Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of monoamines in modulating behavior

Understanding the mechanisms underlying complex behaviors requires a comprehensive investigation of the neurobiological factors that regulate and modulate their expression. Monoamines, such as serotonin, dopamine, and noradrenaline, serve a variety of essential physiological roles in modulating animal behavior. Furthermore, the evolutionary conservation of these aminergic systems spans across both vertebrates and invertebrates, having comparable effects in such diverse processes as learning and memory, aggression, mating behaviors and reproduction, stress responses, locomotion, and collective social behaviors (Dishman 1997; Libersat and Pflueger 2004; Kamhi and Traniello 2013; Bubak et al. 2014a; De Boer et al. 2015). Outstanding research is currently being conducted in this field, uncovering remarkable similarities in neural circuitries even among highly divergent taxa, such as Drosophila and humans. Investigating the neural mechanisms involved in the monoaminergic modulation of behavior across a variety of taxonomically distant species can provide researchers with a better understanding of the origins and functions of these systems. The goal of this special issue is to provide a venue in which colleagues studying similar questions across highly divergent animal systems can present their recent and groundbreaking work in this exciting area of biology. We hope this collection of papers will encourage and stimulate a dialogue on the similarities of monoaminergic function in a wide variety of animals and ultimately promote future comparative approaches when investigating behavioral modulation. In this issue, we aim to highlight a range of animal models systems to illustrate the central role that monoamines play in modulating various behaviors. This special column features seven contributions drawn from the participants in a symposium we organized for the 9th International Congress of Comparative Physiology and Biochemistry, held in Krakow, Poland, in August 2015. Featured animal models include both invertebrates and vertebrates. ### Synthesis, new directions, and reviews The issue starts with … [↵][1]*Address correspondence to John G. Swallow. E-mail: john.swallow{at}ucdenver.edu. [1]: #xref-corresp-1-1
Towards an International Classification for Patient Safety: key concepts and terms

Background Understanding the patient safety literature has been compromised by the inconsistent use of language. Objectives To identify key concepts of relevance to the International Patient Safety Classification (ICPS) proposed by the World Alliance For Patient Safety of the World Health Organization (WHO), and agree on definitions and preferred terms. Methods Six principles were agreed upon—that the concepts and terms should: be applicable across the full spectrum of healthcare; be consistent with concepts from other WHO Classifications; have meanings as close as possible to those in colloquial use; convey the appropriate meanings with respect to patient safety; be brief and clear, without unnecessary or redundant qualifiers; be fit-for-purpose for the ICPS. Results Definitions and preferred terms were agreed for 48 concepts of relevance to the ICPS; these were described and the relationships between them and the ICPS were outlined. Conclusions The consistent use of key concepts, definitions and preferred terms should pave the way for better understanding, for comparisons between facilities and jurisdictions, and for trends to be tracked over time. Changes and improvements, translation into other languages and alignment with other sets of patient safety definitions will be necessary. This work represents the start of an ongoing process of progressively improving a common international understanding of terms and concepts relevant to patient safety.
Identification of errors in the IEDB using ontologies

Abstract The Immune Epitope Database (IEDB) is a free online resource that has manually curated over 18 500 references from the scientific literature. Our database presents experimental data relating to the recognition of immune epitopes by the adaptive immune system in a structured, searchable manner. In order to be consistent and accurate in our data representation across many different journals, authors and curators, we have implemented several quality control measures, such as curation rules, controlled vocabularies and links to external ontologies and other resources. Ontologies and other resources have greatly benefited the IEDB through improved search interfaces, easier curation practices, interoperability between the IEDB and other databases and the identification of errors within our dataset. Here, we will elaborate on how ontology mapping and usage can be used to find and correct errors in a manually curated database. Database URL: www.iedb. org
Genetic and Physiological Diversity in the Diatom Nitzschia inconspicua

