Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic assessment of global Suillus ITS sequences supports morphologically defined species and reveals synonymous and undescribed taxa

Abstract The genus Suillus represents one of the most recognizable groups of mushrooms in conifer forests throughout the Northern Hemisphere. Although for decades the genus has been relatively well defined morphologically, previous molecular phylogenetic assessments have provided important yet preliminary insights into its evolutionary history. We present the first large-scale phylogenetic study of the boundaries of each species in the genus Suillus based on the most current internal transcribed spacer (ITS) barcode sequences available inPUBLIC databases, as well as sequencing of 224 vouchered specimens and cultures, 15 of which were type specimens from North America. We found that species boundaries delimited by morphological data are broadly congruent with those based on ITS sequences. However, some species appear to have been described several times under different names, several species groups cannot be resolved by ITS sequences alone, and undescribed taxa are apparent, especially in Asia. Therefore, we elevated S. tomentosus var. discolor to S. discolor; proposed synonymies of S. neoalbidipes with S. glandulosipes, S. borealis with S. brunnescens, Boletus serotinus and B. solidipes with Suillus elbensis, S. lactifluus with S. granulatus, S. himalayensis with S. americanus; and proposed usage of the names S. clintonianus in the place of the North American S. grevillei, S. weaverae for North American S. granulatus, S. ampliporus in the place of the North American S. cavipes, and S. elbensis in place of the North American S. viscidus. We showed that the majority of Suillus species have strong affinities for particular host genera. Although deep node support was low, geographic differentiation was apparent, with species from North America, Eurasia, and Asia often forming their own clades. Collectively, this comprehensive genus-level phylogenetic integration of currently available Suillus ITS molecular data and metadata will aid future taxonomic and ecological work on an important group of ectomycorrhizal fungi.
Young children and tablets: A systematic review of effects on learning and development

Mobile applications are popular among young children, yet there is a dearth of studies examining their impact on learning and development. A systematic review identified 19 studies reporting learning effects on children 2 to 5 years old. The number of children participating in experimental, quasi‐experimental, or mixed‐method studies was 862 and in descriptive or correlation studies, 941. The majority of studies reported positive effects on literacy development, mathematics, science, problem‐solving, and self‐efficacy. Among the factors explaining observed effects were design features, the role of adults, and a similarity between applications and transfer context. Although drawing firm conclusions remains a challenge, this review forms a first step towards systematic research in the field and contributes to shaping directions for future research.
A Human Mixture Risk Assessment for Neurodevelopmental Toxicity Associated with Polybrominated Diphenyl Ethers Used as Flame Retardants

Background: The European Food Safety Authority recently concluded that the exposure of small children (1–3 y old) to brominated diphenyl ether (BDE)-99 may exceed acceptable levels defined in relation to neurodevelopmental toxicity in rodents. The flame retardant BDE-209 may release BDE-99 and other lower brominated BDEs through biotic and abiotic degradation, and all age groups are exposed not only to BDE-209 and -99 but also to a cocktail of BDE congeners with evidence of neurodevelopmental toxicity. The possible risks from combined exposures to these substances have not been evaluated. Objectives: We performed a congener-specific mixture risk assessment (MRA) of human exposure to combinations of BDE-209 and other BDEs based on estimated exposures via diet and dust intake and on measured levels in biologic samples. Methods: We employed the Hazard Index (HI) method by using BDE congener-specific reference doses for neurodevelopmental toxicity. Results: Our HI analysis suggests that combined exposures to polybrominated diphenyl ethers (PBDEs) may exceed acceptable levels in breastfeeding infants (0–3 mo old) and in small children (1–3 y old), even for moderate (vs. high) exposure scenarios. Our estimates also suggest that acceptable levels of combined PBDEs may be exceeded in adults whose diets are high in fish. Small children had the highest combined exposures, with some estimated body burdens that were similar to body burdens associated with developmental neurotoxicity in rodents. Conclusions: Our estimates corroborate reports from several recent epidemiological studies of associations between PBDE exposures and neurobehavioral outcomes, and they support the inclusion of BDE-209 in the persistent organic pollutant (POP) convention as well as the need for strategies to reduce exposures to PBDE mixtures, including maximum residue limits for PBDEs in food and measures for limiting the release of PBDEs from consumer waste. https://doi.org/10.1289/EHP826
Knee Ligament Injury and the Clinical Application of Tissue Engineering Techniques: A Systematic Review.

