Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple gene sequencing for risk assessment in patients with early-onset or familial breast cancer

Since BRCA mutations are only responsible for 10–20% of cases of breast cancer in patients with early-onset or a family history and since next-generation sequencing technology allows the simultaneous sequencing of a large number of target genes, testing for multiple cancer-predisposing genes is now being considered, but its significance in clinical practice remains unclear. We then developed a sequencing panel containing 68 genes that had cancer risk association for patients with early-onset or familial breast cancer. A total of 133 patients were enrolled and 30 (22.6%) were found to carry germline deleterious mutations, 9 in BRCA1, 11 in BRCA2, 2 in RAD50, 2 in TP53 and one each in ATM, BRIP1, FANCI, MSH2, MUTYH, and RAD51C. Triple-negative breast cancer (TNBC) was associated with the highest mutation rate (45.5%, p = 0.025). Seven of the 9 BRCA1 mutations and the single FANCI mutation were in the TNBC group; 9 of the 11 BRCA2, 1 of the 2 RAD50 as well as BRIP1, MSH2, MUTYH, and RAD51C mutations were in the hormone receptor (HR)(+)Her2(−) group, and the other RAD50, ATM, and TP53 mutations were in the HR(+)Her2(+) group. Mutation carriers were considered as high-risk to develop malignancy and advised to receive cancer screening. Screening protocols of non-BRCA genes were based on their biologic functions; for example, patients carrying RAD51C mutation received a screening protocol similar to that for BRCA, since BRCA and RAD51C are both involved in homologous recombination. In conclusion, we consider that multiple gene sequencing in cancer risk assessment is clinically valuable.
Functional Organization of the Genome May Shape the Species Boundary in the House Mouse

Genomic features such as rate of recombination and differentiation have been suggested to play a role in species divergence. However, the relationship of these phenomena to functional organization of the genome in the context of reproductive isolation remains unexplored. Here, we examine genomic characteristics of the species boundaries between two house mouse subspecies (Mus musculus musculus/M. m. domesticus). These taxa form a narrow semipermeable zone of secondary contact across Central Europe. Due to the incomplete nature of reproductive isolation, gene flow in the zone varies across the genome. We present an analysis of genomic differentiation, rate of recombination, and functional composition of genes relative to varying amounts of introgression. We assessed introgression using 1,316 autosomal single nucleotide polymorphism markers, previously genotyped in hybrid populations from three transects. We found a significant relationship between amounts of introgression and both genomic differentiation and rate of recombination with genomic regions of reduced introgression associated with higher genomic differentiation and lower rates of recombination, and the opposite for genomic regions of extensive introgression. We also found a striking functional polarization of genes based on where they are expressed in the cell. Regions of elevated introgression exhibit a disproportionate number of genes involved in signal transduction functioning at the cell periphery, among which olfactory receptor genes were found to be the most prominent group. Conversely, genes expressed intracellularly and involved in DNA binding were the most prevalent in regions of reduced introgression. We hypothesize that functional organization of the genome is an important driver of species divergence.
Generalizing from social media data: a formal theory approach

ABSTRACT Researchers increasingly draw on social media data to answer big questions about social patterns and dynamics. However, as with any data source, social media data present both opportunities and significant challenges. One major critique of social media data is that the data are not generalizable outside of the platforms from which the data originate. Problems of generalizability stem from non-universal participation rates on various platforms, demographically biased samples, as well as limited access to data based on infrastructural constraints and/or user privacy practices. We suggest that instead of empirical generalizability, social media data are theoretically generalizable in the formal theory tradition. Through a case example in which we use YouTube comments to test and extend a key tenet of identity theory, we show how social media data can instantiate theoretical variables and thus generalize to theoretical propositions. Mediated through formal theory, social media data maintain the capacity to address broad social questions while upholding methodological integrity.
Different exercise modalities have distinct effects on the integrin-linked kinase (ILK) and Ca2+ signaling pathways in the male rat bone

Mechanical loading is essential to maintain optimal skeletal health. Despite the fact that early‐life exercise has positive, long‐lasting effects on the musculo‐skeletal system, the response of the musculo‐skeletal system to spontaneous low‐impact exercise has been poorly studied. Previously, we identified subtle morphological changes in the femoral diaphysis of exercised animals compared to nonexercised controls. We hypothesized that significant changes in gene expression of cells should precede significant measurable phenotypic changes in the tissues of which they are part. Here, we employed RNA‐Seq to analyse the transcriptome of the cortical bone from the femoral mid‐diaphysis of prepubertal male Sprague‐Dawley rats that were assigned to control (CON); bipedal stance (BPS); or wheel exercise (WEX) groups for 15 days. We identified 808 and 324 differentially expressed transcripts in the BPS and WEX animals respectively. While a number of transcripts change their levels in an exercise‐specific manner, we identified 191 transcripts that were differentially expressed in both BPS and WEX. Importantly, we observed that the exercise mode had diametrically opposite effects on transcripts for multiple genes within the integrin‐linked kinase (ILK) and Ca2+ signaling pathways such that they were up‐regulated in BPS and down‐regulated in WEX. The findings are important for our understanding of possible ways in which different exercise regimens might affect bone when normal activities apply mechanical stimuli during postnatal growth and development.
Delays and Oscillations in Networks of Spiking Neurons: A Two-Timescale Analysis

