Miracle-dz/UniFAR-FTUs huggingface dataset:
Cardiac Cell Generation from Encapsulated Embryonic Stem Cells in Static and Scalable Culture Systems

Heart diseases are major causes of morbidity and mortality linked to extensive loss of cardiac cells. Embryonic stem cells (ESCs) give rise to cardiomyocyte-like cells, which may be used in heart cell replacement therapies. Most cardiogenic differentiation protocols involve the culture of ESCs as embryoid bodies (EBs). Stirred-suspension bioreactor cultures of ESC aggregates may be employed for scaling up the production of cardiomyocyte progeny but the wide range of EB sizes and the unknown effects of the hydrodynamic environment on differentiating EBs are some of the major challenges in tightly controlling the differentiation outcome. Here, we explored the cardiogenic potential of mouse ESCs (mESCs) and human ESCs (hESCs) encapsulated in poly-l-lysine (pLL)-coated alginate capsules. Liquefaction of the capsule core led to the formation of single ESC aggregates within each bead and their average size depended on the concentration of seeded ESCs. Encapsulated mESCs were directed along cardiomyogenic lineages in dishes under serum-free conditions with the addition of bone morphogenetic protein 4 (BMP4). Human ESCs in pLL-layered liquid core (LC) alginate beads were also differentiated towards heart cells in serum-containing media. Besides the robust cell proliferation, higher fractions of cells expressing cardiac markers were detected in ESCs encapsulated in LC than in solid beads. Furthermore, we demonstrated for the first time that ESCs encapsulated in pLL-layered LC alginate beads can be coaxed towards heart cells in stirred-suspension bioreactors. Encapsulated ESCs yielded higher fractions of Nkx2.5- and GATA4-positive cells in the bioreactor compared to dish cultures. Differentiated cells formed beating foci that responded to chronotropic agents in an organotypic manner. Our findings warrant further development and implementation of microencapsulation technologies in conjunction with bioreactor cultivation to enable the production of stem cell-derived cardiac cells appropriate for clinical therapies and applications.
Analysis of Computer Intrusions Using Sequences of Function Calls

This paper demonstrates the value of analyzing sequences of function calls for forensic analysis. Although this approach has been used for intrusion detection (that is, determining that a system has been attacked), its value in isolating the cause and effects of the attack has not previously been shown. We also look for not only the presence of unexpected events but also the absence of expected events. We tested these techniques using reconstructed exploits in su, ssh, and lpr, as well as proof-of-concept code, and, in all cases, were able to detect the anomaly and the nature of the vulnerability.
A Functional Misexpression Screen Uncovers a Role for Enabled in Progressive Neurodegeneration

Drosophila is a well-established model to study the molecular basis of neurodegenerative diseases. We carried out a misexpression screen to identify genes involved in neurodegeneration examining locomotor behavior in young and aged flies. We hypothesized that a progressive loss of rhythmic activity could reveal novel genes involved in neurodegenerative mechanisms. One of the interesting candidates showing progressive arrhythmicity has reduced enabled (ena) levels. ena down-regulation gave rise to progressive vacuolization in specific regions of the adult brain. Abnormal staining of pre-synaptic markers such as cystein string protein (CSP) suggest that axonal transport could underlie the neurodegeneration observed in the mutant. Reduced ena levels correlated with increased apoptosis, which could be rescued in the presence of p35, a general Caspase inhibitor. Thus, this mutant recapitulates two important features of human neurodegenerative diseases, i.e., vulnerability of certain neuronal populations and progressive degeneration, offering a unique scenario in which to unravel the specific mechanisms in an easily tractable organism.
Semantic similarity of short texts

This paper presents a method for measuring the semantic similarity of texts using a corpus based measure of semantic word similarity and a normalized and modified versions of the Longest Common Subsequence (LCS) string matching algorithm. Existing methods for computing text similarity have focused mainly on either large documents or individual words. In this paper, we focus on computing the similarity between two sentence or between two short paragraphs. The proposed method can be exploited in a variety of applications involving textual knowledge representation and knowledge discovery. Evaluation results on two different data sets show that our method outperforms several competing methods.
Mutation of the priA Gene of Neisseria gonorrhoeae Affects DNA Transformation and DNA Repair

