Miracle-dz/UniFAR-FTUs huggingface dataset:
Pre-mRNA Secondary Structures Influence Exon Recognition

The secondary structure of a pre-mRNA influences a number of processing steps including alternative splicing. Since most splicing regulatory proteins bind to single-stranded RNA, the sequestration of RNA into double strands could prevent their binding. Here, we analyzed the secondary structure context of experimentally determined splicing enhancer and silencer motifs in their natural pre-mRNA context. We found that these splicing motifs are significantly more single-stranded than controls. These findings were validated by transfection experiments, where the effect of enhancer or silencer motifs on exon skipping was much more pronounced in single-stranded conformation. We also found that the structural context of predicted splicing motifs is under selection, suggesting a general importance of secondary structures on splicing and adding another level of evolutionary constraints on pre-mRNAs. Our results explain the action of mutations that affect splicing and indicate that the structural context of splicing motifs is part of the mRNA splicing code.
An Empirical Approach to Studying Intonation Tendencies in Polyphonic Vocal Performances

Background in music theory and analysis. Polyphonic vocal intonation practices have been addressed in a number of studies on vocal acoustics. Our research both builds on this work and supplements it with a theoretical paradigm based on work done in the areas of sensory consonance and tonal attraction. Background in computing. Recent work in the field of music information retrieval has discussed the main obstacles related to tracking pitches in a polyphonic signal and has provided some techniques for working around these problems. Our method for analyzing the pitch content of recorded performances draws extensively on this work and on the knowledge made available to us by the musical scores of the pieces being performed. Aims. Our research is focused on the study and modeling of polyphonic vocal intonation practices through the intersection of computational and theoretical approaches. We present a methodology that allows for a detailed model of this aspect of polyphonic vocal performance practice to be built from analyses of numerous recordings of real-world performances, while working within a robust theoretical paradigm. Main contribution. In the computational component of the research a number of a cappella polyphonic vocal recordings are analyzed with signal processing techniques to estimate the perceived fundamental frequencies for the sung notes. These observations can be related to the musical context of the score through machine learning techniques to determine likely intonation tendencies for regularly occurring musical patterns. A major issue in developing a theory of intonation practices is the potential conflict between the vertical and horizontal intonational impetuses. To assess this conflict in greater detail we have constructed a theoretical approach where theories of sensory consonance account for vertical tuning tendencies and theories of tonal attraction account for the horizontal tendencies. Implications. In the field of music cognition, our research relates to work being done in the area of musical expression. If the intonation tendencies inferred from the end results of this research are taken as a norm, then deviations from this norm, when these deviations are musically appropriate, can be viewed as expressive phenomena. Computer software implementing such results will allow composers and musicologists to hear more intonationally accurate digital re-creations and may also function as a training guide for vocalists.
Numerical Investigation of Propagation of Ultrasonic Waves in the Waveguides with Mode Conversion

Ultrasonic investigation techniques are widely used in materials characterisation and non-destructive testing applications. In special cases of applications, such as investigation of properties of melted polymers, metals and hot liquids, measurements must be performed in a wide temperature range. However conventional piezoelectric transducers cannot withstand higher temperatures than the Curie temperature. Therefore in order to protect conventional ultrasonic transducers from influence of a high temperature and to avoid depolarization, measurements must be performed using special waveguides with a low thermal conductivity between the object under investigation and the ultrasonic transducer. For measurements of the material properties, such as viscoelastic properties of materials, additional shear wave transducers must be used. In this work approach how to excite both, longitudinal and shear waves using special waveguides with mode conversion, using pair of conventional ultrasonic longitudinal wave transducers is presented. In this work numerical investigation of propagation of longitudinal and shear ultrasonic waves in the waveguides with mode conversion using finite element method and CIVA software was carried out. Modelling of propagation of simultaneously generated longitudinal and shear waves using pair of longitudinal ultrasonic transducers was performed. Influence of temperature gradient to the required incidence angle of the longitudinal wave was evaluated.
Power-efficient prefetching for embedded processors

