Miracle-dz/UniFAR-FTUs huggingface dataset:
SARS-CoV-2 surveillance in Norway rats (Rattus norvegicus) from Antwerp sewer system, Belgium

Background SARS-CoV-2 human-to-animal transmission can lead to the establishment of novel reservoirs and the evolution of new variants with the potential to start new outbreaks in humans. Aim We tested Norway rats inhabiting the sewer system of Antwerp, Belgium, for the presence of SARS-CoV-2 following a local COVID-19 epidemic peak. In addition, we discuss the use and interpretation of SARS-CoV-2 serological tests on non-human samples. Methods Between November and December 2020, Norway rat oral swabs, feces and tissues from the sewer system of Antwerp were collected to be tested by RT-qPCR for the presence of SARS-CoV-2. Serum samples were screened for the presence of anti-SARS-CoV-2 IgG antibodies using a Luminex microsphere immunoassay (MIA). Samples considered positive were then checked for neutralizing antibodies using a conventional viral neutralization test (cVNT). Results The serum of 35 rats was tested by MIA showing 3 potentially positive sera that were later shown to be negative by cVNT. All tissue samples of 39 rats analyzed tested negative for SARS-CoV-2 RNA. Conclusion This is the first study that evaluates SARS-CoV-2 infection in urban rats. We can conclude that the sample of 39 rats had never been infected with SARS-CoV-2. We show that diagnostic serology tests can give misleading results when applied on non-human samples. SARS-CoV-2 monitoring activities should continue due to the emergence of new variants prone to infect Muridae rodents.
A Machine Learning Approach for Detecting Vicarious Trial and Error Behaviors

Vicarious trial and error behaviors (VTEs) indicate periods of indecision during decision-making, and have been proposed as a behavioral marker of deliberation. In order to understand the neural underpinnings of these putative bridges between behavior and neural dynamics, researchers need the ability to readily distinguish VTEs from non-VTEs. Here we utilize a small set of trajectory-based features and standard machine learning classifiers to identify VTEs from non-VTEs for rats performing a spatial delayed alternation task (SDA) on an elevated plus maze. We also show that previously reported features of the hippocampal field potential oscillation can be used in the same types of classifiers to separate VTEs from non-VTEs with above chance performance. However, we caution that the modest classifier success using hippocampal population dynamics is not sufficient for identifying trials where VTEs occur, and show that combining oscillation-based features with trajectory-based features degrades classifier performance compared to trajectory-based features alone. Overall, we propose a standard set of features useful for trajectory-based VTE classification and support previous suggestions that VTEs are supported by a network including, but likely extending beyond, the hippocampus.
Collective behavior emerges from genetically controlled simple behavioral motifs in zebrafish

Since Darwin, coordinated movement of animal groups has been believed to be essential to species survival, but it is not understood how changes in the genetic makeup of individuals might alter behavior of the collective. Here we find that even at the early larval stage, zebrafish regulate their proximity and alignment with each other. Two simple visual responses, one that measures relative visual field occupancy and the other global visual motion, suffice to account for the group behavior that emerges. We analyze how mutations in genes known to affect social behavior of humans perturb these simple reflexes in larval zebrafish and thereby affect their collective behaviors. We use model simulations to show that changes in reflexive responses of individual mutant animals predict well the distinctive collective patterns that emerge in a group. Hence group behaviors reflect in part genetically defined primitive sensorimotor “motifs”, which are evident even in young larvae.
Competitive binding of MatP and topoisomerase IV to the MukB dimerization hinge

