bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Evaluation of Curriculum change in Physiology: A Mixed method research design
Authors: Teli Shivayogappa. S. , M. Senthil velou , K. Soundariya , Velusami Deepika , K Senthamil selvi , S Mangani Mangalavalli 
Published: April 2021

AbstractIntroductionThe quality of both teaching and learning techniques in health sciences determines the competency of the doctors produced and the patient care. Realizing the necessity of active learning at the undergraduate level, curricular reforms were crucial to ensure that students play an active role in the learning process and imbibe all the prerequisite qualities of a competent health professional. The objective of this study was to implement and evaluate case-based learning in the physiology curriculum.MethodsThe study included 150 first-year MBBS students. We followed a mixed research design in this study. A short lecture on anemia was followed by two sessions of CBL with a gap of one week. A structured questionnaire on a 5-point Likert scale was used to collect students’ perceptions. The internal consistency of the questionnaire was Cronbach α-statistic = 0.8. Faculties’ feedback was collected through Focus Group Discussion (FGD).ResultsOut of 145 participants, 117 responded to feedback. Students perceived that the CBL method was effective in understanding anemia topic (71%); promoted meaningful learning (83%); encouraged teamwork (69%); improved communication skills (65%); helps in future application of knowledge (81%); motivated self-directed learning (66%); helped to understand physiology concepts better (72%); leads to the development of problem-solving abilities (70%); and better student-teacher relationship (72%). Faculties suggested developing an assessment plan for future CBL sessions.ConclusionIn our experience, CBL is an effective, active teaching-learning tool that improves students’ understanding of basic concepts, clinical knowledge, problem-solving abilities, teamwork, communication skills, student-teacher relationship, and self-directed learning.
Positive modulation of cerebellar α6GABAAreceptors for treating essential tremor: a proof-of-concept study in harmaline-treated mice
Authors: Huang Ya-Hsien , Lee Ming Tatt , Sieghart Werner , Knutson Daniel E. , Wimmer Laurin R. , Sharmin Dishary , Cook James , Mihovilovic Marko D. , Chiou Lih-Chu 
Published: April 2021

AbstractBackgroundThe etiology of essential tremor (ET) remains unclear but may involve abnormal firing of Purkinje cells, which receive excitatory inputs from granule cells in the cerebellum. Since α6 subunit-containing GABAAreceptors (α6GABAARs) are abundantly expressed in granule cells, we validated a hypothesis that α6GABAAR-selective positive allosteric modulators (PAMs) are promising pharmacological interventions for ET therapy.MethodsEmploying the harmaline-induced ET model in male ICR mice, we evaluated the possible anti-tremor effects of four α6GABAAR-selective PAMs, the pyrazoloquinolinones Compound 6 and LAU-463 and their respective deuterated derivatives. Propranolol, a clinical anti-tremor agent, was employed as positive control. To investigate the involvement of cerebellar α6GABAARs in the antitremor effect of intraperitoneal (i.p.) Compound 6, furosemide, an α6GABAAR antagonist, was intracerebellarly (i.cb.) co-administered with Compound 6. The burrowing activity, an indicator of wellbeing in rodents, was measured concurrently.ResultsHarmaline (10-30 mg/kg,s.c.) induced action tremor in ICR mice dose-dependently and markedly reduced their burrowing activity. Compound 6 (3 and 10 mg/kg,i.p.) significantly attenuated harmaline (20 mg/kg)-induced action tremor and burrowing activity impairment. Propranolol (20 mg/kg,i.p.) diminished tremor but failed to restore the burrowing activity in harmaline-treated mice. Importantly, both anti-tremor and burrowing activity restorative effects of Compound 6 (10 mg/kg,i.p.) was significantly reversed by co-administration ofi.cb.furosemide at a dose (10 nmol/0.5 μl) having no effectper se. All four α6GABAAR PAMs exhibited a similar therapeutic efficacy.Conclusionα6GABAAR-selective PAMs significantly attenuated action tremor and restored physical well-being in a mouse model mimicking ET by acting in the cerebellum. Thus, α6GABAAR-selective PAMs may be potential therapeutic agents for ET.
Controlled Fluorescent Labelling of Metal Oxide Nanoparticles for Artefact-free Live Cell Microscopy
Authors: Kokot Boštjan , Kokot Hana , Umek Polona , van Midden Katarina Petra , Pajk Stane , Garvas Maja , Eggeling Christian , Koklič Tilen , Urbančič Iztok , Štrancar Janez 
Published: April 2021

