Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Three Endotypes in Pediatric Acute Respiratory Distress Syndrome by Nasal Transcriptomic Profiling

Acute respiratory distress syndrome (ARDS) and pediatric ARDS (PARDS) can be triggered by multiple pulmonary and non-pulmonary insults and are the source of substantial morbidity and mortality. The nasal epithelium is similar to that of the lower conducting airways and nasal transcriptomic profiling identifies disease and endotypes in lung cancer, COPD, and asthma. We conducted a prospective trial of testing whether this technique could identify PARDS endotypes in 26 control and 25 PARDS subjects <18 admitted to the PICU extracting RNA from inferior turbinate brushings on days 1, 3, 7, and 14. Standard RNA processing and mRNA-seq yielded ~25% usable specimens and a modified, low-input RNA protocol yielded 95% usable specimens. Sixty-four low-input specimens from 10 control and 15 PARDS subjects were used for initial analysis. Control and some PARDS subjects clustered together in both by-day and combined analysis into Groups A while some day 1, 3, and 7 specimens from the same subjects clustered into Groups B and C with specimens from these subjects moving to Group A with PARDS resolution. In multivariate analysis, the only clinical variables predictive of Group B or C status was severity of lung injury or viral PARDS trigger. Compared to Group A, Group B had upregulation of innate immune processes and group C had upregulation of cilia-associated processes. Analysis of the 15 specimens processed and analyzed by standard techniques identified the same processes as differentiating Groups A, B, and C. Mortality appeared to be higher in group B (25%) and C subjects (28.6%) compared to A subject (5%, p=0.1). Our findings demonstrate three distinct PARDS endotypes which may be useful for prognostic and therapeutic enrichment. ClinicalTrials.gov Identifier NCT03539783
Effects of carrot psyllid (Trioza apicalis) feeding on carrot yield and content of sugars and phenolic compounds

Carrot psyllid, Trioza apicalis, is a serious pest of carrot in Northern Europe, as it can significantly damage young carrot seedlings in a period as short as 3 days. This study was conducted to investigate effects of carrot psyllid feeding at different plant growth stages on carrot yield and to assess changes in content of sugars, phenolics and related compounds in carrot roots resulting from the psyllid feeding. In addition, reflectance of carrot leaves was measured to assess the intensity of discolouration in damaged leaves. Results showed that carrot yield was significantly reduced by a 3-day carrot psyllid feeding period when the seedlings were exposed to psyllids at 1- or 2-leaf stage. However, at 4-leaf stage feeding by one carrot psyllid did not reduce yield. Sucrose concentration in the damaged roots was significantly decreased, whereas concentrations of some phenolic compounds were significantly increased. The reflectance of leaves of damaged carrots differed significantly from those of undamaged control leaves. These observations indicate that carrot psyllid damage has potential to lower not only the carrot yield, but also the carrot crop quality. No phytoplasma was detected in the carrots exposed to psyllids, but recently, T. apicalis has been associated with ‘Candidatus Liberibacter solanacearum’. The role of carrot psyllid feeding and the psyllid-associated bacterium in the damage formation are discussed.
Molecular detection of SARS-CoV-2 using a reagent-free approach

Shortage of reagents and consumables required for the extraction and molecular detection of SARS-CoV-2 RNA in respiratory samples has led many laboratories to investigate alternative approaches for sample preparation. Fomsgaard et al 2020 recently presented results using heat-processing of respiratory samples prior to RT-qPCR as an economical method enabling an extremely fast streamlining of the processes at virtually no cost. Here, we present our results using this method and highlight some major pitfalls that diagnostics laboratories should be aware of before proceeding with this technique. We first investigated various treatments using different temperatures, incubation times and sample volumes based on the above study to optimise the heat-treatment conditions. Although the initial data confirmed the published results, further investigations revealed unexpected inhibitory properties of some commonly used virus transport media (VTMs) on some commercially available RT-qPCR mixes, emphasising the critical importance of a thorough validation process to determine the most adapted reagents to be used depending on the sample types to be tested. In conclusion, although the method works, with very consistent Ct values and an excellent sensitivity when compared to a conventional RNA extraction method, it is critical to include an internal control to check each sample for potential inhibition.
Domination by Reptiles in a Terrestrial Food Web of the Bahamas Prior to Human Occupation

