Miracle-dz/UniFAR-FTUs huggingface dataset:
Dysregulated IP3 Signaling in Cortical Neurons of Knock-In Mice Expressing an Alzheimer's-Linked Mutation in Presenilin1 Results in Exaggerated Ca2+ Signals and Altered Membrane Excitability

Disruptions in intracellular Ca2+ signaling are proposed to underlie the pathophysiology of Alzheimer's disease (AD), and it has recently been shown that AD-linked mutations in the presenilin 1 gene (PS1) enhance inositol triphosphate (IP3)-mediated Ca2+ liberation in nonexcitable cells. However, little is known of these actions in neurons, which are the principal locus of AD pathology. We therefore sought to determine how PS1 mutations affect Ca2+ signals and their subsequent downstream effector functions in cortical neurons. Using whole-cell patch-clamp recording, flash photolysis, and two-photon imaging in brain slices from 4-5-week-old mice, we show that IP3-evoked Ca2+ responses are more than threefold greater in PS1M146V knock-in mice relative to age-matched nontransgenic controls. Electrical excitability is thereby reduced via enhanced Ca2+ activation of K+ conductances. Action potential-evoked Ca2+ signals were unchanged, indicating that PS1M146V mutations specifically disrupt intracellular Ca2+ liberation rather than reduce cytosolic Ca2+ buffering or clearance. Moreover, IP3 receptor levels are not different in cortical homogenates, further suggesting that the exaggerated cytosolic Ca2+ signals may result from increased store filling and not from increased flux through additional IP3-gated channels. Even in young animals, PS1 mutations have profound effects on neuronal Ca2+ and electrical signaling: cumulatively, these disruptions may contribute to the long-term pathophysiology of AD.
Affect recognition in real-life acoustic conditions - a new perspective on feature selection

Automatic emotion recognition and computational paralinguis-tics have matured to some robustness under controlled laboratory settings, however, the accuracies are degraded in real-life conditions such as the presence of noise and reverberation. In this paper we take a look at the relevance of acoustic features for expression of valence, arousal, and interest conveyed by a speaker’s voice. Experiments are conducted on the GEMEP and TUM AVIC databases. To simulate realistically degraded conditions the audio is corrupted with real room impulse responses and real-life noise recordings. Features well correlated with the target (emotion) over a wide range of acoustic conditions are analysed and an interpretation is given. Classiﬁcation results in matched and mismatched settings with multi-condition training are provided to validate the beneﬁt of the feature selection method. Our proposed way of selecting features over a range of noise types considerably boosts the generalisation ability of the classiﬁers.
CanGEM: mining gene copy number changes in cancer

The use of genome-wide and high-throughput screening methods on large sample sizes is a well-grounded approach when studying a process as complex and heterogeneous as tumorigenesis. Gene copy number changes are one of the main mechanisms causing cancerous alterations in gene expression and can be detected using array comparative genomic hybridization (aCGH). Microarrays are well suited for the integrative systems biology approach, but none of the existing microarray databases is focusing on copy number changes. We present here CanGEM (Cancer GEnome Mine), which is a public, web-based database for storing quantitative microarray data and relevant metadata about the measurements and samples. CanGEM supports the MIAME standard and in addition, stores clinical information using standardized controlled vocabularies whenever possible. Microarray probes are re-annotated with their physical coordinates in the human genome and aCGH data is analyzed to yield gene-specific copy numbers. Users can build custom datasets by querying for specific clinical sample characteristics or copy number changes of individual genes. Aberration frequencies can be calculated for these datasets, and the data can be visualized on the human genome map with gene annotations. Furthermore, the original data files are available for more detailed analysis. The CanGEM database can be accessed at http://www.cangem. org/.
Long thermal interactions of PAW with normal tooth structure and different dental biomaterials