Oscillations are a ubiquitous feature of many neural systems, spanning many orders of magnitude in frequency. One of the most prominent oscillatory patterns, with possible functional implications, is that occurring in the mammalian thalamocortical system during sleep. This system is characterized by relatively long delays (reaching up to 40 msec) and gives rise to low-frequency oscillatory waves. Motivated by these phenomena, we study networks of excitatory and inhibitory integrate-and-fire neurons within a Fokker-Planck delay partial differential equation formalism and establish explicit conditions for the emergence of oscillatory solutions, and for the amplitude and period of the ensuing oscillations, for relatively large values of the delays. When a two-timescale analysis is employed, the full partial differential equation is replaced in this limit by a discrete time iterative map, leading to a relatively simple dynamic interpretation. This asymptotic result is shown numerically to hold, to a good approximation, over a wide range of parameter values, leading to an accurate characterization of the behavior in terms of the underlying physical parameters. Our results provide a simple mechanistic explanation for one type of slow oscillation based on delayed inhibition, which may play an important role in the slow spindle oscillations occurring during sleep. Moreover, they are consistent with experimental findings related to human motor behavior with visual feedback.
Link sharing in high capacity Bluetooth voice access networks

Bluetooth is currently being integrated into many different types of cellphones and other portable devices. Future access networks can use this connectivity to provide real-time voice services in public places such as airports, convention centers and shopping malls. To obtain good statistical performance a large number of potential Bluetooth voice links would he provided throughout the desired coverage area. In the results presented we show that Bluetooth SCO voice links are inadequate for this purpose. Unfortunately, when coverage is such that significant Bluetooth base station and link sharing is possible. SCO packet loss rates are unacceptable. The alternative is to operate such a network using voice over Bluetooth ACL links (VoACL). and a simple VoACL scheme is proposed and investigated. A finite windowed loss rate model is also proposed and is used to characterize these designs. Analytic and simulation models show that VoACL can result in acceptable voice packet loss performance compared with SCO voice designs and that the call blocking rate is about the same between the ACL and SCU systems.
“Being a Presence to Each Other”: Adult Educators Who Foster Empowerment With Incarcerated Women

Our research explored the experiences of educators who teach in a gender-responsive program for women in a jail. We interrogated how educators fostered empowerment in their classes, what their motivations were for teaching in the program, and the tensions that existed for them when using emancipatory teaching practices in jail. Findings indicate that educators used Freirean concepts to foster empowerment, were motivated to share their knowledge, were motivated to counter dehumanization, and recognized their commonalities and privilege. Trust and agency created tensions while using an emancipatory pedagogy at a jail. Findings have implications for educators teaching marginalized populations.
Association Rule Mining for Multiple Tables With Fuzzy Taxonomic Structures

Most of the existing data mining algorithms handle databases consisting of single table to find association rules an large databases. Few algorithms work on multiple tables having fuzzy data with taxonomic structures. This paper proposes 'Multi level Fuzzy rules for ER Models' algorithm. The study focuses on the issue of mining association rules in databases having multiple levels containing fuzzy data with taxonomy and tables to be designed using Entity-Relationship (ER) Models. The study aims to incorporate the previous developed algorithms Extended Apriori and Apriori star to a new algorithm. The study will help in standardizing algorithms for finding appropriate results from database tables containing data with fuzzy taxonomic structures.
Damping of Low-Energy Excitations of a Trapped Bose-Einstein Condensate at Finite Temperatures

We present the theory of damping of low-energy excitations of a trapped Bose condensate at finite temperatures, where the damping is provided by the interaction of these excitations with the thermal excitations. We emphasize the key role of stochastization in the behavior of the thermal excitations for damping in non-spherical traps. The damping rates of the lowest excitations, following from our theory, are in fair agreement with the data of recent JILA and MIT experiments. The damping of quasiclassical excitations is determined by the condensate boundary region, and the result for the damping rate is drastically different from that in a spatially homogeneous gas. After the discovery of Bose-Einstein condensation (BEC) [1–3], one of the major directions in the physics of ultra-cold gases has been the investigation of collective many-body effects. Especially interesting is the behavior of low-energy collective excitations of a trapped condensate. The JILA [4,6] and MIT [5,7] experimental studies of the excitations related to shape oscillations of the condensate show that these excitations are damped and provide us with interesting results on the temperature dependence of the damping rates and frequency shifts. In this letter we develop the theory of damping of excitations of a trapped condensate in the Thomas-Fermi regime at finite temperatures, where the presence of a thermal component is important. We confine ourselves to the damping of low-energy excitations, i.e.,
Permanent magnet synchronous motor: finite element torque calculations