SMC complexes have ubiquitous roles in chromosome organisation. In Escherichia coli, the interplay between the SMC complex, MukBEF, and matS-bound MatP in the replication termination region, ter, results in depletion of MukBEF from ter, thus promoting chromosome individualisation by directing replichores to separate cell halves. MukBEF also interacts with topoisomerase IV ParC2E2 heterotetramers, to direct its chromosomal distribution to mirror that of MukBEF, thereby facilitating coordination between chromosome organisation and decatenation by topoisomerase IV. Here we demonstrate that the MukB dimerization hinge binds ParC and MatP with the same dimer to dimer stoichiometry. MatP and ParC have an overlapping binding interface on the MukB hinge, leading to their mutually exclusive binding. Furthermore, the MukB hinge fails to stably associate with matS-bound MatP, while MatP mutants deficient in matS binding are impaired in MukB hinge binding, demonstrating that mats competes with the hinge for MatP binding. Cells expressing MukBEF complexes containing a mutation in the MukB hinge interface for ParC/MatP binding are deficient in ParC binding in vivo, despite having a Muk+ topoisomerase IV+ phenotype. This mutant protein is also impaired in MatP binding in vitro, and cells expressing this variant exhibit a MukBEF cellular localisation consistent with impaired MatP binding.
Concept design of a bionic grasp to capture the hand motion

This study has focused on designing a device allowing the user to perform hand exercise motions, in relation with previous methods with good effects in stroke rehabilitation. The project is mainly aimed at designing a low cost, easy to handle and easy to manufacture smart glove to assist users with finger flexion and extensions, which can at the same time transfer data to an application. The methodology used here includes research, design, simulation testing and finalised design. It started with research and investigations on the needs of the users and previous efficient stroke rehabilitation methods. This has been followed with 4 concept designs, which has been tested and evaluated in the next stage for possible optimizations using a computer modelling technique. At the final step, the virtual prototype and product design specification (PDS) of the finalise concept for the interactive device has been illustrated.
The dielectric breakdown of gases at low pressure

The Townsend theory of dielectric breakdown of gases does not apply at low gas density, where the mean free path of electrons maybe of the order of the dimensions of the discharge chamber. An alternative model of breakdown for this region between true gas breakdown and vacuum was presented recently, and shown to apply in the case of mercury vapour. The mathematical model has been extended to lower pressures than previously, and now includes an analysis of possible secondary mechanisms. The theoretical section is complemented by experimental work, again at lower pressures and for a different gas, namely argon. It is shown that the alternative model of breakdown still applies at the lower gas pressures.
Referential Values of Testicular Volume Measured by Ultrasonography in Normal Children and Adolescents: Z-Score Establishment

Objective: To establish Z-score regression equation derived from age for testicular volume measured by ultrasonography in normal boys aged 0 to 18 years old. Method: The length (L), width (W), and height (H) of 3,328 testicles from 1,664 Chinese boys were measured by ultrasonography. Lambert's formula: L × W × H × 0.71 was used to calculate testicular volume. Z-score regression equation derived from age was established by regression analysis of predicted values of testicular volume and standard deviations. Result: There was no significant difference between left and right testicular volumes. Testicular volume was positively correlated with age, and logarithmic transformation of testicular volume can show a fine curve fit with age. To establish Z-score regression equation derived from age, the predicted values of testicular volume used cubic regression equations, and the standard deviation used square regression equations. The Z-score regression equation derived from age was calculated by the formula: z = [lg (L × W × H × 0.71) – (−0.3524-0.01759 × x+0.009417 × x2-0.0001840 × x3)]/(0.1059+0.01434 × x-0.0005324 × x2). Conclusion: The current study provided a reference value for testicular volume of boys aged 0 to 18 years old. Z-score regression equation derived from age for testicular volume can be established. Z-score will be of great value for the testicular development assessment and disease diagnosis and follow-up.
Abnormal Brain Glucose Metabolism in Papillary Thyroid Cancer Patients 4 Weeks After Withdrawal of Levothyroxine: A Cross-Sectional Study Using 18F-FDG PET/CT