BACKGROUND The incidence of knee ligament injury is increasing and represents a significant cost to healthcare providers. Current interventions include tissue grafts, suture repair and non-surgical management. These techniques have demonstrated good patient outcomes but have been associated graft rejection, infection, long term immobilization and reduced joint function. The limitations of traditional management strategies have prompted research into tissue engineering of knee ligaments. OBJECTIVE This paper aims to evaluate whether tissue engineering of knee ligaments offers a viable alternative in the clinical management of knee ligament injuries. A search of existing literature was performed using OVID Medline, Embase, AMED, PubMed and Google Scholar, and a manual review of citations identified within these papers. RESULTS Silk, polymer and extracellular matrix based scaffolds can all improve graft healing and collagen production. Fibroblasts and stem cells demonstrate compatibility with scaffolds, and have been shown to increase organized collagen production. These effects can be augmented using growth factors and extracellular matrix derivatives. Animal studies have shown tissue engineered ligaments can provide the biomechanical characteristics required for effective treatment of knee ligament injuries. CONCLUSION There is a growing clinical demand for a tissue engineered alternative to traditional management strategies. Currently, there is limited consensus regarding material selection for use in tissue engineered ligaments. Further research is required to optimize tissue engineered ligament production before clinical application. Controlled clinical trials comparing the use of tissue engineered ligaments and traditional management in patients with knee ligament injury could determine whether they can provide a cost-effective alternative.
The Unexplored Diversity of Pleolipoviruses: The Surprising Case of Two Viruses with Identical Major Structural Modules

Extremely halophilic Archaea are the only known hosts for pleolipoviruses which are pleomorphic non-lytic viruses resembling cellular membrane vesicles. Recently, pleolipoviruses have been acknowledged by the International Committee on Taxonomy of Viruses (ICTV) as the first virus family that contains related viruses with different DNA genomes. Genomic diversity of pleolipoviruses includes single-stranded and double-stranded DNA molecules and their combinations as linear or circular molecules. To date, only eight viruses belong to the family Pleolipoviridae. In order to obtain more information about the diversity of pleolipoviruses, further isolates are needed. Here we describe the characterization of a new halophilic virus isolate, Haloarcula hispanica pleomorphic virus 4 (HHPV4). All pleolipoviruses and related proviruses contain a conserved core of approximately five genes designating this virus family, but the sequence similarity among different isolates is low. We demonstrate that over half of HHPV4 genome is identical to the genome of pleomorphic virus HHPV3. The genomic regions encoding known virion components are identical between the two viruses, but HHPV4 includes unique genetic elements, e.g., a putative integrase gene. The co-evolution of these two viruses demonstrates the presence of high recombination frequency in halophilic microbiota and can provide new insights considering links between viruses, membrane vesicles, and plasmids.
Measurement of Steel Phase Transformation Kinetics by Dilatometry and in-Situ Neutron Diffraction – a Comparative Study

Solid-state phase transformation kinetics between ferrite (α) and austenite (γ) phases in a C-Mn steel were investigated by the dilatometry and in-situ neutron diffraction methods, respectively. Dilatometry is commonly used to study the phase transformation kinetics. It infers the allotropic phase transformation from the overall dimensional changes, e.g., the diameter changes of the specimen, during heating and/or cooling. In this regard, it is an indirect measurement technique. Alternatively, neutron diffraction directly detects and measures the individual phases as they present during different stages of phase transformation. A comparative study was made in this work between the dilatometry and the in-situ neutron diffraction methods. The comparison shows that dilatometry analysis would cause the under-estimation of austenite phase evolution as a function of temperature due to the drastic deviation of linear expansion assumption of austenite as function of temperature.
Effect of selection for delayed amelanosis on immune response in chickens. 2. Cell-mediated immunity.

