Miracle-dz/UniFAR-FTUs huggingface dataset:
What rhythmic perception and amusia can tell us about vocal social communication in schizophrenia

Background Perceiving social intent throughvocal intonation is impaired in schizophrenia; thisdysprosodia partly arisingfrom impaired pitch perception.Individuals with amusia (tone-deafness) are insensitive to pitch change andalso demonstrate prosody deficits. Sensitivity to rhythm is reduced in amusia when tonal sequences contain pitch changes (polytonic), but is normal for monotonic sequences, suggesting perceptual impairment originates at a secondary processing stage where pitch- and time-relatedcues are yoked. Here, we sought to ascertain: 1) whether schizophreniapatients demonstrate rhythmic deficits, 2) whether suchdeficits are restricted to polytonic sequences, and 3) how pitch and rhythm perception relate to prosodic processing. Methods Seventy-sixparticipants (33 schizophrenia) completed tasks assessing pitch and prosody perception, as well as monotonic and polytonic rhythmic perception. Results Increasing tone-deafness correlated with pitch-dependent rhythm detection impairments. Pitch and prosody correlated across all participants. Schizophreniapatients displayed basic time and pitch deficits. Correlations and path analyses indicated prosodic processing is an associatedfunction of pitch and pitch-dependent rhythm perception,with pure temporal processing playing an indirect role.In schizophrenia, deficits in monotonic and polytonic rhythmic perception did not contribute to prosodic processing dysfunction, and montonic rhythmic dysfunction and pitch perception did not covary. Conclusions Exploring similarities between amusia and schizophrenia focused our characterization of prosodic processing as the function of sub-processes reflecting pitch and time perception,whichare prerequisite for prosodic processing. The uniqueness of dysprosodia in schizophrenia relative to other illnesses may be measured by idiosyncrasy in the pattern and magnitude of the sub-process task relationships.
Setting the stage: host invasion by HIV

Florian Hladik* ‡§ and M. Juliana McElrath* ‡|| Abstract | For more than two decades, HIV has infected millions of people worldwide each year through mucosal transmission. Our knowledge of how HIV secures a foothold at both the molecular and cellular levels has been expanded by recent investigations that have applied new technologies and used improved techniques to isolate ex vivo human tissue and generate in vitro cellular models, as well as more relevant in vivo animal challenge systems. Here, we review the current concepts of the immediate events that follow viral exposure at genital mucosal sites where most documented transmissions occur. Furthermore, we discuss the gaps in our knowledge that are relevant to future studies, which will shape strategies for effective HIV prevention.
Interspecific and intraspecific variation in corolla tube length in Pedicularis species achieved by both cell anisotropy and division

The association between plants with long corolla tubes and pollinators with long tongues has evolved repeatedly in diverse pollination systems. However, the morphogenesis of long corolla tubes involved in diverse plant groups remains largely unexplored, limiting our understanding of the evolution and maintenance of long corolla tubes. Corolla tubes of Himalayan Pedicularis species exhibit striking length diversity, ranging from less than 10 mm to more than 120 mm. We investigated the role of cell division and cell expansion in determining the corolla tube morphology in eight Pedicularis species and in an experimental population of P. siphonantha Don in which corolla tubes were elongated under shading and watering treatments. Among species, the corolla tube length was positively correlated with both cell number and cell length but not cell width. Our analyses of intraspecific variation in corolla tube length indicated that it was positively correlated with cell length in all eight species but with cell number in only four of the species, indicating that corolla tube development in Pedicularis generally involves anisotropic cell expansion. The elongation of corolla tubes in P. siphonantha under experimental conditions was caused by the anisotropic elongation of cells; cell number of tube‐elongated flowers was not significantly increased. Our results showed that intraspecific variation in corolla tube length in Pedicularis species was largely attributable to changes in cell anisotropy, but the evolutionary innovation underlying the rapid radiation of Pedicularis corolla tubes was attributable to both cell division and cell expansion.
Physiological Responses of Cotton Genotypes to Water-Deficit Stress during Reproductive Development

