Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of action potential backpropagation in basal dendrites of prefrontal cortical pyramidal neurons

Basal dendrites of neocortical pyramidal neurons are relatively short and directly attached to the cell body. This allows electrical signals arising in basal dendrites to strongly influence the neuronal output. Likewise, somatic action potentials (APs) should readily propagate back into the basilar dendritic tree to influence synaptic plasticity. Two recent studies, however, determined that sodium APs are severely attenuated in basal dendrites of cortical pyramidal cells, so that they completely fail in distal dendritic segments. Here we used the latest improvements in the voltage‐sensitive dye imaging technique ( Zhou et al., 2007 ) to study AP backpropagation in basal dendrites of layer 5 pyramidal neurons of the rat prefrontal cortex. With a signal‐to‐noise ratio of > 15 and minimal temporal averaging (only four sweeps) we were able to sample AP waveforms from the very last segments of individual dendritic branches (dendritic tips). We found that in short‐ (< 150 µm) and medium (150–200 µm in length)‐range basal dendrites APs backpropagated with modest changes in AP half‐width or AP rise‐time. The lack of substantial changes in AP shape and dynamics of rise is inconsistent with the AP‐failure model. The lack of substantial amplitude boosting of the third AP in the high‐frequency burst also suggests that in short‐ and medium‐range basal dendrites backpropagating APs were not severely attenuated. Our results show that the AP‐failure concept does not apply in all basal dendrites of the rat prefrontal cortex. The majority of synaptic contacts in the basilar dendritic tree actually received significant AP‐associated electrical and calcium transients.
Performance modeling of message-driven based energy-efficient routing in delay-tolerant networks with individual node selfishness

Delay-Tolerant Networks (DTNs) are wireless mobile networks having intermittent connectivity among the nodes. DTN nodes mostly operate on limited battery power. Hence, in such networks, there is an immediate need to have energy efficient routing protocol, allowing the network to perform better and live longer for a message with lifetime Et and delivery probability Dp. Most of the work in DTN assumes that all the nodes are co-operative in nature, but in real world, all nodes are not always co-operative, and show some form of selfishness. We propose a message-driven based algorithm add-on to the existing routing protocols (such as Epidemic Routing (ER) and Two-Hop Routing (2HR)), that enables forwards based on individual message lifetime and delivery requirements, there by improving energy efficiency. Further we analytically model the performance of these protocols with energy-efficiency add-on in DTN, with individual node selfishness using Ordinary Differential Equations (ODEs). The results show that the proposed energy-efficient add-on improves the energy efficiency up to 90% for both ER and 2HR protocols. The analysis is validated through extensive simulation.
Guidelines to Evaluate Human Observational Studies for Quantitative Risk Assessment

Background Careful evaluation of the quality of human observational studies (HOS) is required to assess the suitability of HOS for quantitative risk assessment (QRA). In particular, the quality of quantitative exposure assessment is a crucial aspect of HOS to be considered for QRA. Objective We aimed to develop guidelines for the evaluation of HOS for QRA and to apply these guidelines to case–control and cohort studies on the relation between exposure to benzene and acute myeloid leukemia (AML). Methods We developed a three-tiered framework specific for the evaluation of HOS for QRA and used it to evaluate HOS on the relation between exposure to benzene and AML. Results The developed framework consists of 20 evaluation criteria. A specific focus of the framework was on the quality of exposure assessment applied in HOS. Seven HOS on the relation of benzene and AML were eligible for evaluation. Of these studies, five were suitable for QRA and were ranked based on the quality of the study design, conduct, and reporting on the study. Conclusion The developed guidelines facilitate a structured evaluation that is transparent in its application and harmonizes the evaluation of HOS for QRA. With the application of the guidelines, it was possible to identify studies suitable for QRA of benzene and AML and rank these studies based on their quality. Application of the guidelines in QRA will be a valuable addition to the assessment of the weight of evidence of HOS for QRA.
On the maximum density of fixed strongly connected subtournaments

