Miracle-dz/UniFAR-FTUs huggingface dataset:
MICRO PROPAGATION AND TISSUE CULTURE OF THE ENDANGERED MEDICINAL PLANT WITHANIA SOMNIFERA BY THE DIRECT SHOOT AND ROOT INITIATION METHOD

Leaf and Cotyledon explants of Withania somnifera (L). Dunal were used to evaluate the effect of different growth regulators on the in vitro direct shoot and root initiation methods. Four different explants were used to establish callus shoot and root direct regeneration. In the first experiment leaf segments were cultured on MS basal supplemented with 2,4 - Dichlorophenoxyacetic acid (2,4 - D, 0.1-20.0 mg/L), with combination of Naphthalene acetic acid (NAA 0.1-20 mg/L) and Benzylaminopurin (0.1-20 mg/L). This new protocol was standardized for easy mass propagation of W. somnifera medicinal plant. Callus initiation was observed best in MS media with (2,4- D 1.0-5.0 mg/L) after 16-20 days (93%). Highest maximum number of multiple shoots was obtained on MS medium (BAP 3.0 - 5.0 mg/L). The shoots were seaperated from the multiple-shoots, transferred to MS medium supplemented with 1.5 - 20 mg/L NAA favored roots formation occurred in most of the shoot let 88% were successfully achieved in the MS media. The rooted plantlets were transferred to polythene bags which was containing vermi compost, sand and red soil in the ratio of 1:2:2 and kept in a mist house. After acclimatization in the mist house for 2-months, it transferred to greenhouse. The plantlets were successfully planted in the field.
Biodiversity study of endophytic fungi associated with two Quercus species in Iran

Aim of study: In this study, frequency and diversity of fungal endophyte communities inhabiting twigs and branches of apparently healthy Q. macranthera and Q. brantii in East Azerbaijan and Lorestan provinces of Iran is presented.Area of study: East Azerbaijan and Lorestan provinces in Iran.Materials and methods: Culturable fungal endophytes were recovered from wood tissues using routine technique for isolation of fungal endophytes. The identity of fungal isolates were determined based on morphological characteristics and sequences data of ITS-rDNA region and Beta-tubulin gene. Frequency and diversity among fungal communities were analyzed using chi-square test and biodiversity indices.Main results: The highest frequency and diversity was detected for fungal endophyte community recovered from Q. macranthera and East Azerbaijan province. The assemblage of endophytic fungi characterized in this study in healthy tissues of oak trees indicates that some of the fungi are possible latent pathogens such as Biscogniauxia mediterranea with 18.28% frequency followed by Alternaria alternata and Trichothecium roseum respectively. Two fungal taxa of Pyronema domesticum and Valsa persoonii are reported for the first time in Iran. Overall, the results of this study show that the plant species and growth location influence frequency and diversity of culturable fungal endophytic communities of Quercus in Iran.Keywords: Quercus macranthera, Quercus brantii, Fungal endophytes, Molecular identification.Abbreviations used: CBS (Centraal Bureau voor Schimmelcultures); CCTU (Culture Collection of University of Tabriz); GTR (General Time Reversible); HKY (Hasegawa Kishino Yano); ITS-rDNA (Internal Transcribed Space); km (kilometer) ; PDA (Potato Dextrose Agar); TUB (Tubulin).
Effects of tianeptine on symptoms of fibromyalgia via BDNF signaling in a fibromyalgia animal model

