Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular analysis of the choroideremia gene related clinical findings in two families with choroideremia

Purpose To investigate the choroideremia (CHM) gene in two families with CHM and to characterize the related clinical features. Methods Two families underwent complete ophthalmic examinations and three males were diagnosed with CHM. Genomic DNA was extracted from the leukocytes of peripheral blood collected from the two families and from 100 unrelated control subjects from the same population. Exons 1–15 of CHM were amplified by PCR and directly sequenced. Ophthalmic examinations included best-corrected visual acuity, slit-lamp examination, fundus examination, visual field, optical coherence tomography, electroretinogram, and Pentacam. Results The affected men were hemizygous and had night blindness, chorioretinal atrophy spreading from the posterior pole to the mid-periphery, and bareness of the sclera. A novel c.1488delGinsATAAC mutation was detected in CHM in family 1. Another mutation c.1703 C>G (S558X) within exon 14 of CHM was identified in family 2, which caused the serine 558 codon (TCA) to be changed to a stop codon (TGA). Conclusions This study identified a novel mutation in CHM associated with CHM and its related clinical features. Our findings expand the genotypic spectrum of CHM mutations associated with CHM and confirm the role of Rab escort protein-1 in the pathogenesis of CHM.
Diel rhythms of basal and stress-induced corticosterone in a wild, seasonal vertebrate, Gambel's white-crowned sparrow.

Glucocorticoids have a wide array of actions in vertebrates. Daily fluctuations in basal levels of glucocorticoids are thought to regulate homeostatic mechanisms. In contrast, elevated levels secreted in response to stress stimulate changes in physiology and behavior. These changes are thought to aid an animal in avoiding chronic stress or death. Twenty-four-hour rhythms in basal and stress-induced glucocorticoids have been detected in laboratory mammals, but studies in wild, seasonal vertebrates are rare. Identification of plasticity in hormone secretion in wild vertebrates is critical to understanding the effects of hormones on physiology and behavior, and therefore the success of an animal in its natural environment. In the present study, we characterized diel patterns of basal and stress-induced corticosterone (the avian glucocorticoid) under two photoperiods in Gambel's white-crowned sparrow (Zonotrichia leucophrys gambelii). In contrast to previous findings in the white-crowned sparrow, we demonstrated a robust rhythm in basal corticosterone secretion, in which corticosterone reaches peak levels at the end of the inactive period, and has returned to trough levels just after the active period has begun. We also demonstrated a diel rhythm in secretion of corticosterone in response to a stressor, showing the greatest response at the beginning of the active period. Patterns of CORT secretion were similar under both photoperiods. These patterns show interesting similarities and differences to classical mammalian rhythms.
Analysis, simulation and modeling of mobile Rayleigh fading channel using LabVIEW

The term fading, in the context of mobile communications, refers to the interference caused by the reception of numerous scattered copies of a given signal at an antenna. Fading can produce significant random variations of signal power — in the scale of 10s of dBs over fractions of a wavelength- and hence, can be extremely destructive to the signal. Therefore, in order to achieve reliable mobile communications, provisions must be considered to counter the effects of fading. Indeed, a first step towards this end is to understand these effects through producing models of and simulating this phenomenon. An approximation method is applied to simulate a mobile radio fading channel using Matlab and LabVIEW environment, based on a somewhat simplified mathematical model. Clearly the simplified model might not present a very realistic view of the highly complex and random nature of fading; nevertheless, this simulation serves as an extremely useful research tool for comparing and measuring the effectiveness of different communication techniques.
Novel delta zero crossing regression features for gait pattern classification

Many recent research works on gait pattern classification indicates that static features are used. This paper describes of extracting novel dynamic features as complimentary features for the gait pattern classification. The dynamic features are obtained by using regression on the delta zero crossing counts (ΔZCC) of the acceleration signal. The classification results using the filterbank features with the novel dynamic features showed an overall accuracy of 97% was achieved. This is an improvement of 3% from using the filterbank features alone.
Influence of Chemically Treated Palygorskite Over the Rheological Behavior of Polypropylene Nanocomposites Influencia de paligorskita químicamente tratada sobre el comportamiento reológico de nanomateriales compuestos de polipropileno

