Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Transcription of Compatible Solute Transporters by the General Stress Sigma Factor, σB, in Listeria monocytogenes

ABSTRACT Listeria monocytogenes is well known for its durable physiological characteristics, which allow the organism to grow at low temperature and pH and high osmolarity. Growth under high osmolarity depends on the accumulation of compatible solutes, among which glycine betaine and carnitine are the preferred solutes for this organism. Three different transport systems, Gbu, BetL, and OpuC, have been identified in L. monocytogenes which serve to scavenge the preferred compatible solutes. The general stress response regulator σB has been shown to play an important role in osmotic adaptation in L. monocytogenes, presumably by directing transcription from one or more of the solute transport genes. In the studies presented here, we have used primer extension analyses to identify the promoter elements responsible for transcription of the opuC, gbuA, and betL genes. All three genes are osmotically inducible to some degree. betL is transcribed from a σB-independent promoter, while gbuA is transcribed from dual promoters, one of which is σB dependent. opuC is transcribed exclusively from a σB-dependent promoter. The betL promoter is similar in sequence to the σB-independent gbuAP1 promoter. Kinetic analysis of transcript accumulation after osmotic upshift demonstrated that σB-dependent transcripts from gbuAP2 and sigB accumulate for an extended period after upshift, suggesting that σB activity may provide a mechanism for sustained high-level expression during osmotic challenge. In contrast to osmotic upshift, expression from the σB-dependent opuC and gbuAP2 promoters after temperature upshift and ethanol stress was minimal, suggesting that additional mechanisms may also participate in regulating transcription from these σB-dependent promoters.
Automatic synthesis of deadlock free connectors for COM/DCOM applications

Many software projects are based on the integration of independently designed software components that are acquired on the market rather than developed within the project itself. Sometimes interoperability and composition mechanisms provided by component based integration frameworks cannot solve the problem of binary component integration in an automatic way. Notably, in the context of component based concurrent systems, the binary component integration may cause deadlocks within the system. In this paper we present a technique to allow connectors synthesis for deadlock-free component based architectures [2] in a real scale context, namely in the context of COM/DCOM applications. This technique is based on an architectural, connector-based approach which consists of synthesizing a COM/DCOM connector as a COM/DCOM server that can route requests of the clients through a deadlock free policy. This work also provides guide lines to implement an automatic tool that derives the implementation of routing dead-lock-free policy within the connector from the dynamic behavior specification of the COM components. It is then possible to avoid the deadlock by using COM composition mechanisms to insert the synthesized connector within the system while letting the system COM servers unimodified. We present a sucessful application of this technique on the (COM version of the) problem known as "The dining philosophers". Depending on the type of deadlock we have a strategy that automatically operates on the connector part of the system architecture in order to obtain a suitably equivalent version of the system which is deadlock-free.
Murine cardiac progenitor cells require visceral embryonic endoderm and primitive streak for terminal differentiation

