Miracle-dz/UniFAR-FTUs huggingface dataset:
Clarifying the relationship between body size and extinction risk in amphibians by complete mapping of model space

In vertebrates, large body size is often a key diagnostic feature of species threatened with extinction. However, in amphibians the link between body size and extinction risk is highly uncertain, with previous studies suggesting positive, negative, u-shaped, or no relationship. Part of the reason for this uncertainty is “researcher degrees of freedom”: the subjectivity and selectivity in choices associated with model specification. Here I clarify the size – threat association in amphibians using Specification Curve Analysis, an analytical approach from the social sciences that attempts to minimize this problem by complete mapping of model space. I find strong support for prevailing negative associations between body size and threat status, the opposite of patterns typical in other vertebrates. This pattern is largely explained by smaller species having smaller geographic ranges, but smaller amphibian species also appear to lack some of the life-history advantages (e.g. higher reproductive output) that are often assumed to “protect” small species in other taxa. These results highlight the need for a renewed conservation focus on the smallest species of the world’s most threatened class of vertebrates, as aquatic habitats become increasingly degraded by human activity.
Derivation of human extended pluripotent stem cells in feeder-free condition

Human extended pluripotent stem cells (EPSCs), with bidirectional chimeric ability to contribute to both embryonic and extra-embryonic lineages, can be obtained and maintained by converting embryonic stem cells (ESCs) using chemicals. However, the transition system is based on inactivated mouse fibroblast, which greatly hinders the mechanistic studies of extended pluripotency and further applications. Here we reported a Matrigel-based feeder-free method to convert human ESCs and iPSCs into EPSCs and demonstrated the extended pluripotency in terms of molecular features, chimeric ability, and transcriptome. We further improved the protocol by applying chemicals targeting glycolysis and histone methyltransferase. Altogether, our data established a feeder-free system to generate human EPSCs and provided additional insights into the acquisition of extended pluripotency.
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models

Several studies suggested that transcription factor (TF) binding to DNA may be impaired or enhanced by DNA methylation. We present MeDeMo, a toolbox for TF motif analysis that combines information about DNA methylation with models capturing intra-motif dependencies. In a large-scale study using ChIP-seq data for 335 TFs, we identify novel TFs that are affected by DNA methylation. Overall, we find that CpG methylation decreases the likelihood of binding for the majority of TFs. For a considerable subset of TFs, we show that intra-motif dependencies are pivotal for accurately modelling the impact of DNA methylation on TF binding.
HIV-1 gp120 impairs spatial memory through CREB

HIV-associated neurocognitive disorders (HAND) remains an unsolved problem in the clinical management of HIV-1 carriers, because existing anti-retroviral therapy while suppressing viral replication, do not prevent neurocognitive impairment (e.g. spatial memory loss). HIV-1 gp120 protein has been proposed to contribute to HAND because it is shed by infected cells and the use of antibodies revealed its presence in cerebrospinal fluid (CSF) even in the combinatory antiretroviral therapy (cART) era. The cyclic AMP response element-binding protein (CREB) has long been known to be a star player in memory. CREB exerts its effect partially through regulating the genes for peroxisome proliferator-activated receptor gamma coactivator (PGC)-1α and brain-derived neurotrophic factor (BDNF). CREB, PGC-1α, and BDNF levels are low in the brains of patients with neurodegenerative diseases and a dearth of either protein is associated with cognitive decline. We have obtained data showing that gp120 contributes to neurodegeneration by altering CREB phosphorylation on serine residue 133 thus disrupting mitochondrial movement and synaptic plasticity leading to spatial memory loss. Inhibition of CREB function was also associated with a decrease of ATP levels and lower mitochondrial DNA copy numbers. Our data was validated in vitro (primary mouse neurons and neuronal cell line, SH-SY5Y) and in vivo (gp120-tg mice and mice injected with gp120). The negative effect of gp120 was alleviated in cells and animals in the presence of Rolipram. Hence, we conclude that HIV-1 gp120 protein contributes to spatial memory impairment via inhibition of CREB protein activity.
Optimal design of a minimum set of clinical tests for the identification and characterization of Von Willebrand disease

Von Willebrand disease (VWD) is one of the most common bleeding disorders visible in humans, caused by qualitative or quantitative deficiencies of von Willebrand factor (VWF), a multimeric glycoprotein fundamental in the coagulation process. The overall objective of this project is to optimally design a minimal set of basal clinical tests for the identification of the PK model of VWD in order to decrease the time and effort required for disease characterization and diagnosis
Requirements for the containment of COVID-19 disease outbreaks through periodic testing, isolation, and quarantine

