Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracellular Matrix is an Important Component of Limbal Stem Cell Niche

Extracellular matrix plays an important role in stem cell niche which maintains the undifferentiated stem cell phenotype. Human corneal epithelial stem cells are presumed to reside mainly at the limbal basal epithelium. Efforts have been made to characterize different components of the extracellular matrix that are preferentially expressed at the limbus. Mounting evidence from experimental data suggest that these components are part of the stem cell niche and play a role in the homeostasis of limbal stem cells. The extracellular matrix provides a mechanical and structural support as well as regulates cellular functions such as adhesion, migration, proliferation, self-renewal and differentiation. Optimization of the extracellular matrix components might be able to recreate an ex vivo stem cell niche to expand limbal stem cells.
Simulation of random fields via local average subdivision

A fast and accurate method of generating realizations of a homogeneous Gaussian scalar random process in one, two, or three dimensions is presented. The resulting discrete process represents local averages of a homogeneous random function defined by its mean and covariance function, the averaging being performed over incremental domains formed by different levels of discretization of the field. The approach is motivated first by the need to represent engineering properties as local averages (since many properties are not well defined at a point and show significant scale effects), and second to be able to condition the realization easily to incorporate known data or change resolution within sub‐regions. The ability to condition the realization or increase the resolution in certain regions is an important contribution to finite element modeling of random phenomena. The Ornstein‐Uhlenbeck and fractional Gaussian noise processes are used as illustrations.
Towards Feature Selection In Actor-Critic Algorithms

Abstract : Choosing features for the critic in actor-critic algorithms with function approximation is known to be a challenge. Too few critic features can lead to degeneracy of the actor gradient, and too many features may lead to slower convergence of the learner. In this paper, the authors show that a well-studied class of actor policies satisfy the known requirements for convergence when the actor features are selected carefully. They demonstrate that two popular representations for value methods -- the barycentric interpolators and the graph Laplacian proto-value functions -- can be used to represent the actor so as to satisfy these conditions. A consequence of this work is a generalization of the proto-value function methods to the continuous action actor-critic domain. Finally, they analyze the performance of this approach using a simulation of a torque-limited inverted pendulum.
Complexin induces a conformational change at the membrane-proximal C-terminal end of the SNARE complex

Complexin regulates spontaneous and activates Ca2+-triggered neurotransmitter release, yet the molecular mechanisms are still unclear. Here we performed single molecule fluorescence resonance energy transfer experiments and uncovered two conformations of complexin-1 bound to the ternary SNARE complex. In the cis conformation, complexin-1 induces a conformational change at the membrane-proximal C-terminal end of the ternary SNARE complex that specifically depends on the N-terminal, accessory, and central domains of complexin-1. The complexin-1 induced conformation of the ternary SNARE complex may be related to a conformation that is juxtaposing the synaptic vesicle and plasma membranes. In the trans conformation, complexin-1 can simultaneously interact with a ternary SNARE complex via the central domain and a binary SNARE complex consisting of syntaxin-1A and SNAP-25A via the accessory domain. The cis conformation may be involved in activation of synchronous neurotransmitter release, whereas both conformations may be involved in regulating spontaneous release. DOI: http://dx.doi. org/10.7554/eLife.16886. 001
Influence of local provision of specialty health care service on patient access to care.

INTRODUCTION The impact of local provision of specialty service on patients' access to care was studied in Canada's 13 health care jurisdictions where distance may be a barrier limiting access. METHODS A cross-sectional study of routinely collected registry data in Ontario and Nova Scotia was performed. Liver transplant was chosen as an indicator service. Transplant rate, disease severity, urgency and outcome were studied in adult recipients of first liver transplants from 1993 to 2002. Provinces that provided liver transplants were compared with those that did not; Ontario regions that provided the service were compared with those that did not; and the period of time when liver transplants were available in Nova Scotia was compared with the time when they were not. RESULTS Use varied widely between jurisdictions but was consistently higher in provider provinces, at 10.9 per million population (pmp) compared with 8.9 pmp in nonprovider provinces (p < 0.005). Use was higher in district health councils of Ontario that provided transplantation. A larger proportion of patients in provider regions had viral or alcoholic etiologies of disease than did those from nonprovider regions, who tended to have superior survival after transplant. Service interruption in Nova Scotia did not change use rates, with transplant rates remaining above average, at 12.0 pmp. CONCLUSIONS Differences in use between provider and nonprovider regions may reflect local service availability as well as local patterns of disease and patient referral. Expectations of patients that are established by local service availability persist after service is removed.
Sample suitability for the detection of minor white cell populations (microchimerism) by polymerase chain reaction

