Miracle-dz/UniFAR-FTUs huggingface dataset:
Prognostic Gene Expression Signature for Squamous Cell Carcinoma of Lung

Purpose: This study aimed to identify and validate a gene expression signature for squamous cell carcinoma of the lung (SQCC). Experimental Design: A published microarray dataset from 129 SQCC patients was used as a training set to identify the minimal gene set prognostic signature. This was selected using the MAximizing R Square Algorithm (MARSA), a novel heuristic signature optimization procedure based on goodness-of-fit (R square). The signature was tested internally by leave-one-out-cross-validation (LOOCV), and then externally in three independent public lung cancer microarray datasets: two datasets of non–small cell lung cancer (NSCLC) and one of adenocarcinoma (ADC) only. Quantitative-PCR (qPCR) was used to validate the signature in a fourth independent SQCC cohort. Results: A 12-gene signature that passed the internal LOOCV validation was identified. The signature was independently prognostic for SQCC in two NSCLC datasets (total n = 223) but not in ADC. The lack of prognostic significance in ADC was confirmed in the Director's Challenge ADC dataset (n = 442). The prognostic significance of the signature was validated further by qPCR in another independent cohort containing 62 SQCC samples (hazard ratio, 3.76; 95% confidence interval, 1.10-12.87; P = 0.035). Conclusions: We identified a novel 12-gene prognostic signature specific for SQCC and showed the effectiveness of MARSA to identify prognostic gene expression signatures. Clin Cancer Res; 16(20); 5038–47. ©2010 AACR.
Manhood constructions among engaged African American male collegians: influences, experiences, and contexts

The manhood constructions and collegiate experiences of twenty-four engaged African American men enrolled across twelve, four-year colleges were explored. The purpose of this study was to inform colleges about the ways in which these men construct their manhood. The manifestations of these constructions in African American college men’s behavior, enrollment, and campus engagement were also investigated. The participants, who represented a range of college engagement, were enrolled in colleges that are situated across the nineteen southern and border states of the United States of America. The institutional selection matrix was further disaggregated according to predominant population (HBCU, HWI) and institutional funding type (public, private). A qualitative research approach was used to forward this study. Specifically, a combination of grounded theory, phenomenological, and case study methodologies examined the nexus between African American manhood and collegiate experiences. The combined research methods were applied to data gleaned from face-to-face interviews that lasted over two hours. Six trustworthiness techniques support the following emergent themes of manhood constructions and collegiate experiences: (1) self-expectations (2) relationships and responsibilities to family (3) worldviews and life philosophies (4) double-consciousness (5) institutional recognition (6) constructing faculty/student relationships (7) mentoring and supporting (8) bridging campus and community. Respondents reported differences in the ways in which they were treated and engaged in historically black and white institutions, also reinforcing various manhood constructs. Emerging divergent perspectives informed a grouping of these men into the following manhood typologies: (1) sexualizer (2) transgressor (3) misogynist and (4) self-actualizer.
The social context of video game play: Relationships with the player experience and wellbeing

This thesis examines the relationships between different social contexts of video game play, the player experience and wellbeing. In doing so it challenges the notion that video game play is socially isolating and shows that there are potential benefits to all contexts of play, including solitary play. Four studies utilizing different methodologies (survey, interview, experiment) collectively demonstrate how different social contexts of play provide distinct opportunities to maintain or enhance wellbeing.
Digital circuit placement in FPGA based on efficient particle swarm optimization techniques

Field programmable gate array (FPGA) is a widely used programmable integrated circuit (IC) for fast realization of digital circuits in all electronic systems. Its reconfigurability has made this mode of digital circuit synthesis more popular among the system designers. But unlike other ICs it provides a restricted hardware structure for circuit implementation and hence the computer aided design (CAD) software is also constrained. The placement being a very vital step in the design process needs to be performed optimally for high performance circuits. In these work novel techniques for placement based on constricted particle swarm optimization (PSO), adaptive PSO and time varying inertia weight (TVIW) PSO are proposed. The results of simulation reveal a competitive performance of the circuits implemented. The technique proposed here also offer faster convergence to a placement solution. The performance of a single BCD counter circuit is studied in details by using the different PSO algorithms. The netlist generated from the Xilinx design tool is used for placement and optimization results are reported here.
Manipulations of zinc in the spinal cord, by intrathecal injection of zinc chloride, disodium-calcium-EDTA, or dipicolinic acid, alter nociceptive activity in mice.

