Miracle-dz/UniFAR-FTUs huggingface dataset:
Principal component analysis of odor coding at the level of third‐order olfactory neurons in Drosophila

Olfactory information in Drosophila is conveyed by projection neurons from olfactory sensory neurons to Kenyon cells (KCs) in the mushroom body (MB). A subset of KCs responds to a given odor molecule, and the combination of these KCs represents a part of the neuronal olfactory code. KCs are also thought to function as coincidence detectors for memory formation, associating odor information with a coincident punishment or reward stimulus. Associative conditioning has been shown to modify KC output. This plasticity occurs in the vertical lobes of MBs containing α/α' branches of KCs, which is shown by measuring the average Ca2+ levels in the branch of each lobe. We devised a method to quantitatively describe the population activity patterns recorded from axons of >1000 KCs at the α/α' branches using two‐photon Ca2+ imaging. Principal component analysis of the population activity patterns clearly differentiated the responses to distinct odors.
ROSE: Compiler Support for Object-Oriented Frameworks

ROSE is a preprocessor generation tool for the support of compile time performance optimizations in Overture. The Overture framework is an object-oriented environment for solving partial differential equations in two and three space dimensions. It is a collection of C++ libraries that enables the use of finite difference and finite volume methods at a level that hides the details of the associated data structures. Overture can be used to solve problems in complicated, moving geometries using the method of overlapping grids. It has support for grid generation, difference operators, boundary conditions, database access and graphics. In this paper we briefly present Overture, and discuss our approach toward performance within Overture and the A++P++ array class abstractions upon which Overture depends, this work represents some of the newest work in Overture. The results we present show that the abstractions represented within Overture and the A++P++ array class library can be used to obtain application codes with performance equivalent to that of optimized C and Fortran 77. ROSE, the preprocessor generation tool, is general in its application to any object-oriented framework or application and is not specific to Overture.
Personality traits detection using a parallelized modified SFFS algorithm

We present in this paper a contribution to the INTERSPEECH 2012 Speaker Trait Challenge. We participated in the Personality Sub-Challenge, where the main characteristics of speakers according to the five OCEAN dimensions had to be determined based on short audio recordings solely. We considered the task as a general optimization problem and applied a modified version of the SFFS algorithm, wrapped around a SVM classifier, along with parallelized parameter tuning. Our system has yielded higher than baseline scores on all five dimensions for the development set, adding almost 14 percentage points to the recognition score of the Openness dimension.
Projection-based curve clustering

This paper focuses on unsupervised curve classification in the context of nuclear industry. At the Commissariat à l'Energie Atomique (CEA), Cadarache (France), the thermal-hydraulic computer code CATHARE is used to study the reliability of reactor vessels. The code inputs are physical parameters and the outputs are time evolution curves of a few other physical quantities. As the CATHARE code is quite complex and CPU time-consuming, it has to be approximated by a regression model. This regression process involves a clustering step. In the present paper, the CATHARE output curves are clustered using a k-means scheme, with a projection onto a lower dimensional space. We study the properties of the empirically optimal cluster centres found by the clustering method based on projections, compared with the ‘true’ ones. The choice of the projection basis is discussed, and an algorithm is implemented to select the best projection basis among a library of orthonormal bases. The approach is illustrated on a simulated example and then applied to the industrial problem.
Robotic Models for Studying Undulatory Locomotion in Fishes

Many fish swim using body undulations to generate thrust and maneuver in threedimensions.Thepatternofbodybendingduringsteadyrectilinearlocomotion has similar general characteristics in many fishes and involves a wave of increasing amplitude passing from the head region toward the tail. While great progress has been made in understanding the mechanics of undulatory propulsion in fishes, the inability to control and precisely alter individual parameters such as oscillation frequency, body shape, and body stiffness, and the difficulty of measuring forces on freely swimming fishes have greatly hampered our ability to understand the fundamental mechanics of the undulatory mode of locomotion in aquatic systems. In this paper, we present the use of a robotic flapping foil apparatus that allows these parameters to be individually altered and forces measured on self-propelling flapping flexible foils that produce a wave-like motion very similar to that of freely swimming fishes. We use this robotic device to explore the effects of changing swimming speed, foil length, and foil-trailing edge shape on locomotor hydrodynamics, the cost of transport, and the shape of the undulating foil during locomotion. We also examine the passive swimming capabilities of a freshly dead fish body. Finally, wemodel fin-fininteractionsin fishesusingdual-flappingfoilsandshowthatthrust can be enhanced under correct conditions of foil phasing and spacing as a result of the downstream foil making use of vortical energy released by the upstream foil.
Title The dynamics of visual experience , an EEG Study of subjectivepattern formation

