Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular identification of Pleurotus ostreatus strains from Patagonia and their ability to retain laccase activity at low temperature

Antecedentes: Pleurotus spp. son hongos reconocidos por su capacidad de degradar biologicamente materiales lignocelulosicos. En Argentina se conocen 6 especies de Pleurotus nativas, siendo P. pulmonarius y P. ostreatus las de mayor interes biotecnologico. Objetivo: Determinar las relaciones filogeneticas de cepas de Pleurotus de la Patagonia y su capacidad enzimatica (lacasa) a bajas temperaturas. Metodos: Se realizo un analisis filogenetico de las regiones ITS de 8 cepas de Pleurotus de Patagonia y la region de Parana en el noreste y centro de la Argentina. Para cuantificar la actividad lacasa se uso dimetoxifenol (DMP) como sustrato, incubando a 30 y 10 oC, con y sin tratamiento previo de calor a 80 oC. Resultados y conclusiones: El analisis filogenetico determino que las cepas provenientes de la Patagonia (5) correspondian a P. ostreatus, y las no patagonicas a P. pulmonarius (3). Con respecto a la actividad de lacasa, no se observo una relacion entre la capacidad de retencion y el origen de las cepas, registrandose mas del 50 % de retencion de la actividad a 10 oC, por lo que su uso en procesos biotecnologicos que requieren condiciones de bajas temperaturas es potencialmente viable.
Natural and anthropic forest fragments have distinct ecological behavior due to their different origin and landscape context

We tested the hypothesis that plant populations in natural fragments have distinct ecological behavior in relation to anthropic fragments. We selected the species Myrcia splendens (SW.) DC. in 2 forest fragments located in southeastern Brazil that present different origins and landscape contexts. The natural fragment originates from landscape relief variations and is inserted in a native grassland matrix, while the anthropic fragment originates from fragmentation due to area conversion and is inserted in an agricultural matrix. We established transects covering an area from one border to the other in each fragment, and we established subunits of 400 m2 within them. Within each subunit we measured all individuals of M. splendens at all establishment stages (seedlings to established trees). We monitored population behavior in the two fragments for 4 years, evaluating their spatial structure, temporal behavior, and age structure. The two populations present distinct ecological behaviors associated with their different origins and landscape contexts; the natural fragment is exposed to disturbances it has adapted to throughout the evolutionary process, whereas the anthropic fragment is subject to new evolutionary disturbances, such as effect edge, cattle, and recurrent fire.
Improving interpretability of deep learning models: splicing codes as a case study

Despite the success and fast adaptation of deep learning models in a wide range of fields, lack of interpretability remains an issue, especially in biomedical domains. A recent promising method to address this limitation is Integrated Gradients (IG), which identifies features associated with a prediction by traversing a linear path from a baseline to a sample. We extend IG with nonlinear paths, embedding in latent space, alternative baselines, and a framework to identify important features which make it suitable for interpretation of deep models for genomics.
Sequencing and analysis of the complete mitochondrial genome of large-toothed Siberian shrew (Sorex daphaenodon)

Absstract The mitochondrial genome of Sorex daphaenodon was sequenced and analyzed for the first time using muscle tissue. This genome was 17351 bp in length and contained 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, 1 control region and 1 rep_origin. The phylogenetic analysis basis of 12 protein-coding genes except for ND6 gene of 13 species shows that Sorex daphaenodon close with Sorex tundrensis, and was farthest related to Sorex cylindricauda in the genus of Sorex.
Pareto-optimality for lethality and collateral risk in the airstrike multi-objective problem

