Miracle-dz/UniFAR-FTUs huggingface dataset:
A blind sparse deconvolution method for neural spike identification

We consider the problem of estimating neural spikes from extracellular voltage recordings. Most current methods are based on clustering, which requires substantial human supervision and produces systematic errors by failing to properly handle temporally overlapping spikes. We formulate the problem as one of statistical inference, in which the recorded voltage is a noisy sum of the spike trains of each neuron convolved with its associated spike waveform. Joint maximum-a-posteriori (MAP) estimation of the waveforms and spikes is then a blind deconvolution problem in which the coefficients are sparse. We develop a block-coordinate descent method for approximating the MAP solution. We validate our method on data simulated according to the generative model, as well as on real data for which ground truth is available via simultaneous intracellular recordings. In both cases, our method substantially reduces the number of missed spikes and false positives when compared to a standard clustering algorithm, primarily by recovering temporally overlapping spikes. The method offers a fully automated alternative to clustering methods that is less susceptible to systematic errors.
A Cascade of CNN and LSTM Network with 3D Anchors for Mitotic Cell Detection in 4D Microscopic Image

Mitotic event detection is a fundamental step in investigating of cell behaviors. The event can be used to analyze various diseases, but most mitotic event detections performed previously focused only on two-dimensional (2D) images with time information. Owing to the complex background (normal cells) and mitotic event orientations, the 2D detection methods yield many false positive and false negative results. To solve this problem, we proposed a 2.5 dimensional (2.5D) cascaded end-to-end network combined with 3D anchors for accurate detection of mitotic events in 4D microscopic images. Our proposed network uses a convolutional long short-term memory to handle issues relating to time sequence; this helps to improve the detection accuracy (reduction of false positives). Furthermore, it uses 3D anchors to capture volume information used to address the orientation problem (reduction of false negatives). The experimental results show that the proposed method can achieve higher precision and recall compared with state-of-the-art methods.
Impact of Airflow Communication between Nasal Cavities on Nasal Ventilation

Objective: To investigate the impact of airflow communication between bilateral nostril sides on nasal ventilation. In addition, we try to validate the efficacy of the Draf III procedure from the aerodynamics perspective. Methods: One health model and two disease models were constructed. These included 2 patients with nasal septum perforation and 1 patient who received the Draf III procedure. With the computational fluid dynamics method, indices such as airflow velocity and wall shear stress in the nasal cavity were detected and compared among the 3 subjects. Results: The main pathway for airflow in the nasal cavity is the common meatus. Little airflow exchange occurred in the patient who underwent the Draf III procedure, and the wall shear stress around the communication site was as low as in the adjacent areas. However, when airflow communication occurred in the lower part of the nasal cavity, the airflow velocity and wall shear stress were obviously altered, and the ventilation function of the nasal cavity was impaired. Conclusion: Airflow communication in the upper part of the nasal cavity has little impact on nasal ventilation. Nonetheless, airflow communication occurring in the lower part of the nasal cavity disturbs the overall airflow distribution and a repair procedure is necessary.
The Role of the Primary Visual Cortex in Perceptual Suppression of Salient Visual Stimuli

The role of primary visual cortex (area V1) in subjective perception has intrigued students of vision for decades. Specifically, the extent to which the activity of different types of cells (monocular versus binocular) and electrophysiological signals (i.e., local field potentials versus spiking activity) reflect perception is still debated. To address these questions we recorded from area V1 of the macaque using tetrodes during the paradigm of binocular flash suppression, where incongruent images presented dichoptically compete for perceptual dominance. We found that the activity of a minority (20%) of neurons reflect the perceived visual stimulus and these cells exhibited perceptual modulations substantially weaker compared with their sensory modulation induced by congruent stimuli. Importantly, perceptual modulations were found equally often for monocular and binocular cells, demonstrating that perceptual competition in V1 involves mechanisms across both types of neurons. The power of the local field potential (LFP) also showed moderate perceptual modulations with similar percentages of sites showing significant effects across frequency bands (18–22%). The possibility remains that perception may be strongly reflected in more elaborate aspects of activity in V1 circuits (e.g., specific neuronal subtypes) or perceptual states might have a modulatory role on more intricate aspects of V1 firing patterns (e.g., synchronization), not necessarily altering the firing rates of single cells or the LFP power dramatically.
Efficient Approximation Algorithms for Repairing Inconsistent Databases

