Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantification of postsynaptic density proteins: Glutamate receptor subunits and scaffolding proteins

The postsynaptic density (PSD) protein complex has long been a major target of proteomics in neuroscience. As the number of glutamate receptors on a synapse is one of the main determinants of synaptic efficacy, determining the absolute numbers of receptors in the PSD is necessary for estimating the amplitude of the excitatory postsynaptic current (EPSC) in individual synapses. Moreover, as the receptor molecules are embedded in a macromolecular complex within the PSD, stoichiometry between the receptors and other PSD proteins could help explain the functional and regional specialization of the synapses and their possible roles in synaptic plasticity. Here, I review various studies concerned with the quantification of PSD proteins. © 2011 Wiley Periodicals, Inc.
Castration-Resistant Prostate Cancer Bone Metastasis Response Measured by 18F-Fluoride PET After Treatment with Dasatinib and Correlation with Progression-Free Survival: Results from American College of Radiology Imaging Network 6687

18F-fluoride PET quantitatively images bone metabolism and may serve as a pharmacodynamic assessment for systemic therapy such as dasatinib, a potent SRC kinase inhibitor, with activity in bone. Methods: This was an imaging companion trial (American College of Radiology Imaging Network [ACRIN] 6687) to a multicenter metastatic castration-resistant prostate cancer (CRPC) tissue biomarker–guided therapeutic trial (NCT00918385). Men with bone metastatic CRPC underwent 18F-fluoride PET before and 12 weeks after initiation of dasatinib (100 mg daily). Dynamic imaging was performed over a 15-cm field of view for trial assessments. The primary endpoint was to determine whether changes in 18F-fluoride incorporation in tumor and normal bone occurred in response to dasatinib. Other endpoints included differential effect of dasatinib between 18F-fluoride incorporation in tumor and normal bone, 18F-fluoride transport in bone metastases, correlation with progression-free survival (PFS), prostate-specific antigen, and markers of bone turnover. Results: Eighteen participants enrolled, and 17 underwent interpretable baseline 18F-fluoride PET imaging before initiation of dasatinib. Twelve of 17 patients underwent on-treatment PET imaging. Statistically significant changes in response to dasatinib were identified by the SUVmaxavg (average of maximum standardized uptake value [SUVmax] for up to 5 tumors within the dynamic field of view) in bone metastases (P = 0.0002), with a significant differential 18F-fluoride PET response between tumor and normal bone (P < 0.0001). Changes in 18F-fluoride incorporation in bone metastases had borderline correlation with PFS by SUVmaxavg (hazard ratio, 0.91; 95% confidence interval, 0.82–1.00; P = 0.056). Changes by SUVmaxavg correlated with bone alkaline phosphatase (P = 0.0014) but not prostate-specific antigen (P = 0.47). Conclusion: This trial provides evidence of the ability 18F-fluoride PET to delineate treatment response of dasatinib in CRPC bone metastases with borderline correlation with PFS.
Real-Time Video Convolutional Face Finder on Embedded Platforms

A high-level optimization methodology is applied for implementing the well-known convolutional face finder (CFF) algorithm for real-time applications on mobile phones, such as teleconferencing, advanced user interfaces, image indexing, and security access control. CFF is based on a feature extraction and classification technique which consists of a pipeline of convolutions and subsampling operations. The design of embedded systems requires a good trade-off between performance and code size due to the limited amount of available resources. The followed methodology copes with the main drawbacks of the original implementation of CFF such as floating-point computation and memory allocation, in order to allow parallelism exploitation and perform algorithm optimizations. Experimental results show that our embedded face detection system can accurately locate faces with less computational load and memory cost. It runs on a 275 MHz Starcore DSP at 35 QCIF images/s with state-of-the-art detection rates and very low false alarm rates.
QACO: exploiting partial execution in web servers