Drought stress is one of the major abiotic factors affecting crop growth and limiting production worldwide. Cotton genotypes vary in drought tolerance, and the effects of drought stress on the anatomy and physiology of cotton leaves and roots have been reported. However, information on physiological and metabolic processes of leaves and flowers of modern cotton cultivars under water-deficit stress during reproductive development is not well elucidated. It was hypothesized that water-deficit stress during squaring and flowering stages would impair stomatal conductance and photosynthetic efficiency of leaves, which consequently would result in osmotic adjustment through accumulation of compatible solutes, increased activity of enzymes, and perturbation of carbohydrates metabolism in leaves and flowers of cotton plants, and differences in drought tolerance among the genotypes would exist. Therefore, field and growth room experiments were conducted to evaluate the effects of water-deficit stress during reproductive development on the physiology and metabolism of leaves and flowers of a diverse range of cotton genotypes. Results indicated that water-deficit stress significantly decreased stomatal conductance of cotton plants. Water-deficit stress during the early squaring stage increased activity of antioxidant enzymes, and decreased photosynthetic efficiency and concentrations of pigments of cotton leaves. Carbohydrate metabolism in cotton flowers and subtending leaves was also compromised by water-deficit conditions, with a shift in the carbohydrate partitioning being promoted by the stress, with subtending leaves and bracts as main sources and pistils as main sinks, mainly for sucrose and soluble sugars. In addition, osmotic adjustment through proline accumulation and changes in osmotic potential is a mechanism used by cotton plants to tolerate drought stress. Leaves are more sensitive to waterdeficit stress than ovaries, thus with higher osmotic adjustment. Finally, genotypes varied in tolerance to drought, with genotypes that showed higher osmotic adjustment in leaves and flowers indicating higher tolerance to drought episodes. Osmotic adjustment through accumulation of compatible solutes could be used as an effective tool for drought-tolerant genotypes in plant biotechnology. However, further research is needed for complete elucidation of osmotic adjustment and carbohydrate metabolism in flower tissues of cotton genotypes under drought conditions during the flower development.
Antioxidační aktivity okřehku Lemna minor L. v abiotickém stresu

Perzistentni organicke polutanty a pesticidy maji na rostliny obecně skodlivý vliv. Cilem bakalařske prace bylo sledovat a zhodnotit vliv koncentraci (0,5 mg/l a 5 mg/l) flurochloridonu a fluorantenu na rostliny okřehku mensiho (Lemna minor L.). Z morfologickeho hlediska byly pozorovany změny vzhledu a růstu rostlin ohřehku. Byl zjistěn znacný vliv flurochloridonu na rostliny. Z fyziologickeho hlediska byl sledovan vliv na biologicke membrany -- měřeni obsahu malonyldialdehydu pomoci spektrofotometrie a vliv na miru stresu v rostlině -- stanoveni kyseliny abscisove pomoci radioimunoanalýzy. Ve ctvrtem dni kultivace na uvedených xenobioticich měly vsechny experimentalni varianty zvýsený obsah kyseliny abscisove oproti kontrole. Zatimco malonyldialdehyd jako marker stresu způsobeneho poskozenim lipidů se měnil z hlediska kvantity u jednotlivých variant nerovnoměrně.
15 Bacterial Behavior

E. R # Sp Patterns of Flagellation . 290 Patterns of Swimming . 290 Swarming . 293 Flagella Structure . 293 Motor Structure . 294 Gene Expression and Assembly . 296
Down-regulation of BmCREB by shRNA in Bombyx mori cell lines

Short hairpin RNA (shRNA) is an effective method for interfering gene expression and gene function research. CREB (cAMP response element binding protein), an important and conservative transcriptional factor in eukaryote, regulates many physiological functions. According to our previous research, Bombyx mori CREB (BmCREB) is closely relative to the diapause induction in the silkworm. In order to clarify the molecular mechanism of BmCREB in diapause induction, we constructed the interfering vector pMD18-U6-shRNA of BmCREB shRNA and transfected in a Bombyx mori ovary cell line (BmN). The expression of BmCREB was detected by Western blot and RT-PCR. The results showed that BmCREB was efficiently reduced by 63.0% with the transfection of 1 μg T-227 plasmid in 72 hours. The down-regulation of BmCREB was significant within different shRNA plasmids. Plasmid T-227 had the best efficiency. These results would lay a foundation for the further research on BmCREB mechanism of the Bombyx mori diapause by shRNA in vivo.
Effects of rice husk and rice husk biochar on root rot disease of ginseng (Panax ginseng) and on soil organisms

