Miracle-dz/UniFAR-FTUs huggingface dataset:
Análise proteômica comparativa do processo de diferenciação celular do fungo patogênico Paracoccidioides brasiliensis

Paracoccidioides spp. e o agente etiologico da paracoccidioidomicose, a mais importante micose sistemica endemica da America Latina. Paracoccidioides spp. e um fungo dimorfico, que apresenta alteracao morfologica de acordo com a temperatura do ambiente. A forma miceliana e encontrada no solo a temperaturas inferiores a 25 oC, enquanto que em tecidos do hospedeiro e sob temperaturas de 36-37 oC o fungo assume forma leveduriforme. A infeccao se inicia com a inalacao de conidios presentes na forma filamentosa do fungo, os quais ao atingirem os pulmoes se diferenciam na forma leveduriforme, estabelecendo a paracoccidioidomicose. A transicao de micelio para levedura esta envolvida na virulencia desse patogeno e esse aspecto da morfogenese do fungo nao esta totalmente compreendido. No presente estudo, foi utilizada a cromatografia liquida acoplada a espectrometria de massas (nanoUPLC-MSE) para avaliar o perfil proteomico durante a transicao de micelio para levedura apos 22 h da mudanca da temperatura de 22oC para 36oC (P. brasiliensis – isolado Pb18). Um total de 991 proteinas foram identificadas (350 em micelio, 288 na transicao e 353 em levedrua) e 251 foram diferencialmente expressas durante o processo de diferenciacao celular. Entre as proteinas que foram abundantes em micelio estao as subunidades da ATPase que participa na cadeia transportadora de eletrons e enzimas envolvidas na fermentacao alcoolica. Proteinas relacionadas a via glicolitica e alguns potenciais fatores de virulencia comecam sua acumulacao apos 22 h do inicio da transicao morfologica. Em levedura enzimas relacionadas com a glicolise e a beta-oxidacao tiveram alta expressao. As analises das categorias funcionais a que essas proteinas pertencem, forneceram uma melhor compreensao da reorganizacao metabolica que ocorre durante a transicao morfologica de micelio para levedura, incluindo possiveis fatores de virulencia.
Insights into the genus Austrella (Pannariaceae, Peltigerales), including a new species from the Falkland Islands

Abstract The new species Austrella isidioidea, which is unique in the genus in having isidioid structures on the thallus lobe ends as well as apothecia lacking a thalline margin, is described from the Falkland Islands. A collection with an identical mtSSU rDNA sequence to A. arachnoidea but with significant morphological differences (viz. a variable apothecial margin ranging from an arachnoid hyphal weft to a corticated regular margin) is reported from Îles Kerguelen. The phylogenetic and biogeographical implications of these new records are discussed.
The twin-arginine translocation network of Bacillus subtilis

Het transport van eiwitten over biologische membranen is van cruciaal belang voor alle levende organismen, omdat de getransporteerde eiwitten veelal betrokken zijn bij essentiele processen. Carmine Monteferrante verrichtte onderzoek naar de gram-positieve bodembacterie Bacillus subtilis, een van de micro-organismen die vaak worden ingezet voor fundamenteel onderzoek naar eiwittransport. B. subtilis bezit verschillende eiwitsecretieroutes, die er voor zorgen dat eiwitten naar verschillende bestemmingen binnen en buiten de cel gedirigeerd worden. Een van deze routes, de zogenaamde twin-arginine translocatie (tat-)route, herkent eiwitten met twee naast elkaar liggende arginine residuen in het signaalpeptide. Deze eiwitten worden vervolgens in een volledig gevouwen conformatie via de tat-route gesecreteerd. Het onderzoek levert nieuwe inzichten op in de globale netwerkorganisatie, de driedimensionale structuur en de mechanismen voor kwaliteitscontrole, die relevant zijn voor eiwittransport via de tat-route naar de cytoplasmamembraan, de celwand of het externe milieu van B. subtilis. Bovendien toonde Monteferrante aan dat milieuomstandigheden een sterke invloed hebben op de specificiteit van eiwittransport via de tat-route. Deze inzichten kunnen onder meer bijdragen aan de ontwikkeling van nieuwe medicijnen.
The food habits of the Madagascar Long-eared Owl Asio madagascariensis in southeastern Madagascar

