Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical and mechanical extracellular matrix properties dictate mammary epithelial cell motility and assembly

Biochemical and mechanical cues of the extracellular matrix have been shown to play important roles in cell‐matrix and cell‐cell interactions. We have experimentally tested the combined influence of these cues to better understand cell motility, force generation, cell‐cell interaction, and assembly in an in vitro breast cancer model. MCF‐10A non‐tumorigenic mammary epithelial cells were observed on surfaces with varying fibronectin ligand concentration and polyacrylamide gel rigidity. Our data show that cell velocity is biphasic in both matrix rigidity and adhesiveness. The maximum cell migration velocity occurs only at specific combination of substrate stiffness and ligand density. We found cell‐cell interactions reduce migration velocity. However, the traction forces cells exert onto the substrate increase linearly with both cues, with cells in pairs exerting higher maximum tractions observed over single cells. A relationship between force and motility shows a maximum in single cell velocity not observed in cell pairs. Cell‐cell adhesion becomes strongly favored on softer gels with elasticity ≤1250 Pascals (Pa), implying the existence of a compliance threshold that promotes cell‐cell over cell‐matrix adhesion. Finally on gels with stiffness similar to pre‐malignant breast tissue, 400 Pa, cells undergo multicellular assembly and division into 3D spherical aggregates on a 2D surface.
Efficient network coding-based end-to-end reliable multicast in multi-hop wireless networks

In multihop wireless networks, many applications require end-to-end reliable multicast communication with 100% packet delivery ratio. Recently, network coding has been applied to the reliable link-level multicast in wireless networks, where multiple lost packets with distinct intended receivers are XOR-ed together as one packet and forwarded via single retransmission, resulting in a significant reduction of bandwidth consumption in the scenarios of many receivers. However, the simple XOR operation cannot fully exploit the potential coding opportunities. Moreover, for the reliable multicast in multihop wireless networks, the number of receivers of link-level multicast is usually not large and thus this coding-based link-level multicast cannot provide a promising gain. In this work, we propose a new network coding-based reliable multicast scheme which exploits both network coding and the physical-layer broadcast nature. Specifically, first, at each link-level multicast the source node performs the more general coding operations instead of XOR and conducts the random linear packet coding such that more coding gain can be achieved. Second, each node snoops on all communications over the wireless medium and stores the overheard packets for packet decoding, such that an additional coding gain can be obtained. Extensive simulations demonstrate that the proposed scheme can greatly improve the transmission efficiency, especially in the case of large-group multicast.
Phylogeny-Directed Search for Murine Leukemia Virus-Like Retroviruses in Vertebrate Genomes and in Patients Suffering from Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Prostate Cancer

Gammaretrovirus-like sequences occur in most vertebrate genomes. Murine Leukemia Virus (MLV) like retroviruses (MLLVs) are a subset, which may be pathogenic and spread cross-species. Retroviruses highly similar to MLLVs (xenotropic murine retrovirus related virus (XMRV) and Human Mouse retrovirus-like RetroViruses (HMRVs)) reported from patients suffering from prostate cancer (PC) and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) raise the possibility that also humans have been infected. Structurally intact, potentially infectious MLLVs occur in the genomes of some mammals, especially mouse. Mouse MLLVs contain three major groups. One, MERV G3, contained MLVs and XMRV/HMRV. Its presence in mouse DNA, and the abundance of xenotropic MLVs in biologicals, is a source of false positivity. Theoretically, XMRV/HMRV could be one of several MLLV transspecies infections. MLLV pathobiology and diversity indicate optimal strategies for investigating XMRV/HMRV in humans and raise ethical concerns. The alternatives that XMRV/HMRV may give a hard-to-detect “stealth” infection, or that XMRV/HMRV never reached humans, have to be considered.
Minimal Graphics

Photorealistic rendering of graphical models continues to be a topic of considerable research effort in the computer graphics community. However, photorealism isn't the only criterion for judging an image's value. In visualization, where rendering is the conduit through which abstract, nonrealistic forms (such as isosurfaces or streamtubes) become perceivable to users, photorealism may neither be the most useful nor appropriate property. This article describes our long-term research vision in an area that, in our view, should gain a lot of importance in the future.
Netrins: versatile extracellular cues with diverse functions

Netrins are secreted proteins that were first identified as guidance cues, directing cell and axon migration during neural development. Subsequent findings have demonstrated that netrins can influence the formation of multiple tissues, including the vasculature, lung, pancreas, muscle and mammary gland, by mediating cell migration, cell-cell interactions and cell-extracellular matrix adhesion. Recent evidence also implicates the ongoing expression of netrins and netrin receptors in the maintenance of cell-cell organisation in mature tissues. Here, we review the mechanisms involved in netrin signalling in vertebrate and invertebrate systems and discuss the functions of netrin signalling during the development of neural and non-neural tissues.
Efficient network aware search in collaborative tagging sites

