Miracle-dz/UniFAR-FTUs huggingface dataset:
Anaerobic and Aerobic Degradation of Cyanophycin by the Denitrifying Bacterium Pseudomonas alcaligenes Strain DIP1 and Role of Three Other Coisolates in a Mixed Bacterial Consortium

ABSTRACT Four bacterial strains were isolated from a cyanophycin granule polypeptide (CGP)-degrading anaerobic consortium, identified by 16S rRNA gene sequencing, and assigned to species of the genera Pseudomonas, Enterococcus, Clostridium, and Paenibacillus. The consortium member responsible for CGP degradation was assigned as Pseudomonas alcaligenes strain DIP1. The growth of and CGP degradation by strain DIP1 under anaerobic conditions were enhanced but not dependent on the presence of nitrate as an electron acceptor. CGP was hydrolyzed to its constituting β-Asp-Arg dipeptides, which were then completely utilized within 25 and 4 days under anaerobic and aerobic conditions, respectively. The end products of CGP degradation by strain DIP1 were alanine, succinate, and ornithine as determined by high-performance liquid chromatography analysis. The facultative anaerobic Enterococcus casseliflavus strain ELS3 and the strictly anaerobic Clostridium sulfidogenes strain SGB2 were coisolates and utilized the β-linked isodipeptides from the common pool available to the mixed consortium, while the fourth isolate, Paenibacillus odorifer strain PNF4, did not play a direct role in the biodegradation of CGP. Several syntrophic interactions affecting CGP degradation, such as substrate utilization, the reduction of electron acceptors, and aeration, were elucidated. This study demonstrates the first investigation of CGP degradation under both anaerobic and aerobic conditions by one bacterial strain, with regard to the physiological role of other bacteria in a mixed consortium.
Pathway Cross-Talk Analysis in Detecting Significant Pathways in Barrett’s Esophagus Patients

Background The pathological mechanism of Barrett’s esophagus (BE) is still unclear. In the present study, pathway cross-talks were analyzed to identify hub pathways for BE, with the purpose of finding an efficient and cost-effective detection method to discover BE at its early stage and take steps to prevent its progression. Material/Methods We collected and preprocessed gene expression profile data, original pathway data, and protein-protein interaction (PPI) data. Then, we constructed a background pathway cross-talk network (BPCN) based on the original pathway data and PPI data, and a disease pathway cross-talk network (DPCN) based on the differential pathways between the PPI data and the BE and normal control. Finally, a comprehensive analysis was conducted on these 2 networks to identify hub pathway cross-talks for BE, so as to better understand the pathological mechanism of BE from the pathway level. Results A total of 12 411 genes, 300 pathways (6919 genes), and 787 896 PPI interactions (16 730 genes) were separately obtained from their own databases. Then, we constructed a BPCN with 300 nodes (42 293 interactions) and a DPCN with 296 nodes (15 073 interactions). We identified 4 hub pathways: AMP signaling pathway, cGMP-PKG signaling pathway, natural killer cell-mediated cytotoxicity, and osteoclast differentiation. We found that these pathways might play important roles during the occurrence and development of BE. Conclusions We predicted that these pathways (such as AMP signaling pathway and cAMP signaling pathway) could be used as potential biomarkers for early diagnosis and therapy of BE.
Soccer robot based on ant colony method of obstacle avoidance

A new method of path planning approach to moving robot 2 soccer in dynamic environment based on ant colony algorithm is presented in this paper. For the path planning, a method of adaptive ref resh strategy is used to plan the best path, two simplified and perfect probability function and fusion function are derived for the adaptive ref resh to optimize the path of obstacle 2 avoiding for Robot 2 soccer. The results of simulated experiment show that the method is effective in the path planning for Robot 2 soccer under the condition of meeting obstacles.
Identification des facteurs de succès d'implantation des SI en gestion documentaire moderne: une étude empirique