Melt compounding was used to prepare thermoplastic composites reinforced with palygorskite; the chemical modification of the palygorskite surface and the control of extrusion parameters were used to promote good dispersion and a good interface with the matrix, affecting the rheological properties of the mixture, since the melt viscoelastic behavior is sensitive to changes in the molecular structures at nanoscale and mesoscale. The palygorskite nanoclay (diameter 30 nm) was extracted from a site in the southeast of the state of Yucatan, Mexico; the palygorskite was subjected to purification and then superficially modified with 3-aminopropyltrimetoxysilane. These processes generated three types of specimens: unpurified, purified and purified-silanized palygorskite; which were subsequently incorporated (0.5 w%) to a polypropylene matrix by twin extrusion. Frequency sweeps were used to evaluate the interaction between the matrix and the nano-reinforcement. The master curves of storage modulus (G’), loss modulus (G”) and complex viscosity (η*) vs angular frequency (ω x ) show a change of the interfacial interaction polypropylene/palygorskite when the palygorskite was chemically modified.
Additively Weighted Voronoi Diagram on the Oriented Projective Plane

We consider Voronoi diagrams deened on the oriented projective plane T 2. In this geometry, the closest and furthest site diagrams are antipodal. We give a simple on-line incremental algorithm for constructing the additively weighted diagram. This diagram, which may be disconnected in Euclidean plane, is always connected in T 2 and has exactly 3n 6 edges and 2n 4 vertices, where n is the number of sites.
Hierarchical parallelization of the multilevel fast multipole algorithm (MLFMA)

Due to its O(N log N) complexity, the multilevel fast multipole algorithm (MLFMA) is one of the most prized algorithms of computational electromagnetics and certain other disciplines. Various implementations of this algorithm have been used for rigorous solutions of large-scale scattering, radiation, and miscellaneous other electromagnetics problems involving 3-D objects with arbitrary geometries. Parallelization of MLFMA is crucial for solving real-life problems discretized with hundreds of millions of unknowns. This paper presents the hierarchical partitioning strategy, which provides a very efficient parallelization of MLFMA on distributed-memory architectures. We discuss the advantages of the hierarchical strategy over previous approaches and demonstrate the improved efficiency on scattering problems discretized with millions of unknowns.
The MIR Perspective on the Evolution of Dynamics in Mainstream Music

Understanding the evolution of mainstream music is of high interest for the music production industry. In this context, we argue that a MIR perspective may be used to highlight, in particular, relations between dynamics and various properties of mainstream music. We illustrate this claim with two results obtained from a diachronic analysis performed on 7200 tracks released between 1967 and 2014. This analysis suggests that 1) the so-called “loudness war” has peaked in 2007, and 2) its influence has been important enough to override the impact of genre on dynamics. In other words, dynamics in mainstream music are primarily related to a track’s year of release, rather than to its genre.
Area-constrained coverage optimization by robotic sensor networks

This paper studies robotic sensor networks performing coverage optimization tasks with area constraints. The network coverage of the environment is a function of the robot locations and the partition of the space. The area of the region assigned to each robot is constrained to be a pre-specified amount. We characterize the optimal configurations as center generalized Voronoi configurations. The generalized Voronoi partition depends on a set of weights, one per robot, assigned to the network. We design a Jacobi iterative algorithm to find the weight assignment whose corresponding generalized Voronoi partition satisfies the area constraints. This algorithm is distributed over the generalized Delaunay graph. We also design the ¿move-to-center-and-compute-weight¿ coordination algorithm that steers the robotic network towards the set of center generalized Voronoi configurations while monotonically optimizing coverage. Various simulations illustrate our results.
Thermal imaging based condition based monitoring on Android platform