Plasma activated water (PAW) has been widely considered to be an effective method for decontamination. Recently, numerous studies report that plasma-activated water (PAW) also has antibacterial ability to prevent or treat dental caries and periodontal related diseases. In this context, this study presents the first report to evaluate the plasma activated water effect on vital teeth enamel and different dental biomaterials. In this context, this study presents the first report to evaluate long thermal interactions of plasma activated water effect on vital teeth enamel and different dental biomaterials without organic substrate. The results suggest that the long-thermal of treatment with PAW of enamel without organic substrate can dissolve the apatite crystallites which are highly organized hierarchical structures.
ULisboa: Recognition and Normalization of Medical Concepts

This paper describes a system developed for the disorder identification subtask within task 14 of SemEval 2015. The developed system is based on a chain of two modules, one for recognition and another for normalization. The recognition module is based on an adapted version of the Stanford NER system to train CRF models in order to recognize disorder mentions. CRF models were build based on a novel encoding of entity spans as token classifications to also consider non-continuous entities, along with a rich set of features based on (i) domain lexicons and (ii) Brown clusters inferred from a large collection of clinical texts. For disorder normalization, we (i) generated a non ambiguous dictionary of abbreviations from the labelled files, using it together with (ii) an heuristic method based on similarity search and (iii) a comparison method based on the information content of each disorder. The system achieved an F-measure of 0.740 (the second best), with a precision of 0.779, a recall of 0.705.
Aggregation and comparison of trajectories

Dealing with moving objects necessitates having available complete geographical traces for determining exact or possible locations that objects have had, have or will have. This is where trajectory determination plays an important role, and on which classification, aggregation and comparison methods must be built. The purpose of aggregation is to identify similar trajectories and to represent them by a single trajectory.Although much work has been done in similarity measurements for time series data, they mainly deal with one dimensional time series. On the other hand, they are good for short time series and in absence of noise, which is definitely not the case for moving objects. This paper describes different approaches to aggregate similar trajectories.
Perceptions of Diversity on Git Hub: A User Survey

Understanding one's work environment is important for one's success, especially when working in teams. In virtual collaborative environments this amounts to being aware of the technical and social attributes of one's team members. Focusing on Open Source Software teams, naturally very diverse both socially and technically, we report the results of a user survey that tries to resolve how teamwork and individual attributes are perceived by developers collaborating on GITHUB, and how those perceptions influence their work. Our findings can be used as complementary data to quantitative studies of developers' behavior on GITHUB.
Adjustable Parameter-Based Distributed Fault Estimation Observer Design for Multiagent Systems With Directed Graphs

In this paper, a novel adjustable parameter (AP)-based distributed fault estimation observer (DFEO) is proposed for multiagent systems (MASs) with the directed communication topology. First, a relative output estimation error is defined based on the communication topology of MASs. Then a DFEO with AP is constructed with the purpose of improving the accuracy of fault estimation. Based on <inline-formula> <tex-math notation="LaTeX">${H} _{{\infty }}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">${H} _{{2}}$ </tex-math></inline-formula> with pole placement, multiconstrained design is given to calculate the gain of DFEO. Finally, simulation results are presented to illustrate the feasibility and effectiveness of the proposed DFEO design with AP.
Manufacturing of biodegradable polyurethane scaffolds based on polycaprolactone using a phase separation method: physical properties and in vitro assay

Background Biodegradable polyurethanes have found widespread use in soft tissue engineering due to their suitable mechanical properties and biocompatibility. Methods In this study, polyurethane samples were synthesized from polycaprolactone, hexamethylene diisocyanate, and a copolymer of 1,4-butanediol as a chain extender. Polyurethane scaffolds were fabricated by a combination of liquid–liquid phase separation and salt leaching techniques. The effect of the NCO:OH ratio on porosity content and pore morphology was investigated. Results Scanning electron micrographs demonstrated that the scaffolds had a regular distribution of interconnected pores, with pore diameters of 50–300 μm, and porosities of 64%–83%. It was observed that, by increasing the NCO:OH ratio, the average pore size, compressive strength, and compressive modulus increased. L929 fibroblast and chondrocytes were cultured on the scaffolds, and all samples exhibited suitable cell attachment and growth, with a high level of biocompatibility. Conclusion These biodegradable polyurethane scaffolds demonstrate potential for soft tissue engineering applications.
Efficient Testing Of Clock Regenerator Circuits In Scan Designs

