Miracle-dz/UniFAR-FTUs huggingface dataset:
Time-Resolved Transcriptomics and Bioinformatic Analyses Reveal Intrinsic Stress Responses during Batch Culture of Bacillus subtilis

We have determined the time-resolved transcriptome of the model gram-positive organism B. subtilis during growth in a batch fermentor on rich medium. DNA microarrays were used to monitor gene transcription using 10-minute intervals at 40 consecutive time points. From the growth curve and analysis of all gene expression levels, we identified 4 distinct growth phases and one clear transition point: a lag phase, an exponential growth phase, the transition point and the very clearly separated early and late stationary growth phases. The gene expression profiles suggest the occurrence of stress responses at specific times although no external stresses were applied. The first one is a small induction of the SigB regulon that occurs at the transition point. Remarkably, a very strong response is observed for the SigW regulon, which is highly upregulated at the onset of the late stationary phase. Bioinformatic analyses that were performed on our data set suggest several novel putative motifs for regulator binding. In addition, the expression profiles of several genes appeared to correlate with the oxygen concentration. This data set of the expression profiles of all B. subtilis genes during the entire growth curve on rich medium constitutes a rich repository that can be further mined by the scientific community.
Traac Characterisation and Eeective Bandwidths for Broadband Network Traces

The trend of current developments in telecommunication networks is towards systems which will allow a number of widely disparate traac streams to share common resources through statistical sharing. How eeciently this can be managed depends critically upon the statistical characteristics of the traac. Our aim in this paper is to investigate the application of a simple and robust graphical descriptor of a given traac stream, designed to emphasize those aspects of the data that are important for the statistical sharing of common resources. Two examples considered in detail are an MPEG-1 video encoding of the Star Wars movie and traces of ethernet traac taken at Bellcore.
Embedding maximum entropy models in algebraic varieties by Gröbner bases methods

The main aim of this paper is to present some notions on how results from commutative algebra and algebraic geometry could be used in representation and computation of maximum entropy (ME) models in the cases, where an integer valued sufficient statistic exists. We give an implicit description of ME-models by embedding them in algebraic varieties for which we use Gröbner bases methods. We prove that in the case of ME, both the model and the data can be represented by algebraic varieties.
Effect of interleukin (IL)-35 on IL-17 expression and production by human CD4+ T cells

Background Interleukin (IL)-17 produced by mainly T helper 17 (Th17) cells may play an important destructive role in chronic periodontitis (CP). Thus, anti-inflammatory cytokines, such as IL-35, might have a beneficial effect in periodontitis by inhibiting differentiation of Th17 cells. Th17 differentiation is regulated by the retinoic acid receptor-related orphan receptor (ROR) α (encoded by RORA) and RORγt (encoded by RORC). However, the role of IL-35 in periodontitis is not clear and the effect of IL-35 on the function of Th17 cells is still incompletely understood. Therefore, we investigated the effects of IL-35 on Th17 cells. Methods Peripheral blood mononuclear cells (PBMCs) were sampled from three healthy volunteers and three CP patients and were analyzed by flow cytometry for T cell population. Th17 cells differentiated by a cytokine cocktail (recombinant transforming growth factor-β, rIL-6, rIL-1β, anti-interferon (IFN)-γ, anti-IL-2 and anti-IL-4) from PBMCs were cultured with or without rIL-35. IL17A (which usually refers to IL-17), RORA and RORCmRNA expression was analyzed by quantitative polymerase chain reaction, and IL-17A production was determined by enzyme-linked immunosorbent assay. Results The proportion of IL-17A+CD4+ slightly increased in CP patients compared with healthy controls, however, there were no significant differences in the percentage of IL-17A+CD4+ as well as IFN-γ+CD4+ and Foxp3+CD4+ T cells between healthy controls and CP patients. IL17A, RORA and RORC mRNA expression was significantly increased in Th17 cells induced by the cytokine cocktail, and the induction was significantly inhibited by addition of rIL-35 (1 ng/mL). IL-17A production in Th17 cells was significantly inhibited by rIL-35 addition (1 ng/mL). Discussion The present study suggests that IL-35 could directly suppress IL-17 expression via RORα and RORγt inhibition and might play an important role in inflammatory diseases such as periodontitis.
PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data

