Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Profiling of Chondrogenically Induced Multipotent Stromal Cell Aggregates Reveals Transcriptomic and Emergent Morphological Phenotypes Predictive of Differentiation Capacity

Multipotent stromal cells (MSCs) are an attractive cell source for bone and cartilage tissue repair strategies. However, the functional heterogeneity of MSCs derived from different donors and manufacturing conditions has limited clinical translation, emphasizing the need for improved methods to assess MSC chondrogenic capacity. We used functionally relevant morphological profiling to dynamically monitor emergent morphological phenotypes of chondrogenically induced MSC aggregates to identify morphological features indicative of MSC chondrogenesis. Toward this goal, we characterized the morphology of chondrogenically stimulated MSC aggregates from eight different human cell‐lines at multiple passages and demonstrated that MSC aggregates exhibited unique morphological dynamics that were both cell line‐ and passage‐dependent. This variation in 3D morphology was shown to be informative of long‐term MSC chondrogenesis based on multiple quantitative functional assays. We found that the specific morphological features of spheroid area, radius, minimum feret diameter, and minor axis length to be strongly correlated with MSC chondrogenic synthetic activity but not gene expression as early as day 4 in 3D culture. Our high‐throughput, nondestructive approach could potentially serve as a tool to identify MSC lines with desired chondrogenic capacity toward improving manufacturing strategies for MSC‐based cellular products for cartilage tissue repair. Stem Cells Translational Medicine 2018;1–12
Immunomodulatory, Apoptosis Induction and Antitumor Activities of Aqueous and Methanolic Extract of Calvatia Craniiformis in Mice Transfected with Murine Hepatocellular Carcinoma Cells

OBJECTIVES: To evaluate the Immunomodulatory, apoptosis induction and antitumor effects of aqueous and methanolic extracts of Calvatia craniiformis regarding the size of tumour mass, caspase-8 expression and apoptotic index (AI%) in mice transfected with murine hepatocellular carcinoma cell line (H22) as an experimental therapeutic system for human hepatocellular carcinoma. MATERIAL AND METHODS: Forty-eight Balb/C albino mice were transfected in legs with H22 cells. Tumour size was measured twice a week. Caspase-8 protein expression and apoptotic index determination evaluated by Immunohistochemistry. RESULTS: Tumor size significantly differed between the two groups of mice transfected with H22 cells; the first was treated with C. craniiformis aqueous extract (0.3, 0.6, 1.2) mg/kg and the second group was treated with C. craniiformis methanolic extract (0.25, 0.5, 1.0) mg/kg compared with control group. The inhibitory activity of aqueous and methanolic extracts was dose and duration dependent. The size of the tumour mass was reduced up to 87.9% when treated with 1.2 mg/kg aqueous extract and 1 mg/kg for methanolic extract. Caspase-8 expression was increased in a dose-dependent manner among H22 bearing mice treated with C. craniiformis aqueous extract (0.3, 0.6, 1.2) mg/kg. At 0.3 mg/kg, the intensity of expression was strong in (33.33%) and very strong in (66.67%). While at 0.6 mg/kg and 1.2 mg/kg the intensity of expression was strong in (33.33%) and very strong in (100%) with a significant difference (P ≤ 0.001). H22 bearing mice treated with (0.25, 0.5, 1.0) mg/kg C. craniiformis methanolic extract shows increased caspase-8 expression in a dose-dependent manner. At 0.25 mg/kg, the intensity of expression was strong in (33.33%) and very strong in (66.67%). While at 0.5 mg/kg, the intensity of expression was strong in (33.33%) and very strong in (100%). At 1.0 mg/kg, the intensity of expression was strong in (16.67%) and very strong in (83.33%) with significant difference (P ≤ 0.001). AI% of H22 bearing mice treated with C. craniiformis aqueous and methanolic extracts were significantly increased (P ≤ 0.05) compared with the untreated control group. No significant difference was reported in AI% between aqueous and methanolic extracts treated groups. CONCLUSIONS: Extracts of C. craniiformis were highly efficient in tumour growth inhibition, causing a reduction in the tumour size clinically and increase the expression of caspase-8 gene product in tumour tissue, causing increase apoptotic index of H22 cells taken from the legs of inoculated mice leading to loss of legs due to bone necrosis. Antitumor activity of C. craniiformis aqueous, and the methanolic extract was dose and duration dependent.
HldE Is Important for Virulence Phenotypes in Enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) is one of the most common causes of diarrheal illness in third world countries and it especially affects children and travelers visiting these regions. ETEC causes disease by adhering tightly to the epithelial cells in a concerted effort by adhesins, flagella, and other virulence-factors. When attached ETEC secretes toxins targeting the small intestine host-cells, which ultimately leads to osmotic diarrhea. HldE is a bifunctional protein that catalyzes the nucleotide-activated heptose precursors used in the biosynthesis of lipopolysaccharide (LPS) and in post-translational protein glycosylation. Both mechanisms have been linked to ETEC virulence: Lipopolysaccharide (LPS) is a major component of the bacterial outer membrane and is needed for transport of heat-labile toxins to the host cells, and ETEC glycoproteins have been shown to play an important role for bacterial adhesion to host epithelia. Here, we report that HldE plays an important role for ETEC virulence. Deletion of hldE resulted in markedly reduced binding to the human intestinal cells due to reduced expression of colonization factor CFA/I on the bacterial surface. Deletion of hldE also affected ETEC motility in a flagella-dependent fashion. Expression of both colonization factors and flagella was inhibited at the level of transcription. In addition, the hldE mutant displayed altered growth, increased biofilm formation and clumping in minimal growth medium. Investigation of an orthogonal LPS-deficient mutant combined with mass spectrometric analysis of protein glycosylation indicated that HldE exerts its role on ETEC virulence both through protein glycosylation and correct LPS configuration. These results place HldE as an attractive target for the development of future antimicrobial therapeutics.
Novel Sophoridine Derivatives Bearing Phosphoramide Mustard Moiety Exhibit Potent Antitumor Activities In Vitro and In Vivo

