Miracle-dz/UniFAR-FTUs huggingface dataset:
Leachate From Expanded Polystyrene Cups Is Toxic to Aquatic Invertebrates (Ceriodaphnia dubia)

Expanded polystyrene (EPS) products and their associated chemicals (e.g., styrenes) are widespread in the marine environment. As a consequence, bans on their use for single-use packaging materials are being proposed in several municipalities. To better understand how science can inform decision-making, we looked at the available scientific literature about contamination and effects and conducted experiments to measure chemical leachate from polystyrene products and toxicity from the leachate. We conducted leaching experiments with common food matrices (water, soup broth, gravy, black coffee and coffee with cream and sugar) at relevant temperatures (70oC and 95oC) that are consumed in or with several polystyrene products (coffee cup lids, polystyrene stir sticks, polystyrene spoons, EPS cups, EPS bowls and EPS takeout containers). We analyzed each sample for styrene, ethylbenzene, toluene, benzene, meta- and para- xylene, isopropylbenzene, and isopropyltoluene – chemicals associated with polystyrene products. To determine whether the leachates are toxic, we conducted chronic toxicity tests, measuring survival and reproductive output in Ceriodaphnia dubia. Toxicity tests included nine treatments: seven concentrations of ethylbenzene, EPS cup leachate and a negative control. Overall, we found that temperature has a significant effect on leaching. We only detected leachates in trials conducted at higher temperature – 95oC. Ethylbenzene was the only target analyte with final concentrations above the method limit of detection, and was present in the greatest concentrations in EPS and with soup broth. Measurable concentrations of ethylbenzene in the leachate ranged from 1.3 to 3.4 µg/L. In toxicity tests, the calculated LC50 for ethylbenzene was 14 mg/L and the calculated LC20 was 210 µg/L. For the treatment exposed to the EPS cup leachate, mortality was 40% - four times greater than the negative control. Finally, there was no significant difference (p = 0.17) between reproductive output for any treatment with ethylbenzene, but there was a significant reduction (p = 0.01) in reproductive output for the treatment exposed to the EPS leachate compared to the negative control. Thus, although the target analyte ethylbenzene was not toxic at concentrations detected in the leachate, significant adverse effects were detected in the whole EPS cup leachate sample.
Retracted: Is immunosuppression, induced by neonatal thymectomy, compatible with poor reproductive performance in adult male rats?

With increasing knowledge that the immune system has a major impact on reproductive ‎health, the potential for cells arising in organs such as the thymus to alleviate oxidative stress ‎has been revealed. This study addresses the impact of neonatal thymectomy on male ‎reproductive function in pubertal and adult animals. Neonatal Sprague Dawley rats were allotted to four treatments consisting of fully thymectomized, partially thymectomized, intact, and sham‐operated rats. Half of the rats in each treatment were sacrificed at 40 and the other half at 80 days of age. Testicular volume, ventral prostate and spleen weight, several sperm attributes (concentration, motility, livability, membrane integrity, sperm penetration into mucus, total antioxidant capacity, mitochondrial dehydrogenase activity), plasma superoxide dismutase, glutathione, and testosterone level as well as fertility decreased in thymectomized rats. Adrenal gland weight, sperm malondialdehyde level, indices of oxidative stress, sperm abnormality, testicular and sperm lipid peroxidation, protein carbonylation, and sperm reactive oxygen species generation increased in thymectomized rats. In thymectomized rats, the testes contained high levels of malondialdehyde but low levels of glutathione and ferric‐reducing antioxidant power. Epididymal sperm reactive oxygen species, blood lipid peroxidation, and oxidative stress indices ‎‎in blood and spermatozoa were highest in fully thymectomized, intermediate ‎in partially thymectomized, and lowest in both pubertal and mature control rats. Blood levels of superoxide dismutase, lipid peroxidation indices, and ‎testosterone, and mitochondrial adenosine triphosphate and ‎dehydrogenase activities in epididymal spermatozoa were lowest in fully thymectomized, ‎intermediate in partially thymectomized, and highest in both pubertal and mature control rats. ‎ The data indicated that increased oxidative stress and mitochondrial dysfunction might play a role in the mechanism of immunosuppression‐induced testicular and sperm abnormalities.
Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts

Chitin-binding LysM effectors contribute to virulence of various plant pathogenic fungi that are causal agents of foliar diseases. Here, we report on LysM effectors of the soil-borne fungal vascular wilt pathogen Verticillium dahliae. Comparative genomics revealed three core LysM effectors that are conserved in a collection of V. dahliae strains. Remarkably, and in contrast to the previously studied LysM effectors of other plant pathogens, no expression of core LysM effectors was monitored in planta in a taxonomically diverse panel of host plants. Moreover, targeted deletion of the individual LysM effector genes in V. dahliae strain JR2 did not compromise virulence in infections on Arabidopsis, tomato or Nicotiana benthamiana. Interestingly, an additional lineage-specific LysM effector is encoded in the genome of V. dahliae strain VdLs17 but not in any other V. dahliae strain sequenced to date. Remarkably, this lineage-specific effector is expressed in planta and contributes to virulence of V. dahliae strain VdLs17 on tomato, but not on Arabidopsis or on N. benthamiana. Functional analysis revealed that this LysM effector binds chitin, is able to suppress chitin-induced immune responses, and protects fungal hyphae against hydrolysis by plant hydrolytic enzymes. Thus, in contrast to the core LysM effectors of V. dahliae, this lineage-specific LysM effector of strain VdLs17 contributes to virulence in planta.
Establishment of the Reference Intervals of Lymphocyte Function in Healthy Adults Based on IFN-γ Secretion Assay upon Phorbol-12-Myristate-13-Acetate/Ionomycin Stimulation

The function of lymphocytes is the key to reflect the immune status of hosts. Evaluation of lymphocyte function is a useful tool to monitor the effect of immunosuppressive treatment and predict the prognosis of immune-mediated diseases (e.g., cancer, autoimmune diseases, and infectious diseases). As the lymphocytes have various activities, such as activation, cytotoxicity, and cytokine secretion, it is a challenge to evaluate the function of lymphocytes in clinical practice and the reference intervals (RIs) of lymphocyte function are rarely reported. The present study showed that the secretion of IFN-γ was well correlated with the activation, chemotaxis, and cytotoxicity of CD4+, CD8+ T cells, and NK cells, which suggests that IFN-γ production can be used as a symbol of lymphocyte function. We therefore created a simple method to detect the function of CD4+, CD8+ T cells, and NK cells simultaneously according to IFN-γ secretion by using whole blood instead of peripheral blood mononuclear cells. We further established the RIs of lymphocyte function (CD4+ T cells: 15.31–34.98%; CD8+ T cells: 26.11–66.59%; NK cells: 39.43–70.79%) in healthy adults. This method showed good reproducibility for the evaluation of lymphocyte function. The established RIs were suitable for use in other centers based on the validation data. We also validated the RIs in individuals with different immune status, and the results showed that kidney transplant recipients and infants (0–1 year) had a decreased lymphocyte function, whereas T cells in systemic lupus erythematosus patients exhibited an opposite trend. Overall, we have successfully established the RIs of lymphocyte function in healthy adults in a simple way, which might be of important clinical value in the diagnosis, monitoring, and prognosis of immune-related diseases.
The road to opportunities: landscape change promotes body-size divergence in a highly mobile species

Abstract Landscape change provides a suitable framework for investigating population-level responses to novel ecological pressures. However, relatively little attention has been paid to examine the potential influence of landscape change on the geographic scale of population differentiation. Here, we tested for morphological differentiation of red-necked nightjars Caprimulgus ruficollis breeding in a managed property and a natural reserve situated less than 10 km apart. At both sites, we also estimated site fidelity over 5 years and quantified the potential foraging opportunities for nightjars. Breeding birds in the managed habitat were significantly larger in size—as indexed by keel length—than those in the natural one. However, there were no significant differences in wing or tail length. Immigration from neighboring areas was almost negligible and, furthermore, no individual (out of 1130 captures overall) exchanged habitats between years, indicating strong site fidelity. Food supply for nightjars was equally abundant in both habitats, but the availability of foraging sites was remarkably higher in the managed property. As a result, nightjars—particularly fledglings—in the latter habitat benefited from increased foraging opportunities in relation to those in the natural site. It seems likely that the fine-scale variation in nightjar morphology reflects a phenotypic response to unequal local conditions, since non-random dispersal or differential mortality had been determined not to be influential. High site fidelity appears to contribute to the maintenance of body-size differences between the two habitats. Results from this nightjar population highlight the potential of human-induced landscape change to promote population-level responses at exceedingly small geographic scales.
A Mechanistic Overview of Triptolide and Celastrol, Natural Products from Tripterygium wilfordii Hook F