The lack of reproducibility with animal phenotyping experiments is a growing concern among the biomedical community. One contributing factor is the inadequate description of statistical analysis methods that prevents researchers from replicating results even when the original data are provided. Here we present PhenStat – a freely available R package that provides a variety of statistical methods for the identification of phenotypic associations. The methods have been developed for high throughput phenotyping pipelines implemented across various experimental designs with an emphasis on managing temporal variation. PhenStat is targeted to two user groups: small-scale users who wish to interact and test data from large resources and large-scale users who require an automated statistical analysis pipeline. The software provides guidance to the user for selecting appropriate analysis methods based on the dataset and is designed to allow for additions and modifications as needed. The package was tested on mouse and rat data and is used by the International Mouse Phenotyping Consortium (IMPC). By providing raw data and the version of PhenStat used, resources like the IMPC give users the ability to replicate and explore results within their own computing environment.
Alleviation of Salt Stress by Enterobacter sp. EJ01 in Tomato and Arabidopsis Is Accompanied by Up-Regulation of Conserved Salinity Responsive Factors in Plants

Microbiota in the niches of the rhizosphere zones can affect plant growth and responses to environmental stress conditions via mutualistic interactions with host plants. Specifically, some beneficial bacteria, collectively referred to as Plant Growth Promoting Rhizobacteria (PGPRs), increase plant biomass and innate immunity potential. Here, we report that Enterobacter sp. EJ01, a bacterium isolated from sea china pink (Dianthus japonicus thunb) in reclaimed land of Gyehwa-do in Korea, improved the vegetative growth and alleviated salt stress in tomato and Arabidopsis. EJ01 was capable of producing 1-aminocy-clopropane-1-carboxylate (ACC) deaminase and also exhibited indole-3-acetic acid (IAA) production. The isolate EJ01 conferred increases in fresh weight, dry weight, and plant height of tomato and Arabidopsis under both normal and high salinity conditions. At the molecular level, short-term treatment with EJ01 increased the expression of salt stress responsive genes such as DREB2b, RD29A, RD29B, and RAB18 in Arabidopsis. The expression of proline biosynthetic genes (i.e. P5CS1 and P5CS2) and of genes related to priming processes (i.e. MPK3 and MPK6) were also up-regulated. In addition, reactive oxygen species scavenging activities were enhanced in tomatoes treated with EJ01 in stressed conditions. GFP-tagged EJ01 displayed colonization in the rhizosphere and endosphere in the roots of Arabidopsis. In conclusion, the newly isolated Enterobacter sp. EJ01 is a likely PGPR and alleviates salt stress in host plants through multiple mechanisms, including the rapid up-regulation of conserved plant salt stress responsive signaling pathways.
Demo: a mobility aware cooperative scheme for MAC reconfiguration in cognitive wireless networks

