Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Modeling of Cod-Capelin Dynamics in the Newfoundland-Labrador Shelves and Barents Sea Ecosystems

The Atlantic cod (Gadus morhua) stocks in the Newfoundland-Labrador Shelves (NL) and Barents Sea (BS) ecosystems have shown divergent trajectories over the last 40 years. Both stocks experienced either an important decline (BS) or a collapse (NL) in the mid-1980s and early 1990s, respectively. After these population reductions, the BS stock quickly rebounded and it is currently at record high levels, while the NL stock, despite showing some improvement since the mid-2000s, remains at low levels. Fishing and environmental conditions are known to be important drivers of cod dynamics in both ecosystems, especially the availability of high energy prey like capelin (Mallotus villosus), however, the question of how different or similar these two stocks truly are remains. Could, for example, the NL cod stock rebuild if presented to conditions like the ones experienced by BS cod? To explore such questions, we developed a simple biomass dynamic model for cod using a bioenergetic-allometric approach. This model includes fisheries catches and capelin availability as external drivers and was implemented for both ecosystems. Despite the contrasting trends, the model produced very good fits, and showed some remarkably similar estimated parameters in both systems. We explored these similarities by (a) performing the thought experiment of transferring cod stocks between ecosystems by switching estimated key parameters between models and comparing the output, and (b) implementing an integrated model architecture which allowed fitting common parameters for both stocks to evaluate the similarity of key vital rates. Our results indicate that cod trajectories in NL and BS can be reliably described using simple bioenergetic-allometric arguments, fishery catches, and capelin availability. Model parameters that encapsulate intrinsic vital rates were not significantly different between stocks. This indicates that NL and BS cod stocks are biologically similar, and that the differences in their trajectories are driven by the ecosystem context in which these stocks are embedded, and suggests that the NL stock would be expected to rebuild if enough capelin were available. This also indicates that capelin status and trend should be an important consideration for effective management of these cod stocks.
Towards a Sustainable Vector-Control Strategy in the Post Kala-Azar Elimination Era

Visceral leishmaniasis (VL) is a potentially deadly parasitic disease. In the Indian sub-continent, VL is caused by Leishmania donovani and transmitted via the bite of an infected Phlebotomus argentipes female sand fly, the only competent vector species in the region. The highest disease burden is in the northern part of the Indian sub-continent, especially in the state of Bihar. India, Bangladesh, and Nepal embarked on an initiative, coordinated by World Health Organization, to eliminate VL as a public health problem by the year 2020. The main goal is to reduce VL incidence below one case per 10,000 people through early case-detection, prompt diagnosis and treatment, and reduction of transmission using vector control measures. Indoor residual spraying, a major pillar of the elimination program, is the only vector control strategy used by the government of India. Though India is close to its VL elimination target, important aspects of vector bionomics and sand fly transmission dynamics are yet to be determined. To achieve sustained elimination and to prevent a resurgence of VL, knowledge gaps in vector biology and behavior, and the constraints they may pose to current vector control methods, need to be addressed. Herein, we discuss the successes and failures of previous and current vector-control strategies implemented to combat kala-azar in Bihar, India, and identify gaps in our understanding of vector transmission towards development of innovative tools to ensure sustained vector control in the post-elimination period.
Divers as Citizen Scientists: Response Time, Accuracy and Precision of Water Temperature Measurement Using Dive Computers