Si d'aucuns s'entendent sur l'importance de gerer efficacement l'information electronique toujours croissante dans nos organisations, il importe de mesurer le degre de succes de l'implantation des systemes d'information (SI). L'auteure offre le fruit de ses recherches sur le modele permettant de mesurer le succes d'implantation des systemes d'information de l'appareil gouvernemental quebecois. Apres avoir resume les projets du gouvernement du Quebec en matiere de gestion integree des documents ainsi que la norme internationale Open Archival Information System (OAIS); modele conceptuel definissant l'organisation d'un systeme d'archivage, l'auteure expose la problematique et les buts vises par sa recherche. Appuyee de schemas et de tableaux explicatifs, elle compare certains modeles existants, notamment aux niveaux des facteurs conditionnels et fonctionnels, de leurs qualites et de leurs benefices. Tout en admettant les limites de son etude, l'auteure invite la communaute archivistique a poursuivre la recherche dans ce domaine en constante evolution.
Frequency domain distributed OFDM source detection

We consider distributed detection of an orthogonal frequency-division multiplexing (OFDM) random source using a cooperative set of sensors. Assuming that the observations of different sensors are independent, we derive/propose several frequency-domain detectors: the Neyman-Pearson detector for known SNRs and noise variances and three generalized likelihood ratio detectors for unknown SNRs and/or noise variances assuming that the transmit power is either uniformly allocated to all the subcarriers or not. Our theoretical analysis matches our simulation results and show that the proposed detectors, despite their lower computational complexity, outperform the state-of-the-art time-domain detectors in practical cases.
A Statistical Study of Solar Active Regions That Produce Extremely Fast Coronal Mass Ejections

We present statistical results on the properties of the solar source regions that produced the 57 fastest (≥1500 km s−1) front-side coronal mass ejections (CMEs) from 1996 June to 2007 January. The properties of these fast-CME-producing regions, 35 in total, are compared with those of all 1143 active regions (ARs) in the period studied. An automated method, based on SOHO MDI magnetic synoptic charts, is used to select and characterize the ARs. For each, a set of parameters is derived that includes the areas (positive, negative, and total, denoted AP, AN, and AT, respectively), the magnetic fluxes (positive, negative, and total, FP, FN, and FT), the average magnetic field strength (Bavg), a quasi elongation (e) characterizing the overall shape of the AR, the number and length of polarity inversion lines (PILs, or neutral lines, NPIL and LPIL, respectively), and the average and maximum magnetic gradient on the PILs (GOPavg and GOPmax). Our statistical analysis shows a general trend between the scales of an AR and the likelihood of its producing a fast CME; that is, the larger the geometric size (AT), the larger the magnetic flux (FT), the stronger the magnetic field (Bavg), and the more complex the magnetic configuration (NPIL and LPIL), the greater the possibility of producing a fast CME. When all the ARs are sorted into three evenly sized groups with low, intermediate, and high values of these parameters, we find that for all the parameters, more than 60% of extremely fast CMEs are from the high-value group. The two PIL parameters are the best indicators of fast-CME production, with more than 80% coming from the high-value group.
Independent of Plasmacytoid Dendritic Cell (pDC) infection, pDC Triggered by Virus-Infected Cells Mount Enhanced Type I IFN Responses of Different Composition as Opposed to pDC Stimulated with Free Virus