Web servers provide content to users, with the requirement of providing high response quality within a short response time. Meeting these requirements is challenging, especially in the event of load spikes. Meanwhile, we observe that a response to a request can be adapted or partially executed depending on current resource availability at the server. For example, a web server can choose to send a low or medium resolution image instead of sending the original high resolution image under resource contention. In this paper, we exploit partial execution to expose a trade off between resource consumption and service quality. We show how to manage server resources to improve service quality and responsiveness. Specifically, we develop a framework, called Quota-based Control Optimization (QACO). The quota represents the total amount of resources available for all pending requests. QACO consists of two modules: (1) A control module adjusts the quota to meet the response time target. (2) An optimization module exploits partial execution and allocates the quota to pending requests in a manner that improves total response quality. We evaluate the framework using a system implementation in the Apache Web server, and using a simulation study of a Video-on-Demand server. The results show that under a response time target, QACO achieves a higher response quality than traditional techniques that admit or reject requests without exploiting partial execution.
Review Article Peroxisome Proliferator-activated Receptors and Progression of Colorectal Cancer

The peroxisome proliferator-activated receptors (PPARs) are members of the nuclear hormone receptor superfamily. These receptors are also ligand-dependent transcription factors responsible for the regulation of cellular events that range from glucose and lipid homeostases to cell differentiation and apoptosis. The importance of these receptors in lipid homeostasis and energy balance is well established. In addition to these metabolic and anti-inflammatory properties, emerging evidence indicates that PPARs can function as either tumor suppressors or accelerators, suggesting that these receptors are potential candidates as drug targets for cancer prevention and treatment. However, conflicting results have emerged regarding the role of PPARs on colon carcinogenesis. Therefore, further investigation is warranted prior to considering modulation of PPARs as an efficacious therapy for colorectal cancer chemoprevention and treatment.
Recognition and representation of text characters using rubber band

An important step in the communication of text including unknown characters is the representation of characters. To realize bilateral exchange of texts, representation of unknown characters, such as foreign characters, created characters, design characters, and historical characters which are not being widely used nowadays is an essential subject. In particular, although many Asian countries are using Chinese characters commonly, the fonts and glyphs are different. A method to recognize the configuration by composition of common components called strokes is proposed. In this method, a character is first analyzed into small elements called parts. Then, parts are merged to form a stroke. Experimental results on Chinese characters are given. <<ETX>>
Gamut Mapping Spatially Varying Reflectance with an Improved BRDF Similarity Metric

Recent spatially varying reflectance (svBRDF) printing systems can reproduce an input document as a combination of matte, glossy and metallic inks. Due to the limited number of inks, this reproduction process incurs some distortion. In this work, we present an svBRDF gamut mapping algorithm that minimizes distortions in the angular and spatial domains. To preserve a material's perceived variation with lighting and view, we introduce an improved BRDF similarity metric that builds on both experimental results on reflectance perception and on the statistics of natural lighting environments. Our experiments show better preservation of object color and highlights, as validated quantitatively as well as through a perceptual study. As for the spatial domain, we show how to adapt traditional color gamut mapping methods to svBRDFs. Our solution takes into account the contrast between regions, achieving better preservation of textures and edges.
CELL JUNCTIONS IN AMPHIBIAN SKIN