Because of stringent power constraints, aggressive latency-hiding approaches, such as prefetching, are absent in the state-of-the-art embedded processors. There are two main reasons that make prefetching power inefficient. First, compiler-inserted prefetch instructions increase code size and, therefore, could increase I-cache power. Second, inaccurate prefetching (especially for hardware prefetching) leads to high D-cache power consumption because of useless accesses. In this work, we show that it is possible to support power-efficient prefetching through bit-differential offset assignment. We target the prefetching of relocatable stack variables with a high degree of precision. By assigning the offsets of stack variables in such a way that most consecutive addresses differ by 1 bit, we can prefetch them with compact prefetch instructions to save I-cache power. The compiler first generates an access graph of consecutive memory references and then attempts a layout of the memory locations in the smallest hypercube. Each dimension of the hypercube represents a 1-bit differential addressing. The embedding is carried out in as compact a hypercube as possible in order to save memory space. Each load/store instruction carries a hint regarding prefetching the next memory reference by encoding its differential address with respect to the current one. To reduce D-cache power cost, we further attempt to assign offsets so that most of the consecutive accesses map to the same cache line. Our prefetching is done using a one entry line buffer [Wilson et al. 1996]. Consequently, many look-ups in D-cache reduce to incremental ones. This results in D-cache activity reduction and power savings. Our prefetcher requires both compiler and hardware support. In this paper, we provide implementation on the processor model close to ARM with small modification to the ISA. We tackle issues such as out-of-order commit, predication, and speculation through simple modifications to the processor pipeline on noncritical paths. Our goal in this work is to boost performance while maintaining/lowering power consumption. Our results show 12% speedup and slight power reduction. The runtime virtual space loss for stack and static data is about 11.8%.
SLAM solution based on particle filter with outliers filtering in dynamic environments

Our work presents a proposal for SLAM (Simultaneous Localization and Mapping) problem in dynamic environments. A method for robot self-localization is described. During operations in dynamic environments, only static landmarks are used. For this purpose, an outliers filter was designed. It separates static and mobile landmarks that are included in a set of neglectable marks. A modified particle filter is proposed which estimates the pose of a robot by a new way. Furthermore, it resamples a new set of particles at each estimative of the pose of the robot. Set of particles is based on current observations made by robot using RGBD camera. ROS (Robot Operating System) platform is used in order to integrate all hardware and our application.
WPRiMA Tool: Managing Risks in Web Projects

Risk management is an essential fraction of project management, which plays a significant role in project success. Many failures associated with Web projects are the consequences of poor awareness of the risks involved and lack of process models that can serve as a guideline for the development of Web based applications. To circumvent this problem, contemporary process models have been devised for the development of conventional software. This paper introduces the WPRiMA (Web Project Risk Management Assessment) as the tool, which is used to implement RIAP, the risk identification architecture pattern model, which focuses upon the data from the proprietor’s and vendor’s perspectives. The paper also illustrates how WPRiMA tool works and how it can be used to calculate the risk level for a given Web project, to generate recommendations in order to facilitate risk avoidance in a project, and to improve the prospects of early risk management. Keywords—Architecture pattern model, risk factors, risk identification, Web project, Web project risk management assessment.
Characterization of silk proteins from African wild silkworm cocoons and application of fibroin matrices as biomaterials

ii Dedication. iv Acknowledgements . v List of Figures . x List of Tables. xiii Scientific contributions . xiv CHAPTER 1: Introduction . 1 1.1 General Introduction . 1 1.2 Background . 2 1.3 Motivation of the study . 3 1.4 Objectives. 5 1.5 Thesis Layout . 5 CHAPTER 2: Silk and its properties . 7 2.
Evaluation of Salmonella enterica Serovar Typhimurium TTSS-2 Deficient fur Mutant as Safe Live-Attenuated Vaccine Candidate for Immunocompromised Mice

