Miracle-dz/UniFAR-FTUs huggingface dataset:
Encoding and Decoding Dynamic Sensory Signals with Recurrent Neural Networks: An Application of Conceptors to Birdsongs

In a constantly changing environment the brain has to make sense of dynamic patterns of sensory input. These patterns can refer to stimuli with a complex and hierarchical structure which has to be inferred from the neural activity of sensory areas in the brain. Such areas were found to be locally recurrently structured as well as hierarchically organized within a given sensory domain. While there is a great body of work identifying neural representations of various sensory stimuli at different hierarchical levels, less is known about the nature of these representations. In this work, we propose a model that describes a way to encode and decode sensory stimuli based on the activity patterns of multiple, recurrently connected neural populations with different receptive fields. We demonstrate the ability of our model to learn and recognize complex, dynamic stimuli using birdsongs as exemplary data. These birdsongs can be described by a 2-level hierarchical structure, i.e. as sequences of syllables. Our model matches this hierarchy by learning single syllables on a first level and sequences of these syllables on a top level. Model performance on recognition tasks is investigated for an increasing number of syllables or songs to recognize and compared to state-of-the-art machine learning approaches. Finally, we discuss the implications of our model for the understanding of sensory pattern processing in the brain. We conclude that the employed encoding and decoding mechanisms might capture general computational principles of how the brain extracts relevant information from the activity of recurrently connected neural populations.
The distinct roles of Argonaute protein 2 in the growth, stress responses and pathogenicity of the apple tree canker pathogen

Summary Valsa mali (V. mali), the causal agent of apple tree Valsa canker, severely damages apple production, a major economic crop in China. To date, our understanding of the molecular mechanisms associated with the pathogenicity of V. mali is still limited. RNA interference participates in various biological processes in multicellular organisms. The Argonaute proteins (AGOs), which are a core component of the RNA interference system, play key roles in vegetable growth, environmental responses and fungal pathogenicity. Previously, transcriptome analysis revealed that the AGO2 gene (VMAGO2) was up-regulated during V. mali infection, suggesting that VMAGO2 plays a potential role in pathogenicity. In this study, we investigated the potential roles of VMAGO2 in the growth, stress responses and pathogenicity of V. mali. VMAGO2 was isolated and found to be orthologous to AGO2 of Neurospora crassa and Fusarium graminearum. Real-time quantitative PCR analysis showed that VMAGO2 expression was 3.4-fold higher than that of the control (mycelium) at 24 hr post-inoculation (hpi). Six positive VMAGO2 mutants were generated using double-joint PCR and PEG-mediated transformation. Deletion of VMAGO2 did not result in any obvious phenotypic change when compared with that of wild-type strain 03-8. Furthermore, the colonial morphology was not obviously affected when the mutants were subjected to osmotic and pH stress treatments. However, the knockout mutants did not grow on PDA with 0.05% H2O2. More importantly, infection assays showed that the average lesion diameter/length resulting from mutant infections was 34.8% and 19.8% smaller on apple leaves and twigs, respectively, than those resulting from wild-type infections. All six positive mutants showed a consistent phenotype, and the defects of the mutants were fully complemented by re-introducing the WTVMAGO2 allele. Our results demonstrated that VMAGO2 plays an important role in H2O2 tolerance and the pathogenicity of V. mali.
Phylogeography of the common vole Microtus arvalis and genetic diversity in populations of the common vole and field vole Microtus agrestis

