Miracle-dz/UniFAR-FTUs huggingface dataset:
The structure of developing muscle insertions in insects

The relationship between muscles and the components of the integument in muscle insertions have been studied with the electron microscope in two insects, Calpodes ethlius (Hesperiidae, Lepidoptera) and Rhodnius prolixus (Reduviidae, Hemiptera). The area of contact between the muscles and the epidermis is increased by interdigitating processes whose membranes are joined by intermediate junctions. The junctions occur at the level of a Z line so that actin filaments attach directly to them. Within the epidermis, microtubules extend from the junctions of the myoepidermal connection to the cuticle, where they attach to hemidesmosomes which line deep indentations of the membrane. The microtubules probably enable the tendinous epidermal cells to withstand the tensions exerted upon them by the muscles. The epidermis is anchored to the cuticle by tonofibrillae, homogeneous rods secreted in the deep indentations of the plasma membrane. Since the tonofibrillae of successive instars are continous, they penetrate and attach to the cuticulin, the outermost layer of the epicuticle.
Chlamydophila felis CF0218 Is a Novel TMH Family Protein with Potential as a Diagnostic Antigen for Diagnosis of C. felis Infection

ABSTRACT Chlamydophila felis is a causative agent of acute and chronic conjunctivitis and pneumonia in cats (feline chlamydiosis). Also, C. felis is a suspected zoonotic agent of such diseases as non-Chlamydia trachomatis conjunctivitis in humans, although this is controversial. At present, there is no serodiagnostic system that specifically detects C. felis infection conveniently. Current systems use antigens such as lipopolysaccharide that cross-react with all chlamydia species. In addition, it is difficult to distinguish between cats that are vaccinated with the commercial vaccine against C. felis and cats that are infected with C. felis. Here, we describe a new candidate diagnostic antigen for diagnosis of C. felis infection, CF0218, that was obtained by screening a genomic expression library of C. felis Fe/C-56 with C. felis-immunized serum. CF0218 was a putative transmembrane head (TMH) family protein with bilobed hydrophobic motifs at its N terminus, and orthologues of CF0218 were not found in the Chlamydophila pneumoniae or Chlamydia trachomatis genomes. The recombinant CF0218 was not recognized by antiserum against C. trachomatis, suggesting that CF0218 is C. felis specific. CF0218 transcription during the course of C. felis infection was confirmed by reverse transcription-PCR. By indirect immunofluorescence analysis, CF0218 was colocalized with the C. felis-formed inclusion bodies in the infected cells. The antibody response against CF0218 was elevated following C. felis infection but not by vaccination in experimentally vaccinated and infected cats. These results suggest that CF0218, a novel TMH family protein of C. felis, possesses potential as a C. felis infection-specific diagnostic antigen.
Virtual Electrode Effects in Transvenous Defibrillation‐Modulation by Structure and Interface: Evidence from Bidomain Simulations and Optical Mapping

Virtual Electrodes, Bidomain Model, and Defibrillation. Introduction: Our goal in this combined modeling and experimental study was to gain insight into the transmembrane potential changes in defibrillation conditions, namely, when shocks are delivered by an implantable cardioverter defibrillator (ICD). Two hypotheses concerning the presence and characteristics of virtual electrode effects (VEE) during an ICD shock were tested numerically and experimentally: (H1) anisotropy‐dependent VEE are induced over a considerable portion of the “bulk” myocardium; and (H2) surface (epicardial and endocardial) VEE are generated under special tissue bath conditions and are not fully anisotropy determined.
Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013