Abstract Human activities in the Bahamas and other oceanic islands have damaged terrestrial ecosystems irreparably through the extinction of indigenous species. Tortoise and crocodile bones from Abaco Island in the Bahamas sampled for 14C-dating revealed a small overlap between the last occurrence of these large reptiles and early human settlement in the Bahamas. Before their extermination approximately 1,000 years ago, the dominant herbivore and carnivore on Abaco Island were the endemic Albury's Tortoise (Chelonoidis alburyorum) and the formerly widespread Cuban Crocodile (Crocodylus rhombifer). Stable isotope data from carbon (δ13C) and nitrogen (δ15N) in bone collagen from Late Holocene fossils suggest that these large reptiles were part of a terrestrial rather than marine or estuarine food web. Our proposal that Cuban Crocodiles were once the apex terrestrial predator in the Bahamas is supported by comparisons with published δ13C values for modern marine/estuarine crocodylians as compared to those of nonmarine reptilian and mammalian carnivores. For reptiles to occupy terrestrial trophic roles distinguishes Bahamian Islands from nearby Greater Antillean Islands (Cuba, Jamaica, Hispaniola, Puerto Rico) where endemic mammals represent the largest herbivores and carnivores in prehuman times. This distinction is even greater when compared with Late Quaternary mammals of prehuman vertebrate communities in neighboring North America.
PROGRESSION OF MYOPIA AT KING ABDUL

Introduction: appear in focus. increasing t Objective: The primary objective of this study was to measure the prevalence medical students, and the secondary objective was to study electronic and Methods: staged sampling for myopia. Results: complained of a progressive worsening of their symptoms. (74%) 37% of non-electronic type of study was significant (p Conclusion: significant: chi and the progression of
Ecto-parasites Infestation of Nile Tilapia (Oreochromis niloticus) in Concrete Ponds in Tamale, Ghana

The demand for concrete pond culture in the Northern Ghana is increasing. The safety and health of Nile tilapia produced in concrete ponds is of public concern. This study investigated the prevalence and mean intensities of ecto-parasites on the gills, skin and the fin of Nile tilapia (Oreochromis niloticus) in some concrete ponds in Tamale, Northern Region of Ghana. A total number of 240 randomly sampled fish specimens consisting fingerlings and adult fish of Nile tilapia were examined using microscope and hand-held lens from November, 2013 to April, 2014. Physico-chemical characteristics of the pond were suitable for culture. Mean temperature was 28.48 ℃ ± 2.31, mean dissolved oxygen was 4.32 mg/l ± 0.38, mean pH was 6.17 ± 0.23 and mean nitrate was 30.60 ppm ± 1.03. A total of 35 of the specimens examined were infested with ecto-parasites representing a prevalence of 15% during the study period. Out of 155 fingerlings examined, 14.8% were infested while 85 adult fish examined had 14.1% infested with ecto-parasites. The prevalence rate encountered was Ichthyophthirius multifilis (60%) ≥ Trichodina sp (23%) ≥ monogeneans (17%). The mean intensity of Trichodina sp ranged from 0 to 2.5. Monogeneans and Ichthyophthirius multifilis mean intensity ranged from 0 to 1.7. The low prevalence and intensities of ecto-parasites recorded indicated that with good water quality, ecto-parasites may not pose a threat to O. niloticus production in concrete pond.
New HL‐A Alleles

Summary. By immunization within specially selected donor‐recipient pairs it was possible to produce antibodies against three new HL‐A antigens. One of these was later found identical to Dn17, the other two are called Li of the LA series, and LND of the Four series of antigens. The antigens behaved in population and family studies as if they were determined by alleles at the LA and Four nib‐loci. The present status of the HL‐A system seems to be that 8 La alleles and 9 Four alleles are well defined. However, unknown HL‐A antigens of low frequency still remain to be identified. The reported method seems to he very useful for this purpose.
A functional screen of translated pancreatic lncRNAs identifies a microprotein-independent role for LINC00261 in endocrine cell differentiation

