Miracle-dz/UniFAR-FTUs huggingface dataset:
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing

Motivation: One of the most deadly cancer diagnoses is the carcinoma of unknown primary origin. Without the knowledge of the site of origin, treatment regimens are limited in their specificity and result in high mortality rates. Though supervised classification methods have been developed to predict the site of origin based on gene expression data, they require large numbers of previously classified tumors for training, in part because they do not account for sample heterogeneity, which limits their application to well-studied cancers. Results: We present ISOLATE, a new statistical method that simultaneously predicts the primary site of origin of cancers and addresses sample heterogeneity, while taking advantage of new high-throughput sequencing technology that promises to bring higher accuracy and reproducibility to gene expression profiling experiments. ISOLATE makes predictions de novo, without having seen any training expression profiles of cancers with identified origin. Compared with previous methods, ISOLATE is able to predict the primary site of origin, de-convolve and remove the effect of sample heterogeneity and identify differentially expressed genes with higher accuracy, across both synthetic and clinical datasets. Methods such as ISOLATE are invaluable tools for clinicians faced with carcinomas of unknown primary origin. Availability: ISOLATE is available for download at: http://morrislab.med.utoronto.ca/software Contact: gerald.quon@utoronto.ca; quaid.morris@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.
A predictive control solution for driveline oscillations damping

This paper deals with the problem of damping driveline oscillations, which is crucial to improving driveability and passenger comfort. Recently, this problem has received an increased interest due to the introduction in several production vehicles of the dual-clutch powershift automatic transmission with dry clutches. This type of transmission improves fuel economy, but it results in a challenging control problem, due to driveline oscillations. These oscillations, also called shuffles, occur during gear-shift, while traversing backlash or when tip-in and tip-out maneuvers are performed. The first contribution of this paper is the derivation of an accurate piecewise affine drivetrain model with three inertias. The second contribution is concerned with the design of a horizon-1 predictive controller based on flexible Lyapunov functions. Several simulations based on realistic scenarios show that the proposed control scheme can handle both the performance and physical constraints, and the strict limitations on the computational complexity.
Hypothesis and Theory Article Hypothesis: Cryptochromes and Brown Fat Are Essential for Adaptation and Affect Mood and Mood-related Behaviors

Solar radiation and ambient temperature have acted as selective physical forces among populations and thereby guided species distributions in the globe. Circadian clocks are universal and evolve when subjected to selection, and their properties contribute to variations in fitness within specific environments. Concerning humans, as compared to the remaining , the " evening owls " have a greater deviation from the 24 h cycle, are under a greater pressure to circadian desynchrony and more prone to a cluster of health hazards with the increased mortality. Because of their position in the hierarchy and repressive actions, cryp-tochromes are the key components of the feedback loops on which circadian clocks are built. Based on the evidence a new hypothesis is formulated in which brown adipocytes with their cryptochromes are responsive to a broad range of physical stimuli from the habitat and through their activity ensure adaptation of the individual. The over-activated brown adipose tissue with deficient cryptochromes might induce disrupted thermoregula-tion and circadian desynchrony, and thereby contribute to lowered mood and pronounced depressive behaviors.
Proteomic and Functional Analyses Reveal MAPK1 Regulates Milk Protein Synthesis

L-Lysine (L-Lys) is an essential amino acid that plays fundamental roles in protein synthesis. Many nuclear phosphorylated proteins such as Stat5 and mTOR regulate milk protein synthesis. However, the details of milk protein synthesis control at the transcript and translational levels are not well known. In this current study, a two-dimensional gel electrophoresis (2-DE)/MS-based proteomic technology was used to identify phosphoproteins responsible for milk protein synthesis in dairy cow mammary epithelial cells (DCMECs). The effect of L-Lys on DCMECs was analyzed by CASY technology and reversed phase high performance liquid chromatography (RP-HPLC). The results showed that cell proliferation ability and β-casein expression were enhanced in DCMECs treated with L-Lys. By phosphoproteomics analysis, six proteins, including MAPK1, were identified up-expressed in DCMECs treated with 1.2 mM L-Lys for 24 h, and were verified by quantitative real-time PCR (qRT-PCR) and western blot. Overexpression and siRNA inhibition of MAPK1 experiments showed that MAPK1 upregulated milk protein synthesis through Stat5 and mTOR pathway. These findings that MAPK1 involves in regulation of milk synthesis shed new insights for understanding the mechanisms of milk protein synthesis.
Comparing Fisheye and Full-Zoom Techniques for Navigation of Hierarchically Clustered Networks

