Miracle-dz/UniFAR-FTUs huggingface dataset:
The partitioning of symbionts effects on host resource acquisition and developmental plasticity

Many symbionts provide nutrients to their host and/or affect its phenotypic plasticity. Such symbiont effects on host resource acquisition and allocation are often simultaneous and difficult to disentangle. Here we partitioned symbiont effects on host resource acquisition and allocation using a new framework based on the analysis of a well-established trade-off between host fitness components. This framework was used to analyze the effect of symbiotic yeast on the larval development of Drosophila larvae in field-realistic conditions. The screening of eighteen yeast fresh isolates showed they had similar effects on the resource acquisition in Drosophila melanogaster, D. simulans and D. suzukii but species-specific effects on resource allocation between either larval development speed or adult size. These differences shed light on the ecology of Drosophila flies and illustrate why distinguishing between these qualitatively different effects of microorganisms on hosts is essential to understand and predict symbiosis evolution.
Morphometric and Karyological Differentiation among Populations of Discoglossus pictus (Discoglossidae: Anura) in Eastern North Africa

Abstract. To assess karyological and morphometric diversity within Discoglossus pictus Otth 1837, morphometric and cytogenetic analyses were carried out on five populations from the northern Tunisia and Algeria. A total of eight morphometric adult traits were evaluated, tadpole oral disc structure was described and chromosome patterns were assessed by means of conventional staining and banding methods (C-, Ag-NOR and CMA3 banding). Karyological data indicated the same chromosome and chromatin characters among the five populations. We observed also the same oral disk structure (LTRF: ⅔) in all studied Discoglossus tadpoles. However, we found significant differences in morphometric parameters of the specimens from these localities. Discriminant Function Analysis (DFA) of morphometric variables correctly classified 88% of individuals to their original localities. The pattern of morphometric variation does not match the genetic observation, which suggests that body shape differences result from the phenotypic plasticity correlated with local climatic factors.
THE DESIGN OF THE WATER DIFFUSER SYSTEM OF A TANK FOR A COGENERATION PLANT WITH RECIPROCATING ENGINES

Integration of thermal energy storage systems into cogeneration plants plays a very important role in their technical and economic operation. The use of storage systems increases the efficiency of the cogeneration plant and its flexibility in operation. The efficiency of the heat storage systems can be improved if the water inside the tank is stratified. In time, water de-stratification results in energy losses. The paper presents the integration of a heat storage system into a cogeneration plant with a reciprocating engine by means of an existing fuel oil tank. At the same time, the water diffusion system is calculated considering a four-ring octagonal system.
vmPFC Drives Hippocampal Processing during Autobiographical Memory Recall Regardless of Remoteness

Our ability to recall past experiences, autobiographical memories (AMs), is crucial to cognition, endowing us with a sense of self and underwriting our capacity for autonomy. Traditional views assume that the hippocampus orchestrates event recall, whereas recent accounts propose that the ventromedial prefrontal cortex (vmPFC) instigates and coordinates hippocampal-dependent processes. Here we sought to characterise the dynamic interplay between hippocampus and vmPFC during AM recall to adjudicate between these perspectives. Leveraging the high temporal resolution of magnetoencephalography, we found that the left hippocampus and the vmPFC showed the greatest power changes during AM retrieval. Moreover, responses in the vmPFC preceded activity in the hippocampus during initiation of AM recall, except during retrieval of the most recent AMs. The vmPFC drove hippocampal activity during recall initiation and also as AMs unfolded over subsequent seconds, and this effect was evident regardless of AM age. These results re-cast the positions of the hippocampus and the vmPFC in the AM retrieval hierarchy, with implications for theoretical accounts of memory processing and systems-level consolidation.
Functional characterization of Neurofilament Light b splicing and misbalance in zebrafish

