Miracle-dz/UniFAR-FTUs huggingface dataset:
A diffusion-based binary digital communication system

Diffusion-based communications refers to the transfer of information using particles as message carriers whose propagation is based on the law of particle diffusion. Though still at an early stage, there have been growing interests and research efforts dedicated to this communication technology. It has been identified that diffusion-based communications is one of the most promising approaches for end-to-end communication between nanoscale devices in the near future. In this paper, the design of a binary digital communication system is proposed based on particle diffusion. Stochastic signaling through On-Off Keying (OOK) for random particle emission and a diffusion channel with memory is considered. The diffusion is considered in the cases of one, two, and three dimensions. The receiver detection problem is formulated by using an information-theoretic approach. The optimal decision threshold for the receiver detection is derived through mutual information maximization for two cases, namely, when the a priori probability of bit transmission is fixed and known to the receiver and when this probability is unknown to the receiver. Numerical results indicate that in the case of diffusion in one or two dimensions, the information of a priori probability plays a key role in optimizing the system performance, while it does not when considering the diffusion in three dimensions.
Calcification in Major Vessel Beds Relates to Vascular Brain Disease

Objective—Calcification in atherosclerotic plaques is a novel marker of atherosclerosis and is related to cardiovascular disease. However, its relationship with cerebrovascular disease has not been investigated extensively. We investigated the relationship between calcification in various vessel beds outside the brain and imaging markers of vascular brain disease. Methods and Results—A total of 885 community-dwelling people (mean age, 66.7 years) underwent computed tomography of the coronary arteries, aortic arch, and extracranial and intracranial carotid arteries to assess arterial calcification. Brain magnetic resonance imaging scans were performed to assess cerebral infarcts, microbleeds, and white matter lesions (WMLs). Calcification in each vessel bed was associated with presence of cerebral infarcts and with larger WML volume. The most prominent associations were found between intracranial carotid calcification and WML volume and between extracranial carotid calcification and infarcts. Adjustment for cardiovascular risk factors or ultrasound carotid plaque scores did not change these results. No associations were found between calcification and cerebral microbleeds. Conclusion—Arterial calcification in major vessel beds is associated with vascular brain disease on magnetic resonance imaging. Most notably, larger intracranial carotid calcification load relates to larger WML volumes, and larger extracranial carotid calcification load relates to the presence of cerebral infarcts, independently of ultrasound carotid plaque score. This suggests that calcification of atherosclerotic plaque yields other information in addition to merely the presence of plaques, providing novel insights into the etiology of vascular brain disease.
Strong Time Dependence of the 76-Gene Prognostic Signature for Node-Negative Breast Cancer Patients in the TRANSBIG Multicenter Independent Validation Series

Purpose: Recently, a 76-gene prognostic signature able to predict distant metastases in lymph node–negative (N−) breast cancer patients was reported. The aims of this study conducted by TRANSBIG were to independently validate these results and to compare the outcome with clinical risk assessment. Experimental Design: Gene expression profiling of frozen samples from 198 N− systemically untreated patients was done at the Bordet Institute, blinded to clinical data and independent of Veridex. Genomic risk was defined by Veridex, blinded to clinical data. Survival analyses, done by an independent statistician, were done with the genomic risk and adjusted for the clinical risk, defined by Adjuvant! Online. Results: The actual 5- and 10-year time to distant metastasis were 98% (88-100%) and 94% (83-98%), respectively, for the good profile group and 76% (68-82%) and 73% (65-79%), respectively, for the poor profile group. The actual 5- and 10-year overall survival were 98% (88-100%) and 87% (73-94%), respectively, for the good profile group and 84% (77-89%) and 72% (63-78%), respectively, for the poor profile group. We observed a strong time dependence of this signature, leading to an adjusted hazard ratio of 13.58 (1.85-99.63) and 8.20 (1.10-60.90) at 5 years and 5.11 (1.57-16.67) and 2.55 (1.07-6.10) at 10 years for time to distant metastasis and overall survival, respectively. Conclusion: This independent validation confirmed the performance of the 76-gene signature and adds to the growing evidence that gene expression signatures are of clinical relevance, especially for identifying patients at high risk of early distant metastases.
Ultrasensitive microarray bioassays using cyanine5 dye-doped silica nanoparticles

Herein we report the use of high brightness Cyanine5-doped silica nanoparticles (NPs) for the detection of antibodies or DNA in microarray bioassays. NP labels showed negligible non-specific binding, greater sensitivity and lower limits of detection when compared to free dye-labelled biomolecules. Moreover, the spotted microarrays used in this study required low NP and antibody concentrations to generate large data sets with improved statistical accuracy. These NPs have significant potential for use in biosensing for disease detection.
Dyna: A Language for Weighted Dynamic Programming