There is a lack of depth-resolved temperature data, especially in coastal areas, which are often commonly dived by SCUBA divers. Many case studies have demonstrated that citizen science can provide high quality data, although users require more confidence in the accuracy of these data. This study examined the response time, accuracy and precision of water temperature measurement in 28 dive computers plus three underwater cameras, from 12 models. A total of 239 temperature response times (τ) were collected from 29 devices over 11 chamber dives. Mean τ by device ranged from (17 ± 6) to (341 ± 69) s, with significant between-model differences found for τ across all models. Clear differences were found in τ by pressure sensor location and material, but not by size. Two models had comparable τ to designed-for-purpose aquatic temperature loggers. 337 mean data points were collected from equilibrated temperatures in hyperbaric chamber (n = 185) and sea (n = 152) dives, compared with baseline mean temperature from Castaway CTDs over the same time period. Mean bias, defined as mean device temperature minus baseline temperature, by model ranged from (0.0 ± 0.5) to (−1.4 ± 2.1) °C and by device from (0.0 ± 0.6) to (−3.4 ± 1.0) °C. Nine of the twelve models were found to have “good” accuracy (≤0.5 °C) overall. Irrespective of model, the overall mean bias of (−0.2 ± 1.1) °C is comparable with existing commonly used coastal temperature data sets, and within global ocean observing system accuracy requirements for in situ temperature. Our research shows that the quality of temperature data in dive computers could be improved, but, with collection of appropriate metadata to allow assessment of data quality, some models of dive computers have a role in future oceanographic monitoring.
Inonotus rickii (Agaricomycetes, Hymenochaetaceae) in Brazilian Cerrado: Expanding Its Geographic Distribution and Host List

Inonotus rickii (Pat.) Reid (Agaricomycetes: Hymenochaetaceae) is a poroid fungus characterized by the expressive production of chlamydospores, in vivo and in vitro, especially during its anamorphic stage. The species plays important ecological roles, standing out as a phytopathogen, affecting several species of ornamental and wild trees, mainly in tropical and subtropical regions. The infected trees develop canker and white rot of the wood, showing symptoms of reduced vegetative vigor and decline of leaves and branches which causes death in some cases. The first record of I. rickii for the Cerrado biome (Brazilian Savanna) and the first record as causal agent of canker in Schinus molle L. in Brazil is reported here. In addition, we present a checklist of its worldwide geographical distribution and known hosts, from an extensive bibliographic search in Google Scholar, SciELO, Scopus, and Web of Science databases. The species is widespread in tropical and subtropical zones; common in the American continent, especially in Central and South America and the Mediterranean region, and rare in temperate zones. We found specimens growing in both living and dead hosts, totalizing 70 species of hosts, distributed in 43 genera and 22 families. Of these, Acer negundo L. (10.5%), Celtis australis L. (6.5%), and Platanus acerifolia (Aiton) Willd. (4.8%), and the Fabaceae (30%), Fagaceae (10%), and Sapindaceae (8.6%) families were the most frequent. We present morphological descriptions and illustrations, as well as the growth characteristics in culture medium. Our study expands the known geographical distribution of I. rickii, including the Cerrado biome, as well as its structural, physiological characteristics, and its hosts.
Immunogenicity Risk Profile of Nanobodies

Nanobodies (Nbs), the variable domains of camelid heavy chain-only antibodies, are a promising class of therapeutics or in vivo imaging reagents entering the clinic. They possess unique characteristics, including a minimal size, providing fast pharmacokinetics, high-target specificity, and an affinity in the (sub-)nanomolar range in conjunction with an easy selection and production, which allow them to outperform conventional antibodies for imaging and radiotherapeutic purposes. As for all protein theranostics, extended safety assessment and investigation of their possible immunogenicity in particular are required. In this study, we assessed the immunogenicity risk profile of two Nbs that are in phase II clinical trials: a first Nb against Human Epidermal growth factor Receptor 2 (HER2) for PET imaging of breast cancer and a second Nb with specificity to the Macrophage Mannose Receptor (MMR) for PET imaging of tumor-associated macrophages. For the anti-HER2 Nb, we show that only one out of 20 patients had a low amount of pre-existing anti-drug antibodies (ADAs), which only marginally increased 3 months after administering the Nb, and without negative effects of safety and pharmacokinetics. Further in vitro immunogenicity assessment assays showed that both non-humanized Nbs were taken up by human dendritic cells but exhibited no or only a marginal capacity to activate dendritic cells or to induce T cell proliferation. From our data, we conclude that monomeric Nbs present a low immunogenicity risk profile, which is encouraging for their future development toward potential clinical applications. One Sentence Summary Nanobodies, the recombinant single domain affinity reagents derived from heavy chain-only antibodies in camelids, are proven to possess a low immunogenicity risk profile, which will facilitate a growing number of Nanobodies to enter the clinic for therapeutic or in vivo diagnostic applications.
Imiquimod Targets Toxoplasmosis Through Modulating Host Toll-Like Receptor-MyD88 Signaling