Upon treatment with vesicular stomatitis virus (VSV) particles, plasmacytoid dendritic cells (pDC) are triggered to mount substantial type I IFN responses, whereas myeloid DC (mDC) are only minor producers. Interestingly, bone marrow–derived (BM-)mDC were more vulnerable to infection with enhanced GFP (eGFP)–expressing VSV (VSVeGFP) than BM-pDC. BM-pDC stimulated with wild-type VSV mounted TLR-dependent IFN responses that were independent of RIG-I–like helicase (RLH) signaling. In contrast, in BM-pDC the VSV variant M2 induced particularly high IFN responses triggered in a TLR- and RLH-dependent manner, whereas BM-mDC stimulation was solely RLH-dependent. Importantly, VSVeGFP treatment of BM-pDC derived from IFN-β yellow fluorescent protein (YFP) reporter mice (messenger of IFN-β) resulted in YFP+ and eGFP+ single-positive cells, whereas among messenger of IFN-β–BM-mDC most YFP+ cells were also eGFP+. This observation indicated that unlike mDC, direct virus infection was not required to trigger IFN responses of pDC. VSV-infected BM-mDC triggered BM-pDC to mount significantly higher IFN responses than free virus particles. Stimulation with infected cells enhanced the percentages of pDC subsets expressing either IFN-β+ or IFN-α6+ plus IFN-β+. Irrespective of whether stimulated with free virus or infected cells, IFN induction was dependent on autophagy of pDC, whereas autophagy of the infected mDC was dispensable. Collectively, these results indicated that productive VSV infection was needed to trigger IFN responses of mDC, but not of pDC, and that IFN responses were primarily induced by virus-infected cells that stimulated pDC in a TLR-dependent manner.
The Discovery of Cepheids and a Distance to NGC 5128

We discuss a new distance to NGC 5128 (Centaurus A) based on Cepheid variables observed with the Hubble Space Telescope. Twelve F555W (V) and six F814W (I) epochs of cosmic-ray-split WFPC2 observations were obtained. A total of 56 bona fide Cepheids were discovered, with periods ranging from 5 to ~50 days; five of these are likely Population II Cepheids of the W Virginis class, associated with the bulge or halo of NGC 5128. Based on the period and V- and I-band luminosities of a subsample of 42 classical (Population I) Cepheids, and adopting an LMC distance modulus and extinction of 18.50 ± 0.10 mag and E(B - V) = 0.10 mag, respectively, the true reddening-corrected distance modulus to NGC 5128 is μ0 = 27.67 ± 0.12 (random) ± 0.16 (systematic) mag, corresponding to a distance of 3.42 ± 0.18 (random) ± 0.25 (systematic) Mpc. The random uncertainty in the distance is dominated by the error on the assumed value for the ratio of total to selective absorption, RV, in NGC 5128, and by the possible metallicity dependence of the Cepheid period-luminosity relation at V and I. This represents the first determination of a Cepheid distance to an early-type galaxy.
On the Consistent Observation of Active Systems

The consistency issues have been well studied in term of methodologies and technologies for the most popular interaction paradigm, namely the client-server. In the agent’s world such a paradigm is used as much as another one, the notification-observation, in which an active system notifies its status changes to registered observer agents. In the client-server paradigm, when a client invokes a read operation of the system, the latter is always able to reply with a consistent status. Also in the notification-observation paradigm, the perception of consistent status changes of the observed system is a requirement, in order to take decision correctly. But the above-mentioned instruments used for the client-server scenario, are not suited for the notificationobservation paradigm. In this paper we highlight the problem and propose an abstraction called observation interface, as an architecture allowing observer agents to perceive consistent status changes of an active system.
Motivational Influences on Memory

Motivation significantly influences learning and memory. While a long history of research has focused on simple forms of associative learning, such as Pavlovian conditioning, recent research is beginning to characterize how motivation influences episodic memory. In this chapter we synthesize findings across behavioral, cognitive, and educational neuroscience to characterize motivation’s influence on memory. We provide evidence that neural systems underlying motivation, namely the mesolimbic dopamine system, interact with and facilitate activity within systems underlying episodic memory, centered on the medial temporal lobes. We focus on two mechanisms of episodic memory enhancement: encoding and consolidation. Together, the reviewed research supports an adaptive model of memory in which an individual’s motivational state (i.e., learning under states of reward or punishment) shapes the nature of memory representations in service of future goals. The impact of motivation on learning and memory, therefore, has very clear implications for and applications to educational settings.
Flexible collaboration transparency: supporting worker independence in replicated application-sharing systems