Abstract This study investigated the effects of rice husk and rice husk biochar on root rot (caused by Cylindrocarpon destructans and Fusarium solani) of ginseng (Panax ginseng) and on soil organisms. The effects were compared between paddy-converted and upland soils characterised by high and low nutrient content, respectively. The prevalence of root rot disease in the upland soil decreased in plots treated with rice husk at 5.2 Mg ha−1 compared to the untreated control. Small differences in soil chemical properties between different treatments suggested the role of biotic factors in the suppression of the disease. In both soils, the lowest hyphal growth of Fusarium solani was observed in soil collected from plots treated with rice husk at 5.2 Mg ha−1. The results suggested that the low incidence of root rot disease was due to the suppressive effect of soil on pathogenic fungi in the treated upland soil. Principal component analysis of phospholipid fatty acid results suggested that changes in microbial community structure contributed to soil suppressiveness in the paddy-converted soil. The highest density of fungivorous nematodes was observed with rice husk at 5.2 Mg ha−1 in the paddy-converted soil, and Aphelenchus sp. collected from the plots were successfully cultured on F. solani and C. destructans. This observation showed that the fungivorous nematodes have potential to suppress pathogenic fungi by feeding on them. It was shown that rice husk can be used in control of root rot disease while promoting the growth of beneficial organisms suppressing pathogenic fungi and that the effect may differ by soil type.
Regulation of maltose transport and metabolism in Saccharomyces cerevisiae

Maltose metabolism in the yeast Saccharomyces cerevisiae is of great importance both for academic and industrial researchers. It requires the presence of at least one of five independent MAL loci: MAL1, MAL2, MAL3, MAL4 and MAL6. Each active locus is made of three genes: two structural genes that encode intracellular enzyme maltase and transport protein for maltose, and the third gene that encodes positive regulatory protein. Maltose is transported unchanged into the cell with the help of specific transmembrane transporter, and then it is hydrolysed by the intracellular maltase into two glucose units which are then channeled through the glycolytic pathway. The maltose metabolism in S. cerevisiae is under the control of three general regulation mechanisms: induction, glucose repression and glucose inactivation. Powerful tools of molecular biology have brought many important discoveries in transport, metabolism and regulation of the uptake of maltose in yeast cells at the molecular level. Although the knowledge on these phenomena is far from being complete, it helps us understand the sugar preference in industrial fermentations on complex substrates but also how glucose effects gene expression and entire metabolic activity in other organisms.
Aflatoxin M1 in Breast Milk, Cow Milk and Milk Products in Minna,Nigeria and their Predisposing Factors

Herein is a focus on incidence and levels of Aflatoxin M1 (AFM1) in milk of breast feeding mothers, cow milk and vended milk products within Minna, Nigeria obtained by analysis of 140 samples of milk and milk products using high performance liquid chromatography (HPLC). The findings reveal; incidence of 77.5% in human milk, and suggests that diet, socioeconomic status and ethnicity influence exposure. Nomadic cow milk samples had the highest incidence of 80%, cheese had 40% incidence, nono had 35% incidence, commercial cow milk had 25% incidence and yoghurt had 10% incidence. In a total of 69 contaminated samples, 51 were at levels above (0.05 μg/L) the EU and Nigerian legislated limit. Exposure to AFM1 from milk and milk products at concentrations demonstrated in this investigation is of great concern as infants in the country are encouraged to be exclusively breast fed for six months after which alternative milk intake sometimes from animal origin can be sourced. Established carcinogenicity and growth impairing potentials of AFM1 stands as sources of concern and hence the need for enforcement of the legislated limit by regulatory agencies in Nigeria.
When conflict cannot be avoided: executive control dominates early selective sensory modulations during cognitive conflict

