Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperature stress induces mites to help their carrion beetle hosts by eliminating rival blowflies

Ecological conditions are known to change the expression of mutualisms though the causal agents driving such changes remain poorly understood. Here we show that temperature stress modulates the harm threatened by a common enemy, and thereby induces a phoretic mite to become a protective mutualist. Our experiments focus on the interactions between the burying beetle Nicrophorus vespilloides, an associated mite species Poecilochirus carabi and their common enemy, blowflies, when all three species reproduce on the same small vertebrate carrion. We show that mites compete with beetle larvae for food in the absence of blowflies, and reduce beetle reproductive success. However, when blowflies breed on the carrion too, mites enhance beetle reproductive success by eating blowfly eggs. High densities of mites are especially effective at promoting beetle reproductive success at higher and lower natural ranges in temperature, when blowfly larvae are more potent rivals for the limited resources on the carcass.
The impact of classroom seating location and computer use on student academic performance

A student’s ability to learn effectively in a classroom setting is subject to many factors. While some factors are difficult to regulate, this study explores two factors that a student, or instructor, has full control over, namely 1) seating position, and 2) computer usage. Both factors have been studied considerably with regard to their effects on student performance, and the results indicate that sitting further from the instructor, or using a computer in the classroom, are related to a decline in grade performance. However, it is unclear if the choice of where to sit and whether or not to use a computer in class are mediated by the same cognitive process. If they are the same, then we would expect to see an interaction between the factors, such that, for example, computer usage would most negatively impact the grades of students who sit near the back of a class. This study aims to answer this question by looking at the individual and combined effects of seating position and computer usage on classroom performance. We sampled 1364 students, collecting nearly 3000 total responses across 5 different introductory psychology courses with 4 different instructors on 3 separate occasions. In agreement with previous research, we found that sitting further from the instructor negatively impacted students' grades (0.75 percentage points/row), and using a computer in class negatively impacted grades (by 3.88 percentage points). Our novel finding is that these deleterious effects combined in an additive manner, such that using a computer had the same harmful effect on grade performance regardless of whether the student sat at the front or back of the classroom.
Effects of shelterwood management on flower-visiting insects and their floral resources

Habitat alteration can affect pollinating-insect community structure, decreasing the efficiency of pollinators on which many agricultural and natural ecosystems rely. Within the Tenderfoot Creek Experimental Forest (TCEF), located in the Little Belt Mountains of Central Montana, two different types of silvicultural techniques, even and group shelterwood, were applied to alter the natural habitats within the lodgepole pine (Pinus contorta) forests. Following logging, surveys of the flower-visiting insects and their floral resources were conducted within four treatments, even and group shelterwood, unlogged and meadow. In addition, individual insects were collected and the pollen removed from their bodies was counted and identified. The density of floral resources and the abundance of flower-visiting insects, as well as several diversity measures of both, were calculated, to examine the response of insects and plants to logging. Spearman rank correlations were used to examine changes over the sample years. Non-metric multi-dimensional scaling (NMS) was used to create ordinations of the treatments while multiple response permutation procedure (MRPP) tested the hypothesis of no difference between treatments with respect to either floral resources or flowervisiting insects. Correlations between the abundances of floral resources and flowervisiting insect taxa were also conducted using Mantel tests. Kruskal-Wallis tests were used to test the hypothesis of no difference between insect taxa with respect to pollen quantity and richness. NMS was used to create ordinations of species within families with respect to types of pollen and quantity carried. Changes in density, abundance, and diversity between years were detected as were differences among treatments. Associations between floral resources and flower-visiting insects were detected. Differences among insect species with respect to pollen type and quantity were detected. Overall, the alteration of the original forest habitats changed the community structure of not only the flower-visiting insects but also their floral resources in the two shelterwood treatments.
Activation of NF‐kB1 by OX40 contributes to antigen‐driven T cell expansion and survival