We study the density of fixed strongly connected subtournaments on 5 vertices in large tournaments. We determine the maximum density asymptotically for five tournaments as well as unique extremal sequences for each tournament. As a byproduct we also characterize tournaments that are recursive blow-ups of a 3-cycle as tournaments that avoid three specific tournaments of size 5.
The Toshiba Mandarin TTS System for the Blizzard Challenge 2009

This paper introduces the Toshiba Mandarin Text-to-Speech (TTS) system submitted to the Mandarin benchmark of the Blizzard Challenge 2009. The basic framework keeps unchanged with the system in 2008 and we modify the system in several aspects: automatically find bad units in the database when preparing the speech corpus, add a G2P procedure after the text analysis to increase accuracy of the predicted pinyin for heteronyms, introduce prosody layer information into the prosody modeling and modify the fusion methods to fuse units in frequency domain. The subjective evaluation results show that these modifications improve the performance.
Measuring resting energy expenditure during extracorporeal membrane oxygenation: preliminary clinical experience with a proposed theoretical model

Extracorporeal membrane oxygenation (ECMO) is increasingly used in patients with severe respiratory failure. Indirect calorimetry (IC) is a safe and non‐invasive method for measuring resting energy expenditure (REE). No data exist on the use of IC in ECMO‐treated patients as oxygen uptake and carbon dioxide elimination are divided between mechanical ventilation and the artificial lung. We report our preliminary clinical experience with a theoretical model that derives REE from IC measurements obtained separately on the ventilator and on the artificial lung.
Comparison of Web Service Similarity- Assessment Methods

Due to the advent of service oriented architecture, web services have gained popularity. The need for efficient web service discovery increases because of the enormous growth of the web services. The main concern of this paper is to addresses the challenge of automated web service discovery and service similarity assessment. It utilizes the WordNet and a traditional information retrieval method, combined with structure matching to identify potentially useful services and estimating their relevance. The objective of this paper is to find the best suitable web service assessment method by comparing the three web service similarity assessment methods namely WordNet-powered vector space model, Structure matching and Semantic structure matching.
Robust Portfolio Rules and Asset Pricing

I present a new approach to the dynamic portfolio and consumption problem of an investor who worries about model uncertainty (in addition to market risk) and seeks robust decisions along the lines of Anderson, Hansen, and Sargent (2002). In accordance with max-min expected utility, a robust investor insures against some endogenous worst case. I first show that robustness dramatically decreases the demand for equities and is observationally equivalent to recursive preferences when removing wealth effects. Unlike standard recursive preferences, however, robustness leads to environment-specific "effective" risk aversion. As an extension, I present a closed-form solution for the portfolio problem of a robust Duffie-Epstein-Zin investor. Finally, robustness increases the equilibrium equity premium and lowers the risk-free rate. Reasonable parameters generate a 4% to 6% equity premium. Copyright 2004, Oxford University Press.
Nonlinear channel equalization in digital satellite systems

A new nonlinear equalizer for digital transmission over a nonlinear satellite channel with a PSK modulation is presented in this paper. The nonlinear channel under consideration is assumed to have a Volterra series representation. By considering the channel equalization as a fixed point problem and taking advantage of the properties of a contraction mapping, we show that the transmitted data symbols can be recovered in an iterative manner. The equalizer has a modular structure for easy implementation. The computer simulation shows that the proposed equalizer has an excellent performance. <<ETX>>
Harsh environments minimally invasive optical sensor using free-space targeted single-crystal silicon carbide

