Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression Profiling of the Response to Interferon Beta in Epstein-Barr-Transformed and Primary B Cells of Patients with Multiple Sclerosis

The effects of interferon-beta (IFN-β), one of the key immunotherapies used in multiple sclerosis (MS), on peripheral blood leukocytes and T cells have been extensively studied. B cells are a less abundant leukocyte type, and accordingly less is known about the B cell-specific response to IFN-β. To identify gene expression changes and pathways induced by IFN-β in B cells, we studied the in vitro response of human Epstein Barr-transformed B cells (lymphoblast cell lines-LCLs), and validated our results in primary B cells. LCLs were derived from an MS patient repository. Whole genome expression analysis identified 115 genes that were more than two-fold differentially up-regulated following IFN-β exposure, with over 50 previously unrecognized as IFN-β response genes. Pathways analysis demonstrated that IFN-β affected LCLs in a similar manner to other cell types by activating known IFN-β canonical pathways. Additionally, IFN-β increased the expression of innate immune response genes, while down-regulating many B cell receptor pathway genes and genes involved in adaptive immune responses. Novel response genes identified herein, NEXN, DDX60L, IGFBP4, and HAPLN3, B cell receptor pathway genes, CD79B and SYK, and lymphocyte activation genes, LAG3 and IL27RA, were validated as IFN-β response genes in primary B cells. In this study new IFN-β response genes were identified in B cells, with possible implications to B cell-specific functions. The study's results emphasize the applicability of LCLs for studies of human B cell drug response. The usage of LCLs from patient-based repositories may facilitate future studies of drug response in MS and other immune-mediated disorders with a B cell component.
Multi-objective no-wait hybrid flowshop scheduling problem with transportation times

This paper studies multi-objective no-wait hybrid flowshop scheduling problems to minimise both makespan and total tardiness. Furthermore, we consider transportation times between machines. This transportation time can be either job-dependent or job-independent. We consider that all transportations are job-independent; and transportations between two machines have to be done by one transporter. This paper presents a new multi-objective electromagnetism algorithm (MOEA). Electromagnetism algorithm is known as a flexible and effective population-based algorithm utilising an attraction/repulsion mechanism to move the particles towards optimality. The algorithm is carefully evaluated for its performance against two available algorithms by means of multi-objective performance measures and statistical tools. The results show that the proposed solution method outperforms the others.
Evaluating virtual router performance for a pluralist future internet

Internet Service Providers resist innovating in the network core, fearing that deploying a new protocol or service compromises the network operation and their profit, as a consequence. Therefore, a new Internet model, called Future Internet, which enables core innovation, must accommodate new protocols and services with the current scenario, isolating each protocol stack from others. Virtualization is the key technique that provides concurrent protocol stack capability to the Future Internet elements. In this paper, we evaluate the performance of three widespread virtualization tools, Xen, VMware, and OpenVZ, considering their use for router virtualization. We conduct experiments with benchmarking tools to measure the overhead introduced by virtualization in terms of memory, processor, network, and disk performance of virtual routers running on commodity hardware. We also evaluate the effects of the increasing number of virtual machines on Xen network virtualization mechanism. Our results show that Xen best fits virtual router requirements. Moreover, Xen fairly shares the network access among virtual routers, but needs further enhancement when multiple virtual machines simultaneously forward traffic.
ANALYZING THE DISCOURSE OF GEOGEBRA COLLABORATIONS

This is a position paper presenting a perspective on fundamental assumptions about doing, teaching and learning mathematics in the presence of computer and communicative technologies. Doing, teaching and learning mathematics are activities that centrally involve discourse. Computer and communication technologies can facilitate collaborative interactions around mathematical topics. This can make the processes of doing, teaching and learning mathematics visible to researchers in the traces of small-group interaction. Analysis of the discourse can reveal processes of mathematical group cognition. We argue for a view of mathematics as discourse and for a specific set of complementary approaches to analyzing collaborative math discourse.
Inappropriate use of inhaled short acting beta-agonists and its association with patient health status