Previous reports have suggested that physical and psychological stresses may trigger fibromyalgia (FM). Stress is an important risk factor in the development of depression and memory impairments. Antidepressants have been used to prevent stress-induced abnormal pain sensation. Among various antidepressants, tianeptine has been reported to be able to prevent neurodegeneration due to chronic stress and reverse decreases in hippocampal volume. To assess the possible effect of tianeptine on FM symptoms, we constructed a FM animal model induced by restraint stress with intermittent cold stress. All mice underwent nociceptive assays using electronic von Frey anesthesiometer and Hargreaves equipment. To assess the relationship between tianeptine and expression levels of brain-derived neurotrophic factor (BDNF), cAMP response element-binding protein (CREB), and phosphorylated cAMP response element-binding protein (p-CREB), western blotting and immunohistochemistry analyses were performed. In behavioral analysis, nociception tests showed that pain threshold was significantly decreased in the FM group compared to that in the control group. Western blot and immunohistochemical analyses of medial prefrontal cortex (mPFC) and hippocampus showed downregulation of BDNF and p-CREB proteins in the FM group compared to the control group. However, tianeptine recovered these changes in behavioral tests and protein level. Therefore, this FM animal model might be useful for investigating mechanisms linking BDNF-CREB pathway and pain. Our results suggest that tianeptine might potentially have therapeutic efficacy for FM.
Modeling Growth and Bacteriocin Production by Lactobacillus amylovorus DCE 471 in Response to Temperature and pH Values Used for Sourdough Fermentations

ABSTRACT The biokinetics of cell growth of Lactobacillus amylovorus DCE 471 and bacteriocin production by this strain were investigated as a function of the temperatures (28 to 44°C) and pH values (pH 4.2 to 6.4) that are characteristic of a sourdough fermentation process. The influence of temperature and pH on microbial behavior is described by using a successfully validated predictive model.
Relationship Between Adherence to Remote Monitoring and Patient Characteristics: Observational Study in Women With Pregnancy-Induced Hypertension

Background Pregnancy-induced hypertension (PIH) is associated with high levels of morbidity and mortality in mothers, fetuses, and newborns. New technologies, such as remote monitoring (RM), were introduced in 2015 into the care of patients at risk of PIH in Ziekenhuis Oost-Limburg (Genk, Belgium) to improve both maternal and neonatal outcomes. In developing new strategies for obstetric care in pregnant women, including RM, it is important to understand the psychosocial characteristics associated with adherence to RM to optimize care. Objective The aim of this study was to explore the role of patients’ psychosocial characteristics (severity of depression or anxiety, cognitive factors, attachment styles, and personality traits) in their adherence to RM. Methods Questionnaires were sent by email to 108 mothers the day after they entered an RM program for pregnant women at risk of PIH. The Generalized Anxiety Disorder Assessment-7 and Patient Health Questionnaire-9 (PHQ-9) were used to assess anxiety and the severity of depression, respectively; an adaptation of the Pain Catastrophizing Scale was used to assess cognitive factors; and attachment and personality were measured with the Experiences in Close Relationships-Revised Scale (ECR-R), the Depressive Experiences Questionnaire, and the Multidimensional Perfectionism Scale, respectively. Results The moderate adherence group showed significantly higher levels of anxiety and depression, negative cognitions, and insecure attachment styles, especially compared with the over adherence group. The low adherence group scored significantly higher than the other groups on other-oriented perfectionism. There were no significant differences between the good and over adherence groups. Single linear regression showed that the answers on the PHQ-9 and ECR-R questionnaires were significantly related to the adherence rate. Conclusions This study demonstrates the relationships between adherence to RM and patient characteristics in women at risk of PIH. Alertness toward the group of women who show less than optimal adherence is essential. These findings call for further research on the management of PIH and the importance of individual tailoring of RM in this patient group. Trial Registration ClinicalTrials.gov NCT03509272; https://clinicaltrials.gov/ct2/show/NCT03509272
Location of the complement factor H binding site on streptococcal M6 protein

The surface M protein of group A streptococci binds factor H, a regulatory protein of the alternative complement pathway, which may contribute to the antiphagocytic activity of the M molecules. To locate the factor H binding domain in the alpha-helical coiled-coil structure of the M molecule, the M protein was cleaved with pepsin at pH 5.8, which separates the molecule approximately in half. Western blot (immunoblot), amino acid sequence, and mass spectrometric analyses revealed that factor H bound to a 14.6-kDa C-terminal fragment of the M molecule. Competitive inhibition of factor H binding to the 14.6-kDa fragment with M protein peptides localized the binding site to amino acids 256 to 292. This segment is located within the surface-exposed region of the M6 protein, identified as the C-repeat region, whose sequence is conserved among heterologous M and M-like molecules. These studies also identified a second pepsin-susceptible site with the sequence ELAK located within the cell wall-associated region of the M molecule.
The R 213 G polymorphism in SOD 3 protects against allergic airway inflammation