Toxoplasma gondii is a prevalent parasite of medical and veterinary importance. Tachyzoïtes and bradyzoïtes are responsible for acute and chronic toxoplasmosis (AT and CT), respectively. In immunocompetent hosts, AT evolves into a persistent CT, which can reactivate in immunocompromised patients with dire consequences. Imiquimod is an efficient immunomodulatory drug against certain viral and parasitic infections. In vivo, treatment with Imiquimod, throughout AT, reduces the number of brain cysts while rendering the remaining cysts un-infectious. Post-establishment of CT, Imiquimod significantly reduces the number of brain cysts, leading to a delay or abortion of reactivation. At the molecular level, Imiquimod upregulates the expression of Toll-like receptors 7, 11, and 12, following interconversion from bradyzoïtes to tachyzoïtes. Consequently, MyD88 pathway is activated, resulting in the induction of the immune response to control reactivated Toxoplasma foci. This study positions Imiquimod as a potent drug against toxoplasmosis and elucidates its mechanism of action particularly against chronic toxoplasmosis, which is the most prevalent form of the disease.
Blood Interferon-α Levels and Severity, Outcomes, and Inflammatory Profiles in Hospitalized COVID-19 Patients

Background: Deficient interferon responses have been proposed as one of the relevant mechanisms prompting severe manifestations of COVID-19. Objective: To evaluate the interferon (IFN)-α levels in a cohort of COVID-19 patients in relation to severity, evolution of the clinical manifestations and immune/inflammatory profile. Methods: This is prospective study recruiting consecutive hospitalized patients with respiratory failure associated with SARS-COV-2 infection and matched controls. After enrollment, patients were assessed every 7 ± 2 days for additional 2 consecutive visits, for a total of 21 days. The severity of the clinical condition was ranked based on the level of respiratory support required. At each time-point blood samples were obtained to assess immune cells and mediators by multiplex immunoassay. Results: Fifty-four COVD-19 and 11 control patients matched for severity were enrolled. At recruitment, lower levels of blood IFN-α were found in COVID-19 patients compared to controls (3.8-fold difference, p < 0.01). Improvements in COVID-19 severity were paralleled by a significant increase of blood IFN-α levels. A significant increase in blood IFN-α was found over the study period in survivors (70% of the study population). A similar trend was found for blood IFN-β with IFN-β levels below the threshold of detectability in a substantial proportion of subjects. Significantly higher values of blood lymphocytes and lower levels of IL-10 were found at each time point in patients who survived compared to patients who died. In patients who clinically improved and survived during the study, we found an inverse association between IL-10 and IFN-α levels. Conclusion: The study identifies a blood immune profile defined by deficient IFN-α levels associated with increased IL-10 expression in patients progressing to severe/life threatening COVID-19 conditions, suggesting the involvement of immunological pathways that could be target of pharmacological intervention. Clinical Trial Registration: ClinicalTrials.gov identifier NCT04343053.
“Motherese” Prosody in Fetal-Directed Speech: An Exploratory Study Using Automatic Social Signal Processing