We present the first version of a new declarative programming language. Dyna has many uses but was designed especially for rapid development of new statistical NLP systems. A Dyna program is a small set of equations, resembling Prolog inference rules, that specify the abstract structure of a dynamic programming algorithm. It compiles into efficient, portable, C++ classes that can be easily invoked from a larger application. By default, these classes run a generalization of agenda-based parsing, prioritizing the partial parses by some figure of merit. The classes can also perform an exact backward (outside) pass in the service of parameter training. The compiler already knows several implementation tricks, algorithmic transforms, and numerical optimization techniques. It will acquire more over time: we intend for it to generalize and encapsulate best practices, and serve as a testbed for new practices. Dyna is now being used for parsing, machine translation, morphological analysis, grammar induction, and finite-state modeling.
Taxonomy of services and its relationship with operations and strategy in electronic commerce

In this study, we propose management challenges and available strategies in electronic commerce (EC) according to two classifying dimensions and classified groups. The two factorised dimensions labelled as: 1. the ease of online interaction and 2. the needs of online interaction that were constructed from five variables were used for the classification. The classification framework used in this study categorises services in EC into mass service, interactive service, ordering service, and professional service.
Measuring and mapping team interaction

Purpose – The purpose of this paper is four‐fold: to highlight the emerging stream of team interaction in research; to present a methodology to measure and map out team interaction; to compare team interaction between US and Spanish MBA teams so as to identify any differences between the two cultures; and to propose team interaction focused programs in educational institutions and organizations.Design/methodology/approach – The study used a quantitative research design and administered a survey that captures ten aspects of team interaction in four major dimensions to 32 US MBA teams (n = 176) and 31 Spanish MBA teams (n = 152) engaged in the same group exercise and used ANOVA analysis to compare the two groups.Findings – The findings show that the US and Spanish teams differ only in the diverging dimension of their actual team interaction (F = 26.42, p < 0.000). A comparative analysis of the ideal team interaction show that both MBA samples desire increased levels of the diverging (F = 3.
The Canadian Environmental Assessment Act, 2012 and Associated Policy: Implications for Aboriginal Peoples

Despite Canada’s positive reputation in international circles regarding environmental protection, there are recent signs that this is no longer warranted. Recent changes to the Canadian Environmental Assessment Act (CEAA) clearly present governmental intentions to focus efforts on stimulating economic growth through more rapid resource exploitation at the expense of the environment. Moreover, when assessing the impact of CEAA 2012 on Aboriginal people, one must look beyond the Act itself and take into account other pieces of policy to see the true effects because there are a number of other governmental initiatives that further weaken Aboriginal peoples’ capacity to participate in the resource development review process for undertakings that affect their traditional lands. The result is the silencing of the people who are most affected by resource development.
Formalizing Push-Relabel Algorithms

We present a formalization of push-relabel algorithms for computing the maximum flow in a network. We start with Goldberg’s et al. generic push-relabel algorithm, for which we show correctness and the time complexity bound of O(V E). We then derive the relabel-tofront and FIFO implementation. Using stepwise refinement techniques, we derive an efficient verified implementation. Our formal proof of the abstract algorithms closely follows a standard textbook proof, and is accessible even without being an expert in Isabelle/HOL— the interactive theorem prover used for the formalization.
Ultra-low power high bandwidth QPSK modulator

A novel method to produce direct QPSK modulation is presented. The key feature of the architecture is the absence of mixers and as a result unwanted mixing products. Bandwidth limitations of previous designs are overcome with a novel phase shifting technique. A prototype is demonstrated at 2.4 GHz to showcase the performance of the modulator. An error vector magnitude (EVM) of less than 5% is obtained over a 600 MHz bandwidth. The power consumption of the circuit is less than 10μW and its 1dB compression point is 17dBm.
Past Visits and the Intention to Revisit a Destination: Place Attachment as the Mediator and Novelty Seeking as the Moderator

The present paper begins from the empirically established positive relationship between the measures of past purchases of a destination and those of the intention to repurchase in the future. It posits that this relationship is mediated by the development of place attachment. It also examines the moderating effect of novelty seeking at two distinct levels: novelty seeking as moderating the relationship between past purchases and place attachment and also that between place attachment and future purchase intention.
On Cognitive Ability and Learning in a Beauty Contest

We reinvestigate a version of the beauty contest originally developed by Keynes (1936) with a focus on cognitive reflection. Using a sample of 166 undergraduate students at a regional university in Florida, we confirm previous research by Burnham et al. (2009) that cognitive reflection, as measured by Frederick's (2005) cognitive reflection test, matters in the first round of the game; players with a higher CRT score pick significantly lower numbers, and their responses cluster more. Unlike previous research, however, we find that cognitive ability is important only when faced with a new situation. In subsequent rounds of the game, cognitive ability is subordinate to a learning effect and players' responses and the variability of responses are not significantly related to CRT scores. This finding is important in financial markets, since it implies that anticipating the decisions and actions of other players is a function of experience, not necessarily cognitive ability.
Deposited in DRO : 20 March 2014 Version of attached le : Published Version Peer-review status of attached le : Peer-reviewed Citation for published item :