We present the design, preparation, results and analysis of the Cancer Genetics (CG) event extraction task, a main task of the BioNLP Shared Task (ST) 2013. The CG task is an information extraction task targeting the recognition of events in text, represented as structured n-ary associations of given physical entities. In addition to addressing the cancer domain, the CG task is differentiated from previous event extraction tasks in the BioNLP ST series in addressing a wide range of pathological processes and multiple levels of biological organization, ranging from the molecular through the cellular and organ levels up to whole organisms. Final test set submissions were accepted from six teams. The highest-performing system achieved an Fscore of 55.4%. This level of performance is broadly comparable with the state of the art for established molecular-level extraction tasks, demonstrating that event extraction resources and methods generalize well to higher levels of biological organization and are applicable to the analysis of scientific texts on cancer. The CG task continues as an open challenge to all interested parties, with tools and resources available from http://2013. bionlp-st.org/.
The Arts in Psychotherapy rts therapies and Schema Focused therapy : A pilot study lsa

Arts therapies and Schema Focused therapy (SFT), use experiential techniques to help patients access and reprocess emotions. We conducted a randomized controlled pilot study to determine the effectiveness of these therapies at evoking emotional states (“schema modes”) in forensic patients, a group that is considered difficult to reach emotionally. Ten male forensic patients with Cluster B personality disorders who were enrolled in a randomized clinical trial of SFT versus usual forensic treatment (“treatment as usual,” TAU) participated in the study. We investigated the effect of Arts therapies versus verbal psychotherapy, and SFT versus TAU on modes. As hypothesized, patients showed significantly more healthier emotional states in their Arts therapy sessions than in their verbal psychotherapy sessions SFT evoked more childmodes than TAU, at a trend level of significance. Patients in the SFT and TAU conditions showed no differences in schema modes early in therapy, and were equivalent on all baseline characteristics. These findings, though requiring replication in a larger sample, suggest that Arts therapies and SFT have potential for evoking emotional states in difficult to reach patients.
The OECD Program to Validate the Rat Hershberger Bioassay to Screen Compounds for in Vivo Androgen and Antiandrogen Responses: Phase 2 Dose–Response Studies

Objective The Organisation for Economic Co-operation and Development (OECD) has completed phase 2 of an international program to validate the rodent Hershberger bioassay. Design The Hershberger bioassay is designed to identify suspected androgens and antiandrogens based on changes in the weights of five androgen-responsive tissues (ventral prostate, paired seminal vesicles and coagulating glands, the levator ani and bulbocavernosus muscles, the glans penis, and paired Cowper’s or bulbourethral glands). Protocol sensitivity and reproducibility were tested using two androgen agonists (17α-methyl testosterone and 17β-trenbolone), four antagonists [procymi-done, vinclozolin, linuron, and 1,1-dichoro-2,2-bis-(p-chlorophenyl)ethylene (p,p’-DDE)], and a 5α-reductase inhibitor (finasteride). Sixteen laboratories from seven countries participated in phase 2. Results In 40 of 41 studies, the laboratories successfully detected substance-related weight changes in one or more tissues. The one exception was with the weakest antiandrogen, linuron, in a laboratory with reduced sensitivity because of high coefficients of variation in all tissue weights. The protocols performed well under different experimental conditions (e.g., strain, diet, housing protocol, bedding, vehicle). There was good agreement and reproducibility among laboratories with regard to the lowest dose inducing significant effects on tissue weights. Conclusions The results show that the OECD Hershberger bioassay protocol is reproducible and transferable across laboratories with androgen agonists, weak androgen antagonists, and a 5α-reductase inhibitor. The next validation phase will employ coded test substances, including positive substances and negative substances having no androgenic or antiandrogenic activity.
Experiences in teaching an advanced computer graphics course

Designed for the experienced computer user, this course provides the opportunity to experiment with a trio of graphics applications to create high quality photo-realistic and 3D artwork. Utilizing the bestselling software Photoshop, Bryce & Poser (demo versions of each included on the course DVD-ROM) soon you will be creating your own professional-quality graphic presentations. After completing this engaging course you will have the knowledge and experience to pass along to your students in a variety of classroom settings including art, journalism, computer applications and vocational education. Hands-on projects maximize the learning experience while focusing on creating useful and meaningful teaching materials. Outcomes are aligned to International Society for Technology in Education (ISTE) standards (NETS-T). At the end of the course participants are asked to correlate assignments to these standards.
AUTOMATIC 3D BUILDING RECONSTRUCTION USING PLANE-ROOF STRUCTURES