Many information systems are represented as twodimensional networks of links and nodes. Because these networks tend to be large and quite complex, people often prefer to view part or all of the network at varying levels of detail. Hierarchical clustering provides a framework for viewing the network at different levels of detail by superimposing a hierarchy on top of it. Nodes are grouped into clusters, and clusters are themselves placed into other clusters. Users can then navigate these clusters until an appropriate level of detail is reached. This paper describes an experiment comparing two methods for viewing hierarchically clustered networks. Traditional full-zoom techniques provide details of only the current level of the hierarchy. In contrast, fisheye views (generated by the “variable zoom” algorithm described in this paper) provide information about higher levels as well. Subjects using both viewing methods were given problem solving tasks requiring them to navigate a network, in this case a simulated telephone system, and to reroute links in it. Results suggest that the greater context provided by fisheye views significantly improved a user’s performance of the tasks. They were quicker to complete their task, and they made fewer unnecessary navigational steps through the hierarchy. This validation of fisheye views is important for designers of interfaces to complicated monitoring systems, such as control rooms for supervisory control and data acquisition systems, where efficient human performance is often critical.
Long‐term scintillation observations of five pulsars at 1540 MHz

From 2001 January to 2002 June, we monitored PSRs B0329+54, B0823+26, B1929+10, B2020+28 and B2021+51 using the Nanshan 25-m radio telescope of the Urumqi Observatory to study their diffractive interstellar scintillation (DISS). The average interval between observations was about 9 d and the observation duration ranged between 2 and 6 h depending on the pulsar. Wide variations in the DISS parameters were observed over the 18-month data span. Despite this, the average scintillation velocities are in excellent agreement with the proper motion velocities. The average two-dimensional autocorrelation function for PSR B0329+54 is well described by a thin-screen Kolmogorov model, at least along the time and frequency axes. Observed modulation indices for the DISS time-scale and bandwidth and the pulsar flux density are greater than values predicted for a Kolmogorov spectrum of electron density fluctuations. Correlated variations over times that are long compared to the nominal refractive scintillation time are observed, suggesting that larger scale density fluctuations are important. For these pulsars, the scintillation bandwidth as a function of frequency has a power-law index (similar to 3.6) much less than that expected for Kolmogorov turbulence (similar to 4.4). Sloping fringes are commonly observed in the dynamic spectra, especially for PSR B0329+54. The detected range of fringe slopes are limited by our observing resolution. Our observations are sensitive to larger-scale fringes and hence smaller refractive angles, corresponding to the central part of the scattering disc.
Legal Obstacles in Shari'ah Corporate Governance of Islamic Financial Institutions in Malaysia

This paper was sent to be published in the Journal of King Abdulaziz University for Islamic Economics. Also, it was presented in different title(1) in the Asia-Pacific Business Research Conference in Malysia, February 2011. The researchers highlighted the significant role of the Shari’ah corporate governance in the effectiveness and stability of Islamic financial Institutions in Malaysia. They outline the roles of corporate governance (in both conventional and Islamic corporation) through which it can be directed, administered and controlled. However, they argue that Shari’ah cooperate governance has different perspective and methodology. The Shari’ah cooperate governance primary is based on the tenet of Islam as the primary law and then on other positive laws, such as laws regulating the interest of the directors and the stakeholders. They described the structure of shari’ah corporate governance in Malaysia in order to emphasize and underscore some legal obstacles in the Shari’ah corporate governance and suggest some practical solutions to reform absence in the law.
Social impact measurement in social entrepreneurial organizations