The popularity of collaborative tagging sites presents a unique opportunity to explore keyword search in a context where query results are determined by the opinion of a network of taggers related to a seeker. In this paper, we present the first in-depth study of network-aware search. We investigate efficient top-k processing when the score of an answer is computed as its popularity among members of a seeker's network. We argue that obvious adaptations of top-k algorithms are too space-intensive, due to the dependence of scores on the seeker's network. We therefore develop algorithms based on maintaining score upper-bounds. The global upper-bound approach maintains a single score upper-bound for every pair of item and tag, over the entire collection of users. The resulting bounds are very coarse. We thus investigate clustering seekers based on similar behavior of their networks. We show that finding the optimal clustering of seekers is intractable, but we provide heuristic methods that give substantial time improvements. We then give an optimization that can benefit smaller populations of seekers based on clustering of taggers. Our results are supported by extensive experiments on del.icio. us datasets.
Mathematical difficulties : psychology and intervention

This book examines the mathematical difficulties in typical and atypical populations. It discusses the behavioral, educational and neuropsychological characteristics of people with mathematical difficulties, and educational interventions to prevent, diagnose, treat or ameliorate such difficulties. The book brings together studies from different disciplines, including developmental psychology, neuroscience and education, and includes perspectives from practicing teachers. The book is divided into three major sections. The first includes chapters about the nature and characteristics of mathematical difficulties in the population as a whole, in relation to both psychology and education. The second deals with mathematical difficulties in children with other problems such as specific language impairment and dyslexia. The third discusses methods of interventions aimed at preventing, treating or ameliorating mathematical difficulties, and will include discussions of assessment and diagnosis.
Etc. frequency processing and cognition

1. Frequency Processing and Cognition: Introduction and Overview THEORETICAL MODELS AND PERSPECTIVES 2. Frequency processing: A twenty-five year perspective 3. Encoding, representing and estimating event frequencies: A multiple strategy perspective 4. In the year 2054: Innumeracy defeated 5. Frequency judgements and retrieval structures: Splitting, zooming and merging the units of the empirical world 6. Experiential and contextual heuristics in frequency judgement: Ease of recall and response scales 7. Tversky and Kahneman's availability approach to frequency judgement: a critical analysis 8. A memory models approach to frequency and probability judgement: Applications of Minerva 2 and Minerva-DM 9. Associative learning and frequency judgements: The PASS model 10. Frequency, contingency and the information processing theory of conditioning ESSENTIAL EMPIRICAL RESULTS 11. Effects of processing fluency on estimates of probability and frequency 12. Frequency judgements of emotions: The cognitive basis of personality assessment 13. Online strategies versus memory-based strategies in frequency estimation 14. Frequency learning and order effects in belief updating 15. The psychophysics metaphor in calibration research PRACTICAL IMPLICATIONS 16. Frequency effects in consumer decision making 17. Free word associations and the frequency of co-occurrence in language use 18. Technology needs Psychology: How natural frequencies foster insight in medical and legal experts 19. Frequency processing and cognition: Stock-taking and outlook
Triangles: tangible interface for manipulation and exploration of digital information topography

This paper presents a system for interacting with digital information, called Triangles. The Triangles system is a physical/digital construction kit, which allows users to use two hands to grasp and manipulate complex digital information. The kit consists of a set of identical flat, plastic triangles, each with a microprocessor inside and magnetic edge connectors. The connectors enable the Triangles to be physically connected to each other and provide tactile feedback of these connections. The connectors also pass electricity, allowing the Triangles to communicate digital information to each other and to a desktop computer. When the pieces contact one another, specific connection information is sent back to a computer that keeps track of the configuration of the system. Specific two and three-dimensional configurations of the pieces can trigger application events. The Triangles system provides a physical embodiment of digital information topography. The individual tiles have a simple geometric form which does not inherit the semantics of everyday physical objects. Their shape, size, and connectors encourage rapid rearrangement and exploration of groups of Triangles. The infinitely reconfigurable 2D and 3D topographies of the Triangles system create a new language for tangible interface.
Direction-Aware Spatial Context Features for Shadow Detection and Removal