Abstract The recent surge in attacks on terrorist organizations within heavily populated areas has brought precision airstrikes to the forefront of discussion topics among partnering nations. In this paper, we present a quick algorithm for accurately creating the Pareto-optimal frontier in the multi-objective airstrike problem. This algorithm, which leverages off specific attributes of lethality and collateral risk, is shown to routinely outperform differential evolution and enumeration algorithms. Once Pareto optimal solutions are found, they can quickly be converted to solutions for the associated goal-programming and weighted sum scalarization problems. The choice of damage function greatly affects the expected lethality and collateral risk in an airstrike underscoring the need for accurate estimation of weapons effects. Notably, the cookie-cutter damage function underestimates collateral risk while overstating lethality in comparison to other damage functions. In addition, we demonstrate that differing guidelines or damage functions significantly alters the optimal location of the optimal aim point in this targeting problem. The methodology presented greatly improves upon existing work in this field, thus ensuring effective precision airstrikes while maximizing civilian safety.
The complete mitochondrial genome of Paracolopha morrisoni (Baker, 1919) (Hemiptera: Aphididae)

Abstract We have determined the mitochondrial genome of Paracolopha morrisoni (Baker, 1919), a gall-forming aphid collected from Korea. The circular mitogenome of Paracolopha morrisoni is 16,330 bp long including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 932 bp. The base composition was AT-biased (84.9%). Gene order of P. morrisoni is identical to all other aphid mitochondrial genomes. Phylogenetic trees show that P. morrisoni is sister to Eriosoma lanigerum both belonging to tribe. The mitochondrial genome of P. morrisoni will be useful in understanding the genetic backgrounds of the species.
Heteroconium sp. nov. from roots of Triticum aestivum in the United Kingdom

Morphological and molecular studies led to the description of Heteroconium triticicola as a new species isolated from roots of wheat in the United Kingdom. The new fungus shares with H. citharexyli, the type species of Heteroconium Petrak, features such as superficial mycelium, macronematous, mononematous, unbranched, straight conidiophores, monoblastic, integrated, terminal, cylindrical conidiogenous cells, and catenate, dry, simple, cylindrical, obclavate, often pale brown, smooth, multiseptate conidia. The genus Heteroconium is proposed as an anamorph within Hyaloscyphaceae.
Effect of xylitol on gut microbiota in an in vitro colonic simulation

Abstract Objective Xylitol has been commonly used as a sweetener and dental caries protective agent. However, how xylitol influences the composition and metabolism of gut microbiota is not known yet. This study aimed to dissect the changes of microbiota and their metabolites under xylitol supplementation in an in vitro colonic simulation. Materials and methods A single-phase continuous fermentation model was used to culture human fecal flora and the 16s rDNA and short chain fatty acid were analyzed. Results and discussion It was found that gut microbiota composition differentiated after xylitol supplementation only for the beginning 3 days. Xylitol significantly enhanced the relative amount of butyrate synthesizing bacteria such as Clostridium and Phascolarctobacterium. Meanwhile, xylitol increased the production of propionic acid and butyrate. An increase of Escherichia population sizes after xylitol supplementation was beyond expectation. By Spearman analysis, a positive relationship between Escherichia and Bifidobacterium was found. Conclusion xylitol can rapidly enhance the total amount of short chain fatty acids, but its influence will disappear after 3 days of fermentation. Results of this investigation can be a guideline for the further investigations on xylitol in relation to gut microbiota and the daily intake determinations.
The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications

Microtubules are cytoskeletal structures involved in structural support, microtubule-based transport and the organization of organelles in the cells. The building blocks of the microtubule, the α- and β-tubulin heterodimers, polymerize into protofilaments, that associate latterly to form the hollow microtubule. There exists a specific type of microtubule structures, termed doublet microtubules, in the cilia where high stability is required for ciliary beating and function. The doublet microtubule consists of a complete A-tubule and a partial B-tubule. The doublet microtubule maintains its stability through the binding of microtubule inner proteins in the lumen of the A- and B-tubules and via unique interactions at its outer and inner junctions, where the A- and B-tubules meet. Here, we present the answer to the long-standing question regarding the identity, localization and structure of the inner junction proteins in Chlamydomonas doublet microtubules. We show that inner junction proteins PACRG and FAP20, together with FAP52, previously unidentified FAP276 and an unknown Tether protein, form an interaction hub at the inner junction, which involves tubulin sites for post-translational modifications. We further compare the Chlamydomonas and Tetrahymena doublet microtubule structures to understand the common and species-specific features of the inner junction.
Teachers’ perception about the contribution of collaborative creation of digital storytelling to the communicative and digital competence in primary education schoolchildren

