Miracle-dz/UniFAR-FTUs huggingface dataset:
Overexpression of Ecdysoneless in Pancreatic Cancer and Its Role in Oncogenesis by Regulating Glycolysis

Purpose: To study the expression and function of a novel cell-cycle regulatory protein, human ecdysoneless (Ecd), during pancreatic cancer pathogenesis. Experimental Design: Immunohistochemical expression profiling of Ecd was done in nonneoplastic normal pancreatic tissues and pancreatic ductal adenocarcinoma lesions (from tissue microarray and Rapid Autopsy program) as well as precancerous PanIN lesions and metastatic organs. To analyze the biological significance of Ecd in pancreatic cancer progression, Ecd was stably knocked down in pancreatic cancer cell line followed by in vitro and in vivo functional assays. Results: Normal pancreatic ducts showed very weak to no Ecd expression compared to significant positive expression in pancreatic cancer tissues (mean ± SE composite score: 0.3 ± 0.2 and 3.8 ± 0.2 respectively, P < 0.0001) as well as in PanIN precursor lesions with a progressive increase in Ecd expression with increasing dysplasia (PanIN-1–PanIN-3). Analysis of matched primary tumors and metastases from patients with pancreatic cancer revealed that Ecd is highly expressed in both primary pancreatic tumor and in distant metastatic sites. Furthermore, knockdown of Ecd suppressed cell proliferation in vitro and tumorigenicity of pancreatic cancer cells in mice orthotopic tumors. Microarray study revealed that Ecd regulates expression of glucose transporter GLUT4 in pancreatic cancer cells and was subsequently shown to modulate glucose uptake, lactate production, and ATP generation by pancreatic cancer cells. Finally, knockdown of Ecd also reduced level of pAkt, key signaling molecule known to regulate aerobic glycolysis in cancer cells. Conclusion: Ecd is a novel tumor-promoting factor that is differentially expressed in pancreatic cancer and potentially regulates glucose metabolism within cancer cells. Clin Cancer Res; 18(22); 6188–98. ©2012 AACR.
Case Studies of Low‐Visibility Forecasting in Falling Snow With WRF Model

Accurate low‐visibility forecasts in falling snow are critical to the safety and efficiency of air traffic. The Weather and Research Forecast (WRF) model successfully captured two unusual snowstorms occurred in Urumqi. On this basis, the quality of 15 parameterizations for predicting visibility in snow is evaluated, using both observations and forecasts of the meteorological variables from WRF model. The parameterizations are mainly based on the relations between the extinction efficient (β) or visibility (Vis) and the snowfall rate (S). Comprehensive evaluations show that most of these parameterizations (13 of 15) are skillful as well as having the ability to predict low visibilities to some extent. Among them, the parameterization Vis = 0.62S−0.59 performs the best, followed by the approach of Stoelinga and Warner. It is also found that the visibility forecasts based on the observations always have considerably higher quality than the visibility forecasts from WRF model. The results suggest that more than one parameterization is promising if the WRF model is able to provide accurate predictions of the relevant meteorological variables. Furthermore, the forecast accuracy of low visibilities strongly depends on the accurate predictions of snowfall rate of greater than or equal to 1.0 mm h−1.
An Analysis of the Use of Social Stories in Teaching Social Skills to Children with Autism Spectrum Disorders.

Social stories play a significant part in the teaching skills and behaviors to children with ASD who lack social skills. The purpose of this study is to analyze studies in which social stories were used for teaching social skills to individuals with Autism Spectrum Disorders (ASD). The present study includes a descriptive review and meta-analysis of single-subject studies that met the criteria. In all studies, social validity, maintenance, and generalization data were collected in 56.25%, 50%, and 31.25% of the respective studies. Although most studies showed that social stories were effective in teaching social skills to children with ASD in the descriptive study, in the meta-analytic study, the mean of Percantage of Non-overlapping Data (PND) scores for all studies was 63.43%, with a range of 0% to 100%. Results suggest that social stories should not yet be considered as evidence based practice for teaching social skills to individuals with ASD. However, social stories seem to be a promising practice that warrants future research. Results will be discussed extensively and future directions for research and practice will be addressed.
5A11 antigen is a cell recognition molecule which is involved in neuronal‐glial interactions in avian neural retina