Zinc is concentrated in the dorsal horn of the spinal cord and has been proposed to alter excitability of primary afferent C-fibers, structures believed to be important in nociceptive transmission. Based on the inhibitory effect of zinc on the activity of various other neurotransmitters that play a role in nociception, we tested the hypothesis that zinc modulates pain transmission. To test this, we examined the effect of exogenous zinc, administered intrathecally (i.t.), on nociception in the mouse. We also assessed the impact of decreased concentrations of endogenously occurring zinc in the extracellular fluid brought about by an i.t. injection of either ethylenediaminetetraacetic acid disodium-calcium salt (Ca++EDTA), a calcium-saturated, membrane-impermeable chelator of divalent cations, or of dipicolinic acid, a zinc chelator. Injection of zinc produced a dose-related antinociceptive effect, optimal at 90 min in the writhing assay, but had no effect on tail-flick response latencies. In contrast, injection of either Ca++EDTA or dipicolinic acid produced a dose-related hyperalgesia in the tail-flick assay at 90 min after injection. Responses induced in the writhing assay were unaffected by Ca++EDTA. Although zinc had no effect on thermal nociception, the hyperalgesic effect of Ca++EDTA was antagonized by coadministration of Ca++EDTA with zinc. Similarly, the antinociceptive effect of zinc on writhing responses was attenuated when coadministered with Ca++EDTA. Zinc also inhibited primary afferent C-fiber activity because 10 ng of zinc i.t. inhibited the behavioral response induced by injection i.t. of 1 nmol of capsaicin. Neither zinc nor Ca++EDTA altered writhing or tail-flick latencies, respectively, when injected intracerebroventricularly. These findings support the hypothesis that endogenous zinc, localized in the dorsal horn of the spinal cord, plays a role in the regulation of pain.
Inhaled antibiotics for stable non-cystic fibrosis bronchiectasis: a systematic review

We conducted a meta-analysis of randomised trials to evaluate the efficacy and safety of inhaled antibiotics in patients with stable non-cystic fibrosis (CF) bronchiectasis. We searched the Cochrane Airways Group Register of Trials from inception until March 2014. 12 trials with 1264 adult patients were included, of which five were unpublished studies. Eight trials on 590 patients contributed data to the meta-analysis. Amikacin, aztreonam, ciprofloxacin, gentamicin, colistin or tobramycin were used for 4 weeks to 12 months. Inhaled antibiotics were more effective than placebo or symptomatic treatment in reducing sputum bacterial load (five trials; weighted mean difference −2.65 log10 CFU·g−1, 95% CI -4.38– -0.92 log10 CFU·g−1), eradicating the bacteria from sputum (six trials; risk ratio 4.2, 95% CI 1.66–10.64) and reducing the risk of acute exacerbations (five trials; risk ratio 0.72, 95% CI 0.55–0.94). Bronchospasm occurred in 10% of patients treated with inhaled antibiotics compared with 2.3% in the control group (seven trials; risk ratio 2.96, 95% CI 1.30–6.73), but the two groups had the same withdrawal rate due to adverse events (12.2%). Inhaled antibiotics may provide an effective suppressive antibiotic therapy with an acceptable safety profile in adult patients with stable non-CF bronchiectasis and chronic bronchial infection. Inhaled antibiotics are effective with an acceptable safety profile in adults with stable non-CF bronchiectasis http://ow.ly/wxsGg
The tidal streams of disrupting subhaloes in cosmological dark matter haloes