AbstractNanotechnologies hold great promise for various applications. To predict and guarantee the safety of novel nanomaterials, it is essential to understand their mechanism of action in an organism, causally connecting adverse outcomes with early molecular events. They are best investigated using non-invasive advanced optical methods, such as high-resolution live-cell fluorescence microscopy, which require stable labelling of nanoparticles with fluorescent dyes. When performed inadequately, unbound fluorophores and inadvertently altered chemical and physical properties of the nanoparticles can, however, result in experimental artefacts and erroneous conclusions.To prevent such unintentional errors, we here describe a minimal combination of experimental methods to enable artefact-free fluorescent labelling of metal-oxide nanoparticles – the largest subpopulation of nanoparticles by industrial production and applications – and demonstrate its application in the case of TiO2nanotubes. We 1) characterize potential changes of the nanoparticles’ surface charge and morphology that might occur during labelling, and 2) assess stable binding of the fluorescent dye to nanomaterial, which ensures correct nanoparticle localization. Together, these steps warrant the reliability and reproducibility of advanced optical tracking, which is necessary to explore nanomaterials’ mechanism of action and will foster widespread and safe use of new nanomaterials.Abstract Figure
Cytosolic fumarase acts as a metabolic fail-safe for both high and low temperature acclimation ofArabidopsis thaliana
Authors: Herrmann Helena A. , Calzadilla Pablo I. , Schwartz Jean-Marc , Johnson Giles N. 
Published: April 2021

SummaryPlants acclimate their photosynthetic capacity in response to changing environmental conditions. InArabidopsis thaliana,photosynthetic acclimation to cold requires the accumulation of the organic acid fumarate, catalysed by a cytosolic fumarase FUM2. However, the role of this accumulation is currently unknown. In this study, we use an integrated experimental and modelling approach to examine the role of FUM2 and fumarate across the physiological temperature range. Using physiological and biochemical analyses, we demonstrate that FUM2 is necessary for high as well as low temperature acclimation. We have adapted a reliability engineering technique, Failure Mode and Effect Analysis (FMEA), to formalize a rigorous approach for ranking metabolites according to the potential risk that they pose to the metabolic system. FMEA identifies fumarate as a low-risk metabolite, while its precursor, malate, is shown to be high-risk and liable to cause system instability. We conclude that the role of cytosolic fumarase, FUM2, is to provide a fail-safe, controlling malate concentration, maintaining system stability in a changing environment. We argue that FMEA is a technique that is not only useful in understanding plant metabolism but can also be used to study reliability in other systems and synthetic pathways.
Origin and diversification of fibroblasts from the sclerotome in zebrafish
Authors: Ma Roger C. , Kocha Katrinka M. , Méndez-Olivos Emilio E. , Ruel Tyler D. , Huang Peng 
Published: April 2021

ABSTRACTFibroblasts play an important role in maintaining tissue integrity by secreting components of the extracellular matrix and initiating response to injury. Although the function of fibroblasts has been extensively studied in adults, the embryonic origin and diversification of different fibroblast subtypes during development remain largely unexplored. Using zebrafish as a model, we show that the sclerotome, a sub-compartment of the somite, is the embryonic source of multiple fibroblast subtypes including tenocytes (tendon fibroblasts), blood vessel associated fibroblasts, fin mesenchymal cells, and interstitial fibroblasts. High-resolution imaging shows that different fibroblast subtypes occupy unique anatomical locations with distinct morphologies. Long-term Cre-mediated lineage tracing reveals that the sclerotome also contributes to cells closely associated with the axial skeleton. Ablation of sclerotome progenitors results in extensive skeletal defects. Using photoconversion-based cell lineage analysis, we find that sclerotome progenitors at different dorsal-ventral and anterior-posterior positions display distinct differentiation potentials. Single-cell clonal analysis combined with in vivo imaging suggests that the sclerotome mostly contains unipotent and bipotent progenitors prior to cell migration, and the fate of their daughter cells is biased by their migration paths and relative positions. Together, our work demonstrates that the sclerotome is the embryonic source of trunk fibroblasts as well as the axial skeleton, and local signals likely contribute to the diversification of distinct fibroblast subtypes.
The mouse papillomavirus epigenetic signature is characterised by DNA hypermethylation after lesion regression
Authors: Tschirley Allison M. , Stockwell Peter A. , Rodger Euan J. , Eltherington Oliver , Morison Ian M. , Christensen Neil , Chatterjee Aniruddha , Hibma Merilyn 
Published: April 2021