Cardiac progenitor cells in avian and amphibian embryos are known to commit to cardiac lineage during gastrulation or early neurulation. These cells require cell interaction with anterior endoderm for their differentiation into cardiomyocytes. However, little is known about cell interaction in mammalian cardiogenesis. We investigated the staging of murine cardiomyocyte commitment and the role of cell interaction in differentiation of cardiac progenitor cells into cardiomyocytes, using cultures of various embryonic regions at 7.25 and 7.5 days post coitum (p.c.), respectively. To evaluate the terminal differentiation of cardiac progenitor cells, we employed three parameters; expression of spontaneous beating, myosin heavy chain (MHC) protein, and cardiac‐specific genes (α myosin heavy chain, Csx/Nkx2.5 and myosin light chain 2V genes). mRNAs of cardiac‐specific genes were detected in 7.25‐day p.c. mesoderm by RT‐PCR, suggesting that the genetic specification to cardiac lineage initiated in the mesoderm by 7.25 days p.c. The 7.25‐day p.c. isolated mesoderm in 48 hr culture, however, failed to differentiate into spontaneous beating cardiomyocytes and exhibited non‐organized MHC protein in 19% of these culture. In contrast, all of the 7.5‐day p.c. isolated mesoderm differentiated into beating cardiomyocytes even in 24 hr culture. The 7.25‐day p.c. mesoderm associated with primitive streak increased MHC protein expression in 93% of these cultures, although they formed beating foci in 3%. The 7.25‐day p.c. explants containing both visceral embryonic endoderm and primitive streak succeeded in terminal differentiation into spontaneous beating cardiomyocytes. Our study suggests that cardiac progenitor cells obtain the potency to complete terminal differentiation autonomously at 7.5 days p.c. , as a consequence of the multistep induction by cell interactions with both the primitive streak and visceral embryonic endoderm, following the genetic specification to cardiac lineage in the early gastrula stage. Dev. Dyn. 1997;210:344–353. © 1997 Wiley‐Liss, Inc.
On Two Filarial Parasites from Dogs in Ceylon, Brugia ceylonensis n.sp. and Dipetalonema sp.inq.

A new species of Brugia, from the lymphatic glands of dogs in Ceylon, is described. It is closely related to B. patei (Buckley, Nelson and Heisch, 1958). Also from dogs in Ceylon, a species of Dipetalonema was recovered whose relationship with other species of Dipetalonema is discussed. In the absence of conclusive evidence that it is a distinct species it is for the present regarded as a species inquirenda.
Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation1

Metabolomics-based integrative approaches provide better understanding of gene function, pathway structure, and regulation. Huge insight into molecular mechanisms and biological network coordination have been achieved following the application of various profiling technologies. Our knowledge of how the different molecular entities of the cell interact with one another suggests that, nevertheless, integration of data from different techniques could drive a more comprehensive understanding of the data emanating from different techniques. Here, we provide an overview of how such data integration is being used to aid the understanding of metabolic pathway structure and regulation. We choose to focus on the pairwise integration of large-scale metabolite data with that of the transcriptomic, proteomics, whole-genome sequence, growth- and yield-associated phenotypes, and archival functional genomic data sets. In doing so, we attempt to provide an update on approaches that integrate data obtained at different levels to reach a better understanding of either single gene function or metabolic pathway structure and regulation within the context of a broader biological process.
L'intention du consommateur de s'immerger dans les mondes virtuels : l'influence de la présence d'interactions sociales, de la persistance et de l'avatar

L’objet de cette recherche est d’etudier les antecedents de l’intention du consommateur de MMO/MMORPG en nous appuyant sur la definition de Bell (2008), qui propose un consensus quant a la definition des mondes virtuels. Par cette definition, tous les mondes virtuels possedent trois concepts qui leur sont inherents : la presence d’interactions sociales, la persistance et l’avatar. Nous avons adapte le modele de l’acceptation technologique en representant ces trois concepts par l’identite sociale pour laquelle nous distinguons la communaute du MMO et la communaute de la guilde, la perception du flow et l’avatar. Notre travail suit une demarche hypothetico-deductive, qui s’est formalisee par l’elaboration d’une analyse qualitative et d’une analyse quantitative, en utilisant les equations structurelles.Les resultats ont montre que les facteurs motivationnels (Yee 2007) d’accomplissement et d’immersion influencent significativement et positivement la personnalisation des determinants de l’avatar (le physique, l’habillement et les attitudes), a contrario du facteur de sociabilite qui l’influence negativement. Les trois concepts inherents aux mondes virtuels ont une influence positive sur l’attitude qui, elle-meme, influence positivement l’intention. Notre adaptation du modele de l’acceptation technologique, en integrant conjointement les trois concepts des MMO/MMORPG que sont l’identite sociale, la perception du flow et la personnalisation des criteres de l’avatar, explique a 27,4 % l’intention du consommateur de mondes virtuels.
Identifying a set of relevant input and output factors within a productivity model for educational services