ABSTRACT In Escherichia coli, PriA is central to the restart of chromosomal replication when replication fork progression is disrupted and is also involved in homologous recombination and DNA repair. To investigate the role of PriA in recombination and repair in Neisseria gonorrhoeae, we identified, cloned, and insertionally inactivated the gonococcal priA homologue. The priA mutant showed a growth deficiency and decreased DNA repair capability and was completely for deficient in DNA transformation compared to the isogenic parental strain. The priA mutant was also more sensitive to the oxidative damaging agents H2O2 and cumene hydroperoxide compared to the parental strain. These phenotypes were complemented by supplying a functional copy of priA elsewhere in the chromosome. The N. gonorrhoeae priA mutant showed no alteration in the frequency of pilin antigenic variation. We conclude that PriA participates in DNA repair and DNA transformation processes but not in pilin antigenic variation.
Gamification of a Reviewing Process Using Self-Setting Question and Game Mechanism in Undergraduate Education

Reviewing a course and preparing for a term exam are very stressful processes for most students. As explained by Csikszentmihalyi, a proper challenge level could be used as an effective motivation for the students to review and prepare a term exam. However, the students face with undue stress and do not think that reviewing a course and preparing for a term exam are interesting in a considerable proportion of cases. To provide a fun experience in reviewing a course and preparing for a term exam is the purpose of this paper. To make a reviewing process fun, this study suggests a gamified reviewing process based on a gamification theory. This study validates the gamified reviewing process using a case study. The proposed reviewing process using a gamification theory could be used as an effective tool which lessens the stress level of the students in education environments.
Sampling Content Distributed Over Graphs

Despite recent effort to estimate topology characteristics of large graphs (i.e., online social networks and peer-to-peer networks), little attention has been given to develop a formal methodology to characterize the vast amount of content distributed over these networks. Due to the large scale nature of these networks, exhaustive enumeration of this content is computationally prohibitive. In this paper, we show how one can obtain content properties by sampling only a small fraction of vertices. We first show that when sampling is naively applied, this can produce a huge bias in content statistics (i.e., average number of content duplications). To remove this bias, one may use maximum likelihood estimation to estimate content characteristics. However our experimental results show that one needs to sample most vertices in the graph to obtain accurate statistics using such a method. To address this challenge, we propose two efficient estimators: special copy estimator (SCE) and weighted copy estimator (WCE) to measure content characteristics using available information in sampled contents. SCE uses the special content copy indicator to compute the estimate, while WCE derives the estimate based on meta-information in sampled vertices. We perform experiments to show WCE and SCE are cost effective and also ``{\em asymptotically unbiased}''. Our methodology provides a new tool for researchers to efficiently query content distributed in large scale networks.
Dynamic Probabilistic Network Based Human Action Recognition

This paper examines use of dynamic probabilistic networks (DPN) for human action recognition. The actions of lifting objects and walking in the room, sitting in the room and neutral standing pose were used for testing the classification. The research used the dynamic interrelation between various different regions of interest (ROI) on the human body (face, body, arms, legs) and the time series based events related to the these ROIs. This dynamic links are then used to recognize the human behavioral aspects in the scene. First a model is developed to identify the human activities in an indoor scene and this model is dependent on the key features and interlinks between the various dynamic events using DPNs. The sub ROI are classified with DPN to associate the combined interlink with a specific human activity. The recognition accuracy performance between indoor (controlled lighting conditions) is compared with the outdoor lighting conditions. The accuracy in outdoor scenes was lower than the controlled environment.
Granulocyte Colony-Stimulating Factor and Its Potential Application for Skeletal Muscle Repair and Regeneration

