Miracle-dz/UniFAR-FTUs huggingface dataset:
H-NS and RpoS regulate emergence of Lac Ara+ mutants of Escherichia coli MCS2

Two master growth-phase regulatory proteins, H-NS and sigmaS, are involved in the formation of araB-lacZ fusion clones of Escherichia coli MCS2. The stationary-phase sigma factor RpoS is strictly required for the appearance of such mutants, whereas the histone-like protein H-NS represses their emergence. Our results support the idea that genetic changes leading to adaptive mutation in this model system are regulated by physiological signal transduction networks.
Hydrogen Sulfide Modulates the S-Nitrosoproteome and the Mitochondrial Morphology in Endothelial Cells.

BACKGROUND Hydrogen sulfide (H2S) is one of the endogenous gaseous molecules promoting the production of nitric oxide (NO) which has cardioprotective functions. However, the role of the H2S-mediated protein S-nitrosoproteome and its subsequent physiological response remains unclear. METHODS Endothelial cells EAhy 926 were treated with 50 μM of H2S for 2 hours. The NO bound S-nitrosoproteins were purified by a biotin-switch and then digested by trypsin. Resulting peptides from control and H2S treatment were separately labeled by isobaric tag for relative and absolute quantitation 114/115, quantified by liquid chromatography tandem-mass spectrometry and analyzed by ingenuity pathway analysis (IPA) software. The microP software was applied to analyze the morphological changes of mitochondria. RESULTS With the treatment of H2S, 416 S-nitrosylated proteins were identified. IPA analysis showed that these proteins were involved in five signaling pathways. The NO-bound cysteine residues and the S-nitrosylation levels (115/114) were shown for ten S-nitrosoproteins. Western blot further verified the S-nitrosylation of thioredoxin-dependant peroxide reductase, cytochrome c oxidase and cytochrome b-c1 complex that are involved in the mitochondrial signaling pathway. H2O2-induced mitochondrial swelling can be reduced by the pretreatment of H2S. CONCLUSIONS The H2S-mediated endothelial S-nitrosoproteome has been confirmed. In the present study, we have proposed the cardioprotective role of H2S via maintaining mitochondrial homeostasis.
Detection of Bovine Viral Diarrhea Virus in some Vaccines, Sera and Cell Cultures

Bovine viral diarrhea virus (BVDV) causes contagious subclinical viral infections among dairy and beef cattle leading to economic losses worldwide. BVDV belongs to Family Flaviviridae, Genus Pestiviruses which is RNA viruses. It has two genotypes (I & II), each genotype has two biotypes, cytopathic (CP) and non-cytopathic (NCP) according to its cytopathology on cell culture. There is a risk factor from using bovine serum as a contaminant of the biological reagents and products prepared on cell cultures as vaccines. The study aimed to detect BVDV contamination in some biological agents such as (cell culture, serum and vaccines) using culture methods, ELISA and quantitate real time PCR. Samples consisted of 13 different attenuated and killed vaccines that are used in farm vaccination, five different serum samples that are used in cell culture and vaccines production in addition to three different cell culture samples that used in cell culture either for virus isolation or vaccines production. All samples inoculated on MDBK cells and examined for cytopathic BVDV revealed negative results. Cell culture and serum samples examined by ELISA technique also gave negative results. All samples were negative with real time PCR except one sample was positive. Comparing between all methods used, there was agreement between their results except in one sample that give positive result only by real time PCR. Therefore, we conclude that the chances of BVDV spread and contamination still there. The qRT – PCR is the most accurate method and can amplify a very little amount of virus. We also approve that all manufactured serum, vaccine samples were good as they were free from contamination with BVDV.
A joint day-ahead scheduling for photovoltaic-storage systems based on extended QV bus-type power flow