In continuing efforts to identify cell‐surface molecules involved in cell‐cell interactions in the developing avian retina, we identified a monoclonal antibody, the 5A11 antibody, which possessed the ability to interfere with contact‐dependent glial cell maturation in vitro. We sought to determine the molecular and biochemical identity of the glycoprotein recognized by this antibody, and using additional criteria, establish whether the 5All antigen is indeed a cell‐recognition molecule in the developing retina. Immuno‐histochemical analyses demonstrate that in the hatchling chick retina and in live cultures of embryonic retina cells, the 5A11 antigen is predominantly associated with Müller glial cells whereas little is observed on neuronal elements. Microsequencing of the major component isolated by immunoaffinity chromatography identifies the HT7 antigen (Seulberger et al.: EMBO Journal 9:2151–2158, 1990), a unique member of the immunoglobulin super gene family (IGSF), as a homologous if not identical protein to the 5A11 antigen. The HT7 antibody, furthermore, recognizes affinity purified 5A11 antigen, and both the HT7 antibody and additional probes generated against the 5A11 antigen recognize a major polypeptide of 45.5 kDa and a minor band of 69 kDa on Western blots of membrane preparations from neural retina. To verify that the 5A11 antigen mediates cell‐cell recognition events in the developing neural retina, we examined the consequences of adding antibody to monolayer cultures of dissociated embryonic retina cells and to dissociated retina cells in rotation‐mediated suspension culture. Addition of the 5A11 antibody to monolayer cultures results in alteration in the development of the stereotypic arrangement of neurons and glia characterized by a reduction in the number and complexity of neural extensions upon the glial‐derived flat cells. Similarly, addition of antibodies generated against the 5A11 antigen to dissociated cells in rotation cultures significantly reduces retina cell reaggregation as monitored by computer‐assisted image analysis of cell aggregate size. These data and the identification of the 5A11 antigen as a member of the IGSF establish a role for the 5A11 antigen as a novel recognition molecule in the developing neural retina. © 1993 wiley‐Liss, Inc.
Deactivation-controlled epidemic routing in disruption tolerant networks with multiple sinks

To characterize the delivery performance of message dissemination in Disruption/Delay Tolerant Networks, various methods have been proposed. However, existing work shares a common simplification that the pairwise meeting rate between any two mobile nodes is exponentially distributed. In this paper, instead of relying on such assumption, we jointly consider the deactivation-rate over relay nodes and the number of sinks deployed in the network as the primary system parameters. Then, an ODE-based theoretical framework is proposed in a stochastic manner, which enables to describe how these two parameters affect the performance of a message delivery process using controlled epidemic routing. Via extensive experiments, the high accuracy of our analytical framework are verified.
A Cool, Nutrient‐Enriched Eastern Equatorial Pacific During the Mid‐Pleistocene Transition

The emergence of high‐amplitude, low‐frequency glacial‐interglacial cycles during the mid‐Pleistocene climate transition (MPT; 800–1,200 ka) is associated with global cooling. In the eastern equatorial Pacific, sea surface temperatures cooled, and the upwelling‐induced cold tongue expanded significantly during the MPT. Here we use sedimentary records of iron, biogenic silica, and nutrient‐nitrogen consumption to evaluate biogeochemical changes hypothesized to accompany the cold tongue expansion. Our results suggest that the eastern equatorial Pacific of the MPT hosted surface waters with higher nitrate contents and biogenic silica production relative to the last 600 ka. Increased production occurred despite low iron supply. We attribute this to enhanced upwelling and nutrient enrichment of thermocline waters, both likely related to the northward migration of Southern Ocean fronts. The return of these fronts to their southward positions after the MPT may be associated with stronger drawdown of nutrients and, potentially, atmospheric CO2 in the Southern Ocean.
A dynamic probabilistic multimedia retrieval model

