Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effect of Crystal Mismatch on the Thermoelectric Performance Enhancement of Nano Cu2Se

In the past decades, Cu2−x Se compounds have attracted great attention due to the inclusion of non-toxic and abundant elements, besides having a promising thermoelectric (TE) performance. In this work, we investigated the effect of a crystal mismatch of a nanoinclusion phase on the TE properties of Cu2−x Se. Nano-Cu2Se was synthesized using microwave assisted thermolysis, while the p-type skutterudite, Fe3.25Co0. 75Sb12 (FeCoSb), compound was synthesized using a chemical alloying route. Nano-Cu2Se, and (nano-Cu2Se)1−x (nano-FeCoSb) x composites, where x = 0.05 and 0.1, were prepared via mechanical alloying followed by Spark Plasma Sintering process. Structural properties were evaluated by PXRD and SEM analysis, while the high temperature transport properties were examined via electrical conductivity, Seebeck coefficient, and thermal conductivity measurements in the temperature range of 300–800 K. Powder X-ray diffraction (PXRD) confirmed a single phase of nano Cu2Se, while the samples with FeCoSb inclusion consist of two phases as Cu2Se and CoSb3. SEM micrographs of all samples show that Cu2Se has randomly oriented grains with different sizes. Cu2Se samples with a FeCoSb inclusion show a rather different structure. In these samples, a rod-shaped FeCoSb phase, with a size varying between 20 and 100 nm, showed an inhomogeneous distribution in the structure and stacked between the Cu2Se layers. Transport data indicate that crystal mismatch between Cu2Se and FeCoSb has a strong effect on the TE transport properties. Electrical conductivity decreases but Seebeck coefficient enhances with nano FeCoSb inclusion. Total thermal conductivity was suppressed by 30% and ZT value enhanced by 15% with 5% nano FeCoSb inclusion at 750 K, likely due to a decrease in the electronic contribution of the thermal conductivity. Structural and transport data show that small amount of nanoinclusion of FeCoSb has a beneficial effect on the TE performance of nano Cu2Se at temperatures below 800 K.
Impact of COVID-19 Pandemic on University Students' Physical Activity Levels: An Early Systematic Review

Purpose: This systematic review aimed to analyze the impact that the COVID-19 lockdown had on the amount of physical activity performed by university students. Materials and Methods: A systematic electronic search for studies providing information regarding physical activity levels pre and during COVID-19 pandemic in university students was performed up to 20th October 2020 in the databases Cochrane Library, PubMed, SPORTDiscus, and Web of Science. The risk of bias of external validity quality of included studies was assessed by means of those the Newcastle-Ottawa Scale (NOS). The quality of the evidence for main outcomes was graded using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. Results and Conclusions: A total of 10 studies were selected. Physical activity levels were assessed by means of questionnaires (10 studies) and accelerometer (1 study). Risk of bias was regarded as low and high in six and four investigations, respectively. The quality of evidence was downgraded to low. A significant reduction of physical activity levels were observed in 9 studies. Compared to pre-lockdown values, five studies showed a reduction of light/mild physical activity (walking) between 32.5 and 365.5%, while seven studies revealed a reduction of high/vigorous physical activity between 2.9 and 52.8%. Walking, moderate, vigorous, and total physical activity levels have been reduced during the COVID-19 pandemic confinements in university students of different countries. Despite of the reductions, those who met the current minimum PA recommendations before the lockdown generally met the recommendations also during the confinements.
Catanionic vesicles from an amphiphilic prodrug molecule: a new concept for drug delivery systems

