Miracle-dz/UniFAR-FTUs huggingface dataset:
Contrasting genetic structure of the Eurasian otter (Lutra lutra) across a latitudinal divide

Abstract The Eurasian otter (Lutra lutra) is recovering from well-documented population declines that occurred during the 20th century. Little is known about the genetic impact of these declines in northern Britain and the current understanding of otter genetic structure in Britain is incomplete. This study reexamines genetic structure in Scotland, one of the otter's major strongholds in the United Kingdom, and combines data with a published microsatellite data set from the remainder of the United Kingdom to produce the 1st comprehensive assessment of genetic structure across the entirety of mainland Britain. We show that there is a remarkable contrast in genetic structure of otters in northern Britain compared to the south. Population fragmentation and high levels of genetic structure were typical of southern Britain, whereas in the north we observed a virtually panmictic population. These results imply very different demographic histories of otters in these 2 regions. Our findings also suggest a more favorable environment for the Eurasian otter in recent times in the north of the United Kingdom, possibly linked to human population density and anthropogenic habitat impacts. This study therefore provides a complete description of population genetics of the Eurasian otter in the United Kingdom, and allows inferences to be made regarding the relative importance of landscape characteristics on the recovery of otter populations.
Efficacy and safety of underwater endoscopic mucosal resection for superficial non-ampullary duodenal epithelial tumors: a systematic review and meta-analysis

Background: Superficial non-ampullary duodenal epithelial tumors (SNADET) are increasingly found during upper endoscopy. Underwater endoscopic mucosal resection (UEMR) is an emerging technique for the endoscopic resection of SNADET. We performed a systematic review and meta-analysis to evaluate the efficacy and safety of this technique. Methods: We conducted a comprehensive search of several databases from inception to August 2019, which included Ovid Cochrane Database of Systematic Reviews, Ovid Embase, Scopus, Ovid Cochrane Central Register of Controlled trials, Ovid MEDLINE®, and In-Process and other non-indexed citations. The primary outcome assessed was the pooled clinical success rate of UEMR. Secondary outcomes included rate of en bloc resection, pooled rate of high-grade dysplasia or intramucosal carcinoma (HGIC), and pooled rate of adverse events. Meta-regression analysis was performed based on tumor size. Results: A total of 8 study arms were included for analysis with UEMR performed in a total of 258 lesions. The pooled clinical success rate was 89.9% (95% confidence interval [CI] 83.4-94.1). En-bloc removal was achieved in 84.6% of treated lesions (95%CI 75.5-90.7). The pooled rate of HGIC was 24.7% (95%CI 10.3-48.3). The pooled rate of adverse events was 6.9% (95%CI 2.5-17.9). This included 10 total adverse events, with the majority being self-limited delayed bleeding. There were no duodenal perforations. Conclusions: UEMR for endoscopic resection of SNADET has a high efficacy. In addition, this technique has a high rate of en bloc resection and an acceptable adverse event profile. Given these data, UEMR should be considered as a method for endoscopic resection of SNADET.
Diet-morphology relationship in a fish assemblage from a medium-sized river of French Guiana: the effect of species taxonomic proximity

We investigated the global relationship between diet and morphology for 42 fish species from a medium-sized river in French Guiana and checked the influence of the species taxonomic proximity on the implication of individual morphological traits in that relation. The 42 species were classified in eight trophic guilds based on analysis of more than 4000 stomach contents. Taxonomic proximity between species was accounted for by an autoregressive model applied to original data of diet and morphology. Original and taxonomic-free data were then submitted to a Canonical Correspondence Analysis in order to detect the relationship between diet and morphology. We compared the results obtained by analyzing the original data and the corrected data. The results confirm the existence of a significant global relationship between diet and morphology. However, morphological traits responsible for that relation were different when considering the taxonomic-free data. Particularly the well known relationship between gut length and detritivory was not observed on the taxonomic free analysis. It is concluded that controlling for phylogeny is essential to the detection of relationships between diet and morphology. It is also concluded that, despite the robustness of some relationships between morphology and diet, many diets cannot be inferred by a ecomorphological approach.
Cysticercoids of three species of Tatria (Cyclophyllidea: Amabiliidae) including T. octacantha sp.nov. from the haemocoele of the damsel-fly nymphs Pyrrhosoma nymphula, Sulz and Enallagma cyathigerum, Charp.