A collection of regurgitated pellets and food remains was found below an occupied roost of the Madagascar Long-eared Owl Asio madagascariensis in southeastern Madagascar. The owls are taking a wide variety of prey including insects, frogs (Boophis), geckos (Uroplatus), birds (Eurystomus, Hypsipetes), bats (large Hipposideros), rodents {Eliurus spp. , Rattus), and lemurs {Microcebus). This is the first quantitative information on the food habits of this owl species.
Salinity Effects on Mineral Nutrients and Performance of Turnip (Brassica Rapa L.) at Different Growth Stages

In order to study the effects of different salinity levels on turnip (Brassica rapa L.), an investigation was conducted at Yasouj University, Iran, in 2010. The effects of four salinity levels including 1.92, 9.87, 19.6 and 21.94 ds m-1 (20:1 ratio of NaCl: CaCl2 in Hoagland solution) on germination, vegetative and maturity stages of turnip (Baherghan landrace) were investigated. The results revealed that the measured traits at the germination stage were significantly affected by salinity treatments. The effect of salinity stress was only significant for leaf area, sodium and potassium contents at the vegetative stage. Salinity had significant effects on all the recorded traits of turnip roots, except for Ca2+, Zn and Fe contents. Based on stress intensity values, salinity affected germination percentage (SI=1.0) on the second day and the seedling root length (SI=0.93) more than other measured traits. The results of SI (stress intensity) showed that salinity affected Na+ content more than other traits at the maturity stage (SI=0.74). Ca2+ showed an inverse response and had the lowest SI (SI=0.001). Based on this study, vegetative growth and root elongation stages were more tolerant and sensitive to salinity, respectively. In addition, seedling root length at germination stage and tissue Na+ content at subsequent growth stages were the most important traits, recommended to be used as selection criteria in turnip breeding programs.
Multiple hidden processes complicate phylogenomic inference of deep Basidiomycota relationships

Resolving deep divergences in the fungal tree of life remains a challenging task even for analyses of genome-scale phylogenetic datasets. Relationships between Basidiomycota subphyla, the rusts (Pucciniomycotina), smuts (Ustilaginomycotina) and mushroom forming fungi (Agaricomycotina) represent a particularly challenging situation that posed problems to both traditional multigene and genome-scale phylogenetic studies. Here, we address basal Basidiomycota relationships using three different phylogenomic datasets, concatenated and gene tree-based analyses and examine the contribution of several potential sources of uncertainty, including fast-evolving sites, putative long-branch taxa, model violation and missing data. We inferred conflicting results with different datasets and under different models. Fast-evolving sites and oversimplified models of amino acid substitution favored the grouping of smuts with mushroom-forming fungi, often leading to maximal bootstrap support in both concatenation and Astral analyses. The most conserved datasets grouped rusts with mushroom forming fungi, although this relationship proved labile, sensitive to model choice, different data subsets and missing data. Excluding putative long branch taxa, genes with the highest proportions of missing data and/or genes with strong signal failed to reveal a consistent trend toward one or the other topology, suggesting that additional sources of conflict are at play too. Our analyses suggest that topologies uniting smuts with mushroom forming fungi can arise as a result of inappropriate modeling of amino acid sites that might be prone to systematic bias. While concatenated analyses yielded strong but conflicting support, individual gene trees mostly provided poor support for rusts, smuts and mushroom-forming fungi, suggesting that the true Basidiomycota tree might be in a part of the tree space that is difficult to access using both concatenation and gene tree based approaches. Thus, basal Basidiomycota relationships remain unresolved and might represent a phylogenetic problem that remains contentious even in the genomic era.
Giant lymphangioma breast – A rare occurrence: Case report and current review