We present a detailed analysis of the properties of tidally stripped material from disrupting substructure haloes or subhaloes in a sample of high-resolution cosmological N-body host haloes ranging from galaxy- to cluster-mass scales. We focus on devising methods to recover the infall mass and infall eccentricity of subhaloes from the properties of their tidally stripped material (i.e. tidal streams). Our analysis reveals that there is a relation between the scatter of stream particles about the best-fitting debris plane and the infall mass of the progenitor subhalo. This allows us to reconstruct the infall mass from the spread of its tidal debris in space. We also find that the spread in radial velocities of the debris material (as measured by an observer located at the centre of the host) correlates with the infall eccentricity of the subhalo, which allows us to reconstruct its orbital parameters. We devise an automated method to identify the leading and trailing arms that can, in principle at least, be applied to observations of stellar streams from satellite galaxies. This method is based on the energy distribution of material in the tidal stream. Using this method, we show that the masses associated with the leading and trailing arms differ. While our analysis indicates that tidal streams can be used to recover certain properties of their progenitor subhaloes (and consequently satellites), we do not find strong correlations between host halo properties and stream properties. This likely reflects the complicated relationship between the stream and the host, which in a cosmological context is characterized by a complex mass accretion history, an asymmetric mass distribution and the abundance of substructure. Finally, we confirm that the so-called ‘backsplash’ subhalo population is present not only in galaxy cluster haloes but also in galaxy haloes. The orbits of backsplash subhaloes brought them inside the virial radius of their host at some earlier time, but they now reside in its outskirts at the present-day, beyond the virial radius. Both backsplash and bound subhaloes experience similar mass loss, but the contribution of the backsplash subhaloes to the overall tidal debris field is negligible.
Opinion digger: an unsupervised opinion miner from unstructured product reviews

Mining customer reviews (opinion mining) has emerged as an interesting new research direction. Most of the reviewing websites such as Epinions.com provide some additional information on top of the review text and overall rating, including a set of predefined aspects and their ratings, and a rating guideline which shows the intended interpretation of the numerical ratings. However, the existing methods have ignored this additional information. We claim that using this information, which is freely available, along with the review text can effectively improve the accuracy of opinion mining. We propose an unsupervised method, called Opinion Digger, which extracts important aspects of a product and determines the overall consumer's satisfaction for each, by estimating a rating in the range from 1 to 5. We demonstrate the improved effectiveness of our methods on a real life dataset that we crawled from Epinions.com.
Unsure What the Future Will Bring? You May Overindulge: Uncertainty Increases the Appeal of Wants over Shoulds

This paper examines the effect of uncertainty about the future on whether individuals select want options (e.g., junk foods, lowbrow films) or instead exert self-control and select should options (e.g., healthy foods, highbrow films). Consistent with the ego-depletion literature, which suggests that self-control resembles an exhaustible muscle, coping with uncertainty about what the future may bring reduces self-control resources and increases individuals’ tendency to favor want options over should options. These results persist when real uncertainty is induced, when the salience of naturally-arising uncertainty is heightened and when individuals are able to make choices contingent upon the outcomes of uncertain events. Overall, this work suggests that reducing uncertainty in a decision maker’s environment may have important spillover effects, leading to less impulsive choices.
Could heart rate variability be associated with weight­ bearing asymmetries in cerebrovascular diseases?

