Miracle-dz/UniFAR-FTUs huggingface dataset:
Making your database available through Wikipedia: the pros and cons

Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis.
On the Origin of Superoxide Dismutase: An Evolutionary Perspective of Superoxide-Mediated Redox Signaling

The field of free radical biology originated with the discovery of superoxide dismutase (SOD) in 1969. Over the last 5 decades, a plethora of research has been performed in species ranging from bacteria to mammals that has elucidated the molecular reaction, subcellular location, and specific isoforms of SOD. However, while humans have only begun to study this class of enzymes over the past 50 years, it has been estimated that these enzymes have existed for billions of years, and may be some of the original enzymes found in primitive life. As life evolved over this expanse of time, these enzymes have taken on new and different functional roles potentially in contrast to how they were originally derived. Herein, examination of the evolutionary history of these enzymes provides both an explanation and further inquiries into the modern-day role of SOD in physiology and disease.
Sensor Saturation Compensated Smoothing Algorithm for Inertial Sensor Based Motion Tracking

In this paper, a smoothing algorithm for compensating inertial sensor saturation is proposed. The sensor saturation happens when a sensor measures a value that is larger than its dynamic range. This can lead to a considerable accumulated error. To compensate the lost information in saturated sensor data, we propose a smoothing algorithm in which the saturation compensation is formulated as an optimization problem. Based on a standard smoothing algorithm with zero velocity intervals, two saturation estimation methods were proposed. Simulation and experiments prove that the proposed methods are effective in compensating the sensor saturation.
Adaptive Topic Modeling for Detection Objectionable Text

Objectionable text content on the Web is harmful to young children. Although keyword-based methods are superior in achieving faster detection, they fail to detect text content that is semantically objectionable. A novel framework based on adaptive topic modeling is proposed to detect objectionable text content. Firstly, a weighted graph is constructed based on several seed words and a set of training texts. Feature words are then selected from the graph according to the measure which shows how likely a word to be sensitive. Adaptive LDA (Latent Dirichlet Allocation) topic model in which topic number can be automatically estimated is proposed to find the latent objectionable topic structure for the text set. An objectionable topic criterion is devised for the adaptive selection method which takes the objectionable topic characteristic into consideration. Finally, detection for a given text is evaluated based on its probability value with respect to the model. Extensive comparison experiments on real world text sets show that the proposed method can effectively detect objectionable text. The performance is superior to that of keyword-based methods with several different approaches to generate keyword list. Experiments also show that the performance is better than that of detection methods based on traditional topic modeling.
The Atmosphere-Ocean Interface Layer of NASA's Goddard Earth Observing System Model and Data Assimilation System Volume 51

The Goddard Earth Observing System (GEOS) general circulation model (GCM) includes modules for sea surface temperature (SST) diurnal warming and cool-skin layers. To support the application of a coupled atmosphere-ocean data assimilation capability, the GCM needs to be flexible enough to support both coupled atmosphere ocean general circulation model (AOGCM) and atmosphere-only (AGCM) configurations, with only minor configuration changes at the user interface. This document presents a formulation of an atmosphere-ocean interface layer (AOIL) that serves this purpose. Previous work by Akella et al. (2017) described a version of a model for near-surface temperature variations, including both both diurnal warming and cool-skin effects, that has been used since 2017 in the near-real-time GEOS FP (forward processing) weather analysis and forecasting system. The diurnal cycle of SST in that version of the GEOS atmospheric data assimilation system (ADAS) undergoes a sharp decay in the late afternoon (local time). The updated AOIL presented here includes a modification of the similarity function used in the diurnal warming model. Results from offline model runs illustrate an improvement in the near-surface (less than 0.5m depth) diurnal cycle compared to the original formulation. The new formulation requires minimal parameter tuning, and the improvements are robust across long (several month) simulation periods. This new model formulation, however, retains some deficiences from the previous module, such as a small warm bias in calm wind conditions for water depths below 1m. Our future work would include surface salinification and sea-ice into the AOIL.
Preservice elementary teachers as information and communication technology designers: an instructional systems design model based on an expanded view of pedagogical content knowledge

Abstract This study discusses the evolution of an instructional systems design (ISD) model that is based on an expanded view of Shulman's concept of pedagogical content knowledge (PCK). An initial model was evaluated in the first iteration of a design experiment, and then it was changed and assessed in two other iterations that followed. The proposed ISD model can be used in educational technology courses, elementary teacher education method courses, and teacher professional development courses to develop information and communication technology (ICT)-related PCK. ICT-related PCK comprises a body of knowledge that educators need to be able to teach with ICT. Evidence from the present study, with preservice elementary teachers, indicates that the evolved model was effective in developing some aspects of ICT-related PCK. Based on the results of the study, more systematic efforts are needed to engage preservice teachers in technology-rich design activities, so that they can adequately develop all aspects of ICT-related PCK. Finally, this study provides baseline data that can be used for comparison purposes in future studies that may be conducted to further validate or modify the suggested ISD model.
Computing loss of efficiency in optimal Bayesian decoders given noisy or incomplete spike trains