We live in a world where accountability (and thus the measurement of inputs and outputs) has become an institution due to the increasing demands of stakeholders, and where what gets measured gets valued. The purpose of the hereby paper is to address change and the impact of change upon society. Whether the change is caused by social innovation, social entrepreneurial organizations or social responsibility actions, it translates into a modification in the status quo of the society. Thus, the discourse of our paper revolves around social value, social problem, social entrepreneurship and it connects them to the social impact they generate by presenting the methods used to measure this impact and their basic assumptions, who applies the methods and what are their effects. The methods for measuring the social impact found in the literature lean on quantifying everything in money and they also tend to overlook the importance of the psychological impact a company might have over its target clients. Furthermore, social impact is measured from the perspective of the companies and of the investors, neglecting the customers who are the target of the impact. Also findings reveal that there is no proper legislation to regulate this field and no specialized control bodies to oversee the activity of the third sector regarding social impact. We propose three principles underpinning our own social impact measurement model (sustainability, added value and scalability (spillovers).
> Replace This Line with Your Paper Identification Number (double-click Here to Edit) <

1  Abstract—We experimentally demonstrate a novel optical physical-layer network coding (PNC) scheme over time-division multiplexing (TDM) passive optical network (PON). Full-duplex error-free communications between optical network units (ONUs) at 2.5 Gb/s are shown for all-optical virtual private network (VPN) applications. Compared to the conventional half-duplex communications setup , our scheme can increase the capacity by 100% with power penalty smaller than 3 dB. Synchronization of ONUs is not required for the proposed VPN scheme.
Mesenchymal Remodeling during Palatal Shelf Elevation Revealed by Extracellular Matrix and F-Actin Expression Patterns

During formation of the secondary palate in mammalian embryos, two vertically oriented palatal shelves rapidly elevate into a horizontal position above the tongue, meet at the midline, and fuse to form a single entity. Previous observations suggested that elevation occurs by a simple 90° rotation of the palatal shelves. More recent findings showed that the presumptive midline epithelial cells are not located at the tips of palatal shelves before elevation, but mostly toward their medial/lingual part. This implied extensive tissue remodeling during shelf elevation. Nevertheless, it is still not known how the shelf mesenchyme reorganizes during this process, and what mechanism drives it. To address this question, we mapped the distinct and restricted expression domains of certain extracellular matrix components within the developing palatal shelves. This procedure allowed to monitor movements of entire mesenchymal regions relative to each other during shelf elevation. Consistent with previous notions, our results confirm a flipping movement of the palatal shelves anteriorly, whereas extensive mesenchymal reorganization is observed more posteriorly. There, the entire lingual portion of the vertical shelves moves close to the midline after elevation, whereas the mesenchyme at the original tip of the shelves ends up ventrolaterally. Moreover, we observed that the mesenchymal cells of elevating palatal shelves substantially align their actin cytoskeleton, their extracellular matrix, and their nuclei in a ventral to medial direction. This indicates that, like in other morphogenetic processes, actin-dependent cell contractility is a major driving force for mesenchymal tissue remodeling during palatogenesis.
Mobile Device Based Personalized Equalizer for Improving Hearing Capability of Human Voices in Particular for Elderly Persons

Mobile device based personalized equalizer for improving the hearing capability of human voices in particular for elderly persons are proposed. Through experiments, it is found that the proposed equalizer does work well for improving hearing capability by 2 to 55 % of voice Recognition success ratio. According to the investigation of the frequency component analysis and formant detections, most of the voice sounds have the formant frequencies for the first to third frequencies within the range of 3445 Hz. Therefore, a nonlinear equalizing multiplier is better to enhance the frequency components for the first to third formants in particular. The experimental results with the voice above input experiments show that a good Percent Correct Recognition: PCR is required for 0 to more than 8000 Hz of frequency components. Also, 8162 Hz cut off frequency would be better for both noise suppressions and keeping a good PCR
A local neural network approach to detect actions of human body