Introduction: Motherese, or emotional infant directed speech (IDS), is the specific form of speech used by parents to address their infants. The prosody of IDS has affective properties, expresses caregiver involvement, is a marker of caregiver-infant interaction quality. IDS prosodic characteristics can be detected with automatic analysis. We aimed to explore whether pregnant women “speak” to their unborn baby, whether they use motherese while speaking and whether anxio-depressive or obstetrical status impacts speaking to the fetus. Participants and Methods: We conducted an observational study of pregnant women with gestational ages from 26 to 38 weeks. Women were recruited in a university hospital department of obstetrics. Thirty-five women agreed to participate in the study, and 26 audio records were exploitable. We collected obstetrical and sociodemographic data, pregnancy outcomes, anxiety and depressive status using the Covy and Raskin Scales, and life events using the Sensations During Pregnancy and Life Event Questionnaire. Each participant was left alone with an audio recorder with a recommendation to feel free to speak to her fetus as she would have done at home. The recording was stopped after 3 min. Audio recordings were analyzed by two methods: psycholinguist experts' annotation and computational objective automatic analyses. Results: Most mothers (89%) reported speaking to their fetuses. We found a correlation between maternal first perceptions of fetal movements and the start of mother's speaking to fetus. Motherese prosody was detected with both annotation and automatic analysis with a significant correlation between the two methods. In this exploratory study, motherese use was not associated with maternal anxiodepressive or obstetrical status. However, the more future mothers were depressed, the less they spoke with their fetuses during the recording. Conclusion: Fetal directed speech (FDS) can be detected during pregnancy, and it contains a period of prosody that shares the same characteristics of motherese that can be described as prenatal motherese or emotional fetal-directed speech (e-FDS). This means that pregnant women start using motherese much earlier than expected. FDS seems to be correlated with maternal first perceptions of fetal movements and depression scores. However, more research is needed to confirm these exploratory results.
Carbon nanotube assisted water self-diffusion across lipid membranes in the absence and presence of electric fields

Water self-diffusion has been investigated by molecular dynamics (MD) simulation through armchair single-walled carbon nanotubes (SWCNTs) implanted in 1-palmytoil-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) membrane patches. Four systems were investigated, each containing one of (5,5), (6,6), (8,8) and (11,11) CNTs with diameters of 6.89, 8.20, 11.04 and 15.02 Å respectively and a length of 36.9 Å, oriented normal to the membrane. The CHARMM27 potential was used, in conjunction with TIP3P water, with particle-mesh Ewald electrostatics. Equilibrium and non-equilibrium MD simulations were performed in the respective absence and presence of a static electric field with an intensity of 0.0065 V/Å, applied along the axis normal to the membrane, i.e. approximately along the axis of the CNTs. It was found that the permeation rate of tracer water molecules was enhanced from 1.13 to 2.6 particles per nanosecond in the presence of the field in the case of (5,5) CNT, whilst the permeation rate per unit area declined in the larger nanotubes vis-à-vis equilibrium zero-field conditions. Single-file diffusion was observed in the (5,5) and (6,6) cases, compared with classical diffusion in the larger pores. From an analysis of the molecular dipole moment distributions, the number of water molecules present in the CNTs and the hydrogen-bonding characteristics of water inside the CNTs and at their mouth, these trends have been rationalised. A significant decrease in the fluctuations in the number of water molecules in the (5,5) CNT due to an enhanced dipole alignment in the electric field resulted in an increased rate of incorporation of the water molecules into this CNT, whereas a sharper alignment of the water dipoles with the field coupled with the greater rotational freedom of the water molecules in the (6,6) nanotube tended to reduced water self-diffusion.
Neurons in the Locus Coeruleus Modulate the Hedonic Effects of Sub-Anesthetic Dose of Propofol

Propofol is a worldwide-used intravenous general anesthetic with ideal effects, but hedonic effects of propofol have been reported and cause addictive issue. There is little known about the neurobiological mechanism of hedonic effects of propofol. Increasing researches have shown that the dopaminergic nervous system of the ventral tegmental area (VTA) and the noradrenergic system of locus coeruleus (LC) play a crucial role in hedonic experiences, which are putative sites for mediating the hedonic effects of propofol. In the present study, rat hedonic response scale and place conditioning paradigm were employed to examine the euphoric effects of propofol. In vivo GCaMP-based (AVV-hSyn-GCaMP6s) fiber photometry calcium imaging was used to monitor the real-time neuronal activity in VTA and LC area in rats exhibiting propofol-induced euphoric behaviors. Then DREADDs (designer receptors exclusively activated by designer drugs) modulation using rAAV-hSyn-hM4D(Gi)-EGFP was performed to confirm the neuronal substrate that mediates the euphoric effects of propofol. The score of hedonic facial responses was significantly increased in the 4 mg/kg group compared with that of the 0 mg/kg group. The locomotor activity in the propofol-paired compartment was significantly increased at the 4 mg/kg dose compared with that of the saline-paired group. When compared with the 0 mg/kg group, the place preference increased in the 4 mg/kg group. Administration of 4 mg/kg of propofol triggers reliable increases in GcaMP fluorescence. However, in the VTA GcaMP-expressing rats, administration of 4 mg/kg of propofol did not induce any change of GcaMP signals. The facial score and the place preference, which increased by 4 mg/kg propofol were abolished by chemogenetic inhibition of the neuronal activity in the LC area. Our results suggest that LC noradrenergic neurons, not VTA dopaminergic neurons, are directly involved in the hedonic effects of sub-anesthetic dose of propofol.
TSC1 Affects the Process of Renal Ischemia-Reperfusion Injury by Controlling Macrophage Polarization

