occur more frequently than expected in lamina-associated domains (LADs) and that a majority reshuffle topologically associating domains (TADs). By applying phased RNA-seq, we observe an enrichment of genes showing allelic imbalanced expression (AIG) within 100 kb around the breakpoints. Interestingly, the AIGs hit by a breakpoint (19/22) display both up- and downregulation, thereby suggesting different mechanisms at play, such as gene disruption and rearrangements of regulatory information. However, the majority of interpretable genes located 200 kb around a breakpoint do not show significant expression changes. Thus, there is an overall robustness in the genome towards large-scale chromosome rearrangements

Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes

Here the authors characterize structural variations (SVs) in a cohort of individuals with complex genomic rearrangements, identifying breakpoints by employing short- and long-read genome sequencing and investigate their impact on gene expression and the three-dimensional chromatin architecture. They find breakpoints are enriched in inactive regions and can result in chromatin domain fusions.Structural variants are a common cause of disease and contribute to a large extent to inter-individual variability, but their detection and interpretation remain a challenge. Here, we investigate 11 individuals with complex genomic rearrangements including germline chromothripsis by combining short- and long-read genome sequencing (GS) with Hi-C. Large-scale genomic rearrangements are identified in Hi-C interaction maps, allowing for an independent assessment of breakpoint calls derived from the GS methods, resulting in >300 genomic junctions. Based on a comprehensive breakpoint detection and Hi-C, we achieve a reconstruction of whole rearranged chromosomes. Integrating information on the three-dimensional organization of chromatin, we observe that breakpoints occur more frequently than expected in lamina-associated domains (LADs) and that a majority reshuffle topologically associating domains (TADs). By applying phased RNA-seq, we observe an enrichment of genes showing allelic imbalanced expression (AIG) within 100 kb around the breakpoints. Interestingly, the AIGs hit by a breakpoint (19/22) display both up- and downregulation, thereby suggesting different mechanisms at play, such as gene disruption and rearrangements of regulatory information. However, the majority of interpretable genes located 200 kb around a breakpoint do not show significant expression changes. Thus, there is an overall robustness in the genome towards large-scale chromosome rearrangements

Modeling of the condyle elements within a biomechanical knee model

The development of a computational multibody knee model able to capture some of the fundamental properties of the human knee articulation is presented. This desideratum is reached by including the kinetics of the real knee articulation. The research question is whether an accurate modeling of the condyle contact in the knee will lead to reproduction of the complex combination of flexion/extension, abduction/adduction and tibial rotation ob-served in the real knee? The model is composed by two anatomic segments, the tibia and the femur, whose characteristics are functions of the geometric and anatomic properties of the real bones. The biomechanical model characterization is developed under the framework of multibody systems methodologies using Cartesian coordinates. The type of approach used in the proposed knee model is the joint surface contact conditions between ellipsoids, represent-ing the two femoral condyles, and points, representing the tibial plateau and the menisci. These elements are closely fitted to the actual knee geometry. This task is undertaken by con-sidering a parameter optimization process to replicate experimental data published in the lit-erature, namely that by Lafortune and his co-workers in 1992. Then, kinematic data in the form of flexion/extension patterns are imposed on the model corresponding to the stance phase of the human gait. From the results obtained, by performing several computational simulations, it can be observed that the knee model approximates the average secondary mo-tion patterns observed in the literature. Because the literature reports considerable inter-individual differences in the secondary motion patterns, the knee model presented here is also used to check whether it is possible to reproduce the observed differences with reasonable variations of bone shape parameters. This task is accomplished by a parameter study, in which the main variables that define the geometry of condyles are taken into account. It was observed that the data reveal a difference in secondary kinematics of the knee in flexion ver-sus extension. The likely explanation for this fact is the elastic component of the secondary motions created by the combination of joint forces and soft tissue deformations. The proposed knee model is, therefore, used to investigate whether this observed behavior can be explained by reasonable elastic deformations of the points representing the menisci in the model.Fundação para a Ciência e a Tecnologia (FCT) - PROPAFE – Design and Development of a Patello-Femoral Prosthesis (PTDC/EME-PME/67687/2006), DACHOR - Multibody Dynamics and Control of Hybrid Active Orthoses MIT-Pt/BSHHMS/0042/2008, BIOJOINTS - Development of advanced biological joint models for human locomotion biomechanics (PTDC/EME-PME/099764/2008)