Long noncoding RNAs (lncRNAs) are a heterogenous group of RNAs, which can encode small proteins. The extent to which developmentally regulated lncRNAs are translated and whether the produced microproteins are relevant for human development is unknown. Here, we show that many lncRNAs in direct vicinity of lineage-determining transcription factors (TFs) are dynamically regulated, predominantly cytosolic, and highly translated during pancreas development. We genetically ablated ten such lncRNAs, most of them translated, and found that nine are dispensable for endocrine cell differentiation. However, deletion of LINC00261 diminishes generation of insulin+ endocrine cells, in a manner independent of the nearby TF FOXA2. Systematic deletion of each of LINC00261’s seven poorly conserved microproteins shows that the RNA, rather than the microproteins, is required for endocrine development. Our work highlights extensive translation of lncRNAs into recently evolved microproteins during human pancreas development and provides a blueprint for dissection of their coding and noncoding roles. Graphical Abstract Highlights Extensive lncRNA translation and microprotein production during human pancreas development A small-scale loss-of-function screen shows most translated lncRNAs are dispensable LINC00261 is highly translated and regulates endocrine cell differentiation Deleting LINC00261’s evolutionary young microproteins reveals no essential roles
Transcriptional analysis of sex pheromone biosynthesis signal genes in Bombyx mori

Abstract Six sex pheromone synthesis signal genes, including acyl coenzyme A (acyl‐CoA) desaturase (desat1), fatty acyl reductase (FAR), pheromone biosynthesis activating neuropeptide receptor (PBANR), fatty acid transport protein (FATP), acyl‐CoA binding protein (ACBP) and store‐operated channel protein (Orai1A), were studied for their transcriptional regulations. The expression profiles of these transcripts at different developmental stages (from –96 to 48 h) revealed that the genes are expressed in an age‐dependent manner. The transcripts of these genes continued to increase despite decapitation, and compared with normally developmental females, decapitation significantly inhibited their expression. Further experiments with a methoprene, a juvenile hormone (JH) analogue, challenge showed that JH was not a key inhibiting factor in the expression of these genes, and mating was found to significantly inhibit the expression of these marker genes. Altogether, the results provide a reference for understanding the mechanism of sex pheromone synthesis.
Extrusion-cooking of potato starch and selected properties of the extrudates

Using single- and twin-screw extrusion cookers samples of potato starch were processed at varying temperature profile in the barrels, and at various feed moisture content. All the expansion, density, shearing stress, characteristics of paste viscosity, water absorption index, water solubility index, glucose content, reaction with iodine, enthalpy of gelatinisation, and resistance to the free radical decomposition at elevated temperature were determined for the extrudates. The product density in the twin-screw cooker increased with the moisture content. The higher temperature in the barrel and die also favoured the product density increase. The expansion ratio of the products depended on these parameters in an opposite manner. The single-screw extrusion cooking provided the product of higher density.
First observation of the marine tardigrades Batillipes mirus and Batillipes noerrevangi (Arthrotardigrada, Batillipedidae) from a strongly brackish part of the Polish Baltic Sea coast

Abstract The tardigrade fauna of Poland is one of the better known in Europe. However, almost all studies have been carried out on the limno-terrestrial species, while marine Tardigrada have been neglected. To the best of our knowledge only one report on marine Tardigrada for Polish waters has been published up to now. In the present study the first records of two marine arthrotardigrade species, Batillipes mirus and Batillipes noerrevangi, from Puck Bay (Baltic Sea) are reported. The lowest salinity value in the study area was 3–4 PSU, and B. noerrevangi should be considered the most brackish water-tolerant arthrotardigrade. Samples were collected from the vegetated seabed (seagrass and macrophytes) and the bare sandy bottom in different seasons. A single specimen of B. mirus was found only during the autumn campaign. Specimens (adults and larval stages) of B. noerrevangi were found in all samples during spring, summer and autumn campaigns. Additionally, morphometric data with detailed microphotographs of B. noerrevangi (PCM, DIC) and B. mirus (PCM) as well as a discussion of the new records are presented. The validity of the occurrence of B. dicrocercus in Poland, which was determined based on a single larva from the Międzyzdroje area by Hummon, is also discussed. The larva from Międzyzdroje should be regarded as an undetermined species; thus, the marine tardigrade fauna from Poland consists of only the two newly recorded species.
REVISION OF THE SUBFAMILY SPHAERIDIINAE OF AMERICA NORTH OF MEXICO (COLEOPTERA: HYDROPHILIDAE). SUPPLEMENTUM 2

