Miracle-dz/UniFAR-FTUs huggingface dataset:
Sulfur Metabolism Pathways in Sulfobacillus acidophilus TPY, A Gram-Positive Moderate Thermoacidophile from a Hydrothermal Vent

Sulfobacillus acidophilus TPY, isolated from a hydrothermal vent in the Pacific Ocean, is a moderately thermoacidophilic Gram-positive bacterium that can oxidize ferrous iron or sulfur compounds to obtain energy. In this study, comparative transcriptomic analyses of S. acidophilus TPY were performed under different redox conditions. Based on these results, pathways involved in sulfur metabolism were proposed. Additional evidence was obtained by analyzing mRNA abundance of selected genes involved in the sulfur metabolism of sulfur oxygenase reductase (SOR)-overexpressed S. acidophilus TPY recombinant under different redox conditions. Comparative transcriptomic analyses of S. acidophilus TPY cultured in the presence of ferrous sulfate (FeSO4) or elemental sulfur (S0) were employed to detect differentially transcribed genes and operons involved in sulfur metabolism. The mRNA abundances of genes involved in sulfur metabolism decreased in cultures containing elemental sulfur, as opposed to cultures in which FeSO4 was present where an increase in the expression of sulfur metabolism genes, particularly sulfite reductase (SiR) involved in the dissimilatory sulfate reduction, was observed. SOR, whose mRNA abundance increased in S0 culture, may play an important role in the initial sulfur oxidation. In order to confirm the pathways, SOR overexpression in S. acidophilus TPY and subsequent mRNA abundance analysis of sulfur metabolism-related genes were carried out. Conjugation-based transformation of pTrc99A derived plasmid from heterotrophic E. coli to facultative autotrophic S. acidophilus TPY was developed in this study. Transconjugation between E. coli and S. acidophilus was performed on modified solid 2:2 medium at pH 4.8 and 37°C for 72 h. The SOR-overexpressed recombinant S. acidophilus TPY-SOR had a SO42−-accumulation increase, higher oxidation/ reduction potentials (ORPs) and lower pH compared with the wild type strain in the late growth stage of S0 culture condition. The transcript level of sor gene in the recombinant strain increased in both S0 and FeSO4 culture conditions, which influenced the transcription of other genes in the proposed sulfur metabolism pathways. Overall, these results expand our understanding of sulfur metabolism within the Sulfobacillus genus and provide a successful gene-manipulation method.
Comparison of Two Algorithms to Reduce Muscular Movement Artifacts in EEG Data

Muscular movement artifacts constitute a major problem in studies involving electroencephalography (EEG) measurements. EEG measurements are used in a variety of different fields like diagnosing epilepsy and other brain related diseases or in biofeedback for athletes. A major drawback is that EEG is susceptible to artifacts of neck muscles due to the low signal amplitude of the electrical activity of the brain. Hence, recording an artifact-free EEG signal during movement or physical exercise is not feasible at the moment. These additional artifacts can be recorded using electromyography (EMG). Various computational methods for the reduction of muscle artifacts in EEG data exist like the ICA algorithm and the AMICA algorithm. However, there exists no objective measure to compare different algorithms concerning their performance on EEG data. We defined a test protocol with specific neck and body movements and measured EEG and EMG simultaneously to compare the ICA algorithm InfoMax and the AMICA algorithm. A novel objective measure enabled to compare both algorithms according to their performance. Results showed that the AMICA algorithm outperformed the ICA algorithm. In further research, we will continue using our novel objective measure to test the performance of other artifact removal algorithms.
The Animate-Inanimate Distinction in Infancy: Developing Sensitivity to Constraints on Human Actions