Neurofilaments (NFs), a major cytoskeletal component of motor neurons, play a key role in their differentiation, establishment and maintenance of their morphology and mechanical strength. The de novo assembly of these neuronal intermediate filaments requires the presence of the neurofilament light subunit, NEFL, which expression is reduced in motor neurons in Amyotrophic Lateral Sclerosis (ALS). This study used zebrafish as a model to characterize the NEFL homologue neflb, which encodes two different isoforms via splicing of the primary transcript (neflbE4 and neflbE3). In vivo imaging showed that neflb is crucial for proper neuronal development, and that disrupting the balance between its two isoforms specifically affects NF assembly and motor axon growth, with resulting motor deficits. This equilibrium is also disrupted upon partial depletion of TDP-43, a RNA binding protein that is mislocalized into cytoplasmic inclusions in ALS. The study supports interaction of NEFL expression and splicing with TDP-43 in a common pathway, both biologically and pathogenetically.
LIMITING NUTRIENTS FOR PLANT GROWTH IN COASTAL SAND DUNE SOILS

(1) A pot-culture experiment and a field experiment were carried out to examine the relative importance of nitrogen, phosphorus and potassium supplies for plant growth on coastal dune soils, using Oenothera erythrosepala as a test plant. (2) The plants grown in pot culture were deficient in phosphorus rather than nitrogen and potassium, while the plants grown in the field were deficient in nitrogen rather than phosphorus and potassium. (3) Dune sands were incubated to examine the differences in nutrient availabilities between pot and field conditions. The incubation resulted in an increased availability of nitrogen and a decreased availability of phosphorus. (4) It is suggested that the low supply of inorganic nitrogen in the field is attributable to restriction of mineralization and nitrification and to leaching of nitrate.
Circular ANRIL isoforms switch from repressors to activators of p15/CDKN2B expression during RAF1 oncogene-induced senescence

Long non-coding RNAs (ncRNAs) are major regulators of gene expression and cell fate. The INK4 locus encodes the tumour suppressor proteins p15INK4b, p16INK4a and p14ARF required for cell cycle arrest and whose expression increases during senescence. ANRIL is a ncRNA antisense to the p15 gene. In proliferative cells, ANRIL prevents senescence by repressing INK4 genes through the recruitment of Polycomb-group proteins. In models of replicative and RASval12 oncogene-induced senescence (OIS), the expression of ANRIL and Polycomb proteins decreases, thus allowing INK4 derepression. Here, we found in a model of RAF1 OIS that ANRIL expression rather increases, due in particular to an increased stability. This led us to search for circular ANRIL isoforms, as circular RNAs are rather stable species. We found that the expression of two circular ANRIL increases in several OIS models (RAF1, MEK1 and BRAF). In proliferative cells, they repress p15 expression, while in RAF1 OIS, they promote full induction of p15, p16 and p14ARF expression. Further analysis of one of these circular ANRIL shows that it interacts with Polycomb proteins and decreases EZH2 Polycomb protein localization and H3K27me3 at the p15 and p16 promoters, respectively. We propose that changes in the ratio between Polycomb proteins and circular ANRIL isoforms allow these isoforms to switch from repressors of p15 gene to activators of all INK4 genes in RAF1 OIS. Our data reveal that regulation of ANRIL expression depends on the senescence inducer and underline the importance of circular ANRIL in the regulation of INK4 gene expression and senescence.
Altered Sensory Neuron Development in CMT2D Mice Is Site-Specific and Linked to Increased GlyRS Levels

Dominant, missense mutations in the widely and constitutively expressed GARS1 gene cause a peripheral neuropathy that usually begins in adolescence and principally impacts the upper limbs. Caused by a toxic gain-of-function in the encoded glycyl-tRNA synthetase (GlyRS) enzyme, the neuropathology appears to be independent of the canonical role of GlyRS in aminoacylation. Patients display progressive, life-long weakness and wasting of muscles in hands followed by feet, with frequently associated deficits in sensation. When dysfunction is observed in motor and sensory nerves, there is a diagnosis of Charcot-Marie-Tooth disease type 2D (CMT2D), or distal hereditary motor neuropathy type V if the symptoms are purely motor. The cause of this varied sensory involvement remains unresolved, as are the pathomechanisms underlying the selective neurodegeneration characteristic of the disease. We have previously identified in CMT2D mice that neuropathy-causing Gars mutations perturb sensory neuron fate and permit mutant GlyRS to aberrantly interact with neurotrophin receptors (Trks). Here, we extend this work by interrogating further the anatomy and function of the CMT2D sensory nervous system in mutant Gars mice, obtaining several key results: 1) sensory pathology is restricted to neurons innervating the hindlimbs; 2) perturbation of sensory development is not common in mouse models of neuromuscular disease; 3) in vitro axonal transport of signalling endosomes is not impaired in afferent neurons of all CMT2D mouse models; and 4) Gars expression is selectively elevated in a subset of sensory neurons and linked to sensory developmental defects. These findings highlight the importance of comparative neurological assessment in mouse models of disease and shed light on key proposed neuropathogenic mechanisms in GARS1-linked neuropathy.
Code Structure Deﬁnition and Veriﬁcation