Background: Since the origin of psychological science a number of studies have reported visual pattern formation in the absence of either physiological stimulation or direct visual-spatial references. Subjective patterns range from simple phosphenes to complex patterns but are highly specific and reported reliably across studies. Methodology/Principal Findings: Using independent-component analysis (ICA) we report a reduction in amplitude variance consistent with subjective-pattern formation in ventral posterior areas of the electroencephalogram (EEG). The EEG exhibits significantly increased power at delta/theta and gamma-frequencies (point and circle patterns) or a series of highfrequency harmonics of a delta oscillation (spiral patterns). Conclusions/Significance: Subjective-pattern formation may be described in a way entirely consistent with identical pattern formation in fluids or granular flows. In this manner, we propose subjective-pattern structure to be represented within a spatio-temporal lattice of harmonic oscillations which bind topographically organized visual-neuronal assemblies by virtue of low frequency modulation. Citation: Elliott MA, Twomey D, Glennon M (2012) The Dynamics of Visual Experience, an EEG Study of Subjective Pattern Formation. PLoS ONE 7(1): e30830. doi:10.1371/journal.pone. 0030830 Editor: Joseph Najbauer, City of Hope National Medical Center and Beckman Research Institute, United States of America Received August 15, 2011; Accepted December 26, 2011; Published January 26, 2012 Copyright: 2012 Elliott et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The authors have no support or funding report. Competing Interests: The authors have declared that no competing interests exist. * E-mail: mark.elliott@nuigalway.ie
Screening and Identification of Inhibitors of Trypanosoma brucei Cathepsin L with Antitrypanosomal Activity

Current treatment options for human African trypanosomiasis (HAT) are ineffective, and they have several well‐known clinical limitations. In our continued efforts to identify chemotypes that can be developed into clinically useful drugs, we screened a targeted compound library against the major cathepsin L (rhodesain) in T. brucei. We report the antirhodesain activity and antitrypanosomal activity of the compounds in this letter. The identified compounds can serve as starting points for structure‐ and/or phenotype‐based lead optimization strategy against Trypanosoma brucei.
Effects of lung volume reduction surgery on distribution of ventilation and perfusion

Lung volume reduction surgery (LVRS) results in functional improvements in most patients. The mechanisms behind the improvements are not clear. We hypothesized that reduced inequalities in ventilation to perfusion ratio (V/Q) may be a contributing explanation. Nine patients who underwent LVRS were investigated by ventilation and perfusion scintigrams before and after surgery. In addition, 8 healthy subjects were investigated once. The relative ventilation, perfusion and V/Q were calculated in 1 × 1 cm lung elements. Normal range of the element count‐rate was determined by the corresponding results in the normal subjects. Results of this small study show a significant effect of LVRS on V/Q, with reduction of shunt‐like elements. We conclude that the functional improvement after LVRS to some extent may be explained by decreased V/Q inequality.
Telemedicine with digital video transport system in Asia-Pacific area

We have established a medical network in Asia-Pacific area with high-quality moving image on a super broad-banded Internet line since February 2003. Broadcasting real-time surgery and teleconference with medical-quality videos with digital video transport system (DVTS) were so useful to learn surgical techniques and other medical procedures beyond borders. We have conducted 20 events in categories of teleconference (8 times), live transmission of medical procedure (6 times), and remote attendance to scientific medical meetings (6 times) until September 2004. We had teleconferences among 3 countries in APAN-Hawaii in January 2004 (Japan, Korea and USA), and in APAN-Cairns in July 2004 (Japan, Korea and Australia). There have been no serious transmission/ethical problems so far. With these experiences and current achievements, we hope to extend this advanced network system to whole Asia-Pacific countries to share medical skills and knowledge.
Crystallization and preliminary X‐ray crystallographic properties of Hsc20, a J‐motif co‐chaperone protein from Escherichia coli