The costimulatory molecule OX40 (CD134) is strongly required in many instances for effective T cell‐mediated immunity, controlling proliferation and survival of T cells after encountering specific antigen. We previously found that the functional targets of OX40 are survivin and aurora B that regulate proliferation, and Bcl‐2 anti‐apoptotic family members that regulate survival. However, the intracellular pathways from OX40 that mediate these effects are unclear. Here, we show that OX40 signaling can target the canonical NF‐kB (NF‐kB1) pathway in peripheral antigen‐responding CD4 T cells. Phosphorylation of IkBalpha which leads to NF‐kB1 (p50)/RelA nuclear translocation is impaired in OX40‐deficient T cells. Retroviral transduction of active IKKbeta that constitutively activates NF‐kB1 rescues the poor proliferation and survival of OX40‐deficient T cells, directly correlating with increased expression and activity of survivin, aurora B, and Bcl‐2 family members. Moreover, active IKKbeta expression alone is sufficient to restore the defective proliferation and survival of OX40‐deficient T cells in vivo when responding to antigen. Thus, OX40 signals regulate T cell number and viability through the NF‐kB1 pathway that controls expression and activity of intracellular targets for proliferation and survival.
Capturing Entity Hierarchy in Data-to-Text Generative Models

We aim at generating summary from structured data (i.e. tables, entity-relation triplets, .). Most previous approaches relies on an encoder-decoder architecture in which data are linearized into a sequence of elements. In contrast, we propose to take into account entities forming the data structure in a hierarchical model. More-over, we introduce the Transformer encoder in data-to-text models to ensure robust encoding of each element/entities in comparison to all others, no matter their initial positioning. Our model is evaluated on the RotoWire benchmark (statistical tables of NBA basketball games). This paper has been accepted at ECIR 2020.
IDENTIFICATION OF OESTROGEN-RESPONSIVE TRANSCRIPTS IN POTAMOPYRGUS ANTIPODARUM

The freshwater caenogastropod Potamopyrgus antipodarum is a promising test species for partial lifecycle toxicity testing and also for studies of endocrine disruptors. However, endocrine signalling pathways and the genes/transcripts involved are barely identified and characterized in this snail. We therefore performed whole transcriptome sequencing (454 pyrosequencing), selected transcripts that are known to be hormone-responsive in vertebrates and determined their expression via quantitative real-time PCR after 24 h exposure to the oestrogens 17a-ethinyloestradiol (EE2) and 17b-oestradiol (E2). Examined mRNAs were: nuclear receptors [oestrogen receptor (ER), chicken ovalbumin upstream promoter-transcription factor (COUP-TF), ecdysone-induced protein (E75)], repressors of oestrogen-induced activity [prohibitin-2 (PHB-2), striatin (STRN)] and the egg yolk precursor vitellogenin (VTG). Significantly increased expression by EE2 and E2 treatment was detected for ER and VTG. E2 induced significant upregulation of E75, PHB-2 and STRN, while EE2 did not. COUP-TF expression was unaffected by EE2 or by E2. Variations between replicates were higher in snails exposed to EE2 than to E2. The identification of these oestrogen-responsive transcripts contributes to a better characterization of the endocrine system of P. antipodarum and provides possible biomarkers for the detection of endocrine disruption.
Lack of exotic hydrilla infestation effects on plant, fish and aquatic bird community measures

Abstract The invasion of hydrilla into North American lakes has provoked concern over loss of native flora and fauna and resulted in costly suppression efforts. We used two data sets to determine if common measures of ecosystem health; abundance, species richness, diversity and evenness, were affected by the presence of hydrilla. Data Set 1 consisted of 27 Florida lakes, 11 of which had hydrilla present for approximately 4–8 years in varying abundances, and 16 did not have hydrilla. Given the number of lakes, each was sampled only once in the summers of 1986–1990 for community measures of aquatic plants, birds, and fish. Data Set 2 consisted of 12 lakes, six with abundant hydrilla for over 23 years and six without hydrilla. These lakes were sampled every year in the summer (with a few exceptions due to weather conditions) between 1999 and 2006 for community measures of aquatic plants and fish. The results for both data sets show that presence of hydrilla had no statistically significant effect (P > 0.05) on all community measures tested (i.e., richness, diversity, abundance). Our conclusions support the hypothesis that hydrilla in these Florida lakes has occupied a mostly vacant ecological niche and has not affected the occurrence or relative composition of native species of aquatic plants, birds, and fish. Because pond experiments have found negative effects of hydrilla, further focused research is needed to assist management decisions when considerable resources are to be spent each year on hydrilla suppression.
ACE2 isoform diversity predicts the host susceptibility of SARS‐CoV‐2