Cell junctions have been investigated in the amphibian epidermis, a stratified squamous epithelium, and compared to those described previously in simple columnar epithelia of mammalian cavitary organs. In adult frogs and toads, and in larvae approaching metamorphosis, belts of membrane fusion or zonulae occludentes of considerable depth are regularly found between adjoining cells of the outermost layer of the stratum corneum, binding the cells together into a continuous, uninterrupted sheet. Another set of occluding zonules appears in the second cornified layer (when such a layer is present), and a third set usually occurs in the outermost layer of the stratum granulosum. Specialized elements described as "modified" and "composite" desmosomes are encountered along the lateral and basal aspects, respectively, of the cornified cells; ordinary desmosomes and maculae occludentes (i.e., spots of membrane fusion) are found in all other strata. The usual 200 A intercellular gap is generally maintained between the cells of the stratum germinativum at the basal ends of the intercellular spaces. Hence, the intercellular spaces of the epidermis form a largely continuous network, closed to the external medium and open to the dermal interstitia. The situation is comparable to that found in columnar epithelia, except that the intercellular spaces are much more extensive, and an extracellular subcompartment (or two) apparently exists in the stratum corneum and between the latter and the stratum granulosum. The last subcompartment is usually filled with a dense substance, probably derived from discharged secretory granules. The tripartite junctional complex characteristic of lumen-lining epithelia (i.e., a zonula occludens followed by a zonula adhaerens, and desmosome) is seen only in early larvae; in adults and in larvae approaching metamorphosis, the occluding zonule is followed directly by a series of modified desmosomes. Interpreted in the light of current physiological data, these findings suggest that the diffusion of water, ions, and small, water-soluble molecules is impeded along the intercellular spaces of the epidermis by zonulae occludentes while it is facilitated from cell to cell within the epidermis by zonulae and maculae occludentes.
Analysis of Recurrent Patterns in Toroidal Magnetic Fields

In the development of magnetic confinement fusion which will potentially be a future source for low cost power, physicists must be able to analyze the magnetic field that confines the burning plasma. While the magnetic field can be described as a vector field, traditional techniques for analyzing the field's topology cannot be used because of its Hamiltonian nature. In this paper we describe a technique developed as a collaboration between physicists and computer scientists that determines the topology of a toroidal magnetic field using fieldlines with near minimal lengths. More specifically, we analyze the Poincaré map of the sampled fieldlines in a Poincaré section including identifying critical points and other topological features of interest to physicists. The technique has been deployed into an interactiveparallel visualization tool which physicists are using to gain new insight into simulations of magnetically confined burning plasmas.
Quality Metrics of Test Suites in Testdriven Designed Applications

As software engineering methodologies continue to progress, new techniques for writing and developing software have developed. One of these methods is known as Test-Driven Development (TDD). In TDD, tests are written first, prior to code development. Due to the nature of TDD, no code should be written without first having a test to execute it. Thus, in terms of code coverage, the quality of test suites written using TDD should be high. However, it is unclear if test suites developed using TDD exhibit high quality in terms of other metrics such as mutation score. Moreover, the association between coverage and mutation score is little studied. In this work, we analyze applications written using TDD and more traditional techniques. Specifically, we demonstrate the quality of the associated test suites based on two quality metrics: 1) structure-based criterion represented by branch coverage and statement coverage, 2) fault-based criterion represented by mutation scores. We hypothesize that test suites with high test coverage will also have high mutation scores, and we especially intend to show this in the case of TDD applications. We found that Test-Driven Development is an efficient approach that improves the quality of the test code to cover more of the source code and also to reveal more faults based on mutation analysis.
A History of Autism: Conversations with the Pioneers

Acknowledgments ix Foreword by Dame Stephanie Shirley xv Introduction 1 1 The Two Great Pioneers 9 2 The 1950s: The Seeds of Understanding 37 3 Blaming the Parents 54 4 The 1960s: The Parents Fight Back 76 5 The Two Teaching Pioneers 117 6 The 1970s: Major Steps Forward 139 7 Definition, Diagnosis, and Assessment: The History of the Tool 165 8 The 1980s and 1990s: Theories and Concepts 203 9 Autism in the Developing Nations 233 10 Where the Future Lies 265 Notes 298 Bibliography 339 Index 367
Incorporating post-click behaviors into a click model