Hsc20 is a 20‐kDa auxiliary protein that functions with the molecular chaperone Hsc66 in Escherichia coli. Crystals of Hsc20 suitable for X‐ray diffraction analysis were grown using the hanging drop vapor diffusion technique in polyethylene glycol 400 containing dioxane as an additive to slow growth. The crystals are monoclinic and belong to the space group C2 with unit cell dimensions α = 125.4 Å, b = 71.9 Å, c = 68.8 Å, and β = 97.0°. The crystals diffract to a minimum d‐spacing of ∼2.5 Å resolution, and a native data set was collected to 2.7 Å. The results of a self‐rotation function analysis revealed threefold symmetry, suggesting three molecules of Hsc20 in the asymmetric unit and, hence, 12 molecules in the unit cell; this corresponds to a Vm value of 2.6 Å3/Da and a solvent content of ∼53% in the crystals. Structure determination by isomorphous replacement is in progress.
NooSphere: an activity-centric infrastructure for distributed interaction

Distributed interaction is a computing paradigm in which the interaction with a computer system is distributed over multiple devices, users and locations. Designing and developing distributed interaction systems is intrinsically difficult as it requires the engineering of a stable infrastructure to support the actual system and user interface. As an approach to this re-engineering problem, we introduce NooSphere, an activity-centric infrastructure and programming framework that provides a set of fundamental distributed services that enables quick development and deployment of distributed interactive systems. In this paper, we describe the requirements, design and implementation of NooSphere and validate the infrastructure by implementing three canonical real deployable applications constructed on top of the NooSphere infrastructure.
An improved man-machine system Incident Tree model considering incident dependence

The Incident Tree Analysis methodology (ITA) can consider the uncertain characteristics of accident by combining fuzzy logic and information flow approaches together. But the dependence of man-machine interaction is not considered in ITA approach, which ignores the differences of task scenarios meanwhile. In this paper, we put forward an Improved Incident Tree Analysis methodology (IITA) taking this dependence into account, and present its mathematic method. Firstly, information quantity and control sequence quantity are introduced and reformed to show the dependence of the man-machine interaction process at the information level. And then the steps of determining the two parameters values in different task scenarios are given. A vehicle-leaving-roadway accident is taken as an example to illustrate the proposed method. Contrasting with the results of ITA, IITA is proved better to evaluate the risk of complex man-machine systems.
Identification of cellular factors that bind specifically to the Epstein-Barr virus origin of DNA replication

The specific binding of HeLa cell factors to DNA sequences at the Epstein-Barr virus (EBV) latent origin of DNA replication was detected by gel shift experiments and DNase I footprinting analysis. These cellular proteins protected at least five discrete regions of the DNA replication origin. The viral protein required for EBV plasmid replication, EBV nuclear antigen 1 (EBNA-1), binds to specific sequences within the origin region. The HeLa cell proteins competed with EBNA-1 for binding to EBV origin DNA in vitro, leading to the possibility that these cellular proteins regulate EBV DNA replication by displacing EBNA-1 at the origin sites.
Specific protein phosphorylation in interferon-treated uninfected and virus-infected mouse L929 cells: enhancement by double-stranded RNA