ABSTRACTThe β genus of human papillomaviruses (HPVs) infect cutaneous epidermis. They contribute to the development of cutaneous squamous cell carcinoma (cSCC) in individuals with epidermodysplasia verruciformis, and increase susceptibility to UV-induced cSCC. This has been demonstrated in UV-exposed mice previously infected with mouse papillomavirus (MmuPV1). However, the mechanism by which β-HPVs contribute to cSCC is unclear. We propose that viral infection leaves a DNA methylation signature following resolution of the active lesion that may contribute to increased susceptibility to UV-induced cSCC.To test this, we carried out Reduced Representation Bisulphite Sequencing on DNA from tail skin of mice with actively infected lesions, MmuPV1-infected then healed lesions (regressed infection), and mock-infected control mice. Genome-scale DNA methylation libraries were generated and analysed for differentially methylated regions throughout the genome, and for HPV sequences.We found that DNA of active lesions was not differentially methylated compared to matched control mice. In contrast, 834 differentially methylated fragments were identified in regressed lesions compared to mock-infected control skin. An analysis of MmuPV1 viral DNA demonstrated retention of viral DNA in some of the lesions that had regressed. Overall, the viral sequences identified showed over-representation of sequences from the E4 region. The DNA hypermethylation that we found in regressed MmuPV1 lesions may be a factor in the increased susceptibility of mice to UV-induced cSCC.AUTHOR SUMMARYPapillomavirus infections can be asymptomatic, can cause warts, and in some cases can lead to cancer. There is direct evidence for mouse papillomavirus infection resulting in increased susceptibility to UV-induced cutaneous squamous cell carcinoma in a mouse model. We propose that DNA methylation following viral infection may contribute to the increased susceptibility. We describe the DNA methylation landscape during an active infection with mouse papillomavirus and following regression of the lesion. We found that there were very few differentially methylated DNA fragments during active infection. In contrast, over 800 differentially methylated DNA fragments were identified following regression of the lesion. This is the first description of the genome-wide DNA methylation landscape for mouse papillomavirus, to our knowledge. The dramatic DNA hypermethylation that we observe following resolution of infection may contribute to a ‘hit and run’ mechanism for the increased susceptibility to UV-induced cancer by papillomaviruses.
occAssess: An R package for assessing potential biases in species occurrence data
Authors: Boyd R. J. , Powney G. , Carvell C. , Pescott O. L. 
Published: April 2021

AbstractSpecies occurrence records from a variety of sources are increasingly aggregated into heterogeneous databases and made available to ecologists for immediate analytical use. However, these data are typically biased, i.e. they are not a probability sample of the target population of interest, meaning that the information they provide may not be an accurate reflection of reality. It is therefore crucial that species occurrence data are properly scrutinised before they are used for research. In this article, we introduce occAssess, an R package that enables straightforward screening of species occurrence data for potential biases. The package contains a number of discrete functions, each of which returns a measure of the potential for bias in one or more of the taxonomic, temporal, spatial and environmental dimensions. Users can opt to provide a set of time periods into which the data will be split; in this case separate outputs will be provided for each period, making the package particularly useful for assessing the suitability of a dataset for estimating temporal trends in species’ distributions. The outputs are provided visually (as ggplot2 objects) and do not include a formal recommendation as to whether data are of sufficient quality for any given inferential use. Instead, they should be used as ancillary information and viewed in the context of the question that is being asked, and the methods that are being used to answer it. We demonstrate the utility of occAssess by applying it to data on two key pollinator taxa in South America: leaf-nosed bats (Phyllostomidae) and hoverflies (Syrphidae). In this worked example, we briefly assess the degree to which various aspects of data coverage appear to have changed over time. We then discuss additional applications of the package, highlight its limitations, and point to future development opportunities.
What canonical online and offline measures of statistical learning can and cannot tell us
Authors: Kiai Ava , Melloni Lucia 
Published: April 2021

AbstractStatistical learning (SL) allows individuals to rapidly detect regularities in the sensory environment. We replicated previous findings showing that adult participants become sensitive to the implicit structure in a continuous speech stream of repeating tri-syllabic pseudowords within minutes, as measured by standard tests in the SL literature: a target detection task and a 2AFC word recognition task. Consistent with previous findings, we found only a weak correlation between these two measures of learning, leading us to question whether there is overlap between the information captured by these two tasks. Representational similarity analysis on reaction times measured during the target detection task revealed that reaction time data reflect sensitivity to transitional probability, triplet position, word grouping, and duplet pairings of syllables. However, individual performance on the word recognition task was not predicted by similarity measures derived for any of these four features. We conclude that online detection tasks provide richer and multi-faceted information about the SL process, as compared with 2AFC recognition tasks, and may be preferable for gaining insight into the dynamic aspects of SL.
Fine tuning the mechanism of Antigen 43 self-association to modulate aggregation levels ofEscherichia colipathogens
Authors: Vo Julieanne L , Martínez Ortiz Gabriela C , Totsika Makrina , Lo Alvin , Whitten Andrew E. , Hor Lilian , Peters Kate M , Ageorges Valentin , Caccia Nelly , Desvaux Mickaël , Schembri Mark A , Paxman Jason J , Heras Begoña 
Published: April 2021