We describe the application of a probabilistic multimedia model to video retrieval. From video shots, we compute Gaussian-mixture models that capture correlations in time and space, such as the appearance and disappearance of objects. These models improve the precision of "query by example/s" results in the TRECVID 2003 collection when compared to models that only make use of static visual information. Furthermore, integrated with information from automatic speech recognition (ASR) transcripts, they outperform ASR only results.
Regulation of the Cellular Heat Shock Response in Caenorhabditis elegans by Thermosensory Neurons

Temperature pervasively affects all cellular processes. In response to a rapid increase in temperature, all cells undergo a heat shock response, an ancient and highly conserved program of stress-inducible gene expression, to reestablish cellular homeostasis. In isolated cells, the heat shock response is initiated by the presence of misfolded proteins and therefore thought to be cell-autonomous. In contrast, we show that within the metazoan Caenorhabditis elegans, the heat shock response of somatic cells is not cell-autonomous but rather depends on the thermosensory neuron, AFD, which senses ambient temperature and regulates temperature-dependent behavior. We propose a model whereby this loss of cell autonomy serves to integrate behavioral, metabolic, and stress-related responses to establish an organismal response to environmental change.
Anomaly Detection Using the Dempster-Shafer Method

In this paper, we implement an anomaly detection system using the Dempster-Shafer method. Using two standard benchmark problems we show that by combining multiple signals it is possible to achieve better results than by using a single signal. We further show that by applying this approach to a real-world email dataset the algorithm works for email worm detection. Dempster-Shafer can be a promising method for anomaly detection problems with multiple features (data sources), and two or more classes.
A New Perceptron Algorithm for Sequence Labeling with Non-Local Features

We cannot use non-local features with current major methods of sequence labeling such as CRFs due to concerns about complexity. We propose a new perceptron algorithm that can use non-local features. Our algorithm allows the use of all types of non-local features whose values are determined from the sequence and the labels. The weights of local and non-local features are learned together in the training process with guaranteed convergence. We present experimental results from the CoNLL 2003 named entity recognition (NER) task to demonstrate the performance of the proposed algorithm.
Intrinsic and extrinsic contributions to stochasticity in gene expression

Gene expression is a stochastic, or “noisy,” process. This noise comes about in two ways. The inherent stochasticity of biochemical processes such as transcription and translation generates “intrinsic” noise. In addition, fluctuations in the amounts or states of other cellular components lead indirectly to variation in the expression of a particular gene and thus represent “extrinsic” noise. Here, we show how the total variation in the level of expression of a given gene can be decomposed into its intrinsic and extrinsic components. We demonstrate theoretically that simultaneous measurement of two identical genes per cell enables discrimination of these two types of noise. Analytic expressions for intrinsic noise are given for a model that involves all the major steps in transcription and translation. These expressions give the sensitivity to various parameters, quantify the deviation from Poisson statistics, and provide a way of fitting experiment. Transcription dominates the intrinsic noise when the average number of proteins made per mRNA transcript is greater than ≃2. Below this number, translational effects also become important. Gene replication and cell division, included in the model, cause protein numbers to tend to a limit cycle. We calculate a general form for the extrinsic noise and illustrate it with the particular case of a single fluctuating extrinsic variable—a repressor protein, which acts on the gene of interest. All results are confirmed by stochastic simulation using plausible parameters for Escherichia coli.
Sterol carrier protein 2 gene transfer changes lipid metabolism and enterohepatic sterol circulation in mice.