Salmonella enterica serovar Typhimurium has been extensively exploited as live attenuated vaccines (LAV) which generally confers better protection than killed or subunit vaccines. However, many LAV are limited by their inherent ability to access systemic organs in many of the vaccinated hosts, especially those which are immunocompromised. We evaluated the efficacy of a live-attenuated SPI2-deficient (ΔssaV) S. Typhimurium vaccine candidate (MT13) that additionally devoids the ferric uptake regulator (fur). We used specific pathogen free (SPF) streptomycin-pretreated mouse colitis model that included healthy C57BL/6 and immunocompromised iNos −/−, IL10−/− and CD40L−/− in the background of C57BL/6 mice to assess the efficacy of developed vaccine candidate. In our study, the S. Typhimurium MT13 strain was established as a safe vaccine candidate to be administered in immunocompromised mice as it was found to be systemically attenuated without conferring significant pathological signs and growth defect within the host. In bacterial challenge experiment, the MT13-vaccinated C57BL/6 mice were protected from subsequent wild-type S. Typhimurium infection by inducing proficient mucosal immunity. The MT13 strain elicited efficient O-antigen specific mucosal secretory IgA associated protective response which was comparable with its parental ssaV mutant. Vaccination with MT13 also showed proficient T-cell activation in host mice; which has direct relation with pathogen clearance from host tissues. Collectively, these data implicate the possible application of SPI-2 deficient fur mutant (MT13) as a novel live attenuated vaccine strain with adept immunogenicity and improved safety, even in immunocompromised hosts. Further, this vaccine candidate can be employed to express heterologous antigens targeted against several other diseases, especially related to enterocolitic pathogens.
The Build-Up of Strain Fields in Czochralski-Si Observed in Real Time by High Energy X-Ray Diffraction

The build-up of strain fields caused by the precipitation of oxygen in Czochralski-silicon during annealing up to 1200°C and for process times up to 70 hours has been observed in real time by high energy x-ray diffraction. Five different processes are distinguished in the temperature evolution of the intensity and of the rocking width of the silicon 220-reflection. These features are attributed to different precipitation mechanisms. A fit to part of the data with a diffusion limited precipitation model leads to an activation energy for oxygen diffusion in silicon of 2.2 eV in the temperature range from 700°C to 950°C.
FT-RANSAC: Towards robust multi-modal homography estimation

As the golden standard in robust estimation, the classic RANSAC approach has undergone extensive research that contributed to further enhancements in run-time performance, robustness, and multi-structure support to name a few. Yet, the accelerating growth of multi-modal co-registered datasets requires a new adaptation of the RANSAC algorithm. In this paper, we propose a multi-modal fault-tolerant extension to RANSAC, termed FT-RANSAC, with a model-independent tolerance to degenerate configurations. Besides building on state-of-the-art RANSAC variants, such as PROSAC, our approach introduces a Hough inspired dimensionality reduction and consistency voting processes, to enable robust estimation in the presence of non-homogenous multi-modal correspondence sets. Through experimental evaluation using homography estimation of RGB-D data, we demonstrate that our approach outperforms the classic single-modality RANSAC in robustness and tolerance to degenerate configurations. Finally, the proposed approach lends itself to parallel multi-core implementations, and could be adapted to specialized RANSAC extensions found in the literature.
Updating Accounting Systems : Long-Run Evidence from the Health Care Sector

This paper provides evidence on the determinants of and economic outcomes associated with updates of accounting systems over a 24-year time-span in a large novel sample of U.S. hospitals. We document that a set of previously unidentified determinants drive the updating decision including the way in which hospitals initially adopted their accounting systems, “waves” of updates that are taking place across hospitals, and implementation of price transparency websites at state level that increase hospitals’ demand for high quality costing and budgeting information. Using vendor-pushed updates as an instrumental variable, we document that updating of most types of accounting systems results in immediate and significant reductions in operating expenses. Our findings have implications for settings outside of the health care sector, but they are also important in their own right given the prominence of health care in the economy and the current public policy crisis concerning rising costs of medical care.
The Human Cytomegalovirus Major Immediate-Early Proteins as Antagonists of Intrinsic and Innate Antiviral Host Responses