The common vole (Microtus arvalis) and the field vole (Microtus agrestis) are morphologically similar species but are ecological distinctive and differ in the details of their evolutionary history as revealed by mitochondrial DNA (mtDNA). The aim of this study is to describe patterns of genetic variability using microsatellite markers in populations of the common and field vole in Poland using museum specimens, to assess the degree of congruence with mtDNA variation and thereby determine the factors that influence current patterns of gene flow. We genotyped 190 individuals of the common vole at 11 loci and 190 individuals of the field vole at 13 loci. Overall differentiation based on FSTwas higher for the common vole than in the field vole. We detected a significant isolation by distance pattern for both species. Bayesian analysis in STRUCTURE identified Eastern and Western geographic groups in Poland based on microsatellites for both species. The location of river barriers is likely to be the main factor in these partitions. The eastern-western subdivision with microsatellites does not coincide with the distribution of mtDNA lineages for either species. Unlike previous studies in the common and field vole elsewhere in Europe, we found no evidence of reproductive isolation between the mtDNA lineages of these species at their contact zones in Poland. This study highlights the different roles of evolutionary history and landscape in shaping contemporary genetic structure in voles in Poland.
Inhibitory effects of 6-methylsulfinylhexyl isothiocyanate on superoxide anion generation from differentiated HL-60 human promyelocytic leukemia cells

Wasabi is a plant of Japanese origin. It belongs to the Brassicaceae family and produces various isothiocyanates (ITCs). Because 6-methylsulfinylhexyl isothiocyanate (6-MSITC) is particularly stable among wasabi ITCs, it has potential as a functional compound. To clarify the antioxidative activity of 6-MSITC, we investigated its inhibitory effect on superoxide anion (O2• ) generation from phorbol 12-myristate 13-acetate (PMA)-stimulated differentiated HL-60 human promyelocytic leukemia cells. Our results showed that 6-MSITC inhibited O2• − generation in these cells (IC50 value: 28.9 μM). 6-MSITC at 0.8, 4, and 20 μM significantly inhibited the consumption of exogenously added NADH compared with the control. On the other hand, < 263 μM 6-MSITC did not scavenge O2• − in cell-free experiments. Therefore, we suggest that 6-MSITC inhibited O2• − generation by decreasing an enzymatic reaction with NADPH oxidase. Thus, 6-MSITC may be useful as a functional compound.
Identification of Novel Ligands and Structural Requirements for Heterodimerization of the Liver X Receptor Alpha

Bedi, Shimpi Ph.D., Biomedical Sciences Ph.D. program, Department of Biochemistry and Molecular Biology, Wright State University, 2017. Identification of novel ligands and structural requirements for heterodimerization of the liver X receptor alpha. LXRs, LXRα (NR1H3) and LXRβ (NR1H2), are ligand-activated transcription factors that are members of the nuclear receptor superfamily. Oxysterols and nonsteroidal synthetic compounds bind directly to LXRs and influence the expression of LXR dependent genes. The use of murine models and LXR-selective agonists have established the important role of LXRs as sterol sensors that govern the absorption, transport, and catabolism of cholesterol. Upon activation, these receptors have been shown to increase reverse cholesterol transport from the macrophage back to the liver to aid in the removal of excess cholesterol. Not surprisingly, LXR dysregulation is a feature of several human diseases, including metabolic syndrome. Due to their roles in the regulation of lipid and cholesterol metabolism, LXRs are potentially attractive pharmaceutical targets. As ligand binding and dimerization play pivotal roles in modulating LXR activity, the identification of novel ligands and requirements for LXR dimerization can potentially aid the drug development process. Herein, using a variety of biophysical assays, including fluorescence based assays coupled with in silico molecular modeling, I have identified medium chain fatty acids and/or their metabolites as the novel endogenous agonists of LXRα. There is mounting evidence that ligand induced dimerization regulates the transcriptional output of nuclear receptors. Thus, it is important to identify factors that
Comparison of three different methods for DNA extraction from bugs of family Pentatomidae (Hemiptera) for PCR

Developing a simple, time and cost efficient method for the extraction of DNA is essential when a large number of samples have to be processed. The success of PCR depends on the purity and quality of the DNA template and for this the method of specimen storage is equally critical as the DNA extraction methods. This study is an attempt to find the most suitable method of DNA extraction and the effect of killing method and storage conditions for extraction and purification of intact DNA in Pentatomid bugs.
Mechanism of Nuclear Protein Import and Export an In Vitro Approach