This paper focuses on voltage fluctuation and the mismatch between generation and load demand caused by photovoltaic access to distribution network, using energy storage to solve negative effects brought by photovoltaic. According to the characteristics of point of common coupling (PCC) photovoltaic and energy storage accessed to, extended QV bus-type is put forward in order to describe the feature of PCC more reasonably. The solution of power flow calculation with QV bus-type is also shown in this paper. Furthermore, a joint day-ahead scheduling of photovoltaic-storage is put forward in core view of voltage control at PCC. The two scenarios where whether the power output of energy storage system is beyond the limit are considered. When the power output beyond its limit, the bus-type is transformed. As a consequence, node voltage curve and joint power curves of photovoltaic-storage are thus gained. The result is comprehensively compared with the case where photovoltaic and energy storage operate with constant power. It shows that the strategy this paper proposed has a significant effect on suppressing voltage fluctuation, improving power flow, peak load shifting and so on.
Functional Study of Mammalian Neph Proteins in Drosophila melanogaster

Neph molecules are highly conserved immunoglobulin superfamily proteins (IgSF) which are essential for multiple morphogenetic processes, including glomerular development in mammals and neuronal as well as nephrocyte development in D. melanogaster. While D. melanogaster expresses two Neph-like proteins (Kirre and IrreC/Rst), three Neph proteins (Neph1–3) are expressed in the mammalian system. However, although these molecules are highly abundant, their molecular functions are still poorly understood. Here we report on a fly system in which we overexpress and replace endogenous Neph homologs with mammalian Neph1–3 proteins to identify functional Neph protein networks required for neuronal and nephrocyte development. Misexpression of Neph1, but neither Neph2 nor Neph3, phenocopies the overexpression of endogenous Neph molecules suggesting a functional diversity of mammalian Neph family proteins. Moreover, structure-function analysis identified a conserved and specific Neph1 protein motif that appears to be required for the functional replacement of Kirre. Hereby, we establish D. melanogaster as a genetic system to specifically model molecular Neph1 functions in vivo and identify a conserved amino acid motif linking Neph1 to Drosophila Kirre function.
Encapsulation of ionic electromechanically active polymer actuators

Biomimetic movement and low operating voltage have made ionic electroactive polymer actuators (iEAPs) interesting for applications where interactions with living organisms occur, such as haptic devices operating mainly in air or minimally invasive or chronically implanted medical devices operating in biological fluids. However, not all materials that are typically used in the fabrication of iEAPs are biofriendly, nor are the biological environments with various electrolyte compositions safe or optimal for the actuator. This paper presents a comprehensive overview of materials and methods that have been previously used to encapsulate ionic electroactive polymer actuators. Recently, increasing emphasis has been given to the miniaturization of actuators for the biomedical field, and therefore in the detailed overview we have focused on automated, tunable and industrially applicable coating methods, together with promising biocompatible encapsulant materials. In the final section, we introduce a carbon-based actuator that has been dip-coated with polydimethylsiloxane elastomer that shows extended lifetime during actuation in water.
Visible-light-driven photocatalysts for hydrogen production by water splitting

ABSTRACT Two photocatalysts, namely, graphene oxide and TiO2/CdS/CNT nanocomposite for hydrogen production from pure water and seawater were synthesized by modified Hummer’s method and sol-gel method, respectively. The photocatalysts were characterized by X-Ray Diffraction (XRD), Scanning Electron Microscope (SEM), Energy Dispersive Spectroscope (EDS) and UV-Visible Diffuse Reflectance Spectroscope (UV-DRS). The particle size of graphene oxide and TiO2/CdS/CNT nanocomposite was measured to be 14.84 nm and 9.03 nm, respectively. The photocatalytic activity on hydrogen generation from pure water and seawater was investigated under visible-light irradiation (λ ≥ 420 nm) at room temperature. It was observed that TiO2/CdS/CNT nanocomposite showed higher photocatalytic H2 production rate (3502 µmol/h from pure water and 1373 µmol/h from seawater) than graphene oxide (2548 µmol/h from pure water and 995 µmol/h from seawater). The experimental results indicate that the improved photoactivity of TiO2/CdS/CNT nanocomposite is due to the presence of MWCNTs which enhances hydrogen production, improves the photo-stability of CdS and retards the recombination rate of electron-hole pairs. The present study reveals that the photocatalytic activity of ternary nanocomposite is superior to graphene oxide. Thus, the novel photocatalyst TiO2/CdS/CNT nanocomposite holds high stability and photo-activity and improves the quantity of hydrogen produced from 1 l of water.
Incremental Neuroevolution of Reactive and Deliberative 3D Agents