Novel mustard functionalized sophoridine derivatives were synthesized and evaluated for their cytotoxicity against of a panel of various cancer cell lines. They were shown to be more sensitive to S180 and H22 tumor cells with IC50 values ranging from 1.01–3.65 μM, and distinctly were more cytotoxic to cancer cells than normal cell L929. In addition, compounds 7a, 7c, and 7e displayed moderate tumor suppression without apparent organ toxicity in vivo against mice bearing H22 liver tumors. Furthermore, they arrested tumor cells in the G1 phase and induced cellular apoptosis. Their potential binding modes with DNA-Top I complex have also been investigated.
BIGMOMAL: Big Data Analytics for Mobile Malware Detection

Mobile malware is on the rise. Indeed, due to their popularity, smartphones represent an attractive target for cybercriminals, especially because of private user data, as these devices incorporate a lot of sensitive information about users, even more than a personal computer. As a matter of fact, besides personal information such as documents, accounts, passwords, and contacts, smartphone sensors centralise other sensitive data including user location and physical activities. In this paper, we study the problem of malware detection in smartphones, relying on supervised-machine-learning models and big-data analytics frameworks. Using the SherLock dataset, a large, publicly available dataset for smartphone-data analysis, we train and benchmark tree-based models to identify running applications and to detect malware activity. We verify their accuracy, and initial results suggest that decision trees are capable of identifying running apps and malware activity with high accuracy.
Idiopathic Pulmonary Fibrosis (IPF): An Overview

Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease characterised by chronic, progressive scarring of the lungs and the pathological hallmark of usual interstitial pneumonia. Current paradigms suggest alveolar epithelial cell damage is a key initiating factor. Globally, incidence of the disease is rising, with associated high morbidity, mortality, and economic healthcare burden. Diagnosis relies on a multidisciplinary team approach with exclusion of other causes of interstitial lung disease. Over recent years, two novel antifibrotic therapies, pirfenidone and nintedanib, have been developed, providing treatment options for many patients with IPF, with several other agents in early clinical trials. Current efforts are directed at identifying key biomarkers that may direct more customized patient-centred healthcare to improve outcomes for these patients in the future.
GraMap: QoS-Aware Indoor Mapping Through Crowd-Sensing Point Clouds with Grammar Support