Local events in a video sequence can be captured by local space-time features, these features helps to extract motion descriptors which capture motion sequence in the video. In the proposed work, the actions of human body is detected by detecting interest points called STIP, in each frame of the video and for each interest point, a motion descriptors called HOG are extracted around each interest point. The dictionary of Bag of Visual Features (BoVF) is created by using HOG descriptors from which normalized histograms are constructed for each action video to train and test the classifier. Feed forward neural Network (FFNN) with Backpropagation classifier is used to classify the actions of human body.
Interferometric observations of the Mira star o Ceti with the VLTI/VINCI instrument in the near-infrared

We present K-band commissioning observations of the Mira star prototype o Cet obtained at the ESO Very Large Telescope Interferometer (VLTI) with the VINCI instrument and two siderostats. The observations were carried out between 2001 October and December, in 2002 January and December, and in 2003 January. Rosseland angular radii are derived from the measured visibilities by fitting theoretical visibility functions obtained from center-to-limb intensity variations (CLVs) of Mira star models. Using the derived Rosseland angular radii and the spectral energy distributions (SEDs) reconstructed from available photometric and spectrophotometric data, we find effective temperatures ranging from T_eff=3192 +/- 200 K at phase 0.13 to 2918 +/- 183 K at phase 0.26. Comparison of these Rosseland radii, effective temperatures, and the shape of the observed visibility functions with model predictions suggests that o Cet is a fundamental mode pulsator. Furthermore, we investigated the variation of visibility function and diameter with phase. The Rosseland angular diameter of o Cet increased from 28.9 +/- 0.3 mas (corresponding to a Rosseland radius of 332 +/- 38 Rsun for a distance of D=107 +/- 12 pc) at phase 0.13 to 34.9 +/- 0.4 mas (402 +/- 46 Rsun) at phase 0.4. The observational error of the Rosseland linear radius almost entirely results from the error of the parallax, since the error of the angular diameter is only approximately 1%.
Hubungan dinamik antara inflasi kemeruapan inflasi dan pertumbuhan output: Bukti empirikal di Malaysia

Purpose – The main purpose of this study was to analyse the dynamic relationship between inflation, inflation uncertainty and output growth in Malaysia for the period 1980 to 2004. Design/Methodology/Approach – The EGARCH model was used to estimate the infl ation uncertainty and the Vector Autoregressive (VAR) technique, which includes the Granger causality test, was employed in the investigation of dynamic relationships between these variables. Findings – There was significant evidence on the existence of one way positive relationships between inflation and inflation uncertainty in Malaysia. Further investigation showed that a high inflation level tends to have a negative effect on output growth. However, there was no significant evidence on the relationship between inflation uncertainty and output growth. Originality/Value – This paper explores the time varying volatility of inflation in Malaysia and investigates the dynamic relationship between inflation, inflation uncertainty, and output growth.
Effect of Periodontal Treatment on Glycemic Control of Diabetic Patients

OBJECTIVE There is growing evidence that periodontitis may affect general health. This study was assigned to explore the robustness of observations that periodontal therapy leads to the improvement of glycemic control in diabetic patients. RESEARCH DESIGN AND METHODS A literature search (until March 2009) was carried out using two databases (MEDLINE and the Cochrane Library) with language restriction to English. Selection of publications was based on 1) original investigations, 2) controlled periodontal intervention studies where the diabetic control group received no periodontal treatment, and 3) study duration of ≥3 months. RESULTS Screening of the initial 639 identified studies and reference checking resulted in five suitable articles. A total of 371 patients were included in this analysis with periodontitis as predictor and the actual absolute change in A1C (ΔA1C) as the outcome. The duration of follow-up was 3–9 months. All studies described a research population of type 2 diabetic patients in whom glycemic control improved after periodontal therapy compared with the control group (range ΔA1C: Δ−1.17 up to Δ−0.05%). The studies in a meta-analysis demonstrated a weighted mean difference of ΔA1C before and after therapy of −0.40% (95% CI −0.77 to −0.04%, P = 0.03) favoring periodontal intervention in type 2 diabetic patients. Nevertheless, this improvement in %A1C must be interpreted with care due to limited robustness as evidenced by heterogeneity among studies (59.5%, P = 0.04). CONCLUSIONS The present meta-analysis suggests that periodontal treatment leads to an improvement of glycemic control in type 2 diabetic patients for at least 3 months.
An oral selective M3 cholinergic receptor antagonist in COPD