Abstract Digital storytelling (DST) is an innovative narrative practice based on the creation of multimodal stories, which promotes communicative as well as digital competences. This research verifies teachers’ perception about the progress in communicative and digital competences in primary education children (N= 201) participating in a collaborative digital storytelling project supported by the Department of Education of the Principality of Asturias (Spain). The descriptive analysis shows teachers’ qualitative assessment, related to the change perceived after DST creation. The teachers used an instrument consisting of 15 qualitative indicators and based on an assessment rubric, which was validated by means of the Delphi method. The results reveal that − according to these instructors’ perception − such a collaborative digital narrative helped to foster both competences in the participating students. They all improve qualitatively, especially students enrolled in the higher stages, through the production of written compositions for DST (thus practicing with vocabulary, spelling and punctuation, as well as verb tenses), the elaboration of scripts with coherent characters and settings, and the expression of the purpose sought with their stories. As for digital competence, the higher stages developed it to a greater extent, due to the greater complexity of the tools used to create DST. In conclusion, teachers see collaborative DST creation as an educational practice which significantly activates schoolchildren’s expression and communication skills, since it provides them with suitable environments to acquire story-related competences and abilities, supported by several technological resources and audiovisual techniques.
The complete chloroplast genome of an Antarctic moss Syntrichia filaris (Müll.Hal.) R.H. Zander

Abstract Syntrichia filaris is one of the common mosses in the northern maritime Antarctic. In this study, we determined the complete chloroplast genome of S. filaris (GenBank accession number MK852705) to provide a genetic resource for phylogenetic study on Bryophytes. It is of 136,227 bp length, containing 8 ribosomal RNA (rRNA), 37 transfer RNA, and 85 protein-coding genes. The chloroplast genome structure and gene order were similar to other bryophytes. Phylogenetic tree based on combined amino acids sequences of 72 chloroplast genes common in S. filaris, 7 Bryophyta, 1 Anthocerotophyta, and 2 Marchantiophyta, was congruent with the traditional position of Pottiales in Bryophytes.
Spatiotemporal dynamics of RNA virus diversity in a phyllosphere microbial community

Although metagenomics reveals that natural virus communities harbor vast genetic diversity, the spatiotemporal dynamics of viral diversity in the wild are seldom tested, especially across small geographic scales. This problem is usefully examined in the above-ground phyllosphere, because terrestrial plants are frequently infected by taxonomically-diverse RNA viruses, whose elevated mutation rates generate abundant allele diversity. Here, we studied the problem by comparative analysis of RNA virus samples over time from three spatially-separated patches of a common perennial legume, white clover (Trifolium repens L.), growing in a grassy lawn in Woods Hole Village (Falmouth, MA, USA). We predicted that clover samples would show similarly high levels of virus species (alpha) diversity across space, but differing among-patch diversity of non-dominant virus taxa over time (4 samples spanning 6 weeks). Results showed that recognizable alpha diversity in clover patches was consistently dominated by RNA virus family Alphaflexiviridae across space, but that all patches showed inconsistent spatiotemporal presence of a diversity of minority virus families. Also, we observed that white clover mosaic virus (WClMV) dominated all patches across space and time. The high coverage of WClMV fostered an haplotype analysis, which revealed that two strains of the virus consistently infected clover plants during the 6-week period.
SCAR FORMATION AND DECREASED CARDIAC FUNCTION FOLLOWING ISCHEMIA/REPERFUSION INJURY IN 1-MONTH-OLD SWINE