Abstract Pelosoma pecki is described as new from specimens from the Florida Keys (Upper Matacumba Key) and from Mexico (Oaxaca). The genus Genyon Smetana 1978 (type-species Cercyon navicularis Zimmerman 1869, from eastern North America) is placed in synonymy with Tectosternum Balfour-Browne 1958 (type-species T. exstriatum Balfour-Browne 1958, from equatorial Africa). A lectotype is designated for Pelosoma prosternale Sharp 1882, and Pelosoma praecursor Smetana 1978 is placed in synonymy with P. prosternale Sharp 1882. Omicrus intermedius Smetana and the genus Cycrillum Knisch, with the species C. strigicolle (Sharp), are recorded for the first time from North America. Additional data on bionomics, geographical distribution, and synonymy of many species are presented. Résumé Une espèce nouvelle pour la science, Pelosoma pecki, est décrite à partir d'exemplaires des Keys de la Floride (Upper Matacumba Key) et du Mexique (Oaxaca). Le genre Genyon Smetana 1978 (espèce-type Cercyon navicularis Zimmerman 1869, de l'est de l'Amérique du Nord) est placé en synonymie avec Tectosternum Balfour-Browne 1958 (espèce-type T. exstriatum Balfour-Browne 1958, de l'Afrique équatoriale). Un lectotype est désigné pour Pelosoma prosternale Sharp 1882, et Pelosoma praecursor Smetana 1978 est placé en synonymie avec P. prosternale Sharp 1882. Omicrus intermedius Smetana et le genre Cycrillum Knisch, avec l'espèce C. strigicolle (Sharp), sont mentionnés pour la première fois en provenance d'Amérique du Nord. Des données additionnelles sur l'habitat, la répartition géographique et la synonymie de plusieurs espèces sont incluses.
Regulation of seed and pollinator production in the fig-fig wasp mutualism

Female agaonine fig wasps enter Ficus fruits (figs), where they pollinate the flowers and oviposit into the ovaries of a proportion of the flowers via their styles. The fig trees are totally dependent on these fig wasps for sexual reproduction, as the wasps fertilize the figs' seeds and transfer pollen between trees, while the wasps need the fig trees' ovaries as feeding sites (galled seeds) for their progeny. Since the wasp progeny destroy seeds, the question arises as to why selection has not led to increasingly higher fig wasp fecundities and the eventual collapse of the mutualism. The stability of the mutualism could be maintained by pollinators having short ovipositors, restricting oviposition to short-styled flowers so that long-styled flowers produce seeds. However, in most of the monoecious Ficus species where measurements were taken, pollinators generally possessed ovipositors of sufficient length to reach the ovaries of a large majority of the flowers. This was confirmed by the presence of pollinator progeny in flowers with long styles. Complete seed destruction may also be avoided by a proportion of fig ovaries being inviolate to oviposition by fig wasps, independent of their style lengths. However, experimental increases in pollinator foundresses per fig in F. burtt-davyi showed that all the ovaries that could be reached by the wasps' ovipositors were potentially exploitable by agaonine fig wasps. Relative production of wasps and seeds was found to be largely dependent on the interplay between the number of eggs inside each wasp, the number of accessible ovaries in individual figs, and the average number of foundresses entering each fig. On average, there were not enough foundresses entering each fig to utilize all accessible ovaries. Possible factors affecting the total entry numbers of wasps into figs include ostiolar closure rates and wasp population densities in the areas surrounding fig trees. As many ovaries remain unused because of a frequent shortage of wasp eggs per fig, fig trees can continue to produce enough seeds for the continued evolutionary stability of the fig-fig wasp mutualism.
Analysis of microsatellite variation in the spider mite pest Tetranychus turkestani (Acari: Tetranychidae) reveals population genetic structure and raises questions about related ecological factors