Introduction: Cerebrovascular diseases result in sensory­motor deficits disturbing postural control that is observed by weight­bearing asymmetries commonly named as hemiparesis. Besides hemiparetic impairments, first observed after stroke, many studies have pointed cardiac failure and risk of sudden death as the main factors responsible for death of stroke survivors. This case series characterized weight­bearing asymmetries and heart rate variability, and describes relationships between these parameters in hemiparesis. Case Series: Five Brazilian male subjects with chronic hemiparesis acquired after ischemic stroke in the middle cerebral artery were selected to study heart rate variability obtained by Root Mean Square Successive Difference. Also, weight­bearing asymmetries were measured by Symmetry Ratio calculated by weight­bearing recorded between each foot. The Symmetry Ratio was 1.1±0.43 for all cases presenting a symmetry case (n = 1) and different types of asymmetries cases (n = 4) during upright position. Root Mean Square Successive Difference was 9.9±3.4, presenting strong and significant (p < 0.05) positive correlation with age and a strong but not significant (0.05 < p < 0.10) negative correlation with hemiparesis chronicity. A strong but not significant negative correlation was observed between the Root Mean Square Successive Difference and the Symmetry Rate values. Conclusion: A characteristic pattern of heart rate variability for patients with cerebrovascular disease was observed in these cases, associated significantly with age. Still, this behavior seems to be influenced by chronicity and by different types of asymmetries in the distribution of weight bearing that could be investigated in more appropriate clinical research designs.
Joint Design of Multiple Non-Regenerative MIMO Relaying Matrices With Power Constraints

This paper investigates the joint design of multiple non-regenerative multiple-input multiple-output (MIMO) relaying matrices, with the purpose of minimizing the mean square error (MSE) between the transmitted signals from the source and the received signals at the destination. Two types of constraints on the transmit power of the relays are considered separately: 1) a weighted sum power constraint, and 2) per-relay power constraints. As opposed to using general-purpose interior-point methods, we exploit the inherent structure of the problems to develop more efficient algorithms. Under the weighted sum power constraint, the optimal solution is expressed as a function of a Lagrangian parameter. By introducing a complex scaling factor at the destination, we derive a closed-form expression for this parameter, thereby avoiding the need to solve an implicit nonlinear equation numerically. Under the per-relay power constraints, the optimal solution is the same as that under the weighted sum power constraint if particular weights are chosen. We then propose an iterative power balancing algorithm to compute these weights. In addition, under both types of constraints, we investigate the joint design of a MIMO equalizer at the destination and the relaying matrices, using block coordinate descent or steepest descent. The bit-error rate (BER) simulation results demonstrate that all the proposed designs, under either type of constraints, with or without the equalizer, perform much better than previous methods.
Synaptotagmin-2 Is a Reliable Marker for Parvalbumin Positive Inhibitory Boutons in the Mouse Visual Cortex

Background Inhibitory innervation by parvalbumin (PV) expressing interneurons has been implicated in the onset of the sensitive period of visual plasticity. Immunohistochemical analysis of the development and plasticity of these inhibitory inputs is difficult because PV expression is low in young animals and strongly influenced by neuronal activity. Moreover, the synaptic boutons that PV neurons form onto each other cannot be distinguished from the innervated cell bodies by immunostaining for this protein because it is present throughout the cells. These problems call for the availability of a synaptic, activity-independent marker for PV+ inhibitory boutons that is expressed before sensitive period onset. We investigated whether synaptotagmin-2 (Syt2) fulfills these properties in the visual cortex. Syt2 is a synaptic vesicle protein involved in fast Ca2+ dependent neurotransmitter release. Its mRNA expression follows a pattern similar to that of PV throughout the brain and is present in 30–40% of hippocampal PV expressing basket cells. Up to now, no quantitative analyses of Syt2 expression in the visual cortex have been carried out. Methodology/Principal Findings We used immunohistochemistry to analyze colocalization of Syt2 with multiple interneuron markers including vesicular GABA transporter VGAT, calbindin, calretinin, somatostatin and PV in the primary visual cortex of mice during development and after dark-rearing. Conclusions/Significance We show that in the adult visual cortex Syt2 is only found in inhibitory, VGAT positive boutons. Practically all Syt2 positive boutons also contain PV and vice versa. During development, Syt2 expression can be detected in synaptic boutons prior to PV and in contrast to PV expression, Syt2 is not down-regulated by dark-rearing. These properties of Syt2 make it an excellent marker for analyzing the development and plasticity of perisomatic inhibitory innervations onto both excitatory and inhibitory neurons in the visual cortex.
Automatically Determining Compatibility of Evolving Services