ABSTRACT Background: Despite the widespread distribution of guidelines on the proper use of inhaled asthma medication, the overuse of short acting bronchodilators (SABs) persists. This study aims to examine how inhaled asthma medications are used in the US and to examine whether inappropriate use of inhaled SABs is associated with poor patient health. Research design and methods: The study design was a retrospective analysis of the Medical Expenditure Panel Survey (MEPS) for asthmatic patients 5 years or older who had used SAB medication during the period from 1996 through 2000. Use of SAB medication was defined as inappropriate when a patient inhaled more than 225 defined daily doses (DDDs) of SABs but less than 45.625 DDDs of corticosteroids per year. Health status was evaluated using survey respondents’ perceptions on a 5‐point Likert scale. Five functional limitations (activities of daily living, instrumental activities of daily living, walking, social function, and cognitive function) were rated on a dichotomous scale. Results: A total of 2386 asthmatic patients were identified as having used a SAB in the period 1996 through 2000. Of these, 272 (11.4%) used excessive doses of SABs, and of this group of excessive users, 151 (55.5%) underused corticosteroids. Compared to appropriate users of SAB medication, inappropriate users had lower perceptions of their overall health (adjusted mean: 3.21 vs. 2.94, p < 0.05) and mental health (adjusted mean: 2.39 vs. 2.13, p < 0.05). They were also at an increased risk of limitations in walking (relative risk [RR]: 1.76, 95% confidence interval [CI]:1.15–2.71) and in cognitive function (RR: 2.32, 95% CI: 1.37–3.93). Conclusion: Despite the national guidelines concerning the proper use of inhaled asthma medication, over-reliance on SAB medication and under-use of corticosteroids persists in the US. Those not using asthma medication according to the guidelines had poor perceptions of their health and were subject to an increased risk of limitations in walking and cognitive function.
Impact of the clients' position on performance of VoD systems based on collocated APs

This paper investigates the impact of clients' position in scalable wireless VoD systems, based on collocated access points. In particular, it evaluates the use of several transmission modes provided by the 802.11a standard, aiming to service different area sizes, using the CINAPS (Cluster of Inexpensive Access Points) system, which was extended with a novel distance-aware association control heuristic. Overall, our simulated results showed that the clients' position influences only when the blockage rate of requests given by the other system variables is up to the uncovered area coefficient. Moreover, they suggest that an adaptive approach of transmission mode choice could achieve a slightly better average blockage rate but significantly far from the ideal values.Este artigo investiga o impacto da posição dos clientes no desempenho de sistemas de VoD sem fio escal´veis, baseados em pontos de acesso co-localizados. Em particular, é avaliado o uso de v´rios modos de transmissão do padrão 802.11a, visando atender ´reas de diferentes tamanhos, utilizando como base o sistema CINAPS (Cluster of Inexpensive Access Points), estendido com uma nova heurĩstica de controle de associação distance-aware. Os resultados mostram que o posicionamento dos clientes influencia apenas quando a taxa de bloqueio determinada pelas demais vari´veis do sistema é inferior ao coeficiente de ´rea descoberta. Além disso, eles sugerem que uma abordagem adaptativa de escolha de modo de transmissão poderia melhorar levemente a taxa de bloqueio média mas ainda distante dos valores ideais.
Prohormone processing in the trans-Golgi network: endoproteolytic cleavage of prosomatostatin and formation of nascent secretory vesicles in permeabilized cells

Many peptide hormones are synthesized as larger precursors which undergo endoproteolytic cleavage at paired basic residues to generate a bioactive molecule. Morphological evidence from several laboratories has implicated either the TGN or immature secretory granules as the site of prohormone cleavage. To identify the site where prohormone cleavage is initiated, we have used retrovirally infected rat anterior pituitary GH3 cells which express high levels of prosomatostatin (proSRIF) (Stoller, T. J., and D. Shields. J. Cell Biol. 1988. 107:2087- 2095). By incubating these cells at 20 degrees C, a temperature that prevents exit from the Golgi apparatus, proSRIF accumulated quantitatively in the TGN and no proteolytic processing was evident; processing resumed upon shifting the cells back to 37 degrees C. After the 20 degrees C block, the cells were mechanically permeabilized and pro-SRIF processing determined. Cleavage of proSRIF to the mature hormone was approximately 35-50% efficient, required incubation at 37 degrees C and ATP hydrolysis, but was independent of GTP or cytosol. The in vitro ATP-dependent proSRIF processing was inhibited by inclusion of chloroquine, a weak base, CCCP, a protonophore, or by preincubating the permeabilized cells with low concentrations of N- ethylmaleimide, an inhibitor of vacuolar-type ATP-dependent proton pumps. These data suggest that: (a) proSRIF cleavage is initiated in the TGN, and (b) this reaction requires an acidic pH which is facilitated by a Golgi-associated vacuolar-type ATPase. A characteristic feature of polypeptide hormone-producing cells is their ability to store the mature hormone in dense core secretory granules. To investigate the mechanism of protein sorting to secretory granules, the budding of nascent secretory vesicles from the TGN was determined. No vesicle formation occurred at 20 degrees C; in contrast, at 37 degrees C, the budding of secretory vesicles was approximately 40% efficient and was dependent on ATP, GTP, and cytosolic factors. Vesicle formation was inhibited by GTP gamma S suggesting a role for GTP- binding proteins in this process. Vesicle budding was dependent on cytosolic factors that were tightly membrane associated and could be removed only by treating the permeabilized cells with high salt. After high salt treatment, vesicle formation was dependent on added cytosol or the dialyzed salt extract. The formation of nascent secretory vesicles contrasts with prosomatostatin processing which required only ATP for efficient cleavage. Our results demonstrate that prohormone cleavage which is initiated in the TGN, precedes vesicle formation and that processing can be uncoupled from the generation of nascent secretory vesicles.
Comparison of model evaluation methods to develop a comprehensive watershed simulation model.