Toxicity and low entrapment efficiency are the main problems for pharmaceutical applications of catanionic vesicles. In order to minimize surfactant toxicity, increase the drug loading content and simultaneously reduce the need for tedious chemical synthesis, we use oleic acid as the biocompatible surfactant, which reacts with the selected drug molecules (amlodipine) to produce an amphiphilic prodrug molecule for the straightforward fabrication of catanionic vesicles. The prodrug molecules are easily obtained by proton transfer between amlodipine and oleic acid molecules. The characterization of prodrug molecules and their aggregation behaviours in aqueous solutions are investigated by using Fourier transform infrared spectrophotometry (FTIR), 1H-nuclear magnetic resonance (1H-NMR), differential scanning calorimetry (DSC), surface tension measurement, transmission electron microscopy (TEM), dynamic light scattering (DLS), conductivity and zeta potential (ζ). The results demonstrate that vesicles could be easily formed with the prodrug amphiphilic molecules dispersed in aqueous solutions. Particularly, the drug release behaviour of the as-prepared catanionic vesicles exhibits excellent sustained drug release properties, which demonstrates their promising application in the newly designed drug delivery system.
ASSESSMENT OF GLUCOSINOLATES IN BROCCOLI BY THREE DIFFERENT METHODOLOGIES

Three different methodologies were used to assess the glucosinolate content in four broccoli cultivars. The assessment was performed by the thymol, enzyme immobilization and gas liquid chromatography (GLC) techniques. The cultivars used were Green Valiant, Green Duke, Marathon and Samurai. The three techniques demonstrated that Samurai and Green Valiant were the cultivars with the highest content of glucosinolates. It was also evident that, compared to stem and leaves, the floret of the four cultivars exhibited in general the highest amount of this component. Of the tested methodologies, the GLC technique showed the lowest data variability, although this technique was unable to estimate all the glucosinolates present in the broccoli samples because of its poor performance for the quantitation of indole and sulfinyl glucosinolates. In conclusion, the thymol technique appeared the most adequate procedure for the assessment of glucosinolates in broccoli samples.
Morphological variability in the mucosal attachment site of Trichuris muris revealed by X-ray microcomputed tomography

Parasitic infections can be challenging to study, because light and electron microscopy are often limited in visualising complex and inaccessible attachment sites. Exemplifying this, Trichuris spp. inhabits a tunnel of epithelial cells within the host caecum and colon. A significant global burden of this infection persists partly because available anthelminthics lack efficacy, although the mechanisms underlying this remain unknown. Consequently, there is a need to pioneer new approaches to better characterize the parasite niche within the host and investigate how variation in its morphology and integrity may contribute to resistance to therapeutic intervention. To address these aims, we exploited 3D X-ray micro-computed tomography (microCT) to image the mouse whipworm T. muris in caeca of wild-type C57BL/6 and SCID mice ex vivo. Using osmium tetroxide staining to effectively enhance contrast of worms, we found that a subset exhibited preferential positioning towards the bases of the intestinal crypts. Moreover, in one rare event, we demonstrate whipworm traversal of the lamina propria. This morphological variability contradicts widely accepted conclusions from conventional microscopy of the parasite niche, showing Trichuris in close contact with the host proliferative and immune compartments that may facilitate immunomodulation. Furthermore, by using a skeletonization-based approach we demonstrate considerable variation in tunnel length and integrity which may represent an indicator of tunnel “health”. The qualitative and quantitative observations provide a new morphological point of reference for future in vitro study of Trichuris-host interactions and highlight the potential of microCT to more accurately characterise enigmatic host-parasite interactions. Author Summary Parasites are often difficult to observe once established within host tissues, presenting a barrier to biological understanding and therapeutic innovation. Whipworms (Trichuris spp.) affect 500 million people worldwide, causing significant disability, and appear partially resistant to widely used “deworming” drugs. However, the inaccessibility of worms within the cells of the host intestine makes them highly challenging to image and study. By investigating Trichuris attachment sites in 3D, using X-ray micro-computed tomography, we found that the niche is highly variable in size and, contrary to reports in all previous studies, can also penetrate different layers of intestinal tissue. By showing that worms are positioned much closer to host immune cells that previously appreciated, we provide a morphological reference point for future studies on how Trichuris effectively avoids clearance by the host. The non-invasive imaging approach used represents an excellent opportunity to clarify the lifecycles of other difficult-to-study parasites.
Apathogenic proxies for transmission dynamics of a fatal virus