We employ individual-based Monte Carlo computer simulations of a stochastic SEIR model variant on a two-dimensional Newman–Watts small-world network to investigate the control of epidemic outbreaks through periodic testing and isolation of infectious individuals, and subsequent quarantine of their immediate contacts. Using disease parameters informed by the COVID-19 pandemic, we investigate the effects of various crucial mitigation features on the epidemic spreading: fraction of the infectious population that is identifiable through the tests; testing frequency; time delay between testing and isolation of positively tested individuals; and the further time delay until quarantining their contacts as well as the quarantine duration. We thus determine the required ranges for these intervention parameters to yield effective control of the disease through both considerable delaying the epidemic peak and massively reducing the total number of sustained infections.
Testing the Role of Δ9-Tetrahydrocannabinol During Adolescence as a Gateway Drug: Behavioural, Brain Imaging and Transcriptomic Studies

Cannabis is widely consumed by adolescents, and is also a potential prior step leading to the use of other drugs later in life (Gateway Hypothesis); however, the evidence for this hypothesis is controversial. This work aimed to increase our understanding of the long-term consequences of adolescent exposure to Δ9-tetrahydrocannabinol (THC) and to test the Gateway Hypothesis, experimentally. We exposed rats of both sexes to THC and studied its effects on reward-related processes, brain morphology (MRI), metabolism (1H-MRS), function (PET) and the transcriptomic profiles of the nucleus accumbens (RNASeq). Lastly, we studied cocaine-induced cellular activation (c-Fos) and cocaine addiction-like behaviours. THC exposure increased Pavlovian to instrumental transfer in males, goal-tracking (regardless of the sex) and impulsivity, but did not affect habit formation. Adolescent THC reduced striatal volume (in females), commissural integrity and ventricular volume. Also, there were lower levels of choline compounds in the cortex of THC-exposed rats and cerebellar hypoactivation in THC-females. THC also modified some of the gene expression programs of the nucleus accumbens, which could contribute to the behavioural features observed. Lastly, THC exposure increased cocaine-induced c-Fos levels in cortical and hypothalamic areas and increased the motivation for cocaine, followed by a higher rebound of use in THC-females after reestablishing low-effort conditions. Critically, acquisition of cocaine self-administration, compulsive seeking, intake under extended access or the incubation of seeking were unaltered. These results suggest that adolescent THC exposure alters psychological and brain development and that the Gateway Hypothesis does not entirely pass the test of preclinical enquiry.
Signatures of Selection in Composite Vrindavani Cattle of India

Vrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle in the 1960s. About 190,000 semen doses of Vrindavani bulls have been distributed to the farmers till date. The animals are under artificial and natural selection for higher milk production and adaptation to the tropical climate, respectively. However, the selection response for production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in the Vrindavani genome. 96 Vrindavani cattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). Vrindavani was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST). Selection of signature identifies 11 common region identified by more than one harbouring genes such as LRP1B, TNNI3K, APOB, CACNA2D1, FAM110B and SPATA17 associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield.
Systematics and biogeography of Spinoctenus, a new genus of wandering spider from Colombia (Ctenidae)

Abstract. Among ctenid spiders, ctenines comprise the most diverse subfamily. In this study, a new genus of Cteninae, Spinoctenus, is proposed to include the type species S. yotoco, sp. nov. Ten new species are also described: S. escalerete, S. pericos, S. eberhardi, S. spinosus, S. stephaniae, S. nambi, S. florezi, S. tequendama, S. chocoensis and S. flammigerus. Results of the parsimony and Bayesian phylogenetic analyses using morphological and behavioural characters indicate the monophyly of this genus, closely related to Phoneutria Perty, 1883 and Ctenus Walckenaer, 1805. This genus can be distinguished from the remaining Ctenidae by three unambiguous synapomorphies: embolus with folded process, tegulum with median process, and RTA curved internally close to the cymbium. A dispersal-vicariance biogeographical analysis of the genus in the Andean and Chocó regions indicates the origin of Spinoctenus in the Western and Central Andean Cordilleras. From this region, three events of dispersal occurred to the other regions (one to the Chocó and two to the Eastern Cordillera), which were subsequently followed by three events of vicariance, suggesting that dispersal and vicariance were equally important in shaping the current distribution patterns of Spinoctenus species. The discovery of this new genus containing a large number of new species in the Andean and Chocó regions highlights the current poor knowledge of the Colombian biodiversity.
“Entraining” to speech, generating language?