Cysticercoids of three species of Tatria have been recovered from the haemocoele of two species of damsel-fly nymphs from a lake in Mid-Wales. This is the first record of Tatria in Britain. The cysticercoids are enclosed each in a transparent capsule of host origin permanently attached to the midgut of the host. The cysticercoids of the three species are indistinguishable superficially. Specific diagnosis depending on the armature of the scolex. Tatria octacantha sp.nov. differs from the other eight species by the presence of eight apical rostellar hooks and 48 small spines on the rostellar surface. One mature adult was found in a little grebe Podiceps ruficollis ruficollis (Pallas) from the same lake and is described briefly. The cysticercoids are described in general terms and the scolex of T. octacantha in detail including the mode of operation of the rostellum and the ultrastructure of the surface layers. A layer of fibres occurs below the superficial longitudinal muscles of the rostellum providing additional support for this mobile organ. A revised key to the nine species of Tatria is included.
OPTIMIZATION OF PROCESS PARAMETERS FOR THE PRODUCTION OF CYCLODEXTRIN GLYCOSYLTRANSFERASE BY NEWLY ISOLATED BACILLUS SP. TPR71H BY CONVENTIONAL METHOD

The extracellular enzyme cyclodextrin glucanotransf erase (CGTase) synthesizes cyclic malto-oligosaccharides called cyclodextrins (CDs) from starch and related glucans. CGTases are produced by a variety of bacte ria, mainly Bacillus species, by submerged culture in complex medium. CGTases differ in the amount and types of CDs produced. In addition, CGTase production is highly dependent on the strain, medium composition and culture conditions. Therefore we undertook this stu dy with a newly isolated strain of Bacillus sp. TPR71H . CGTase activity produced from Bacillus sp. TPR71H was optimised in shake flasks using conventional method. Effects of nutrients, including several carbon, nit rogen and mineral sources, and environmental conditions like pH, temperature were assayed. The selected minimal medium consisted of 1.0 % starch, 0.5 % yeast extra ct, 0.5 % peptone, 0.1 % disodium hydrogen phosphate, 0.02 % magnesium sulphate and distilled water. The process parameters were optimized by changing one independent variable, while fixing the others at a certain l evel. Maximum CGTase activity obtained in supernatants was 30.34 U/mL. In this study we have screened condit ions for optimal CGTase production by newly isolate bacillus sp. TPR71H. From this study we found that the optimized parameters for the production of CGTase by Bacillus sp. TPR71H were Soluble Starch 3%, Yeast Extract 0.5%, K 2HPO 4 0.1%, Inoculum Level 3.5%, Inoculum Age 24h, Incubation Period 36h, rpm 220, Incubation Temperature 32°C and the pH of 7.5.
Microplastics as a Vector for Exposure to Hydrophobic Organic Chemicals in Fish: A Comparison of Two Polymers and Silica Particles Spiked With Three Model Compounds

The role of microplastics as chemical vectors delivering environmental contaminants into biota has been proposed, but their environmental relevance remains an issue of a debate. In this paper we compared the propensity and relative importance of synthetic polymer microparticles [glassy polystyrene (PS) and rubbery polyethylene (PE)] and silica glass particles (SG) to act as vectors for hydrophobic organic chemicals (HOCs) into fish after ingestion. Particles were spiked with three HOCs [17α-ethinylestradiol, chlorpyrifos and benzo(α)pyrene], which differ in hydrophobicity and induce well-known biomarker responses. Three-spined stickleback were exposed to 8 different diets: control diets (1), diets with non-spiked particles (2–4), diets containing a mixture of particles spiked with 3 model contaminants (5–7) and, finally, diets loaded with only the chemical mixture (8), for 14 days. Chemical sorption onto the particles was quantified and chemical transfer into the fish was investigated via biomarkers (CYP1a, ERα, VTG, and AChE) in fish intestine, liver and brain and quantification of HOCs in fish muscle. Results demonstrated particle-mediated chemical transfer of moderately hydrophobic contaminants into fish. While PS and PE particles mediated higher chemical transfer and tissue accumulation of 17α-ethinylestradiol and chlorpyrifos than SG, the overall chemical transfer was found to be very low. The present work suggested that chemical sorption, desorption and subsequent transfer of chemicals in vivo depends on multiple interconnected factors, including physicochemical properties of particles and contaminants, as well as toxicokinetic and toxicodynamic interactions. The biomarker approach was, however, suboptimal for assessing chemical transfer when addressing particle-associated chemical mixtures.
Host preferences of aphidophagous hoverflies from field distribution of their larvae

The patterns of occurrences among aphid colonies of the larvae of two species of highly polyphagous predatory hoverflies, Episyrphus balteatus (de Geer) and Syrphus ribesii (L.) (Diptera: Syrphidae), were assessed in three areas (Nottingham, Cardiff (UK) and the Czech Republic); in the last two sites, larvae of other syrphid species were also identified. The two syrphid species showed considerable diet overlap, their larvae using many of the same aphids as food, but with significant exceptions. Together with information from the literature, even for these very generalist species there was a consistent pattern of preference among aphid species. Most other species showed restricted preferences. Larvae were more frequent on developed aphid colonies than on colonies that were younger or had almost disappeared.
Structural Covariance Network Disruption and Functional Compensation in Parkinson’s Disease