When different sources of sensory information suggest competing behavioral responses, the efficiency of decision-making is impaired. Prior work suggests that at least two mechanisms may play a role in mitigating this interference: using early selective attention to extract the most relevant sensory inputs to avoid conflict or increasing the efficiency of the executive control network to resolve conflict during post-perceptual processing. To test these alternatives, we combined a stimulus-frequency tagging technique with a classic color-word Stroop paradigm, where color-bar targets and letter-string distractors were simultaneously flickered at different frequencies. Using electroencephalography (EEG), we measured the quality of early sensory processing by assessing the amplitude of steady-state visually evoked potentials (SSVEPs) elicited by the targets and distractors. We also measured the engagement of the executive control network by assessing changes in frontal theta (4-7Hz) and posterior alpha oscillations (8-14Hz). Counter to the ‘early selective sensory modulation’ account, the amplitude of the SSVEP response was not modulated by manipulations of color/word congruency, while the frontal theta activity increased and the posterior alpha activity decreased in response to conflict. Moreover, target-related SSVEP amplitude was not correlated with response times (RTs) and a higher (not lower) distractor-related SSVEP amplitude predicted faster RTs. On the other hand, the amplitude of the frontal theta and alpha activity was highly correlated with RTs, irrespective of conflict levels. Over all, these results highlight the dominant role of the executive control network in conflict resolution during post-perceptual processing. Significance Statement Conflicting information interferes with decision-making. However, this interference can be mitigated either by extracting the most relevant inputs during early sensory processing or by increasing the efficiency of the executive control processes to resolve conflict. By measuring electroencephalography (EEG) in humans performing a modified color-word Stroop task, we examined early sensory responses evoked by targets and distractors while simultaneously monitoring frontal theta and posterior alpha oscillations to index the activation of the executive control network. We found evidence that the executive control network played a more prominent role in resolving conflict.
Integrative Analysis of Transcriptomic Data Applied to Prostate Cancer Metastasis

Prostate cancer is the most common non-dermatological cancer amongst men in the developed world. The disease is manageable if detected early; treatment is thus becoming highly individualized, placing emphasis on detection and prediction of disease prognosis. This thesis is concerned with the integrative analysis of gene expression data from prostate cancer, to reveal molecular signatures of metastases and the mechanisms of disease progression. Meta-analytic procedures are used to integrate three datasets and compare primary tumors based on metastatic outcome. Four datasets are also integrated to compare primary and metastatic tumour tissue types. This statistical integration provides a more robust and accurate characterization of gene expression signatures, and helps minimize microarray noise and study-specific effects. Multiple methods of integration are explored. Once integrated, a subset of significantly differentiated transcripts is selected to form a tentative expression signature. A support vector machine was used to construct a predictive model of metastatic outcome based on the identified expression signature. Its performance was assessed using a nested cross-validation procedure and out-of-sample testing. Data integration and network analysis have proved to be useful tools in providing context to the complex systems studied in system biology. This thesis makes
Microbial diversity in Rohu fish gut and inland saline aquaculture sediment and variations associated with next-generation sequencing of 16S rRNA gene

Next-Generation Sequencing (NGS) based 16S rRNA gene metagenomics studies are significantly contributing to understand microbial diversities in relatively unexplored agricultural sub-disciplines. However, experimental variations such as primer selection and polymerase chain reaction (PCR) bias can have great impact on outcomes of these studies. Here, we compared two 16S rRNA variable (V3 and V4) region specific primer pairs for study of microbial diversity in sediment and fish (Labeo rohita) gut samples. Clear bias in terms of diversity and community representation was observed in NGS dataset generated from V3 primers, whereas V4 primer showed much better results. Overall diversity in sediment sample was found to be much higher than gut sample. Proteobacteria followed by Verrucomicrobia were most dominant phyla in sediment and fish gut samples. Presence of known cellulose degraders (Clostridium spp., Ruminococcus spp., Eubacterium spp. and Bacteroides spp.) and Short Chain Fatty Acid (SCFA) producers (Faecalibacterium prausnitzii, Veillonella spp. and Megasphaera spp.) suggested that gut microbiota played an important role in digestion, physiology, metabolism and health of L. rohita. Gut microbiota also harbored potentially fish and human pathogenic bacteria. Very few sequences belonging to known probiotic bacteria (Bacillus spp., Streptococcus spp. and Bifidobacterium spp.) were observed. This study serves as preliminary investigation of microbial diversity in aquaculture environment and impact of primer specific variations on estimated diversity. © 2017 The Authors. Published by JFLS. This is an open access article under the CC BY-NC-ND license (https://creativecommons.org/licenses/by-nc-nd/4.0). A R T I C L E I N F O Received: 03 May 2017 Accepted: 10 June 2017 Available online: 30 June 2017
Fluid dynamic factors as a cause and effect of biofilm formation of Staphylococcus aureus biofilms