Development of a planar multi-body model of the human knee joint

The aim of this work is to develop a dynamic model for the biological human knee joint. The model is formulated in the framework of multibody systems methodologies, as a system of two bodies, the femur and the tibia. For the purpose of describing the formulation, the relative motion of the tibia with respect to the femur is considered. Due to their higher stiffness compared to that of the articular cartilages, the femur and tibia are considered as rigid bodies. The femur and tibia cartilages are considered to be deformable structures with specific material characteristics. The rotation and gliding motions of the tibia relative to the femur can not be modeled with any conventional kinematic joint, but rather in terms of the action of the knee ligaments and potential contact between the bones. Based on medical imaging techniques, the femur and tibia profiles in the sagittal plane are extracted and used to define the interface geometric conditions for contact. When a contact is detected, a continuous non-linear contact force law is applied which calculates the contact forces developed at the interface as a function of the relative indentation between the two bodies. The four basic cruciate and collateral ligaments present in the knee are also taken into account in the proposed knee joint model, which are modeled as non-linear elastic springs. The forces produced in the ligaments, together with the contact forces, are introduced into the system’s equations of motion as external forces. In addition, an external force is applied on the center of mass of the tibia, in order to actuate the system mimicking a normal gait motion. Finally, numerical results obtained from computational simulations are used to address the assumptions and procedures adopted in this study.Fundação para a Ciência e a Tecnologia (FCT

Investigating the effectiveness of self-shading strategy on overall thermal transfer value and window size in high rise buildings

So much energy is used in high rise buildings to fulfill the basic needs of users such as lighting and thermal comfort. Malaysia has hot and humid climate, buildings especially high rise buildings receive unnecessary solar radiation that cause more solar heat gain. Energy use specially electricity consumption in high rise buildings has increased. There have been growing concerns about energy consumption and its effect on environment. Building, energy and the environment are important issues that the designers should consider to them. Self protected form is one of possible ways against the impact of solar radiation in high rise buildings. The Energy performance of building envelopes was investigated in term of the Overall Thermal Transfer Value (OT TV).In this paper, the amount of OT TV reduction was calculated through OT TV Equations to clear the effectiveness of self shading strategy on minimizing energy consumption for cooling interior spaces in high rise buildings which has considerable envelope areas against solar radiation. Also increasing the optimum window area was investigated using self-shading strategy in designing high rise buildings. As result, the significant reduction in OT TV was shown based on WWR.In addition slight increase was demonstrated in WWR that can influence on visible comfort interior spaces