Purpose: To investigate the structural covariance network disruption in Parkinson’s disease (PD), and explore the functional alterations of disrupted structural covariance network. Methods: A cohort of 100 PD patients and 70 healthy participants underwent structural and functional magnetic resonance scanning. Independent component analysis (ICA) was applied separately to both deformation-based morphometry (DBM) maps and functional maps with the same calculating parameters (both decomposed into 20 independent components (ICs) and computed 20 times the Infomax algorithm in ICASSO). Disrupted structural covariance network in PD patients was identified, and then, we performed goodness of fit analysis to obtain the functional network that showed the highest spatial overlap with it. We investigated the relationship between structural covariance network and functional network alterations. Finally, to further understand the structural and functional alterations over time, we performed a longitudinal subgroup analysis (51 patients were followed up for 2 years) with the same procedures. Results: In a cross-sectional analysis, PD patients showed decreased structural covariance between anterior and posterior cingulate subnetworks. The functional components showed best overlap with anterior and posterior cingulate structural subnetworks were selected as anterior and posterior cingulate functional subnetworks. The functional connectivity between them was significantly increased [assessed by Functional Network Connectivity (FNC) toolbox]; and the increased functional connectivity was negatively correlated with cingulate structural covariance network integrity. Longitudinal subgroup analysis showed cingulate structural covariance network disruption was worse at follow-up, while the functional connectivity between anterior and posterior cingulate network was increased at baseline and decreased at follow-up. Conclusion: This study indicated that the cingulate structural covariance network displayed a high susceptibility in PD patients. This study indicated that the cingulate structural covariance network displayed a high susceptibility in PD patients. Considering that disrupted structural covariance network coexisted with enhanced/remained functional activity during disease development, enhanced functional activity underlying the disrupted cingulate structural covariance network might represent a temporal compensation for maintaining clinical performance.
Water Flow Behavior and Storage Potential of the Semi-Arid Ephemeral River System in the Mara Basin of Kenya

Alluvial corridors of ephemeral river systems provide viable opportunities for natural water storage in dry lands. Whilst alluvial corridors are widely recognized as water buffers, particularly for areas experiencing constant water scarcity, little research has been undertaken in Sub-Saharan Africa to explore their hydrological variability and water resource potential as alternative water sources for nearby communities. This study investigated the water flow behavior and storage potential of an ephemeral river system in the Mara Basin of Kenya for purposes of supporting water resources development and ecological sustainability. The water flow processes – including the recharge rates and water loss processes – from existing sand storage systems were established through monitoring of ground and surface water levels. Water samples along the alluvial corridor were collected and analyzed for major ions and isotopic signatures required to establish the water storage dynamics. The storage potential was estimated through Probing and Electrical Resistivity Tomography techniques, augmented with in-situ measurements of hydraulic conductivities and channel bed porosities. The mean annual storage volume in the alluvium of the study reach was estimated at 1.1 Mm3, potentially capable of providing for the annual domestic and livestock water demands of the area. Transmission losses into the alluvium beneath the ephemeral channel-bed were noted to attenuate the flood peak discharges, depending on the level of saturation of the alluvial bed. However, water storage in the alluvium was subject to losses through evapotranspiration and seepage through fractured bedrocks. The study demonstrated the potential of alluvial corridors as water storage buffers providing alternative water sources to communities within the dry land regions with water scarcity, thereby to supporting ecosystem sustainability.
Possible new intranuclear symbionts of Paramecium caudatum

Summary Intranuclear bacteria inhabiting macronucleus of Paramecium caudatum isolated from three populations from North America and Eastern Europe were studied. Interference contrast and electron microscopy was used to describe symbiont morphology. Symbiotic bacteria from such distant populations are rather similar. They are rod-shaped with 1–2 µm length and 0.3–0.4 µm diameter; cell wall is typical for gram-negative bacteria; membrane vesicles on the surface of some bacteria indicate the secretion of some periplasm material into the nucleus. According to the in situ hybridization with group-specific probes, these symbionts belong to a-Proteobacteria subdivision. The proposal of α -Proteobacteria advantages for intracellular and intranuclear life are discussed.
The Broad Spectrum of LMNA Cardiac Diseases: From Molecular Mechanisms to Clinical Phenotype