We investigate Bayesian methods for optimal decoding of noisy or incompletely-observed spike trains. Information about neural identity or temporal resolution may be lost during spike detection and sorting, or spike times measured near the soma may be corrupted with noise due to stochastic membrane channel effects in the axon. We focus on neural encoding models in which the (discrete) neural state evolves according to stimulus-dependent Markovian dynamics. Such models are sufficiently flexible that we may incorporate realistic stimulus encoding and spiking dynamics, but nonetheless permit exact computation via efficient hidden Markov model forward-backward methods. We analyze two types of signal degradation. First, we quantify the information lost due to jitter or downsampling in the spike-times. Second, we quantify the information lost when knowledge of the identities of different spiking neurons is corrupted. In each case the methods introduced here make it possible to quantify the dependence of the information loss on biophysical parameters such as firing rate, spike jitter amplitude, spike observation noise, etc. In particular, decoders that model the probability distribution of spike-neuron assignments significantly outperform decoders that use only the most likely spike assignments, and are ignorant of the posterior spike assignment uncertainty.
Feldspar: A System for Finding Information by Association

We present Feldspar, the first system that allows people to find personal information on the computer by specifying chains of other information that it is associated with, emulating the information retrieval process of human associative memory. Feldspar’s contributions include (1) a user interface for constructing retrieval queries that consist of multiple levels of associations, such as “find the folder containing the email attachment from the person I met at an event ”; and (2) algorithms for collecting the association information and for providing answers to associative queries in real-time. A user study showed that Feldspar is easy to use, and is superior to conventional browsing and searching for these kinds of retrieval tasks. We have reported Feldspar’s implementation and evaluation in our long paper at CHI 2008. Here, our discussion focuses on the design and implementation ideas that we have tried, or are currently investigating. We hope this will stimulate further discussions and help inspire more design ideas.
The effect of riverbank erosion on lives and livelihoods of rural people: a study on Nolian village, Khulna, Bangladesh

For any information: ask.author@journalbinet.com The effect and magnitude of river bank erosion are multiple because of its polygonal impact. It creates a great loss of physical and natural resources which makes the life of people more vulnerable. This study was an initiative to explore the effects of riverbank erosion on living and livelihood of rural people of Nolian village of Dacope Upazila, Khulna, Bangladesh. The current study applied survey method because the household heads were considered as the respondents. Applying face-toface interview method author collected data through an interview schedule form 336 household head. Findings revealed that 94% of respondents were affected by river bank erosion up to 9 times during their lifetimes. The inferential statistics describes that after riverbank erosion income of the household declined, in addition, their expenditure decreased. (42.0%) strongly agreed that food cost and medical cost due to riverbank tremendously increased. Majority (32.70%) household lost more than (1 to 3) metric tons of rice, and another (29.20%) lost (4 to 6) metric tons of rice. This study also explored that (36%) people and households lost (1-5) bighas of land, while (35%) household lost (6-10) bighas of land and the rest 59(10.5%) household lost (above-10) bighas of plough lands and homestead. The river bank erosion problem is increasing in Bangladesh due to lack of proper initiatives. The prevalence of river bank erosion dares to question the initiatives which had already been taken and implemented in different times in Bangladesh. Adequate measures need to be taken for stopping this situation while this study would assist the interested researchers for taking further extensive researches on this issue. Citation: Khan, B. , Nabia, S. A. and Rahman, M. A. (2018). The effect of riverbank erosion on lives and livelihoods of rural people: a study on Nolian village, Khulna, Bangladesh. Journal of Science, Technology and Environment Informatics, 06(01), 466-473. Crossref: https://doi.org/10.18801/jstei.060118. 49
Cardiac Resynchronization Therapy in Infant with Dilated Cardiomyopathy during Extracorporeal Membrane Oxygenator