This paper describes the use of a high-level view (functionalview) of a clock regenerator circuit for generating effective andinexpensive manufacturing tests. It is shown that the tests generatedfrom the traditional, structural view add hardwareoverhead, increase design time and potentially lower effectiveyield when compared to the tests generated from the functionalview. A test generation procedure is described and successfullyused on a microprocessor design.
Glutamine Deamidation and Dysfunction of Ubiquitin/NEDD8 Induced by a Bacterial Effector Family

Gee-Up, NEDD8 Diverse bacterial pathogens, such as Burkholderia pseudomallei and enteropathogenic Escherichia coli (EPEC), inject effector proteins into eukaryotic host cells to subvert host cell biology. Cui et al. (p. 1215; published online 5 August) show that certain bacterial effector proteins promoted the glutamine deamidation of ubiquitin and the ubiquitin-related protein, NEDD8. The modification of ubiquitin inhibited the formation of polyubiquitin chains while, unexpectedly, the same chemical alteration on NEDD8 interfered with the cell cycle, offering insights not only into the cytopathic effects of bacterial infection but also into mechanisms that may operate during viral infection and cancer. Pathogenic bacterial proteins interfere with eukaryotic ubiquitination pathways to induce cytopathic effects. A family of bacterial effectors including Cif homolog from Burkholderia pseudomallei (CHBP) and Cif from Enteropathogenic Escherichia coli (EPEC) adopt a functionally important papain-like hydrolytic fold. We show here that CHBP was a potent inhibitor of the eukaryotic ubiquitination pathway. CHBP acted as a deamidase that specifically and efficiently deamidated Gln40 in ubiquitin and ubiquitin-like protein NEDD8 both in vitro and during Burkholderia infection. Deamidated ubiquitin was impaired in supporting ubiquitin-chain synthesis. Cif selectively deamidated NEDD8, which abolished the activity of neddylated Cullin-RING ubiquitin ligases (CRLs). Ubiquitination and ubiquitin-dependent degradation of multiple CRL substrates were impaired by Cif in EPEC-infected cells. Mutations of substrate-contacting residues in Cif abolished or attenuated EPEC-induced cytopathic phenotypes of cell cycle arrest and actin stress fiber formation.
Targeting of De Novo DNA Methylation Throughout the Oct-4 Gene Regulatory Region in Differentiating Embryonic Stem Cells

Differentiation of embryonic stem (ES) cells is accompanied by silencing of the Oct-4 gene and de novo DNA methylation of its regulatory region. Previous studies have focused on the requirements for promoter region methylation. We therefore undertook to analyse the progression of DNA methylation of the ∼2000 base pair regulatory region of Oct-4 in ES cells that are wildtype or deficient for key proteins. We find that de novo methylation is initially seeded at two discrete sites, the proximal enhancer and distal promoter, spreading later to neighboring regions, including the remainder of the promoter. De novo methyltransferases Dnmt3a and Dnmt3b cooperate in the initial targeted stage of de novo methylation. Efficient completion of the pattern requires Dnmt3a and Dnmt1, but not Dnmt3b. Methylation of the Oct-4 promoter depends on the histone H3 lysine 9 methyltransferase G9a, as shown previously, but CpG methylation throughout most of the regulatory region accumulates even in the absence of G9a. Analysis of the Oct-4 regulatory domain as a whole has allowed us to detect targeted de novo methylation and to refine our understanding the roles of key protein components in this process.
An OpenCL Candidate Slicing Frequent Pattern Mining algorithm on graphic processing units