Rohit Gaurav,1 Jason T. Varasteh,1 Michael R. Weaver,1 Sean R. Jacobson,1 Laura Hernandez-Lagunas,2 Qing Liu,3 Eva Nozik-Grayck,2 Hong Wei Chu,1 Rafeul Alam,1 Børge G. Nordestgaard,4,5 Camilla J. Kobylecki,4 Shoaib Afzal,4,5 Geoffrey L. Chupp,3 and Russell P. Bowler1 1Department of Medicine, National Jewish Health, Denver, Colorado, USA. 2Cardiovascular Pulmonary Research Laboratories and Department of Pediatrics, University of Colorado, Aurora, Colorado, USA. 3Department of Internal Medicine, Yale University, New Haven, Connecticut, USA. 4Department of Clinical Biochemistry, Herlev and Gentofte Hospital, and 5Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Transgenic Mice Expressing the Nucleoprotein of Borna Disease Virus in either Neurons or Astrocytes: Decreased Susceptibility to Homotypic Infection and Disease

ABSTRACT The nucleoprotein (N) of Borna disease virus (BDV) is the major target of the disease-inducing antiviral CD8 T-cell response in the central nervous system of mice. We established two transgenic mouse lines which express BDV-N in either neurons (Neuro-N) or astrocytes (Astro-N). Despite strong transgene expression, neurological disease or gross behavioral abnormalities were not observed in these animals. When Neuro-N mice were infected as adults, replication of BDV was severely impaired and was restricted to brain areas with a low density of transgene-expressing cells. Notably, the virus failed to replicate in the transgene-expressing granular and pyramidal neurons of the hippocampus (which are usually the preferred host cells of BDV). When Neuro-N mice were infected within the first 5 days of life, replication of BDV was not suppressed in most neurons, presumably because the onset of transgene expression in the brain occurred after these cells became infected with BDV. Astro-N mice remained susceptible to BDV infection, but they were resistant to BDV-induced neurological disorder. Unlike their nontransgenic littermates, Neuro-N mice with persistent BDV infection did not develop neurological disease after immunization with a vaccinia virus vector expressing BDV-N. In contrast to the situation in wild-type mice, this treatment also failed to induce N-specific CD8 T cells in the spleens of both transgenic mouse lines. Thus, while resistance to BDV infection in N-expressing neurons appeared to result from untimely expression of a viral nucleocapsid component, the resistance to BDV-induced neuropathology probably resulted from immunological tolerance.
Should We Abandon the t-Test in the Analysis of Gene Expression Microarray Data: A Comparison of Variance Modeling Strategies

High-throughput post-genomic studies are now routinely and promisingly investigated in biological and biomedical research. The main statistical approach to select genes differentially expressed between two groups is to apply a t-test, which is subject of criticism in the literature. Numerous alternatives have been developed based on different and innovative variance modeling strategies. However, a critical issue is that selecting a different test usually leads to a different gene list. In this context and given the current tendency to apply the t-test, identifying the most efficient approach in practice remains crucial. To provide elements to answer, we conduct a comparison of eight tests representative of variance modeling strategies in gene expression data: Welch's t-test, ANOVA [1], Wilcoxon's test, SAM [2], RVM [3], limma [4], VarMixt [5] and SMVar [6]. Our comparison process relies on four steps (gene list analysis, simulations, spike-in data and re-sampling) to formulate comprehensive and robust conclusions about test performance, in terms of statistical power, false-positive rate, execution time and ease of use. Our results raise concerns about the ability of some methods to control the expected number of false positives at a desirable level. Besides, two tests (limma and VarMixt) show significant improvement compared to the t-test, in particular to deal with small sample sizes. In addition limma presents several practical advantages, so we advocate its application to analyze gene expression data.
Evolving an intelligent vehicle for tactical reasoning in traffic