Following earlier work on the neuroevolution of deliberative behaviour to solve increasingly challenging tasks in a twodimensional dynamic world, this paper presents the results of extending the original system to a three-dimensional rigid body simulation. The 3D physically based setting requires that a successful agent continually and deliberately adjust its gait, turning and other motor control over the many stages and sub-stages of these tasks, within its individual evaluation. Achieving such complex interplay between motor control and deliberative control, within a neuroevolutionary framework, is the focus of this work. To this end, a novel neural architecture is presented and an incremental evolutionary approach used to bootstrap the locomotive behaviour of the agents. Agent morphology is fixed as a quadruped with three degrees of freedom per limb. Agent populations have no initial knowledge of the problem domain, and evolve to move around and then solve progressively more difficult challenges in the environment using a tournament-based co-evolutionary algorithm. The results demonstrate not only success at the tasks but also a variety of intricate lifelike behaviours being used, separately and in combination, to achieve this success. Given the problem-agnostic controller architecture, these results indicate a potential for discovering yet more advanced behaviours in yet more complex environments.
RGB-D sensor setup for multiple tasks of home robots and experimental results

While navigation based on 2D laser data is well understood, the application of robots at home environments requires seeing more than a slice of the world. RGB-D cameras have been used to perceive the full scenes and solutions exist consuming extensive computing power. We propose a setup with two RGB-D cameras that covers the need for conflicting requirements regarding localization, obstacle avoidance, object search and recognition, and gesture recognition. We show that this setup provides sufficient data to enable navigation at homes and we present how ROS modules can be configured to use virtual RGB-D scans instead of laser data for operation in real-time (10Hz). Finally, we present first results of exploiting this versatile setup for a home service robot that picks up things from the floor to prevent potential falls of its future users.
Karadeniz’de (Sinop Yarımadası Civarı) Avlanan İzmarit Balığı, Spicara smaris (Linnaeus, 1758), Etinin LC-MS/MS Kullanarak Amino Asit İçeriğinin Tespiti ve Ağırlık-Boy İlişkisi

Bu calismada Karadeniz’de Sinop yarimadasi civarinda yakalanan izmarit baligi ( Spicara smaris ) etinin amino asit icerigi ve bu baligin boy agirlik iliskisi belirlenmistir. Amino asit iceriginin belirlenmesinde; bir karisimdaki istenen maddeyi ileri duzeyde ayirip tanimlayabilir ve olcebilir ozellikteki LC-MS / MS (Sivi Kromatografi Kutle Spektrometresi) cihazi kullanilmis ve bu yontemle izmarit baliklari icin sonuclar ilk kez rapor edilmistir. Bu calismada esansiyel (EAA) ve esansiyel olmayan (NEAA) toplam 19 adet amino asit tespit edilmistir. Esansiyel amino asitler toplam amino asit miktarinin %52,44’unu olusturmustur. Izmarit etinde en yuksek oranda tespit edilen EAA miktarlari sirasiyla lysin (2,10±0,215 g/100 g), leucine (1,68±0,115 g/100 g), arginine (1,18±0,030 g/100 g) ve valine (1,09±0,070 g/100 g) seklindedir. Izmarit etinde en yuksek oranda tespit edilen NEAA miktarlari ise sirasiyla glutamic asit (2,88±0,010 g/100 g), aspartik asit (2,16±0,280 g/100 g), alanine (1,32±0,000 g/100 g) ve glycine (1,05±0,060 g/100 g) seklindedir. Arastirmada incelenen baliklarin agirlik - boy iliskisi W = 0,0044TL 3,3423 , R 2 = 0,990, N = 45, P < 0,05 seklinde hesaplanmistir. Agirlik boy - iliskisi (WLR) denkleminin korelasyon katsayisi ( r ) istatistiksel olarak sifirdan farkli ( P < 0,05), b degeri ise istatistiksel olarak b = 3 den (izometrik buyume) farkli bulunmustur (Pauly t test P < 0,05). Bu sonuclar Karadeniz’de uzatma aglariyla avlanan izmarit baliklarinin AA bakimindan zengin ve pozitif allometrik buyume ozelligi gosterdigini ortaya koymustur.
Curiosity in Time

