Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing the Clinical Relevance of an Embryonic Stem Cell Phenotype in Lung Adenocarcinoma

Purpose: Cancer cells possess traits reminiscent of those ascribed to normal stem cells. It is unclear whether these phenotypic similarities are the result of a common biological phenotype, such as regulatory pathways. Experimental Design: Lung cancer cell lines with corresponding gene expression data and genes associated with an embryonic stem cell identity were used to develop a signature of embryonic stemness (ES) activity specific to lung adenocarcinoma. Biological characteristics were elucidated as a function of cancer biology/oncogenic pathway dysregulation. The ES signature was applied to three independent early-stage (I-IIIa) lung adenocarcinoma data sets with clinically annotated gene expression data. The relationship between the ES phenotype and cisplatin (current standard of care) sensitivity was evaluated. Results: Pathway analysis identified specific regulatory networks [Ras (P = 0.0005), Myc (P = 0.0224), wound healing (P < 0.0001), chromosomal instability (P < 0.0001), and invasiveness (P < 0.0001)] associated with the ES phenotype. The prognostic relevance of the ES signature, as related to patient survival, was characterized in three cohorts [CALGB 9761 (n = 82; P = 0.0001), National Cancer Institute Director's Challenge Consortium (n = 442; P = 0.0002), and Duke (n = 45; P = 0.06)]. The ES signature was not prognostic in prostate, breast, or ovarian adenocarcinomas. Lung tumors (n = 569) and adenocarcinoma cell lines (n = 31) expressing the ES phenotype were more likely to be resistant to cisplatin (P < 0.0001 and P = 0.006, respectively). Conclusions: Lung adenocarcinomas that share a common gene expression pattern with normal human embryonic stem cells were associated with decreased survival, increased biological complexity, and increased likelihood of resistance to cisplatin. This indicates the aggressiveness of these tumors. (Clin Cancer Res 2009;15(24):7553–61)
Precursors of chondroitin sulfate proteoglycan are segregated within a subcompartment of the chondrocyte endoplasmic reticulum

Immunocytochemical methods were used at the levels of light and electron microscopy to examine the intracellular compartments of chondrocytes involved in extracellular matrix biosynthesis. The results of our studies provide morphological evidence for the compartmentalization of secretory proteins in the ER. Precursors of the large chondroitin sulfate proteoglycan (CSPG), the major proteoglycan species produced by chondrocytes, were present in the Golgi complex. In addition, CSPG precursors were localized in specialized regions of the ER. Link protein, a separate gene product which functions to stabilize extracellular aggregates of CSPG monomers with hyaluronic acid, was segregated similarly. In contrast, type II procollagen, another major secretory molecule produced by chondrocytes, was found homogeneously distributed throughout the ER. The CSPG precursor-containing ER compartment exhibits a variable tubulo-vesicular morphology but is invariably recognized as an electronlucent, smooth membrane-bounded region continuous with typical ribosome-studded elements of the rough ER. The observation that this ER structure does not stain with antibodies against resident ER proteins also suggests that the compartment is a specialized region distinct from the main part of the ER. These results support recent studies that consider the ER as a compartmentalized organelle and are discussed in light of the possible implications for proteoglycan biosynthesis and processing.
Swimming Performance and Physiological Responses to Exhaustive Exercise in Radio-Tagged and Untagged Pacific Lampreys

Abstract Populations of Pacific lamprey Lampetra tridentata have declined in the Columbia River basin. One factor that may have contributed to this reduction in population size is an excessive use of energy by adult lampreys as they negotiate fishways at dams during spawning migrations. To gain an understanding of the performance capacity of Pacific lampreys, we estimated the critical swimming speed (U crit) and documented physiological responses of radio-tagged and untagged adult lampreys exercised to exhaustion. The mean (±SD) U crit of untagged lampreys was 86.2 ± 7.5 cm/s at 15°C, whereas the U crit for radio-tagged lampreys was 81.5 ± 7.0 cm/s, a speed that was significantly lower than that of untagged fish. The physiological responses of tagged and untagged lampreys subjected to exhaustive exercise included decreases in blood pH of 0.3–0.5 units, a 40% decrease in muscle glycogen levels, a 22% increase in hematocrit for untagged fish only, and a 4- to 5-fold increase in muscle and a 40- to 100-fold .
Reservoir Management Using Artificial Neural Networks