The major immediate-early (IE) gene of human cytomegalovirus (CMV) is believed to have a decisive role in acute infection and its activity is an important indicator of viral reactivation from latency. Although a variety of gene products are expressed from this region, the 72-kDa IE1 and the 86-kDa IE2 nuclear phosphoproteins are the most abundant and important. Both proteins have long been recognized as promiscuous transcriptional regulators. More recently, a critical role of the IE1 and IE2 proteins in counteracting non-adaptive host cell defense mechanisms has been revealed. In this review we will briefly summarize the available literature on IE1- and IE2-dependent mechanisms contributing to CMV evasion from intrinsic and innate immune responses.
HLA-A*24:02 as a common risk factor for antiepileptic drug–induced cutaneous adverse reactions

Objective: To investigate the involvement of human leukocyte antigen (HLA) loci in aromatic antiepileptic drug–induced cutaneous adverse reactions. Methods: A case-control study was performed to detect HLA loci involved in aromatic antiepileptic drug–induced Stevens-Johnson syndrome in a southern Han Chinese population. Between January 1, 2006, and December 31, 2015, 91 cases of Stevens-Johnson syndrome induced by aromatic antiepileptic drugs and 322 matched drug-tolerant controls were enrolled from 8 centers. Important genotypes were replicated in cases with maculopapular eruption and in the meta-analyses of data from other populations. Sequence-based typing determined the HLA-A, HLA-B, HLA-C, and HLA-DRB1 genotypes. Results: HLA-B*15:02 was confirmed as strongly associated with carbamazepine-induced Stevens-Johnson syndrome (p = 5.63 × 10−15). In addition, HLA-A*24:02 was associated significantly with Stevens-Johnson syndrome induced by the aromatic antiepileptic drugs as a group (p = 1.02 × 10−5) and by individual drugs (carbamazepine p = 0.015, lamotrigine p = 0.005, phenytoin p = 0.027). Logistic regression analysis revealed a multiplicative interaction between HLA-B*15:02 and HLA-A*24:02. Positivity for HLA-A*24:02 and/or HLA-B*15:02 showed a sensitivity of 72.5% and a specificity of 69.0%. The presence of HLA-A*24:02 in cases with maculopapular exanthema was also significantly higher than in controls (p = 0.023). Meta-analysis of data from Japan, Korea, Malaysia, Mexico, Norway, and China revealed a similar association. Conclusions: HLA-A*24:02 is a common genetic risk factor for cutaneous adverse reactions induced by aromatic antiepileptic drugs in the southern Han Chinese and possibly other ethnic populations. Pretreatment screening is recommended for people in southern China.
SOMA: mutual approval for included content in web pages

Unrestricted information flows are a key security weakness of current web design. Cross-site scripting, cross-site request forgery, and other attacks typically require that information be sent or retrieved from arbitrary, often malicious, web servers. In this paper we propose Same Origin Mutual Approval (SOMA), a new policy for controlling information flows that prevents common web vulnerabilities. By requiring site operators to specify approved external domains for sending or receiving information, and by requiring those external domains to also approve interactions, we prevent page content from being retrieved from malicious servers and sensitive information from being communicated to an attacker. SOMA is compatible with current web applications and is incrementally deployable, providing immediate benefits for clients and servers that implement it. SOMA has an overhead of one additional HTTP request per domain accessed and can be implemented with minimal effort by application and web browser developers. To evaluate our proposal, we have developed a Firefox SOMA add-on.
A Systems Approach Reveals Regulatory Circuitry for Arabidopsis Trichome Initiation by the GL3 and GL1 Selectors