Studies in mice show a brief neonatal period of cardiac regeneration with minimal scar formation. Less is known about reparative mechanisms in large mammals. A transient cardiac injury approach (ischemia/reperfusion, IR) was used in weaned postnatal day (P)30 pigs, to assess regenerative repair in young large mammals. Female and male P30 pigs were subjected to cardiac ischemia (1 hour) by occlusion of the left anterior descending artery followed by reperfusion, or to sham operation. Following IR, myocardial damage occurred, with cardiac ejection fraction significantly decreased 2 hours post-ischemia. No improvement or worsening of cardiac function to the 4 week study end-point was observed. Histology demonstrated cardiomyocyte (CM) cell cycling at 2-months-of-age in multinucleated CMs in both sham-operated and IR pigs. Regional scar formation and inflammation in the epicardial region proximal to injury were observed 4 weeks post-IR. Sex differences were found, suggestive of females creating a greater fibrotic response with worse cardiac function, highlighting the importance of representing both sexes in cardiac injury studies. Together, our results describe an effective novel cardiac injury model in P30 swine, at a time when CMs are still cycling. Pigs subjected to IR show myocardial damage with a prolonged decrease in cardiac function, formation of a small, regional scar with increased inflammation. These data demonstrate that P30 pigs do not regenerate myocardium, even in the presence of CM mitotic activity, but form a scar after transient IR injury. NEW & NOTEWORTHY Here, we report for the first time ischemia/reperfusion (IR) cardiac injury in 1-month-old (P30) pigs. This model of IR injury highlights lack of cardiac regeneration, even in the presence of cardiomyocyte (CM) cell cycling in young swine. An effective injury approach is described for use in large mammals to investigate cardiac function, CM cell cycling, extracellular matrix (ECM) remodeling, and gene expression changes, while highlighting the importance of studying both sexes.
A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis

Formalin fixation and paraffin-embedding (FFPE) is the most common method to preserve human tissue for clinical diagnosis and FFPE archives represent an invaluable resource for biomedical research. Proteins in FFPE material are stable over decades but their efficient extraction and streamlined analysis by mass spectrometry (MS)-based proteomics has so far proven challenging. Here, we describe an MS-based proteomic workflow for quantitative profiling of large FFPE tissue cohorts directly from pathology glass slides. We demonstrate broad applicability of the workflow to clinical pathology specimens and variable sample amounts, including less than 10,000 cancer cells isolated by laser-capture microdissection. Using state-of-the-art data dependent acquisition (DDA) and data independent (DIA) MS workflows, we consistently quantify a large part of the proteome in 100 min single-run analyses. In an adenoma cohort comprising more than 100 samples, total work up took less than a day. We observed a moderate trend towards lower protein identifications in long-term stored samples (>15 years) but clustering into distinct proteomic subtypes was independent of archival time. Our results underline the great promise of FFPE tissues for patient phenotyping using unbiased proteomics and prove the feasibility of analyzing large tissue cohorts in a robust, timely and streamlined manner.
Geophysical, evolutionary and ecological processes interact to drive phylogenetic dispersion in angiosperm assemblages along the longest elevational gradient in the world

Ecologists have embraced phylogenetic measures of assemblage structure, in large part for the promise of better mechanistic inferences. However, phylogenetic structure is driven by a wide array of factors from local biotic interactions to biogeographical history, complicating the mechanistic interpretation of a pattern. This may be particularly problematic along elevational gradients, where rapidly changing physical and biological conditions overlap with geological and biogeographical history, potentially producing complex patterns of phylogenetic dispersion (relatedness). We focus on the longest elevational gradient of vegetation in the world (i.e. c. 6000 m in Nepal) to explore patterns of phylogenetic dispersion for angiosperms (flowering plants) along this elevational gradient. We used the net relatedness index to quantify phylogenetic dispersion for each elevational band of 100 m. We found a zig-zag pattern of phylogenetic dispersion along this elevational gradient. With increasing elevation, the phylogenetic relatedness of species decreased for the elevational segment between 0 and c. 2100 m, increased for the elevational segment between 2100 and c. 4200 m, and decreased for the elevational segment above c. 4200 m. We consider this pattern to be a result of the interaction of geophysical (e.g. plate tectonics) and eco-evolutionary processes (e.g. niche conservatism and trait convergence). We speculate on the mechanisms that might have generated this zig-zag pattern of phylogenetic dispersion.
PHYSICOCHEMICAL, MICROBIOLOGICAL AND SENSORY CHARACTERISTICS OF PERSIMMON FRUIT LEATHER