Comprehensive environmental models such as the Soil and Water Assessment Tool (SWAT) are becoming an integral part of decision making processes for effective planning and management of natural resources. Before their use as decision making aid, however, models must be properly evaluated to improve their prediction accuracy and reduce the likelihood of making decisions that could lead to undesirable policy outcomes. Model evaluation refers to practices such as quality analysis of input data, sensitivity analysis, calibration and verification, and uncertainty analysis. Many methodologies have been developed for model evaluations over the years. One of the major limitations of the existing model evaluation methods, in particular model calibration methods, is their computational inefficiency, especially when used to calibrate comprehensive watershed simulation models. It may take weeks to months of CPU time, depending on the problem size, to successfully calibrate a comprehensive watershed simulation model on a standard PC. In this study, two sensitivity analysis methods and four calibration methods are used to evaluate SWAT to improve its streamflow prediction accuracy for the Morro Bay watershed located on the central coast of California. Parameter sensitivity analysis was performed using step-wise-regression analysis and the one-factor-at-a time screening method. Calibration was performed using PEST, Genetic Algorithms, the Shuffled Complex Evolution, and the Dynamically Dimensioned Search using observed data from multiple sites in the watershed. The model evaluation methods are compared in terms of their computational efficiency as well as effectiveness to determine “accurate” results. The developed SWAT model can be used to evaluate effectiveness of the Best Management Practices installed in the Morro Bay watershed, and to also prioritize sites where BMPs may be implemented in the future to further improve ecological integrity of the Morro Bay Estuary, which is one of the most important wetlands in California as it supports wide variety of habitats including numerous sensitive and endangered plant and animal species.
Association of interleukin-1beta (IL1B) polymorphisms with Graves' ophthalmopathy in Taiwan Chinese patients.

PURPOSE To evaluate whether variations in the IL1B gene could be associated with Graves' ophthalmopathy (GO) in patients with Graves' disease (GD). METHOD This case-control study included 471 Taiwan Chinese patients with GD (200 with GO and 271 without GO) and 160 healthy volunteers. Eight single-nucleotide polymorphisms (SNPs) in IL1B were genotyped with an allele-specific extension and ligation assay. RESULTS In the IL1B SNPs examined, the C allele of rs1143634 was associated with GD, whereas the T/T genotype of the SNPs rs1143634 and rs16944 were less associated with the disease. The A/A genotype of the SNPs rs3917368 and rs1143643, which had the strongest interaction, may increase the risk of GO (P = 0.024 and P = 0.017, respectively). Several GD susceptibility and insusceptibility IL1B haplotypes have been identified, and the Ht4-GCGCCTCC haplotype, composed of eight SNPs and associated with low circulating IL1β levels, may be protective against the development of GO (P = 0.025). Moreover, that the GO-susceptible genotype was associated with lower plasma IL1β concentrations implies that the origin of GO may go beyond the IL1B polymorphism-associated elevation of circulating IL1β. CONCLUSIONS The data for IL1B polymorphisms and the association of GD and GO with plasma IL1β levels show that IL1B polymorphisms may be associated with the development of GD and GO.
An Autoethnographic Account of Knowledge Creation: Seeing and Feeling Knowledge Creation in Project Teams

An autoethnographic study was used to explore the combination capability of a project team that facilitates knowledge creation. Both emotional and analytical approaches contributed to the ability to ‘see’ knowledge creation. An emotional ‘ahha’ was associated with acknowledgement the team created something new. This ‘ahha’ occurred when an individual team member(s) had done some independent ‘percolation’ work and introduced this work as a boundary object. Team members had to authorize the individual to introduce the stimulus and the individual presenting the object had to be willing to see their ideas ‘torn apart’ in the process of achieving joint understanding and subsequently knowledge creation. In this process of joint sense-making our data shows that it is important for ideas to be visually captured in a shared space and for each member to demonstrate care of and about the ideas of others.
Comparison of ultrasound imaging in transverse median and parasagittal oblique planes for thoracic epidurals: A pilot study