The study aims to develop a comprehensive set of input and output factors for educational services. In the frame of the study, a set of input, throughput and output factors is presented. These factors were collected in a workshop with lecturers having a long-time experience in teaching, since the authors assume that they have a great amount of implicit knowledge about the productive delivery of educational services. So far, no further refinement on the different factors was conducted, thus an actual usage of the taxonomy is not possible. Hence, it is necessary, to find a comprehensive set of factors, which helps to operationalize the factors which consequently can be converted into an applicable productivity measurement model. Based on the workshop results, further details to a beforehand developed productivity model is added, which combines and classifies input and output factors. The advanced productivity model will allow classifying existing learning scenarios and enables scientists to derive appropriate measurement tools to measure the productivity of educational services. Based on the workshop findings an approach for an learning scorecard is presented.
The effects of low levels of fatigue on face recognition among individuals and team members

The ability to identify particular faces among a crowd or line up is important in various contexts. However, little is known about how fatigue due to sleep deficit affects performance nor about the moderating role of team membership. UK Army Reservists (n = 182) indicated whether line ups of four faces included either of two target faces. They did this while either alone or in a team and while fatigued or alert. Among individuals, fatigue led to a greater bias toward identifying targets as absent. Fatigued team members experienced bias toward absent responses but to a lesser extent than did fatigued individuals. This did not translate into improved performance; fatigued teams had an equal proportion of hits but more false alarms than fatigued individuals.
The Ongoing Challenge of Hematopoietic Stem Cell-Based Gene Therapy for β-Thalassemia

β-thalassemia is characterized by reduced or absence of β-globin production, resulting in anemia. Current therapies include blood transfusion combined with iron chelation. BM transplantation, although curative, is restricted by the matched donor limitation. Gene therapy, on the other hand, is promising, and its success lies primarily on designing efficient globin vectors that can effectively and stably transduce HSCs. The major breakthrough in β-thalassemia gene therapy occurred a decade ago with the development of globin LVs. Since then, researchers focused on designing efficient and safe vectors, which can successfully deliver the therapeutic transgene, demonstrating no insertional mutagenesis. Furthermore, as human HSCs have intrinsic barriers to HIV-1 infection, attention is drawn towards their ex vivo manipulation, aiming to achieve higher yield of genetically modified HSCs. This paper presents the current status of gene therapy for β-thalassemia, its success and limitations, and the novel promising strategies available involving the therapeutic role of HSCs.
BCCI - A Bidirectional Cortical Communication Interface

Therapeutic methods based on efferent signals from the patients’ brain have been studied extensively in the field of brain-computer interfaces and applied to paralysed and stroke patients. Invasive stimulation is used as a therapeutic tool for patients with Parkinson disease, intractable chronic pain and other neurological diseases. We give a short review of currently used applications for cortical stimulation for stroke patients and braincomputer interfaces for paralyzed patients. We propose a refined approach for stroke rehabilitation as well as the extension of the use of invasive cortical stimulation to ALS patients with an experimental setup inspired by classical conditioning to facilitate the communication with brain-computer interfaces for LIS and CLIS patients. A closed-loop system is described with sophisticated methods for the identification of recording and stimulation sites, feature extraction and adaptation of stimulation algorithms to the patient in order to design a bidirectional cortical communication interface (BCCI).
Multilayer Periodic and Random Metamaterial Structures: Analysis and Applications