BACKGROUND & AIMS Sterol carrier protein 2 (SCP-2) enhances sterol cycling and facilitates cholesterol translocation between intracellular organelles and plasma membrane in cultured cells, including hepatocytes. We examined the role of SCP-2 in hepatic cholesterol and lipid trafficking through the sinusoidal and canalicular secretory pathways of the liver in vivo. METHODS Recombinant adenovirus-mediated SCP-2 gene transfer was used to obtain hepatic overexpression of SCP-2 in C57BL/6 mice. RESULTS SCP-2 overexpression in the mouse liver resulted in an 8-fold increase of SCP-2 protein levels and determined various effects on lipid metabolism. It decreased high-density lipoprotein cholesterol and increased low-density lipoprotein (LDL) cholesterol concentrations. The expressions of hepatic LDL receptor, apolipoprotein (apo) A-I, apoB, and apoE were decreased. SCP-2 overexpression also increased hepatic cholesterol concentration, associated with decreased cholesterol neosynthesis. Increased biliary cholesterol and bile acid secretion, bile acid pool size, and intestinal cholesterol absorption were also observed. CONCLUSIONS These results indicate that modulation of SCP-2 expression in the liver determines important modifications on lipoprotein metabolism, hepatic cholesterol synthesis and storage, biliary lipid secretion, bile acid metabolism, and intestinal cholesterol absorption.
Gradient Magnitude Similarity Deviation: A Highly Efficient Perceptual Image Quality Index

It is an important task to faithfully evaluate the perceptual quality of output images in many applications, such as image compression, image restoration, and multimedia streaming. A good image quality assessment (IQA) model should not only deliver high quality prediction accuracy, but also be computationally efficient. The efficiency of IQA metrics is becoming particularly important due to the increasing proliferation of high-volume visual data in high-speed networks. We present a new effective and efficient IQA model, called gradient magnitude similarity deviation (GMSD). The image gradients are sensitive to image distortions, while different local structures in a distorted image suffer different degrees of degradations. This motivates us to explore the use of global variation of gradient based local quality map for overall image quality prediction. We find that the pixel-wise gradient magnitude similarity (GMS) between the reference and distorted images combined with a novel pooling strategy-the standard deviation of the GMS map-can predict accurately perceptual image quality. The resulting GMSD algorithm is much faster than most state-of-the-art IQA methods, and delivers highly competitive prediction accuracy. MATLAB source code of GMSD can be downloaded at http://www4.comp.polyu.edu. hk/~cslzhang/IQA/GMSD/GMSD.htm.
Arithmetic-Based Address Translation for Energy-Efficient Virtual Memory Support in Low-Power, Real-Time Embedded Systems

In this paper, we present an arithmetic-based address translation scheme for low-power and real-time embedded processors with virtual memory support. General-purpose virtual memory support comes with its fundamental disadvantages of excessive power consumption and nondeterministic execution times. These disadvantages have been the main reason for not adopting virtual memory and its associated benefits in embedded systems where energy efficiency and real-time operations are major requirements. To address these issues, we propose a novel scheme for application-driven address translation where most of the virtual address translations, which are traditionally performed as lookups in the translation lookaside buffer (TLB), are replaced with fast and energy efficient arithmetic add operations. To achieve this, a program and system-wide information is used to identify sequences of consecutive virtual page numbers, which are mapped to sequences of consecutive physical page frames. For such pairs of virtual and physical page sequences, only the addition of a constant to the virtual page number is needed to produce the physical page frame. The proposed methodology relies on the combined efforts of compiler, operating system, and hardware architecture to achieve a significant power reduction. As the approach fundamentally eliminates conflicts inherent in the hardware translation table, execution time is not only improved but also made predictable during system design time. The experiments that we have performed on a set of embedded applications show power reductions in the range of 80% to 95% compared to a general-purpose translation lookaside buffer (TLB)
GSVD based multi-user multi-stream MIMO linear precoding with limited feedback

We present a generalized singular value decomposition (GSVD) based multi-user (MU) multi-stream multiple-input multiple-output (MIMO) precoding scheme with limited feedback. Our precoding scheme maximizes the signal to leakage and noise ratio (SLNR), so that it does not require any iterations to obtain precoding matrices. However, in MU-MIMO system, the precoding matrix should be computed at transmit side, because the precoding matrix of a user affects those of other users. Accordingly, full channel state information (CSI) for all users is required at the transmitter, which prevents MU-MIMO precoding implementable. To overcome this problem, an efficient limited feedback algorithm optimized to the GSVD based MU-MIMO precoding is proposed. Here, by extracting the parameters to be utilized in GSVD based precoding from the full CSI, the amount of feedback information is reduced. Furthermore, by analyzing their statistical properties, the parameters are efficiently quantized according to their probability densities. Finally, we develop a modified GSVD based precoding considering the channel quantization errors due to the limited feedback.
Regulation of Complement C3 Expression by the Bile Acid Receptor FXR*