This article presents a critique of conventional collaboration transparency systems, also called “application-sharing” systems, which provide the real-time shared use of legacy single-user applications. We find that conventional collaboration transparency systems are inefficient in their use of network resources and lack support for key groupware principles: concurrent work, relaxed WYSIWIS, and group awareness. Next, we present an alternative approach to implementing collaboration transparency that provides many features previously seen only in collaboration-aware applicaitons. Our approach is based on a replicated architecture where selected single-user interface components are dynamically replaced by multiuser versions. The replacement occurs at run-time and is transparent to the single-user application and its developers. As an instance of this approach, we describe its incorporation into a Java-based collaboration transparency system for serializable, Swing-based Java applications, called Flexible JAMM (Java Applets Made Multiuser). To validate that the flexible collaboration transparency system is truly an improvement over conventional systems, we conducted an empirical study of collaborators performing both tightly and loosely coupled tasks using Flexible JAMM versus a representative conventional collaboration transparency system, Microsoft NetMeeting. Completion times were significantly faster in the loosely coupled task using Flexible JAMM and were not adversely affected in the tightly coupled task. Accuracy was equivalent for both systems. Participants greatly preferred Flexible JAMM.
Assembly, Gene Annotation and Marker Development Using 454 Floral Transcriptome Sequences in Ziziphus Celata (Rhamnaceae), a Highly Endangered, Florida Endemic Plant

Large-scale DNA sequence data may enable development of genetic resources in endangered species, thereby facilitating conservation efforts. Ziziphus celata, a federally endangered, self-incompatible plant species occurring in Florida, USA, is one species for which genetic resources are necessary to facilitate new introductions and augmentations essential for recovery of the species. We used 454 pyrosequencing of a Z. celata normalized floral cDNA library to create a genomic resource for gene and marker discovery. A half-plate GS-FLX Titanium run yielded 655 337 reads averaging 250 bp. A total of 474 025 reads were assembled de novo into 84 645 contigs averaging 408 bp, while 181 312 reads remained unassembled. Forty-seven and 43% of contig consensus sequences had BLAST matches to known proteins in the Uniref50 and TAIR9 annotated protein databases, respectively; many contigs fully represented orthologous proteins in TAIR9. A total of 22 707 unique genes were sequenced, indicating substantial coverage of the Z. celata transcriptome. We detected single-nucleotide polymorphisms and simple sequence repeats (SSRs) and developed thousands of SSR primers for use in future genetic studies. As a first step towards understanding self-incompatibility in Z. celata, we identified sequences belonging to the gene family encoding self-incompatibility. This study demonstrates the efficacy of 454 transcriptome sequencing for rapid gene and marker discovery in an endangered plant.
Analysis of IEEE 802.11e for QoS support in wireless LANs

The IEEE 802.11e medium access control protocol is an emerging standard for wireless local area networks providing quality of service. An overview of this standard based on the current draft is presented on this article. We analyze the enhancements in 802.11 standard. The new hybrid coordination function of the IEEE 802.11e with its contention-based and contention-free (controlled) medium access control schemes is evaluated. The capability to provide QoS support is discussed by means of simulations.
CANNET: Context aware nonlocal convolutional networks for semantic image segmentation

Semantic segmentation has long been a hot topic, most methods are the region based method, which lost connection information to their neighbors. In this paper we propose to encode context information into convolutional networks on this semantic labeling task. Firstly, we propose the nonlocal convolution kernel, which extracts feature from larger neighbor regions without introducing more parameters. Then we build up a context aware module, which takes both local patch and nonlocal neighbor information into account. At last we embed the module into convolutional networks and tested the improvement on benchmark datasets.
Increased levels of noisy splicing in cancers, but not for oncogene-derived transcripts