A major advantage of Service-Oriented Architectures (SOA) is composition and coordination of loosely coupled services. Because the development lifecycles of services and clients are decoupled, multiple service versions have to be maintained to continue supporting older clients. Typically versions are managed within the SOA by updating service descriptions using conventions on version numbers and namespaces. In all cases, the compatibility among services description must be evaluated, which can be hard, error-prone and costly if performed manually, particularly for complex descriptions. In this paper, we describe a method to automatically determine when two service descriptions are backward compatible. We then describe a case study to illustrate how we leveraged version compatibility information in a SOA environment and present initial performance overheads of doing so. By automatically exploring compatibility information, a) service developers can assess the impact of proposed changes; b) proper versioning requirements can be put in client implementations guaranteeing that incompatibilities will not occur during run-time; and c) messages exchanged in the SOA can be validated to ensure that only expected messages or compatible ones are exchanged.
A metadata-based approach to personalized mobile resource sharing

Along with the rapid development of mobile devices, resources become more and more dispersive, which poses a new challenge on how to support resource sharing and exchanging mechanism among the mobile users. To address such issues, we describe our approach on building up mobile information resource exchange system (MIRES). The design of MIRES makes use of a central server to enable instant resources sharing. Metadata is introduced in our system to help record the characteristics of the shared resources. It is shown in this paper that by proper management of the metadata, mobile resource exchanging can be turned into a highly efficient and user-friendly procedure.
Differences in the state of differentiation of THP‐1 cells induced by phorbol ester and 1,25‐dihydroxyvitamin D3

Human THP‐1 leukemia cells differentiate along the monocytic lineage following exposure to phorbol‐12‐myristate‐13‐acetate (PMA) or 1,25‐dihydroxyvitamin D3 (VD3). In the monocytic cell line THP‐1, PMA treatment resulted in a more differentiated phenotype than VD3, according to adherence, loss of proliferation, phagocytosis of latex beads, and expression of GD11b and CD14. Both differentiating substances induced similar effects in the release of superoxide anions (O2 ‐). VD3‐differentiated cells did not release prostaglandin E2 (PGE2), in contrast to PMA‐differentiated cells, and in PMA‐differentiated cells phospholipase A2 (PLA2) activity and expression was increased. Lipopolysaccharide (LPS)‐stimulated tumor necrosis factor‐α (TNF‐α) release was higher in PMA‐treated cells. PMA‐ but not VD3‐differentiation resulted in a translocation of protein kinase C (PKC) isoenzymes to membrane fractions. Both differentiating agents up‐regulated the expression of PKC isoenzymes. Whereas VD3 elevated mainly the expression of PKC‐β, PMA caused a strong increase in PKC‐δ and a weak increase in PKC‐α, PKC‐, and PKC‐ expression. These results indicate that phorbol ester and the active metabolite of vitamin D induce different signal pathways, which might result in different achievement of differentiation.
Automatic Musical Instrument Recognition Preface

First and foremost, I wish to express my gratitude to Mr Anssi Klapuri, who was the initiator of this research and provided guidance, advice and support of all kinds for this work. I wish to thank Professor Jaakko Astola for his advice and comments. I am grateful for the staff at the Audio Research Group and Insitute of Signal Processing for providing a stimulating working atmosphere. During the recent years, many persons have become as much friends as colleagues. I want to thank Mr Jari Yli-Hietanen and Professor Pauli Kuosmanen for providing the opportunity to start working at the Audio Research Group even before I had learned the basics of DSP. I wish to thank my parents for understanding the long periods I have been working and not having time to visit them. Finally, I wish to thank Katri for her love and support.