Infants aged 4 and 6 months were presented with events in which a person acted so as to set another person, or an inanimate object, in motion. In one condition, the actor spoke to the person (natural) or inanimate object (unnatural); in the other condition, the actor grasped and manipulated the person (unnatural) or object (natural). Six-month-old infants looked reliably longer at the natural actions than at the unnatural actions. A follow-up experiment revealed that their preference depended on the naturalness of the human actions themselves, not on the features or motions of the person or object that was acted upon. Looking preferences at 4 months were equivocal, consistent with the thesis that sensitivity to the natural actions develops over the first 6 months of age. We discuss these findings in relation to the development of social understanding, social gaze, and visual exploration.
Web Spam Detection Using Link-Based Ant Colony Optimization

Web spam is one of the most important problems which degrade quality and efficiency of web search engines. In this paper, we present a novel link-based ant colony optimization learning algorithm for spam host detection. The host graph is first constructed by aggregating pages' hyperlink structure. Following the Trust Rank assumption, ants start walking from a normal host and randomly follow host links with a probability distribution. Then, the classification rules are appropriately generated according to common features of normal hosts sequentially discovered by ants. From the experiments with the WEBSPAM-UK2006 dataset, the proposed learning model provides much accuracy in classifying both normal and spam hosts than several baselines, including a state of the art C4.5. Moreover, we also provide an analysis in parameter tuning for better results.
Enlarged Peroxisomes Are Present in Oleic Acid–grown Yarrowia lipolytica Overexpressing the PEX16 Gene Encoding an Intraperoxisomal Peripheral Membrane Peroxin

Pex mutants of the yeast Yarrowia lipolytica are defective in peroxisome assembly. The mutant strain pex16-1 lacks morphologically recognizable peroxisomes. Most peroxisomal proteins are mislocalized to a subcellular fraction enriched for cytosol in pex16 strains, but a subset of peroxisomal proteins is localized at, or near, wild-type levels to a fraction typically enriched for peroxisomes. The PEX16 gene was isolated by functional complementation of the pex16-1 strain and encodes a protein, Pex16p, of 391 amino acids (44,479 D). Pex16p has no known homologues. Pex16p is a peripheral protein located at the matrix face of the peroxisomal membrane. Substitution of the carboxylterminal tripeptide Ser-Thr-Leu, which is similar to the consensus sequence of peroxisomal targeting signal 1, does not affect targeting of Pex16p to peroxisomes. Pex16p is synthesized in wild-type cells grown in glucose-containing media, and its levels are modestly increased by growth of cells in oleic acid–containing medium. Overexpression of the PEX16 gene in oleic acid– grown Y. lipolytica leads to the appearance of a small number of enlarged peroxisomes, which contain the normal complement of peroxisomal proteins at levels approaching those of wild-type peroxisomes.
Social sensing model and analysis for event detection and estimation with twitter

Twitter is an Online Social Networking (OSN) service, in which users instantly share short messages with their followers. Active use of Twitter during major events turns it into a participatory sensor network, where each user acts as a sensor by sharing its observation through Twitter, and the observations may be utilized for estimation of various events. There are several studies on event detection in Twitter, which are primarily based on semantic analysis of collected tweets. To the best of our knowledge, there exists no analytical study on the accuracy of event detection and estimation of event signal with Twitter using observations collected. In this study, a communication theoretical model is developed for tweet propagation, and the accuracy of the estimated signal is explored with mean square error analysis. The results indicate that, in addition to user observations and network conditions, the accuracy of the estimation is also affected by user behavior patterns.
Mini-max feedback control as a computational theory of sensorimotor control in the presence of structural uncertainty

We propose a mini-max feedback control (MMFC) model as a robust approach to human motor control under conditions of uncertain dynamics, such as structural uncertainty. The MMFC model is an expansion of the optimal feedback control (OFC) model. According to this scheme, motor commands are generated to minimize the maximal cost, based on an assumption of worst-case uncertainty, characterized by familiarity with novel dynamics. We simulated linear dynamic systems with different types of force fields–stable and unstable dynamics–and compared the performance of MMFC to that of OFC. MMFC delivered better performance than OFC in terms of stability and the achievement of tasks. Moreover, the gain in positional feedback with the MMFC model in the unstable dynamics was tuned to the direction of instability. It is assumed that the shape modulations of the gain in positional feedback in unstable dynamics played the same role as that played by end-point stiffness observed in human studies. Accordingly, we suggest that MMFC is a plausible model that predicts motor behavior under conditions of uncertain dynamics.
An analysis of the socio-technical gap in social networking sites

