Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection and Mitigation of Spurious Antisense Reads with RoSA

Motivation Antisense transcription is known to have a range of impacts on sense gene expression, including (but not limited to) impeding transcription initiation, disrupting post-transcriptional processes, and enhancing, slowing, or even preventing transcription of the sense gene. Strand-specific RNA-Seq protocols preserve the strand information of the original RNA in the data, and so can be used to identify where antisense transcription may be implicated in regulating gene expression. However, our analysis of 199 strand-specific RNA-Seq experiments reveals that spurious antisense reads are often present in these datasets at levels greater than 1% of sense gene expression levels. Furthermore, these levels can vary substantially even between replicates in the same experiment, potentially disrupting any downstream analysis, if the incorrectly assigned antisense counts dominate the set of genes with high antisense transcription levels. Currently, no tools exist to detect or correct for this spurious antisense signal. Results Our tool, RoSA (Removal of Spurious Antisense), detects the presence of high levels of spurious antisense read alignments in strand-specific RNA-Seq datasets. It uses incorrectly spliced reads on the antisense strand and/or ERCC spike-ins (if present in the data) to calculate both global and gene-specific antisense correction factors. We demonstrate the utility of our tool to filter out spurious antisense transcript counts in an Arabidopsis thaliana RNA-Seq experiment. Availability RoSA is open source software available under the GPL licence via the Barton Group GitHub page https://github.com/bartongroup. Contact g.j.barton@dundee.ac. uk, g.g. simpson@dundee.ac. uk
The Association between The Degree of Liver Cirrhosis Severity and Zinc Serum Level

Background: Impaired liver function in LC (Liver Cirrhosis) can cause Zinc deficiency (Zn). One of the causes of Zn deficiency in LC is decreased albumin synthesis, whereas albumin is required as the main Zn binding protein in plasma. However, some studies of the severity of LC with Zn serum levels still provide controversial results. Objective: To determine the association between the degree of LC severity and Zn serum level. Methods: The subjects of this study were LC patients in Gastroentero-Hepatology Unit and In ternal medicine wards in of Dr. Soetomo General Hospital Surabaya for three months. Diagnosis of LC was based on clinical examination according to Soehardjno- S oebandiri criteria and other findings (ultrasound or endoscopy). The degree of LC severity was determined based on the CTP score (Child-Turcotte-Pugh). Serum Zn concentration was measured by atomic absorption spectrophotometry method. The research design used the cross-sectional method. The statistical test used was Spearman correlation. Results: Forty-three patients fulfilled the study criteria. The subjects consisted of 27 males (62.8%) and 16 females (37.2%) with the mean age of 53.81 ± 8.67 years. Based on the CTP scores, we obtained CTP A of 4 patients (9.3%), CTP B of 19 patients (44.2%) and CTP C of 20 patients (46.5%). The mean of Zn serum level in CTP A, CT P B, and CT P C score was 58.3 ± 19.6 μg/dl, 43.4 ± 14.5 μg/dl and 31.6 ± 10 μg/dl respectively. The result of the statistical test showed a significant correlation between LC severity and Zn serum level (p <0.05 and r = -0.583). Conclusion: The heavier the severity of LC, the lower Zn serum levels.
Biochromic silole derivatives: a single dye for differentiation, quantitation and imaging of live/dead cells

Differentiating between live and dead cells is a critical step for biological researchers, clinical doctors and pharmaceutical engineers when evaluating cell viability, for determining compound cytotoxicity and in the development of effective treatments for many diseases. Usually, careful selection and combination of two different dyes are required to differentiate and image both live and dead cells. In this work, we present a new method that can differentiate, quantify and image both live and dead cells concurrently through the use of a single, cell-permeable, biochromic fluorescent dye. Two silole-based hemicyanine dyes, Silo-Cy and Silo-2Cy are designed and synthesized. These dyes exhibit green fluorescence in both live and dead cells but much stronger green and red fluorescence only from dead cells. By collecting signals from the two distinct channels, we are able to image and discriminate between live and dead cells through fluorescence microscopy and quantify the cell viability via flow cytometry.
Towards grizzly bear population recovery in a modern landscape

1Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada 2Department of Forest Resources Management, University of British Columbia, Vancouver, BC, Canada 3Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada 4RGL Recovery Wildlife Health & Veterinary Services, Saskatoon, SK, Canada 5Grizzly Bear Program, fRI Research, Hinton, AB, Canada
Effect of domestic processing on the antioxidant activities of edible mushrooms

This study evaluated the effect of domestic cooking practices (boiling, steaming and pan-frying) on the antioxidant activities of Pleurotus sajor-caju (Grey oyster mushroom), Lentinus edodes (Shiitake) and Auricularia polytricha (Black jelly mushroom). Four different antioxidant assays, namely ABTS, DPPH, FRAP and ORAC were conducted to determine the antioxidant properties after cooking treatments. Colour change in Shiitake and black jelly mushroom was more marked as stated by higher I”E values as compared to steamed samples. Interestingly, lightness (L * ), redness (a *) and yellow (b* ) of black jelly mushroom was markedly increased upon all cooking methods. Shiitake (15 minutes) had the highest Total Phenolic Content (TPC) among all the boiled samples whereas black jelly mushroom (5 minutes) had the highest after steaming. Boiling had detrimental effect on TPC of black jelly mushroom, which caused almost 100% lost. The losses of phenolics were associated to unexceptionally high phenolic content (34.08Â±0.19 mg GAE/g extract) that released into the cooking water. This had led to tremendous reduction of DPPH radical scavenging activity after boiled for 15 minutes. However, steamed grey oyster mushroom showed the FRAP and ORAC values increased 4 fold after steamed for 20 minutes. Phenolic compounds namely catechin, syringic acid, (-) Epicatechin, naringin, quercetin and kaempferol were present in all three mushroom species except catechin was found absent in grey oyster and Shiitake mushrooms. No phenolic compounds were detected in both mushroom species after pan-frying at 3 minutes. Black jelly mushroom is the only species that contained catechin. The principle component of grey oyster mushroom correlated well with FRAP, TPC, ORAC and moderately with ABTS whereas high inter-relationship among FRAP and ABTS was observed among Shiitake. Similarly, PCA of black jelly mushroom demonstrated phenolic content of mushroom extracts were highly related with DPPH radical scavenging activity. In conclusion, the present findings demonstrated that domestic cooking methods significantly affected antioxidant activities of the studied mushroom species. Steaming seems to be the best cooking methods for edible mushrooms, as it appeared to efficiently increase bio-accessibility of polyphenols while preserving or even enhancing antioxidant actions in edible mushrooms.
De novo transcriptome combined with spectrophotometry and gas chromatography-mass spectrometer (GC-MS) reveals differentially expressed genes during accumulation of secondary metabolites in purple-leaf tea (Camellia sinensis cv Hongyafoshou)

ABSTRACT To investigate differences in secondary metabolites and their related molecular mechanisms between purple-leaf tea and green-leaf tea, the transcriptomes and the secondary product profiles of the Camellia sinensis cultivars ‘Hongyafoshou’ (HF) and cultivar ‘Lvyafoshou’ (LF) were analysed and compared using GC-MS and spectrophotometric methods. The contents of anthocyanins, carotenoids, and total catechins were higher in HF than in LF. In total, 8,406 differentially expressed genes (DEGs) between HF and LF were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the flavonoids, carotenoids and terpenoids metabolic pathways were highly enriched with DEGs. Differences in the expression of DEGs involved in these three pathways might be responsible for the high accumulation of secondary metabolites in HF. The small miRNA miR529 plays regulatory roles in these secondary metabolic pathways. The sensory quality of purple-leaf tea is higher than that of green-leaf tea, and these results from the combination of flavonoids, carotenoids, and terpenoids biosynthesis. Our study provides further insights into the molecular mechanisms underlying differences in secondary metabolite accumulation between HF and LF.
“Quantitative analysis reveals the basic behavioural repertoire of the urochordate Ciona intestinalis”