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) causes the ongoing coronavirus disease 2019 (COVID‐19) pandemic. Angiotensin‐converting enzyme 2 (ACE2) is the functional receptor for SARS‐CoV‐2. In our current study, we found that two types of deficient ACE2 isoforms from different mammals compete with full‐length ACE2 for association with S protein. One type of ACE2 is a natural soluble isoform, the other type of ACE2 only associates with one loop of the receptor‐binding domain (RBD) of the SARS‐CoV‐2 S protein. Mammals with either type of ACE2 will be deficient in support of SARS‐CoV‐2 entry. By combining S recognition and isoform analysis of ACE2, we predict that felids, mustelids, hamsters, and sheep are susceptible to SARS‐CoV‐2, while canids, swines, cattle, and goats are not permissive for SARS‐CoV‐2. Thus, the differential susceptibilities of mammals with SARS‐CoV‐2 infection could be partially explained by the ACE2 isoform diversity. Our findings will shed important light on predicting the host range of other zoonotic viruses.
The Current Trends of Biosensors in Tissue Engineering

Biosensors constitute selective, sensitive, and rapid tools for disease diagnosis in tissue engineering applications. Compared to standard enzyme-linked immunosorbent assay (ELISA) analytical technology, biosensors provide a strategy to real-time and on-site monitor micro biophysiological signals via a combination of biological, chemical, and physical technologies. This review summarizes the recent and significant advances made in various biosensor technologies for different applications of biological and biomedical interest, especially on tissue engineering applications. Different fabrication techniques utilized for tissue engineering purposes, such as computer numeric control (CNC), photolithographic, casting, and 3D printing technologies are also discussed. Key developments in the cell/tissue-based biosensors, biomolecular sensing strategies, and the expansion of several biochip approaches such as organs-on-chips, paper based-biochips, and flexible biosensors are available. Cell polarity and cell behaviors such as proliferation, differentiation, stimulation response, and metabolism detection are included. Biosensors for diagnosing tissue disease modes such as brain, heart, lung, and liver systems and for bioimaging are discussed. Finally, we discuss the challenges faced by current biosensing techniques and highlight future prospects of biosensors for tissue engineering applications.
Smarca5 mediated epigenetic programming facilitates fetal HSPC development in vertebrates.

Nascent HSPCs acquire definitive hematopoietic characteristics only when they develop into fetal HSPCs; however, the mechanisms underlying fetal HSPC development are poorly understood. Here, we profiled the chromatin accessibility and transcriptional features of zebrafish nascent- and fetal HSPCs using ATAC-seq and RNA-seq and revealed dynamic changes during HSPC transition. Functional assays demonstrated that chromatin remodeler-mediated epigenetic programming facilitates fetal HSPC development in vertebrates. Systematical screening of chromatin remodeler-related genes identified that smarca5 is responsible for the maintenance of chromatin accessibility at promoters of hematopoiesis-related genes in fetal HSPCs. Mechanistically, Smarca5 interacts with Nucleolin to promote chromatin remodeling, thereby facilitating genomic binding of transcription factors to regulate expression of hematopoietic regulators such as bcl11ab. Our results unravel a new role of epigenetic regulation and reveal that Smarca5-mediated epigenetic programming is responsible for fetal HSPC development, which will provide new insights into the generation of functional HSPCs both in vivo and in vitro.
Living-Donor Uterus Transplantation: Pre-, Intra-, and Postoperative Parameters Relevant to Surgical Success, Pregnancy, and Obstetrics with Live Births

