Miracle-dz/UniFAR-FTUs huggingface dataset:
Bifurcation Analysis of Cardiac Alternans Using δ-Decidability

We present a bifurcation analysis of electrical alternans in the two-current Mitchell-Schaeffer (MS) cardiac-cell model using the theory of δ-decidability over the reals. Electrical alternans is a phenomenon characterized by a variation in the successive Action Potential Durations (APDs) generated by a single cardiac cell or tissue. Alternans are known to initiate re-entrant waves and are an important physiological indicator of an impending life-threatening arrhythmia such as ventricular fibrillation. The bifurcation analysis we perform determines, for each control parameter τ of the MS model, the bifurcation point in the range of τ such that a small perturbation to this value results in a transition from alternans to non-alternans behavior. To the best of our knowledge, our analysis represents the first formal verification of non-trivial dynamics in a numerical cardiac-cell model. Our approach to this problem rests on encoding alternans-like behavior in the MS model as a 11-mode, multinomial hybrid automaton (HA). For each model parameter, we then apply a sophisticated, guided-searchbased reachability analysis to this HA to estimate parameter ranges for both alternans and non-alternans behavior. The bifurcation point separates these two ranges, but with an uncertainty region due to the underlying δ-decision procedure. This uncertainty region, however, can be reduced by decreasing δ at the expense of increasing the model exploration time. Experimental results are provided that highlight the effectiveness of this method.
Demonstration of composite microsphere cavity and surface enhanced raman spectroscopy for improved sensitivity

Surface enhanced Raman spectroscopy (SERS) has widely been used for material composition analysis because it can provide good selectivity and sensitivity without the labeling process required by fluorescence detection. SERS enhancements on the order of 1014 have been demonstrated, which can enable the detection of a single molecule. However, further enhancement is necessary to increase the sensitivity of SERS systems, and to make single molecule detection and analysis more practical. In this work, we demonstrate a composite system of silver nanoparticles and an optical microsphere resonator to create an even higher average Raman enhancement than SERS alone. The Raman pump is coupled into the microsphere resonator, where it repeatedly circulates around the surface via total internal reflection in the form of whispering gallery modes (WGMs). Microsphere resonators can have Q-factor values higher than 106, which results in a tremendous local field enhancement. The evanescent field of the WGM interacts with the silver nanoparticles and target analytes, which are adsorbed onto the surface of the microsphere. With this composite system, we demonstrate an increase in Raman enhancement of approximately 300. Engineering improvements to this experimental prototype system may increase the enhancement by an order of magnitude. Further improvements that can leverage the microsphere resonator system to promote stimulated Raman scattering (SRS) may result in a dramatic increase in sensitivity. Ultimately, this composite system will increase the sensitivity of SERS sensor systems, and will bring single molecule detection and analysis systems closer to practical implementation.
DNA Content of broad bean (Vicia faba) internodes in connection with tumor induction by Agrobacterium tumefaciens.

This paper is concerned with changes which occur in the deoxyribonucleic acid (DNA) content of Vicia faba during tumor induction by Agrobacterium tum.efaciens. Thus far, the phenomenon has been described in several ways. Oft quoted is the work of Klein (2, 3), who claimed that unlike responses to wounding or inoculation with attenuated bacteria, tumor induction by a virulent bacterium evokes first a marked increase in DNA. His analyses were made by conventional chemical methods. Rasch, Swift, and Klein (5) analyzed infected tissues by microspectrophotometric methods and found no evidence for a sharp increase in DNA during the inductive phase. Robson, Budd, and Yost (6) compared tissue cultures of tumorous and non-tumorous tissue and concluded that tumor cells contain more DNA than normal ones and that the excess may be of non-chromosomal origin. The latter conclusion might be interpreted to mean that induction of tumor is tied to some novel pathway of DNA metabolism. Simply put, the problem is reduced to ascertaining whether direct chemical analysis of plant tissues during the tumor induction phase is or is not at variance with histochemical measurements. At issue is the nature of the primary act of the tumor-inducing principle. If a marked increase in DNA such as noted by Klein (2, 3) precedes other observable events, then a primary alteration in DNA metabolism would appear likely; if the contrary is true, then subtler changes such as those discussed by Braun and Stonier (1) must be sought for.
PKCθ and HIV-1 Transcriptional Regulator Tat Co-exist at the LTR Promoter in CD4+ T Cells