With increasing wireless communication applications, assigning dedicated spectral resource to each application is becoming impractical. Cognitive radios are emerging as a possible solution for enabling coexistence among networks and higher spectrum utilization by opportunistically using spectral holes through dynamic spectrum access schemes [1]. Since the spectral environment for a node can be highly dynamic and unstable due to mobility and spectrum sharing with other networks, medium access schemes must be flexible and adaptable in order to provide a stable and high Quality of Service (QoS). Classically, protocols are implemented in a monolithic fashion which restricts reconfigurability required in a dynamic spectrum access paradigm and mobile environment. One common approach for reconfiguration is by appropriately setting the parameters of a particular protocol such as the selection of the modulation and coding schemes in LTE [2]. MultiMAC [3] switches among a few pre-defined standalone protocols based on QoS requirements. Although these approaches aim at providing flexibility, the design choice is limited to the subset of the tunable parameter values and pre-selected options. In our demonstration, we will use a toolchain for runtime protocol realization (TRUMP) [4] which is built based on Decomposable MAC Framework [5]. It enables flexible adaptation of MAC behaviour on-the-fly resulting from spectral and network dynamics, mobility and varying QoS application demands. Reconfiguration at individual nodes may lead to possibly incoherent MAC schemes in a neighbourhood. Therefore, we have designed and implemented a cooperative mechanism where coexistence of different MAC solutions is allowed in the same network without disruption in communication links. Furthermore, the cooperative scheme allows the neighbouring nodes to adapt their MAC behaviour in order to maximize the performance characteristics. This is achieved through a controlling mechanism which monitors the MAC behaviour of its neighbours and disseminates this information. Demo This demonstration will provide an opportunity to the audience to interactively change the protocol configuration at individual nodes, spectral conditions and/or the network topology and correspondingly observe the resulting performance characteristics. The demonstration will show how our cooperative scheme enables MAC reconfiguration in a network neighbourhood. The demo will also show that our cooperative scheme allows nodes to reconfigure
A real-time software framework for indoor navigation

We introduce an initial implementation of a real-time component-based software framework for autonomous mobile robots. We argue that real-world autonomous mobile robots shall be controlled by self-contained software systems able to meet hard timing constraints. The proposed solution empowers specialized roboticists to contribute software components that can be integrated into complete real-time systems. The framework also facilitates robotic software components reuse and portability across hardware platforms. Based on an indoor navigation case study we evaluate the advantages and the limitations of the framework in terms of ease of use, modularity and real-time capabilities.
Semantics Enhanced Composition Planner for Distributed Resources

The composition of distributed resources is a pervasive challenge facing almost all modern application fields, especially for large-scale scientific applications. In most of these applications, several resources need to be integrated in order to fulfill the requirements of a complex scientific task. However, even though current Web Services have emerged as a paradigm for managing complex distributed resources, the lack of machine readability in representation prevents Web Services from supporting the efficient composition of resources. This paper presents SECPlanner, a new Web Services composition approach which combines the AI Planning Graph technique with semantics enabled matchmaking algorithm to find the optimal composition candidates. The composition result will afterwards be represented as a scientific workflow for future reuse.
Metabolic Syndrome and Benign Prostatic Hyperplasia: Evidence of a Potential Relationship, Hypothesized Etiology, and Prevention

Benign prostatic hyperplasia (BPH) is highly prevalent in older men and causes substantial adverse effects on health. The pathogenesis of this disease is not totally clear. Recent reports have suggested a possible relationship between metabolic syndrome (MetS) and BPH. Single components of MetS (obesity, dyslipidemia, hypertension, and insulin resistance) as well as the syndrome itself may predispose patients to a higher risk of BPH and lower urinary tract symptoms (LUTS). This may stem from changes in insulin resistance, increased autonomic activity, impaired nitrergic innervation, increased Rho kinase activity, pro-inflammatory status, and changes in sex hormones that occur in association with MetS. However, the exact underlying mechanisms that regulate the potential relationship between MetS and BPH/LUTS still need to be clarified. Increased physical activity and dietary strategies may help in decreasing the incidence of MetS and its impact on BPH/LUTS. However, differences in the definitions used to address the examined predictors and endpoints preclude the possibility of arriving at definitive conclusions.
Contranarratieven van Marokkaanse ouders: een weerwoord op discriminatie, paternalisme em stigmatisering

“Wij weten hoe we onze kinderen moeten opvoeden. Wij proberen ze op te voeden zoals wij dat willen, maar dat gaat hier niet. De opvoeding hier in de scholen leidt naar niets. Als onze kinderen problemen veroorzaken kijkt iedereen naar ons. Maar het is het probleem van de samenleving, niet dat van ons. Ze moeten het niet altijd op de vreemdeling duwen. Het zijn niet wij die slecht opvoeden maar de school. Op school laten ze de kinderen doen wat zij willen. Ze zijn niet streng genoeg. De kinderen zijn van acht tot vier op school. Dan is het eten, huiswerk maken en slapen. Dus ze zijn meer op school dan thuis. De school heeft dus meer invloed op hen dan wij. De staat wil dat de kinderen vanaf twee en een half jaar naar school gaan. Het is de school en de staat. De scholen hebben kinderen nodig, dus telefoneren ze om de haverklap om je kind te krijgen als het bijna zo oud is. Maar op die leeftijd begint het te begrijpen en te praten en te leren wat mag en wat niet mag. Dan heeft het zijn moeder nodig. Maar het moet naar school. Ze leren Frans en vergeten hun moedertaal. ” (Marokkaanse moeder, Brussel)
Postrefractive surgery dry eye