Although heart transplantation is a final therapeutic option in pediatric patients with dilated cardiomyopathy (DCMP), the shortage of pediatric heart donors is a major obstacle. In adults with DCMP characterized by cardiac dyssynchrony, cardiac resynchronization therapy (CRT) is known to be an effective treatment option. However, there is a lack of evidence on the effectiveness of CRT in infants with DCMP. Several studies have reported improvement in hemodynamics and cardiac performance following CRT in infants with DCMP. Here, we report CRT in an infant with DCMP during extracorporeal membrane oxygenation with 5 months of follow-up.
A Bayesian Computation for The Prediction Of Football Match Results Using Artificial Neural Network

The problem of modelling football data has become increasingly popular in the last few years and many different models have been proposed with the aim of estimating the characteristics that bring a team to lose or win a game, or to predict the score of a particular match. We propose a Bayesian model to test its predictive strength on data for the Turkish Super League 2008-2009. We compare the predictive performance of Bayesian approach with a Poisson Log linear approach and Artificial Neural Network approaches.
Variational Bayes for Spatiotemporal Identification of Event-Related Potential Subcomponents

We propose a novel method for detection and tracking of event-related potential (ERP) subcomponents. The ERP subcomponent sources are assumed to be electric current dipoles (ECDs), and their locations and parameters (amplitude, latency, and width) are estimated and tracked from trial to trial. Variational Bayes implies that the parameters can be estimated separately using the likelihood function of each parameter. Estimations of ECD locations, which have nonlinear relations to the measurement, are obtained by particle filtering. Estimations of the amplitude and noise covariance matrix of the measurement are optimally given by the maximum likelihood (ML) approach, while estimations of the latency and the width are obtained by the Newton-Raphson technique. New recursive methods are introduced for both the ML and Newton-Raphson approaches to prevent divergence in the filtering procedure where there is a very low SNR. The main advantage of the method is the ability to track varying ECD locations. The proposed method is assessed using simulated as well as real data, and the results emphasize the potential of this new approach for the analysis of real-time measures of neural activity.
Implications of diabetes in patients with acute coronary syndromes. The Global Registry of Acute Coronary Events.

BACKGROUND There are limited data describing the presenting characteristics, management, and outcomes of diabetic and nondiabetic patients with an acute coronary syndrome (ACS). OBJECTIVE To examine differences in these factors, patients with ST-segment elevation acute myocardial infarction, non-ST-segment elevation acute myocardial infarction, and unstable angina were enrolled in a large multinational coronary disease registry. METHODS The Global Registry of Acute Coronary Events is a prospective observational study of patients hospitalized with an ACS at 94 hospitals in 14 countries. The study sample consisted of 5403 patients with ST-segment elevation acute myocardial infarction, 4725 with non-ST-segment elevation acute myocardial infarction, and 5988 with unstable angina. RESULTS Approximately 1 in 4 patients presented to participating hospitals with a history of diabetes. Patients with diabetes were older, more often women, with a greater prevalence of comorbidities, and they were less likely to be treated with effective cardiac therapies than nondiabetic patients. Patients with diabetes who developed an ACS were at increased risk for each hospital outcome examined including heart failure, renal failure, cardiogenic shock, and death. These differences remained after adjustment for potentially confounding prognostic factors. CONCLUSIONS A considerable proportion of patients with an ACS has diabetes and is at increased risk for adverse outcomes compared with patients without diabetes. There are certain proven therapeutic strategies that remain underused in the diabetic population. A more widespread awareness of this increased risk and a more diligent use of proven cardiac treatment approaches are indicated for patients with diabetes who develop an ACS.
The effect of 1,25‐dihydroxyvitamin D3 on the cytoskeleton of rat calvaria and rat osteosarcoma (ROS 17/2.8) osteoblastic cells

1,25‐dihydroxy vitamin D3 produces pronounced shape changes in fetal rat calvaria and osteosarcoma‐derived (ROS 17/2.8) osteoblastic cells, characterized by retracting processes and cell rounding followed by aggregation of cells. The 1,25(OH)2D3 effect on ROS 17/2.8 morphology was determined morphometrically on scanning electron micrographs. The hormone effect was found to be dose dependent between 10−12 and 10−9 M. The shape changes appeared 12 h after hormone (10−10 M) addition and were present in 80% of the ROS 17/2.8 cells and in 50% of the calvaria cells at 72 h. Cycloheximide at 1 μM, inhibited the hormone‐dependent change in morphology. The 1,25(OH)2D3 effects were partially mimicked by 10−8 M 25(OH)D3 but not by 10−10 M 25(OH)D3 or 10−11‐10−8 M 24,25(OH)2D3. 1,25‐dihydroxy vitamin D3 also increased cell proliferation twofold at 14 days in serum‐free medium.
Production of Biofuels from Microalgae