Uterus transplantation (UTx) can provide a route to motherhood for women with Mayer–Rokitansky–Küster–Hauser syndrome (MRKHS), a congenital disorder characterized by uterovaginal aplasia, but with functional ovaries. Based on our four successful living-donor transplantations and two resulting births, this analysis presents parameters relevant to standardizing recipient/donor selection, UTx surgery, and postoperative treatment, and their implementation in routine settings. We descriptively analyzed prospectively collected observational data from our four uterus recipients, all with MRKHS, their living donors, and the two newborns born to two recipients, including 1-year postnatal follow-ups. Analysis included only living-donor/recipient pairs with completed donor/recipient surgery. Two recipients, both requiring ovarian restimulation under immunosuppression after missed pregnancy loss in one case and no pregnancy in the other, each delivered a healthy boy by cesarean section. We conclude that parameters crucial to successful transplantation, pregnancy, and childbirth include careful selection of donor/recipient pairs, donor organ quality, meticulous surgical technique, a multidisciplinary team approach, and comprehensive follow-up. Surgery duration and blood vessel selection await further optimization, as do the choice and duration of immunosuppression, which are crucial to timing the first embryo transfer. Data need to be collected in an international registry due to the low prevalence of MRKHS.
Lysosomal accumulation of the hormone-receptor complex during receptor- mediated endocytosis of human choriogonadotropin

The experiments presented herein were designed to determine the fate of the human choriogonadotropin (hCG) receptor during endocytosis of the receptor-bound hCG. Using several biochemical approaches, it is shown that the receptor is internalized together with the hormone into endocytic vesicles and transferred to lysosomes without ligand dissociation. Once delivered to the lysosomes, the hCG-receptor complex dissociates, and the free hormone is degraded. This pathway appears to prevent receptor recycling and probably promotes receptor degradation.
Soundscape of green turtle foraging habitats in Fiji, South Pacific

The soundscape features of the marine environment provide crucial information about ecosystem health for many species, and they are defined by the local biological, geophysical, and anthropogenic components. In this study, we investigated the soundscape at green turtle neritic foraging habitats in Fiji, South Pacific, with the aims of characterizing the contribution of each component and of comparing the levels of acoustic pressure among sites with different abundances of sea turtles. Four sites were selected at two islands, and one hydrophone was deployed at each site. Generalized additive models highlighted that sound pressure levels (SPLs) at low frequencies (125–250 Hz) were especially affected by wind conditions, while at higher frequencies (>250 Hz) SPLs were mostly influenced by fish and crustacean acoustic activity. Higher abundances of green turtles were found at sites with the highest levels of SPLs and the highest number of acoustic emissions by fishes and crustaceans but were not related to maximum seagrass and macroalgae coverage, or the highest number of fish. The selected coastal habitats have negligible anthropogenic noise, thus this study informs physiological and behavioral studies of the acoustic signatures that sea turtles might target and provides a baseline against which potential impact of soundscape changes on sea turtle spatial abundance and distribution can be evaluated.
Sites of contamination and numbers of Erwinia carotovora present in stored seed potato stocks in Scotland

SUMMARY Forty-eight bulk and crate stored commercial seed potato stocks from the east of Scotland were examined for contamination by Erwinia carotovora in 1967 and 1968. Both E. carotovora var. carotovora and E. carotovora var. atroseptica were present, the latter, the blackleg pathogen, being detected four times more frequently. Most contamination was located on the tuber surface and in the lenticels; it was rare in the vascular ring and the organism was never detected in the cortex. The level of contamination of lenticels was only slightly affected after winter storage, which, however, substantially reduced surface contamination. More than 103 cells were detected on the surface of tubers in over half the stocks and in half the stocks each lenticel sampled contained more than 102 bacteria.
Immunothrombotic Dysregulation in COVID-19 Pneumonia Is Associated With Respiratory Failure and Coagulopathy