Background There is no doubt that thyroid dysfunction is associated with psychiatric disorders. A large amount of thyroid carcinoma patients displayed mood disorders after the withdrawal of levothyroxine (LT4). However, it is unclear whether the disorders are related to the transient withdrawal of LT4, and if yes, what the possible underlying mechanism is. This study aims to investigate the abnormal regional cerebral glucose metabolism (rCMRglu) in a group of papillary thyroid cancer (PTC) patients without LT4 for 4 weeks and prove the relationship between the abnormal rCMRglu with depression and anxiety. Methods Brain 18F-FDG PET/CT data of 38 consecutive PTC patients with high/intermediate-risk from June 2016 to December 2017 have been analyzed. Of the 38 patients, 23 are in the LT4 withdrawal group (WG) and 15 in the LT4 replacement group (RG). These patients were also evaluated for depressive and anxiety symptoms within 24 h after the scans based on the Hamilton Depression Rating Scale (17 items, HRDS-17) and the Hamilton Anxiety Rating Scale (HAMA) respectively. Results Thirty-eight patients (12 men, 26 women; age range, 25–69 years; mean age, 45.8 years) were selected in the study. Compared with the RG, patients in WG showed depression and anxiety with higher total scores of HRDS-17 and HAMA (14.7 ± 5.8 vs 3.8 ± 5.5, t = −5.74, p = 0.00; 9.3 ± 4.3 vs 2.7 ± 4.1, t = −4.74, p = 0.00, respectively). In the brain glucose metabolism analysis, the WG patients showed lower rCMRglu in Occipital_Mid_R and Postcentral_L. On the other hand, data illustrated significant rCMRglu increases in the Frontal_Sup_Orb_L. Compared with the healthy group (HG), the rCMRglu of the Postcentral_L and Precuneus_L showed hypoactivity, but the Hippocampus_R and the Temporal_Inf_L showed hyperactivity. This analysis yielded a significant correlation between abnormal rCMRglu with the free thyroxine level, the serum thyroid-stimulating hormone level, HRDS-17, and HAMA scores. Conclusions The findings showed that more PTC patients exhibited depression and anxiety after LT4 withdrawal for 4 weeks. More attention should be paid to these hypothyroid patients while they were in the hospital. Such a short-term LT4 withdrawal also likely induced abnormal rCMRglu. Our study attempts to explain the possible mechanism of mood disorders related to transient hypothyroidism.
Biofilm formation: hydrodynamic effects on internal diffusion and structure

Diffusion in microbial films produced by Pseudomonas fluorescens under turbulent flow conditions was studied using an inert substance (LiCl). Mass transfer coefficients in the biofilm were measured during formation of the biological deposits and for biofilms developed under different fluid velocities. Mass transfer rates in the biofilm decreased with time, and more quickly in the case of biofilms subjected to high shear stresses. The latter show lower final thicknesses and lower internal diffusivities. The so‐called “active layer”;, if it exists, does not seem to have a fixed thickness (as proposed by some authors), since it will depend on the environmental conditions, particularly on fluid velocities.
Abilities, Motivations, and Opportunities of Furloughed Employees in the Context of Covid-19: Preliminary Evidence From the UK

The Covid-19 global pandemic is a crisis like no other, forcing governments to implement prolonged national lockdowns in an effort to limit the spread of the disease. As organizations aim to adapt and remain operational, employers can suspend or reduce work activity for events related to Covid-19 and claim government support to subsidize employee wages. In this way, some employees are placed on furlough (i.e., temporary unemployment) as opposed to being made redundant. While the impact of such schemes on global economy attracted much attention, their micro-level impact on individual employees is still unknown. Building on the ability-motivation-opportunity (AMO) framework, this pilot study explores how employees' perceptions of abilities, motivation, and opportunities are affected as a result of furlough. Rapid ethnography including interviews, observations, and document analysis in a British organization provided insights into the perceptions and experiences of employees put on furlough and highlighted that all three elements of AMO are affected by the current situation, either positively or negatively. We identify theoretical contributions and suggest a number of AMO enhancing practices in the context of furlough.
Complete Metamorphosis in Manduca sexta Involves Specific Changes in DNA Methylation Patterns