De novo and haplotype assembly of polyploid genomes

In this thesis, we focus on the problem of reconstructing haplotypes for polyploid genomes and the utilization of called haplotypes in de novo assembly of these genomes. We approach this topic exploring short read sequence data of the highly heterozygous hexaploid sweet potato genome. First, we investigate the role of heterozygosity and ploidy number in reconstructing haplotypes with short reads. In short, higher heterozygosity provides higher number of useful reads for reconstructing haplotypes while being polyploid introduces a challenge in assembling reads into longer sequences; we called it the problem of Ambiguity of Merging fragments. However, we address this problem and show that reads can be assembled into haplotypes with high accuracy using short reads. To this end, we propose a new algorithm, called Ranbow, and evaluate its performance on real and simulated datasets from tetraploid Capsella bursa-pastoris (Shepherd's Purse), and hexaploid Ipomoea batatas (sweet potato) genomes. We are able to show that our method achieves higher accuracy and longer assembled haplotypes than the other methods. Next, we present the de novo assembly pipeline of the sweet potato genome utilizing computed haplotypes for genome assembly improvement. This novel approach, called haplo-scaffolders, uses the assembled haplotypes in order to rescue a set of potential connections which were hidden due to the differences of true haplotypes and the reference sequence. These connections are obtained by mapping the reads into haplotypes and transforming the connection information to the reference level. This process can be repeated by updating the scaffold set to further improve the genome assembly. We show that this strategy improves substantially the N50 and maximum scaffold length of assembled sweet potato genome.Diese Dissertation widmet sich dem Problem der Rekonstruktion von Haplotypen in polyploiden Genomen, und der Verwendung der Haplotypen für das “de novo assembly" dieser Genome. Der gewählte Ansatz stützt sich auf “short read" Sequenzierdaten des höchst heterozygoten hexaploiden Genoms der Süßkartoffel. Zunächst wird die Rolle der Heterozygosität und Ploidie im Kontext der Rekonstruktion von Haplotypen durch "short reads" untersucht. Höhere Heterozygosität macht mehr "reads" für die Rekonstruktion von Haplotypen nutzbar, während die Polyploidie das Zusammenfügen der reads in längere Sequenzen erschwert. Dieses Problem wird hier "Ambiguity of Merging Fragments" genannt und durch den beschriebenen Algorithmus Ranbow adressiert. Die Leistung von Ranbow wird mit Hilfe von realen und simulierten Datensätzen des tetraploiden Genoms des Hirtentäschelkrauts ("Capsella bursa-pastoris") und des hexaploiden Genoms der Süßkartoffel ("Ipomoea batatas") evaluiert. Der Vergleich mit anderen Methoden zeigt, dass man mit Ranbow die höchste Genauigkeit und die längsten Haplotypen erreicht. Anschließend wird eine Pipeline für das verbesserte "de novo assembly" des Süßkartoffelgenoms präsentiert, die die zuvor errechneten Haplotypen nutzt. Diese neue Methode, genannt "haplo-scaffolders", deckt mit Hilfe der Haplotypen einen Satz an möglichen Verbindungen zwischen "scaffolds" auf, die zuvor durch die Unterschiede zwischen echten Haplotypen und der Referenzsequenz versteckt blieben. Diese Verbindungen werden aufgedeckt, indem die "reads" den Haplotypen zugeordnet werden und die Verbindungen auf das Referenzlevel übertragen werden. Der Prozess kann wiederholt werden, in dem der "scaffold" Satz aktualisiert wird, um das Genom “assembly" weiter zu verbessern. Es wird gezeigt, dass diese Strategie den N50-Wert und die maximale Scaffold-Länge des Süßkartoffelgenoms signifikant verbessern

Evaluation of the effect of angiotensin converting enzyme2 in corona pandemic affect female infertility: A review article

Background: Recently in 2019, a novel virus from coronavirus family (Sars-CoV-2) was introduced in China. ACE2 is a zinc metalloprotease played role in the angiotensin system. Earliest reports indicate that 2019-nCoV and SARS-CoV tend to cells that express ACE2 on their surface. ACE2 is expressed in the female reproductive system, and therefore can help Sars-CoV-2 to enter this system and cause infertility or other disorders of the female reproductive system. Materials and Methods: In July 2020, it was researched on the PubMed and Google Scholar databases. Articles were excluded that had an unrelated title or abstract. Finally, the studies that were most relevant to our research subject were selected. Results: Studies to date up to now have shown an invasion of new coronavirus into female reproductive system. Conclusion: SARS-CoV-2 has the potential to impair female fertility. With the assist of ACE2, the virus which invades the female genital tissues, can upset the process of steroidogenesis, folliculogenesis and ovulation, and may eventually lead to menstrual irregularities, miscarriages and even infertility. To date, there have been no reports of coronavirus in the female reproductive system, although at present, there is no evidence that the SARS-CoV-2 virus uses ACE2 receptors in the reproductive system or how they moderate oocyte quality, ensuing pregnancy or fetal growth