We consider the problem of repairing a database that is inconsistent wrt a set of integrity constraints by updating numerical values. In particular, we concentrate on denial integrity constraints with numerical built-in predicates. So far research in this context has concentrated in computational complexity analysis. In this paper we focus on efficient approximation algorithms to obtain a database repair and we present an algorithm that runs in O(n log n) wrt the size of the database. Our experimental evaluations show that even for large databases an approximate repair of the database can be computed efficiently despite the fact that the exact problem is computationally intractable. Finally, we show that our results can also be applied to database repairs obtained by a minimal number of tuple deletions.
Expression of a Tetraheme Protein,Desulfovibrio vulgaris Miyazaki F Cytochromec3, in Shewanella oneidensisMR-1

ABSTRACT Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F was successfully expressed in the facultative aerobe Shewanella oneidensis MR-1 under anaerobic, microaerophilic, and aerobic conditions, with yields of 0.3 to 0.5 mg of cytochrome/g of cells. A derivative of the broad-host-range plasmid pRK415 containing the cytochrome c3 gene fromD. vulgaris Miyazaki F was used for transformation ofS. oneidensis MR-1, resulting in the production of protein product that was indistinguishable from that produced by D. vulgaris Miyazaki F, except for the presence of one extra alanine residue at the N terminus.
Railroad: virtual infrastructure for data dissemination in wireless sensor networks

In this paper, we present Railroad, a data dissemination architecture for large-scale wireless sensor networks. Railroad system proactively exploits a virtual infrastructure called Rail, which is an area where all the metadata of event data are stored. There is only one Rail in the network and it acts as a rendezvous area of the events and the queries. Rail is placed in the middle area of the field so that every node can easily access it. Once a query is issued, it circulates around Rail and searches relevant data stored in Rail. When a relevant metadata is found, the source node of the data transmits the corresponding data to the sink node which has issued the query. By using Rail, Railroad achieves a scalable and energy-efficient data dissemination architecture under dynamic conditions with multiple mobile observers and targets. We evaluate and compare the communication cost and the hot spot message complexity of Railroad with previous approaches.
Interaction of verotoxin 2e with pig intestine

In pigs with edema disease, verotoxin 2e (VT2e) is produced in the intestine and transported to tissues, but neither the mechanism by which toxin passes through the intestine nor its failure to induce an enterotoxic reaction is understood. Binding of VT2e to pig intestine was examined by enzyme-linked immunosorbent assay involving microvillus membranes (MVM) and crude mucus; thin-layer chromatographic overlay immunoassay with total lipids extracted from MVM; and indirect immunofluorescence of toxin bound to thin sections of jejunum, ileum, and colon. VT2e bound significantly to MVM from pig jejunum and ileum but not to crude mucus. Verotoxin 2e-binding glycolipids, globotetraosylceramide and globotriaosylceramide, were detected by thin-layer chromatographic overlay immunoassay in extracts of MVM from jejunum and ileum. Indirect immunofluorescence showed that VT2e bound to vessels within the submucosa and muscularis mucosa of the jejunum, ileum, and colon and to enterocytes at the lower portion but not at the tips of villi in the jejunum and ileum. Receptors for VT2e are therefore present in the intestine of the pig, but their role in absorption of VT2e is unclear since intraintestinal inoculation of pigs with large quantities of VT2e does not result in edema disease. Previously reported lack of enterotoxicity of verotoxins in pig intestine may be explained by the absence of toxin receptors in the villus absorptive enterocytes.
Corticotropin releasing hormone and related peptides can act as bioregulatory factors in human keratinocytes