Cystic lymphangiomas are rare benign tumor and are due to congenital malformations of lymphatic vessels. Majority occur either at birth or up to 2 years age. These are slow-growing lesions and infiltrate into the surrounding tissues. Malignancy is quite rare in these lesions. Common sites are head and neck, axilla, and mediastinum and rarely in breast. Hereby, we report a case of a 13-year-old female who presented with a gradually increasing painless swelling in the upper outer quadrant of her left breast for the last 12 years. Magnetic resonance imaging of the breast showed multiple, irregular, hypoechoic lesions associated with irregular duct dilatation. As the treatment of choice is complete excision, the cystic mass was excised in toto and sent for histopathology, which revealed cystic lymphangioma.
Electroconvulsive therapy during the COVID-19 pandemic

The COVID-19 pandemic has forced substantial changes in the practice of psychiatry, including that of electroconvulsive therapy (ECT). There is higher risk of transmission of the SARS-CoV-2 virus during ECT unless due care is taken. However, in many cases, ECT cannot be avoided. In this paper, we discuss various measures that may be adapted to reduce the risk of transmission of the virus during ECT. We also suggest certain modifications to the practice of ECT in order to achieve a balance between risks and benefits of the procedure during the pandemic.
Drought tolerance of two perennial ryegrass cultivars with and without AR37 endophyte

ABSTRACT The objectives of this research were to investigate Lolium perenne L. responses to water deficit, compare drought tolerance of two cultivars derived from different germplasm and the role of endophyte in drought tolerance of the host cultivar. Plants of cultivars Ceres One50 and Grasslands Commando with and without AR37 endophyte were kept irrigated or unirrigated for two weeks and then rehydrated for one month in a glasshouse. A positive correlation between the extent of osmotic adjustment (OA) and leaf dry matter regrowth indicated that OA was correlated with the plant regrowth during recovery. For One50, the reduction in leaf elongation rate was less and the increase in proline was greater in response to drought, compared to Commando. From this observation, it was inferred One50 has enhanced capacity to continue growth, and had greater intra-cellular protection than Commando. Endophyte status did not affect plant responses to drought in this experiment.
Distribution and population genetic analysis of the agents of invasive needle and shoot diseases of conifers in Northern Europe

For the northern Baltic region, Diplodia sapinea (Fr.) Fuckel, a well-known around the world pine pathogen, was first recorded in Estonia on Austrian pine (Pinus nigra Arn.) in 2007. Wider monitoring of the fungus was promptly started. Shortly, in 2012, the native Scots pine (P. sylvestris L.) was found symptomatic: first in Estonia, then in Latvia, and in 2013 in north-west Russia. Several individuals of exotic Mountain pine (P. mugo Turra) and some Bosnian pines (Pinus leucodermis Ant.) were also found to be infected. By the end of 2013, the front of the northward enlargement of the range of D. sapinea had reached to central Estonia. Early detection and continuous monitoring of this pathogen on native and introduced ornamental pine species will support forest and green belt management specialists with timely information, if an epidemic, as it occurred previously with the invasive Dothistroma needle blight, would emerge.
Systematic review on alternative methods for caries removal in permanent teeth