This paper introduces a new method for automatic 3D building reconstruction using plane-roof structures. A boundary representation (b-rep) of a coarse building hypothesis is constructed in a bottom-up approach from simple geometric primitives in image domain to more complex geometric primitives (roof structure) in object domain. Subsequently, a hypothesis model verification is performed in a top-down approach by back projecting the constructed model to the corresponding aerial images. A number of issues in an autonomous image analysis system are covered. The various processes and components essential to the proposed method are reported and the experimental results are also presented.
On cloaking for elasticity and physical equations with a transformation invariant form

In this paper, we investigate how the form of the conventional elastodynamic equations changes under curvilinear transformations. The equations get mapped to a more general form in which the density is anisotropic and additional terms appear which couple the stress not only with the strain but also with the velocity, and the momentum gets coupled not only with the velocity but also with the strain. These are a special case of equations which describe the elastodynamic response of composite materials, and which it has been argued should apply to any material which has microstructure below the scale of continuum modelling. If composites could be designed with the required moduli then it could be possible to design elastic cloaking devices where an object is cloaked from elastic waves of a given frequency. To an outside observer it would appear as though the waves were propagating in a homogeneous medium, with the object and surrounding cloaking shell invisible. Other new elastodynamic equations also retain their form under curvilinear transformations. The question is raised as to whether all equations of microstructured continua have a form which is invariant under curvilinear space or space-time coordinate transformations. We show that the non-local bianisotropic electrodynamic equations have this invariance under space-time transformations and that the standard non-local, time-harmonic, electromagnetic equations are invariant under space transformations.
Assignment 1 of the bovine C 10 orf 2 gene to bovine 26 q 13 → q 21 by fluorescence in situ hybridization and confirmation by radiation hybrid mapping

Mutations in coding regions of the C10orf2 (chromosome 10 open reading frame 2) gene encoding the mitochondrial protein twinkle were shown to co-segregate in man with autosomal dominant progressive external ophthalmoplegia (adPEO) in several pedigrees of various ethnic origin (Spelbrink et al., 2001). A specific feature of the disease is accumulation of multiple deletions of mtDNA in tissues, mostly in the brain, muscle and heart, which results in a lack of the respiratory chain proteins thus leading to defective energy production and muscle weakness, most severely in the ocular muscles (Soumalainen et al., 1995). The human C10orf2 gene is located on HSA10q24.31 (http://www.ensembl.org). The objective of this study was to map the C10orf2 gene by fluorescence in situ hybridization and radiation hybrid mapping in cattle. C10orf2 appears as an appropriate candidate gene for bilateral convergent strabismus with exophthalmus (BCSE) in cattle, because the phenotype of BCSE in cattle shows striking similarities to the heterogeneous dominant and recessive forms of PEO in man (Distl, 1993). BCSE is similarly to adPEO characterized by a progressive symmetrical insufficient function of the eye muscles recti laterals and retractores. Furthermore, in German Brown cattle a monogenic, autosomal dominant inheritance proved to be most probable using complex segregation analysis (Distl, 1993). Due to the wide dissemination of BCSE in many cattle breeds, the late onset in life not earlier than by an age of 1–2 years, and a high incidence of 0.9% of this inherited anomaly in German Brown cattle, the development of an effective genetic program based on molecular genetic tests is strongly warranted.
Comparison of viral load and duration of virus shedding in symptomatic and asymptomatic neonatal rotavirus infections