We explore the idea of adding the ability to learn time dependent tasks into the Intelligent Adaptive Curiosity (IAC) learning scheme as presented by Oudeyer, et al. [2004, 2006]. We use a three layer architecture (IGE) consisting of a bottom-level IAC brain, an Elman network, and a toplevel IAC brain. For both IAC brains we use the equilibrium Growing Neural Gas (GNG) algorithm to cluster the regions rather than k-means clustering. The bottom-level IAC brain takes as input the robot’s sensors and motors and outputs actions, while the Elman network takes as input the regions of the lower-level IAC brain and attempts to predict the next region. The upper-level IAC brain takes the hidden unit activations of the Elman network and uses these to decide on actions for the robot. Our environment consists of a square where each corridor of the square has a different color scheme. Thus, each corridor is, in itself, predictable by the original IAC architecture, but the corners where the corridors join require time-dependence to predict. Upon running the experiments, we found that using GNG to cluster the regions allows the robot to learn the environment with only 20-25 regions, which is a significant improvement over the approximately 200 that would be formed by k-means clustering. However, while the robot was able to make accurate predictions in the corridors, it could not learn the time-dependence of the environment. We hypothesize that this occurred because the robot’s behavior when controlled by IAC is too unstructured to be used as input to the Elman network. We conclude, therefore, that an Elman network may be helpful in introducing time-dependence to IAC, but only if trained off-line or if the lower-level brain produces more structured actions than those of IAC.
Phonophoresis in animals- A review

Phonophoresis is a transdermal drug-delivery system that uses ultrasound to enhance the delivery of topically-applied drugs. Use of ultrasound in therapeutics and drug delivery has gained importance in recent years in human-medicine while it is still a new frontier in veterinary medicine. The primary challenge in developing these systems is rooted in the wide differences in skin structure and function seen in species ranging from cats to cows. The following review focuses on the mechanism of phonophoresis and encompasses a discussion on the possible applications of phonophoresis, phonophoretic-systems used in humans and future trends to develop a drug and species-specific phonophoretic-systems. The paper concludes with a section detailing the scope of research in future in veterinary medicine. The purpose of this article is to build a theoretical foundation for understanding phonophoresis and review the efficacy of phonophoresis as a clinical treatment in physical-therapy in humans as well as in animals.
Approaches to assessment in time-limited Mentalization-Based Therapy for Children (MBT-C)

In this article we describe our clinical approach to assessment, formulation and the identification of a therapeutic focus in the context of time-limited Mentalization-Based Treatment for Children (MBT-C) aged between 6 and 12. Rather than seeing the capacity to mentalize as a global construct, we set out an approach to assessing the developmental ‘building blocks’ of the capacity to mentalize the self and others, including the capacity for attention regulation, emotion regulation, and explicit mentalization. Assessing the child’s strengths and vulnerabilities in each of these domains provides a more nuanced picture of the child’s mentalizing capacities and difficulties, and can provide a useful approach to case formulation. The article sets out an approach to assessment that includes a consideration of mentalizing strengths and difficulties in both the child and the parents, and shows how this can be used to help develop a mutually agreed treatment focus. A clinical vignette illustrates the approach taken to assessment and connects it to routine clinical practice.
Expression of dopamine and adrenergic receptors in mouse embryonic stem cells and preimplantation embryos