The management of the water resources is of crucial importance since it directly affects the design and operation of many water resources structures. Conventional procedures for design and analysis are basically iterative trial-and-error procedures. The methods that are used for the reservoir operation study are especially based on the continuity equation. The storage capacity of the dam, the inflow to the reservoir, the evaporation losses in the reservoir and the demand are the main parameters of the continuity equation. In these methods the aim is to optimize the reservoir volume (that is storage) for abstracting sufficient amount of water from the dam reservoir. At the stage of the planning of the reservoir size this is a very important subject. Here the monthly total inflow of the reservoir is the main data series. It is better to have a data record length as long as possible. Artificial neural networks (ANN) are black box models that are used for forecasting and estimating purposes in so many different areas of the science and engineering. In this research two artificial neural network (ANN) approaches were used for the reservoir management and operation purpose. It is aimed to see that if the artificial neural network (ANN) approaches are applicable and useful for the operation and management of the reservoirs. At first the monthly inflow data of a given reservoir was forecasted for the future. Then the study continued with the monthly evaporation forecasts on the same reservoir. After this, the total volume of the reservoir at the end of each month was estimated. The ANN methods employed in the study are Radial Basis Functions (RBF) and Feed Forward Back Propagation (FFBP) methods. The data were divided into two parts. The first part that has a data length of 35 years was used for training of the Artificial neural networks (ANN). The remaining data were used for testing. At the end of the study the results of the artificial neural networks were compared with those of the reservoir operation programs that are commonly used by the General Directorate of State Hydraulic Works (DSI) of Turkey.
Mechanisms of voice processing in dementia

Perception of nonverbal vocal information is essential in our daily lives. Patients with degenerative dementias commonly have difficulty with such aspects of vocal communication; however voice processing has seldom been studied in these diseases. This thesis comprises a series of linked studies of voice processing in canonical dementias: Alzheimer’s disease, behavioural variant frontotemporal dementia, semantic dementia and progressive nonfluent aphasia. A series of neuropsychological tests were developed to examine perceptual and semantic stages of voice processing and to assess two aspects of accent processing: comprehension of foreign accented speech and recognition of regional and foreign accents; patient performance was referenced to healthy control subjects. Neuroanatomical associations of voice processing performance were assessed using voxel based morphometry. Following a symptom-led approach, a syndrome of progressive associative phonagnosia was characterised in two detailed case studies. Following a disease-led approach, this work was extended systematically to cohorts of patients representing the target diseases and assessing voice processing in relation to other aspects of person recognition (faces and names). This work provided evidence for separable profiles of voice processing impairment in different diseases: associative deficits were particularly severe in semantic dementia, whilst perceptual deficits showed relative specificity for Alzheimer’s disease. Neuroanatomical associations were identified for voice recognition in the right temporal pole and anterior fusiform gyrus, and for voice discrimination in the right inferior parietal lobe. The final phase of this work addressed the neuropsychological and neuroanatomical basis of accent processing, as an important dimension of nonverbal vocal analysis that is not dependent on voice identity. This work provides evidence for impaired processing of accents in progressive nonfluent aphasia and Alzheimer’s with neuroanatomical associations in the anterior and superior temporal lobe. The thesis contributes new information about voice processing in the degenerative dementias and furthers our understanding of the mechanisms of human voice analysis.
High performance parallel backprojection on multi-GPU