Triptolide and celastrol are predominantly active natural products isolated from the medicinal plant Tripterygium wilfordii Hook F. These compounds exhibit similar pharmacological activities, including anti-cancer, anti-inflammation, anti-obesity, and anti-diabetic activities. Triptolide and celastrol also provide neuroprotection and prevent cardiovascular and metabolic diseases. However, toxicity restricts the further development of triptolide and celastrol. In this review, we comprehensively review therapeutic targets and mechanisms of action, and translational study of triptolide and celastrol. We systemically discuss the structure-activity-relationship of triptolide, celastrol, and their derivatives. Furthermore, we propose the use of structural derivatives, targeted therapy, and combination treatment as possible solutions to reduce toxicity and increase therapeutic window of these potent natural products from T. wilfordii Hook F.
Modeling conservative updates in multi-hash approximate count sketches

Multi-hash-based count sketches are fast and memory efficient probabilistic data structures that are widely used in scalable online traffic monitoring applications. Their accuracy significantly improves with an optimization, called conservative update, which is especially effective when the aim is to discriminate a relatively small number of heavy hitters in a traffic stream consisting of an extremely large number of flows. Despite its widespread application, a thorough understanding of the conservative update operation has lagged behind, perhaps because of the significant modeling complexity involved. In this work we attempt to fill this gap. Our proposed modeling approach builds on a practically important empirical finding: simulation results (as well as experimental ones over real traffic traces) obtained for skewed load scenarios exhibit a sharp waterfall-type behaviour. That is, the approximate count provided by the sketch response remains accurate until an “error floor” is reached. Flows below this error flow level are on average approximated by the same error floor count value, irrespective of their exact count. The error floor itself appears to be maximal in the case of uniform load. Leveraging the simplifications made possible when the load is uniform, we derive an analytic model capable of accurately predicting the transient growth behavior of the (tightly correlated) counters deployed in the data structure and obtain an upper bound on the error floor level.
Highly parallel direct RNA sequencing on an array of nanopores

Sequencing the RNA in a biological sample can unlock a wealth of information, including the identity of bacteria and viruses, the nuances of alternative splicing or the transcriptional state of organisms. However, current methods have limitations due to short read lengths and reverse transcription or amplification biases. Here we demonstrate nanopore direct RNA-seq, a highly parallel, real-time, single-molecule method that circumvents reverse transcription or amplification steps. This method yields full-length, strand-specific RNA sequences and enables the direct detection of nucleotide analogs in RNA.
The determinants of antimicrobial prescribing among hospital doctors in England: a framework to inform tailored stewardship interventions.

AIM Little is known about the determinants of antimicrobial prescribing behaviour (APB), how they vary between hospital prescribers or the mechanism by which interventions are effective. Yet, interventions based on a sound theoretical understanding of APB are more likely to be successful in changing outcomes. This study sought to quantify the potential determinants of APB among hospital doctors in south-west England. METHODS This multicentre, quantitative study employed a closed answer questionnaire to garner hospital doctors' views on factors influencing their APB. Underlying constructs within the data were identified using exploratory factor analysis and subsequent pairwise comparisons assessed for variance between groups of prescribers. RESULTS The questionnaire was completed by 301 doctors across four centres (response rate ≥ 74%) and three key factors were identified: autonomy, guidelines adherence and antibiotic awareness. The internal consistency for the questionnaire scale and for each factor subscale was good (α ≥ 0.7). Subgroup analysis identified significant differences between groups of prescribers: autonomy scores increased with grade until at the specialist trainee level (P ≤ 0.009), foundation doctors scored higher for guidelines adherence than consultants (P = 0.004) and specialist trainees (P = 0.003) and United Kingdom trained doctors scored higher than those trained abroad for antibiotic awareness (P < 0.0005). Scores did not vary significantly between doctors from different centres. CONCLUSION Autonomy, guidelines adherence and antibiotic awareness were identified as important factors relevant to APB, which vary with experience and training. A theoretical framework is offered to facilitate development of more effective, tailored interventions to change APBs.
Communicating about obesity and weight-related topics with children with a physical disability and their families: spina bifida as an example