In recent years, multilayer photonic bandgap structures comprising stacks of alternating layers of positive and negative index have been proposed for a variety of applications, such as perfect imaging, filters, sensors, coatings for tailored emittance, absorptance, etc. Following a brief review of the history of negative index materials, the performance of such stacks is reviewed, with emphasis on analysis of plane wave and beam propagation, and possible applications in sensing. First, the use of the transfer matrix method to analyze plane wave propagation in such structures to determine the transmittance and reflectance is developed. Examples of cases where the Bragg bandgap and the so-called zero <;\(n \) > gap can be used for possible applications in sensing are illustrated. Next, the transfer matrix approach is extended to simulate the spatial evolution of a collection of propagating and nonpropagating TE and TM plane waves (or plane wave spectra) incident on such multilayer structures. The use of the complex Poynting theorem in checking the computations, as well as monitoring powers and the stored electric or magnetic energy in any section of the multilayer stack, is illustrated, along with its use in designing alternating positive and negative index structures with optimal gain to compensate for losses in the negative index material. Finally, the robustness of PIM-NIM stacks with respect to randomness in the dimensions of the PIM-NIM structure is examined. This should be useful in determining the performance of such structures when they are physically fabricated.
Bio-inspired active vision for obstacle avoidance

Reliable distance estimation of objects in a visual scene is essential for any artificial vision system designed to serve as the main sensing unit on robotic platforms. This paper describes a vision-centric framework for a mobile robot which makes use of bio-inspired techniques to solve visual tasks, in particular to estimate disparity. Such framework features robustness to noise, high speed in data processing, good performance in 3D reconstruction, the possibility to orientate the cameras independently and it requires no explicit estimation of the extrinsic parameters of the cameras. These features permit navigation with obstacle avoidance allowing active exploration of the scene. Furthermore, the modular design allows the integration of new modules with more advanced functionalities.
Effect of Cross-Language IR in Bilingual Lexicon Acquisition from Comparable Corpora

Within the framework of translation knowledge acquisition from WWW news sites, this paper studies issues on the effect of cross-language retrieval of relevant texts in bilingual lexicon acquisition from comparable corpora. We experimentally show that it is quite effective to reduce the candidate bilingual term pairs against which bilingual term correspondences are estimated, in terms of both computational complexity and the performance of precise estimation of bilingual term correspondences.
Optical Fiber Humidity Sensors Using PVdF Electrospun Nanowebs

In this paper, a new optical fiber humidity sensor based on PVdF nanowebs is presented. The electrospinning technique has been used to create a nanometric scale membrane onto the surface of a hollow core fiber (HCF). The fabricated sensor has demonstrated a repetitive response in the range from 50 to 70% of relative humidity with a rise time of 100 ms. Among other applications, this sensor is intended to be used for monitoring the human breathing. Therefore, high dynamic performances are required, especially in the higher relative humidity ranges.
Protective Effects of PARP-1 Knockout on Dyslipidemia-Induced Autonomic and Vascular Dysfunction in ApoE−/− Mice: Effects on eNOS and Oxidative Stress

The aims of this study were to investigate the role of poly(ADP-ribose) polymerase (PARP)-1 in dyslipidemia-associated vascular dysfunction as well as autonomic nervous system dysregulation. Apolipoprotein (ApoE)−/− mice fed a high-fat diet were used as a model of atherosclerosis. Vascular and autonomic functions were measured in conscious mice using telemetry. The study revealed that PARP-1 plays an important role in dyslipidemia-associated vascular and autonomic dysfunction. Inhibition of this enzyme by gene knockout partially restored baroreflex sensitivity in ApoE−/− mice without affecting baseline heart-rate and arterial pressure, and also improved heart-rate responses following selective blockade of the autonomic nervous system. The protective effect of PARP-1 gene deletion against dyslipidemia-induced endothelial dysfunction was associated with preservation of eNOS activity. Dyslipidemia induced PARP-1 activation was accompanied by oxidative tissue damage, as evidenced by increased expression of iNOS and subsequent protein nitration. PARP-1 gene deletion reversed these effects, suggesting that PARP-1 may contribute to vascular and autonomic pathologies by promoting oxidative tissue injury. Further, inhibition of this oxidative damage may account for protective effects of PARP-1 gene deletion on vascular and autonomic functions. This study demonstrates that PARP-1 participates in dyslipidemia-mediated dysregulation of the autonomic nervous system and that PARP-1 gene deletion normalizes autonomic and vascular dysfunctions. Maintenance of eNOS activity may be associated with the protective effect of PARP-1 gene deletion against dyslipidemia-induced endothelial dysfunction.
Integrating N-gram model information for Chinese word segmentation based on conditional random fields