The enhanced phosphorylation of specific protein(s) observed in extracts from interferon-treated cells (in the presence of ATP and double-stranded [ds] RNA) was also seen in intact mouse L929 cells upon treatment with dsRNA, polyriboinosinic.polyribocytidylic acid [poly(rI.rC)] or reovirus dsRNA, using 32Pi as radiolabel. Labeling of a 65,000-dalton protein(s) with 32P was greatly increased in interferon-treated cells in the presence of added dsRNA, suggesting that the expression in vivo of the kinase activity involved is regulated by dsRNA. This was used as a test system to investigate whether the activity of interferon-induced enzyme(s) is stimulated following virus infection, possibly owing to the accumulation of dsRNA. No obvious increase in 32P-labeling of 65,000-dalton protein(s) was observed upon infection of interferon-treated cells with mengovirus or vesicular stomatitis virus. A basal level of 32P-labeling of the 65,000-dalton protein(s) was detected in interferon-treated cells in the absence of added dsRNA, indicating a basal level of expression of the kinase activity involved. The possible implications of these results are discussed.
Comparison of the Penner and Lior methods for serotyping Campylobacter spp

We compared two Campylobacter serotyping systems by using 1,405 isolates of Campylobacter collected from human, animal, and environmental sources during epidemiologic investigations and special studies. We found 96.1% of isolates to be typable by the Penner method for heat-stable antigens, which involved the use of an indirect hemagglutination technique, and 92.1% of isolates to be typable by the Lior method for heat-labile antigens, which involved the use of a slide agglutination technique and absorbed antisera. Absorbed antisera were not required for the Penner method, making that method less difficult to implement. The Lior method was simpler to perform and gave more rapid results than did the Penner method. Cultures frequently reacted in multiple antisera with the Penner method, whereas multiple reactions were rare with the Lior method. Thus, results were easier to interpret with the Lior system. Strains of a single serotype in one system were sometimes found to be multiple serotypes in the other system; hence, the two methods have the potential to be complementary. Both systems were comparable in serotyping isolates from human and nonhuman sources and for evaluating the relationship of strains collected during outbreak investigations.
Downregulation of hPMC2 imparts chemotherapeutic sensitivity to alkylating agents in breast cancer cells

Triple negative breast cancer cell lines have been reported to be resistant to the cyotoxic effects of temozolomide (TMZ). We have shown previously that a novel protein, human homolog of Xenopus gene which Prevents Mitotic Catastrophe (hPMC2) has a role in the repair of estrogen-induced abasic sites. Our present study provides evidence that downregulation of hPMC2 in MDA-MB-231 and MDA-MB-468 breast cancer cells treated with temozolomide (TMZ) decreases cell survival. This increased sensitivity to TMZ is associated with an increase in number of apurinic/apyrimidinic (AP) sites in the DNA. We also show that treatment with another alkylating agent, BCNU, results in an increase in AP sites and decrease in cell survival. Quantification of western blot analyses and immunofluorescence experiments reveal that treatment of hPMC2 downregulated cells with TMZ results in an increase in γ-H2AX levels, suggesting an increase in double strand DNA breaks. The enhancement of DNA double strand breaks in TMZ treated cells upon downregulation of hPCM2 is also revealed by the comet assay. Overall, we provide evidence that downregulation of hPMC2 in breast cancer cells increases cytotoxicity of alkylating agents, representing a novel mechanism of treatment for breast cancer. Our data thus has important clinical implications in the management of breast cancer and brings forth potentially new therapeutic strategies.
The value of point-of-Care CD4 and Laboratory viral Load in tailoring ART monitoring Strategies to resource limitations.

OBJECTIVE To examine the clinical and economic value of point-of-care CD4 (POC-CD4) or viral load (VL) monitoring compared to current practices in Mozambique, a country representative of the diverse resource limitations encountered by HIV treatment programs in sub-Saharan Africa. DESIGN/METHODS We use the CEPAC-I model to examine the clinical impact, cost (2014 US$), and incremental cost-effectiveness ratio (ICER, $/year of life saved [YLS]) of ART monitoring strategies in Mozambique. We compare: 1) monitoring for clinical disease progression (CLIN) vs. annual POC-CD4 in rural settings without laboratory services and 2) biannual laboratory CD4 (LAB-CD4), biannual POC-CD4, and annual VL in urban settings with laboratory services. We examine the impact of a range of values in sensitivity analyses, using Mozambique's 2014 per capita GDP ($620) as a benchmark cost-effectiveness threshold. RESULTS In rural settings, annual POC-CD4 compared to CLIN improves life expectancy by 2.8 years, reduces time on failed ART by 0.6 years, and yields an ICER of $480/YLS. In urban settings, biannual POC-CD4 is more expensive and less effective than VL. Compared to biannual LAB-CD4, VL improves life expectancy by 0.6 years, reduces time on failed ART by 1.0 year, and is cost-effective ($440/YLS). CONCLUSIONS In rural settings, annual POC-CD4 improves clinical outcomes and is cost-effective compared to CLIN. In urban settings, VL has the greatest clinical benefit and is cost-effective compared to biannual POC-CD4 or LAB-CD4. Tailoring ART monitoring strategies to specific settings with different available resources can improve clinical outcomes while remaining economically efficient.
Familial restless legs with periodic movements in sleep