Position-dependent cell fate determination and pattern formation are unique aspects of the development of plant structures. The establishment of single-celled leaf hairs (trichomes) from pluripotent epidermal (protodermal) cells in Arabidopsis provides a powerful system to determine the gene regulatory networks involved in cell fate determination. To obtain a holistic view of the regulatory events associated with the differentiation of Arabidopsis epidermal cells into trichomes, we combined expression and genome-wide location analyses (ChIP-chip) on the trichome developmental selectors GLABRA3 (GL3) and GLABRA1 (GL1), encoding basic helix-loop-helix (bHLH) and MYB transcription factors, respectively. Meta-analysis was used to integrate genome-wide expression results contrasting wild type and gl3 or gl1 mutants with changes in gene expression over time using inducible versions of GL3 and GL1. This resulted in the identification of a minimal set of genes associated with the differentiation of epidermal cells into trichomes. ChIP-chip experiments, complemented by the targeted examination of factors known to participate in trichome initiation or patterning, identified about 20 novel GL3/GL1 direct targets. In addition to genes involved in the control of gene expression, such as the transcription factors SCL8 and MYC1, we identified SIM (SIAMESE), encoding a cyclin-dependent kinase inhibitor, and RBR1 (RETINOBLASTOMA RELATED1), corresponding to a negative regulator of the cell cycle transcription factor E2F, as GL3/GL1 immediate targets, directly implicating these trichome regulators in the control of the endocycle. The expression of many of the identified GL3/GL1 direct targets was specific to very early stages of trichome initiation, suggesting that they participate in some of the earliest known processes associated with protodermal cell differentiation. By combining this knowledge with the analysis of genes associated with trichome formation, our results reveal the architecture of the top tiers of the hierarchical structure of the regulatory network involved in epidermal cell differentiation and trichome formation.
MONTE CARLO MODELING OF CATHODOLUMINESCENCE GENERATION USING ELECTRON ENERGY LOSS CURVES

This work demonstrates the validity of approximating cathodoluminescence generation throughout the electron interaction volume by the total electron energy loss profile. The energy loss profiles in multilayer specimens were accurately calculated using the Monte Carlo simulation CASINO. Resolution of cathodoluminescence images can be estimated from the electron beam spot diameter, the electron penetration range, and the minority carrier diffusion length.
A Healthcare Decision-Making Model Using a Classifier-Based Disease Reasoning

This paper proposes a Healthcare Decision-making Model using a Classifier-based Disease Reasoning. The proposed model consists of a Classifier-based Filtering Module (CFM) and a Disease Reasoning Module (DRM). The CFM extracts only the data necessary for a Decision-making by filtering Disease and Therapy data with a Classifier based Feature Elimination (CFE) algorithm. The DRM generates disease reasoning rules with the data extracted from the CFM by using Markov Process and makes a decision with the generated reasoning rules. The experimental result, the precision of CFE algorithm is improved better than that of the SVM by average 4.7%. In addition, the reasoning result generated by the DRM excels the C 4.5 algorithm by 2% in precision.
Trends in Hypertension Control Among the Older Population of Spain From 2000 to 2001 to 2008 to 2010: Role of Frequency and Intensity of Drug Treatment

Background— The use of antihypertensive medication and hypertension control has significantly increased during recent decades in some developed countries, but the impact of improved drug treatment on blood pressure (BP) control in the population is unknown. Methods and Results— Data were taken from 2 surveys representative of the population aged ≥60 years in Spain conducted with the same methodology in 2000 to 2001 and in 2008 to 2010. BP was measured 6×. The first BP reading was discarded, and the average of the remaining 3 to 5 BP readings was taken for analysis. Hypertension prevalence was 68.7% in 2000 to 2001 and 66.0% in 2008 to 2010. Between both time periods there was an improvement in hypertension awareness (63.6%–67.7%), drug treatment among those aware (84.5%–87.5%), and BP control among treated hypertensives (30.3%–42.9%). Overall, BP control among all hypertensives increased from 16.3% to 25.4%. After adjustment for age, sex, education, hypertension duration, smoking, alcohol consumption, body mass index, sedentary behavior, diabetes mellitus, cardiovascular disease, and visits to the physician through logistic regression, ≈7% of the improvement in BP control among all hypertensives was explained by higher hypertension awareness, and 36.2% was explained by a higher treatment rate. Among the treated hypertensives, 22.6% of the progress in BP control was because of the increase in the number of BP medications used in each patient. Conclusions— BP control among the older hypertensive population in Spain has improved from 2000 to 2001 to 2008 to 2010 because of a higher treatment rate and more intense antihypertensive drug treatment.