SummaryFollowing previous findings in human skin of the functional expression of genes for the corticotropin releasing hormone (CHR) receptor type 1 (CRH-R1) and CRH itself, we searched for local phenotypic effects for peptides related to CRH. We now report that CRH, sauvagine, and urocortin inhibit proliferation of human HaCaT keratinocytes in a dose-dependent manner. The peptides produced variable cyclic adenosine 3′∶5′-monophosphate stimulation with CRH having the highest potency. Binding of iodine 125 CRH to intact keratinocytes was inhibited by increasing doses of CRH, sauvagine, or urocortin, all showing equal inhibitory potency. Immunocytochemistry identified CRH-R1 immunoreactivity in HaCaT keratinocytes. In conclusion, CRH (exogenous or produced locally) and the related urocortin and sauvagine peptides can modify human keratinocyte phenotype through a receptor-mediated pathway.
Necdin: A multi functional protein with potential tumor suppressor role?

Necdin (NDN), a member of the melanoma‐associated antigen (MAGE) family of proteins was first identified in mouse stem cells of embryonal carcinoma origin induced to differentiate by treatment with retinoic acid. The human gene maps to chromosome 15q11. This imprinted region is implicated in the pathogenesis of Prader–Willi syndrome (PWS), a neurodevelopmental disorder, where NDN is one of multiple genes silenced by deletion, maternal uniparental disomy or translocation. Due to this association, much interest has focused on the role of NDN in neuronal development and differentiation. However, a considerable number of studies have identified additional functions of NDN. Taken together these studies suggest a pleiotropic protein with diverse functions some of which may be relevant to tumorigenesis. Downregulation of NDN occurs in carcinoma cell lines and primary tumors, suggesting a tumor suppressor role. Our working hypothesis is that NDN is a worthy candidate for further studies with regard to a potential tumor suppressor role. In this article we outline the considerable evidence supporting the hypothesis that NDN has multiple functions, some of which indicate that it could be a tumor suppressor. The roles of NDN in key processes such as interaction with p53 and E2F‐1, hematopoietic stem cell quiescence, transcriptional repression, angiogenesis, differentiation and interaction with the polycomb group gene BMI1 are discussed. Confirmation of NDN as a tumor suppressor may have implications for monitoring of PWS patients and could present a novel cancer therapeutic target. © 2009 Wiley‐Liss, Inc.
In Vitro Regeneration Protocol of Kenyan Adapted Groundnut (Arachis hypogaea L.) Genotypes using Cotyledonary Node Explants

A reproducible regeneration protocol for ICGV 12991, CG 7 and Red Valencia groundnut genotypes using Cotyledonary Node explants has been optimized. The effect of different BAP concentrations combined with either 2,4-D or TDZ was tested to determine optimum conditions for high shoot induction. Different BAP concentrations were tested to determine an optimum concentration for shoot elongation. Different NAA concentrations were similarly evaluated to determine the best concentration for rooting. Media containing combination of 5 mg/L BAP and 1 mg/L TDZ was the best concentration for shoot induction while media containing BAP at 5 mg/L was the best for elongation of shoots. NAA concentration of 1 mg/L gave the highest number of plants with roots. This works provides a very good protocol which will be beneficial during groundnut tissue culture as well as genetic transformation of groundnuts.
Inter-Subject Alignment of MEG Datasets in a Common Representational Space