Much work has attempted to model a user's click-through behavior by mining the click logs. The task is not trivial due to the well-known position bias problem. Some break-throughs have been made: two newly proposed click models, DBN and CCM, addressed this problem and improved document relevance estimation. However, to further improve the estimation, we need a model that can capture more sophisticated user behaviors. In particular, after clicking a search result, a user's behavior (such as the dwell time on the clicked document, and whether there are further clicks on the clicked document) can be highly indicative of the relevance of the document. Unfortunately, such measures have not been incorporated in previous click models. In this paper, we introduce a novel click model, called the post-click click model (PCC), which provides an unbiased estimation of document relevance through leveraging both click behaviors on the search page and post-click behaviors beyond the search page. The PCC model is based on the Bayesian approach, and because of its incremental nature, it is highly scalable to large scale and constantly growing log data. Extensive experimental results illustrate that the proposed method significantly outperforms the state of the art methods merely relying on click logs.
Gene expression as a circular process

Studies on the regulation of gene expression in eukaryotes in the past 20 years have consistently revealed increasing levels of complexity. Thirty years ago it seemed that we had understood the basic principles of gene regulation in eukaryotes. It was thought that regulation of transcription was the first and most important stage at which gene expression was regulated, and transcriptional regulation was considered to be very simple, with DNA-binding activators and repressors talking to the basic transcription machinery. This simple model was overthrown when it became clear that other stages of gene expression are also highly regulated. More recently, other dogmas have started to collapse. In particular, the idea that a linkage between the different steps in gene expression is restricted to processes ongoing in the same compartment has fallen out of favor. It is now evident that functional and physical linkage occurs in eukaryotes. We know that factors contributing to transcription in the nucleus can be found in the cytoplasm, and that RNA binding proteins that contribute to RNA decay in the cytoplasm are present in the nucleus. However, shuttling of such factors between nucleus and cytoplasm has traditionally been thought to serve a simple regulatory purpose, for instance, to avoid untimely activation of a transcription factor in the nucleus. Alternatively, it was thought to be necessary to recruit RNA binding proteins to the relevant RNAs. The notion that is now emerging is that factors thought to have evolved to specialize in regulating a single step of gene regulation in one cellular compartment may be contributing to the regulation of mRNAs at multiple steps along the lifecycle of an mRNA.
The first membrane spanning region of the lamin B receptor is sufficient for sorting to the inner nuclear membrane

The lamin B receptor (LBR) is a polytopic integral membrane protein localized exclusively in the inner nuclear membrane domain of the nuclear envelope. Its cDNA deduced primary structure consists of a highly charged amino-terminal domain of 205 residues that faces the nucleoplasm followed by a hydrophobic domain with eight potential transmembrane segments. To identify determinants that sort LBR from its site of integration (RER and outer nuclear membrane) to the inner nuclear membrane, we prepared full-length, truncated, and chimeric cDNA constructs of chick LBR, transfected these into mammalian cells and detected the expressed protein by immunofluorescence microscopy using appropriate antibodies. Surprisingly, we found that the determinants for sorting of LBR to the inner nuclear membrane reside in a region comprising its first transmembrane sequence plus flanking residues on either side. The other transmembrane regions as well as the nucleoplasmic domain are not required for sorting. We propose that the first transmembrane segment of LBR interacts specifically with another transmembrane segment and consider several mechanisms by which such specific interaction could result in sorting to the inner nuclear membrane.
Adherence to Prescription Medications Among Medical Professionals

Background. We evaluated adherence to medication usage by health care professionals to estimate the expected upper limit of adherence among the general population. Methods. In a self-administered survey, physicians and nurses were asked about their use of prescribed medications for acute and chronic illnesses. The settings were a teaching hospital, employee health service, medical college, and educational conferences. Results. Among 435 respondents, 301 physicians and nurses had medications prescribed for acute and/or chronic illnesses within 2 years of the survey. Of 610 prescribed medications, ≥80% were taken as prescribed, with a 77% compliance rate for short-term medications and 84% for long-term medications. Older age was associated with better adherence, whereas a greater number of doses per day was associated with poorer adherence. Conclusions. Approximately 80% of respondents reported properly taking prescription medications ≥80% of the time. Given the nature of the study population, it is unlikely that a nonclinical trial population will consistently achieve better adherence without specific interventions.
Dietary Omega-3 Fatty Acids Do Not Change Resistance of Rat Brain or Liver Mitochondria to Ca2+ and/or Prooxidants