Recently, several approaches have been proposed to automatically model indoor environments. Most of such efforts principally rely on the crowd to sense data such as motion traces, images, and WiFi footprints. However, large datasets are usually required to derive precise indoor models which can negatively affect the energy efficiency of the mobile devices participating in the crowd-sensing system. Furthermore, the aforementioned data types are hardly suitable for deriving 3D indoor models. To overcome these challenges, we propose GraMap, a QoS-aware automatic indoor modeling approach through crowd-sensing 3D point clouds. GraMap exploits a recently-developed sensors fusion mechanism, namely Tango technology, to cooperatively collect point clouds from the crowd. Afterward, a set of backend servers extracts the required geometrical information to derive indoor models. For the sake of improving the energy efficiency of the mobile devices, GraMap performs data quality assurance along with 3D data compression. Specifically, we propose a probabilistic quality model---implemented on the mobile devices---to ensure high-quality of the captured point clouds. In this manner, we conserve energy via sidestepping the repetition of sensing queries due to uploading low-quality point clouds. Nevertheless, the resultant indoor models may still suffer from incompleteness and inaccuracies. Therefore, GraMap leverages formal grammars which encode design-time knowledge, i.e. structural information about the building, to enhance the quality of the derived models. To demonstrate the effectiveness of GraMap, we implemented a crowd-sensing Android App to collect point clouds from volunteers. We show that GraMap derives highly-accurate models while reducing the energy costs of pre-processing and reporting the point clouds.
Policy Injection: A Cloud Dataplane DoS Attack

Enterprises continue to migrate their services to the cloud on a massive scale, but the increasing attack surface has become a natural target for malevolent actors. We show policy injection, a novel algorithmic complexity attack that enables a tenant to add specially tailored ACLs into the data center fabric to mount a denial-of-service attack through exploiting the built-in security mechanisms of the cloud management systems (CMS). Our insight is that certain ACLs, when fed with special covert packets by an attacker, may be very difficult to evaluate, leading to an exhaustion of cloud resources. We show how a tenant can inject seemingly harmless ACLs into the cloud data plane to abuse an algorithmic deficiency in the most popular cloud hypervisor switch, Open vSwitch, and reduce its effective peak performance by 80--90%, and, in certain cases, denying network access altogether.
Screening Method for Anti-Colon Cancer Drugs Using Two Sensor Cell Lines with Human β4-Galactosyltransferase 4 Gene Promoters

The increased expression of β4-galactosyltransferase (β4GalT) 4 is closely associated with poor prognosis of colon cancer. Recently, we showed that the expression of the β4GalT4 gene is regulated by the 0.17 kb core promoter region containing one binding site for Specificity protein 1 (Sp1). To develop a screening method for anti-colon cancer drugs, two sensor cell lines having the luciferase gene under the control of two β4GalT4 gene promoters that differed in length were established from SW480 human colon cancer cells. The hGT4-0.17-sensor cells possessed the luciferase reporter driven by the 0.17 kb promoter, while the hGT4-0.3-sensor cells possessed the luciferase reporter driven by the 0.3 kb promoter containing one binding site each for colon cancer-related transcription factors including activator protein 2, E2F, caudal-related homeobox transcription factors, and Runt-related transcription factors besides Sp1. Upon treatment with mitogen-activated protein kinase signaling inhibitor U0126, the promoter activities of the hGT4-0.3-sensor cells decreased significantly, while those of the hGT4-0.17-sensor cells remained unchanged. These results suggest that the responsiveness to U0126 differs between two sensor cell lines due to the different regulation of the luciferase reporters. This study provides the screening method for anti-colon cancer drugs by the combination of two sensor cell lines.
Cancer Classification by Gene Subset Selection from Microarray Dataset