Quantitative analysis of animal behaviour in model organisms is becoming an increasingly essential approach for tackling the great challenge of understanding how activity in the brain gives rise to behaviour. In addition, behavioural analysis can provide insight on the molecular basis of nervous system development and function as demonstrated by genetic screens focused on behavioural phenotyping in some genetically tractable model organisms. The progress in building low-cost automated tracking setups, together with advances in computer vision machine learning have expanded the repertoire of organisms which are amenable to quantitative behavioural analysis. Here we used automated image-based tracking to extract behavioural features from an organism of great importance in understanding the evolution of chordates, the free swimming larval form of the tunicate Ciona intestinalis which has a compact and fully mapped nervous system composed of only 231 neurons. We analysed hundreds of videos of larvae and we extracted basic geometric and physical descriptors of larval behaviour. Most importantly, we used machine learning methods to create an objective ontology of behaviours for C. intestinalis larvae. We identified eleven behavioural modes using agglomerative clustering. This approach enabled us to produce a quantitative description of the basic larval behavioural repertoire. Furthermore, we tested the robustness of this repertoire by comparing different rearing conditions and ages. Using our pipeline for quantitative behavioural analysis, we successfully reproduced the known photoresponsive behaviour and the first demonstration to our knowledge that C. intestinalis larvae exhibit sensory arousal and thigmotaxis, both of which can be modulated by the anxiotropic drug modafinil. Remarkably, by comparing the behaviour between animals assayed individually or in small groups, we found that crowd size influences larval behaviour. This study shows that C. intestinalis larval behaviour can be broken down to a set of stereotyped behaviours that are used to different extents in a context-dependent manner. Furthermore, it raises exciting possibilities such as mapping behaviour to specific neurons of this compact chordate nervous system and it paves the way for comparative quantitative behavioural studies as a means to reconstruct the evolution of behaviour, especially in the chordate lineage.
UNA REVISIÓN A LA MINERIA DE OPINIONES Y LOS RETOS DEL PNL

En los ultimos anos se ha generado un crecimiento en el analisis de las redes sociales para tener una idea de lo que la gente piensa sobre los temas de interes actuales, sin embargo, los sistemas de mineria de texto originalmente disenados para tipos de textos mas regulares, como los articulos de noticias, pueden necesitar adaptarse para tratar publicaciones de redes sociales como Facebook, tweets, etc. En este articulo, se presenta una reflexion sobre temas relacionados con la mineria de opinion de las redes sociales y los desafios que imponen en un sistema de procesamiento de lenguaje natural (PNL). DOI: http://dx.doi. org/10.21017/rimci.2020. v7.n13. a80
Desarrollo de un sistema de regulación sintético mediado por “Quorum Sensing” en Cupriavidus pinatubonensis JMP134, para controlar la expresión de genes promotores del crecimiento de plantas

11 Resumen . 12 1. Introducción . 13 1.1 Bacterias promotoras del crecimiento de plantas . 13 1.2 “Quorum Sensing” en la interacción planta-bacteria . 14 1.3 Biología Sintética. 17 2. Hipótesis . 20 3. Objetivo general . 20 4. Objetivos específicos . 20 5. Materiales y Métodos . 21 5.1 Materiales . 21 5.1.1 Reactivos . 21 5.1.2 Material biológico . 21 5.1.3. Medios de cultivo . 23 5.1.3.1 Medio Luria-Bertani (LB) . 23 5.1.3.2 Medio Dorn . 23 5.1.3.3 Medio basal Murashige Skoog (MS) . 24 5.2 Métodos . 24 5.2. 1 Amplificación de fragmentos de DNA por la reacción en cadena de la polimerasa (PCR). 24 5.2. 2 Electroforesis de DNA en geles de agarosa. 24 5.2. 3 Partidores. 24 5.2. 4 Ensamblaje por Gibson . 26 5.2. 5 Transformación de bacterias . 26 5.2. 6 Condiciones de cultivo . 28 5.2. 7 Curvas de crecimiento . 28 5.2. 8 Detección de ácido indol acético (AIA) . 28 5.2. 9 Evaluación de motilidad por swimming . 29 5.2. 10 Ensayo de biopelículas . 29 5.2. 11 Medición de fluorescencia. 30 5.2. 12 Ensayo de crecimiento en plantas . 30 5.2. 13 Ensayo de colonización . 31 5.2. 14 Análisis por microscopía confocal . 31
Transcriptional Regulation of The Porcine GnRH Receptor Gene by Glucocorticoids