The farnesoid X receptor (FXR; NR1H4) is an intracellular bile acid-sensing transcription factor that plays a critical role in the regulation of synthesis and transport of bile acids as well as lipid metabolism. Although the reciprocal relationship between bile acid and triglyceride levels is well known, the mechanism underlying this link is not clearly defined. In this study, we demonstrate that FXR regulates the expression of at least two secreted factors, complement component C3 and FGF15, the rat ortholog of FGF19, known to influence lipid metabolism. The analysis of the human complement C3 gene reveals the presence of functional FXR response elements in the proximal promoter of C3. Furthermore, rats given a single dose of an FXR agonist exhibit an increase in the plasma concentration of complement C3 protein. These studies demonstrate a mechanism by which FXR, a nuclear receptor with a limited tissue expression pattern, regulates secretion of factors that ultimately can affect lipid metabolism in an endocrine or paracrine manner.
Incremental updates for efficient bidirectional transformations

A bidirectional transformation is a pair of mappings between source and view data objects, one in each direction. When the view is modified, the source is updated accordingly. The key to handling large data objects that are subject to relatively small modifications is to process the updates incrementally. Incrementality has been explored in the semi-structured settings of relational databases and graph transformations; this flexibility in structure makes it relatively easy to divide the data into separate parts that can be transformed and updated independently. The same is not true if the data is to be encoded with more general-purpose algebraic datatypes, with transformations defined as functions: dividing data into well-typed separate parts is tricky, and recursions typically create interdependencies. In this paper, we study transformations that support incremental updates, and devise a constructive process to achieve this incrementality.
Role of FDG-PET scans in staging, response assessment, and follow-up care for non-small cell lung cancer

The integral role of positron-emission tomography (PET) using the glucose analog tracer fluorine-18 fluorodeoxyglucose (FDG) in the staging of non-small cell lung cancer (NSCLC) is well established. Evidence is emerging for the role of PET in response assessment to neoadjuvant therapy, combined-modality therapy, and early detection of recurrence. Here, we review the current literature on these aspects of PET in the management of NSCLC. FDG-PET, particularly integrated 18F-FDG-PET/CT, scans have become a standard test in the staging of local tumor extent, mediastinal lymph node involvement, and distant metastatic disease in NSCLC. 18F-FDG-PET sensitivity is generally superior to computed tomography (CT) scans alone. Local tumor extent and T stage can be more accurately determined with FDG-PET in certain cases, especially in areas of post-obstructive atelectasis or low CT density variation. FDG-PET sensitivity is decreased in tumors <1 cm, at least in part due to respiratory motion. False-negative results can occur in areas of low tumor burden, e.g., small lymph nodes or ground-glass opacities. 18F-FDG-PET-CT nodal staging is more accurate than CT alone, as hilar and mediastinal involvement is often detected first on 18F-FDG-PET scan when CT criteria for malignant involvement are not met. 18F-FDG-PET scans have widely replaced bone scintography for assessing distant metastases, except for the brain, which still warrants dedicated brain imaging. 18F-FDG uptake has also been shown to vary between histologies, with adenocarcinomas generally being less FDG avid than squamous cell carcinomas. 18F-FDG-PET scans are useful to detect recurrences, but are currently not recommended for routine follow-up. Typically, patients are followed with chest CT scans every 3–6 months, using 18F-FDG-PET to evaluate equivocal CT findings. As high 18F-FDG uptake can occur in infectious, inflammatory, and other non-neoplastic conditions, 18F-FDG-PET-positive findings require pathological confirmation in most cases. There is increased interest in the prognostic and predictive role of FDG-PET scans. Studies show that absence of metabolic response to neoadjuvant therapy correlates with poor pathologic response, and a favorable 18F-FDG-PET response appears to be associated with improved survival. Further work is underway to identify subsets of patients that might benefit individualized management based on FDG-PET.