Cholinergic antagonists have been used since the early 1900s as bronchodilators for chronic obstructive pulmonary disease (COPD). The present study investigated whether an oral muscarinic M3-selective anticholinergic agent (OrM3) would provide an improved therapeutic advantage compared with an inhaled anticholinergic agent in patients with COPD. A 6-week, multicentre, randomised, placebo- and active-controlled, parallel-group study was performed at 56 sites in the USA. In total, 412 male and female patients (aged 35–86 yrs) with a clinical history consistent with COPD were randomised to receive OrM3 0.5, 2, 3 or 4 mg orally once daily, ipratropium bromide 36 μg by inhalation four times daily or placebo. OrM3 demonstrated a significant dose-related improvement in serial forced expiratory volume in one second and a trend for dose-related improvement in patient-reported symptoms compared with placebo. However, at a dose that provided efficacy less than that of ipratropium, the incidence of dose-related, mechanism-based side-effects for OrM3 exceeded those observed for ipratropium. In patients with chronic obstructive pulmonary disease, the oral M3-selective agent did not offer a therapeutic advantage over inhaled ipratropium. These results do not support the hypothesis that high selectivity for muscarinic M3 receptors over airway neuronal M2 receptors will represent a more effective therapy than current inhaled anticholinergics in obstructive airway disease.
"Screening" of universal Casimir terms by Coulomb gases in a fully-finite two-dimensional geometry

Abstract. This paper is a continuation of a previous one [Jancovici B and Šamaj L, 2004 JSTAT P08006] dealing with classical Casimir phenomena in semi-infinite wall geometries. In that paper, using microscopic Coulomb systems, the long-ranged Casimir force due to thermal fluctuations in conducting walls was shown to be screened by the presence of an electrolyte between the walls into some residual short-ranged force. Here, we aim to extend the study of the screening (cancellation) phenomena to universal Casimir terms appearing in the large-size expansions of the grand potentials for microscopic Coulomb systems confined in fully-finite 2D geometries, in particular the disc geometry. Two cases are solved exactly: the high-temperature (Debye-Hückel) limit and the Thirring free-fermion point. Similarities and fundamental differences between fully-finite and semi-finite geometries are pointed out.
Measuring dynamic effects of display advertising in the absence of user tracking information

In this paper, we develop a time series approach, based on Dynamic Linear Models (DLM), to estimate the impact of ad impressions on the daily number of commercial actions when no user tracking is possible. The proposed method uses aggregate data, and hence it is simple to implement without expensive infrastructure. Specifically, we model the impact of daily number of ad impressions on daily number of commercial actions. We incorporate persistence of campaign effects on actions assuming a decay factor. We relax the assumption of a linear impact of ads on actions using the logtransformation. We also account for outliers with long-tailed distributions fitted and estimated automatically without a pre-defined threshold. This is applied to observational data post-campaign and does not require an experimental set-up. We apply the method to data from the Advertising.com ad network on 2,885 campaigns for 1,251 products during six months, to calibrate and perform model selection. We set up a randomized experiment for two campaigns where user tracking is feasible. We find that the output of the proposed method is consistent with the results of A/B testing with similar confidence intervals. Finally, we validate our model with a synthetic public data set, PROMO, and identify 84% of effective campaigns correctly.