ABSTRACT Could meaning be read from acoustics, or from the refraction rate of pyramidal cells innervated by the cochlea, everyone would be an omniglot. Speech does not contain sufficient acoustic cues to identify linguistic units such as morphemes, words, and phrases without prior knowledge. Our target article (Meyer, L., Sun, Y., & Martin, A. E. (2019). Synchronous, but not entrained: Exogenous and endogenous cortical rhythms of speech and language processing. Language, Cognition and Neuroscience, 1–11. https://doi.org/10.1080/23273798.2019. 1693050) thus questioned the concept of “entrainment” of neural oscillations to such units. We suggested that synchronicity with these points to the existence of endogenous functional “oscillators”—or population rhythmic activity in Giraud’s (2020) terms—that underlie the inference, generation, and prediction of linguistic units. Here, we address a series of inspirational commentaries by our colleagues. As apparent from these, some issues raised by our target article have already been raised in the literature. Psycho– and neurolinguists might still benefit from our reply, as “oscillations are an old concept in vision and motor functions, but a new one in linguistics” (Giraud, A.-L. 2020. Oscillations for all A commentary on Meyer, Sun & Martin (2020). Language, Cognition and Neuroscience, 1–8).
Novel Asgard archaea phylum Hermodarchaeota degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway

Asgard superphylum is composed of a group of uncultivated archaea that are deemed the closest relatives of eukaryotes. These archaea are widely distributed in anaerobic environments and suggested to be important players in carbon cycling of sediments. Alkanes and aromatics are refractory organic compounds and abundant in sediments. However, little is known about degradation of these compounds by Asgard archaea to date. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered in metagenomes from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those found in alkanes-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes for alkyl-coenzyme A and benzoyl-coenzyme A oxidation, and the Wood–Ljungdahl pathway, as well as nitrate reductases. Furthermore, transcripts for these enzymes have been frequently detected in metatranscriptomes from mangrove sediments. This indicates that members of this phylum are able to anaerobically oxidize alkanes and aromatic compounds, coupling the reduction of nitrate. Genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in a range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.
Increased risk of incident dementia following use of anticholinergic agents: A systematic literature review and meta‐analysis

Long‐term treatment with anticholinergic agents may increase the risk of cognitive impairment or dementia. This systematic literature review and meta‐analysis aimed to assess the impact of ≥3 months of exposure to anticholinergics as a class on the risk of dementia, mild cognitive impairment, and change in cognitive function. The impact of anticholinergic agents specifically used to treat overactive bladder was also evaluated.
Formulation of Creams Containing Spirulina Platensis Powder with Different Nonionic Surfactants for the Treatment of Acne Vulgaris

Natural products used in the treatment of acne vulgaris may be promising alternative therapies with fewer side effects and without antibiotic resistance. The objective of this study was to formulate creams containing Spirulina (Arthrospira) platensis to be used in acne therapy. Spirulina platensis belongs to the group of micro algae and contains valuable active ingredients. The aim was to select the appropriate nonionic surfactants for the formulations in order to enhance the diffusion of the active substance and to certify the antioxidant and antibacterial activity of Spirulina platensis-containing creams. Lyophilized Spirulina platensis powder (SPP) was dissolved in Transcutol HP (TC) and different types of nonionic surfactants (Polysorbate 60 (P60), Cremophor A6:A25 (CR) (1:1), Tefose 63 (TFS), or sucrose ester SP 70 (SP70)) were incorporated in creams as emulsifying agents. The drug release was evaluated by the Franz diffusion method and biocompatibility was tested on HaCaT cells. In vitro antioxidant assays were also performed, and superoxide dismutase (SOD) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays were executed. Antimicrobial activities of the selected compositions were checked against Staphylococcus aureus (S. aureus) and Cutibacterium acnes (C. acnes) (formerly Propionibacterium acnes) with the broth microdilution method. Formulations containing SP 70 surfactant with TC showed the most favorable dissolution profiles and were found to be nontoxic. This composition also showed significant increase in free radical scavenger activity compared to the blank sample and the highest SOD enzyme activity was also detected after treatment with the cream samples. In antibacterial studies, significant differences were observed between the treated and control groups after an incubation time of 6 h.
Enrichment of Olive Fruits in Antioxidant Content by Pre-Harvest Salicylic Acid Treatment

We here study the effect of the pre-harvest application of salicylic acid at two different concentrations on the olive phenolic composition. Influence of the cultivar and harvesting day were considered. As a result, the total phenol content increased significantly, particularly when using 200 mg mL−1 of salicylic acid. However, the free radical scavenging activity was cultivar dependent. For instance, when the olives were harvested on day 3 and treated with 200 mg mL−1 of salicylic acid, the antioxidant activity decreased from 161 to 278 µg mL−1 for Arbequina, whereas it increased from 397 to 258 µg mL−1 for Picual. Generally speaking, oleuropein and hydroxytyrosol contents enhanced with the application of 200 mg mL−1 of salicylic acid. The results found suggest that exogenous salicylic acid is an interesting agronomic practice to enrich olive fruits in antioxidants.
COVID-19 in transplant recipients: The Spanish experience