BACKGROUND: There is increasing use of highly sensitive testing with polymerase chain reaction (PCR) to study white cell microchimerism after transfusion and transplantation. This study investigated possible artifactual sources of allogeneic sample contamination before PCR testing. STUDY DESIGN AND METHODS: Quantitative Y‐chromosome PCR was used to study microchimerism among transfused patients with sickle cell disease (SCD) and thalassemia by using residual specimens from the clinical laboratory. High levels of circulating male white cells among transfused patients with SCD but not thalassemia led to concern over the artifactual origin of male cells. To investigate, paired specimens were collected from 26 female SCD patients: one specimen underwent processing only for PCR, while the other underwent testing in the clinical laboratory before PCR as a process control. All laboratory instruments were also assessed for their ability to impart male allogeneic cells to aliquots of female blood. RESULTS: Thirty‐three (31%) of 107 SCD samples, but 0 of 20 thalassemia samples, gave a high‐ level PCR signal. One of 26 paired samples that was not exposed to clinical laboratory equipment had low‐level PCR positivity while 10 of the 26 became strongly positive after testing on a blood cell analyzer and a reticulocyte analyzer. Sixteen of 32 female samples became positive after reticulocyte analysis, while none became positive after blood cell analysis. Samples from thalassemia patients tested PCR‐ negative because reticulocyte counts had not been performed. CONCLUSION: Allogeneic cell contamination is common with clinical laboratory equipment. These samples may not be suitable for microchimerism studies. In addition to method controls, process controls should be employed where appropriate.
Visualisation of direct interaction of MDA5 and the dsRNA replicative intermediate form of positive strand RNA viruses

Summary The innate immune system is a vital part of the body's defences against viral pathogens. The proteins retinoic acid-inducible gene-I (RIG-I) and melanoma differentiation associated gene 5 (MDA5) function as cytoplasmic pattern recognition receptors that are involved in the elimination of actively replicating RNA viruses. Their location and their differential responses to RNA viruses emphasises the complexity of the innate detection system. Despite the wealth of information on the types of RNA that trigger RIG-I, much less is known about the nature of the RNAs that act as agonists for MDA5. In order to identify which RNA species triggers MDA5 activation during infection, we isolated viral ssRNA and replicative intermediates of RNA from positive sense ssRNA viruses. We reveal that MDA5 recognises not the genomic ssRNA but the dsRNA generated by the replication of these viruses. Furthermore, using fluorescent imaging we present the first report of the visualisation of dsRNA and MDA5, which provides unique evidence of the relationship between viral dsRNA and MDA5 and proves without a doubt that MDA5 is the key sensor for the dsRNA replicative intermediate form of positive sense ssRNA viruses.
Reducing Idle Mode Power in Software Defined Radio Terminals

In this paper, we propose a processor which is optimized for idle mode operation of a software defined radio (SDR) terminal. Since a SDR terminal spends most of its time in the idle mode, reducing the power consumption in this mode directly translates to longer terminal standby time. Workload analysis of idle mode operations of contemporary standards showed that these are dominated by FIR filtering, which can be easily parallelized. This analysis was used in the design of the idle mode processor. The key architectural components are an SIMD unit for the parallel computations that dominate the workload, a conventional scalar unit for the sequential computations, and a control unit which supports efficient data memory access and loop control. The idle mode processor was modeled with Verilog and synthesized using standard cells in 0.13 micron technology. It consumes about 9mW at 1.08V
Processing private queries over untrusted data cloud through privacy homomorphism

Query processing that preserves both the data privacy of the owner and the query privacy of the client is a new research problem. It shows increasing importance as cloud computing drives more businesses to outsource their data and querying services. However, most existing studies, including those on data outsourcing, address the data privacy and query privacy separately and cannot be applied to this problem. In this paper, we propose a holistic and efficient solution that comprises a secure traversal framework and an encryption scheme based on privacy homomorphism. The framework is scalable to large datasets by leveraging an index-based approach. Based on this framework, we devise secure protocols for processing typical queries such as k-nearest-neighbor queries (kNN) on R-tree index. Moreover, several optimization techniques are presented to improve the efficiency of the query processing protocols. Our solution is verified by both theoretical analysis and performance study.
Submitted to the Annals of Statistics INFERENCE OF WEIGHTED V-STATISTICS FOR NON-STATIONARY TIME SERIES AND ITS APPLICATIONS By

We investigate the behavior of Fourier transforms for a wide class of non-stationary nonlinear processes. Asymptotic central and noncentral limit theorems are established for a class of non-degenerate and degenerate weighted V-statistics through the angle of Fourier analysis. The established theory for V-statistics provides a unified treatment for many important time and spectral domain problems in the analysis of non-stationary time series, ranging from nonparametric estimation to the inference of periodograms and spectral densities.
Qualitative Research Methods in Psychology