Studies were conducted to compare the cell-mediated immune response of the Delayed Amelanotic (DAM) line of chickens with that of the line from which it originated, the Brown (BR) line, and a distantly related environmental control, the Light Brown Leghorn (LBL) line. Assays used to evaluate cell-mediated immunity were graft versus host (GvH) splenomegaly and the phytohemagglutinin (PHA) skin response. The three genetic stocks showed different responses to both tests with a variation in ranking between the tests. The GvH response of BR birds was significantly greater (P less than .01) than that of DAM birds, which was in turn significantly greater (P less than .001) than that of LBL birds. In the PHA skin test, the responses of BR and LBL birds did not differ but were significantly greater (P less than .001) than those of DAM line birds.
Encapsulation of FBG Sensor into the PDMS and its Effect on Spectral and Temperature Characteristics

Fiber Bragg Grating (FBG) is the most distributed type of fiber-optic sensors. FBGs are primarily sensitive to the effects of temperature and deformation. By employing different transformation techniques, it is possible to use FBG to monitor any physical quantity. To use them as parts of sensor applications, it is essential to encapsulate FBGs to achieve their maximum protection against external effects and damage. Another reason to encapsulate is increasing of sensitivity to the measured quantity. Polydimethylsiloxane (PDMS) encapsulation appears to be an interesting alternative due to convenient temperature and flexibility of the elastomer. This article describes an experimental proposal of FBG PDMS encapsulation process, also providing an analysis of the FBG spectral characteristics and temperature sensitivity, both influenced by high temperature and the process of polydimethylsiloxane curing itself. As for the PDMS type, Sylgard 184 was employed. Encapsulation consisted of several steps: allocation of FBG to PDMS in its liquid state, curing PDMS at the temperature of 80°C ± 5 %, and a 50-minute relaxation necessary to stabilize a Bragg wavelength. A broadband light source and an optical spectrum analyzer were both used to monitor the parameters during the processes of curing and relaxation. Presented results imply that such a method of encapsulation does not have any influence on the structure or functionality of the FBG. At the same time, a fourfold increase of temperature sensitivity was monitored when compared to a bare FBG.
A Conceptual Model for Researching the Creation and Operation of Supply Networks

This paper presents a conceptual model for the creation and operation of supply networks. Existing conceptual research relating to interorganizational relationships and networks is reviewed in terms of its relevance to understanding supply networks; this research is drawn from the fields of strategic management, channel management, industrial marketing and purchasing, organizational behaviour and supply-chain management. The different perspectives each field has on networks are highlighted. Contributions made by each in assisting to understand supply networks are discussed and synthesized. Findings from an exploratory survey are used to structure the design of a conceptual model for analysing the processes involved in the creation and operation of supply networks. The authors identify nine different types of networking activities and discuss the nature of these activities in the context of supply. Four different types of contextual factors relating to supply networks are identified. The model is tested in eight in-depth case studies and a validating survey of 58 focal firm networks. It is concluded that it provides a robust structure that enabled complex, cross-case analysis of multi-variable, multi-disciplinary data from interorganization product/service supply networks, but that further testing by other researchers is required.
Influence of photoperiod and age of photostimulation on the incidence of polycystic ovarian follicle syndrome in turkey breeder hens.