PKCθ is essential for the activation of CD4+ T cells. Upon TCR/CD28 stimulation, PKCθ is phosphorylated and migrates to the immunological synapse, inducing the activation of cellular transcription factors such as NF-κB and kinases as ERK that are critical for HIV-1 replication. We previously demonstrated that PKCθ is also necessary for HIV-1 replication but the precise mechanism is unknown. Efficient HIV-1 transcription and elongation are absolutely dependent on the synergy between NF-κB and the viral regulator Tat. Tat exerts its function by binding a RNA stem-loop structure proximal to the viral mRNA cap site termed TAR. Besides, due to its effect on cellular metabolic pathways, Tat causes profound changes in infected CD4+ T cells such as the activation of NF-κB and ERK. We hypothesized that the aberrant upregulation of Tat-mediated activation of NF-κB and ERK occurred through PKCθ signaling. In fact, Jurkat TetOff cells with stable and doxycycline-repressible expression of Tat (Jurkat-Tat) expressed high levels of mRNA for PKCθ. In these cells, PKCθ located at the plasma membrane was phosphorylated at T538 residue in undivided cells, in the absence of stimulation. Treatment with doxycycline inhibited PKCθ phosphorylation in Jurkat-Tat, suggesting that Tat expression was directly related to the activation of PKCθ. Both NF-κB and Ras/Raf/MEK/ERK signaling pathway were significantly activated in Jurkat-Tat cells, and this correlated with high transactivation of HIV-1 LTR promoter. RNA interference for PKCθ inhibited NF-κB and ERK activity, as well as LTR-mediated transactivation even in the presence of Tat. In addition to Tat-mediated activation of PKCθ in the cytosol, we demonstrated by sequential ChIP that Tat and PKCθ coexisted in the same complex bound at the HIV-1 LTR promoter, specifically at the region containing TAR loop. In conclusion, PKCθ-Tat interaction seemed to be essential for HIV-1 replication in CD4+ T cells and could be used as a therapeutic target.
Effect of Moisture and Temperature on the Functional Properties of Composite Flour Extrudates from Beans (Phaseolus vulgaris) and Nixtamalized Corn (Zea mays)

Beans have high protein content. Bean and corn flours can complement each other with essential amino acids. There has been little research on the production of snacks or extruded feed with bean–corn composite flours. The aim of this study was to obtain a bean–corn snack with high protein content for low-income families in the world. Bean–corn composite flours (60/40) were extruded. The effect of temperature and moisture during extrusion on the end quality of the product was analyzed. The expansion index, apparent density, water solubility index, water absorption index and the initial viscosity were measured and were significantly (p < 0.05) higher when bean–corn flour was extruded in high temperature and low moisture conditions. The best bean–corn extrudates was obtained in extrusion conditions of 190 oC and 14.5% moisture. The results show that bean proteins can be complemented by corn proteins to obtain highly valuable protein flour. Extrusion is an alternative processing method for obtaining extruded products with high protein content for human or animal consumption.
An improved complex field network coding scheme for wireless relay system in asymmetric link environment

In this paper, a complex field network coding (CFNC) scheme is presented, which focuses on improving transmission efficiency by reducing time slots that are needed to exchange data frames. Conventional CFNC scheme has the advantage of minimizing the number of time slots required for information exchanges. However, there exists serious performance deterioration because the transmit signals are interfered with each other. Also, considering a typical asymmetric link whose data traffic is biased in downlink such as orthogonal frequency division multiple access (OFDMA) system, conventional CFNC scheme cannot obtain sufficient coding gain due to frequency selective fading. In order to overcome these problems, we propose a repetition-based CFNC scheme as well as the corresponding maximum likelihood (ML) decision rule. The proposed repetition scheme is considered for obtaining frequency diversity gain, which is used to improve the decision accuracy in the proposed ML decision process. Simulation results verify that the proposed scheme has superior coded bit error rate (BER) performance compared with the conventional scheme.
Testing alternative hypotheses regarding the association between behavioral inhibition and language development in toddlerhood.

Studies have reported an inverse association between language development and behavioral inhibition or shyness across childhood, but the direction of this association remains unclear. This study tested alternative hypotheses regarding this association in a large sample of toddlers. Data on behavioral inhibition and expressive and receptive language abilities were collected from 816 twins at ages 14, 20, and 24 months. Growth and regression models were fit to the data to assess the longitudinal associations between behavioral inhibition and language development from 14 to 24 months. Overall, there were significant associations between behavioral inhibition and expressive language, and minimal associations with receptive language, indicating that the association is better explained by reticence to respond rather than deficient language development.
Clopidogrel-Induced Neutropenia after Coronary Stenting: Is Cilostazol a Good Alternative?