The speed of image reconstruction is an important indicator of the three-dimensional Computed Tomography (CT) imaging systems. GPU has become a focus of the research in CT reconstruction due to its characteristic of parallel computing. In this paper, the acceleration of backprojection, which is the most time consuming step of reconstruction, was implemented on multi-GPU hardware and OpenCL platform. The optimization techniques of parallelization strategy and memory management were explored and studied. The experimental results showed that the method obtained a considerable speedup, and the calculation times of total backprojection using 2 GPUs that were 1.67 times faster than using a single GPU. The method may be taken as the useful reference for researchers working on GPU applications and high-performance applications.
Effects of increasing ruminally degraded nitrogen and abomasal casein infusion on net portal flux of nutrients in yearling heifers consuming a high-grain diet.

Seven Meat Animal Research Center (MARC) III heifers (410+/-25 kg) fitted with hepatic portal, mesenteric venous, carotid catheters, and an abomasal cannula were used in a 7 x 5 incomplete Latin square design experiment. The objective was to evaluate the effects of increasing levels of ruminally degradable N (RDN) with or without the addition of abomasally infused casein on portal-drained visceral (PDV) flux of nutrients. Treatments consisted of dietary CP percentage levels of 9.5 (control), control plus . 72% dietary urea (11.5U), control plus 1.44% dietary urea (13.5U), control plus abomasally infused casein (250 g/d; 11.5C), or control plus . 72% dietary urea and abomasally infused casein (250 g/d; 13.5UC). All diets contained (DM basis) 80% ground corn, 15% corn silage, and 5% dry supplement and were provided for ad libitum consumption. Nitrogen intake increased (linear, P < .001) as CP increased from 9.5 to 13.5%. Portal-drained visceral release of ammonia N increased (linear, P < .10) as RDN increased, and was greater (P < .05) when protein was fed compared with heifers fed control (P < .10). Urea N removal by PDV was not affected ( P > . 10) by level of RDN but was greatest when 11.5C was fed and least when 13.5UC was fed. Net alpha-amino N (AAN) release by PDV was greatest when 13.5UC was fed (309 mmol/h), least when 9.5% CP was fed (112 mmol/h), and intermediate for the other groups (205 to 252 mmol/h). These data suggest that removal of N by the PDV may promote microbial protein synthesis when dietary RDN is low. When RDN needs have been met and amino acids are deficient for the host, escape protein should be fed to increase amino acid absorption.
A basal ganglia-forebrain circuit in the songbird biases motor output to avoid vocal errors

In songbirds, as in mammals, basal ganglia-forebrain circuits are necessary for the learning and production of complex motor behaviors; however, the precise role of these circuits remains unknown. It has recently been shown that a basal ganglia-forebrain circuit in the songbird, which projects directly to vocal–motor circuitry, has a premotor function driving exploration necessary for vocal learning. It has also been hypothesized that this circuit, known as the anterior forebrain pathway (AFP), may generate an instructive signal that improves performance in the motor pathway. Here, we show that the output of the AFP directly implements a motor correction that reduces vocal errors. We use disruptive auditory feedback, contingent on song pitch, to induce learned changes in song structure over the course of hours and find that reversible inactivation of the output of the AFP produces an immediate regression of these learned changes. Thus, the AFP is involved in generating an error-reducing bias, which could increase the efficiency of vocal exploration and instruct synaptic changes in the motor pathway. We also find that learned changes in the song generated by the AFP are incorporated into the motor pathway within 1 day. Our observations support a view that basal ganglia-related circuits directly implement behavioral adaptations that minimize errors and subsequently stabilize these adaptations by training premotor cortical areas.
Perceptual Tuning and Feedback-Related Brain Activity in Gambling Tasks.