Pooling neural imaging data across subjects requires aligning recordings from different subjects. In magnetoencephalography (MEG) recordings, sensors across subjects are poorly correlated both because of differences in the exact location of the sensors, and structural and functional differences in the brains. It is possible to achieve alignment by assuming that the same regions of different brains correspond across subjects. However, this relies on both the assumption that brain anatomy and function are well correlated, and the strong assumptions that go into solving the underdetermined inverse problem given the high dimensional source space. In this paper, we investigated an alternative method that bypasses source-localization. Instead, it analyzes the sensor recordings themselves and aligns their temporal signatures across subjects. We used a multivariate approach, multi-set canonical correlation analysis (M-CCA), to transform individual subject data to a low dimensional common representational space. We evaluated the robustness of this approach over a synthetic dataset, by examining the effect of different factors that add to the noise and individual differences in the data. On a MEG dataset, we demonstrated that M-CCA performs better than a method that assumes perfect sensor correspondence and a method that applies source localization. Lastly, we described how the standard M-CCA algorithm could be further improved with a regularization term that incorporates spatial sensor information.
No effect of moderate hypohydration or hyperthermia on anaerobic exercise performance.

PURPOSE This study examined the effects of hypohydration and moderate hyperthermia (core temperature elevation) on anaerobic exercise performance in a temperate environment. METHODS Eight active males completed two passive heat exposure trials (180 min, 45 degrees C, 50% rh) with (EUH) and without (HYP) fluid replacement. A single 15-s Wingate anaerobic test (WAnT) was used to assess anaerobic performance (peak power, mean power, and fatigue index) before (-180 min) and again at three time points after passive heat exposure to include immediately (0 min), 30 min, and 60 min after in a temperate environment (22 degrees C). Rectal temperature (Tc) was measured throughout the experiment. RESULTS HYP reduced body mass (2.7+/-0.7%) (P<0.05) but had no effect on any WAnT performance measure. Passive heat exposure elicited moderate hyperthermia in both trials (EUH: 0.6 degrees C; HYP: 1.0 degrees C) and returned to baseline within 30-60 min following similar decay curves. HYP Tc remained higher (0.4 degrees C) than EUH throughout testing (P<0.05), but moderate hyperthermia itself produced no independent effect on anaerobic exercise performance in either trial. CONCLUSIONS This study demonstrates that neither moderate HYP nor the moderate hyperthermia accompanying HYP by passive heat exposure affect anaerobic exercise performance in a temperate environment.
Atg5- and Atg7-dependent autophagy in dopaminergic neurons regulates cellular and behavioral responses to morphine

ABSTRACT The molecular basis of chronic morphine exposure remains unknown. In this study, we hypothesized that macroautophagy/autophagy of dopaminergic neurons would mediate the alterations of neuronal dendritic morphology and behavioral responses induced by morphine. Chronic morphine exposure caused Atg5 (autophagy-related 5)- and Atg7 (autophagy-related 7)-dependent and dopaminergic neuron-specific autophagy resulting in decreased neuron dendritic spines and the onset of addictive behaviors. In cultured primary midbrain neurons, morphine treatment significantly reduced total dendritic length and complexity, and this effect could be reversed by knockdown of Atg5 or Atg7. Mice deficient for Atg5 or Atg7 specifically in the dopaminergic neurons were less sensitive to developing a morphine reward response, behavioral sensitization, analgesic tolerance and physical dependence compared to wild-type mice. Taken together, our findings suggested that the Atg5- and Atg7-dependent autophagy of dopaminergic neurons contributed to cellular and behavioral responses to morphine and may have implications for the future treatment of drug addiction.
QoI-Aware Unified Framework for Node Classification and Self-Reconfiguration Within Heterogeneous Visual Sensor Networks

Due to energy and throughput constraints of visual sensing nodes, in-node energy conservation is one of the prime concerns in visual sensor networks (VSNs) with wireless transceiving capability. To cope with these constraints, the energy efficiency of a VSN for a given level of reliability can be enhanced by reconfiguring its nodes dynamically to achieve optimal configurations. In this paper, a unified framework for node classification and dynamic self-reconfiguration in VSNs is proposed. The proposed framework incorporates quality-of-information (QoI) awareness using peak signal-to-noise ratio-based representative metric to support a diverse range of applications. First, for a given application, the proposed framework provides a feasible solution for the classification of visual sensing nodes based on their field-of-view by exploiting the heterogeneity of the targeted QoI within the sensing region. Second, with the dynamic realization of QoI, a strategy is devised for selecting suitable configurations of visual sensing nodes to reduce redundant visual content prior to transmission without sacrificing the expected information retrieval reliability. The robustness of the proposed framework is evaluated under various scenarios by considering: 1) target QoI thresholds; 2) degree of heterogeneity; and 3) compression schemes. From the simulation results, it is observed that for the second degree of heterogeneity in targeted QoI, the unified framework outperforms its existing counterparts and results in up to 72% energy savings with as low as 94% reliability.
An approach to sentiment analysis of short Chinese texts based on SVMs