Dual antiplatelet therapy with aspirin plus thienopyridines has become the standard treatment of patients undergoing coronary stenting. Clopidogrel has mostly replaced the use of ticlopidine due to its more favourable adverse event profile. However, also the use of clopidogrel is not without side effects. Clopidogrel major adverse events are represented by marrow suppression, manifesting with aplastic anaemia, thrombocytopenia and neutropenia. When clopidogrel toxicity occurs, there are few and unsubstantiated alternative treatments and thus, in these cases, medical decisions may be very difficult. We report a case of clopidogrel-induced bone marrow toxicity manifesting with severe neutropenia in a patient treated with multiple coronary stents and provide suggestions for an alternative treatment.
A 20Gb/s Burst-Mode CDR Circuit Using Injection-Locking Technique

The design and experimental verification of a 20Gb/s CDR circuit based on injection-locking technique is presented. Fabricated in 90nm CMOS technology, this circuit achieves a BER of <10-9 for both continuous and burst modes. It has tunability of over 800Mb/s while consuming 175mW. The re-acquisition time of this CDR is 1b interval.
Title : Software for Automated Classification of probe-based Confocal Laser Endomicroscopy Videos of Colorectal Polyps Running title : Automated pCLE Classification of Colonic Polyps

AIM To support probe-based confocal laser endomicroscopy (pCLE) diagnosis by designing a software for automated classification of colonic polyps. MATERIALS AND METHODS Intravenous fluorescein pCLE imaging of colorectal lesions was performed on patients undergoing screening and surveillance colonoscopies, followed by polypectomies. All resected specimens were reviewed by a reference gastrointestinal pathologist blinded to pCLE information. Histopathology was used as criterion standard for the differentiation between neoplastic and non-neoplastic lesions. The pCLE video sequences, recorded for each polyp, were analyzed off-line by 2 expert endoscopists who were blinded to the endoscopic characteristics and histopathology. These pCLE videos, along with their histopathology diagnosis, were used to train the automated classification software which is a Content-Based Image Retrieval (CBIR) technique followed by k-nearest neighbor classification. The performances of the off-line diagnosis of pCLE videos established by the 2 expert endoscopists were compared with those of automated pCLE software classification. All evaluations were performed using leave-onepatient-out cross-validation to avoid bias. RESULTS 135 colorectal lesions were imaged in 71 patients. Based on histopathology, 93 of these 135 lesions were neoplastic and 42 were nonneoplastic. The study finds no statistical significance for the difference between the performance of automated pCLE software classification (accuracy 89.6%, sensitivity 92.5%, specificity 83.3%, using leave-onepatient-out cross-validation) and the performance of the off-line diagnosis of pCLE videos established by the 2 expert endoscopists (accuracy 89.6%, sensitivity 91.4%, specificity 85.7%). There is very low power (< 6%) to
Compatibility Is Not Transparency: VMM Detection Myths and Realities

Recent work on applications ranging from realistic honeypots to stealthier rootkits has speculated about building transparent VMMs - VMMs that are indistinguishable from native hardware, even to a dedicated adversary. We survey anomalies between real and virtual hardware and consider methods for detecting such anomalies, as well as possible countermeasures. We conclude that building a transparent VMM is fundamentally infeasible, as well as impractical from a performance and engineering standpoint.
Optimization of surgical planning of total hip arthroplasty based on computational anatomy

This paper describes a method for automated optimization of total hip arthroplasty (THA) planning incorporating joint functionalities. The optimal planning is formulated as maximum a posterior (MAP) estimation, which ensures the best-balance of joint functionalities and bone-implant spatial relations based on their statistical models derived from the training datasets prepared by an experienced surgeon. According to the performance evaluation, four of the six functionalities of the automatically optimized plans were almost equivalent to those of surgeon's plans, and two of them were improved. We consider these results showed a potential usefulness of the proposed method.
Construction and analysis of cDNA libraries from the antennae of Batocera horsfieldi and expression pattern of putative odorant binding proteins

Abstract A high-quality cDNA library was constructed from female and male antenna of the longhorned beetle, Batocera horsfieldi (Hope) (Coleoptera: Cerambycidae), a serious pest of Populus (Salicales: Salicaceae). The titer was approximately 2.37 × 106 pfu/mL, and this complies with the test requirement. From the libraries, 692 clones were selected randomly, sequenced, and further analyzed, and the recombinational efficiency reached 93.85%. By alignment and cluster analysis, we identified four odorant binding proteins, two pheromone-binding proteins (have the characteristic six conserved cysteine residues), four Minus-C odorant binding proteins (lost two conserved cysteines), and three chemosensory proteins. In this study, we describe the identification and characterization of four new cDNAs that encode Minus-C odorant binding proteins (Minus-C OBPs) from B. horsfieldi antennal cDNA libraries. Our investigation focused on the expression pattern of the Minus-C OBP genes in various tissues in both sexes at different developmental stages, using reverse transcription PCR (RT-PCR) and real-time PCR (qPCR) strategies. Minus-C OBP1, 2, and 3 were expressed in all tested tissues, with the exception of the head (without antenna, labial palps, and maxillary palps). Minus-C OBP4 was expressed in the antenna, legs, and abdomen, but not in the labial palps, maxillary palps, or head. The qPCR results revealed Minus- C OBPs were expressed in the antenna throughout the adult life, and that the transcript levels of these genes depended on the sex, age, and mating status of adults.
Understanding and Supporting Emerging Domestic Energy Practices Conference or Workshop Item