This paper compares two diﬀerent languages resp. toolkits to deﬁne and verify code structures, i.e., object-oriented design patterns. Informal descriptions of design patterns are transformed into formal notations. It is revealed that UML class diagrams are not best suited for automated veriﬁcation of those code structures. Instead, the formal languages LePUS3 and Class-Z and SPQR are presented. Concrete examples are given by the factory method pattern and the adapter object pattern. The evaluation and results show that SPQR is more complex but more powerful, whereas LePUS3 and Class-Z are more easy to read and understand but still powerful enough to model most design patterns.
CARACTERISATION DES BACTERIES ISOLEES A PARTIR DES NODULES DES ESPECES DE LEGUMINEUSES DU GENRE HEDYSARUM : H. pallidum desf., H. spinosissimum subsp. capitatum, H. carnosum desf. et H. naudinianum coss

Des bacteries ont ete isolees a partir des nodules des especes de plantes legumineuses du genre Hedysarum : H. pallidum Desf. , H. spinosissimum subsp. capitatum, H. carnosum Desf. et H. naudinianum Coss. Pour l’espece H. naudinianum Coss, c’est la premiere fois qu’une etude est faite pour mettre en evidence l’association symbiotique plante-bacterie. La caracterisation des bacteries isolees porte sur une identification phenotypique qui englobe une serie de tests en plus de la determination du profil proteique par SDS-PAGE et le test de nodulation et une caracterisation moleculaire des isolats. Les resultats de la caracterisation phenotypique et phylogenetique (l’ARDRA et le sequencage de l’ADNr16S) montrent que les isolats appartiennent a la classe des Gammaproteobacteria specifiquement les especes de Pseudomonas sp et Pantoea agglomerans
Arctic ground squirrels Urocitellus parryii as drivers and indicators of change in northern ecosystems

Global warming and increasing human activity are altering northern ecosystems. In these strongly seasonal environments, small herbivorous mammals may have a significant role in determining the trajectory of ecosystem transitions from one state to another. Arctic ground squirrels Urocitellus parryii are a key component of northern terrestrial food webs and are considered ecosystem engineers, exerting a large impact on their habitat through bioturbation. We review and synthesize diverse information about current and past distribution and density of arctic ground squirrels, their physiology and ecological interactions with other species. Factors that appear to affect the distribution and abundance of arctic ground squirrels include increasing temperatures, changes in flooding probability, permafrost thaw, shifting phenology, habitat change, new predators and invasive diseases. Increases in the distribution and density of arctic ground squirrels in northern latitudes and high altitudes could accelerate ecosystem change through facilitation of disturbance-tolerant species, while decreases in southern and milder climates could remove an important agent of disturbance and prey item. Despite their pervasive ecological influence throughout most of their range, arctic ground squirrels are underrepresented in ecological research, based on a comparison of the number of publications about arctic ground squirrels with the number about other species of the same genus, and about other arctic herbivores. The widespread distribution of arctic ground squirrels, along with their potential to exacerbate and alter trajectories of ecosystem change under global warming, makes them a valuable indicator of ecosystem change and therefore a candidate for increased monitoring.
Biological basis for variation in residual feed intake in beef cattle 1: Review of potential mechanisms