Supplemental Digital Content is available in the text. Background: Severe acute respiratory syndrome corona virus 2 infection causes severe pneumonia (coronavirus disease 2019 [COVID-19]), but the mechanisms of subsequent respiratory failure and complicating renal and myocardial involvement are poorly understood. In addition, a systemic prothrombotic phenotype has been reported in patients with COVID-19. Methods: A total of 62 subjects were included in our study (n=38 patients with reverse transcriptase polymerase chain reaction–confirmed COVID-19 and n=24 non–COVID-19 controls). We performed histopathologic assessment of autopsy cases, surface marker–based phenotyping of neutrophils and platelets, and functional assays for platelet, neutrophil functions, and coagulation tests, as well. Results: We provide evidence that organ involvement and prothrombotic features in COVID-19 are linked by immunothrombosis. We show that, in COVID-19, inflammatory microvascular thrombi are present in the lung, kidney, and heart, containing neutrophil extracellular traps associated with platelets and fibrin. Patients with COVID-19 also present with neutrophil-platelet aggregates and a distinct neutrophil and platelet activation pattern in blood, which changes with disease severity. Whereas cases of intermediate severity show an exhausted platelet and hyporeactive neutrophil phenotype, patients severely affected with COVID-19 are characterized by excessive platelet and neutrophil activation in comparison with healthy controls and non–COVID-19 pneumonia. Dysregulated immunothrombosis in severe acute respiratory syndrome corona virus 2 pneumonia is linked to both acute respiratory distress syndrome and systemic hypercoagulability. Conclusions: Taken together, our data point to immunothrombotic dysregulation as a key marker of disease severity in COVID-19. Further work is necessary to determine the role of immunothrombosis in COVID-19.
The effect of hydration status on plasma FGF21 concentrations in humans: A subanalysis of a randomised crossover trial

Aim Fibroblast growth factor 21 (FGF21) has recently been implicated in thirst in rodent models. The mechanisms for this are currently uncertain, and it is unclear whether hydration status can alter FGF21 concentrations, potentially providing an additional mechanism by which hypohydration induces thirst. The aim of this study is therefore to understand whether hydration status can alter circulating FGF21 in humans. Methods Using a heat tent and fluid restriction, we induced hypohydration (1.9% body mass loss) in 16 healthy participants (n = 8 men), and compared their glycaemic regulation to a rehydration protocol (heat tent and fluid replacement) in a randomised crossover design. Results After the hypohydration procedure, urine specific gravity, urine and serum osmolality, and plasma copeptin (as a marker for arginine vasopressin) increased as expected, with no change after the rehydration protocol. In the fasted state, the median paired difference in plasma FGF21 concentrations from the rehydrated to hypohydrated trial arm was -37 (interquartile range -125, 10) pg∙mL-1(P = 0.278), with average concentrations being 458 ± 462 pg∙mL-1 after hypohydration and 467 ± 438 pg∙mL-1 after rehydration; mean difference -9 ± 173 pg∙mL-1. Conclusion To our knowledge, these are the first causal data in humans investigating hydration and FGF21, demonstrating that an acute bout of hypohydration does not impact fasted plasma FGF21 concentrations. These data may suggest that whilst previous research has found FGF21 administration can induce thirst and drinking behaviours, a physiological state implicated in increased thirst (hypohydration) does not appear to impact plasma FGF21 concentrations in humans.
Rule Extraction via Dynamic Discretization with an Application to Air Quality Modelling

Association rule extraction is a very well-known and important problem in machine learning, and especially in the sub-ﬁeld of explainable machine learning. Association rules are naturally extracted from data sets with Boolean (or at least categorical) attributes. In order for rule extraction algorithms to be applicable to data sets with numerical attributes as well, data must be suitably discretized, and a great amount of work has been devoted to ﬁnding good discretization algorithms, taking into account that optimal discretization is a NP-hard problem. Motivated by a speciﬁc application, in this paper we provide a novel discretization algorithm deﬁned as an (heuristic) optimization problem and solved by an evolutionary algorithm, and we test its performances against well-known available solutions, proving (experimentally) that we are able to extract more rules in a easier way.