To the best of our knowledge, for the first time, a single-crystal silicon carbide (SiC)-based minimally invasive smart optical sensor suited for harsh environments has been designed and demonstrated. The novel sensor design is based on an agile wavelength source, instantaneous single-wavelength strong two-beam interferometry, full optical power cycle data acquisition, free-space targeted laser beams, multiple single-crystal-thick SiC optical front-end chips, and multiwavelength signal processing for unambiguous temperature measurements to form a fast and distributed smart optical sensor system. Experiments conducted using a 1550-nm eye-safe band-tunable laser and a 300-mum coating-free thick SiC chip demonstrate temperature sensing from room temperature to 1000degC with an estimated average 1.3degC resolution. Applications for the proposed sensor include use in fossil fuel-based power systems, aerospace/aircraft systems, satellite systems, deep-space exploration systems, and drilling and oil mining industries
User Interest Analysis with Hidden Topic in News Recommendation System

To take advantage of the Internet - vast but complicated information resources, Recommendation systems help users find out information they need by providing them personalized suggestions. This research area is receiving more and more attention from researchers and used in some famous websites like EBay, Amazon, etc. In this paper, we proposed a Recommendation System for Vietnamese electronic newspaper which uses content-based filtering techniques associating with the attention of users shown in user’s profile. These users’ attentions are determined by inferring a set of common Hidden Topics from the documents which users preferred. Experimental results showed that approach is feasible with positive results and its capabilities for reality development.
Bayesian Stochastic Mortality Modelling for Two Populations

Abstract This paper introduces a new framework for modelling the joint development over time of mortality rates in a pair of related populations with the primary aim of producing consistent mortality forecasts for the two populations. The primary aim is achieved by combining a number of recent and novel developments in stochastic mortality modelling, but these, additionally, provide us with a number of side benefits and insights for stochastic mortality modelling. By way of example, we propose an Age-Period-Cohort model which incorporates a mean-reverting stochastic spread that allows for different trends in mortality improvement rates in the short-run, but parallel improvements in the long run. Second, we fit the model using a Bayesian framework that allows us to combine estimation of the unobservable state variables and the parameters of the stochastic processes driving them into a single procedure. Key benefits of this include dampening down of the impact of Poisson variation in death counts, full allowance for paramater uncertainty, and the flexibility to deal with missing data. The framework is designed for large populations coupled with a small sub-population and is applied to the England & Wales national and Continuous Mortality Investigation assured lives males populations. We compare and contrast results based on the two-population approach with single-population results.
Reibergram and oligoclonal bands in diagnosis of multiple sclerosis.

INTRODUCTION In this study authors have analyzed the correlation between the IgG immunoglobulins in cerebrospinal fluid and the findings of oligoclonal bands on gel. Immunoglobulin IgG in cerebrospinal fluid (CSF) can be detected in neurological diseasses (infections and inflammatory neurological diseases and in demyelinating diseases, like multiple sclerosis (MS)). Quantitative IgG in CSF can be expressed by different formulae Reiber (Reiber and Felgenhauer 1987), Tourtellotte (Tourtellotte 1970), Schuller (Schuller and Sagar 1983) and IgG Index (Link and Tibbling 1977). In this study we used Reibergram. Qualitative CSF IgG can be measured by electrophoresis and isoelectric focusing (IEF). We used IEF for analysig CSF and seum because of its higher sensitivity. AIMS OF THE STUDY To determine the correlation of immunoglobulins IgG positivity in CSF with the finding of oligoclonal bands on the gel. MATERIAL AND METHODS The retrospective study based on data processed in OJ Clinical Immunology KCUS. Patients were suspicious of multiple sclerosis according to clinical findings and magnetic resonance imaging. All CSF and serum samples were processed by nephelometry, isoelectric focusing on the gel. Statistical analysis of intrathecal synthesis was also performed according to Reibergram. RESULTS Analyses were performed on 76 samples of cerebrospinal fluid and serum of patients from neurological clinic, suspected of multiple sclerosis. We received following results: 42 samples tested had type 1.25 samples tested showed type 2.3 samples had type 3.5 samples had type 4.1 sample had a fifth type. When we compare these results with values obtained by intrathecal synthesis of which is determined by Reibergram we obtained the following values: 16 samples had intrathecal synthesis of 20%-60%, 9 samples had a negative value of intrathecal synthesis of 10% or less. DISCUSSION AND CONCLUSION For most patients with established MS we found intrathecal humoral response, type two, and the number and arrangement of IgG bands generally does not change during the disease, because they reflect long-term non-specific immune stimulation rather than a specific immune response that during infectious disease changes (quantitatively and qualitatively).
Named Entity Disambiguation in Streaming Data