Recent research in automated highway systems has ranged from low-level vision-based controllers to high-level route-guidance software. However there is currently no system for tactical-level reasoning. Such a system should address tasks such as passing cars, making exits on time, and merging into a traffic stream. Our approach to this intermediate-level planning combines a distributed reasoning system (PolySAPIENT) with a novel evolutionary optimization strategy (PBIL). PBIL automatically tunes PolySAPIENT module parameters in simulation by evaluating candidate modules on various traffic scenarios. Since the control interface to the simulated vehicles is identical to that on the Carnegie Mellon Navlab vehicles, modules developed using this process can be directly ported to existing hardware. This method is currently being applied to the automated highway system domain; it also generalizes to many complex robotics tasks where multiple interacting modules must simultaneously be configured without individual module feedback.
Persistent Autoantibody-Production by Intermediates between Short-and Long-Lived Plasma Cells in Inflamed Lymph Nodes of Experimental Epidermolysis Bullosa Acquisita

Autoantibodies are believed to be maintained by either the continuous generation of short-lived plasma cells in secondary lymphoid tissues or by long-lived plasma cells localized in bone marrow and spleen. Here, we show in a mouse model for the autoimmune blistering skin disease epidermolysis bullosa acquisita (EBA) that chronic autoantibody production can also be maintained in inflamed lymph nodes, by plasma cells exhibiting intermediate lifetimes. After EBA induction by immunization with a mCOL7c-GST-fusion protein, antigen-specific plasma cells and CD4 T cells were analyzed. Plasma cells were maintained for months in stable numbers in the draining lymph nodes, but not in spleen and bone marrow. In contrast, localization of mCOL7c-GST -specific CD4 T cells was not restricted to lymph nodes, indicating that availability of T cell help does not limit plasma cell localization to this site. BrdU-incorporation studies indicated that pathogenic mCOL7c- and non-pathogenic GST-specific plasma cells resemble intermediates between short-and long-lived plasma cells with half-lives of about 7 weeks. Immunization with mCOL7c-GST also yielded considerable numbers of plasma cells neither specific for mCOL7c- nor GST. These bystander-activated plasma cells exhibited much shorter half-lives and higher population turnover, suggesting that plasma cell lifetimes were only partly determined by the lymph node environment but also by the mode of activation. These results indicate that inflamed lymph nodes can harbor pathogenic plasma cells exhibiting distinct properties and hence may resemble a so far neglected site for chronic autoantibody production.
Model Checking Constraint LTL over Trees

Constraint automata are an adaptation of B\"uchi-automata that process data words where the data comes from some relational structure S. Every transition of such an automaton comes with constraints in terms of the relations of S. A transition can only be fired if the current and the next data values satisfy all constraints of this transition. These automata have been used in the setting where S is a linear order for deciding constraint LTL with constraints over S. In this paper, S is the infinitely branching infinite order tree T. We provide a PSPACE algorithm for emptiness of T-constraint automata. This result implies PSPACE-completeness of the satisfiability and the model checking problem for constraint LTL with constraints over T.
Apoptosis of larval cells during amphibian metamorphosis

Programmed cell death occurs in a variety of organs during amphibian metamorphosis and is usually identified by electron microscopy as apoptosis or its modifications. Because of the massive cell death that occurs during a short period, amphibian organs serve as an ideal model system for the study of mechanisms underlying programmed cell death. In this article, a series of morphological changes in apoptosis from their nuclear changes to removal by phagocytic macrophages is reviewed, mainly in the small intestine of metamorphosing Xenopus laevis tadpoles. It is well known that cell death during amphibian metamorphosis is under the control of thyroid hormone (TH), and changes in gene expression induced by TH have been recently analyzed in a few Xenopus organs. On the other hand, there is a growing body of evidence that cell death is regulated by various kinds of local factors. For example, roles of interactions with other tissue cells and/or participation of immunocompetent cells in cell death have been experimentally shown. Therefore, to clarify the mechanisms of this complicated process, it is important at present that TH‐induced changes in gene expression of each cell type comprising the organ are chronologically examined by combining morphological and molecular biological techniques. © 1996 Wiley‐Liss, Inc.
Optimizing Cost of Continuous Overlapping Queries over Data Streams by Filter Adaption