Restless legs syndrome was present in nine members of a family over a span of five generations. In three subjects, the diagnosis was confirmed by all-night sleep recordings and concomitant EMG. Two of these three subjects also had periodic movements in sleep. The frequency of leg movements decreased from wakefulness to stages 1 and 2 non-REM sleep. There was an increase of free dopamine and homovanillic acid in CSF of the propositus. Clonazepam effectively controlled restless legs in the propositus and his mother.
Myoblast Transplantation in Whole Muscle of Nonhuman Primates

The goal of the present study was to determine the feasibility, success, and toxicity of myoblast transplantation (MT) in the whole muscle of primates. Allogenic myoblasts transduced with the β-galactosidase (β-Gal) gene were transplanted in the whole Biceps brachii of 5 monkeys immunosuppressed with FK506. Myoblast injections were spaced at every 1 to 1.5 mm in 7 muscles, as well as at every 5 mm in 2 muscles. Myoblasts were resuspended in HBSS, notexin 1 μg/ml or notexin 5 μg/ml. Depending on the number of β-Gal labeled myoblasts and the injection protocol, biopsies of transplanted muscles exhibited 7% to 74% β-Gal+ fibers 1 month after MT. β-Gal+ fibers were present in muscle biopsies made 3, 8, and 12 months after MT. Myoglobinuria and hyperkalemia, the risk factors after extensive muscle damage and notexin toxicity, were not observed. The withdrawal of immunosuppression led to histological evidences of cellular rejection of the graft. We concluded that MT can be successfully performed in large primate muscles without toxicity due to muscle damage. An effective immunosuppression allowed the maintenance of β-Gal+ fibers up to 1 year after MT. These results suggest parameters that may allow effective MT in humans.
Compensatory evolution facilitates the acquisition of multiple plasmids in bacteria

The coexistence of multicopy plasmids is a common phenomenon. However, the evolutionary forces promoting these genotypes are poorly understood. In this study, we have analyzed multiple ColE1 plasmids (pB1000, pB1005 and pB1006) coexisting within Haemophilus influenzae RdKW20 in all possible combinations. When transformed into the naïve host, each plasmid type presented a particular copy number and produced a specific resistance profile and biological cost, whether alone or coexisting with the other plasmids. Therefore, there was no fitness advantage associated with plasmid coexistence that could explain these common plasmid associations in nature. Using experimental evolution, we showed how H. influenzae Rd was able to completely compensate the fitness cost produced by any of these plasmids. Crucially, once the bacterium has compensated for a first plasmid, the acquisition of new multicopy plasmid(s) did not produced any extra biological cost. We argue therefore that compensatory adaptation pave the way for the acquisition of multiple coexisting ColE1 plasmids. Importance Antibiotic resistance is a major concern for human and animal health. Plasmids play a major role in the acquisition and dissemination of antimicrobial resistance genes. In this report we investigate, for the first time, how plasmids are capable to cohabit stably in populations. This coexistence of plasmids is driven by compensatory evolution alleviating the cost of a first plasmid, which potentiates the acquisition of further plasmids at no extra cost. This phenomenon explains the high prevalence of plasmids coexistance in wild type bacteria, which generates multiresistant clones and contributes to the maintenance and spread of antibiotic resistance genes within bacterial populations.