The named entity disambiguation task is to resolve the many-to-many correspondence between ambiguous names and the unique real-world entity. This task can be modeled as a classification problem, provided that positive and negative examples are available for learning binary classifiers. High-quality sense-annotated data, however, are hard to be obtained in streaming environments, since the training corpus would have to be constantly updated in order to accomodate the fresh data coming on the stream. On the other hand, few positive examples plus large amounts of unlabeled data may be easily acquired. Producing binary classifiers directly from this data, however, leads to poor disambiguation performance. Thus, we propose to enhance the quality of the classifiers using finer-grained variations of the well-known Expectation-Maximization (EM) algorithm. We conducted a systematic evaluation using Twitter streaming data and the results show that our classifiers are extremely effective, providing improvements ranging from 1% to 20%, when compared to the current state-of-the-art biased SVMs, being more than 120 times faster.
Computing galled networks from real data

Motivation: Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area. Although promising approaches exist, there are no tools available that biologists could easily and routinely use to compute rooted phylogenetic networks on real datasets containing tens or hundreds of taxa. Biologists are interested in clades, i.e. groups of monophyletic taxa, and these are usually represented by clusters in a rooted phylogenetic tree. The problem of computing an optimal rooted phylogenetic network from a set of clusters, is hard, in general. Indeed, even the problem of just determining whether a given network contains a given cluster is hard. Hence, some researchers have focused on topologically restricted classes of networks, such as galled trees and level-k networks, that are more tractable, but have the practical draw-back that a given set of clusters will usually not possess such a representation. Results: In this article, we argue that galled networks (a generalization of galled trees) provide a good trade-off between level of generality and tractability. Any set of clusters can be represented by some galled network and the question whether a cluster is contained in such a network is easy to solve. Although the computation of an optimal galled network involves successively solving instances of two different NP-complete problems, in practice our algorithm solves this problem exactly on large datasets containing hundreds of taxa and many reticulations in seconds, as illustrated by a dataset containing 279 prokaryotes. Availability: We provide a fast, robust and easy-to-use implementation of this work in version 2.0 of our tree-handling software Dendroscope, freely available from http://www.dendroscope. org. Contact: huson@informatik.uni-tuebingen.de
Sense-antisense gene-pairs in breast cancer and associated pathological pathways

More than 30% of human protein-coding genes form hereditary complex genome architectures composed of sense-antisense (SA) gene pairs (SAGPs) transcribing their RNAs from both strands of a given locus. Such architectures represent important novel components of genome complexity contributing to gene expression deregulation in cancer cells. Therefore, the architectures might be involved in cancer pathways and, in turn, be used for novel drug targets discovery. However, the global roles of SAGPs in cancer pathways has not been studied. Here we investigated SAGPs associated with breast cancer (BC)-related pathways using systems biology, prognostic survival and experimental methods. Gene expression analysis identified 73 BC-relevant SAGPs that are highly correlated in BC. Survival modelling and metadata analysis of the 1161 BC patients allowed us to develop a novel patient prognostic grouping method selecting the 12 survival-significant SAGPs. The qRT-PCR-validated 12-SAGP prognostic signature reproducibly stratified BC patients into low- and high-risk prognostic subgroups. The 1381 SAGP-defined differentially expressed genes common across three studied cohorts were identified. The functional enrichment analysis of these genes revealed the GABPA gene network, including BC-relevant SAGPs, specific gene sets involved in cell cycle, spliceosomal and proteasomal pathways. The co-regulatory function of GABPA in BC cells was supported using siRNA knockdown studies. Thus, we demonstrated SAGPs as the synergistically functional genome architectures interconnected with cancer-related pathways and associated with BC patient clinical outcomes. Taken together, SAGPs represent an important component of genome complexity which can be used to identify novel aspects of coordinated pathological gene networks in cancers.
An enhanced appearance model for ultrasound image segmentation