Nitzschia inconspicua is an ecologically important diatom species, which is believed to have a widespread distribution and to be tolerant to salinity and to organic or nutrient pollution. However, its identification is not straightforward and there is no information on genetic and ecophysiological diversity within the species. We used morphological, molecular (rbcL and LSU D1–D3), ecophysiological and reproductive data to investigate whether N. inconspicua constitutes a single species with a broad ecological tolerance or two or more cryptic species with shared or different ecological preferences. Molecular genetic data for clones from upstream and deltaic sites in the Ebro River basin (Catalonia, Spain) revealed seven N. inconspicua rbcL + LSU genotypes grouped into three major clades. Two of the clades were related to other Nitzschia and Denticula species, making N. inconspicua paraphyletic and suggesting the need for taxonomic revision. Most clones were observed to be automictic, exhibiting paedogamy, and so the biological species concept cannot be used to establish species boundaries. Although there were morphological differences among clones, we found no consistent differences among genotypes belonging to different clades, which are definable only through sequence data. Nevertheless, separating the genotypes could be important for ecological purposes because two different ecophysiological responses were encountered among them.
SECURITY USING CRYPTOGRAPHIC TECHNIQUES FOR IMAGE PROCESSING

This paper focuses mainly on the different kinds of image security techniques. The digital techniques for transmitting and storing images are increasing, it becomes an important issue that how to protect the confidentiality, integrity and authenticity of images. There are lots of other techniques which enhance the security of images in the field of encryption and decryption Image security is protecting image and the systems from unauthorized access, use, disclosure, disruption, modification, inspection, recording or destruction. Therefore it is necessary to apply effective encryption/decryption methods to achieve data security. In this paper a Survey of different secure image techniques and Biometrics are the two most prominent solutions for user authentication, data integrity preservation, and trustworthy verification. By combining biometrics with image security techniques, high level of security can be achieved. It additionally focuses on the functionality of Image encryption and decryption techniques.
Rapid flooding-induced adventitious root development from preformed primordia in Solanum dulcamara

Flooding strongly affects plant growth, as it leads to low oxygen concentrations in the submerged tissues. Understanding plant responses to flooding may benefit both management of wetland ecosystems and improve progress in creating flood-tolerant crop species. Bittersweet (Solanum dulcamara), a species related to tomato and eggplant, has dormant primordia on the stem that develop into adventitious roots within 3 days of flooding. Changes in gene expression were present within 2 hours and included activation of hypoxia and ethylene signalling genes. Unexpectedly, these early changes in gene expression were closely similar in primordia and adjacent stem tissue, suggesting a dominant general response in tissues during early flooding.
mRNA decay: an adaptation tool for the environmental fungal pathogen Cryptococcus neoformans

Fungi are ubiquitous in the environment and humans constantly encounter them in the soil, air, water, and food. The vast majority of these interactions are inconsequential. However, in the context of immunodeficiency precipitated by HIV infection, hematologic malignancy, or transplantation, a small subset of fungi can cause devastating, systemic infection. The most deadly of the opportunistic environmental fungi, Cryptococcus neoformans, is estimated to cause hundreds of thousands of deaths per year, mostly in the context of HIV co‐infection. The cellular processes that mediate adaptation to the host environment are of great interest as potential novel therapeutic targets. One such cellular process important for host adaptation is mRNA decay, which mediates the specific degradation of subsets of functionally related mRNAs in response to stressors relevant to pathogenesis, including human core body temperature, carbon limitation, and reactive oxygen stress. Thus, for C. neoformans, host adaptation requires mRNA decay to mediate rapid transcriptome remodeling in the face of stressors encountered in the host. Several nodes of stress‐responsive signaling that govern the stress‐responsive transcriptome also control the decay rate of mRNAs cleared from the ribosome during stress, suggesting an additional layer of coupling between mRNA synthesis and decay that allows C. neoformans to be a successful pathogen of humans. WIREs RNA 2017, 8:e1424. doi: 10.1002/wrna.1424
A Differential Privacy Mechanism Design Under Matrix-Valued Query