This chapter views social networking sites as supporting social capital and the advantages which derive from it, namely emotional support, information exchange, and a capacity for concerted action. Social capital is subdivided in three types: relational, cognitive, and structural. The authors derive a number of social needs from these types of social capital and discuss how the social networking sites considered in this study support or fail to support these needs with technical features. The contributions of this chapter include the dimensionalisation of the socio-technical gap in social networking systems and a discussion of elements that reside in the gap.
Deceased-donor kidney transplantation: improvement in long-term survival.

BACKGROUND Despite marked improvement in short-term renal allograft survival rates (GSR) in recent years, improvement in long-term GSR remained elusive. METHODS We analysed the kidney transplant experience at our centre accrued over four decades to evaluate how short-term and long-term GSR had changed and to identify risk factors affecting graft survival. The study included 1476 adult recipients of a deceased-donor kidney transplant who were transplanted between 1963 and 2006 and who had received one of five distinct immunosuppressive protocols. RESULTS Five-year actual GSR steadily improved over the years as immunosuppressive therapy evolved (22-86%, P < 0.001) in spite of an increasing trend in the transplantation of higher-risk donor-recipient pairings. For those whose grafts functioned for the first year, subsequent 4-year GSR (5-year conditional GSR) also improved significantly (63-92%, P < 0.001). Acute rejection and delayed graft function (DGF) were the most significant risk factors for actual graft survival, while acute rejection was the only significant risk factor for conditional GSR. Use of kidneys from expanded-criteria donors (ECD) was not a risk factor, compared to the use of standard-criteria donor kidneys for either 5-year actual or conditional GSR. There was an impressive decline in the incidence of acute rejection events (77.4-5.8%, P < 0.001). While the DGF rate had decreased, it still remained high (68.7-38.5%, P < 0.001). CONCLUSIONS We found a significant improvement in both short-term and long-term GSR of deceased-donor kidney transplants over the last four decades. These improvements are most likely related to the decreased incidence of acute rejection episodes. Minimizing acute rejection events and preventing DGF could result in further improvement in the GSR. Our experience in the judicious use of ECD kidneys suggests that this source of kidneys could be expanded further.
Modeling of OFDM based System with Optical Components for BW Reconfiguration

In this paper, an optical network model is presented where ISI is reduced considerably. The input to the network is optical orthogonal frequency division multiplexed (OOFDM) signal. Optimization of all optical components in the network is done to reconfigure the bandwidth, to minimize the bit error rate (BER). While modeling, the advantages and disadvantages of OFDM system are considered to ensure minimum distortion. The transmitter in the proposed model consists of 16Laser sources with frequency ranging from 193.035 THz to 193.785 THz; the channel spacing is set to 50 GHz. The optical signal is launched onto a 200 km fiber link. Along the fiber link, after 100 km, a 4channel optical add drop multiplexer (OADM) is used to select and to add channels. The dropped channels are detected by the receiver with an appropriate electrical filtering. Erbium doped fiber amplifier (EDFA) is being used in the link. All three types of compensation techniques such as pre post and symmetric using dispersion compensation fiber (DCF) is employed to enhance the network performance.
The C. elegans homologs of nephrocystin-1 and nephrocystin-4 are cilia transition zone proteins involved in chemosensory perception