The problem we aim to address is the optimization of cost management for executing multiple continuous queries on data streams, where each query is defined by several filters, each of which monitors certain status of the data stream. Specially, the filter can be shared by different queries and expensive to evaluate. The conventional objective for such a problem is to minimize the overall execution cost to solve all queries, by planning the order of filter evaluation in shared strategy. However, in the streaming scenario, the characteristics of data items may change in process, which can bring some uncertainty to the outcome of individual filter evaluation, and affect the plan of query execution as well as the overall execution cost. In our work, considering the influence of the uncertain variation of data characteristics, we propose a framework to deal with the dynamic adjustment of filter ordering for query execution on data stream, and focus on the issues of cost management. By incrementally monitoring and analyzing the results of filter evaluation, our proposed approach can be effectively adaptive to the varied stream behavior and adjust the optimal ordering of filter evaluation, so as to optimize the execution cost. In order to achieve satisfactory performance and efficiency, we also discuss the trade-off between the adaptivity of our framework and the overhead incurred by filter adaption. The experimental results on synthetic and two real data sets (traffic and multimedia) show that our framework can effectively reduce and balance the overall query execution cost and keep high adaptivity in streaming scenario.
Towards Service-Oriented Enterprise Architectures for Big Data Applications in the Cloud

Applications with Service-oriented Enterprise Architectures in the Cloud are emerging and will shape future trends in technology and communication. The development of such applications integrates Enterprise Architecture and Management with Architectures for Services & Cloud Computing, Web Services, Semantics and Knowledge-based Systems, Big Data Management, among other Architecture Frameworks and Software Engineering Methods. In the present work in progress research, we explore Service-oriented Enterprise Architectures and application systems in the context of Big Data applications in cloud settings. Using a Big Data scenario, we investigate the integration of Services and Cloud Computing architectures with new capabilities of Enterprise Architectures and Management. The underlying architecture reference model can be used to support semantic analysis and program comprehension of service-oriented Big Data Applications. Enterprise Services Computing is the current trend for powerful large-scale information systems, which increasingly converge with Cloud Computing environments. In this paper we combine architectures for services with cloud computing. We propose a new integration model for service-oriented Enterprise Architectures on basis of ESARC - Enterprise Services Architecture Reference Cube, which is our previous developed service-oriented enterprise architecture classification framework, with MFESA - Method Framework for Engineering System Architectures - for the design of service-oriented enterprise architectures, and the systematic development, diagnostics and optimization of architecture artifacts of service-oriented cloud-based enterprise systems for Big Data applications.
The PrimeGame Revolutions: A cloud-based collaborative environment for teaching introductory programming

The PrimeGame is an established mathematical programming game that has been used successfully in undergraduate computer science teaching since 2003. To meet the increasing demand for innovative programming tools in undergraduate tertiary and secondary education, we have created SoGaCo, a novel platform to deliver the PrimeGame and similar games to a wide audience via standard web browsers. SoGaCo is designed to have a very low total cost of ownership. This is achieved by enabling teachers to provision a customised collaborative development environment on commodity cloud computing infrastructure. Amongst the unique features of the platform are its social networking features and support for polyglot programming. In this paper, we describe the requirements for this system, its design and implementation. We focus on how the scalability and security challenges of an open web-based development environment are addressed. This includes a discussion of the sandboxing and verification techniques we have developed in order to safeguard server-side code execution on the Java Virtual Machine.
Closed-Form Solutions for Physically Based Shape Modeling and Recognition

The authors present a closed-form, physically based solution for recovering a three-dimensional (3-D) solid model from collections of 3-D surface measurements. Given a sufficient number of independent measurements, the solution is overconstrained and unique except for rotational symmetries. The proposed approach is based on the finite element method (FEM) and parametric solid modeling using implicit functions. This approach provides both the convenience of parametric modeling and the expressiveness of the physically based mesh formulation and, in addition, can provide great accuracy at physical simulation. A physically based object-recognition method that allows simple, closed-form comparisons of recovered 3-D solid models is presented. The performance of these methods is evaluated using both synthetic range data with various signal-to-noise ratios and using laser rangefinder data. >