2008 ii To my family iii Acknowledgment I would like to express my gratitude to all those people who have made this dissertation possible. for taking the time to work with me during this endeavor, and thanks for the distinct expertise and knowledge that each person brought to this dissertation study. I am deeply indebted to my academic advisor and dissertation chair, William J. Gehring, who has given me generous support, intellectually and emotionally, for the past five years. He allowed me to have total freedom to pursue my intellectual interest and provided timely and thoughtful guidance. He set an example of an extraordinary scholar and a good person. His professional and personal influence on me will be felt in the years to come. I offer my thanks to my dear friend Mason R. Smith for proofreading my dissertation, and to my colleague Joseph Orr for giving me constructive comments on the dissertation draft. I thank my friend and colleague Poyu Chen for assisting me in collecting the last experiment data during her visit in our lab. I thank my boy friend Yu-chun Kao for listening to my complaints all the time and undertaking all the housekeeping work during my dissertation writing. The greatest support throughout my graduate program comes from my family. My parents Shiwen Liu and Yuli Gao always give me unconditional love and support. My brother Guodong Liu encouraged me to study abroad to pursue my intellectual interests and shares the joy and sorrow in my oversea graduate study life.
Quantitative Magnetic Resonance Imaging Analysis of Neovasculature Volume in Carotid Atherosclerotic Plaque

Background—Neovasculature within atherosclerotic plaques is believed to be associated with infiltration of inflammatory cells and plaque destabilization. The aim of the present investigation was to determine whether the amount of neovasculature present in advanced carotid plaques can be noninvasively measured by dynamic, contrast-enhanced MRI. Methods and Results—A total of 20 consecutive patients scheduled for carotid endarterectomy were recruited to participate in an MRI study. Images were obtained at 15-second intervals, and a gadolinium contrast agent was injected coincident with the second of 10 images in the sequence. The resulting image intensity within the plaque was tracked over time, and a kinetic model was used to estimate the fractional blood volume. For validation, matched sections from subsequent endarterectomy were stained with ULEX and CD-31 antibody to highlight microvessels. Finally, all microvessels within the matched sections were identified, and their total area was computed as a fraction of the plaque area. Results were obtained from 16 participants, which showed fractional blood volumes ranging from 2% to 41%. These levels were significantly higher than the histological measurements of fractional vascular area. Nevertheless, the 2 measurements were highly correlated, with a correlation coefficient of 0.80 (P <0.001). Conclusions—Dynamic contrast-enhanced MRI provides an indication of the extent of neovasculature within carotid atherosclerotic plaque. MRI therefore provides a means for prospectively studying the link between neovasculature and plaque vulnerability.
Linking Network Structure to Ecommerce Demand: Theory and Evidence from Amazon.com's Copurchase Network

We report on a research project that studies how network structures affect demand in electronic commerce, using daily data about the graph structure of Amazon.com’s co-purchase network for over 250,000 products, gathered over this year. We describe how the presence of such network structures alters demand patterns by changing the distribution of traffic between ecommerce web pages. When this traffic distribution generated by the presence of the network is less skewed than the intrinsic or “real world” traffic distribution, such network structures will even out demand across products, leading to a demand distribution with a longer tail. We estimate an econometric model to validate this theory, and report on preliminary confirmation by contrasting the demand distributions of products in over 200 distinct categories on Amazon.com. We measure the overall extent to which a product influences the network by adapting Google’s PageRank algorithm, applying it to a weighted composite of graphs over four distinct 7-day periods, and we characterize the demand distribution of each category using its Gini coefficient. Our results establish that categories whose products are influenced more by the network structure have significantly flatter demand distributions, which provides an additional explanation for the widely documented phenomenon of the long tail of ecommerce demand.
Chattering Elimination in Fuzzy Sliding Mode Control of Fractional Chaotic Systems Using a Fractional Adaptive Proportional Integral Controller