In the scientific community, and particularly in psychology and health, there has been an active and ongoing debate on the relative merits of adopting either quantitative or qualitative methods, especially when researching into human behaviour (Bowling, 2009; Oakley, 2000; Smith, 1995a, 1995b; Smith, 1998). In part, this debate formed a component of the development in the 1970s of our thinking about science. Andrew Pickering has described this movement as the "sociology of scientific knowledge" (SSK), where our scientific understanding, developing scientific ‘products’ and 'know-how', became identified as forming components in a wider engagement with society’s environmental and social context (Pickering, 1992: 1). Since that time, the debate has continued so that today there is an increasing acceptance of the use of qualitative methods in the social sciences (Denzin & Lincoln, 2000; Morse, 1994; Punch, 2011; Robson, 2011) and health sciences (Bowling, 2009; Greenhalgh & Hurwitz, 1998; Murphy & Dingwall, 1998). The utility of qualitative methods has also been recognised in psychology. As Nollaig Frost (2011) observes, authors such as Carla Willig and Wendy Stainton Rogers consider qualitative psychology is much more accepted today and that it has moved from "the margins to the mainstream in psychology in the UK. " (Willig & Stainton Rogers, 2008: 8). Nevertheless, in psychology, qualitative methodologies are still considered to be relatively 'new' (Banister, Bunn, Burman, et al., 2011; Hayes, 1998; Richardson, 1996) despite clear evidence to the contrary (see, for example, the discussion on this point by Rapport et al., 2005). Nicki Hayes observes, scanning the content of some early journals from the 1920s – 1930s that many of these more historical papers "discuss personal experiences as freely as statistical data" (Hayes, 1998, 1). This can be viewed as an early development of the case-study approach, now an accepted methodological approach in psychological, health care and medical research, where our knowledge about people is enhanced by our understanding of the individual 'case' (May & Perry, 2011; Radley & Chamberlain, 2001; Ragin, 2011; Smith, 1998).
Effect of compliance location in series elastic actuators

SUMMARY Series elastic actuators have beneficial properties for some robot applications. Several recent implementations contain alternative placements of the compliant element to improve instrumentation design. We use a class 1 versus class 2 lever model and energy-port methods to demonstrate in this paper that these alternative placements should still be classified as series elastic actuators. We also note that the compliance of proximal series elastic actuators is reflected by an augmented gear ratio dependent on the nominal gear ratio, which is significant for small gear ratios and approaches unity for large gear ratios. This reflected compliance is shown to differ depending on the sign of the gear ratio. We demonstrate that although the reflected compliance is only marginally influenced by the magnitude of the gear ratio, there are several notable differences, particularly for small gear ratios.
Skill acquisition and self-improvement for environmental change adaptation of mobile robot

Learning and development are essential processes for an animat to adapt itself to environmental changes so as to accomplish a given task. This paper proposes a single mechanism for learning and self-improvement that results in learning curves similar to the “U-shape” phenomena observed in several psychological experiments concerning the human learning process such as in language acquisition. The basic idea is that (1) the animat monitors its success rate in goal achievement so as to perceive environmental changes instead of relying on signals from a teacher, and (2) in order to reuse acquired knowledge and accelerate reinforcement learning, the animat does not memorize the action values but transfers only the learned policy. The resultant policy (a state transition map where transitions indicate the best actions) may not be optimal in any given environment but it may be able to better handle differences between environments. We apply this model to a mobile robot navigation problem for which the task is to reach the target while avoiding obstacles by means of uninterpreted sonar and visual information. Our experimental results demonstrate the validity of the model.
Anomalous regulation of the Drosophila Na(+)-Ca2+ exchanger by Ca2+

The Na(+)-Ca2+ exchanger from Drosophila was expressed in Xenopus and characterized electrophysiologically using the giant excised patch technique. This protein, termed Calx, shares 49% amino acid identity to the canine cardiac Na(+)-Ca2+ exchanger, NCX1. Calx exhibits properties similar to previously characterized Na(+)-Ca2+ exchangers including intracellular Na+ affinities, current-voltage relationships, and sensitivity to the peptide inhibitor, XIP. However, the Drosophila Na(+)-Ca2+ exchanger shows a completely opposite response to cytoplasmic Ca2+. Previously cloned Na(+)-Ca2+ exchangers (NCX1 and NCX2) are stimulated by cytoplasmic Ca2+ in the micromolar range (0.1- 10 microM). This stimulation of exchange current is mediated by occupancy of a regulatory Ca2+ binding site separate from the Ca2+ transport site. In contrast, Calx is inhibited by cytoplasmic Ca2+ over this same concentration range. The inhibition of exchange current is evident for both forward and reverse modes of transport. The characteristics of the inhibition are consistent with the binding of Ca2+ at a regulatory site distinct from the transport site. These data provide a rational basis for subsequent structure-function studies targeting the intracellular Ca2+ regulatory mechanism.
An eclectic approach for change impact analysis