Identifying drivers of transmission prior to an epidemic—especially of an emerging pathogen—is a formidable challenge for proactive disease management efforts. We tested a novel approach in the Florida panther, hypothesizing that apathogenic feline immunodeficiency virus (FIV) transmission could predict transmission dynamics for pathogenic feline leukemia virus (FeLV). We derived a transmission network using FIV whole genome sequences, and used exponential random graph models to determine drivers structuring this network. We used these drivers to predict FeLV transmission pathways among panthers and compared predicted outbreak dynamics against empirical FeLV outbreak data. FIV transmission was primarily driven by panther age class and distances between panther home range centroids. Prospective FIV-based modeling predicted FeLV dynamics at least as well as simpler, often retrospective approaches, with evidence that FIV-based predictions captured the spatial structuring of the observed FeLV outbreak. Our finding that an apathogenic agent can predict transmission of an analogously transmitted pathogen is an innovative approach that warrants testing in other host-pathogen systems to determine generalizability. Use of such apathogenic agents holds promise for improving predictions of pathogen transmission in novel host populations, and could thereby provide new strategies for proactive pathogen management in human and animal systems.
Humanization of antibodies using a machine learning approach on large-scale repertoire data

Monoclonal antibody therapeutics are often produced from non-human sources (typically murine), and can therefore generate immunogenic responses in humans. Humanization procedures aim to produce antibody therapeutics that do not elicit an immune response and are safe for human use, without impacting efficacy. Humanization is normally carried out in a largely trial-and-error experimental process. We have built machine learning classifiers that can discriminate between human and non-human antibody variable domain sequences using the large amount of repertoire data now available. Our classifiers consistently outperform existing best-in-class models, and our output scores exhibit a negative relationship with the experimental immunogenicity of existing antibody therapeutics. We used our classifiers to develop a novel, computational humanization tool, Hu-mAb, that suggests mutations to an input sequence to reduce its immunogenicity. For a set of existing therapeutics with known precursor sequences, the mutations suggested by Hu-mAb show significant overlap with those deduced experimentally. Hu-mAb is therefore an effective replacement for trial- and-error humanization experiments, producing similar results in a fraction of the time. Hu-mAb is freely available to use at opig.stats. ox.ac. uk/webapps/humab.
Dysregulation of the basal ganglia indirect pathway prior to cell loss in the Q175 mouse model of Huntington’s disease

The psychomotor symptoms of Huntington’s disease (HD) are linked to degeneration of the basal ganglia indirect pathway. To determine how this pathway is perturbed prior to cell loss, optogenetic- and reporter-guided electrophysiological interrogation approaches were applied to early symptomatic 6-month-old Q175 HD mice. Although cortical activity was unaffected, indirect pathway striatal projection neurons were hypoactive in vivo, consistent with reduced cortical input strength and dendritic excitability. Downstream parvalbumin-expressing prototypic external globus pallidus (GPe) neurons were hyperactive in vivo and exhibited elevated autonomous firing ex vivo. Optogenetic inhibition of prototypic GPe neurons ameliorated the abnormal hypoactivity of postsynaptic subthalamic nucleus (STN) and putative arkypallidal neurons in vivo. In contrast to STN neurons, autonomous arkypallidal activity was unimpaired ex vivo. Together with previous studies, these findings demonstrate that basal ganglia indirect pathway neurons are highly dysregulated in Q175 mice through changes in presynaptic activity and/or intrinsic properties 6-12 months before cell loss.
ADF and cofilin-1 collaborate to promote cortical actin flow and the leader bleb-based migration of confined cells

Melanoma cells have been shown to undergo fast amoeboid (leader bleb-based) migration, requiring a single large bleb for migration. In leader blebs, is a rapid flow of cortical actin that drives the cell forward. Using RNAi, we find that co-depleting cofilin-1 and ADF led to a large increase in cortical actin, suggesting that both proteins regulate cortical actin. Furthermore, severing factors can promote contractility through the regulation of actin architecture. However, RNAi of cofilin-1 but not ADF led to a significant decrease in cell stiffness. We found cofilin-1 to be enriched at leader bleb necks, whereas RNAi of cofilin-1 and ADF reduced bleb sizes and the frequency of motile cells. Strikingly, cells without cofilin-1 and ADF had blebs with abnormally long necks. Many of these blebs failed to retract and displayed slow actin turnover. Collectively, our data identifies cofilin-1 and ADF as actin remodeling factors required for fast amoeboid migration.
Altered A-Type Potassium Channel Function Impairs Dendritic Spike Initiation and Temporoammonic Long-Term Potentiation in Fragile X Syndrome