Microarray dataset contains huge number of genes, many of which are irrelevant regarding cancer classification and as a result classification accuracy is reduced. Therefore, the dataset should be pre-processed to filter out these redundant genes. In this paper, initially a Pareto optimality based Multi-objective Genetic Algorithm has been proposed where non-linear cellular automata is employed to overcome the demerits of random initialization to generate initial population in high dimensional space. The fitness functions are defined based on both attribute dependency and boundary region exploration of rough set theory and Log-Likelihood ratio to select the informative genes. The chromosomes are hybridized by applying multi-point crossover; whereas proximity mutation builds on Flip-bit mutation with a little modification to produce fittest offspring. Finally, the gene subset with strong biological significance in cancer treatment is obtained from the Pareto dominant solutions. Performances are investigated on publicly available microarray cancer datasets and compared with the state-of-the-art methods to demonstrate the effectiveness of the proposed method.
The effect of skeleton screens: Users' perception of speed and ease of navigation

Progression bars and spinners have long been the norm when providing feedback during wait times on the web. However, a more recent trend is the use of skeleton screens. This paper aims to evaluate the usefulness of skeleton screens as an alternative to spinners. This is done user testing a fictional news site with two variations, one showing skeleton screens before content is loaded, and another utilizing spinners. Both a questionnaire and measuring timing while finding a specified article when entering a website for the first time was used. The results show that the page using skeleton screens, scored higher on average on both perceived speed and ease of navigation. However, people using the page with spinners were faster at finding the article when entering the site for the first time. The results of this paper cannot show any significant differences in any of the comparisons between the web pages.
On the Optimality of the Kautz-Singleton Construction in Probabilistic Group Testing

We consider the probabilistic group testing problem where d random defective items in a large population of N items are identified with high probability by applying binary tests. It is known that $\Theta(d\log N)$ tests are necessary and sufficient to recover the defective set with vanishing probability of error. However, to the best of our knowledge, there is no explicit (deterministic) construction achieving $\Theta(d\log N)$ tests in general. In this work, we show that a famous construction introduced by Kautz and Singleton for the combinatorial group testing problem (which is known to be suboptimal for combinatorial group testing for moderate values of d) achieves the order optimal $\Theta(d\log N)$ tests in the probabilistic group testing problem. This provides the first strongly explicit construction achieving the order optimal result in the probabilistic group testing setting. To prove the order-optimality of Kautz and Singleton’s construction in the probabilistic setting, we provide a novel analysis of the probability of a non-defective item being covered by a random defective set directly, rather than arguing from combinatorial properties of the underlying code, which has been the main approach in the literature. Furthermore, we use a recursive technique to convert this construction into one that can also be efficiently decoded with only a log-log factor increase in the number of tests.
Retweeting Risk Communication: The Role of Threat and Efficacy

Social media platforms like Twitter and Facebook provide risk communicators with the opportunity to quickly reach their constituents at the time of an emerging infectious disease. On these platforms, messages gain exposure through message passing (called “sharing” on Facebook and “retweeting” on Twitter). This raises the question of how to optimize risk messages for diffusion across networks and, as a result, increase message exposure. In this study we add to this growing body of research by identifying message‐level strategies to increase message passing during high‐ambiguity events. In addition, we draw on the extended parallel process model to examine how threat and efficacy information influence the passing of Zika risk messages. In August 2016, we collected 1,409 Twitter messages about Zika sent by U.S. public health agencies’ accounts. Using content analysis methods, we identified intrinsic message features and then analyzed the influence of those features, the account sending the message, the network surrounding the account, and the saliency of Zika as a topic, using negative binomial regression. The results suggest that severity and efficacy information increase how frequently messages get passed on to others. Drawing on the results of this study, previous research on message passing, and diffusion theories, we identify a framework for risk communication on social media. This framework includes four key variables that influence message passing and identifies a core set of message strategies, including message timing, to increase exposure to risk messages on social media during high‐ambiguity events.
Correlates of the Timely Initiation of Complementary Feeding among Children Aged 6–23 Months in Rupandehi District, Nepal