1 Chapter 1: Introduction to nuclear protein transport. 2 1.1 Nuclear protein transport occurs through the nuclear pore complex 2 1.2 Nuclear import of endogenous proteins is signal dependent. 6 1.3 Identification of a nuclear localization signal. 8 1.4 The rate of nuclear protein import depends on the number of NLSs 9 1.5 Nuclear protein import consists of two steps: docking of a cNLS-containing protein at the NPC, and translocation across the NPC 1 0 1.6 Identification of different factors that mediate docking of a cNLScontaining protein at the NPC, and subsequent translocation 12 1.7 The small GTPase Ran and its regulators . 14
The emergence of words from vocal imitations

People have long pondered the origins of language, especially the words that compose them. Here, we report a series of experiments investigating how conventional spoken words might emerge from imitations of environmental sounds. Does the repeated imitation of an environmental sound gradually give rise to novel word forms? In what ways do these words resemble the original sounds that motivated them? Participants played a version of the children’s game “Telephone”. The first generation of participants imitated recognizable environmental sounds (e.g., glass breaking, water splashing). Subsequent generations imitated the imitations for a maximum of 8 generations. The results showed that the imitations became more stable and word-like, and later imitations were easier to learn as category labels. At the same time, even after 8 generations, both spoken imitations and their written transcriptions could be matched above chance to the category of environmental sound that motivated them. These results show how repeated imitation can create progressively more word-like forms while continuing to retain a resemblance to the original sound that motivated them, and speak to the possible role of human vocal imitation in explaining the origins of at least some spoken words.
In Vitro ACTIVITY OF PROPOLIS ON DOMESTIC ANIMAL VIRUSES: A REVIEW

espanolEl propoleo es una mezcla resinosa natural producida por las abejas a base de sustancias recogidas de las plantas and sus exudados. Los antiguos griegos, romanos and egipcios eran conscientes de las propiedades curativas del propoleo and se le otorgo un amplio uso en la medicina. El propoleo varia en componentes and proporcion de sustancias activas en funcion de la flora de cada region donde es producido. Se ha demostrado que el propoleo posee importantes propiedades biologicas como bactericida, anti-parasitario, fungicida, inmunomodulador, antioxidante and antiviral. El objetivo de este trabajo fue explorar el uso del propoleo en estudios con virus de origen animal mediante una minuciosa busqueda de informacion en las principales bases de datos disponibles. Se reportan los principales efectos encontrados con el uso del propoleo in vitro sobre virus de animales domesticos and se muestran las perspectivas en este campo de estudio emergente. EnglishPropolis is a natural resinous mixture produced by bees, based on substances collected from plants and its exudates. The ancient Greeks, Romans and Egyptians were aware of the healing properties of propolis and granted it extensive use in medicine. Propolis varies in components and proportion of active substances depending on the flora of each region where it is produced. Important biological properties of propolis as a bactericide, anti-parasitic, fungicide, immunomodulatory, antioxidant and antiviral agent have been demonstrated. The objective of this work was to explore the uses of propolis in studies of animal viral diseases through a thorough search of information in the main available databases. The paper reviews the main reported in vitro effects of propolis on viruses that cause domestic animal diseases, showing the prospects in this emerging field of study. portuguesO propolis e uma mistura resinosa natural produzida pelas abelhas a base de substâncias recolhidas das plantas e seus exudados. Os antigos gregos, romanos e egipcios eram conscientes das propriedades curativas do propolis ao qual lhe foi outorgado um amplo uso na medicina. O propolis varia em componentes e proporcao de substâncias ativas em funcao da flora de cada regiao onde e produzido. Tem sido demonstrado que o propolis possui importantes propriedades biologicas como bactericida, anti-parasitario, fungicida, imunomodulador, antioxidante e antiviral. O objetivo deste trabalho foi explorar o uso do propolis em estudos com virus de origem animal mediante uma minuciosa busca de informacao nas principais bases de dados disponiveis. Relatam-se os principais efeitos encontrados com o uso do propolis in vitro sobre virus de animais domesticos e se mostram as perspectivas neste campo de estudo emergente
Premna integrifolia L. on Enzymatic Biomarkers in Atherosclerosis