Nephronophthisis (NPH) is a cystic kidney disorder that causes end-stage renal failure in children. Five nephrocystin (nephrocystin-1 to nephrocystin-5) genes, whose function is disrupted in NPH patients, have been identified and data indicate they form a complex at cell junctions and focal adhesions. More recently, the nephrocystin proteins have also been identified in cilia, as have multiple other cystic kidney disease related proteins. Significant insights into this cilia and cystic kidney disease connection have come from analyses in simpler eukaryotic organisms such as Caenorhabditis elegans. In this regard, we became interested in the C. elegans homologs of nephrocystin-1 (nph-1) and nephrocystin-4 (nph-4) from a database screen to identify genes coordinately regulated by the ciliogenic transcription factor DAF-19. Here we show that expression of nph-1 and nph-4 is DAF-19 dependent, that their expression is restricted to ciliated sensory neurons, and that both NPH-1 and NPH-4 concentrate at the transition zones at the base of the cilia, but are not found in the cilium axoneme. In addition, NPH-4 is required for the localization of NPH-1 to this domain. Interestingly, nph-1 or nph-4 mutants have no obvious cilia assembly defects; however, they do have abnormalities in cilia-mediated sensory functions as evidenced by abnormal chemotaxis and lifespan regulation. Our data suggest that rather than having a ciliogenic role, the NPH proteins play an important function as part of the sensory or signaling machinery of this organelle. These findings suggest that the defects in human NPH patients may not be the result of aberrant ciliogenesis but abnormal cilia-sensory functions.
Stability of switched linear discrete-time descriptor systems: A commutation condition

In this paper, we study stability of switched linear discrete-time descriptor systems. Under the assumption that all subsystems are stable and there is no impulse occurring at the switching instants, we establish a new pairwise commutation condition under which the switched system is stable. We also show that when the proposed commutation condition holds, there exists a common quadratic Lyapunov function (CQLΓ) for the subsystems. These results are natural and important extensions to the existing results for switched systems in the state space representation.
A new class of ranking functions for DCG-like evaluation metrics using conditional probability models October 29 , 2010

In the context oflearning to rankfor information retrieval [15], we study a general class of “DCG-like” ranking loss functions which include DCG [13] and approximate ERR [6] as specific cases. We then study the Bayes optimal ranking function for this class, which is a function of the conditional distribution of graded document relevance levels. Our main contribution is a novel class of ranking functions building upon the Bayes optimality result. Specifically, our ranking function class uses the conditional expectation of a function of the document features with respect to an ostensible multiclass logistic regression model. We empirically evaluate our proposals with respect to NDCG on seven standard learning to rank datasets [16] and three different surrogate evaluation metrics. Results show our proposed ranking functions improve accuracy across datasets and surrogate evaluation metrics, achieving 10.6% improvement on average and as high as 25% in the best case.
Blood leucocyte telomere DNA content predicts vascular telomere DNA content in humans with and without vascular disease.

AIMS Previous studies have suggested that reduced telomere length in circulating leucocytes in humans is associated with premature vascular disease and by implication, accelerated vascular ageing. Importantly, a link between telomere length in circulating leucocytes and the blood vessel wall has never been established. We, thus, investigated the relationship between vascular wall and circulating leucocyte telomere length in humans with and without overt vascular disease. METHODS AND RESULTS Aortic biopsies and paired blood leucocytes were obtained from 20 patients with asymptomatic abdominal aortic aneurysms (AAAs), undergoing elective open repair, and 12 morphologically normal aortas from a group of cadaveric organ donors of similar mean age. Telomere content was compared by quantitative PCR and expressed as telomere:genomic DNA ratio. The telomere:genomic DNA content was significantly reduced in wall biopsies of AAA vs. normal aorta, and this difference remained after adjusting for age and gender. There were strong correlations between leucocyte and vascular telomere content when the AAA and control groups were analysed either separately or grouped irrespective of the presence of vascular disease (r = 0.62, P < 0.001). CONCLUSION The findings demonstrate that leucocyte DNA content is predictive of vascular telomere content and is an accurate surrogate for human vascular age.
Evolutionary algorithm based offline/online path planner for UAV navigation