Renal ischemia-reperfusion injury (IRI) contributes to acute kidney injury (AKI), increases morbidity and mortality, and is a significant risk factor for chronic kidney disease (CKD). Macrophage infiltration is a common feature after renal IRI, and infiltrating macrophages can be polarized into the following two distinct types: M1 macrophages, i.e., classically activated macrophages, which can not only inhibit infection but also accelerate renal injury, and M2 macrophages, i.e., alternatively activated macrophages, which have a repair phenotype that can promote wound healing and subsequent fibrosis. The role of TSC1, which is a negative regulator of mTOR signaling that regulates macrophage polarization in inflammation-linked diseases, has been well documented, but whether TSC1 contributes to macrophage polarization in the process of IRI is still unknown. Here, by using a mouse model of renal ischemia-reperfusion, we found that myeloid cell-specific TSC1 knockout mice (termed Lyz-TSC1 cKO mice) had higher serum creatinine levels, more severe histological damage, and greater proinflammatory cytokine production than wild-type (WT) mice during the early phase after renal ischemia-reperfusion. Furthermore, the Lyz-TSC1 cKO mice showed attenuated renal fibrosis during the repair phase of IRI with decreased levels of M2 markers on macrophages in the operated kidneys, which was further confirmed in a cell model of hypoxia-reoxygenation (H/R) in vitro. Mechanistically, by using RNA sequencing of sorted renal macrophages, we found that the expression of most M1-related genes was upregulated in the Lyz-TSC1 cKO group (Supplemental Table 1) during the early phase. However, C/EBPβ and CD206 expression was decreased during the repair phase compared to in the WT group. Overall, our findings demonstrate that the expression of TSC1 in macrophages contributes to the whole process of IRI but serves as an inflammation suppressor during the early phase and a fibrosis promoter during the repair phase.
COVID-19 Mortality and Case-Fatality Rates in Sergipe State, Northeast Brazil, From April to June 2020

Information on how coronavirus disease 2019 (COVID-19) mortality is related to population characteristics in low- and middle-income countries is still limited. We described the deaths from COVID-19 in Sergipe state, Northeast Brazil, from April 2 to June 27, 2020. For this purpose, we conducted a study composed of (i) a case series study of all deaths due to COVID-19 and (ii) a population-based study to verify the behavior of the mortality and case-fatality rates (CFR) related to COVID-19. Data from 605 deaths due to COVID-19 were used to describe the characteristics of individuals with the disease, as well as the differences in gender, age, and comorbidities. Additionally, population data were extracted to estimate the mortality and CFR by population stratum. We also performed an adjusted CFR analysis including a time lag of 14 days between the onset of symptoms and reporting deaths. Of the 605 patients included in this study, 321 (53.1%) were males and the median age was 67.0 years. Most patients (n = 447, 73.9%) who died from COVID-19 had at least one pre-existing clinical condition. The mortality rate was 29.3 deaths per 100,000 inhabitants and the crude CRF was 2.6% (95% CI 2.4–2.8). CFR was higher in males (3.1%, 95% CI 2.8–3.4; p < 0.001) and people aged ≥60 years (14.2%, 95% CI 13.0–15.6; p = 0.042). About 25% of patients died during the first 24-h post-hospital admission. The adjusted CFR for a 14-day time lag was ~2-fold higher than the crude CFR over the study period.