The Maxwell stress tensor method is modified by the authors to yield an area integration which takes into account the field distribution in the airgap of a machine, resulting in an improvement in accuracy and the elimination of sensitivity to contour selection. A second technique, based on the co-energy derivative method, is also developed. This needs only one finite-element (FE) solution and eliminates the trial-and-error procedure of selecting a proper displacement for the derivative determination, thus shortening the computational time. The torque characteristics of a permanent magnet synchronous motor (PMSM) evaluated from the above methods compare favourably with each other as well as with those from the Lorentz method and an analytical model based on an equivalent circuit of the machine. The torque calculating techniques are used to select the geometry of the permanent magnets for the rotor of a 30 hp machine using a criterion which takes into account the torque per unit stator current, efficiency-power-factor product, overload capability of the machine, and volume (cost) of permanent magnet material. <<ETX>>
Nonlinear conjugate gradient method for spectral tomosynthesis

Image reconstruction in spectral digital breast tomosynthesis (DBT) requires solving a large-scale nonlinear inverse problem. Most numerical approaches on real data used a simplified linear (and hence incorrect) mathematical model to reduce the computational costs. The aim of this paper is to consider the use of a nonlinear conjugate gradient method for very large-scale nonlinear least squares problems, and apply it to spectral DBT. Numerical experiments on 3-dimensional phantom images illustrate the effectiveness and efficiency of the proposed scheme.
Language Identification using Classifier Ensembles

In this paper we describe the language identiﬁcation system we developed for the Discriminating Similar Languages (DSL) 2015 shared task. We constructed a clas-siﬁer ensemble composed of several Support Vector Machine (SVM) base classi-ﬁers, each trained on a single feature type. Our feature types include character 1 – 6 grams and word unigrams and bigrams. Using this system we were able to outperform the other entries in the closed training track of the DSL 2015 shared task, achieving the best accuracy of 95 . 54% .
Regional Analysis of Potentials of Flexibility Options in the Electricity System for the Study Regions Prignitz in Brandenburg and Anhalt-Bitterfeld-Wittenberg in Saxony-Anhalt

The electricity system is changing. Due to the climate targets, the share of fluctuating renewable energy will continue to rise in the next few years, and conventional, fossil fuels will increasingly take a back seat. This creates the challenge of balancing supply and demand in the power system and increases the need for flexibility in the electricity system. In this article flexibility in energy systems is introduced, flexibility options are categorised along existing literature and a method is explained to approach the estimation of flexibility potential by means of two example regions. Therefore, 13 flexibility options in the electricity system in four categories are analysed: flexible generators, demand side management, storage, and power-to-X. By means of the two study regions Prignitz in Brandenburg and Anhalt-Bitterfeld-Wittenberg in Saxony-Anhalt, a practicable, transferable method to quantify and compare the technical potentials of the flexibility options at a high regional level is developed.
Application of construal level and value-belief norm theories to undergraduate decision-making on a wildlife socio-scientific issue

ABSTRACT One aim of science education is to develop scientific literacy for decision-making in daily life. Socio-scientific issues (SSI) and structured decision-making frameworks can help students reach these objectives. This research uses value belief norm (VBN) theory and construal level theory (CLT) to explore students’ use of personal values in their decision-making processes and the relationship between abstract and concrete problematization and their decision-making. Using mixed methods, we conclude that the level of abstraction with which students problematise a prairie dog agricultural production and ecosystem preservation issue has a significant relationship to the values students used in the decision-making process. However, neither abstraction of the problem statement nor students’ surveyed value orientations were significantly related to students’ final decisions. These results may help inform teachers’ understanding of students and their use of a structured-decision making tool in a classroom, and aid researchers in understanding if these tools help students remain objective in their analyses of complex SSIs.
UML 2 . 0-Based Systems Engineering Using a Model-Driven Development Approach