There is a growing body of evidence that there is genetic variation in beef cattle feed intake relative to their liveweight and weight gain. Difference in feed intake, above and below that expected or predicted on the basis of size and growth, is measured as residual feed intake. Variation in residual feed intake must be underpinned by measurable differences in biological processes. This paper summarises some plausible mechanisms by which variation in efficiency of nutrient use may occur and presents several testable hypotheses for such variation. A companion paper [Richardson and Herd (2004) Aust. J. Exp. Ag. 44, 431–441] presents results from experiments on cattle following divergent selection for residual feed intake. There were at least 5 major processes identified by which variation in efficiency can arise. These are associated with variation in intake of feed, digestion of feed, metabolism (anabolism and catabolism associated with and including variation in body composition), activity and thermoregulation. The percentage contribution of different mechanisms, to variation in residual feed intake, was: 9% for differences in heat increment of feeding; 14% for differences in digestion; 5% for differences in body composition; and 5% for differences in activity. Together, these mechanisms may be responsible for about one-third of the variation in residual feed intake. The remaining two-thirds were likely to be associated with heat loss due to variation in other processes, such as protein turnover and ion transport. There is no shortage of candidate mechanisms that, singularly or in combination, might contribute to genetic variation in energy utilisation in ruminants. Further research in beef cattle, to better define these mechanisms and enable their incorporation into breeding programmes, may lead not only to cattle which eat less for the same performance, but are superior in other traits as well.
Decontamination of filtering facepiece respirators in primary care using medical autoclave

Objective: There are widespread shortages of personal protective equipment as a result of the coronavirus disease 2019 (COVID-19) pandemic. Reprocessing filtering facepiece respirators may provide an alternative solution in keeping health care professionals safe. Design: prospective, bench-to-bedside Setting: A primary care-based study using filtering facepiece particles (FFP) type 2 respirators without exhalation valve (3M Aura 1862+, Maco Pharma ZZM002), FFP2 respirators with valve (3M Aura 9322+ and San Huei 2920V), and valved FFP type 3 respirators (Safe Worker 1016). Interventions: All masks were reprocessed using a medical autoclave (34-minute total cycle time of steam sterilization, with 17 minutes at 121 degrees Celsius) and subsequently tested up to 3 times whether these decontaminated respirators retained their integrity (seal check, pressure drop) and ability to filter small particles (0.3-5.0 microns) in the laboratory using a particle penetration test. Results: We tested 32 respirators, and 63 samples for filter capacity. All 27 FFP-2 respirators retained their shape, whereas half of the sterilized FFP-3 respirators (Safe Worker 1116) showed deformities and failed the seal check. The filtering capacity of the 3M Aura 1862 was best retained after 1, 2, and 3 sterilization cycles (0.3 microns: 99.3+/-0.3% (new) versus 97.0+/-1.3, 94.2+/-1.3% or 94.4+/-1.6, p<0.001). Of the other FFP-2 respirators, the San Huei 2920V had 95.5+/-0.7% at baseline versus 92.3+/-1.7% versus 90.0+/-0.7 after one- and two-time sterilization, respectively (p<0.001). The tested FFP-3 respirator (Safe Worker 1016) had a filter capacity of 96.5+/-0.7% at baseline and 60.3+/-5.7% after one-time sterilization (p<0.001). Breathing and pressure resistance tests indicated no relevant pressure changes between respirators that were used once, twice or thrice. Conclusion: This study shows that selected FFP2-type respirators may be reprocessed for use in primary care, as the tested masks retain their shape, ability to retain particles and breathing comfort after decontamination using a medical autoclave.
Dinosaur Systematics: A review of Vectisaurus valdensis , with comments on the family Iguanodontidae

Abstract Vectisaurus valdensis is considered to be the imperfectly preserved remains of juvenile Iguanodon . Based on juvenile material of Iguanodon recovered from Nehden (Federal Republic of Germany), Vectisaurus is most probably referrable to I. atherfieldensis . Ornithopod relationships have been evaluated by reference to the detailed recent systematic reviews of the Ornithischia. Results from this study suggest that the family Iguanodontidae is valid, if more restricted than previously argued; that Tenontosaurus tilletti is more closely related to hypsilophodontians than iguanodontians; and, that Probactrosaurus gobiensis is the sister-taxon of the Hadrosauridae. A revised cladogram of advanced ornithopod dinosaurs is proposed. Introduction In 1879, John Wittaker Hulke described the partial, associated skeleton of a small ornithopod that had been recovered from the Wealden Marls near Brixton (Brighstone) Chine (Isle of Wight, southern England). In the description of this material (Figs. 11.1, 11.2, 11.3), which included five dorsal vertebrae, an anterior caudal centrum, and a partial ilium, Hulke recognised several characters that merited the erection of a new genus and species distinct from the then known ornithopods from the Isle of Wight ( Hypsilophodon foxii and Iguanodon mantelli ). The principal characters by which Hulke distinguished this new taxon were: opisthocoelous dorsal centra with a nearly flat anterior articular surface, a heart-shaped posterior articular surface, a blunt ventral keel on the centra, and the quadrangular appearance of the anterior caudal centrum. Based on the preacetabular process of the ilium, Hulke referred this species to the family Iguanodontidae.
Coyote diets in the Chihuahuan Desert, more evidence for optimal foraging