A single rotavirus strain causing asymptomatic infections as well as severe gastrointestinal disease has been described in the neonatal nurseries of the Christian Medical College, Vellore. In this study, quantitative real‐time RT‐PCR was used to determine the association of viral load with the presence of gastrointestinal symptoms in neonates. Viral load was estimated in terms of the crossing point [C(t) value] at which the amplicon could be detected in the real‐time PCR assay. The study was carried out on 103 neonates, including 33 asymptomatic neonates and 70 neonates with different gastrointestinal symptoms. The duration of virus shedding was also compared between five symptomatic and four asymptomatic neonates using real‐time RT‐PCR. There was no significant difference in viral load between symptomatic and asymptomatic neonates (P = 0.087). Among neonates with different gastrointestinal symptoms, those presenting with feed intolerance and abdominal distension had a significantly higher viral load than those with other gastrointestinal symptoms (P = 0.02). For the study on virus shedding, nine neonates were followed up for a median duration of 53 days, with a median of 31 samples tested per child. Extended shedding of low copies of rotavirus was found, with no significant differences in pattern of shedding between symptomatic and asymptomatic neonates. The lack of correlation between viral load and gastrointestinal disease demonstrates yet another difference between neonatal rotavirus infection and infection in older children where higher viral load correlates with severe disease. J. Med. Virol. 82:1803–1807, 2010. © 2010 Wiley‐Liss, Inc.
Energy-Efficient Static Priority and Speed Assignment for Real-Time Tasks with Non-deterministic Release Times

Dynamic Voltage Scaling (DVS) has been widely used for decreasing the dynamic power dissipation of processors. For real-time systems, DVS techniques have been developed that permit to meet the timing constraints of multiple real-time tasks and at the same time reduce the overall dynamic energy consumption. Known methods for static priority DVS scheduling are, however, either restricted to simple periodic/sporadic task release patterns or presume full a priori knowledge of task release times. Moreover, none of the present approaches considers the optimization of task priorities for reducing the energy consumption. In this paper we explore how to determine the static priorities and individual execution speeds (supply voltages) of multiple tasks with non-deterministic release times bounded by arrival curves such that the energy consumption is reduced and the real-time constraints are met. The result are different heuristics for the design of DVS-based real-time systems with static priorities. We show that the proposed methodology leads to energy-efficient system designs and demonstrate the applicability of the approach by means of experiments.
Performance analysis for two-tier cellular systems based on probabilistic distance models

Tiered networks have been introduced to mitigate the issues related to poor cellular coverage in dead zones and indoor environments. However, the large-scale deployment of multiple tiers can result in severe intra-tier and inter-tier interference that can considerably degrade the performance of users in all tiers. Thus, the network interference analysis has been an important topic in tiered networks. In this paper, we focus on the uplink resource reusing scenario in a two-tier cellular network consisting of a macro cell and multiple femto cells. Without imposing any limitations on the shape of the macro/femto cells (as long as they are approximated by polygons), for the first time in the literature, we obtain the distance distributions associated with tiered structures. Utilizing these distance distributions and the path-loss model in an interference-limited environment, we obtain the distributions of the received signal and interference for both tiers. Further, we give details on how our approach applies to the downlink resource reusing scenario as well as a network with multiple macro cells. Our performance study provides insights into the Signal-to-Interference Ratio and outage probability for macro/femto-cell base stations.
Gas Flow Method for Detecting Local Preform Defects by Inverse Estimation of Space-Varying Permeability

A method using gas flow is proposed for testing the quality of fibrous preforms in the resin transfer molding process. The method is based on the idea that preform defects cause variation in permeability and deviation from Darcy's law. This paper presents a gradient-based inverse method that estimate space-varying permeability by examining the consistency between computed and measured pressures at various locations in the mold during steady-state gas flow through the enclosed preform. Such consistency is achieved by the conjugate gradient method. The computed pressures are obtained by the control volume finite element method (CVFEM). The proposed method was demonstrated by using a specially designed mold with multiple ports for gas injection and pressure measurement, and testing for various cases with and without defects.
Comparison of mean-field theories for vortices in trapped Bose-Einstein condensates