Background: Animal studies have suggested that the hippocampus may play an important role in anxiety as part of the Behavioural Inhibition System (BIS), which mediates reactivity to threat and punishment and can predict an individual’s response to anxiety-relevant cues in a given environment. The aim of the present structural magnetic resonance imaging (MRI) study was to examine the relationship between individual differences in BIS and hippocampal structure, since this has not received sufficient attention in non-clinical populations. Thirty healthy right-handed participants with no history of alcohol or drug abuse, neurological or psychiatric disorders, or traumatic brain injury were recruited (16 male, 14 female, age 18 to 32 years). T1-weighted structural MRI scans were used to derive estimates of total intracranial volume, and hippocampal and amygdala gray matter volume using FreeSurfer. To relate brain structure to Gray’s BIS, participants completed the Sensitivity to Punishment questionnaire. They also completed questionnaires assessing other measures potentially associated with hippocampal volume (Beck Depression Inventory, Negative Life Experience Survey), and two other measures of anxiety (Spielberger Trait Anxiety Inventory and the Beck Anxiety Inventory). Results: We found that high scores on the Sensitivity to Punishment scale were positively associated with hippocampal volume, and that this phenomenon was lateralized to the right side. In other words, greater levels of behavioural inhibition (BIS) were positively associated with right hippocampal volume. Conclusions: Our data suggest that hippocampal volume is related to the cognitive and affective dimensions of anxiety indexed by the Sensitivity to Punishment, and support the idea that morphological differences in the hippocampal formation may be associated with behavioural inhibition contributions to anxiety.
Photogrammetry for use in biological surface acquisition: investigation of use, geometric accuracy and consequence on analysis

Medical imaging has advanced medical and scientific understanding of disease since its implementation. However, a wealth of information that may be beneficial for detailed surgical review, surgical-specific device design and retrospective case studies is not gathered. In this study, a single-camera photogrammetry method is proposed to investigate a feasible method of capturing exposed in vivo geometric data in an open surgical environment. To address current restrictions, the method must be rapid, cost-effective and not an impede surgical protocol performance. The tool is validated for geometry reconstruction fidelity against an anatomically complex model of known dimensions using three test criteria: geometry, structural simulation and fluid simulation. Each reconstruction was subject to three levels of smoothing to test solution sensitivity and feature erosion. The model was reconstructed three times to test variability of the reconstruction. All reconstructions were carried out using a freely available webservice. The models were geometrically accurate, with half of the model area below 1% error (0.5 mm) and 75–84% area below 2% error (1 mm). Finite element analysis and computational fluid dynamics simulations carried out found that over 84% and 90% of the model, for both the structural and fluid simulations, were within 10% of the control value, respectively. The results and conclusions reported illustrate the capability of using photogrammetry for geometric reconstruction and computational analysis of in vivo geometries.
The statistical evaluation of social network dynamics

A class of statistical models is proposed for longitudinal network data. The dependent variable is the changing (or evolving) relation network, represented by two or more observations of a directed graph with a fixed set of actors. The network evolution is modeled as the consequence of the actors making new choices, or withdrawing existing choices, on the basis of functions, with fixed and random components, that the actors try to maximize. Individual and dyadic exogenous variables can be used as covariates. The change in the network is modeled as the stochastic result of network effects (reciprocity, transitivity, etc.) and these covariates. The existing network structure is a dynamic constraint for the evolution of the structure itself. The models are continuous-time Markov chain models that can be implemented as simulation models. The model parameters are estimated from observed data. For estimating and testing these models, statistical procedures are proposed that are based on the method of moments. The statistical procedures are implemented using a stochastic approximation algorithm based on computer simulations of the network evolution process.
Context-free error analysis by evaluation of algebraic power series

Optimal error analysis with respect to a context-free language may be viewed as the evaluation of an algebraic power series. By generalization of the nodal span context-free recognition algorithm, any algebraic power series is computable in O(n3) steps. The closure of algebraic power series under sequential transduction yields a generous class of reasonable error measures for which optimal analysis is O(n3). Included is minimizing the number of symbol insertions, deletions and/or replacements needed for correction, a special case which has been studied separately.
Correlations Without Synchrony