Premna integrifolia L. belongs to family Verbenaceae and it is believed to prevent cardiovascular disease as per Ayurveda. In order to evaluate the cardiac biomarkers and treatment efficacy of hydroalcoholic extract (HAE) of root bark in atherosclerosis. Sixty Wistar rats were divided into six groups and ten animals in each group. Rats fed with high fat diet and various concentrations of HAE treatment were studied and standard drug, atorvastatin was compared with HAE. This extract showed a significant action against atherosclerosis in a dose dependent manner which was studied in terms of lactate dehydrogenase activity, HMG-CoA/Mevalonate ratio, collagen content in aorta, levels of transaminases, calcium and other marker enzymes indirectly involved in the cardio protection. Alteration in collagen deposition in aorta of histopathological evaluation was noticed in treated animals. Anti-atherosclerotic activity of HAE of P. integrifolia was due to its modulatory activity on cholesterol metabolism and our results contribute towards validation of the traditional use of P. integrifolia in high fat diet induced atherosclerosis. Short Research Article Chitra et al.; IJBCRR, 17(3): 1-9, 2017; Article no.IJBCRR. 34232 2
Urease-Producing Halophilic Bacteria Isolated from Bahr Al-Milh Salt Lake, Karbala, Iraq

Salt lakes represent an extreme habitat for prokaryotes which tolerate significant concentration of NaCl. Many studies on screening and characterization of these microorganisms have been done, however, very little reported about urease producer halophilic bacteria. The present study aimed to isolate urease positive bacteria from Bahr Al-Milh Salt Lake, Karbala, Iraq. A total of 161 gram positive and 57 gram negative bacteria were found which one third of them showed the ability to produce urease. 16S rDNA sequencing analysis showed the isolated bacteria belong to genus Bacillus, Virgibacillus, Halobacillus and Staphylococcus. Further studies focusing on the enzyme structures and encoding genes are suggested.
Evaluation of Pseudomonas putida and Pseudoalteromonas haloplanktis as Alternative Hosts for Recombinant Gene Expression - by Evaluating the xylS/Pm Expression System with mCherry as Reporter Gene

Different species of bacteria have different intracellular environments. Escherichia coli (E. coli) is widely used as an expression host for microbial production of recombinant proteins and therapeutics. However, its intracellular environment is not necessarily the best to obtain correct folding of all proteins expressed. Changing the expression host to a species with a more suitable intracellular environment can cause benefits like proper folding for some proteins. Thus, downstream processing after expression to achieve correct folding is no longer needed, resulting in simplified and more inexpensive production. In this thesis, two alternative expression hosts proved to be favorable for recombinant gene expression, Pseudomonas putida (P. putida) and Pseudoalteromonas haloplanktis (P. haloplanktis) were compared to E. coli for production of recombinant proteins. The expression vectors used in this thesis includes the xylS/Pm expression cassette from the TOL plasmid and is expected to function well in P. putida since it originates from this bacterium. The different expression vectors used were shown to function well in E. coli by high expression of the reporter gene mCherry. The expression vectors pVB-1B0B1-mCh, and pVB-1M0B1-mCh resulted in highest expression of the reporter gene for both soluble and insoluble protein fractions. These vectors carried the mutated 5’-UTR region H39 in combination with wild type (pVB-1M0B1-mCh) and mutated Pm promoter ML2-5 (pVB-1B0B1-mCh). However, in P. putida these plasmid vectors resulted in no expression of mCherry. This might be caused by the medium copy number caused by the cop271 -mutation of trfA embedded in the RK2 vectors. The evaluation of P. haloplanktis resulted in the establishment of favorable growth conditions, as well as a functioning protocol for conjugation and detection of positive conjugants. However, the preservation of these must be optimized further, so the strains are easier to revive after freezing and evaluation of the expression can be performed more thoroughly and compared to E. coli.
Nutrient distribution in a shallow subtropical lagoon, south Brazil, subjected to seasonal hypoxic and anoxic events