Fragile X syndrome (FXS) is the leading monogenetic cause of cognitive impairment and autism spectrum disorder. Area CA1 of the hippocampus receives current information about the external world from the entorhinal cortex via the temporoammonic (TA) pathway. Given its role in learning and memory, it is surprising that little is known about TA long-term potentiation (TA-LTP) in FXS. We found that TA-LTP was impaired in male fmr1 KO mice. Although there were no significant differences in basal synaptic transmission, synaptically evoked dendritic calcium signals were smaller in KO neurons. Using dendritic recording, we found no difference in complex spikes or pharmacologically isolated Ca2+ spikes; however, the threshold for fast, Na+-dependent dendritic spikes was depolarized in fmr1 KO mice. Cell-attached patch-clamp recordings found no difference in Na+ channels between wild-type and fmr1 KO CA1 dendrites. Dendritic spike threshold and TA-LTP were restored by blocking A-type K+ channels with either 150 µm Ba2+ or the more specific toxin AmmTx3. The impairment of TA-LTP shown here, coupled with previously described enhanced Schaffer collateral LTP, may contribute to spatial memory alterations in FXS. Furthermore, as both of these LTP phenotypes are attributed to changes in A-type K+ channels in FXS, our findings provide a potential therapeutic target to treat cognitive impairments in FXS. SIGNIFICANCE STATEMENT Alterations in synaptic function and plasticity are likely contributors to learning and memory impairments in many neurologic disorders. Fragile X syndrome is marked by dysfunctional learning and memory and changes in synaptic structure and function. This study shows a lack of LTP at temporoammonic synapses in CA1 neurons associated with biophysical differences in A-type K+ channels in fmr1 KO CA1 neurons. Our results, along with previous findings on A-type K+ channel effects on Schaffer collateral LTP, reveal differential effects of a single ion channelopathy on LTP at the two major excitatory pathways of CA1 pyramidal neurons. These findings expand our understanding of memory deficits in FXS and provide a potential therapeutic target for the treatment of memory dysfunction in FXS.
The duration of antibiotic treatment is associated with carriage of toxigenic and non-toxigenic strains of Clostridioides difficile in dogs

Clostridioides difficile is a leading cause of human antibiotic-associated diarrhoeal disease globally. Zoonotic reservoirs of infection are increasingly suspected to play a role in the emergence of this disease in the community and dogs are considered as one potential source. Here we use a canine case-control study at a referral veterinary hospital in Scotland to assess: i) the risk factors associated with carriage of C. difficile by dogs, ii) whether carriage of C. difficile is associated with clinical disease in dogs and iii) the similarity of strains isolated from dogs with local human clinical surveillance. The overall prevalence of C. difficile carriage in dogs was 18.7% (95% CI 14.8-23.2%, n=61/327) of which 36% (n=22/61) were toxigenic strains. We found risk factors related to prior antibiotic treatment were significantly associated with C. difficile carriage by dogs. However, the presence of toxigenic strains of C. difficile in a canine faecal sample was not associated with diarrhoeal disease in dogs. Active toxin was infrequently detected in canine faecal samples carrying toxigenic strains (2/11 samples). Both dogs in which active toxin was detected had no clinical evidence of gastrointestinal disease. Among the ten toxigenic ribotypes of C. difficile detected in dogs in this study, six of these (012, 014, 020, 026, 078, 106) were ribotypes commonly associated with human clinical disease in Scotland, while atoxigenic isolates largely belonged to 010 and 039 ribotypes. Whilst C. difficile does not appear commonly associated with diarrhoeal disease in dogs, antibiotic treatment increases carriage of this bacteria including toxigenic strains commonly found in human clinical disease.
Easymap: A User-Friendly Software Package for Rapid Mapping-by-Sequencing of Point Mutations and Large Insertions