Recent genome-wide analyses have detected numerous cancer-specific alternative splicing (AS) events. Whether transcripts containing cancer-specific AS events are likely to be translated into functional proteins or simply reflect noisy splicing, thereby determining their clinical relevance, is not known. Here we show that consistent with a noisy-splicing model, cancer-specific AS events generally tend to be rare, containing more premature stop codons and have less identifiable functional domains in both the human and mouse. Interestingly, common cancer-derived AS transcripts from tumour suppressor and oncogenes show marked changes in premature stop-codon frequency; with tumour suppressor genes exhibiting increased levels of premature stop codons whereas oncogenes have the opposite pattern. We conclude that tumours tend to have faithful oncogene splicing and a higher incidence of premature stop codons among tumour suppressor and cancer-specific splice variants showing the importance of considering splicing noise when analysing cancer-specific splicing changes.
Architecture migration using DSM in a large-scale software project

In product line development (PLD), maintaining architecture against the rapid changes in market requirements and the technical environment is important. When maintaining architecture, architecture migration is often necessary to keep the architecture up to date. An issue in architecture migration is the continuity of the products. Because architecture is the basis of the development of core assets, architecture migration can result in core asset redesign or reimplementation, which can have a big impact on existing products. In large-scale PLD, this problem becomes very serious. Furthermore, our project required architecture migration along with real product development. This short paper outlines our approach towards architecture migration of effectively using DSM for a large-scale software project.
Identification and Gene Expression Analysis of a Taxonomically Restricted Cysteine-Rich Protein Family in Reef-Building Corals

The amount of genomic sequence information continues to grow at an exponential rate, while the identification and characterization of genes without known homologs remains a major challenge. For non-model organisms with limited resources for manipulative studies, high-throughput transcriptomic data combined with bioinformatics methods provide a powerful approach to obtain initial insights into the function of unknown genes. In this study, we report the identification and characterization of a novel family of putatively secreted, small, cysteine-rich proteins herein named Small Cysteine-Rich Proteins (SCRiPs). Their discovery in expressed sequence tag (EST) libraries from the coral Montastraea faveolata required the performance of an iterative search strategy based on BLAST and Hidden-Markov-Model algorithms. While a discernible homolog could neither be identified in the genome of the sea anemone Nematostella vectensis, nor in a large EST dataset from the symbiotic sea anemone Aiptasia pallida, we identified SCRiP sequences in multiple scleractinian coral species. Therefore, we postulate that this gene family is an example of lineage-specific gene expansion in reef-building corals. Previously published gene expression microarray data suggest that a sub-group of SCRiPs is highly responsive to thermal stress. Furthermore, data from microarray experiments investigating developmental gene expression in the coral Acropora millepora suggest that different SCRiPs may play distinct roles in the development of corals. The function of these proteins remains to be elucidated, but our results from in silico, transcriptomic, and phylogenetic analyses provide initial insights into the evolution of SCRiPs, a novel, taxonomically restricted gene family that may be responsible for a lineage-specific trait in scleractinian corals.
TASI Lectures on Perturbative String Theories

These lecture notes are based on a course on string theories given by Hirosi Ooguri in the first week of TASI 96 Summer School at Boulder, Colorado. It is an introductory course designed to provide students with minimum knowledge before they attend more advanced courses on non-perturbative aspects of string theories in the School. The course consists of five lectures: 1. Bosonic String, 2. Toroidal Compactifications, 3. Superstrings, 4. Heterotic Strings, and 5. Orbifold Compactifications.
Constrained Navigation with Mandatory Waypoints in Uncertain Environment

This paper presents a hybrid solving method for vehicle path planning problems. As part of the vehicle system architecture (vetronic), planning is dynamic and has to be activated on-line, which requires response times to be compatible with mission execution. The proposed approach combines constraint solving techniques with an Ant Colony Optimization (ACO). The hybridization relies on a static probing technique which builds up a search strategy using a distance information between problem variables and a heuristic solution. Various forms of this approach are compared and evaluated on real world scenarios. Preliminary results exhibit response times close to vehicle control requirements, on realistic problem instances.