Although the predictors of the timely initiation of complementary feeding are well-known elsewhere, there is less awareness of the topic in Nepal. The current study was undertaken to identify the correlates of timely initiation of complementary feeding among children aged 6–23 months. A community-based cross-sectional study was conducted in the Rupandehi district, Nepal. A total of 155 mother-child pairs were selected using a simple random sampling technique. Logistic regression with adjustment for potential confounders was employed to examine the independent association between risk factors and the timely initiation of complementary feeding. Fewer than 3 in 5 children aged 6–23 months received complementary feeding at the recommended time. Literate mothers and a maternal occupation in the service or business sectors were found to be associated with complementary feeding at 6 months. In addition, child characteristics such as birth order, male children, and those fed micronutrients were also more likely to have been received complementary feeding at 6 months than their counterparts. Maternal education and occupation, and child characteristics such as, birth order, male gender, and micronutrient consumption, which are correlates of the timely initiation of complementary feeding, suggest that the Nepalese Infant and Young Child Feeding (IYCF) programme should target these predictors while designing preventive strategies.
Real-time monitoring of DNA G-quadruplexes in living cells with a small-molecule fluorescent probe

Abstract G-quadruplex DNA has been viewed as a prospective anti-cancer target owing to its potential biological relevance. Real-time monitoring of DNA G-quadruplex structures in living cells can provide valuable insights into the relationship between G-quadruplex formation and its cellular consequences. However, the probes capable of detecting DNA G-quadruplexes in living cells are still very limited. Herein, we reported a new fluorescent probe, IMT, for real-time visualization of DNA G-quadruplex structures in living cells. Using IMT as a fluorescent indicator, the quantity changes of DNA G-quadruplex at different points in time during continuous cellular progression responding to Aphidicolin and Hydroxyurea treatment have been directly visualized. Our data demonstrate that IMT will be a valuable tool for exploring DNA G-quadruplexes in live cells. Further application of IMT in fluorescence imaging may reveal more information on the roles of DNA G-quadruplexes in biological systems.
An Analysis of Quorum-based Abstractions: A Case Study using Gorums to Implement Raft

Gorums is a novel RPC framework aimed at simplifying development of fault tolerant distributed systems. In this paper, we want to assess whether Gorums can simplify the implementation of a practical fault tolerant service that supports reconfiguration. To this end, we implemented the Raft consensus algorithm using Gorums, and show that Gorums's abstractions are useful for simplifying reconfiguration and Raft's leader election protocol. We do however discover that Raft's log replication protocol is problematic to implement with Gorums's abstractions. We attribute this difficulty to Raft's highly monolithic design, due to bundling multiple protocol features into a single RPC, violating the separation of concerns design principle. We solve this issue by developing extensions to Raft and Gorums. Our performance evaluation shows that our Raft implementation with these extensions performs better or on par with two state-of-the-art implementations. We evaluate both latency and overall throughput during normal operation, as well as under a network partition scenario.
Blimp-1 Mediates Tracheal Lumen Maturation in Drosophila melanogaster

The specification of tissue identity during embryonic development requires precise spatio-temporal coordination of gene expression. Many transcription factors required for the development of organs have been identified and their expression patterns are known; however, the mechanisms through which they coordinate gene expression in time remain poorly understood. Here, we show that hormone-induced transcription factor Blimp-1 participates in the temporal coordination of tubulogenesis in Drosophila melanogaster by regulating the expression of many genes involved in tube maturation. In particular, we demonstrate that Blimp-1 regulates the expression of genes involved in chitin deposition and F-actin organization. We show that Blimp-1 is involved in the temporal control of lumen maturation by regulating the beginning of chitin deposition. We also report that Blimp-1 represses a variety of genes involved in tracheal maturation. Finally, we reveal that the kinase Btk29A serves as a link between Blimp-1 transcriptional repression and apical extracellular matrix organization.