Shadow detection and shadow removal are fundamental and challenging tasks, requiring an understanding of the global image semantics. This paper presents a novel deep neural network design for shadow detection and removal by analyzing the spatial image context in a direction-aware manner. To achieve this, we first formulate the direction-aware attention mechanism in a spatial recurrent neural network (RNN) by introducing attention weights when aggregating spatial context features in the RNN. By learning these weights through training, we can recover direction-aware spatial context (DSC) for detecting and removing shadows. This design is developed into the DSC module and embedded in a convolutional neural network (CNN) to learn the DSC features at different levels. Moreover, we design a weighted cross entropy loss to make effective the training for shadow detection and further adopt the network for shadow removal by using a euclidean loss function and formulating a color transfer function to address the color and luminosity inconsistencies in the training pairs. We employed two shadow detection benchmark datasets and two shadow removal benchmark datasets, and performed various experiments to evaluate our method. Experimental results show that our method performs favorably against the state-of-the-art methods for both shadow detection and shadow removal.
Evidence That Phospholipase δ1 Is the Effector in the Gh (Transglutaminase II)-mediated Signaling*

A new class of GTP-binding protein transglutaminase II (Gh) couples to a 69-kDa phospholipase C (PLC). An 8-amino acid region (Leu665-Lys672) of the α-subunit of Gh (Gαh) is involved in interaction and activation of PLC, an observation that has now been used to characterize the 69-kDa PLC further. A 20-amino acid peptide corresponding to Leu654-Leu673 of Gαh was used to prepare an affinity resin. On incubation with a partially purified PLC preparation from rat liver membranes, the affinity resin-bound ∼69- and 85-kDa proteins were recognized by an antibody to the 69-kDa PLC. Both purified 69-kDa PLC and PLC-δ1 bound to the affinity resin; moreover, antibodies to PLC-δ1 recognized the 69-kDa PLC, and antibodies to the 69-kDa PLC recognized PLC-δ1. A synthetic peptide corresponding to Leu661-Lys672 of Gαh inhibited the binding of PLC-δ1 to the affinity resin and also stimulated PLC-δ1. Reconstitution of PLC-δ1 with GTPγS (guanosine 5′-3-O-(thio)triphosphate)-activated Gh resulted in activation of PLC-δ1. Antibodies to Gαh also coimmunoprecipitated PLC-δ1 upon activation of Gh. These findings indicate that PLC-δ1 is the effector of Gh-mediated signaling.
Age-Related Surgical Outcomes of Laminoplasty for Cervical Spondylotic Myelopathy

Study Design Retrospective clinical study. Objective To investigate the age-related surgical outcomes of laminoplasty. Methods One hundred patients who underwent an en bloc laminoplasty for cervical spondylotic myelopathy from 2004 to 2008 and were followed for at least 1 year were included in this study. The clinical outcomes were assessed with the Japanese Orthopaedic Association (JOA) score. Acquired points (postoperative JOA score minus preoperative JOA score) were also calculated. To investigate the age-related effect for laminoplasty, two analyses were conducted: (1) the correlation between age and clinical outcome; and (2) the clinical outcomes by decade. Patients were divided into four groups according to their age at the time of operation as follows: group 50s, 50 to 59 years old; group 60s, 60 to 69 years; group 70s, 70 to 79 years; and group 80s, 80 to 89 years. The pre- and postoperative JOA scores, acquired points, preoperative comorbidities, and postoperative complications were then compared among the groups. Results Significant correlations were detected between age and JOA scores at the preoperative (p = 0.03), postoperative maximum (p < 0.0001), and final assessments (p < 0.0001). An age-related decline of JOA scores was observed over all periods. The analysis by decades showed the same results. On the other hand, the significant differences were not found for acquired points over all periods by either method. The preoperative comorbidities of hypertension and diabetes mellitus increased with age. Delirium was more common postoperatively in elderly patients. Conclusions Although an age-related decline of JOA scores was found over all periods, there were no severe sequelae and no differences in the acquired points that were age-related.
Data Mining with Decision Trees

In this tutorial, we survey recent developments in learning tree-based models for classification and regression called predictor trees. The tutorial has three parts: (1) A general overview of tree-based classification and regression. (2) A survey of methods to construct predictor trees. (3) An overview of scalable data access methods to construct predictor trees from very large training databases.
Performance Optimization and Modeling of Blocked Sparse Kernels

We present a method for automatically selecting optimal implementations of sparse matrix-vector operations. Our software “AcCELS” (Accelerated Compress-storage Elements for Linear Solvers) involves a setup phase that probes machine characteristics, and a run-time phase where stored characteristics are combined with a measure of the actual sparse matrix to find the optimal kernel implementation. We present a performance model that is shown to be accurate over a large range of matrices.
Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species.
A Yeast Metabolite Extraction Protocol Optimised for Time-Series Analyses