An arrest in egg laying associated with a polycystic ovarian follicle syndrome (PCOF) has been recently reported early in the egg production period in turkey hens photostimulated at 30 wk of age (WOA) with continuous light. When autopsied 2 to 3 wk after laying ceased, the ovaries of PCOF hens contained an increased number of mature size (F1) yolky follicles in comparison with normally laying hens plus several larger cystic follicles, while their oviducts were equal in weight to oviducts of hens laying normally. Four experiments were conducted to examine effects of age at photostimulation and photoperiod [14L:10D (14L) or continuous lighting 24L:0D (24L)] on the incidence of the PCOF syndrome. Turkey hens of the egg line were given short-day photostimulation of 6L:18D at 16 WOA and then photostimulated with either 14L or 24L at various ages between 26 to 70 WOA. Egg production was followed for 6 to 8 wk, and hens that stopped laying eggs during this period were autopsied 2 to 3 wk later to determine presence and incidence of the PCOF syndrome. At 26 WOA, the PCOF incidence was 80% with 24L lighting and 31% with 14L lighting (P = 0.006). At 28 WOA, the PCOF incidence was 56% with 24L lighting and 25% with 14L lighting (P = 0.072). At 31, 34, and 41 WOA, there were no differences (P > or = 0.10) in incidence of the PCOF syndrome between the 24L and 14L treatments. Within the 24L treatment, the PCOF incidence at 26 and 28 WOA (80 and 56%) were greater than at 31 WOA and older ages (< or = 20%; P < or = 0.025). Within the 14L lighting treatment, the PCOF incidence was not different among ages (26 WOA, 31% to 48 WOA, 0%; P > or = 0.05). It was concluded that the incidence of the PCOF syndrome is greater when photosensitive Egg line turkey hens are photostimulated at relatively young ages (less than 31WOA) and with 24L in comparison to 14L lighting.
Cannabis: Does it have a medicinal value?

Use of cannabis can have a variety of psychological effects. It generally causes a sense of heightened mood or “high. ” This can lead to decreased anxiety and increased social interaction. It can also lead to perceptual changes where sensory stimuli are exaggerated to heightened, such as colors and sound. It also leads to slower to reaction times, impaired coordination, and short-term memory. Chronic use can also to “a motivational syndrome” characterized by lack of energy and motivation. Long-term use can also lead to tolerance and withdrawal symptoms.
Muscle Weakness and 5-Year Survival in Acute Respiratory Distress Syndrome Survivors*

Objectives: To longitudinally evaluate the association of post-ICU muscle weakness and associated trajectories of weakness over time with 5-year survival. Design: Longitudinal prospective cohort study over 5 years of follow-up. Setting: Thirteen ICUs in four hospitals in Baltimore, MD. Patients: One hundred fifty-six acute respiratory distress syndrome survivors. Interventions: None. Measurements and Main Results: Strength was evaluated with standardized manual muscle testing using the Medical Research Council sum score (range, 0–60; higher is better), with post-ICU weakness defined as sum score less than 48. Muscle strength was assessed at hospital discharge and at 3, 6, 12, 24, 36, and 48 months after acute respiratory distress syndrome. At discharge, 38% of patients had muscle weakness. Every one point increase in sum score at discharge was associated with improved survival (hazard ratio [95% CI], 0.96 [0.94–0.98]), with similar findings longitudinally (0.95 [0.93–0.98]). Having weakness at discharge was associated with worse 5-year survival (1.75 [1.01–3.03]), but the association was attenuated (1.54 [0.82–2.89]) when evaluated longitudinally over follow-up. Persisting and resolving trajectories of muscle weakness, occurring in 50% of patients during follow-up, were associated with worse survival (3.01 [1.12-8.04]; and 3.14 [1.40-7.03], respectively) compared to a trajectory of maintaining no muscle weakness. Conclusions: At hospital discharge, greater than one third of acute respiratory distress syndrome survivors had muscle weakness. Greater strength at discharge and throughout follow-up was associated with improved 5-year survival. In patients with post-ICU weakness, both persisting and resolving trajectories were commonly experienced and associated with worse survival during follow-up.
Rate of food passage (transit time) as influenced by level of supplemental fat.