Introduction: Dental caries is the most common chronic dental disease in the world. It is defined as a multifactorial microbial infectious disease characterized by demineralization of the inorganic and destruction of the organic substance of the tooth. The host, flora, and the substrate should be there for the formation of dental caries. There are various microorganisms responsible for caries. The treatment for caries is essential to prevent teeth from involving pulp, leading to further damage. There are various methods in removing caries such as minimally invasive technique, rotary method with different types of burs, chemomechanical caries removal, and lasers. There are no data in literature for various methods of removing caries in permanent teeth. Materials and Methods: Research question was formulated based on the PICO strategy. A comprehensive electronic literature search was conducted, independently by two reviewers. Based on the specified inclusion and exclusion criteria's, the selected articles were subjected to quality assessment and the risk of bias was evaluated. Objective: The objective of this study was to evaluate the efficiency of caries removal by various methods in permanent teeth. Search Strategy: A search was performed in electronic database (i.e. PubMed and Medline) using search terms alone and in combination by means of PubMed search builder from January 1985 to January 2018. Selection Criteria: Studies were selected if they met the following criteria: in vivo studies comparing various methods of caries removal in permanent teeth. Results: The search identified 338 publications, out of which 328 were excluded after examination of the title and 2 were excluded after examination of the abstract. Through the hand search, three articles were included. Eight articles were retrieved for more detailed evaluation from the search. A total of 11 publications fulfilled all the criteria for inclusion. Conclusion: With the available evidence, this review concludes that the studies included in this review have a high risk of quality evidence.
The incidence of nickel-titanium endodontic hand file fractures: A 7-year retrospective study in a tertiary care hospital

Aim: The present retrospective cross-sectional study aims to evaluate the incidence and factors associated with nickel-titanium hand file fractures in root canal-treated teeth in a tertiary care hospital of western India. Methodology: The diagnostic records of intraoral periapical (IOPA) radiographs were analyzed to check for file fractures in the root canal-treated teeth. As a part of standardized departmental protocol, Hand ProTaper Universal file system (Dentsply, India) was used for chemomechanical preparation for root canal treatment. The file fractures were analyzed with reference to age group, type of teeth, curvature of the canal, site of file fracture in the canal, length of file fracture, level of file fracture, distance of the file fracture from the apex, and obturation status of the file-fractured tooth. Chi-square test was applied to assess the significance difference between the tested groups. Results: A total of 19,810 IOPA X-rays were screened and 2728 root canal-treated teeth were found and of these 2728 cases, 109 file-fractured teeth were observed. Conclusion: The total incidence of file fractures was 3.9/100 root canal-treated cases, and mandibular molars with severely curved canals (>25°) had shown the maximum incidence of file fractures.
Growth dynamics of Chattonella antiqua in relation to nutrients in the Yatsushiro Sea

八代海において，Chattonella antiqua の増殖および栄養塩との関係について検討した。 まず，本種を用いた現場海水のバイオアッセイ試験を行った。 その結果，培地成分のうち，窒素，リンまたは鉄源を添加しなかった場合に増殖速度は低下し，海水試料に N 源を単独で添加した場合に向上した。 また，2008 年の本種ブルームの発生直前には DIN および DIP 濃度の上昇が認められた。 本研究より，八代海において C. antiqua の増殖は第一に窒素，次にリンおよび鉄源によって制限されていることが推定された。
The complete mitochondrial genome of a medicinal fungus, Tolypocladium ophioglossoides

Abstract As part of a genome sequencing project for Tolypocladium ophioglossoides (T. ophioglossoides), a complete mitochondrial (mt) genome was assembled as a single circular dsDNA of 35,159 bp. Conserved genes including the large and small rRNA subunits, 25 tRNA and 15 protein-coding genes, were identified. In addition, 4 non-conserved open reading frames (ncORFs) in the intergenic and intronic regions were also identified. Transcription analyses using RNA-seq validated the expression of most conserved genes and ncORFs. Seven introns (groups I and II) were found within conserved genes, accounting for 21% of the mitogenome. All structural genes are located on one strand and are apparently transcribed in one direction. The complete mt genomes of T. ophioglossoides would be useful for future investigation of genetics, evolution and clinical identification of Tolypocladium species.
Modelling of berseem (Trifolium Alexandrinum L.) growth and biomass yield under different levels of water stress in Tadla, Morocco.