Purpose of review To report the recently published literature on ocular surface changes after refractive surgery, as well as the outcomes of treatment modalities on postrefractive surgery dry eye. Recent findings Cyclosporine, the first US Food and Drug Administration approved agent to treat the underlying pathological mechanism of chronic dry eye, has demonstrated promising results in dry eye patients. Further, there may be an additive effect of topical cyclosporine and punctal occlusion. Femtosecond lasers for corneal flaps in laser in-situ keratomileusis seem to induce fewer signs and symptoms of dry eye and may be attributed to the creation of thinner flaps. Summary Dry eye is one of the most common complications after photorefractive keratectomy and laser in-situ keratomileusis. Keratorefractive surgery is known to cause damage to the corneal sensory nerves. Several studies have demonstrated a decrease in corneal sensation, tear secretion, and tear film stability several months after keratorefractive surgery. For patients with preoperative dry eye, the ocular surface must be treated accordingly prior to surgery.
Coordination context-based spectrum sharing for 5G millimeter-wave networks

Spectrum sharing is particularly promising for 5G-oriented millimeter-wave (MMW) networks, since MMW network deployments are predominantly expected to be only partially overlapping or adjacent islands, and it would not make sense to assign a dedicated sub-band to each operator in this case. However, inter-network interference may degrade the performance of both networks. Therefore coordination is needed to further improve the network performance. In this paper, a link-specific coordination context (CC) concept is proposed. The CC here for one link represents a constraint that needs to be considered by the scheduler in each AN in a sense that certain transmissions are only scheduled on “allowed” radio resources. To determine CC for each link that suffer non-negligible interference from other networks, the coordination procedure and algorithm is designed in both centralized and distributed structure in this paper. Finally, the performance is evaluated for spectrum sharing of two networks in corridor scenario with realistic ray-tracing propagation channel and steering directional horn antenna models in 60GHz. The results show that high gain beamforming enables more aggressive resource reuse and CC scheme can bring coordination gain over both blind full re-use (i.e. without coordination) and fixed orthogonal re-use (no sharing).
Dynamic Effects of Repeating a Timed Writing Task in Two EFL University Courses: Multi-Element Text Analysis with Coh-Metrix

The longitudinal effects of repeating a timed writing activity on English as a Foreign Language (EFL) students’ second language (L2) writing development were investigated. Data for 46 students in two university classes (23 in each class), each with a different course objective, were collected 30 times in the same way over one year. The students’ compositions were analyzed for fluency, grammatical complexity, and lexical complexity. Text analysis using Coh-Metrix showed that task repetition had an overall effect on L2 writing development. The text analysis was supplemented with a visual analysis using moving min-max graphs. Grammatical complexity developed more prominently than the other aspects of writing in both classes. This counter-predictive result points to the significance of the writers’ reflective consciousness towards their own writing. This study also emphasizes that it is important to study the dynamics in L2 writing development with multi-wave data. DOI: 10.4018/978-1-60960-741-8.ch023
Modelling character emotion in an interactive virtual environment

Expressing emotions plays a critical role in increasing the believability of virtual characters. Our aim is to develop an emotional model that can be integrated into characters in an interactive virtual reality environment. We have adopted mood, personality and emotion in an approach where the human users animates their own virtual character. This approach allows the user to employ all of their social and cultural skills in both decisionmaking and in interaction with other agents. The model so far developed is currently being integrated into a virtual reality training tool for fireman.
Cross-linguistic differences in the immediate serial recall of consonants versus vowels