F or many years, software engineers have successfully applied the Unified Modeling Language (UML) to model-based software engineering. There have been several attempts to introduce UML and the underlying object-oriented methods to systems engineering to unify the overall development process. However, many systems engineers continue to use classically structured analysis techniques and artifacts to define system requirements and designs. One reason for this could be that systems engineering is mostly driven by functional requirements. Speaking in terms of system functionality is still considered the most natural way of expressing a design by most of the domain experts involved in the early phases of system development (electrical engineers , mechanical engineers, test engineers , marketing personnel, and, of course, customers). Given this, the only way to unify the overall development process is to extend UML with regard to function-driven systems engineering, and to define a process that enables a seamless transfer of respective artifacts to UML-based software engineering. The release of UML 2.0 [1] eventually provided the missing artifacts for function-driven systems engineering. The following sections describe a UML 2.0-based process that systems engineers can use to capture requirements and specify architecture. The approach uses model execution as a means for requirements verification and validation. Figure 1 shows the integrated systems and software engineering process by means of the classic V. The left leg of the V describes the top-down design flow, while the right-hand side shows the bottom-up integration phases from unit test to the final system acceptance. Using the notation of state-charts, the iterative characteristic of the process is visualized by the high-level interrupt due to system changes. Whenever changes occur, the process will restart at the requirements analysis phase. Systems engineering is characterized by a sequential top-down workflow from requirements analysis to system analysis and system architectural design. A loop back to the requirements analysis may occur if, during systems analysis or architectural design, functional issues require a reexamination of the higher-level requirements. The software engineering work-flow is characterized by the iterative and incremental cycles through the software analysis and design phase, the implementation phase, and the different levels of integration and testing. It is important to note the creation and reuse of requirements-related test scenarios along the top-down design path. These scenarios are also used to assist the bottom up integration and test phases and, in the case of system changes, regression test cycles. Key objectives of …
Resolving Zero Pronouns in Texts using Textual Structure

This paper proposes a powerful method for the resolution of Japanese zero pronouns in a text with meta information which indicates the textual structure. This method uses not only semantic and pragmatic constraints but also information about the text structure. According to a window test for 480 zero pronouns in a specification with explicit structural information, all of the zero pronouns could be resolved consistently and correctly. Furthermore, 93% of zero pronouns with intersentential antecedents could be resolved correctly using only structural information in the text. This result indicates that, for a text with explicit structural information, the information can be used to effectively resolve zero pronouns with intersentential antecedents.
Dufour-Soret Effects on 3D Convective Viscoelastic Fluid Flow Upon a Stretched Surface

The purpose of this analytical work is to investigate the Dufour-Soret effects on three dimensional unsteady boundary layer flows, mass and heat transfer of a viscoelastic fluid upon a stretched surface in the existence of internal heat generation/absorption. The equations governing the flow are converted using similarity variables into a set of non-linear ordinary differential equations. The series solution is obtained by homotopy analysis. The results are analyzed for the influences of the various pertinent constants involving in the study. The mass and heat transfer rates are calculated by the localized Sherwood and Nusselt numbers along the surface.
VLC physical layer design based on Pulse Position Modulation (PPM) for stable illumination

Visible Light Communication (VLC) is promising new technology to be applied in the lighting system infrastructure. This communication function should not interfere with the existing lighting system. In order to prevent from this interference, the utilized modulation scheme should have a limited dynamic range to avoid flickering and dimming effect. We propose Pulse Position Modulation (PPM) technique in our VLC system due to its very minimum dynamic range feature. This paper describes the design and analysis of VLC physical layer using PPM scheme to obtain a stable illumination. The design of physical layer consists of analog front end (AFE) circuit and the data processing which is implemented in microcontroller and FPGA. Based on the test results of our VLC system using low cost photo detector, the system is able to provide stable illumination while reaching the maximum data transfer rate of 20 kbps.
The multifaceted resources and microevolution of the successful human and animal pathogen methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most important bacterial pathogens based on its incidence and the severity of its associated infections. In addition, severe MRSA infections can occur in hospitalised patients or healthy individuals from the community. Studies have shown the infiltration of MRSA isolates of community origin into hospitals and variants of hospital-associated MRSA have caused infections in the community. These rapid epidemiological changes represent a challenge for the molecular characterisation of such bacteria as a hospital or community-acquired pathogen. To efficiently control the spread of MRSA, it is important to promptly detect the mecA gene, which is the determinant of methicillin resistance, using a polymerase chain reaction-based test or other rapidly and accurate methods that detect the mecA product penicillin-binding protein (PBP)2a or PBP2’. The recent emergence of MRSA isolates that harbour a mecA allotype, i.e., the mecC gene, infecting animals and humans has raised an additional and significant issue regarding MRSA laboratory detection. Antimicrobial drugs for MRSA therapy are becoming depleted and vancomycin is still the main choice in many cases. In this review, we present an overview of MRSA infections in community and healthcare settings with focus on recent changes in the global epidemiology, with special reference to the MRSA picture in Brazil.