Background and Aims: The use of ultrasound (US) scanning to assess the depth of epidural space to prevent neurological complications is established in current practice. In this study, we hypothesised that pre-puncture US scanning for estimating the depth of epidural space for thoracic epidurals is comparable between transverse median (TM) and paramedian sagittal oblique (PSO) planes. Methods: We performed pre-puncture US scanning in 32 patients, posted for open abdominal surgeries. The imaging was done to detect the depth of epidural space from skin (ultrasound depth [UD]) and needle insertion point, in parasagittal oblique plane in PSO group and transverse median plane in TM group. Subsequently, epidural space was localised through the predetermined insertion point by 'loss of resistance' technique and needle depth (ND) to the epidural space was marked. Correlation between the UD and actual ND was calculated and concordance correlation coefficient (CCC) was used to determine the degree of agreement between UD and ND in both the planes. Results: The primary outcome, i.e., the comparison between UD and ND, done using Pearson correlation coefficient, was 0.99 in both PSO and TM groups, and the CCC was 0.93 (95% confidence interval [95% CI]: 0.81–0.97) and 0.90 (95% CI: 0.74–0.96) in PSO and TM groups respectively, which shows a strong positive association between UD and ND in both groups. Conclusion: The use of pre-puncture US scanning in both PSO and TM planes for estimating the depth of epidural space at the level of mid- and lower-thoracic spine is comparable.
Computational differences between whispered and non-whispered speech

Whispering is a common type of speech which is not often studied in speech technology. Perceptual and physiological studies show us that whispered speech is subtly different from phonated speech, and is surprisingly able to carry a tremendous amount of information. In this dissertation we consider the question: What makes whispering a good form of communication? We examine the differences between normal phonated speech and whispered speech, and gauge the effectiveness of state-of-the-art speech recognition algorithms at recognizing whisper. Our perceptual experiments add to the literature on the intelligibility of whispered speech. Comparisons with ASR results yield interesting insights into the differences between the two systems. A method for building speech recognizers for whispered speech using limited whispered speech data is proposed and evaluated. Our approach effectively performs speaker-adaptation for whispered speech acoustic models without needing whispered speech from the target speaker. Results show improvement over the standard speaker-independent models. Our work opens up additional avenues for research, which are outlined in the conclusions.
Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract

Linking taxonomic identity and functional potential at the population-level is important for the study of mixed microbial communities and is greatly facilitated by the availability of microbial reference genomes. While the culture-independent recovery of population-level genomes from environmental samples using the binning of metagenomic data has expanded available reference genome catalogs, several microbial lineages remain underrepresented. Here, we present two reference-independent approaches for the identification, recovery, and refinement of hitherto undescribed population-level genomes. The first approach is aimed at genome recovery of varied taxa and involves multi-sample automated binning using CANOPY CLUSTERING complemented by visualization and human-augmented binning using VIZBIN post hoc. The second approach is particularly well-suited for the study of specific taxa and employs VIZBIN de novo. Using these approaches, we reconstructed a total of six population-level genomes of distinct and divergent representatives of the Alphaproteobacteria class, the Mollicutes class, the Clostridiales order, and the Melainabacteria class from human gastrointestinal tract-derived metagenomic data. Our results demonstrate that, while automated binning approaches provide great potential for large-scale studies of mixed microbial communities, these approaches should be complemented with informative visualizations because expert-driven inspection and refinements are critical for the recovery of high-quality population-level genomes.
Input-output modeling and control of the departure process of congested airports

A simple queueing model of busy air-port departure operations is proposed. This model is calibrated and validated using available runway configuration and traffic data. The model is then used to evaluate preliminary control schemes aimed at alleviating departure traffic congestion on the airport surface. The potential impact of these control strategies on direct operating costs, environmental costs and overall delay is quantified and discussed.
Multi-scale segmentation for remote sensing imagery based on minimum heterogeneity rule

Image segmentation is an essential step toward higher level image processing in remote sensing. However, the traditional image segmentation approaches based on pixels spectral characteristics and single-scale image information extraction methods have obvious flaws in this respect. Currently, multi-scale image segmentation is seen as a promising alternative of traditional segmentation method and is one of the most useful approaches in object oriented classification of remotely sensed images. In this paper, we present a multi-scale segmentation method based on Minimum Heterogeneity Rule (MHR) for merging objects. Segmentation results show that this method can easily adapt its scale parameter to different scale image analysis tasks and any chosen scale object-extraction of interest.