The use of thermal images for condition based monitoring is becoming very popular in industries. This paper presents a simple approach for condition based monitoring of machines using thermal Images on Android Platform. This approach is non-contact, fast and precise for CBM of rotating and non-rotating machines. The proposed approach has been successfully implemented on Android smartphone for CBM of prototype machine. The application uses standard OpenCV library functions to implement processing logic. For this the temperature profile of overall machine from different views was captured and analyzed using thermal images. Regression model was developed to find relation between local temperature and pixel intensity which helped in recognizing the condition of prototype machine.
ABCB1 haplotype and OPRM1 118A > G genotype interaction in methadone maintenance treatment pharmacogenetics

Background: Genetic variability in ABCB1, encoding the P-glycoprotein efflux transporter, has been linked to altered methadone maintenance treatment dose requirements. However, subsequent studies have indicated that additional environmental or genetic factors may confound ABCB1 pharmacogenetics in different methadone maintenance treatment settings. There is evidence that genetic variability in OPRM1, encoding the mu opioid receptor, and ABCB1 may interact to affect morphine response in opposite ways. This study aimed to examine whether a similar gene-gene interaction occurs for methadone in methadone maintenance treatment. Methods: Opioid-dependent subjects (n = 119) maintained on methadone (15–300 mg/day) were genotyped for five single nucleotide polymorphisms of ABCB1 (61A > G; 1199G > A; 1236C > T; 2677G > T; 3435C > T), as well as for the OPRM1 118A > G single nucleotide polymorphism. Subjects’ methadone doses and trough plasma (R)-methadone concentrations (Ctrough) were compared between ABCB1 haplotypes (with and without controlling for OPRM1 genotype), and between OPRM1 genotypes (with and without controlling for ABCB1 haplotype). Results: Among wild-type OPRM1 subjects, an ABCB1 variant haplotype group (subjects with a wild-type and 61A:1199G:1236C:2677T:3435T haplotype combination, or homozygous for the 61A:1199G:1236C:2677T:3435T haplotype) had significantly lower doses (median ± standard deviation 35 ± 5 versus 180 ± 65 mg/day, P < 0.01) and Ctrough (78 ± 22 versus 177 ± 97 ng/mL, P < 0.05) than ABCB1 wild-type subjects. Among subjects with the most common ABCB1 haplotype combination (wild-type with 61A:1199G:1236T:2677T:3435T), the OPRM1 118 A/G genotype was associated with a significantly higher Ctrough than 118 A/A (250 ± 126 versus 108 ± 36 ng/mL, P = 0.016). No ABCB1 haplotype group or OPRM1 genotype was associated with dose or Ctrough without taking into account confounding genetic variability at the other locus. Therefore, two interacting pharmacogenetic determinants of methadone maintenance treatment response were identified, ie, ABCB1, where variants are associated with lower methadone requirements, and OPRM1, where the variant is associated with higher methadone requirements. Conclusion: These opposing pharmacogenetic effects therefore need to be considered in combination when assessing methadone maintenance treatment pharmacogenetics.
Numerical Service Life Model of Chloride Induced Corrosion in Recycled Aggregate Concrete and Design Optimization of Sustainable and Durable Concrete Mixtures