Active appearance model (AAM) had been popular on object segmentation for medical images. However, its performance is not good on ultrasound (US) images. In this paper, we propose an enhanced appearance model which represents the texture by edge structure and reduces the view-dependent feature of US images by a novel data normalization process. In our experiments on general US data, the proposed model shows considerable improvements compared to the original one.
The Stress response in transthyretin amyloidosis

Familial amyloidotic polyneuropathy (FAP) belongs to the group of disorders named amyloidoses. It has a systemic predominance range but it is the peripheral nervous system that is prominently affected. The primary cause of FAP is known: mutations in transthyretin protein lead to decreased conformation stability that alter its solubility making the protein prone to aggregate and form amyloid fibrils in tissues. Screening of diverse families in different populations reveals that the expression of this pathology is a complex process, clearly involving the contribution of other unidentified factors besides the TTR genetic mutation. Study of these modulator factors is very important to understand the pathogenesis of FAP and a way to envisage strategies for ameliorating symptoms or preventing FAP onset. The study of transgenic mice has proven to be a crucial tool for understanding FAP pathogenesis. We chose 3, 6 and 12 months transgenic mice expressing the human TTR V30M to search for a possible influence of an environmental adverse stimulus unpredictable chronic mild stress in the progression of FAP. Stress treatments altered the body weight, food and water consumption of the males, while with females the results were not significantly different. TTR serum levels were not altered during the course of experiments, due to stress. Corticosterone levels were significantly higher at 6 months; while TTR non-fibrillar deposition was similar in control and stressed mice. Amyloid was observed at 6 months (2/12) and 15 months (5/11) while control animals were amyloid free. We conclude that the employed stress stimulus was sufficient to enhance amyloid deposition.
Do ultra-short screening instruments accurately detect depression in primary care? A pooled analysis and meta-analysis of 22 studies.

BACKGROUND Guidance from the National Institute for Health and Clinical Excellence recommends one or two questions as a possible screening method for depression. Ultra-short (one-, two-, three- or four-item) tests have appeal due to their simple administration but their accuracy has not been established. AIM To determine whether ultra-short screening instruments accurately detect depression in primary care. DESIGN OF STUDY Pooled analysis and meta analysis. METHOD A literature search revealed 75 possible studies and from these, 22 STARD-compliant studies (Standards for Reporting of Diagnostic Accuracy) involving ultra-short tests were entered in the analysis. RESULTS Meta-analysis revealed a performance accuracy better than chance (P<0.001). More usefully for clinicians, pooled analysis of single-question tests revealed an overall sensitivity of 32.0% and specificity of 97.0% (positive predictive value [PPV] was 55.6% and negative predictive value [NPV] was 92.3%). For two- and three-item tests, overall sensitivity on pooled analysis was 73.7% and specificity was 74.7% with a PPV of only 38.3% but a pooled NPV of 93.0%. The Youden index for single-item and multiple item tests was 0.289 and 0.47 respectively, suggesting superiority of multiple item tests. Re-analysis examining only 'either or' strategies improved the 'rule in' ability of two- and three-question tests (sensitivity 79.4% and NPV 94.7%) but at the expense of being able to rule out a possible diagnosis if the result was negative. CONCLUSION A one-question test identifies only three out of every 10 patients with depression in primary care, thus unacceptable if relied on alone. Ultra-short two- or three-question tests perform better, identifying eight out of 10 cases. This is at the expense of a high false-positive rate (only four out of 10 cases with a positive score are actually depressed). Ultra-short tests appear to be, at best, a method for ruling out a diagnosis and should only be used when there are sufficient resources for second-stage assessment of those who screen positive.