Abstract Purpose: The purpose of this study was to explore the experiences of children with spina bifida (SB), their families and healthcare professionals (HCPs) when discussing weight-related topics. Method: In-depth qualitative interviews were conducted with HCPs from Canadian outpatient SB clinics (n = 13), children aged 6–18 years with SB (n = 17) and their parents (n = 20). Data were analyzed using a phenomenological approach within an interpretative paradigm. Results: Many HCPs were not confident talking about weight, concerned that they would damage relationships with children and families. Parents wanted routine weight surveillance, but were worried about their children’s self-esteem if their weight was discussed. They wanted HCPs to acknowledge the challenges of weight management in children with a physical disability and provide specialized solutions. Children wanted a positively framed and tailored approach to weight discussions, although this had generally not been their experience. Conclusions: Stakeholders describe therapeutic relationships that are currently disconnected around the issue of weight and obesity. However, children, parents and HCPs all believed that discussing this topic was critical. Positively framed, strengths-based and tailored approaches to weight-related discussions are warranted. Implications for Rehabilitation Rates of overweight and obesity in children and youth with physical disabilities are substantially higher than their typically developing peers. Healthcare professionals, children with physical disabilities and families often find weight-related discussions challenging and disconnected. Weight-related discussions should be tailored to the child and family’s circumstances and priorities. Positively framed and strengths-based approaches to weight-related discussions are warranted.
The epithelial-to-mesenchymal transition activator ZEB1 initiates a prometastatic competing endogenous RNA network.

Epithelial tumor cells undergo epithelial-to-mesenchymal transition (EMT) to gain metastatic activity. Competing endogenous RNAs (ceRNAs) have binding sites for a common set of microRNAs (miRs) and regulate each other’s expression by sponging miRs. Here, we address whether ceRNAs govern metastasis driven by the EMT-activating transcription factor ZEB1. High miR-181b levels were correlated with an improved prognosis in human lung adenocarcinomas, and metastatic tumor cell lines derived from a murine lung adenocarcinoma model in which metastasis is ZEB1-driven were enriched in miR-181b targets. ZEB1 relieved a strong basal repression of α 1 integrin (ITGA1) mRNA, which in turn upregulated adenylyl cyclase 9 mRNA (ADCY9) by sponging miR181b. Ectopic expression of the ITGA1 3′-untranslated region reversed miR-181b–mediated metastasis suppression and increased the levels of adenylyl cyclase 9 protein (AC9), which promoted tumor cell migration and metastasis. In human lung adenocarcinomas, ITGA1 and ADCY9 levels were positively correlated, and an AC9-activated transcriptomic signature had poor-prognostic value. Thus, ZEB1 initiates a miR-181b–regulated ceRNA network to drive metastasis. metastasis is ZEB1-driven were enriched in miR-181b targets. ZEB1 relieved a strong basal repression of α 1 integrin (ITGA1) mRNA, which in turn upregulated adenylyl cyclase 9 mRNA (ADCY9) by sponging miR181b. Ectopic expression of the ITGA1 3 ′ -untranslated region reversed miR-181b–mediated metastasis suppression and increased the levels of adenylyl cyclase 9 protein (AC9), which promoted tumor cell migration and metastasis. In human lung adenocarcinomas, ITGA1 and ADCY9 levels were positively correlated, and an AC9-activated transcriptomic signature had poor-prognostic value. Thus, ZEB1 initiates a miR-181b–regulated ceRNA network to drive metastasis. which identified genes that at least and were increased at least 1.5-metastatic KP cell lines undergo a reversible EMT in response to extracellular cues and demonstrate migratory and invasive activities that are driven by high ZEB1 expression levels, whereas poorly metastatic KP cells do not exhibit such differentiation plasticity and remain in an epithelial state (18). The findings presented here support a model in which ZEB1 increases metastasis through a miR-181b–regulated ceRNA network involving α 1 integrin (ITGA1) and adenylyl cyclase 9 (ADCY9). 120); thyroid carcinoma (THCA, n = 503); uterine carcinosarcoma (UCS, n = 57); and uterine corpus endometrial carcinoma (UCEC, n = 545). P less than 0.05 was considered statistically significant. To analyze a compendium of human lung adenocarcinoma cohorts (48) for the presence or absence of the ADCY9-derived expression signature, we used a t score described elsewhere (29).
Unsupervised consensus cluster analysis of [18F]-fluoroethyl-L-tyrosine positron emission tomography identified textural features for the diagnosis of pseudoprogression in high-grade glioma