Mapping-by-sequencing strategies combine next-generation sequencing (NGS) with classical linkage analysis, allowing rapid identification of the causal mutations of the phenotypes exhibited by mutants isolated in a genetic screen. Computer programs that analyze NGS data obtained from a mapping population of individuals derived from a mutant of interest in order to identify a causal mutation are available; however, the installation and usage of such programs requires bioinformatic skills, modifying or combining pieces of existing software, or purchasing licenses. To ease this process, we developed Easymap, an open-source program that simplifies the data analysis workflows from raw NGS reads to candidate mutations. Easymap can perform bulked segregant mapping of point mutations induced by ethyl methanesulfonate (EMS) with DNA-seq or RNA-seq datasets, as well as tagged-sequence mapping for large insertions, such as transposons or T-DNAs. The mapping analyses implemented in Easymap have been validated with experimental and simulated datasets from different plant and animal model species. Easymap was designed to be accessible to all users regardless of their bioinformatics skills by implementing a user-friendly graphical interface, a simple universal installation script, and detailed mapping reports, including informative images and complementary data for assessment of the mapping results. One sentence summary Easymap is a versatile user-friendly software tool that facilitates mapping-by-sequencing of large insertions and point mutations in plant and animal genomes
Late Pleistocene palaeoecology and phylogeography of woolly rhinoceroses

The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted herbivore, widely distributed from western Europe to north-east Siberia during the Late Pleistocene. Previous studies associate the extinction of the species ~14,000 years before present to climatic and vegetational changes, and suggest that later survival of populations in north-east Siberia may relate to the later persistence of open vegetation in that region. Here, we analyzed carbon (δ13C) and nitrogen (δ15N) stable isotopes and mitochondrial DNA sequences to elucidate the evolutionary ecology of the species. Our dataset comprised 286 woolly rhinoceros isotopic records, including 192 unpublished records, from across the species range, dating from >58,600 14C years to ~14,000 years before present. Crucially, we present the first 71 isotopic records available to date of the 15,000 years preceding woolly rhinoceros extinction. The data reveal ecological flexibility and geographical variation in woolly rhinoceros stable isotope compositions through time. In north-east Siberia, we detected δ15N stability through time. This could reflect long-term environmental stability, and might have enabled the later survival of the species in the region. To further investigate the palaeoecology of woolly rhinoceroses, we compared their isotopic compositions with that of other contemporary herbivores. This analysis suggests possible niche partitioning between woolly rhinoceros and both horse (Equus spp.) and woolly mammoth (Mammuthus primigenius), and isotopic similarities between woolly rhinoceros and both musk ox (Ovibos moschatus) and saiga (Saiga tatarica) at different points in time. To provide phylogeographical context to the isotopic data, we analyzed 61 published mitochondrial control region sequences. The data show a lack of geographic structuring; we found three haplogroups with overlapping distributions, all of which show a signal of expansion during the Last Glacial Maximum. Furthermore, our genetic findings support the notion that environmental stability in Siberia had an impact on the paleoecology of woolly rhinoceroses in the region. Our study highlights the utility of combining stable isotopic records with ancient DNA to advance our knowledge of the evolutionary ecology of past populations and extinct species.
Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression

Cells live in constantly changing environments and employ dynamic signaling pathways to transduce information about the signals they encounter. However, the mechanisms by which dynamic signals are decoded into appropriate gene expression patterns remain poorly understood. Here, we devise networked optogenetic pathways that achieve novel dynamic signal processing functions that recapitulate cellular information processing. Exploiting light-responsive transcriptional regulators with differing response kinetics, we build a falling-edge pulse-detector and show that this circuit can be employed to demultiplex dynamically encoded signals. We combine this demultiplexer with dCas9-based gene networks to construct pulsatile-signal filters and decoders. Applying information theory, we show that dynamic multiplexing significantly increases the information transmission capacity from signal to gene expression state. Finally, we use dynamic multiplexing for precise multidimensional regulation of a heterologous metabolic pathway. Our results elucidate design principles of dynamic information processing and provide original synthetic systems capable of decoding complex signals for biotechnological applications.