An evolutionary algorithm based framework, a combination of modified breeder genetic algorithms incorporating characteristics of classic genetic algorithms, is utilized to design an offline/online path planner for unmanned aerial vehicles (UAVs) autonomous navigation. The path planner calculates a curved path line with desired characteristics in a three-dimensional (3-D) rough terrain environment, represented using B-spline curves, with the coordinates of its control points being the evolutionary algorithm artificial chromosome genes. Given a 3-D rough environment and assuming flight envelope restrictions, two problems are solved: i) UAV navigation using an offline planner in a known environment, and, ii) UAV navigation using an online planner in a completely unknown environment. The offline planner produces a single B-Spline curve that connects the starting and target points with a predefined initial direction. The online planner, based on the offline one, is given on-board radar readings which gradually produces a smooth 3-D trajectory aiming at reaching a predetermined target in an unknown environment; the produced trajectory consists of smaller B-spline curves smoothly connected with each other. Both planners have been tested under different scenarios, and they have been proven effective in guiding an UAV to its final destination, providing near-optimal curved paths quickly and efficiently.
New Adaptive Class of Filter Operators for Salt & Pepper Impulse corrupted Images

The paper proposes two new adaptive filtering algorithms for the restoration of salt & pepper impulse corrupted digital images; the Iterative Adaptive Switching Median Filter(IASMF) and the Adaptive Threshold based Median Filter(ATMF). The IASMF works steadily on the corrupted pixels of the noisy image degraded at all noise ratio whereas ATMF works on highly corrupted environments to give acceptable outputs of better visual quality. Experimental results show that the proposed adaptive filters give enhanced subjectiveness and objectiveness in restoring images than many other impulse filters whose outputs show black and white patches with blurred effects at higher noise levels. They are also computationally efficient than many other reputed impulse filters, the ATMF a slightly complex due to its pixel-wise comparison with the valid median. Keywords— Adaptive filter, image restoration, impulse detection, impulse noise, median filter, pseudo median.
Breastfeeding and sexuality immediately post partum.

OBJECTIVE To examine the relationship between breastfeeding and resumption of vaginal intercourse; to determine the association between these behaviours and age, parity, marital status, mode of delivery, and contraceptive use; and to identify factors associated with resumption of intercourse among Canadian women in the early postpartum period. DESIGN Prospective survey. SETTING Eleven obstetricians' offices in three Ontario communities between August and December 2002. PARTICIPANTS Women attending their first postpartum visit. MAIN OUTCOME MEASURES Resumption of vaginal intercourse. RESULTS Of 316 respondents, 181 (57.3%) were currently breastfeeding, and 167 (52.8%) had not yet resumed vaginal intercourse. Mean age of the mothers was 28.7 +/- 5.3 years; mean age of their babies was 6.5 +/- 1.1 weeks. This was a first child for 50.3% and a second child for 32.6%. Most women (72.8%) were married; another 19.3% were in common-law relationships. Married women were more likely to breastfeed (P = .001), as were those with higher parity (P = .008). Multivariable logistic regression identified five variables significantly associated with resumption of intercourse by 6 weeks post partum. The two most statistically significant variables were breastfeeding (exclusively or supplementing with bottle) and baby's age in weeks (P < .001 for both). Mode of delivery (vaginal delivery with no tearing, compared with cesarean section or vaginal delivery with tearing) was also a highly significant predictor (P = .003), as was higher parity (P = .003). Older maternal age was weakly associated with resumption of intercourse (P = .049). The 167 women who had not resumed intercourse were asked to indicate their main reasons: 161 responded, citing a total of 215 reasons (54 cited more than one reason). The most common reasons were lack of interest (18.6%), being too tired (16.8%), being afraid of intercourse being painful (16.8%), physician told them not to (15.6%), and thinking they should wait 6 weeks (14.4%). CONCLUSION Breastfeeding women who delay resumption of intercourse during the postpartum period might benefit from open discussion of breastfeeding, sexuality, and contraception immediately post partum.