In this paper, a Fractional Adaptive Fuzzy Logic Control (FAFLC) strategy based on active fractional sliding mode (FSM) theory is considered to synchronize chaotic fractional-order systems. Takagi-Sugeno fuzzy systems are used to estimate the plant dynamics represented by unknown fractional order functions. One of the main contributions in this work is to combine an adaptive fractional order PI control law with the fractional-order adaptive sliding mode controller in order to eliminate the chattering action in the control signal. Based on Lyapunov theory, the stability analysis of the proposed control strategy is performed for an acceptable synchronization error level. Numerical simulations illustrate the efficiency of the proposed fractional fuzzy adaptive control scheme through the synchronization of two different fractional order chaotic Duffing systems. We show that the introduction of the additional fractional adaptive PI control action is able to eliminate the chattering phenomena in the control signal.
Optical coherence tomography enables accurate measurement of equine cartilage thickness for determination of speed of sound

Background and purpose — Arthroscopic estimation of articular cartilage thickness is important for scoring of lesion severity, and measurement of cartilage speed of sound (SOS)—a sensitive index of changes in cartilage composition. We investigated the accuracy of optical coherence tomography (OCT) in measurements of cartilage thickness and determined SOS by combining OCT thickness and ultrasound (US) time-of-flight (TOF) measurements. Material and methods — Cartilage thickness measurements from OCT and microscopy images of 94 equine osteochondral samples were compared. Then, SOS in cartilage was determined using simultaneous OCT thickness and US TOF measurements. SOS was then compared with the compositional, structural, and mechanical properties of cartilage. Results — Measurements of non-calcified cartilage thickness using OCT and microscopy were significantly correlated (ρ = 0.92; p < 0.001). With calcified cartilage included, the correlation was ρ = 0.85 (p < 0.001). The mean cartilage SOS (1,636 m/s) was in agreement with the literature. However, SOS and the other properties of cartilage lacked any statistically significant correlation. Interpretation — OCT can give an accurate measurement of articular cartilage thickness. Although SOS measurements lacked accuracy in thin equine cartilage, the concept of SOS measurement using OCT appears promising.
Nonhyperbolic moveout analysis in VTI media using rational interpolation

Anisotropic velocity analysis using qP-waves in transversely isotropic media with a vertical symmetry axis (VTI) usually is done by inferring the anellipticity parameter η and the normal moveout velocity VNMO from the nonhyperbolic character of the moveout. Several approximations explicit in these parameters exist with varying degrees of accuracy. Here, we present a rational interpolation approach to nonhyperbolic moveout analysis in the t-x domain. This method has no additional computational overhead compared to using expressions explicit in η and VNMO . The lack of such overhead stems from the observation that, for fixed η and zero-offset two-way traveltime t0 , the moveout curve for different values of VNMO can be calculated by simple stretching of the offset axis. This observation is based on the assumptions that the traveltimes of qP-waves in transversely isotropic media mainly depend on η and VNMO , and that the shear-wave velocity along the symmetry axis has a negligibleinfluence on these traveltim.
Linear Transmission of Composite Gaussian Measurements Over a Fading Channel Under Delay Constraints

Delay constrained linear transmission (LT) strategies are considered for the transmission of composite Gaussian measurements over an additive white Gaussian noise fading channel under an average power constraint. If the channel state information (CSI) is known by both the encoder and decoder, the optimal LT scheme in terms of the average mean-square error distortion is characterized under a strict delay constraint, and a graphical interpretation of the optimal power allocation strategy is presented. Then, for general delay constraints, two LT strategies are proposed based on the solution to a particular multiple measurements-parallel channels scenario. It is shown that the distortion decreases as the delay constraint is relaxed, and when the delay constraint is completely removed, both strategies achieve the optimal performance under certain matching conditions. If the CSI is known only by the decoder, the optimal LT strategy is derived under a strict delay constraint. The extension to general delay constraints is elusive. As a first step toward understanding the structure of the optimal scheme in this case, it is shown that for the multiple measurements-parallel channels scenario, any LT scheme that uses only a one-to-one linear mapping between measurements and channels is suboptimal in general.