We compute structures of vortex configurations in a harmonically trapped Bose-Einstein condensed atom gas within three different gapless self-consistent mean-field theories. Outside the vortex core region, the density profiles for the condensate and the thermal gas derived from the Hartree-Fock-Bogoliubov-Popov theory are found to differ by only a few per cent from those derived from two of its recently proposed gapless extensions. In the core region, however, the differences between the density profiles are substantial. The structural differences are reflected in the energies of the quasiparticle states localized near the vortex core. In particular, the predictions for the energy of the lowest quasiparticle excitation derived from the theoretical models investigated differ considerably.
Crystallization of polymers studied by temperature-modulated techniques (TMDSC, TMDMA)

Abstract Quasi-isothermal temperature-modulated differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA) measurements (TMDSC and TMDMA, respectively) permit determination of heat capacity and shear modulus as a function of time during crystallization. Nonreversible and reversible phenomena in the crystallization region of polymers can be observed. The combination of TMDSC and TMDMA yields new information about local processes at the surface of polymer crystals, like reversible melting. Reversible melting can be observed in the complex heat capacity and in the amplitude of sheer modulus in response to temperature perturbation. The fraction of material involved in reversible melting, which is established during primary crystallization, remains constant during secondary crystallization for polycaprolactone (PCL) and polyether ether ketone (PEEK). This shows that, also after long crystallization times, the surfaces of the individual crystallites are in equilibrium with the surrounding mel.
Computational environment for the fast calculation of ECT probe signal by field decomposition

Eddy current testing (ECT) probe signal due to cracks can be predicted by separating the calculation steps to the evaluation of the incident field and the reaction of the crack. Finite element (FEM) and boundary integral (BIM) methods can be, for example, advantageously applied for the calculation of the incident and reaction fields, respectively. The computational environment presented in this paper allows the blending of the different calculation methods for the purpose of ECT probe signal calculation. As a result, a fast and versatile tool is obtained to calculate the signal of complicated ECT probes due to cracks. The developed approach is validated through comparisons with experimental data
Why Does Data Prefetching Not Work for Modern Workloads?

Emerging cloud workloads in today’s modern data centers have large memory footprints that make the processor’s caches to be ineffective. Since L1 data cache is in the critical path, high data cache miss rates degrade the performance. To fix the issue in traditional workloads, data prefetchers predict the needed data to hide the memory latency and ultimately improve performance. In this paper, we focus on the L1 data cache to answer the question on why state-of-the-art prefetching methods are inefficient for modern workloads in terms of performance and energy consumption? This is because L1 cache is the most important player affecting the processor performance. Results show that, on the one hand, these workloads suffer from low temporal locality and address repetition, and their consecutive accesses exhibit better spatial locality compared with the traditional workloads. On the other hand, miss patterns are spatially irregular and there is little opportunity to eliminate repetitive miss patterns. Because of these reasons, prefetching methods have poor performance and, with respect to more accesses to the lower memory levels, it is not energy efficient to use prefetchers for modern workloads.
A one-pass sequential Monte Carlo method for Bayesian analysis of massive datasets

For Bayesian analysis of massive data, Markov chain Monte Carlo (MCMC) techniques often prove infeasible due to computational resource con- straints. Standard MCMC methods generally require a complete scan of the dataset for each iteration. Ridgeway and Madigan (2002) and Chopin (2002b) recently presented importance sampling algorithms that combined simulations from a posterior distribution conditioned on a small portion of the dataset with a reweighting of those simulations to condition on the remainder of the dataset. While these algorithms drastically reduce the number of data accesses as compared to traditional MCMC, they still require substantially more than a single pass over the dataset. In this paper, we present \1PFS," an ecien t, one-pass algorithm. The algorithm employs a simple modication of the Ridgeway and Madigan (2002) particle ltering algorithm that replaces the MCMC based \rejuvenation" step with a more ecien t \shrinkage" kernel smoothing based step. To show proof- of-concept and to enable a direct comparison, we demonstrate 1PFS on the same examples presented in Ridgeway and Madigan (2002), namely a mixture model for Markov chains and Bayesian logistic regression. Our results indicate the proposed scheme delivers accurate parameter estimates while employing only a single pass through the data.