This paper presents a Chinese word segmentation system based on conditional random fields, which integrates the result information of N-gram model as features of conditional random fields. Since dictionary-based N-gram model can deal with in-vocabulary words very well, while conditional random fields have the advantage of recognizing out-of-vocabulary words. This approach is evaluated using the PKU data from Sighan Bakeoff 2005. The experimental results have proven that this method achieved an F-measure of 95.0% and higher Roov (85.2%) and Riv (97.9%).
A Framework for Sharing Voluminous Content in P2P Systems

File-sharing applications remain today the most representative and popular realization of the Peerto-Peer paradigm. Large objects receive an increasing amount of interest in such systems. In this paper, we identify several challenges related to sharing voluminous content such as movies, OS distributions, games, etc, in unstructured Peer-to-Peer networks. We then describe our scheme which adaptively expands or contracts system resources in order to improve the sharing process and achieve a fair load distribution among the providers.
Chemical chronology of the Southern Coalsack

We demonstrate how the observed H 2 O ice column densities toward three dense globules in the Southern Coalsack could be used to constrain the ages of these sources. We derive ages of ∼10 5 yr, in agreement with dynamical studies of these objects. We have modelled the chemical evolution of the globules and showed how the molecular abundances are controlled by both the gas density and the initial chemical conditions as the globules formed. Based on our derived ages, we predict the column densities of several species of interest. These predictions should be straightforward to test by performing molecular-line observations.
Predicting personal preferences in subjective video quality assessment

In this paper, we study the problem of predicting the visual quality of a specific test sample (e.g. a video clip) experienced by a specific user, based on the ratings by other users for the same sample and the same user for other samples. A simple linear model and algorithm is presented, where the characteristics of each test sample are represented by a set of parameters, and the individual preferences are represented by weights for the parameters. According to the validation experiment performed on public visual quality databases annotated with raw individual scores, the proposed model can predict the scores by individuals more accurately than the average score for the respective sample computed from the scores given by other individuals. In many cases, the proposed algorithm also outperforms more generic Parametric Probabilistic Matrix Factorization (PPMF) technique developed for collaborative filtering in recommendation systems.
The Lurcher Mutation Identifies δ2 as an AMPA/Kainate Receptor-Like Channel That Is Potentiated by Ca2+

Neurodegeneration in Lurcher (Lc) mice results from constitutive activation of δ2, a subunit of ionotropic glutamate receptors (GluRs) with unknown natural ligands and channel properties. Homo-oligomeric channels of GluR-δ2 with the Lurcher mutation (GluR-δ2Lc) expressed in human embryonic kidney 293 cells showed a doubly rectifying current–voltage relation reminiscent of the block by intracellular polyamines in AMPA/kainate channels. Similarly, the fraction of the total current carried by Ca2+ was ∼2–3%, comparable with that found in Ca2+-permeable AMPA/kainate channels. Currents through GluR-δ2Lc channels were also potentiated by extracellular Ca2+ in a biphasic manner, with maximal potentiation occurring at physiological concentrations of Ca2+. We examined the functional role of the Q/R site in GluR-δ2Lc by replacing glutamine with arginine. Analogous to AMPA/kainate receptors, GluR-δ2Lc(R) channels showed no voltage-dependent block by intracellular polyamines and were nominally impermeable to Ca2+. The potentiation by Ca2+, however, remained intact. Hence, GluR-δ2Lcchannels are functionally similar to the AMPA/kainate receptor channels, consistent with the high-sequence identity shared by these subunits within the channel-lining M2 and M3 segments. Furthermore, potentiation by Ca2+ and a permeability to Ca2+ comparable with that of AMPA/kainate receptors provide a possible cause for cell death in Lurcher mice and may contribute to cerebellar long-term depression under physiological conditions.