ABSTRACT The current study investigated native English and native Arabic speakers’ phonological short-term memory for sequences of consonants and vowels. Phonological short-term memory was assessed in immediate serial recall tasks conducted in Arabic and English for both groups. Participants (n = 39) heard series of six consonant–vowel syllables and wrote down what they recalled. Native speakers of English recalled the vowel series better than consonant series in English and in Arabic, which was not true of native Arabic speakers. An analysis of variance showed that there was an interaction between first language and phoneme type. The results are discussed in light of current research on consonant and vowel processing.
Maternal breastfeeding history and Alzheimer’s risk

Background: The effect of early and midlife factors on later-life cognitive function has attracted scientific and public interest in recent years, especially in terms of hormonal risk factors for dementia. Given the substantial evidence for roles of ovarian hormones, insulin sensitivity, and inflammation in Alzheimer? s Disease (AD) etiology, here it is hypothesized that breastfeeding history may affect women? s risk of AD.Methods: Reproductive history information was collected and Alzheimer? s diagnostic interviews were performed for a cohort of elderly British women (N = 133). Results: Using Cox regression models, we find that history of longer breastfeeding duration corresponded to reduced risk of AD onset in women without family history of AD. This effect was absent in women with family history of AD. Conclusions: Breastfeeding practices are an important modifier of cumulative endogenous hormone exposure for mothers. Progesterone deprivation and/or glucose tolerance benefits of breastfeeding may be responsible for the observed reduction in AD risk. Future studies concerning hormone effects on AD risk should consider how reproductive history leads to variation in endogenous hormone exposure, and the role thismay play in the relationship between hormones and AD.Keywords: Alzheimer? s Disease, risk factors, breastfeeding, lactation, reproductive history, hormones, estrogen, prolactin, inflammation
Detecting Story Analogies from Annotations of Time, Action and Agency

We describe the Story Intention Graph (SIG) as a model of narrative meaning that is amenable to both corpus annotation and computational inference. The relations, focusing on time, action and agency, can express a range of thematic scenarios and lend themselves to the automatic detection of story similarity and analogy. An evaluation finds that such detection outperforms a propositional similarity metric in predicting human judgments of story similarity in the Aesop domain.
A HYBRID MODEL-BASED VENTILATORY DECISION SUPPORT SYSTEM

A hybrid knowledge-and-model-based advisory system for intensive care ventilators has been developed. The system consists of two parts: a knowledge-based toplevel module using neural fuzzy technology and a model-based lower-level module consisting of 4 sub-units. The system generates advice on four ventilator settings (the inspired fraction of oxygen (FiO2), positive end-expiratory pressure (PEEP), peak inspiratory pressure (PINSP) and ventilatory rate) based on the patient’s routine and cardiorespiratory measurements. The validation results of the top-level module were encouraging. Validation of the integrated system using retrospective clinical data is underway. Copyright © 2003 University of Sheffield.
Service-based Business Process Merge Using Process Feature Structure Tree ?

In order to meet the individualization needs, software manufacturing companies have developed a number of individualized services. However, it leads to a lot of redundant software products and low production eciency. In addition, it cannot quickly and eciently respond to changes in demand. In order to solve above problems, the concept of congurable process model was proposed. Given a congurable
Pairs Trading and Accounting Information

This paper examines the impact of accounting information events (i.e., earnings announcements and analysts’ earnings forecasts) on the profitability of a pairs trading strategy proposed by Gatev et al. (2006). Using a portfolio of U.S. stock pairs between 1981 and 2006, we find that pairs trades are frequently triggered around accounting information events. More importantly, we find that pairs positions opened after accounting events are significantly less profitable than pairs positions opened in non-event periods. Furthermore, we find that incremental excess returns can be achieved by delaying the closing of a pairs position until after accounting information events. Overall, our results suggest that drift in stock prices following earnings announcements and analysts’ earnings forecasts is a significant factor affecting the profitability of pairs trades. JEL Classification: G12; G14; M41