The Conceicao Lagoon, located in south Brazil, is a semi-enclosed coastal ecosystem that has seasonal hypoxic and anoxic conditions in its vertically stratified central region, characterized as a site of retention and mineralization of organic matter. This study investigates water column dynamics in the central region of the Conceicao Lagoon (CCL) and its relation to physical and chemical variables, in order to understand the hypoxic and anoxic events. Surface, halocline and bottom waters were evaluated at three sampling sites along the CCL. The samples were collected in triplicate during the summer, fall and winter of 2014. Hypoxic and/or anoxic events occurred in the summer (1/21) at the halocline (3 m) and bottom (4 m) waters, and in the fall (2/5) in the bottom water (4.5 m). Positive values of apparent oxygen utilization showed mineralization processes in the halocline and bottom waters. The lowest vertical stratification index was recorded in August (southern winter), which was associated with wind speed (14.7 m.s-1) and direction (southern quadrant). Nutrient concentrations were higher in winter, related to increasing of water mixing. This was the first study to evaluate the dynamics of hypoxic and anoxic events in the CCL and how nutrients respond to the physical structure of the water column.
Probiotic Lactococcus lactis: A Review

Lactococcus lactis plays a critical role in food, dairy and health sectors. In food and dairy industries, it is found in production processes of various fermented products such as sausages, pickled vegetables, beverages such as beer and wine, breads, soymilk kefir, sour milk, butter, cream, fresh cheese and different types of cheeses, like Cheddar, Colby, Cottage cheese, Camembert, cream cheese, Roquefort and Brie. Additionally, there is an increasing interest towards the possible health benefits of the probiotic activity of this organism which generally is species and strain specific and depends upon the survival in gastrointestinal tract with sufficient number. Certain strains have the ability to produce antimicrobial peptide called nisin which exhibits preservative potential. Therefore, application of bacteriocinogenic Lactococcus lactis in food and dairy sectors to preserve foods as a natural way and contributing health promoting attributes due to probiotic activity would definitely fulfil today’s consumer demands. This paper aimed to review the adaptation, antibiotic resistance, therapeutic and preservation potential of bacteriocinogenic and probiotic Lactococcus lactis.
Dissimilar stem and leaf hydraulic traits suggest varying drought tolerance among co-occurring Eucalyptus grandis × E. urophylla clones

In South Africa, there is currently a phenomenon where a Eucalyptus grandis × E. urophylla clone is dying on a large scale, whereas co-occurring clones in the same plantation area remain healthy. No primary biotic pathogen has been isolated from these dying trees. However, the plantation region has endured severe drought conditions. We hypothesised that the specific E. grandis × E. urophylla clone dieback is due in part to the affected trees having an elevated drought vulnerability. We tested this hypothesis retrospectively by examining how the dying (branch dieback started) as compared with two healthy and co-occurring E. grandis × E. urophylla clones vary in branch xylem anatomy (water transport) and leaf stable carbon isotopes (gas exchange) across two levels of mean annual precipitation in the planted landscape. There was significant intra-hybrid variation in the range of studied hydraulic traits. It appeared that the dying clone is maladapted to drier field conditions relative to the two healthy growing clones. Individuals of the drought-susceptible clone had increased hydraulic conductivity, having both wider vessel lumens and larger lumen fractions, and also did not regulate leaf-level transpiration in the drier landscape as efficiently as the two unaffected clones (lower δ13C ratios). In turn, one of the healthy growing clones had a completely different hydraulic strategy, having higher wood density, lower lumen fractions, and higher δ13C ratios that are widely considered as hydraulically resilient during water stress. The other clone appeared to also gain drought tolerance via higher leaf-level water-use efficiency, although drought tolerance was less clear regarding xylem anatomy. We highlight how variation in relative drought vulnerability can be highly significant even between clones within a single hybrid group. Knowledge of this variation in plant hydraulics between commercially planted and closely related Eucalyptus trees would complement clone deployment programmes in a target landscape.