The current transformation of the domestic energy landscape, including local generation, new consumption and storage, requires rethinking our research approach. This paper reports experiences from two case studies with their implications for future HCI research in the home. Introduction The home energy environment, as part of the smart grid implementation, is starting a deep mutation: (i) householders have started generating their own electricity, (ii) new high electrical demand appliances have appeared such as heat pumps and electric vehicles, significantly increasing consumption, and (iii) domestic electricity storage is now commercially available. These transformations will result in both the challenge of increasing the complexity and the opportunity of closing the gap between producer and consumer – thus making energy more tangible for householders. The increasing evidence of emerging energy behaviors in a domestic context requires us to rethink both how we investigate energy in the home and our approach to contributions to address climate change. In this paper we report on our experience in studying emerging domestic energy practices. We briefly review existing HCI research in home relating to energy. Then, we present two case studies – that of doing laundry and driving an electric vehicle – in the context of domestic solar electricity generation. Finally, we discuss the implications for the domestic energy and HCI research. Jacky Bourgeois
Early events in Epstein-Barr virus infection provide a model for B cell activation

We have used Epstein-Barr virus (EBV) infection in vitro to delineate two distinct stages in B cell activation. Previous studies have shown that the BLAST-2 (EBVCS) (EBV cell surface) activation antigen is expressed on a small fraction of B cells within 24 h of stimulation with a variety of agents, including mitogens and EBV. In this study, we have been able to isolate the BLAST-2 (EBVCS)+ cells early after activation/infection with EBV. These cells are small B cells that are actively synthesizing RNA but not DNA, and are, therefore, clearly distinct from large proliferating lymphoblasts. In addition, they contain multiple copies of the EBV genome, express the viral nuclear antigen (EBNA) and, most importantly, proceed to undergo transformation when placed back in culture. By comparison, the BLAST-2 (EBVCS)- population does not undergo transformation, even though a fraction of these cells are activated for RNA synthesis and express EBNA. Thus, using the EBV system, we have been able to show directly that an activated B cell first expresses the BLAST-2 (EBVCS) antigen concomitant with an increase in RNA synthesis, and then subsequently proceeds to differentiate into a proliferating lymphoblast.
Influence of Expressive Coupling in Ensemble Performance on Musicians' Body Movement

This study aims at investigating if movements executed by musicians during musical performances are related to their expressive intentions. We tested the hypothesis by identifying information patterns on body movement data collected in performances of clarinet duos under different experimental conditions. First, we identified information patterns recurrent enough for the recognition of musicians who performed the excerpts. Then, we found evidence for a change in the “gestural signature” of the instrumentalist follower imposed by the leader, across the different performance conditions.
Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment

Genotypes are frequently used to identify parentage. Such analysis is notoriously vulnerable to genotyping error, and there is ongoing debate regarding how to solve this problem. Many scientists have used the computer program cervus to estimate parentage, and have taken advantage of its option to allow for genotyping error. In this study, we show that the likelihood equations used by versions 1.0 and 2.0 of cervus to accommodate genotyping error miscalculate the probability of observing an erroneous genotype. Computer simulation and reanalysis of paternity in Rum red deer show that correcting this error increases success in paternity assignment, and that there is a clear benefit to accommodating genotyping errors when errors are present. A new version of cervus (3.0) implementing the corrected likelihood equations is available at http://www.fieldgenetics. com.
Enhancing Knowledge Management in Online Collaborative Learning

This paper aims to explore two crucial aspects of collaborative work and learning: on the one hand, the importance of enabling collaborative learning applications to capture and structure the information generated by group activity and, on the other hand, to extract the relevant knowledge in order to provide learners and tutors with efficient awareness, feedback and support with regards to group performance and collaboration. To this end, in this paper we first propose a conceptual model for data analysis and management that identifies and classifies the many kinds of indicators that describe collaboration and learning into high-level aspects of collaboration. Then, we provide a computational platform that, at a first step, collects and classifies both the event information generated asynchronously from the users' actions and the labeled dialogues from the synchronous collaboration according to these indicators. This information is then analyzed in next steps to eventually extract and present to participants the relevant knowledge about the collaboration. The ultimate aim of this platform is to efficiently embed information and knowledge into collaborative learning applications. We eventually suggest a generalization of our approach to be used in diverse collaborative learning situations and domains.