Concrete mixture design is a multi-objective optimization problem that often involves the weighing of trade-offs between fresh-state properties, such as workability, flowability, and set time with hardened-state properties, such as strength, freeze thaw durability, and chloride durability. Substantial time and effort goes into designing, testing, and perfecting single mixture designs for optimal performance in some, but not all, of these properties. Additionally, considerations for mixture cost and environmental impacts, such as embodied energy, and embodied carbon are often included only as a secondary objective. The complex relationships between concrete mixture proportions and resulting constituent properties are investigated herein through two studies that explore mixture design tradeoffs. The first study presents the development, validation, and implementation of a 1D numerical service-life prediction model for reinforced recycled aggregate concrete exposed to internal and external sources of chlorides. The model accounts for the inclusion of supplementary cementitious materials (SCMs), namely (a) fly ash, (b) slag, (c) silica fume, and (d) metakaolin, and recycled aggregates (i) with and (ii) without initial chloride contamination from previous in-service exposure. The model is used to predict time to corrosion-induced cracking for reinforced recycled aggregate concrete in five case-study applications, namely structures in a marine splash zone (Zone I), a marine spray zone (Zone II), within 800 km of coastline (Zone III), within 1.5 km of coastline (Zone IV), and parking structures at locations greater than 1.5 km from the coastline (Zone V) in Los Angeles, California and Anchorage, Alaska. The effects of recycled aggregate size, replacement ratio, degree of aggregate pre-contamination with chloride from previous in-service exposure, water-to-cement ( w/c ) ratio, and SCMs on time-to-cracking of reinforced recycled aggregate concrete are elucidated herein. The potential for SCMs to improve the service life of recycled aggregate concrete is investigated by estimating theoretical additions required to meet a target service life of 50 years. Results indicate that, in addition to geographic location, temperature, and severity of chloride exposure, w/c ratio and aggregate replacement ratio exhibit the greatest impact on time to chloride-induced cracking in reinforced recycled aggregate concrete. Furthermore, initial aggregate chloride contamination and aggregate size impart minimal effects on expected service life. Finally, the results illustrate that the use of either fly ash or slag is most viable in achieving a 50-year service life for recycled aggregate concretes in chloride-laden environments. Broadening the work of the first study, the second study presents the development and implementation of a multi-objective concrete mixture design tool to evaluate tradeoffs of different mixture proportions on the physical, mechanical, and environmental performance of concrete. The model…
Partially Synchronized DEC-MDPs in Dynamic Mechanism Design

In this paper, we combine for the first time the methods of dynamic mechanism design with techniques from decentralized decision making under uncertainty. Consider a multi-agent system with self-interested agents acting in an uncertain environment, each with private actions, states and rewards. There is also a social planner with its own actions, rewards, and states, acting as a coordinator and able to influence the agents via actions (e.g., resource allocations). Agents can only communicate with the center, but may become inaccessible, e.g., when their communication device fails. When accessible to the center, agents can report their local state (and models) and receive recommendations from the center about local policies to follow for the present period and also, should they become inaccessible, until becoming accessible again. Without self-interest, this poses a new problem class which we call partially-synchronized DEC-MDPs, and for which we establish some positive complexity results under reasonable assumptions. Allowing for self-interested agents, we are able to bridge to methods of dynamic mechanism design, aligning incentives so that agents truthfully report local state when accessible and choose to follow the prescribed "emergency policies" of the center.
Hierarchical Sliding Mode Control to Swing up a Pendubot

To swing up a Pendubot, a pendulum robot, this paper presents a hierarchical sliding mode controller with limited control torque. The structure characteristic of the Pendubot system is that it can be treated as two subsystems. Thus, the hierarchical structure of the sliding mode surfaces is designed as follows. The sliding mode surfaces of the two subsystems are defined at first. The sliding mode surface of one subsystem is selected as the first layer sliding mode surface. The second layer sliding mode surface is constructed by the first layer sliding mode surface and the sliding mode surface of the other subsystem. The hierarchical sliding mode control law is deduced in terms of Lyapunov stability theorem. Asymptotic stability of the entire sliding mode surfaces is proven theoretically and control parameter boundaries of the two subsystems are also given theoretically. Finally, simulation results show the validity of this control method and its robustness for external disturbances.
Intravascular Lead Extraction Using Locking Stylets and Sheaths