An experiment involving 35 White Leghorn hens was conducted to study the influence of graded levels of supplemental yellow grease on rate of food passage (transit time). Seven experimental diets (0, 5, 10, 15, 20, 25, and 30% supplemental fat) were formulated. Transit time was determined by utilizing either Cr2O3 or 144Ce as indicators. First appearance of the markers in the excreta and percentages of the markers ingested that were recovered in excreta 10 hr after feeding were criteria used to determine transit time. There was a significant (P less than .01) linear effect of fat on transit time of Cr2O3 whereby the time required for the marker to appear in the excreta increased with increments of supplemental fat. Average first appearance time of Cr2O3 was 193, 219, 214, 227, 251, 250, and 270 min for the diets containing 0, 5, 10, 15, 20, 25, and 30% supplemental fat, respectively. Transit time of 144Ce also was increased slightly (P less than .10) by fat supplementation. Transit time, measured as percentage of marker recovered in excreta 10 hr after feeding, was faster for the control than for the fat-supplemented diets, although the linear effects of fat were not statistically significant (P greater than .10). The results show that supplemental fat increased transit time of ingesta in chickens. This observation may be helpful in understanding the nature of the extrametabolic effect of fat in poultry diets. By increasing transit time, supplemental fats may improve digestibility of other dietary constituents and thereby increase the utilization of dietary energy.
Regulatory logic driving stable levels of defective proventriculus expression during terminal photoreceptor specification in flies

How differential levels of gene expression are controlled in post-mitotic neurons is poorly understood. In the Drosophila retina, expression of the transcription factor Defective Proventriculus (Dve) at distinct cell type-specific levels is required for terminal differentiation of color- and motion-detecting photoreceptors. Here, we find that the activities of two cis-regulatory enhancers are coordinated to drive dve expression in the fly eye. Three transcription factors act on these enhancers to determine cell-type specificity. Negative autoregulation by Dve maintains expression from each enhancer at distinct homeostatic levels. One enhancer acts as an inducible backup (‘dark’ shadow enhancer) that is normally repressed but becomes active in the absence of the other enhancer. Thus, two enhancers integrate combinatorial transcription factor input, feedback and redundancy to generate cell type-specific levels of dve expression and stable photoreceptor fate. This regulatory logic may represent a general paradigm for how precise levels of gene expression are established and maintained in post-mitotic neurons. Summary: The activities of two cis-regulatory enhancers, which integrate combinatorial transcription factor input, feedback and redundancy, are coordinated to drive dve expression in the Drosophila eye.
Residual feed consumption in laying hens. 2. Genetic variation and correlations.

The study described here deals with the quantification of the genetic variation of "residual feed consumption" (RFC) of hens of a White Leghorn population during a 44-wk laying period (20 to 64 wk of age) in 11 time segments of 4 wk each, fed either a commercial or a low-energy diet (11.7 and 10.0 MJ ME/kg, respectively, where 1 MJ = .239 Mcal). The RFC is defined operationally as the difference between the observed feed consumption of a laying hen and its consumption as predicted from a model with metabolic body weight, egg mass production, and body weight gain as independent variables. The RFC was found to be highly heritable in all periods. The heritability of RFC accumulated over the whole laying period (RFC-T) was estimated as . 42 to . 62. For each time segment between 32 and 56 wk of age, genetic correlations between RFC and RFC-T were estimated to be larger than . 91. The genetic sources causing variation in RFC during the first part of lay seem to differ from those causing variation later on, and to be of less importance during the rest of the laying period. It was concluded that RFC shows a considerable systematic and permanent additive genetic variance, and that RFC measurements for selection can be limited to one to three time segments between 32 and 56 wk. Furthermore, less environmental variance and therefore higher heritabilities and genetic correlations seemed to exist for birds fed the low energy diet in comparison with those fed the commercial diet. No clear differences could be found between genetic and phenotypic correlation estimates of RFC with feed consumption, metabolic body weight, egg mass production, and body weight gain.