Abstract Using RT-PCR we examined expression of dopamine and adrenergic receptors in undifferentiated and spontaneously differentiating mouse embryonic stem (ES) cells. We also examined expression of dopamine receptor subtypes in mouse ovulated oocytes and preimplantation embryos. Comparing the expression of catecholamine receptors in undifferentiated mouse ES cells and in blastocysts (from which ES cells are derived), we found that transcripts of all five dopamine receptors were expressed in both cell types. In contrast, we detected eight adrenergic receptor subtypes in undifferentiated mouse ES cells, but only three subtypes were found in mouse blastocysts. In three adrenergic receptors (α1D, α2B, β1), we found higher expression in the spontaneously differentiating ES cells than in undifferentiated ES cells, and the α1B adrenoceptor was not even detectable in the undifferentiated cells. These results indicate that genes encoding all types of catecholamine receptors are transcribed in mouse ES cells, and some of them are differentially expressed during ES cell differentiation. We found several profiles of dopamine receptor mRNA expression during the preimplantation period. The DR3 transcript was present in all examined stages (oocytes, 4-cell embryos, 8- to 16-cell embryos, blastocysts). DR1 and DR4 transcripts were not found in oocytes, but we detected them in preimplantation embryos. The DR2 receptor transcript was found in all examined stages except for the 4-cell embryos, and the DR5 receptor transcript was found in all examined stages except for the 8- to 16-cell embryos. The expression profiles of dopamine receptor transcripts suggest different roles of some receptor subtypes in particular preimplantation developmental stages.
A system for retargeting of streaming video

We present a novel, integrated system for content-aware video retargeting. A simple and interactive framework combines key frame based constraint editing with numerous automatic algorithms for video analysis. This combination gives content producers high level control of the retargeting process. The central component of our framework is a non-uniform, pixel-accurate warp to the target resolution which considers automatic as well as interactively defined features. Automatic features comprise video saliency, edge preservation at the pixel resolution, and scene cut detection to enforce bilateral temporal coherence. Additional high level constraints can be added by the producer to guarantee a consistent scene composition across arbitrary output formats. For high quality video display we adopted a 2D version of EWA splatting eliminating aliasing artifacts known from previous work. Our method seamlessly integrates into postproduction and computes the reformatting in real-time. This allows us to retarget annotated video streams at a high quality to arbitary aspect ratios while retaining the intended cinematographic scene composition. For evaluation we conducted a user study which revealed a strong viewer preference for our method.
Towards model-driven safety analysis

Model-based safety analysis allows very high quality analysis of safety requirements. Both qualitative (i.e. what must go wrong for a system failure) and quantitative aspects (i.e. how probable is a system failure) are of great interest for safety analysis. Traditionally, the analysis of these aspects requires separate, tool-dependent formal models. However, building adequate models for each analysis requires a lot of effort and expertise. Model-driven approaches support this by automating the generation of analysis models. SAML is a tool-independent modeling framework that allows for the construction of models with both non-deterministic and probabilistic behavior. SAML models can automatically be transformed into the input language of different state of the art formal analysis tools — while preserving the semantics — to analyze different aspects of safety. As a consequence both — qualitative and quantitative — model-based safety analysis can be done without any additional generation of models and with transferable results. This approach makes SAML an ideal intermediate language for a model-driven safety analysis approach. Every higher-level language that can be transformed into SAML can be analyzed with all targeted formal analysis tools. New analysis tools can be added and the user benefits from every advancement of the analysis tools.
Altered Oligomerization Properties of N316 Mutants of Escherichia coli TyrR

ABSTRACT The transcriptional regulator TyrR is known to undergo a dimer-to-hexamer conformational change in response to aromatic amino acids, through which it controls gene expression. In this study, we identified N316D as the second-site suppressor of Escherichia coli TyrRE274Q, a mutant protein deficient in hexamer formation. N316 variants exhibited altered in vivo regulatory properties, and the most drastic changes were observed for TyrRN316D and TyrRN316R mutants. Gel filtration analyses revealed that the ligand-mediated oligomer formation was enhanced and diminished for TyrRN316D and TyrRN316R, respectively, compared with the wild-type TyrR. ADP was substituted for ATP in the oligomer formation of TyrRN316D.