Rationale Timely detection of pseudoprogression (PSP) is crucial for the management of patients with high-grade glioma (HGG) but remains difficult. Textural features of O-(2-[18F]fluoroethyl)-L-tyrosine positron emission tomography (FET-PET) mirror tumor uptake heterogeneity; some of them may be associated with tumor progression. Methods Fourteen patients with HGG and suspected of PSP underwent FET-PET imaging. A set of 19 conventional and textural FET-PET features were evaluated and subjected to unsupervised consensus clustering. The final diagnosis of true progression vs. PSP was based on follow-up MRI using RANO criteria. Results Three robust clusters have been identified based on 10 predominantly textural FET-PET features. None of the patients with PSP fell into cluster 2, which was associated with high values for textural FET-PET markers of uptake heterogeneity. Three out of 4 patients with PSP were assigned to cluster 3 that was largely associated with low values of textural FET-PET features. By comparison, tumor-to-normal brain ratio (TNRmax) at the optimal cutoff 2.1 was less predictive of PSP (negative predictive value 57% for detecting true progression, p=0.07 vs. 75% with cluster 3, p=0.04). Principal Conclusions Clustering based on textural O-(2-[18F]fluoroethyl)-L-tyrosine PET features may provide valuable information in assessing the elusive phenomenon of pseudoprogression.
Frequency and intensity of facilitation reveal opposing patterns along a stress gradient

Abstract Disentangling the different processes structuring ecological communities is a long‐standing challenge. In species‐rich ecosystems, most emphasis has so far been given to environmental filtering and competition processes, while facilitative interactions between species remain insufficiently studied. Here, we propose an analysis framework that not only allows for identifying pairs of facilitating and facilitated species, but also estimates the strength of facilitation and its variation along environmental gradients. Our framework combines the analysis of both co‐occurrence and co‐abundance patterns using a moving window approach along environmental gradients to control for potentially confounding effects of environmental filtering in the co‐abundance analysis. We first validate our new approach against community assembly simulations, and exemplify its potential on a large 1,134 plant community plots dataset. Our results generally show that facilitation intensity was strongest under cold stress, whereas the proportion of facilitating and facilitated species was higher under drought stress. Moreover, the functional distance between individual facilitated species and their facilitating species significantly changed along the temperature–moisture gradient, and seemed to influence facilitation intensity, although no general positive or general negative trend was discernible among species. The main advantages of our robust framework are as follows: It enables detecting facilitating and facilitated species in species‐rich systems, and it allows identifying the directionality and intensity of facilitation in species pairs as well as its variation across long environmental gradients. It thus opens numerous opportunities for incorporating functional (and phylogenetic) information in the analysis of facilitation patterns. Our case study indicated high complexity in facilitative interactions across the stress gradient and revealed new evidence that facilitation, similarly to competition, can operate between functionally similar and dissimilar species. Extending the analyses to other taxa and ecosystems will foster our understanding how complex interspecific interactions promote biodiversity.