With 7 years data on coyote prey use and availability, we tested three predictions based on optimal foraging: (1) the proportion eaten of the most profitable item is constant regardless of availability, (2) under a constant density of higher ranked prey, there is no relationship between the proportion eaten of low profitability items and their density, (3) the ratio of number consumed to availability for the highest ranking prey item should be negatively related to availability. We tested these predictions with regression analyses. We found no significant linear relationship between lagomorph availability and use. There was no significant linear relationship between percent frequency of occurrence of rodents nor arthropods and their respective availabilities for two levels of availability of lagomorphs. We found a significant negative relationship between number consumed/number available to availability for lagomorphs but not for rodents nor arthropods. The results supported the three predictions and we concluded that coyotes are foraging optimally.
Deficiency in reverse cholesterol transport in mice augments sepsis

Background Sepsis claims over 215,000 lives and costs $16.7 billion per year in America alone. Recent studies revealed that HDL receptor scavenger receptor BI (SR-BI or Scarb1) plays a critical protective role in sepsis. Using Scarb1I179N mice, a mutant SR-BI mouse model with 90% depletion in hepatic SR-BI, we previously reported that the mutant mice are susceptible to cecal ligation and puncture (CLP)-induced sepsis. However, using a hypo-AlbCreSR-BIfl/fl mouse model, Huby’s group showed that the liver-specific SR-BI KO mice are not more susceptible to CLP-induced sepsis. In this study, we generated a new floxed SR-BI mouse model to clarify the contribution of hepatic SR-BI in sepsis. SR-BI is known as a receptor that plays a key role in reverse cholesterol transport (RCT) by uptaking cholesterol to the liver. So, our established AlbCreSR-BIfl/fl mice (liver-specific SR-BI KO) is an RCT deficiency mice model that can be used to understand the mechanisms of RCT protecting against sepsis and may provide new insight into the pathogenesis of sepsis. Methods and Results We generated SR-BIfl/fl mice by flanking exon 2. We bred the floxed mice with AlbCre mice to generate AlbCreSR-BIfl/fl mice (liver-specific SR-BI KO mice), then the mice were backcrossed to C57BL/6J for 10 generations. As shown in Fig 1, the liver SR-BI expression was normal in SR-BIfl/fl mice as compared to C57BL/6J (B6) mice, but completely depleted in AlbCreSR-BIfl/fl mice. Using this liver-specific SR-BI KO model, we observed that a deficiency in RCT rendered the mice highly susceptible to CLP-induced sepsis as shown by 80% and 14.3% survival of SR-BIfl/fl and AlbCreSR-BIfl/fl mice, respectively. We found aggravated inflammatory cytokine production, altered leukocyte recruitment and slightly increased in the blood and peritoneal bacteria. Moreover, we found RCT deficiency mice increased both free and total cholesterol levels in serum and showed severer hemolysis in AlbCreSR-BIfl/fl mice than SR-BIfl/fl mice during CLP-induced sepsis. Importantly, when we fed AlbCreSR-BIfl/fl mice with probucol to decrease the cholesterol level in serum before performing CLP, the survival rate of AlbCreSR-BIfl/fl mice improved to 88.9%. Conclusions Deficiency RCT resulting in abnormal metabolism of cholesterol and lipid metabolism is a risk factor in sepsis and maintain normal metabolism of cholesterol may provide a new insight for sepsis therapies.