Sherman, Erica, "Fluid dynamic factors as a cause and effect of biofilm formation of Staphylococcus aureus biofilms" (2016). Staphylococcus aureus bacteria are able to form biofilms and distinctive tower structures that facilitate their ability to tolerate treatment and to spread within the human body. The formation of towers, which break off, get carried downstream and serve to initiate biofilms in other parts of the body are of particular interest here. It is known that flow conditions play a role in the development, dispersion and propagation of biofilms in general. The influence of flow on tower formation and ultimately what factors lead to tower formation, however, is not at all understood. This work is focused on the effect of applied shear stress on tower development. The hypothesis being examined is that tower structures form within a specific range of shear stresses and that there is an as yet ill-defined fluid dynamic phenomenon that occurs hours before a tower forms. In this study, a range of shear stresses is examined that brackets 0.6 dynes/cm 2 , the nominal shear stress where towers seem most likely to form. The biofilm structure is known to be a temporally and spatially heterogeneous structure, which must be taken into account when considering the tower formation frequency and the local flow environment. How this structure differs as a function of applied shear, the experimental stage of biofilm development, and the likelihood of tower formation is analyzed. This work includes µPTV measurements and cell density data indicating variations in flow and biofilm evolution as a function of the applied shear. Causal relations between flow and biofilm development will be discussed as well as the presentation of specific biofilm development terms as predictive measures of tower formation. iii DEDICATION This work is dedicated to my grandfather, Enzio Macor. His passion for learning was evident in everything he did and shone through no matter what life sent his way. His example leaves me humbled and sparks a fire in my heart. iv ACKNOWLEDGEMENTS My work is a cumulative result of the support, inspiration, and effort of those around me who have helped me to become who I am today. Each person has played a role, no matter how big or small, which has fostered my growth and for that I am thankful. First and foremost, my parents have provided tremendous support and encouragement to try and keep trying no matter …
Advances in culture and genetic modification approaches to lipid biosynthesis for biofuel production and in silico analysis of enzymatic dominions in proteins related to lipid biosynthesis in algae

Biofuels have been shown to be a promising and highly attractive alternative for minimizing the use of fossil fuels, and microalgae have positioned themselves as potential candidates for production of lipids and other substances of commercial interest. We briefly review recent advances made in microalgae culture conditions and genetic manipulation for improving lipid yields for biofuel production – with both approaches showing similar yields of triacylglycerides, indicating that more work is required for improving lipid yield and accumulation in algae. Aiming at gaining knowledge of algae genetic manipulation and exploring future use of this information for modifying the lipid biosynthesis pathway, we investigated whether some characteristics of enzymes involved in lipid biosynthesis could relate to lipid yield and accumulation in algae. We made an in silico analysis of amino acid sequence of enzymatic domains and modeled tertiary structure of three proteins involved in the biosynthesis of lipids in microalgae: acetyl‐CoA carboxylase, Acyl‐CoA: diacylglycerol acyltransferase, and glycerol‐3‐phosphate acyltransferase. Our results suggest that, based on primary amino acid sequences and tertiary structure of proteins shared by certain algae, it is likely that these proteins may relate to lipid yield and accumulation, which makes bioinformatics a powerful tool for in silico study of proteins and for selecting genes involved in lipid biosynthesis that could be useful for heterologous transformation in algae with the long term objective of improving their yield, accumulation, and fatty acid composition by genetic engineering.