We report the nationwide experience with solid organ transplant (SOT) and hematopoietic stem cell transplant (HSCT) recipients diagnosed with coronavirus disease 2019 (COVID‐19) in Spain until 13 July 2020. We compiled information for 778 (423 kidney, 113 HSCT, 110 liver, 69 heart, 54 lung, 8 pancreas, 1 multivisceral) recipients. Median age at diagnosis was 61 years (interquartile range [IQR]: 52‐70), and 66% were male. The incidence of COVID‐19 in SOT recipients was two‐fold higher compared to the Spanish general population. The median interval from transplantation was 59 months (IQR: 18‐131). Infection was hospital‐acquired in 13% of cases. No donor‐derived COVID‐19 was suspected. Most patients (89%) were admitted to the hospital. Therapies included hydroxychloroquine (84%), azithromycin (53%), protease inhibitors (37%), and interferon‐β (5%), whereas immunomodulation was based on corticosteroids (41%) and tocilizumab (21%). Adjustment of immunosuppression was performed in 85% of patients. At the time of analysis, complete follow‐up was available from 652 patients. Acute respiratory distress syndrome occurred in 35% of patients. Ultimately, 174 (27%) patients died. In univariate analysis, risk factors for death were lung transplantation (odds ratio [OR]: 2.5; 95% CI: 1.4‐4.6), age >60 years (OR: 3.7; 95% CI: 2.5‐5.5), and hospital‐acquired COVID‐19 (OR: 3.0; 95% CI: 1.9‐4.9).
Plants in the Genus Tephrosia: Valuable Resources for Botanical Insecticides

Simple Summary There is an increasing interest in botanical insecticides worldwide. Plants from the genus Tephrosia are rich in bioactive phytochemicals, particularly rotenoids which include rotenone, deguelin, rotenolone, and tephrosin. Rotenoids have strong insecticidal activities against a wider range of pests. However, there has been no treatise thus far focusing on Tephrosia as insecticidal plants. This article is intended to review phytochemicals produced by selected species, their insecticidal activities, and the current status on the use of Tephrosia as botanical insecticidal plants for insect pest control. Abstract Synthetic insecticides are effective in controlling insect pests but can also harm nontarget organisms and the environment. During the last 40 years, there has been an increasing interest in alternative insecticides, particularly those derived from plants, commonly known as botanical insecticides. However, commercially available botanical insecticides remain limited. Rotenone is one of the earliest identified compounds and was used as fish poison and pest management. Due to its link with Parkinson disease, the use of rotenone was banned in many developed countries. Rotenone used to be isolated from Derris spp. and Lonchocarpus spp. , and it can also be isolated from Tephrosia species. In this article, we present basic botanical information on selected Tephrosia species and their major compounds related to insecticidal activities and highlight the current use of extracts derived from some species, Tephrosia vogelii in particular, for control of insect pests in stored grains and crop production. The crude extracts contain multiple bioactive compounds, mainly rotenone, deguelin, rotenolone, and tephrosin, which act in either additive or synergistic fashion, resulting in effective control of insect pests. There are about 400 species in the genus Tephrosia, and species and even strains or variants vary greatly in these active compounds. We argue that a systematic evaluation of bioactive compounds in different species are needed, and species or strains with high insecticidal activities should be selected for use in the sustainable control of insect pests.
Dramatic long-term restoration of an oak woodland due to multiple, sustained management treatments

We measured 34 years of plant community change in a degraded oak woodland undergoing ecological management. Management included regular prescribed fire, control of white-tailed deer populations, repeated sowing of a diverse seed mix, and removal of invasive plants. We tracked change with several conservation metrics. Time series analysis showed no significant changes over time in either plant species richness or the Shannon-Weiner diversity index. Floristic Quality Assessment measures—the Floristic Quality Index (FQI), Cover-weighted FQI, and the Mean Coefficient of Conservatism (Mean C)—all increased dramatically over time, such that their values now surpass those of the highest quality representative of this habitat in the region. Cover-weighted FQI had the added benefit of being quick to respond (negatively and positively) to short-term management changes during the study. This sensitivity highlights its utility for adaptive management, enabling timely, data-driven changes to ongoing management regimes. Plant community composition showed striking changes during the study period, as species of high conservation value replaced weedier species. As a group, conservative woodland species are notoriously slow to recover from degradation, making this flora’s recovery particularly notable. A mid-study cessation of management immediately stalled the woodland’s recovery according to Floristic Quality metrics, but the restoration quickly returned to its positive trajectory with the resumption of management treatments. These results illustrate that impressive plant biodiversity restoration can be achieved, even in highly degraded contemporary oak ecosystems, if ecological management is comprehensive and if it is sustained over time.