BYRD, C.L. , ET AL.: Intravascular Lead Extraction Using Locking Stylets and Sheaths. Chronic lead extraction using intravascular countertraction techniques was studied in patients with over 65 different lead models including passive and active fixation devices. Indications for removal of 115 leads implanted 5 days to 264 months (mean 58 months) in 62 patients (mean 65 years) included septicemia, subcutaneous tissue infection, preerosion, free‐floating lead, lead trapped in valve, too many leads, pain, and vein thrombosis. The superior vena cava (SVC) approach was attempted in 101 leads and was successful in 82 attempts (71% of total leads). The inferior vena cava (IVC) approach via the femoral vein was required to extract 14 (12%) leads inaccessible to the SVC approach and the 19 leads that failed the SVC approach (29% of total leads). The SVC procedure includes a sized stylet locked at the tip and telescoping sheaths advanced over the lead to the heart. An IVC procedure includes placement of a 16 F sheath workstation via a femoral vein into the right atrium. A deflection catheter and Dotter snare in an 11 F sheath were advanced through the workstation into the right atrium. The lead was maneuvered into position, snared, and pulled into the workstation. For both the SVC and IVC approaches, the leads were removed by applying traction on the lead and countertraction with the sheaths. In experienced hands, these techniques have proven safe and effective for removing chronic transvenous leads.
Algorithms for restriction map comparisons

An algorithm is presented which compares two restriction maps, yielding a measure of distance between the maps and relating the maps by an alignment. This new algorithm finds the minimum weighted sum of genetic events required to convert one map into the other, where the genetic events are the appearance/disappearance of restriction sites and changes in the number of bases between restriction sites. The algorithm is illustrated by comparison of the beta-delta region of the globin gene cluster of four primate species. The results are in excellent agreement with known evolutionary relationships.
Adaptive Space-Time Finite Element Methods for Parabolic Optimization Problems

In this paper we derive a posteriori error estimates for space-time finite element discretizations of parabolic optimization problems. The provided error estimates assess the discretization error with respect to a given quantity of interest and separate the influences of different parts of the discretization (time, space, and control discretization). This allows us to set up an efficient adaptive algorithm which successively improves the accuracy of the computed solution by construction of locally refined meshes for time and space discretizations.
Estimating Translational Selection in Eukaryotic Genomes

Natural selection on codon usage is a pervasive force that acts on a large variety of prokaryotic and eukaryotic genomes. Despite this, obtaining reliable estimates of selection on codon usage has proved complicated, perhaps due to the fact that the selection coefficients involved are very small. In this work, a population genetics model is used to measure the strength of selected codon usage bias, S, in 10 eukaryotic genomes. It is shown that the strength of selection is closely linked to expression and that reliable estimates of selection coefficients can only be obtained for genes with very similar expression levels. We compare the strength of selected codon usage for orthologous genes across all 10 genomes classified according to expression categories. Fungi genomes present the largest S values (2.24–2.56), whereas multicellular invertebrate and plant genomes present more moderate values (0.61–1.91). The large mammalian genomes (human and mouse) show low S values (0.22–0.51) for the most highly expressed genes. This might not be evidence for selection in these organisms as the technique used here to estimate S does not properly account for nucleotide composition heterogeneity along such genomes. The relationship between estimated S values and empirical estimates of population size is presented here for the first time. It is shown, as theoretically expected, that population size has an important role in the operativity of translational selection.
Predictability of Genetic Interactions from Functional Gene Modules

Characterizing genetic interactions is crucial to understanding cellular and organismal response to gene-level perturbations. Such knowledge can inform the selection of candidate disease therapy targets, yet experimentally determining whether genes interact is technically nontrivial and time-consuming. High-fidelity prediction of different classes of genetic interactions in multiple organisms would substantially alleviate this experimental burden. Under the hypothesis that functionally related genes tend to share common genetic interaction partners, we evaluate a computational approach to predict genetic interactions in Homo sapiens, Drosophila melanogaster, and Saccharomyces cerevisiae. By leveraging knowledge of functional relationships between genes, we cross-validate predictions on known genetic interactions and observe high predictive power of multiple classes of genetic interactions in all three organisms. Additionally, our method suggests high-confidence candidate interaction pairs that can be directly experimentally tested. A web application is provided for users to query genes for predicted novel genetic interaction partners. Finally, by subsampling the known yeast genetic interaction network, we found that novel genetic interactions are predictable even when knowledge of currently known interactions is minimal.