Granulocyte colony-stimulating factor (G-CSF) was originally discovered in the context of hematopoiesis. However, the identification of the G-CSF receptor (G-CSFR) being expressed outside the hematopoietic system has revealed wider roles for G-CSF, particularly in tissue repair and regeneration. Skeletal muscle damage, including that following strenuous exercise, induces an elevation in plasma G-CSF, implicating it as a potential mediator of skeletal muscle repair. This has been supported by preclinical studies and clinical trials investigating G-CSF as a potential therapeutic agent in relevant disease states. This review focuses on the growing literature associated with G-CSF and G-CSFR in skeletal muscle under healthy and disease conditions and highlights the current controversies.
Exploiting High-Level Semantics for No-Reference Image Quality Assessment of Realistic Blur Images

To guarantee a satisfying Quality of Experience (QoE) for consumers, it is required to measure image quality efficiently and reliably. The neglect of the high-level semantic information may result in predicting a clear blue sky as bad quality, which is inconsistent with human perception. Therefore, in this paper, we tackle this problem by exploiting the high-level semantics and propose a novel no-reference image quality assessment method for realistic blur images. Firstly, the whole image is divided into multiple overlapping patches. Secondly, each patch is represented by the high-level feature extracted from the pre-trained deep convolutional neural network model. Thirdly, three different kinds of statistical structures are adopted to aggregate the information from different patches, which mainly contain some common statistics i.e., the mean & standard deviation, quantiles and moments). Finally, the aggregated features are fed into a linear regression model to predict the image quality. Experiments show that, compared with low-level features, high-level features indeed play a more critical role in resolving the aforementioned challenging problem for quality estimation. Besides, the proposed method significantly outperforms the state-of-the-art methods on two realistic blur image databases and achieves comparable performance on two synthetic blur image databases.
Using the Proteomics Identifications Database (PRIDE)

The Proteomics Identifications Database (PRIDE) is a public data repository designed to store, disseminate, and analyze mass spectrometry based proteomics datasets. The PRIDE database can accommodate any level of detailed metadata about the submitted results, which can be queried, explored, viewed, or downloaded via the PRIDE Web interface. The PRIDE database also provides a simple, yet powerful, access control mechanism that fully supports confidential peer‐reviewing of data related to a manuscript, ensuring that these results remain invisible to the general public while allowing referees and journal editors anonymized access to the data. This unit describes in detail the functionality that PRIDE provides with regards to searching, viewing, and comparing the available data, as well as different options for submitting data to PRIDE. Curr. Protoc. Bioinform. 21:13.8. 1‐13.8. 19. © 2008 by John Wiley & Sons, Inc.
ENGLISH VERB PARTICLES AND THEIR ACQUISITION. A COGNITIVE APPROACH

This paper revisits the issue of English phrasal verbs from the perspective of particles and the meaning they contribute to the composite meaning as a whole. The question it addresses is whether particles are purely idiomatic (i.e. arbitrarily or chaotically used) or whether they rather consist of clusters of related and transparent meanings so that they can be used in a quite motivated, logical way. Following the cognitive linguistic approach, the paper will consider the spatial domain as the source for a large variety of semantic extensions to non-locative domains through metonymy and metaphor and will analyze the meanings of two of the most frequently used particles in English: OUT and UP. Therefore, the analysis is meant to demonstrate that English verb particles disclose figurative related meanings derived from a central/prototypical locative meaning. The abstract senses did not develop at random but systematically, and this systematicity should not be disregarded if we really want to reduce the amount of memory work that learners of English (including non-native speaking teachers and translators) must invest in learning how particles and phrasal verbs are used.
Initiation of lamellipodia and ruffles involves cooperation between mDia1 and the Arp2/3 complex