The incredible increase in world population, which could reach nine billion by 2050, and the rapid progress of globalization in recent decades have put pressure on the food and energy sectors. The resources currently available for energy production are insufficient to meet future demand. These facts are pushing governments and scientific organizations all over the world to search for alternative renewable energy sources. Microalgae present an ideal, resurgent resource for the production of biofuels, especially biodiesel and biogas, because their lipid productivity is greater than that of other terrestrial food crops. However, from a biotechnological point of view, the use of microalgae requires further investigation and development to be economically viable, particularly in regard to cost and biomass production. The most important step in the use of microalgae for biofuel production is strain selection. The optimal strain must be able to withstand outdoor conditions and survive seasonality. Four related manuscripts were prepared during my Ph.D. project. Two of them have been published, one has been submitted for publication, and the fourth is ready for submission. Together, they focus on new strategies for strain selection, lipid production increase, lipid vesicles detection and imaging, total cost reduction strategies, biodiesel production from promising strains, and biogas production from the remaining microalgal residues. From a practical perspective, only a few microalgal species have been investigated for pharmaceutical and industrial applications. Throughout my Ph.D. project, I have identified microalgal strains able to grow at high temperature and under light stress, as a step toward the development of sustainable microalgal fuels. The four manuscripts that have resulted from my project are described below. In the first manuscript, entitled “Isolation and characterization of thermo-tolerant Egyptian marine microalgae as proposed candidates for biodiesel prod
Compassionate revanchism: The blurry geography of homelessness in the USA

In this article we move beyond the binary division between care and punishment in urban studies of homelessness to examine how caring institutions are themselves crucial to the punitive and exclusionary project of capitalist urbanisation. Based on ethnographic and archival analysis of homelessness management in Fresno, California, and Phoenix, Arizona, we show how punitive measures and institutions of care often emerge simultaneously and operate in tandem as part of a broader scheme for urban revitalisation. Further, we show how caring institutions themselves often perform the function of controlling homeless people’s movements in the city, while punitive institutions adopt more caring tactics. Thus, we argue for a focus on how compassion and criminalisation are regularly blurred.
Mutant p53 Attenuates the Anti-Tumorigenic Activity of Fibroblasts-Secreted Interferon Beta

Mutations in the p53 tumor suppressor protein are highly frequent in tumors and often endow cells with tumorigenic capacities. We sought to examine a possible role for mutant p53 in the cross-talk between cancer cells and their surrounding stroma, which is a crucial factor affecting tumor outcome. Here we present a novel model which enables individual monitoring of the response of cancer cells and stromal cells (fibroblasts) to co-culturing. We found that fibroblasts elicit the interferon beta (IFNβ) pathway when in contact with cancer cells, thereby inhibiting their migration. Mutant p53 in the tumor was able to alleviate this response via SOCS1 mediated inhibition of STAT1 phosphorylation. IFNβ on the other hand, reduced mutant p53 RNA levels by restricting its RNA stabilizer, WIG1. These data underscore mutant p53 oncogenic properties in the context of the tumor microenvironment and suggest that mutant p53 positive cancer patients might benefit from IFNβ treatment.
Why do shrews twitter? Communication or simple echo-based orientation

Shrews are very vocal animals. We tested behaviourally whether the high-pitched laryngeal ‘twittering’ calls of as-yet unclear function serve for communication or echo-based orientation. We used a representative species from each of the two largest phylogenetic groups of shrews. In both species, experimental manipulation of substrate density, but not of the likelihood of conspecific presence, affected the shrews' call rate when exploring an unknown environment. This adaptation of call rate to the degree of habitat clutter parallels bat echolocation and suggests that shrews may use the echoes and reverberations of their calls for identifying routes through their habitat or for probing habitat type. To assess the acoustic feasibility of shrew echo orientation, we ensonified shrew habitats in the field with an ‘artificial shrew’ (small speaker mounted close to a sensitive microphone). The data showed that shrew-like calls can indeed yield echo scenes useful for habitat assessment at close range, but beyond the range of the shrews' vibrissae.
The Internet Democracy: A Predictive Model Based on Web Text Mining

This thesis describes an algorithm that predicts events by mining Internet data. A number of specialized Internet search engine queries were designed in order to summarize results from relevant web pages. At the core of these queries was a set of algorithms that embodied the wisdom of crowds hypothesis. This hypothesis states that under the proper conditions the aggregated opinion of a large number of non-experts is more accurate than the opinions of a set of experts. Natural language processing techniques were used to summarize the opinions expressed on a large number of web pages. The specialized queries predicted actual events at a statistically significant level. These data confirmed the hypothesis that the Internet can function as a wise crowd and make accurate predictions of future events.