Traditionally, differential privacy mechanism design has been tailored for a scalar-valued query function. Although many mechanisms such as the Laplace and Gaussian mechanisms can be extended to a matrix-valued query function by adding i.i. d. noise to each element of the matrix, this method is often sub-optimal as it forfeits an opportunity to exploit the structural characteristics typically associated with matrix analysis. In this work, we consider the design of differential privacy mechanism specifically for a matrix-valued query function. The proposed solution is to utilize a matrix-variate noise, as opposed to the traditional scalar-valued noise. Particularly, we propose a novel differential privacy mechanism called the Matrix-Variate Gaussian (MVG) mechanism, which adds a matrix-valued noise drawn from a matrix-variate Gaussian distribution. We prove that the MVG mechanism preserves $(\epsilon,\delta)$-differential privacy, and show that it allows the structural characteristics of the matrix-valued query function to naturally be exploited. Furthermore, due to the multi-dimensional nature of the MVG mechanism and the matrix-valued query, we introduce the concept of directional noise, which can be utilized to mitigate the impact the noise has on the utility of the query. Finally, we demonstrate the performance of the MVG mechanism and the advantages of directional noise using three matrix-valued queries on three privacy-sensitive datasets. We find that the MVG mechanism notably outperforms four previous state-of-the-art approaches, and provides comparable utility to the non-private baseline. Our work thus presents a promising prospect for both future research and implementation of differential privacy for matrix-valued query functions.
Site of Tagging Influences the Ochratoxin Recognition by Peptide NFO4: A Molecular Dynamics Study

Molecular recognition by synthetic peptides is growing in importance in the design of biosensing elements used in the detection and monitoring of a wide variety of hapten bioanlaytes. Conferring specificity via bioimmobilization and subsequent recovery and purification of such sensing elements are aided by the use of affinity tags. However, the tag and its site of placement can potentially compromise the hapten recognition capabilities of the peptide, necessitating a detailed experimental characterization and optimization of the tagged molecular recognition entity. The objective of this study was to assess the impact of site-specific tags on a native peptide's fold and hapten recognition capabilities using an advanced molecular dynamics (MD) simulation approach involving bias-exchange metadynamics and Markov State Models. The in-solution binding preferences of affinity tagged NFO4 (VYMNRKYYKCCK) to chlorinated (OTA) and non-chlorinated (OTB) analogues of ochratoxin were evaluated by appending hexa-histidine tags (6× His-tag) to the peptide's N-terminus (NterNFO4) or C-terminus (CterNFO4), respectively. The untagged NFO4 (NFO4), previously shown to bind with high affinity and selectivity to OTA, served as the control. Results indicate that the addition of site-specific 6× His-tags altered the peptide's native fold and the ochratoxin binding mechanism, with the influence of site-specific affinity tags being most evident on the peptide's interaction with OTA. The tags at the N-terminus of NFO4 preserved the native fold and actively contributed to the nonbonded interactions with OTA. In contrast, the tags at the C-terminus of NFO4 altered the native fold and were agnostic in its nonbonded interactions with OTA. The tags also increased the penalty associated with solvating the peptide-OTA complex. Interestingly, the tags did not significantly influence the nonbonded interactions or the penalty associated with solvating the peptide-OTB complex. Overall, the combined contributions of nonbonded interaction and solvation penalty were responsible for the retention of the native hapten recognition capabilities in NterNFO4 and compromised native recognition capabilities in CterNFO4. Advanced MD approaches can thus provide structural and energetic insights critical to evaluate the impact of site-specific tags and may aid in the selection and optimization of the binding preferences of a specific biosensing element.
Direct experimental visualization of atomic and electron dynamics with attosecond pulses