ABSTRACT Protrusion of lamellipodia and ruffles requires polymerization of branched actin filaments by the Arp2/3 complex. Although regulation of Arp2/3 complex activity has been extensively investigated, the mechanism of initiation of lamellipodia and ruffles remains poorly understood. Here, we show that mDia1 acts in concert with the Arp2/3 complex to promote initiation of lamellipodia and ruffles. We find that mDia1 is an epidermal growth factor (EGF)-regulated actin nucleator involved in membrane ruffling using a combination of knockdown and rescue experiments. At the molecular level, mDia1 polymerizes linear actin filaments, activating the Arp2/3 complex, and localizes within nascent and mature membrane ruffles. We employ functional complementation experiments and optogenetics to show that mDia1 cooperates with the Arp2/3 complex in initiating lamellipodia and ruffles. Finally, we show that genetic and pharmacological interference with this cooperation hampers ruffling and cell migration. Thus, we propose that the lamellipodium- and ruffle-initiating machinery consists of two actin nucleators that act sequentially to regulate membrane protrusion and cell migration. Highlighted Article: The formin mDia1 nucleates linear actin filaments that serve as mother filaments for initial activation of the Arp2/3 complex and formation of lamellipodia and ruffles.
A Generic Method for Identifying Maintainability Requirements Using ISO Standards

ISO 9126 standards for the software product quality; includes maintainability requirements for the software Quality. The software maintainability requirements can be measured internally and externally; According to these standards maintainability requirements shall be apportioned to set of maintainability requirements for lower level products to conform to the maintenance concept, maintainability requirements of the system and the maintainability analysis shall identify maintainability critical items. This paper presents a method for identifying the maintainability requirements. The proposed method suggesting a generic model to locate and measure all maintainability requirements as defined in ISO.
The impact of chronic migraine: The Chronic Migraine Epidemiology and Outcomes (CaMEO) Study methods and baseline results

Background Longitudinal migraine studies have rarely assessed headache frequency and disability variation over a year. Methods The Chronic Migraine Epidemiology and Outcomes (CaMEO) Study is a cross-sectional and longitudinal Internet study designed to characterize the course of episodic migraine (EM) and chronic migraine (CM). Participants were recruited from a Web-panel using quota sampling in an attempt to obtain a sample demographically similar to the US population. Participants who passed the screener were assessed every three months with the Core (baseline, six, and 12 months) and Snapshot (months three and nine) modules, which assessed headache frequency, headache-related disability, treatments, and treatment satisfaction. The Core also assessed resource use, health-related quality of life, and other features. One-time cross-sectional modules measured family burden, barriers to medical care, and comorbidities/endophenotypes. Results Of 489,537 invitees, we obtained 58,418 (11.9%) usable returns including 16,789 individuals who met ICHD-3 beta migraine criteria (EM (<15 headache days/mo): n = 15,313 (91.2%); CM (≥15 headache days/mo): n = 1476 (8.8%)). At baseline, all qualified respondents (n = 16,789) completed the Screener, Core, and Barriers to Care modules. Subsequent modules showed some attrition (Comorbidities/Endophenotypes, n = 12,810; Family Burden (Proband), n = 13,064; Family Burden (Partner), n = 4022; Family Burden (Child), n = 2140; Snapshot (three months), n = 9741; Core (six months), n = 7517; Snapshot (nine months), n = 6362; Core (12 months), n = 5915). A total of 3513 respondents (21.0%) completed all modules, and 3626 (EM: n = 3303 (21.6%); CM: n = 323 (21.9%)) completed all longitudinal assessments. Conclusions The CaMEO Study provides cross-sectional and longitudinal data that will contribute to our understanding of the course of migraine over one year and quantify variations in headache frequency, headache-related disability, comorbidities, treatments, and familial impact.
SIC-MMSE Detection for Filter Bank Multicarrier Systems