This work compares the performance of PILOTE, an operative crop model developed by IRSTA Montpellier France, with that of well established model, CropSyst, in simulating berseem (Trifolium Alexandrinum L.) growth under different water regimes in the semi-arid climate of Tadla (Morocco). Both based on Beer’s law via the intercepted potential active radiation (IPAR) regarding dry matter accumulation, the models differ in the level of complexity describing crop development, biomass growth, root water uptake principle and consequently, in the number of input parameters. The models were calibrated on an unstressed irrigation treatment in 2009/10, and were validated on other stressed and unstressed treatments in 2009/10 and 2010/11. Although PILOTE required fewer input parameters and data than CropSyst, it performed similarly better when simulating both biomass and soil water balance. The use of different numbers of parameters and crop growth modules by the tested models did not influence substantially the simulation results. Therefore, for management purposes and in conditions of limited input information, the use of simpler models should be encouraged. Keywords: Crop models, berseem, PILOTE, CropSyst, water stress, Morocco. Resume Ce travail compare les performances de PILOTE, un modele operationnel developpe par IRSTA de Montpellier-France, avec celles d’un modele plus elabore, CropSyst, dans la simulation de croissance du bersim (Trifolium Alexandrinum L.) conduit sous differents regimes hydriques au Tadla (Maroc). L’accumulation de la matiere seche selon la loi de Beer via la radiation potentielle active interceptee (IPAR) constitue le point commun des deux modeles. Ils different par le niveau de complexite relative a la description du developpement et la croissance de la culture, le principe d’absorption de l’eau par les racines et par consequent le nombre d’input. Les deux modeles ont ete cales sur le regime hydrique non limitant en 2009/10, puis valides sur les autres traitements de 2009/10 et de 2010/11. Bien que PILOTE necessite moins de parametres, il s’avere comparable a CropSyst dans la simulation de la biomasse et du bilan hydrique. L’utilisation d’un nombre different de parametres et de modules par les deux modeles testes n’a pas influence sensiblement les resultats de la simulation. Par consequent, dans un objectif limite a la gestion de l’eau et dans des conditions de manque de parametres culturaux, l’utilisation de modeles plus simples devrait etre encouragee. Mots cles: Modele de culture, bersim, PILOTE, CropSyst, stress hydrique, Maroc
Phytoplankton Abundance and Distribution in Selected Sites of Boracay Island, Malay, Aklan, Central Philippines

This study investigated the impacts of natural and anthropogenic factors on the coastal water quality dynamics in the Island of Boracay, Malay, Aklan, Central Philippines particularly the effects of nutrient pollution on phytoplankton population. The samples were gathered at two month interval for a total of five samplings by filtering 10 liter buckets of surface water through a net with 25μm mesh bag. There were 35 identified genera of phytoplankton belonging to four taxonomic groups. Diatoms had 26 genera, cyanophycean and silicoflagellate and dinoflagellates had one and seven genera, respectively. Diatoms were the dominant group with the highest mean density of 1,588 ind.L-l, followed by silicoflagellate at 399 ind.L-1 represented by Tintinnopsis, cynophycean was represented by Trichodesmium at 204 ind.L-1, while the dinoflagellates had 132 ind.L-l. Genera richness was high when N and P concentrations were relatively lower. Phytoplankton density was highest in Lugotan Cove and Long Beach where nutrients readings were relatively high. This research clearly demonstrated that the growth of Trichodesmium reaching carrying capacity is an indication that the island ecosystem is near its ecological thresholds. The level of nitrate N acts as the limiting nutrient in the coastal water of the island controlling the growth of Trichodesmium and phytoplankton diversity. Changes in phytoplankton assemblages and density in the coastal waters were associated to variations on intensity and frequency of water mixing along with nutrient loading coming from anthropogenic activities and land uses in the island.
Viability of seeds ripened after cutting (pot experiment)

Viability of seeds ripened after cutting (pot experiment) Ulrike Sölter1, Arnd Verschwele1, Uwe Starfinger2 1Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Field Crops and Grassland, Messeweg 11/12, 38104 Braunschweig, Germany; e-mail: ulrike.soelter@julius-kuehn.de; 2Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for National and International Plant Health, Messeweg 11/12, 38104 Braunschweig, Germany