Omega-3 polyunsaturated fatty acids (n-3 PUFAs) block apoptotic neuronal cell death and are strongly neuroprotective in acute and chronic neurodegeneration. Theoretical considerations, indirect data, and consideration of parsimony lead to the hypothesis that modulation of mitochondrial pathway(s) underlies at least some of the neuroprotective effects of n-3 PUFAs. We therefore systematically tested this hypothesis on healthy male FBFN1 rats fed for four weeks with isocaloric, 10% fat-containing diets supplemented with 1, 3, or 10% fish oil (FO). High resolution mass spectrometric analysis confirmed expected diet-driven increases in docosahexaenoic acid (DHA, 22:6, n-3) and eicosapentaenoic acid (EPA, 20:5, n-3) in sera, liver and nonsynaptosomal brain mitochondria. We further evaluated the resistance of brain and liver mitochondria to Ca2+ overload and prooxidants. Under these conditions, neither mitochondrial resistance to Ca2+ overload and prooxidants nor mitochondrial physiology is altered by diet, despite the expected incorporation of DHA and EPA in mitochondrial membranes and plasma. Collectively, the data eliminate one of the previously proposed mechanism(s) that n-3 PUFA induced augmentation of mitochondrial resistance to the oxidant/calcium-driven dysfunction. These data furthermore allow us to define a specific series of follow-up experiments to test related hypotheses about the effect of n-3 PUFAs on brain mitochondria.
Application of Anthromes to Frame Scenario Planning for Landscape-Scale Conservation Decision Making

Complexities in the rates and patterns of change necessitate the consideration of alternate futures in planning processes. These scenarios, and the inputs and assumptions used to build them, should reflect both ecological and social contexts. Considering the regional landscape as an anthrome, a priori, assumes human needs and institutions have a fundamental role and place in these futures, but that institutions incorporate ecological limits in decision making. As a case study of conservation scenario planning under the anthrome paradigm, we used a suite of InVEST models to develop and explore land use and land cover scenarios and to measure the associated change in biodiversity and ecosystem services in a region where dense settlements are expanding into populated and residential woodland anthromes. While tradeoffs between benefits in alternative futures are unavoidable, we found that distinct conservation opportunities arise within and around the protected areas and in the heterogeneous urban core of the county. Reflecting on the process and subsequent findings, we discuss why anthromes can be a more suitable framing for scenarios used in conservation decision making and land use planning. Specifically, we discuss how starting with anthromes influenced assumptions about inputs and opportunities and the decisions related to the planning for human and natural systems.
Folded reflectarray antenna based on a single layer reflector with increased phase angle range

Simple elementary cells for reflectarrays based on a single dielectric layer exhibit only a limited phase angle range not covering the complete 360° range, whereas multilayer substrate arrangements are not acceptable for some commercial applications with high pressure on cost. Therefore, this paper reports investigations on novel elementary reflectarray cells suitable for folded reflectarray antennas, resulting in a flat phase angle slope over geometrical dimensions as well as a phase angle range of more than 500°. A test antenna and a reference antenna with simple rectangular elementary cells were designed, built, and tested. Although the novel antenna exhibits slightly higher losses, it had a larger bandwidth and better performance at frequencies above the design frequency.
Analysis of Spatial, Temporal, and Content Characteristics of Videos in the YFCC100M Dataset

The Yahoo Flickr Creative Commons 100 Million dataset (YFCC100M) is one of the largest public databases containing images and videos and their annotations for research on multimedia analysis. In this paper, we present our study on analysis of characteristics of the 0.8 million videos in the dataset in spatial, temporal, and content perspectives. For this, all the video frames and metadata of the videos are examined. In addition, user-wise analysis of the characteristics is conducted. We make the obtained results publicly available in the form of a metadata dataset for the research community.