Filter bank multicarrier is one of the candidates for next generation mobile radio systems. Using filtered sub-channels reduces side-lopes as well as interference among sub-channels. Symbols overlap in time and are not separated by a cyclic prefix resulting in inter-symbol inference as well as interference from adjacent sub-channels under multi-path propagation. Equalization methods known from OFDM can not be directly applied. However, a linear per-subchannel equalizer with minimum mean-squared error has been proposed. This has also been used for iterative decoding and equalization by remodulating decoded symbols to cancel-out interference. In this short paper, we extend this concept and derive a MMSE equalizer using soft interference cancellation. Using soft-information increases performance and enables turbo equalization for filter bank multicarrier systems.
Inhibition of Gastric Lipase as a Mechanism for Body Weight and Plasma Lipids Reduction in Zucker Rats Fed a Rosemary Extract Rich in Carnosic Acid

Background Rosemary (Rosmarinus officinalis L.) extracts (REs) exhibit hepatoprotective, anti-obesity and anti-inflammatory properties and are widely used in the food industry. REs are rich in carnosic acid (CA) and carnosol which may be responsible for some of the biological activities of REs. The aim of this study was to investigate whether inhibition of lipase activity in the gut may be a mechanism by which a RE enriched in CA (40%) modulates body weight and lipids levels in a rat model of metabolic disorders and obesity. Methods and Principal Findings RE was administered for 64 days to lean (fa/+) and obese (fa/fa) female Zucker rats and body weight, food intake, feces weight and blood biochemical parameters were monitored throughout the study. Lipase activity (hydrolysis of p-nitrophenylbutyrate) was measured in the gastrointestinal tract at the end of the study and the contents of CA, carnosol and methyl carnosate were also determined. Sub-chronic administration of RE moderately reduced body weight gain in both lean and obese animals but did not affect food intake. Serum triglycerides, cholesterol and insulin levels were also markedly decreased in the lean animals supplemented with RE. Importantly, lipase activity was significantly inhibited in the stomach of the RE-supplemented animals where the highest content of intact CA and carnosol was detected. Conclusions Our results confirm that long-term administration of RE enriched in CA moderates weight gain and improves the plasma lipids profile, primarily in the lean animals. Our data also suggest that these effects may be caused, at least in part, by a significant inhibition of gastric lipase and subsequent reduction in fat absorption.
Comparing Meaning in Context (CoMiC)

I Some activities in the middle ground provide explicit, language-based context with predictable contents: I summarization, reading comprehension, information-gap activities, . ⇒ Compile a corpus with answers to reading comprehension exercises written by learners of English (CREE) (Bailey 2008; Bailey & Meurers 2008; Meurers, Ziai, Ott & Bailey 2011). I In the CoMiC project, we focus on learners of German (CREG) (Meurers, Ott & Ziai 2010).
Multiple protein-binding sites in the 5'-flanking region regulate c-fos expression

We tested sequences flanking the mouse c-fos gene for the ability to form specific DNA-protein complexes with factors present in crude nuclear extracts prepared from mammalian cells. Three such complexes were detected. One complex formed in a region necessary for the induction of c-fos expression by serum growth factors. Two additional complexes formed at sequences that contribute to basal c-fos promoter activity in vivo. These complexes represent three novel sequence-specific DNA-binding activities which appear to participate in the regulation of c-fos transcription.
Lightness and Perceptual Transparency

To estimate intrinsic descriptors of objects in the environment, effective biological vision systems must ‘discount’ extrinsic image properties that arise from changes in viewing conditions. In particular, to estimate the reflectance of surfaces, human vision must discount, or ‘take account of’, likely differences in the illumination of surfaces between one image region and another. If human vision possesses any significant degree of lightness constancy, then we would expect a target perceived to be in low illumination to appear lighter than an identical target perceived to be in higher illumination. In this paper, I present lightness illusions that run directly counter to this expectation. I suggest that mid-level and higher-level factors such as image junction structure and perceived illumination and transparency, are ineffective for generating strong lightness illusions on their own, and that these factors are not ‘stronger’ than luminance contrast in determining lightness. I discuss the implications of these results for current models of lightness perception. I also suggest a statistical justification for the highest-luminance anchoring rule for lightness.