Frequent pattern mining (FPM) is important in data mining field with Apriori algorithm to be one of the commonly used approaches to solve it. However, Aprori algorithm encounters an issue that the computation time increases dramatically when data size increases and when the threshold is small. Many parallel algorithms have been proposed to speed up the computation using computer clusters or grid systems. GPUs have also been applied on FPM with only few adopting OpenCL although OpenCL has the advantage of being platform independent. Thus, the aim of this research is to develop efficient parallel Aprori strategy using GPU and OpenCL. Our novel method, Candidate Slicing Frequent Pattern Mining (CSFPM) algorithm, improves over the previous method by slicing candidate information to better balance the load between processing units. This strategy is proved to be more efficient according to our experiments. For example, CSFPM is at most 2.6 times faster than the previous method. Therefore, CSFPM is an efficient parallel Apriori algorithm which can reduce computation time and improve overall performance.
PianoText: transferring musical expertise to text entry

We present PianoText, a text entry method based on a piano keyboard with an optimized mapping between notes and chords of music to letters of the English language. PianoText exemplifies the idea of transferring musical expertise to a text entry task by computationally searching for mappings between frequent motor patterns while considering their n-gram frequency distributions and respecting constraints affecting the playability of music. In the Interactivity session, audience members with piano skills can transcribe text with PianoText, and a trained pianist will show that it allows him to generate text at speeds close to that of professional QWERTY-typists.
Uncertain Location Based Range Aggregates in a Multi-dimensional Space

Uncertain data are inherent in many applications such as environmental surveillance and quantitative economics research. Recently, considerable research efforts have been put into the field of analysing uncertain data. In this paper, we study the problem of processing the uncertain location based range aggregate in a multi-dimensional space. We first formally introduce the problem, then propose a general filtering-and-verification framework to solve the problem. Two filtering techniques, named STF and PCR respectively, are proposed to significantly reduce the verification cost.
Leaf Extraction and Analysis Framework Graphical User Interface: Segmenting and Analyzing the Structure of Leaf Veins and Areoles1[W][OA]

Interest in the structure and function of physical biological networks has spurred the development of a number of theoretical models that predict optimal network structures across a broad array of taxonomic groups, from mammals to plants. In many cases, direct tests of predicted network structure are impossible given the lack of suitable empirical methods to quantify physical network geometry with sufficient scope and resolution. There is a long history of empirical methods to quantify the network structure of plants, from roots, to xylem networks in shoots and within leaves. However, with few exceptions, current methods emphasize the analysis of portions of, rather than entire networks. Here, we introduce the Leaf Extraction and Analysis Framework Graphical User Interface (LEAF GUI), a user-assisted software tool that facilitates improved empirical understanding of leaf network structure. LEAF GUI takes images of leaves where veins have been enhanced relative to the background, and following a series of interactive thresholding and cleaning steps, returns a suite of statistics and information on the structure of leaf venation networks and areoles. Metrics include the dimensions, position, and connectivity of all network veins, and the dimensions, shape, and position of the areoles they surround. Available for free download, the LEAF GUI software promises to facilitate improved understanding of the adaptive and ecological significance of leaf vein network structure.
Thermal imaging systems for real-time applications in smart cities

In the modern world, cities need to keep up with the demand for mobility, efficient infrastructure and environmental sustainability. The future smart cities use intelligent information and communication technologies to raise the quality of life. This includes computer vision as one of the main technologies. It can observe and analyse human activities from a distance in a non-invasive manner. Traditional computer vision utilises RGB cameras, but problems with this sensor include its light dependency, and the privacy issues that can be raised by people being observed. In this paper, we propose the use of thermal imaging in real-time smart city applications. Thermal cameras operate independently of light and measure the radiated infrared waves representing the temperature of the scene. In order to showcase the possibilities, we present five different applications which use thermal imaging only. These include both indoor and outdoor scenarios with the purposes of people detection, counting and tracking, as well as one application for traffic safety evaluation.
Medication Use Patterns Associated with Spirometry in Diagnosing COPD