We illustrate how attosecond light pulses can be used directly in mapping out the time dependence of the motion of atoms in a small molecule, as well as of the correlated motion of two excited electrons in an atom. For simple molecules such as H2 and D2, we show that the vibrational wave packet can be mapped out very accurately, including details due to the broadening and interference. For doubly excited states of a helium atom, we show that the time-dependent correlated motion between the two electrons can be mapped via double ionization with attosecond pulses.
Evolutionary adaptive behavior in noisy multi-agent system

In this paper, we discuss a relationship between perceptual noise and fitness of agents in a multi-agent system. In multi-agent system, agents perceive environmental information and act based on this information. Therefore, in case that the perceptual information contains some noise, a cooperative behavior of agents is more challenging and the resulting fitness of the agents is inferior. In order to develop a behavior of the agents that is robust to the perception noise, we evolved the behavior of the agents in noisy environment. As a result, the evolved behavior, obtained in a noisy environment is superior (in terms of robustness) than that evolved in noiseless environment.
Suppression of tumorigenesis and activation of Wnt signaling by bone morphogenetic protein 4 in human cancer cells

Aberrations in BMP signaling have recently been implicated as a cause of human cancer. Here we demonstrate and define the tumor suppressive properties of BMP4. Consistent with its potential role in a tumor suppressor pathway, BMP4 treatment eliminated the tumorigenic potential of an undifferentiated human cancer cell line. This loss of tumorigenicity was accompanied by an increase in apoptosis, alterations in cell cycle profile, and an increase in cell size. Interestingly, human colon cancer cells were resistant to the growth-suppressive properties of BMP4. To identify putative downstream mediators of BMP4-mediated tumor suppression, Affymetrix Genechips were employed to identify BMP4-regulated genes. The human BMP4 transcriptome was characterized by the modulation of many genes well known to play important roles in differentiation and development, including the induction of numerous genes involved in Wnt signaling. Modulation of Wnt gene expression by BMP4 had several functional consequences - BMP4 treatment led to activation of TCF reporters; complete activation of at least one BMP4-responsive gene required TCF sites; and treatment with a Wnt ligand was sufficient to mimic several of the phenotypic effects of BMP4 treatment. These data demonstrate the tumor suppressive properties of BMP4 signaling, show that colon cancer cells are resistant to BMP4-induced differentiation and growth suppression, further define the BMP4 transcriptome, and raise the intriguing possibility that interactions between the Wnt and BMP signaling pathways may play an important role in differentiation and tumor suppression.
Adaptation to Aerobic Environment of Lactobacillus johnsonii/gasseri Strains

Oxygen is considered one of the main factors affecting probiotic bacteria survival due to the induction of oxidative damages caused by the action of reactive oxygen species (ROS). It has been shown that oxidative stress resistance in lactic acid bacteria is strongly dependent on the type of cell metabolism. Shift from fermentative to respiratory metabolism (through the addition of heme and menaquinone and in presence of oxygen) was associated to increase in biomass, long-term survival, and production of antioxidant enzymes. The aim of this work was to investigate the effect of aerobic (presence of oxygen) and respiratory (presence of oxygen, heme, and menaquinone) cultivation on the growth kinetic, catalase production, oxygen uptake, and oxidative stress response of Lactobacillus johnsonii/gasseri strains previously isolated from infant feces. Seven strains showed to consume oxygen under aerobic and respiratory conditions. The strain AL5 showed a catalase activity in both growth conditions, while AL3 showed this activity only in respiratory condition. Respiratory condition improved their tolerance to oxidative compounds (hydrogen peroxide and ROS generators) and further they showed promising probiotic features. The exploration of respiratory competent phenotypes with probiotic features may be extremely useful for the development of competitive starter or probiotic cultures.
Are Environmental Contaminants Responsiblefor ‘Globesity’?