Peaks in spike train correlograms are usually taken as indicative of spike timing synchronization between neurons. Strictly speaking, however, a peak merely indicates that the two spike trains were not independent. Two biologically plausible ways of departing from independence that are capable of generating peaks very similar to spike timing peaks are described here: covariations over trials in response latency and covariations over trials in neuronal excitability. Since peaks due to these interactions can be similar to spike timing peaks, interpreting a correlogram may be a problem with ambiguous solutions. What peak shapes do latency or excitability interactions generate? When are they similar to spike timing peaks? When can they be ruled out from having caused an observed correlogram peak? These are the questions addressed here. The previous article in this issue proposes quantitative methods to tell cases apart when latency or excitability covariations cannot be ruled out.
High-throughput alternative splicing quantification by primer extension and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Alternative splicing is a significant contributor to transcriptome diversity, and a high-throughput experimental method to quantitatively assess predictions from expressed sequence tag and microarray analyses may help to answer questions about the extent and functional significance of these variants. Here, we describe a method for high-throughput analysis of known or suspected alternative splicing variants (ASVs) using PCR, primer extension and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Reverse-transcribed mRNA is PCR amplified with primers surrounding the site of alternative splicing, followed by a primer extension reaction designed to target sequence disparities between two or more variants. These primer extension products are assayed on a MALDI-TOF mass spectrometer and analyzed automatically. This method is high-throughput, highly accurate and reproducible, allowing for the verification of the existence of splicing variants in a variety of samples. An example given also demonstrates how this method can eliminate potential pitfalls from ordinary gel electrophoretic analysis of splicing variants where heteroduplexes formed from different variants can produce erroneous results. The new method can be used to create alternative variant profiles for cancer markers, to study complex splicing regulation, or to screen potential splicing therapies.
Immunological Aspects of Recombinant Adeno-Associated Virus Delivery to the Mammalian Brain

ABSTRACT Recombinant adeno-associated viruses (rAAV) are highly efficient vectors for gene delivery into the central nervous system (CNS). However, host inflammatory and immune responses may play a critical role in limiting the use of rAAV vectors for gene therapy and functional genomic studies in vivo. Here, we evaluated the effect of repeated injections of five rAAV vectors expressing different genetic sequences (coding or noncoding) in a range of combinations into the rat brain. Specifically, we wished to determine whether a specific immune or inflammatory response appeared in response to the vector and/or the transgene protein after repeated injections under conditions of mannitol coinjection. We show that readministration of the same rAAV to the CNS is possible if the interval between the first and second injection is more than 4 weeks. Furthermore, our data demonstrate that rAAV vectors carrying different genetic sequences can be administered at intervals of 2 weeks. Our data therefore suggest that the AAV capsid structure is altered by the vector genetic sequence, such that secondary structures of the single-stranded genome have an impact on the antigenicity of the virus. This study provides guidelines for more rational design of gene transfer studies in the rodent brain and, in addition, suggests the use of repeated administration of rAAV as a viable form of therapy for the treatment of chronic diseases.
Validation of Salivary Interleukin-6 and Tumor Necrosis Factor-Alpha of Healthy Adult Volunteers by Enzyme Immunoassay

BackgroundDespite the use of saliva with enzyme immunoassay (EIA) methods validated for use with blood to measure interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-&agr;), there has been limited validation of saliva as a matrix for EIA of IL-6 and TNF-&agr;. ObjectivesThe study aims were to (a) validate one vendor’s commercially available EIAs for detecting IL-6 and TNF-&agr; in saliva as an alternative matrix to blood and (b) test the long-term stability of EIA detection of IL-6 and TNF-&agr; after 12-month storage of saliva and plasma. MethodsSpike and recovery and linearity experiments were performed. Concentrations of IL-6 and TNF-&agr; in saliva and plasma from 20 healthy adult volunteers (6 men and 14 women) were correlated; the assays were repeated 12 months later. ResultsSpike and recovery and linearity performance was adequate for salivary IL-6: intra-assay percentage coefficient of variation, less than or equal to 8.4%; sensitivity, 0.11 pg/ml; mean recoveries, 81% in spiked saliva and 110% in spiked controls; and linearity, r = . 995. The association between IL-6 in saliva and plasma was moderate and significant (p = .04). Spike and recovery and linearity performance was inadequate for TNF-&agr;: intra-assay coefficient of variation, 10.8%; sensitivity, 2.3 pg/ml; mean recoveries, 44% in spiked saliva and 92% in spiked controls; and linearity, r = . 950. The association between TNF-&agr; in saliva and plasma was low and insignificant. Plasma and saliva IL-6 levels were significantly higher (p < .0001), and plasma and saliva TNF-&agr; levels were significantly lower (p < .0001) after 12-month storage of specimens. DiscussionWe concluded that (a) saliva can be used to assess IL-6, but not TNF-&agr;, with an EIA validated for use with blood and (b) 12-month storage of plasma and saliva significantly changes the assay results. Validation of other EIAs would expand assay options for investigators.