The binding of GnRH to its receptor results in the synthesis and secretion of the gonadotropins, as well as stimulation of the gene encoding its own receptor. Thus, the interaction between GnRH and GnRHR represents a central point for regulation of reproductive function. Glucocorticoids can alter reproduction by reducing GnRH responsiveness of gonadotropes within the anterior pituitary gland, potentially via transcriptional regulation of the GnRHR gene. Investigation of this possible mechanism, however, revealed that transcription of the murine GnRHR gene is stimulated by glucocorticoids. To determine the effect of glucocorticoids on porcine GnRHR gene expression, gonadotrope-derived αT3-1 cells were transiently transfected with a vector containing 5118 bp of 5’ flanking sequence for the porcine GnRHR gene fused to luciferase for 12 h and treated with increasing concentrations of the glucocorticoid agonist, dexamethasone (0, 1, 10, 100 and 1,000 nM) for an additional 12 h prior to harvest. Maximal induction of luciferase activity was detected at 100 nM of dexamethasone (2-fold over vehicle; P < 0.05), and this response was blocked by the glucocorticoid antagonist, mifepristone (100 pM). Deletion from 274 to 323 bp upstream of the translational start site eliminated glucocorticoid responsiveness, suggesting the presence of a GRE(s) within this region. Electrophoretic mobility shift assays (EMSA)
Apoptosis After Stent Implantation Compared With Balloon Angioplasty in Rabbits

Abstract Both cell proliferation and apoptosis (programmed cell death) are supposed to play a role in restenosis after angioplasty. We studied these processes in smooth muscle cells (SMCs) and macrophages 1, 4, and 12 weeks after balloon angioplasty or Palmaz-Schatz stent implantation in rabbit iliac arteries. Proliferating cells were visualized by immunostaining with antibodies directed against proliferating cell nuclear antigen. Apoptotic cells were detected using the TUNEL (terminal deoxynucleotidyl transferase–mediated dUTP nick end labeling) technique, propidium iodide staining, and transmission electron microscopy. At all time points, the neointimal cross-sectional area of the arteries was twofold to fourfold greater after stent implantation than after balloon angioplasty. The total number of neointimal cells was similar 1 and 12 weeks after both interventions. The neointimal cell density, however, decreased by 58% between the 1st and the 12th week after stent implantation compared with a 20% decrea.
Reduplication in Japanese Pidgin Chinese

: This paper focuses on the descriptions and analysis of reduplication in Japanese Pidgin Chinese (JPC). Reduplication is usually either totally absent or nonproductive and/or without contrasting simple form in pidgins although it is fairly common and even productive in JPC which makes JPC unusual among pidgins. Nouns, verbs and adjectives from both lexifer and substrate can be reduplicated. In this paper, the first language acquisition mechanism reloading is used to interpret the origin of the reduplication in JPC and the research may shed light on the both pidgin and language acquisition devices.
Discrete mechanical growth model for plant tissue

We present a discrete mechanical model to study plant development. The method is built up of mass points, springs and hinges mimicking the plant cell wall’s microstructure. To model plastic growth the resting lengths of springs are adjusted; when springs exceed a threshold length, new mass points, springs and hinges, are added. We formulate a stiffness tensor for the springs and hinges as a function of the fourth rank tensor of elasticity and the geometry of the mesh. This allows us to approximate the material law as a generalized orthotropic Hooke’s law, and control material properties during growth. The material properties of the model are illustrated in numerical simulations for finite strain and plastic growth. To solve the equations of motion of mass points we assume elastostatics and use Verlet integration. The method is demonstrated in simulations when anisotropic growth causes emergent residual strain fields in cell walls and a bending of bulk tissue. The method can be used in multilevel models to study plant development, for example by coupling it to models for cytoskeletal, hormonal and gene regulatory processes.
Modeling decision-making under uncertainty: a direct comparison study between human and mouse gambling data