The transition between morphologically distinct phenotypes during complete metamorphosis in holometabolous insects is accompanied by fundamental transcriptional reprogramming. Using the tobacco hornworm (Manduca sexta), a powerful model for the analysis of insect evolution and development, we conducted a genome-wide comparative analysis of gene expression and DNA methylation in caterpillars and adults to determine whether complete metamorphosis has an epigenetic basis in this species. Bisulfite sequencing indicated a generally low level of DNA methylation with a unimodal CpGO/E distribution. Expression analysis revealed that 24 % of all known M. sexta genes (3.729) were upregulated in last-instar larvae relative to the adult moth, whereas 26 % (4.077) were downregulated. We also identified 4.946 loci and 4.960 regions showing stage-specific differential methylation. Interestingly, genes encoding histone acetyltransferases and histone deacetylases were differentially methylated in the larvae and adults, indicating there is crosstalk between different epigenetic mechanisms. The distinct sets of methylated genes in M. sexta larvae and adults suggest that complete metamorphosis involves epigenetic modifications associated with profound transcriptional reprogramming, involving approximately half of all the genes in this species.
Lack of Effectiveness of Repurposed Drugs for COVID-19 Treatment

The magnitude of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has prompted the repurposing of several drugs to quickly stop the morbidity, mortality, and spread of this new disease. Repurposed drugs tested to fight COVID-19 have been chosen mainly on the basis of promising in vitro efficacy against SARS-CoV-2 or on previous therapeutic results with other human coronavirus diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) (1). Numerous clinical trials have already been completed, but no repurposed drug evaluated to date has been found that could significantly impact the course of COVID-19 pandemic (2). Our experience with previous viral pandemics, such as human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV), has taught us that precise design and target specificity will be essential to obtaining potent and successful antivirals against SARS-CoV-2.
Relationships Between the Life Satisfaction, Meaning in Life, Hope and COVID-19 Fear for Turkish Adults During the COVID-19 Outbreak

The current study investigated whether there are significant relationships between life satisfaction and meaning in life, hope and COVID-19 fear and the extent to which life satisfaction is predicted by these variables. The study group of this research consists of 1,186 adults with the mean age of 41.04. Study group participants are consists of different cities of different regions of Turkey. As the data collection tools, the life satisfaction scale, the meaning in life scale, the dispositional hope scale and the COVID-19 fear scale were used. The results of the analyses have revealed that meaning in life, hope (actuating thinking and alternative ways thinking) are significant predictors of life satisfaction as positively. Besides, it is seen COVID-19 fear, age, gender and the presence of people infected with COVID-19 around aren’t significant predictors of life satisfaction in adults.
Systems Biology Analysis of the Radiation-Attenuated Schistosome Vaccine Reveals a Role for Growth Factors in Protection and Hemostasis Inhibition in Parasite Survival

In spite of several decades of research, an effective vaccine against schistosomiasis remains elusive. The radiation-attenuated (RA) cercarial vaccine is still the best model eliciting high protection levels, although the immune mechanisms have not yet been fully characterized. In order to identify genes and pathways underlying protection we investigated patterns of gene expression in PBMC and skin draining Lymph Nodes (LN) from mice using two exposure comparisons: vaccination with 500 attenuated cercariae versus infection with 500 normal cercariae; one versus three doses. Vaccinated mice were challenged with 120 normal parasites. Integration of PBMC and LN data from the infected group revealed early up-regulation of pathways associated with Th2 skewing and polarization of IgG antibody profiles. Additionally, hemostasis pathways were downregulated in infected mice, correlating with platelet reduction, potentially a mechanism to assist parasite migration through capillary beds. Conversely, up regulation of such mechanisms after vaccination may explain parasite blockade in the lungs. In contrast, a single exposure to attenuated parasites revealed early establishment of a Th1 bias (signaling of IL-1, IFN-γ; and Leishmania infection). Genes encoding chemokines and their receptors were more prominent in vaccinated mice, indicating an enhanced capacity for inflammation, potentially augmenting the inhibition of intravascular migration. Increasing the vaccinations from one to three did not dramatically elevate protection, but there was a clear shift towards antibody-mediated effectors. However, elements of the Th1 bias were still evident. Notable features after three vaccinations were markers of cytotoxicity (including IL-6 and NK cells) together with growth factors and their receptors (FGFR/VEGF/EGF) and the apoptosis pathway. Indeed, there is evidence for the development of anergy after three vaccinations, borne out by the limited responses detected in samples after challenge. We infer that persistence of a Th1 response puts a limit on expression of antibody-mediated mechanisms. This feature may explain the failure of multiple doses to drive protection towards sterile immunity. We suggest that the secretions of lung stage parasites would make a novel cohort of antigens for testing in protection experiments.
The Association of TLR2, TLR3, and TLR9 Gene Polymorphisms With Susceptibility to Talaromycosis Among Han Chinese AIDS Patients in Guangdong