The habitat fragmentation that characterizes agricultural systems made up of an array of sympatric crop and weed biotopes might be a major determinant of the population structure of plant-feeding arthropods. Spider mites are interesting in this regard as several species are highly polyphagous, possibly generating homogenization by plant shifting, but also have the potential of forming host plant races which promotes specialization. This study analyses genetic diversity and structure in natural populations of a spider mite pest, Tetranychus turkestani, collected on both crops and weeds. Five microsatellite markers were used to genotype 283 individuals collected from 15 samples in four locations in southern France. The markers revealed considerable genetic variation, with an average heterozygosity of 0.68. Pairwise ΦST estimates calculated between localities showed differentiation in all comparisons. Although geographical distance appears to be a factor that influences T. turkestani population genetic structure at a regional scale, there was no clear evidence for differentiation between mites living on different host plants. A hierarchical analysis of the distribution of the genetic diversity within and between habitats showed that more than 97% of the observed genetic variation accounted for the differentiation between mites collected on the same host plant in a given locality. Significant heterozygote deficiency was found in 11 out of the 15 samples studied. Considering the biology of the mite, a Wahlund effect and inbreeding might explain such an excess of homozygosity. The data support the view that the plants in a given locality are colonized by mites that originate from diverse sources. They also support previous data suggesting that the demographic structure is made up of small demes of inbred individuals. The agricultural-level implications of the data are discussed, notably the fact that mites may well be capable of moving between host plants, making weeds surrounding the crop fields potential reservoirs for the pest. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82, 69–78.
Slow‐growing species cope best with drought: evidence from long‐term measurements in a tropical semi‐deciduous moist forest of Central Africa

Understanding how drought affects annual tree growth in tropical forests is of crucial importance to predict their response to climate change. Previous studies, mainly led in the Neotropics and in Southeast Asia, have yielded contradictory results which might be explained by differences in species studied, in the tree development stages considered, or by differences in other environmental factors than water availability. Here, we described the growth responses of functional groups of tree species to drought in a Central African semi‐deciduous moist forest. Species groups were automatically defined using a finite mixture model, which grouped species according to their growth model parameters. The growth model considered the variation in species response to drought, and the effect of competition for resources and of tree development stage on growth. Groups were further characterized by species functional traits. Nine species groups were identified. They differed in their ability to acquire, use and conserve resources, as suggested by their differences in maximum growth rate, regeneration guild, maximum dbh, wood density and leaf habit. The species were organized along a light requirement gradient that here closely matched a broader continuum of plant strategies for resource use, from slow‐growing shade‐tolerant conservative species to fast‐growing pioneer acquisitive species. Tree growth decreased with drought intensity, and species drought tolerance was found to be related to resource use strategy: slow‐growing species using a conservative strategy were the least sensitive to variations in water availability, while fast‐growing species using an acquisitive strategy were the most sensitive. Synthesis. Shade‐tolerant species, characterized by a low potential growth rate and thus a conservative strategy of resource use, were found to be the least sensitive to drought. This supports the hypothesis of a single axis summarizing multiple traits that represents a general trade‐off between the conservation and rapid acquisition of resources.
Learning the architectural features that predict functional similarity of neural networks

The mapping of the wiring diagrams of neural circuits promises to allow us to link structure and function of neural networks. Current approaches to analyzing connectomes rely mainly on graph-theoretical tools, but these may downplay the complex nonlinear dynamics of single neurons and networks, and the way networks respond to their inputs. Here, we measure the functional similarity of simulated networks of neurons, by quantifying the similitude of their spiking patterns in response to the same stimuli. We find that common graph theory metrics convey little information about the similarity of networks’ responses. Instead, we learn a functional metric between networks based on their synaptic differences, and show that it accurately predicts the similarity of novel networks, for a wide range of stimuli. We then show that a sparse set of architectural features - the sum of synaptic inputs that each neuron receives and the sum of each neuron’s synaptic outputs - predicts the functional similarity of networks of up to 100 cells, with high accuracy. We thus suggest new architectural design principles that shape the function of neural networks, which conform with experimental evidence of homeostatic mechanisms.