Change impact analysis aims at identifying software artifacts being affected by a change. In the past, this problem has been addressed by approaches relying on static, dynamic, and textual analysis. Recently, techniques based on historical analysis and association rules have been explored. This paper proposes a novel change impact analysis method based on the idea that the mutual relationships between software objects can be inferred with a statistical learning approach. We use the bivariate Granger causality test, a multivariate time series forecasting approach used to verify whether past values of a time series are useful for predicting future values of another time series. Results of a preliminary study performed on the Samba daemon show that change impact relationships inferred with the Granger causality test are complementary to those inferred with association rules. This opens the road towards the development of an eclectic impact analysis approach conceived by combining different techniques.
A simple device for indirect measurement of blood pressure in mice

The pulsating blood flow in the caudal arteries of anaesthetized mice, detected by means of a photoconductive cell, is interrupted by increasing the pressure in a cuff fixed around the tail. Except for the anaesthetizing, the determination of blood pressures by this method requires little time and training.
New prior knowledge based extensions for stable feature selection

In many data sets, there are only hundreds or fewer samples but thousands of features. The relatively small number of samples in high dimensional data results in modest classification performance and feature selection instability. In order to deal with the curse of dimensionality, we propose to investigate research on the effect of integrating background knowledge about some dimensions known to be more relevant, as a means of directing the feature selection process. We propose extensions of three feature selection techniques, two filters and a wrapper, by incorporating prior knowledge in the search procedure of the best features. We study the effect of these extensions on the classification performance and the stability of the feature selection. We experimentally test and compare our proposed approaches with their original versions, which do not integrate prior knowledge, over three high-dimensional datasets. The results show that our proposed techniques outperform other methods in terms of stability of feature selection but also in classification performance in most cases.
A comparison between disturbance observer-based and model-based control of needle in percutaneous applications

In this paper, model-based and disturbance observer (DOB)-based control of needle in precautious applications are compared. In the model-based approach, the force acting on the needle is calculated by evaluating the finite element model (FEM) of the tissue with the tissue deformation. In DOB-based method, the force acting on the needle is considered as an external disturbance and it is estimated using position and velocity of the needle. In both approaches, the calculated/estimated force is used in a sliding mode control scheme to steer the needle to the target. A dynamics equation for the movement of the needle is proposed which includes the force applied by the tissue to the needle. The results are evaluated through simulation and a dynamic finite element model is used to simulate the behavior of the soft tissue. It is shown that the performance of the model-based scheme in presence of the uncertainty in tissue mechanical properties is superior to that of DOB; however it introduces additional system complexity due to the usage of the tissue deformation.
An iterative convex approach for fixed-order robust ℋ2/ℋ∞ control of discrete-time linear systems with parametric uncertainty

This paper presents a convex approach to design fixed-order robust ℋ2/ℋ∞ controllers for discrete-time linear time-invariant (LTI) systems affected by parametric uncertainty. Starting from an a priori computed stabilizing full-order parameter-dependent controller for the same system, which is designed under the assumption that the parameter is exactly known, parameter-dependent sufficient linear matrix inequalities (LMIs) for robust ℋ2/ℋ∞ analysis and synthesis are presented. A novel LMI procedure is proposed to iteratively compute less conservative robust controllers, utilizing a feasible solution of the fixed-order synthesis conditions as a starting point. Assuming polynomial parameter dependencies of all system matrices, tractable LMI formulations that guarantee feasibility of the parameter-dependent conditions are derived using well-known relaxations based on Pólya's theorem. Numerical comparisons with existing methods confirm the potential of the proposed robust controller design approach.
A Semantically Enabled Architecture for Crowdsourced Linked Data Management

Increasing amounts of structured data are exposed on the Web using graph-based representation models and protocols such as RDF and SPARQL. Nevertheless, while the overall volume of such open, or easily accessible, data sources reaches critical mass, the ability of potential consumers to use them in novel applications and services is predicated on the availability of purposeful means to query and manage the data, while taking into account and mastering its essential features in terms of decentralization, heterogeneity of schema, varying quality, and scale. Many aspects of these challenges are necessarily tackled through a combination of algorithmic techniques and manual effort. In the literature on traditional data management the theoretical and technical groundwork to realize and manage such combinations is being established. In this paper we build upon these ideas and propose a semantically enabled architecture for crowdsourced data management systems which uses formal representations of tasks and data to automatically design and optimize the operation and outcomes of human computation projects. The architecture is applied to the context of Linked Data management to address specific challenges of LinkedData query processing such as identity resolution and ontological classification. Starting from a motivational scenario we explain how query-processing tasks can be decomposed and translated into MTurk projects using our semantic approach, and roadmap the extensions to graph-based data management technology that are required to achieve this vision.