Spirometry is necessary to diagnose and assess severity of COPD, but is used infrequently. Therapy with inhaled medications can improve COPD outcomes, but are not without risks. The use of spirometry may help mitigate the therapy risks if treatment is appropriate based on spirometry results. Before determining benefits of spirometry use, it is important to examine use of medications and the use of spirometry. Our objective was to characterize the association between the use of spirometry and respiratory medications in newly diagnosed COPD. This is a retrospective, longitudinal study using data from the Department of Veterans Affairs. We identified patients with a new diagnosis of COPD (index date). Spirometry use was measured two years before to six months after the index date. Respiratory medications were measured within one year following the index date. The association between spirometry and medication use was evaluated using logistic regressions and stratified by quintiles of the propensity scores for the probability of having had spirometry performed. A total of 81,162 patients were included and 30.8% had a spirometry performed. Patients with spirometry were more likely to have been dispensed an inhaled corticosteroid (AOR = 1.22 (95% CI, 1.11–1.36) to 1.61 (1.45–1.79)), long-acting beta-agonists (AOR = 1.41(1.25–1.58) to 1.63(1.45–1.83)), and ipratropium bromide (AOR = 1.25(1.16–1.35) to 1.64 (1.49–1.81)) across quintiles. Patients with spirometry were more likely to have medications added. The use of spirometry around a new diagnosis of COPD was associated with higher likelihood of using and adding respiratory medications after diagnosis
Playgroup Participation and Social Support Outcomes for Mothers of Young Children: A Longitudinal Cohort Study

Objective This study aimed to examine friendship networks and social support outcomes for mothers according to patterns of playgroup participation. Methods Data from the Longitudinal Study of Australian Children were used to examine the extent to which patterns of playgroup participation across the ages of 3–19 months (Wave 1) and 2–3 years (Wave 2) were associated with social support outcomes for mothers at Wave 3 (4–5 years) and four years later at Wave 5 (8–9 years). Analyses were adjusted for initial friendship attachments at Wave 1 and other socio-demographic characteristics. Results Log-binomial regression models estimating relative risks showed that mothers who never participated in a playgroup, or who participated at either Wave 1 or Wave 2 only, were 1.7 and 1.8 times as likely to report having no support from friends when the child was 4–5 years, and 2.0 times as likely to have no support at age 8–9 years, compared with mothers who persistently participated in playgroup at both Wave 1 and Wave 2. Conclusion These results provide evidence that persistent playgroup participation may acts as a protective factor against poor social support outcomes. Socially isolated parents may find playgroups a useful resource to build their social support networks.
Beyond Kyoto: Forest Management in a Time of Rapid Climate Change

Abstract: Policies to reduce global warming by offering credits for carbon sequestration have neglected the effects of forest management on biodiversity. I review properties of forest ecosystems and management options for enhancing the resistance and resilience of forests to climate change. Although forests, as a class, have proved resilient to past changes in climate, today's fragmented and degraded forests are more vulnerable. Adaptation of species to climate change can occur through phenotypic plasticity, evolution, or migration to suitable sites, with the latter probably the most common response in the past. Among the land‐use and management practices likely to maintain forest biodiversity and ecological functions during climate change are (1) representing forest types across environmental gradients in reserves; (2) protecting climatic refugia at multiple scales; (3) protecting primary forests; (4) avoiding fragmentation and providing connectivity, especially parallel to climatic gradients; (5) providing buffer zones for adjustment of reserve boundaries; (6) practicing low‐intensity forestry and preventing conversion of natural forests to plantations; ( 7) maintaining natural fire regimes; (8) maintaining diverse gene pools; and (9) identifying and protecting functional groups and keystone species. Good forest management in a time of rapidly changing climate differs little from good forest management under more static conditions, but there is increased emphasis on protecting climatic refugia and providing connectivity.