Background Talaromycosis (TM) caused by Talaromyces marneffei (T. marneffei) is a growing public health concern. Although Toll-like receptor (TLR) genes play a critical role in the host defense against fungal infection, the influence of polymorphisms in these genes on the susceptibility of acquired immune deficiency syndrome (AIDS) patients to TM remains unknown. This study aims to uncover the associations of single nucleotide polymorphisms (SNPs) in TLR genes with TM susceptibility among patients with AIDS. Methods Altogether 200 AIDS patients complicated with TM, 200 matched AIDS patients without TM, and 76 healthy controls (HCs) were enrolled in this case-control study. In total, 23 SNPs in the TLR2, TLR4, and TLR9 genes, which may influence the susceptibility of AIDS patients to TM, were checked by the time of flight mass spectrometry (TOF/MS) method among these Han Chinese subjects. Results No significant differences in genotype or allele frequencies of selected SNPs were found among the TM group, Non-TM group, and HC group. Haplotype analysis also demonstrated no correlation of these SNPs with TM. However, subgroup analysis showed that the genotype TT and the T allele in TLR2 SNP rs1339 were more frequent in typical TM cases than controls (50.0 vs. 35.8%, 70.5 vs. 59.7%); the frequency of the GT genotype in TLR2 SNP rs7656411 was markedly higher in severe TM cases compared to controls (57.8 vs. 34.4%). Conclusion Our results demonstrate a genetic connection of TLR2 SNPs rs1339 and rs7656411 with an increased susceptibility and severity of TM among Han Chinese populations.
Optimal Candidates to Do Fresh Embryo Transfer in Those Using Oral Contraceptive Pretreatment in IVF Cycles

Objective Concern regarding the adverse impact of pretreatment of oral contraceptives (OC) prior to ovarian stimulation for in vitro fertilization (IVF) on pregnancy outcome has been debated. We investigated factors that may be associated with live birth rate (LBR) in fresh embryo transfer cycles after OC pretreatment. Methods A retrospective study was conducted at the Reproductive Center of Ren Ji Hospital, Shanghai, China. 814 women aged 20–35 years undergoing their first autologous IVF cycle and fresh embryo transfer after OC pretreatment were included. Long gonadotropin releasing hormone (GnRH) agonist (a) or GnRH antagonist (ant) protocol was used for ovarian stimulation. Predictive factors for LBR were identified using multivariate logistic regression analysis. Results Multivariate logistic regression analysis demonstrated that using GnRH-ant protocol for ovarian stimulation was associated with significantly lower LBR (OR 0.70, 95% CI 0.52–0.93), while endometrial thickness on day of hCG trigger was associated with increased LBR (OR 1.16, 95% CI 1.06–1.27). Despite comparable patients’ age, duration of infertility, BMI and basal FSH between GnRH-a and GnRH-ant groups, those using GnRH-ant resulted in significantly lower LBR compared to the GnRH-a group (37.4 vs. 48.5%, p = 0.002). Using ROC analysis and a cut-off endometrial thickness of < and ≥ 9.5 mm, those < 9.5 mm using GnRH-ant resulted in significantly lower LBR (28.5 vs. 43.4%, p = 0.004), while no differences were noted with an endometrial thickness ≥9.5 mm (49.6 vs. 51.1%, p = 0.78). Conclusions Live birth was significantly impacted in OC pre-treated GnRH-ant cycles with an endometrial thickness of <9.5 mm on day of hCG trigger. Cryopreservation of all embryos in these cycles should be considered.