Decision-making is a conserved evolutionary process enabling to choose one option among several alternatives, and relying on reward and cognitive control systems. The Iowa Gambling Task allows to assess human decision-making under uncertainty by presenting four cards decks with various cost-benefit probabilities. Participants seek to maximize their monetary gains by developing long-term optimal choice strategies. Animal versions have been adapted with nutritional rewards but interspecies data comparisons are still scarce. Our study directly compared physiological decision-making performances between humans and wild-type C57BL/6 mice. Human subjects fulfilled an electronic Iowa Gambling Task version while mice performed a maze-based adaptation with four arms baited in a probabilistic way. Our data show closely matching performances among species with similar patterns of choice behaviors. Moreover, both populations clustered into good, intermediate, and poor decision-making categories with similar proportions. Remarkably, mice good decision-makers behaved as humans of the same category, but slight differences among species have been evidenced for the other two subpopulations. Overall, our direct comparative study confirms the good face validity of the rodent gambling task. Extended behavioral characterization and pathological animal models should help strengthen its construct validity and disentangle determinants of decision-making in animals and humans.
Impact of Physical Proximity in Romantic Relationships on Trust, Commitment and Relationship Satisfaction among Young Adults

Background: The present study was aimed at discerning the impact of physical proximity in romantic relationships on trust, commitment and relationship satisfaction among young adults. Methodology: For the purpose, a sample of 40 young adults was taken. The participants were divided into two groups: (young adults involved in long distance relationship and proximally close relationship) on the basis of their physical proximity. Participants were assessed for their trust, commitment and relationship satisfaction, quantitatively with the help of Trust Scale, Sternberg’s Triangular Love Scale and Relationship Assessment scale. Results: The results of the study indicated that there was a significant difference in the levels of trust and commitment, although an insignificant difference was observed in the levels of relationship satisfaction among couples in long distance and proximally close relationship. And it was observed that, young adults involved in long distance relationship elicited higher levels of commitment with a mean of 115.15 as compared to young adults involved in proximally close relationship with a mean of 98.95; while lower levels of trust was observed among young adults in long distance relationship with a mean of 30.45 as compared to young adults in proximally close relationship with a mean of 38.35. Conclusions: There was a significant difference in the levels of trust and commitment, although an insignificant difference was observed in the levels of relationship satisfaction among couples in long distance and proximally close relationship.
Comparison of regenerative neurogenesis in response to CNS injury between adult zebrafish and mice

The difference between adult zebrafish and mice in their regenerative capacity following central nervous system (CNS) injury is influenced by the permissiveness of the brain microenvironment aside from the intrinsic neurogenic potential of the cell population. In adult zebrafish, glia cells largely retain their radial characteristics and neurogenic capacity, and the zebrafish brain shows full recovery after traumatic brain injury (TBI) as well as spinal cord injury (SCI). Conversely, in mice, radial glia (RG) have largely differentiated into astrocytes. Excluding certain brain regions, following TBI, reactive astrocytes that show the potential to become neural stem cells (NSCs) in vitro remain strictly non-neurogenic in vivo due to the presence of inhibitory factors in the microenvironment. Combined with prolonged inflammation and gliosis, injury to the CNS eventually results in formation of a glial scar further impeding regeneration. However in rodents, suppression of neurogenesis may be a protection mechanism against possible detrimental side-effects of neurogenesis in the long term.
Animal-fungal interactions 2: first report of mycophagy by the Eastern European Hedgehog Erinaceus concolor Martin, 1837 (Mammalia: Eulipotyphla: Erinaceidae)

Mycophagy (fungivory) performs numerous important ecosystem functions for fungi, plants, and animals. Fungi serve as food for diverse mammals, ranging from bears, Ursus spp. , to shrews, Sorex spp. However, among the many mammals reported to eat fungi, hedgehogs and other insectivores have been poorly studied. Based on microscopic examination of a fecal sample collected from an Eastern European Hedgehog (Erinaceus concolor) near Ula-Muğla, Turkey, we provide the first confirmed evidence of mycophagy by hedgehogs and review the literature on hedgehog mycophagy.