Persimmon fruit leather is a dehydrated persimmon product, which was consumed as a chewy for preparation of valuable nutritive dessert. The aim of the present study was to utilize persimmon puree in the preparation of persimmon leather and study physicochemical, microbiological and sensory characteristics of persimmon leather. Persimmon fruit leather was prepared by drying a mixture of persimmon puree treated with hot break by steam (HST), mango puree, glucose syrup, sugar, pectin, citric acid and starch. Dehydration was performed in microwave at 55oC for 30 min. Leather was also prepared from persimmon leather using the same ingredients except starch. Results showed that texture properties of leather containing starch was higher than leather without starch. Moisture, ash content and acidity were close to each other in persimmon leathers with or without starch. TSS content in persimmon leather product samples were 78.89o Brix and 79.14o Brix, while total and reducing sugars of leather without starch recorded 83.26 and 45.08%, respectively. Persimmon leather with starch contained total and reducing sugars 81.48 and 44.90%, respectively. Ascorbic acid retained in persimmon leather containing starch was slightly higher (14.26 mg/100g) compared to leather without starch (13.52 mg/100g). Browning index increased when adding starch to the formula. Alcohol insoluble solids (AIS) and crude fibers content were 12.87 and 0.98% in persimmon leather with starch, respectively, whereas the respective values in persimmon leather without starch were 8.73 and 0.82%. Antioxidant activity and carotenoids contents were higher in persimmon leather containing starch than that without starch. Polyphenols, flavonoids and tannins contents were lower in persimmon leather containing starch than leather without starch. Pyrogallol and E-vanillic were the dominant compounds in both of persimmon leathers with and without starch. Vitamin K represented the highest content among all studied vitamins in persimmon leather. Lightness value (L*) was 33.81 in persimmon leather containing starch which is higher than lightness value (L*) in persimmon leather without starch (23.72). The values of (a*) and (b*) were higher in persimmon leather without starch (12.71 and 12.97, respectively) than in persimmon leather containing starch (8.10 and 8.16, respectively). Total bacteria count was 110 CFU/g in just first dilution in persimmon leather with starch but it was not detected in other dilutions, total count bacteria was not detected in persimmon leather without starch in all dilutions. Molds and yeasts and spore forming bacteria counts were not detected in all persimmon leather samples.
The complete mitochondrial genome of Laudakia wui (Iguania; Agamidae)

Abstract In this study, the complete mitochondrial genome of Laudakia wui, has been firstly determined by shotgun sequencing. The overall length of mitogenome is 16,455 bp and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 control regions. Majority of the genes (13 protein-coding genes, 2 rRNA and 14 tRNA) were distributed on the H-strand, in addition to the two ND6 genes and eight tRNA genes, which were encoded on the L-strand. The phylogenetic tree was built by L. wui and 13 other related species. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of L. wui.
Preliminary Phytochemical Screening, Total Phenolic Content, In Vitro Antioxidant and Molluscicidal Activities of the Methanolic Extract of Five Medicinal Plants on Biomphalaria Alexandrina Snails

ABSTRACT Schistosomiasis is a neglected tropical disease caused by blood flukes. Freshwater snails of genus Biomphalaria are the intermediate hosts of Schistosoma mansoni. The present study aimed to investigate the presence of phytochemicals, total phenolic content, antioxidant and molluscicidal activities of the methanolic extract of five plants (Ziziphus spina- christi, Tecoma stans, Carica papaya, Moringa oleifera, and Nerium oleander) on Biomphalaria alexandrina snails. The phytochemical analysis confirmed the presence of tannins, flavonoids, saponins, terpenoids, steroids, anthraquinones, alkaloids, carbohydrates, and coumarins. The results showed that N. oleander, M. oleifera, and C. papaya had higher amount of the total phenolic content while C. papaya, M. oleifera, and T. stans had greater antioxidant activity than others. Z. spina-christi and N. oleander had higher molluscicidal effect (LC50: 108.7 and 138.6 mg L−1) than C. papaya, T. stans, and M. oleifera methanolic extracts (LC50: 172.9, 256.0, and 1125.0 mg L−1, respectively).