There is an increasing call for the absolute quantification of time-resolved metabolite data. However, a number of technical issues exist, such as metabolites being modified/degraded either chemically or enzymatically during the extraction process. Additionally, capillary electrophoresis mass spectrometry (CE-MS) is incompatible with high salt concentrations often used in extraction protocols. In microbial systems, metabolite yield is influenced by the extraction protocol used and the cell disruption rate. Here we present a method that rapidly quenches metabolism using dry-ice ethanol bath and methanol N-ethylmaleimide solution (thus stabilising thiols), disrupts cells efficiently using bead-beating and avoids artefacts created by live-cell pelleting. Rapid sample processing minimised metabolite leaching. Cell weight, number and size distribution was used to calculate metabolites to an attomol/cell level. We apply this method to samples obtained from the respiratory oscillation that occurs when yeast are grown continuously.
An Enhanced Shunt Active Filter with Energy Storage for Microgrids

This paper investigates the use of energy storage added to a shunt active filter configuration in order to enhance its operation in maintaining power quality conditioning at a particular part of a grid system. The specific application considered is for a microgrid. In the proposed configuration the shunt active filter with energy storage (SAFES) can supply both reactive and real power for a short duration, to "fill in" the power required in the presence of load changes within the microgrid until the main generation can respond. In this way voltage quality is maintained and no power is drawn from the main grid. To perform both voltage and harmonic compensation in the presence of a non-linear load a novel control strategy based on the state space pole placement design has been developed for the SAFES installed in a microgrid. Simulation studies and experimental results show that the proposed controller is able to regulate the grid voltage at its nominal value and also control the power sharing between the SAFES and the local supply. It also provides high bandwidth control of current harmonics.
Cancer survivors in the United States: age, health, and disability.

BACKGROUND Relatively little is known about the health and disability of adult cancer survivors. As a way to explore these issues, data from the National Health Interview Survey (years 1998-2000) were analyzed. METHODS Comparisons were made between cancer survivors (n = 4878) and those without a history of cancer (n = 90,737), using both descriptive statistics and logistic-regression models on general health status, psychological disability, limitations in activities of daily living, physical function, and health-related ability to work. Among cancer survivors, health and disability status were assessed by cancer site or type, age at diagnosis, and years since cancer diagnosis. RESULTS Compared with individuals without a history of cancer or other chronic disease, cancer survivors without other chronic diseases were significantly more likely to report being in fair or poor health (odds ratio, or OR, 2.97), a psychological disability (OR 2.18), limitations of activities of daily living or instrumental activities of daily living (OR 2.22), functional limitations (OR 1.74), and, among those under the age of 65, being unable to work because of a health condition (OR 3.22). The likelihood of poor health and disability was much higher among cancer survivors who also reported comorbid chronic conditions. CONCLUSIONS Providers caring for cancer survivors should be made aware of the long-term health consequences of cancer and consider appropriate supportive care for their patients. The identification of long-term effects of cancer that contribute to disability and the interventions needed to ameliorate these and their consequences should become a more prominent aspect of the research agenda.
35 W bi-level supply modulated Doherty amplifier for 3G LTE base station

This paper presents a Doherty power amplifier (DPA) controlled by the optimized bi-level supply modulator to improve an overall efficiency. By utilizing the supply modulation method determined by the probability density function (PDF) of an interest signal, an estimated average efficiency can be improved as much as 8.5 % compared with that of conventional DPA. For the verification the proposed DPA using commercial 120 W GaN devices has been devised. The experimental results show that the proposed DPA delivers a drain efficiency (DE) of 53.8 % and power added efficiency (PAE) of 50 %, with a gain of 11.8 dB at an average output power of 34.7 W for a 2.65 GHz 10 MHz 3G LTE signal with a 9 dB peak-to-average power ratio (PAPR). The measure result reveals that the DE of proposed DPA is 6 % higher than that of conventional one.
The Elements of Automatic Summarization

This thesis is about automatic summarization, with experimental results on multi-document news topics: how to choose a series of sentences that best represents a collection of articles about one topic. I describe prior work and my own improvements on each component of a summarization system, including preprocessing, sentence valuation, sentence selection and compression, sentence ordering, and evaluation of summaries. The centerpiece of this work is an objective function for summarization that I call "maximum coverage". The intuition is that a good summary covers as many possible important facts or concepts in the original documents. It turns out that this objective, while computationally intractable in general, can be solved efficiently for medium-sized problems and has reasonably good fast approximate solutions. Most importantly, the use of an objective function marks a departure from previous algorithmic approaches to summarization.