According to the World Health Organization (WHO), worldwide obesity has nearly doubled since 1980. In the previous year 42 million children under the age of 5 were overweight or obese. The concern of governments, the scientific community, and health services is noticed in the causes behind the prevalence of obesity and its prevention. Taking into consideration the reasons underlying obesity, toxic substances found in the environment and the food system have been receiving significant attention. Thus, the aim of this paper was to explore the associations between numerous environmental contaminants (heavy metals, persistent organic pollutants) and obesity. Our hypothesis was that neuroendocrine system disturbances caused by these xenobiotics play a crucial role in the obesity epidemic. The neurotoxicity of these compounds could be connected with the reward center in the brain as well as the endocrine system, and lead to an increase of food intake and, consequently, obesity. Taking into consideration global health as well as the best interests of society, studies in this area are crucial for understanding this problem.
Massive MIMO for Ultra-reliable Communications with Constellations for Dual Coherent-noncoherent Detection

The stringent requirements of ultra-reliable low-latency communications (URLLC) require rethinking of the physical layer transmission techniques. Massive antenna arrays are seen as an enabler of the emerging $5^\text{th}$ generation systems, due to increases in spectral efficiency and degrees of freedom for transmissions, which can greatly improve reliability under demanding latency requirements. Massive array coherent processing relies on accurate channel state information (CSI) in order to achieve high reliability. In this paper, we investigate the impact of imperfect CSI in a single-input multiple-output (SIMO) system on the coherent receiver. An amplitude-phase keying (APK) symbol constellation is proposed, where each two symmetric symbols reside on distinct power levels. The symbols are demodulated using a dual-stage non-coherent and coherent detection strategy, in order to improve symbol reliability. By means of analysis and simulation, we find an adequate scaling of the constellation and show that for high signal-to-noise ratio (SNR) and inaccurate CSI regime, the proposed scheme enhances receiver performance.
New Miticides for Integrated Pest Management of Varroa destructor (Acari: Varroidae) in Honey Bee Colonies on the Canadian Prairies

ABSTRACT Varroa destructor Anderson and Trueman 2000 (Acari: Varroidae) is an ectoparasitic mite of the honey bee, Apis mellifera L. (Hymenoptera: Apidae). Honey bee colonies require extensive management to prevent mortality caused by varroa mites and the viruses they vector. New miticides (Thymovar and HopGuard) to manage varroa mites were evaluated during the spring and fall treatment windows of the Canadian prairies to determine their effectiveness as part of an integrated management strategy. Thymovar and HopGuard were evaluated alongside the currently used industry standards: Apivar and formic acid. Results demonstrated that Apivar and formic acid remain effective V. destructor management options under spring and fall conditions. Applications of Thymovar during spring were associated with a reduction in brood area, and therefore should be limited to the fall season. The miticide HopGuard was not effective in managing V. destructor, and alteration of the current delivery system is necessary. This study demonstrates the potential for new effective treatment options to supplement currently used V. destructor integrated pest management systems.
Structure of the plant photosystem I.

Plant photosystem I (PSI) is one of the most intricate membrane complexes in nature. It comprises two complexes, a reaction center and light-harvesting complex (LHC), which together form the PSI-LHC supercomplex. The crystal structure of plant PSI was solved with two distinct crystal forms. The first, crystallized at pH 6.5, exhibited P21 symmetry; the second, crystallized at pH 8.5, exhibited P212121 symmetry. The surfaces involved in binding plastocyanin and ferredoxin are identical in both forms. The crystal structure at 2.6 Å resolution revealed 16 subunits, 45 transmembrane helices, and 232 prosthetic groups, including 143 chlorophyll a, 13 chlorophyll b, 27 β-carotene, 7 lutein, 2 xanthophyll, 1 zeaxanthin, 20 monogalactosyl diglyceride, 7 phosphatidyl diglyceride, 5 digalactosyl diglyceride, 2 calcium ions, 2 phylloquinone, and 3 iron sulfur clusters. The model reveals detailed interactions, providing mechanisms for excitation energy transfer and its modulation in one of nature's most efficient photochemical machine.