Mutations of Lamin A/C gene (LMNA) cause laminopathies, a group of disorders associated with a wide spectrum of clinically distinct phenotypes, affecting different tissues and organs. Heart involvement is frequent and leads to cardiolaminopathy LMNA-dependent cardiomyopathy (LMNA-CMP), a form of dilated cardiomyopathy (DCM) typically associated with conduction disorders and arrhythmias, that can manifest either as an isolated event or as part of a multisystem phenotype. Despite the recent clinical and molecular developments in the field, there is still lack of knowledge linking specific LMNA gene mutations to the distinct clinical manifestations. Indeed, the severity and progression of the disease have marked interindividual variability, even amongst members of the same family. Studies conducted so far have described Lamin A/C proteins involved in diverse biological processes, that span from a structural role in the nucleus to the regulation of response to mechanical stress and gene expression, proposing various mechanistic hypotheses. However, none of those is per se able to fully justify functional and clinical phenotypes of LMNA-CMP; therefore, the role of Lamin A/C in cardiac pathophysiology still represents an open question. In this review we provide an update on the state-of-the-art studies on cardiolaminopathy, in the attempt to draw a line connecting molecular mechanisms to clinical manifestations. While investigators in this field still wonder about a clear genotype/phenotype correlation in LMNA-CMP, our intent here is to recapitulate common mechanistic hypotheses that link different mutations to similar clinical presentations.
Active integrins regulate white adipose tissue insulin sensitivity and brown fat thermogenesis

Reorganization of the extracellular matrix is a prerequisite for healthy adipose tissue expansion, whereas fibrosis is a key feature of adipose dysfunction and inflammation. However, very little is known about the direct effects of impaired cell-matrix interaction in adipocyte function and insulin sensitivity. Using adipose selective deletion of β1 integrin (Itgb1adipo-cre) and Kindlin-2 (Kind2adipo-cre), we demonstrate here that active β1 and β3 integrins directly interact with the insulin receptor to regulate white adipocyte insulin action and systemic metabolism. Consequently, loss of adipose integrin activity, similar to loss of adipose insulin receptors, results in lipodystrophy and systemic insulin resistance. Conversely, we find that brown adipose tissue of Kind2adipo-cre and Itgb1adipo-cre mice is chronically hyperactivated, and has increased substrate delivery, reduced endothelial basement membrane thickness, and increased endothelial vesicular transport. Thus, we establish integrin-extracellular matrix interactions as key regulators of white and brown adipose tissue function and whole body metabolism.
Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes revealed its epidemic trend and possible origins

Objectives To reveal epidemic trend and possible origins of SARS-CoV-2 by exploring its evolution and molecular characteristics based on a large number of genomes since it has infected millions of people and spread quickly all over the world. Methods Various evolution analysis methods were employed. Results The estimated Ka/Ks ratio of SARS-CoV-2 is 1.008 or 1.094 based on 622 or 3624 SARS-CoV-2 genomes, and the time to the most recent common ancestor (tMRCA) was inferred in late September 2019. Further 9 key specific sites of highly linkage and four major haplotypes H1, H2, H3 and H4 were found. The Ka/Ks, detected population size and development trends of each major haplotype showed H3 and H4 subgroups were going through a purify evolution and almost disappeared after detection, indicating H3 and H4 might have existed for a long time, while H1 and H2 subgroups were going through a near neutral or neutral evolution and globally increased with time. Notably the frequency of H1 was generally high in Europe and correlated to death rate (r>0.37). Conclusions In this study, the evolution and molecular characteristics of more than 16000 genomic sequences provided a new perspective for revealing epidemiology of SARS-CoV-2.
Pain Catastrophizing Thoughts Explain the Link Between Perceived Caregiver Responses and Pain Behaviors of Patients With Chronic Musculoskeletal Pain

Purpose Caregivers’ responses to pain behaviors of patients with chronic pain have an essential role in how patients perceive their pain condition. The current study investigated the mediating role of pain catastrophizing on the link between perceived caregiver responses and patient pain behaviors. Materials and Methods The sample of this cross-sectional study consisted of 200 patients with chronic pain (mean of age = 44.6; 71.5% were female). Participants responded to measures assessing their perception of their caregiver responses to their pain, their pain catastrophizing thoughts, and their pain behaviors. Results The mediation analyses showed that perceived distracting responses were negatively related to pain catastrophizing level in patients, which in turn was positively associated with expressing pain behaviors. Besides, perceived caregiver negative responses were positively associated with catastrophizing thoughts, which in turn was positively related to expressing pain behaviors. Conclusion Patients’ perceptions regarding how their caregiver responds to their pain condition can be related to their thoughts about their pain and how they react to their pain situation. Investigating the external sources that might have an impact on patients’ reactions to their pain, especially when those external sources are caregivers who, in most situations, are with the patients for a prolonged duration, is essential.
Manipulating genetic architecture to reveal fitness relationships

Traits are often claimed (rather than shown) to be closely related to fitness. Sometimes this leads to contrasting predictions for the direction of the association between the trait value and fitness, a prime example of which is the debate over how (Darwinian) fitness links with the rate of energy turnover at rest (see: Burton et al. 2011, for definitions). To resolve this debate Burton et al. (2011) suggested manipulation of traits and measuring changes in fitness. In this perspective, we propose that we should do the opposite – manipulate genetic architecture underlying fitness and measure the traits response.