This paper uses a machine-learning method to determine the sentiment polarity of short Chinese texts. Firstly, a new way to extend the sentiment dictionary is presented. The sentiment dictionaries from NTU and HowNet are extended by using the word2vec tool provided by Google. The review texts are collected from Internet as datasets. Then the feature weight of the words is enhanced, including the words that appear in the sentiment dictionary that has been extended and the words next to the sentiment words. The reviews are classified into two classes, the positive semantic orientation and the negative semantic orientation. The result of experiment shows the progress in the accuracy.
Analysis of Energy-Based Metrics for Laparoscopic Skills Assessment

<italic>Objective:</italic> The complexity of minimally invasive surgery (MIS) requires that trainees practice MIS skills in numerous training sessions. The goal of these training sessions is to learn how to move the instruments smoothly without damaging the surrounding tissue and achieving operative tasks with accuracy. In order to enhance the efficiency of these training sessions, the proficiency of the trainees should be assessed using an objective assessment method. Several performance metrics have been proposed and analyzed for MIS tasks. The differentiation of various levels of expertise is limited without the presence of an external evaluator. <italic>Methods:</italic> In this study, novel objective performance metrics are proposed based on mechanical energy expenditure and work. The three components of these metrics are potential energy, kinetic energy, and work. These components are optimally combined through both one-step and two-step methods. Evaluation of these metrics is accomplished for suturing and knot-tying tasks based on the performance of 30 subjects across four levels of experience. <italic>Results:</italic> The results of this study show that the one-step combined metric provides 47<inline-formula><tex-math notation="LaTeX"> $\%$</tex-math></inline-formula> and 60<inline-formula><tex-math notation="LaTeX">$\%$</tex-math></inline-formula> accuracy in determining the level of expertise of subjects for the suturing and knot-tying tasks, respectively. The two-step combined metric provided 67<inline-formula><tex-math notation="LaTeX">$\%$</tex-math></inline-formula> accuracy for both of the tasks studied. <italic>Conclusion:</italic> The results indicate that energy expenditure is a useful metric for developing objective and efficient assessment methods. <italic>Significance:</italic> These metrics can be used to evaluate and determine the proficiency levels of trainees, provide feedback and, consequently, enhance surgical simulators.
Scalable Performance of FCbO Algorithm on Museum Data

Formal Concept Analysis – known as a technique for data analysis and visualisation – can also be applied as a means of creating interaction approaches that allow for knowledge discovery within collections of content. These interaction approaches rely on performant algorithms that can generate conceptual neighbourhoods based on a single formal concept, or incrementally compute and update a set of formal concepts given changes to a formal context. Using case studies based on content from museum collections, this paper describes the scalability limitations of existing interaction approaches and presents an implementation and evaluation of the FCbO update algorithm as a means of updating formal concepts from large and dynamically changing museum datasets.
Plasma Fluoride Levels in Man Following Intake of SnF2 in Solution or Toothpaste

The degree and rate of fluoride absorption in five volunteers were studied after ingestion of SnF 2 and NaF solutions or SnF 2 toothpaste. The fluoride concentration in plasma was followed for eight hours. The relative bio-availability of fluoride was calculated and was similar for both the NaF and SnF 2 solutions, although the latter solution showed a somewhat faster absorption rate. The bio-availability of fluoride from the SnF 2 dentifrice was 85%.