AbstractBacterial aggregates and biofilms allow bacteria to colonise a diverse array of surfaces that can ultimately lead to infections, where the protection they afford permits bacteria to resist anti-microbials and host immune factors. Despite these advantages there is a trade-off, whereby bacterial spread is reduced. As such, biofilm development needs to be regulated appropriately to suit the required niche. Here we investigate members from one of largest groups of bacterial adhesins, the autotransporters, for their critical role in the formation of bacterial aggregates and biofilms. We describe the structural and functional characterisation of autotransporter Ag43 homologues from diverse pathogenicEscherichiastrains. We reveal a common mode of trans-association that leads to cell clumping and show that subtle variations in these interactions governs their aggregation kinetics. Our in depth investigation reveals an underlying molecular basis for the ‘tuning’ of bacterial aggregation.
Molecular architecture of black widow spider neurotoxins
Authors: Chen Minghao , Blum Daniel , Engelhard Lena , Raunser Stefan , Wagner Richard , Gatsogiannis Christos 
Published: April 2021

AbstractLatrotoxins (LaTXs) are presynaptic pore-forming neurotoxins found in the venom ofLatrodectusspiders. The venom contains a toxic cocktail of seven LaTXs, with one of them targeting vertebrates (α-latrotoxin (α-LTX)), five specialized on insects (α, β, γ, δ, ɛ-latroinsectotoxins (LITs), and one on crustaceans (α-latrocrustatoxin (α-LCT)). LaTXs bind to specific receptors on the surface of neuronal cells, inducing the release of neurotransmitters either by directly stimulating exocytosis or by forming Ca2+-conductive tetrameric pores in the membrane. Despite extensive studies in the past decades, a high-resolution structure of a LaTX is not yet available and the precise mechanism of LaTX action remains unclear.Here, we report cryoEM structures of the α-LCT monomer and the δ-LIT dimer. The structures reveal that LaTXs are organized in four domains. A C-terminal domain of ankyrin-like repeats shields a central membrane insertion domain of six parallel α-helices. Both domains are flexibly linked via an N-terminal α-helical domain and a small β-sheet domain. A comparison between the structures suggests that oligomerization involves major conformational changes in LaTXs with longer C-terminal domains. Based on our data we propose a cyclic mechanism of oligomerization, taking place prior membrane insertion. Both recombinant α-LCT and δ-LIT form channels in artificial membrane bilayers, that are stabilized by Ca2+ions and allow calcium flux at negative membrane potentials. Our comparative analysis between α-LCT and δ-LIT provides first crucial insights towards understanding the molecular mechanism of the LaTX family.
Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate
Authors: Seim Ian , Posey Ammon E. , Snead Wilton T. , Stormo Benjamin M. , Klotsa Daphne , Pappu Rohit V. , Gladfelter Amy S. 
Published: April 2021

AbstractRibonucleoprotein bodies are exemplars of membraneless biomolecular condensates that can form via spontaneous or driven phase transitions. The fungal protein Whi3 forms ribonucleoprotein condensates with different RNA molecules, and these condensates are implicated in key processes such as cell-cycle control and generating cell polarity. Whi3 has a modular architecture that includes a Q-rich intrinsically disordered region (IDR) and a tandem RNA recognition module. Here, we demonstrate that a 21-residue stretch within the Q-rich IDR has a weak intrinsic preference for forming alpha-helical conformations. Through mutagenesis, we find that increased alpha helicity enhances oligomerization in the dilute phase. One consequence of enhanced oligomerization is a dilution of Whi3 in the dense phase. The opposite behavior is observed when helicity within the 21-residue stretch of the Q-rich region is abrogated. Thus, the formation of dilute phase oligomers, driven by a specific sequence motif and potential synergies with the rest of the IDR, opposes incorporation of the Whi3 protein into the dense phase, thereby altering the dense phase stoichiometry of protein to RNA. Our findings, which stand in contrast to other systems where oligomerization has been shown to enhance the drive for phase separation, point to a novel mechanism that might be operative for influencing compositions of condensates. Our work also points to routes for designing synthetic ribonucleoprotein condensates whereby modulation of protein oligomerization via homotypic interactions can impact dense phase concentrations, stoichiometries, and material properties.SignificanceA large sub-class of biomolecular condensates are linked to RNA regulation and are known as ribonucleoprotein (RNP) bodies. While extensive work has identified driving forces for biomolecular condensate formation, relatively little is known about forces that oppose assembly. Here, using a fungal RNP protein, Whi3, we show that a portion of its intrinsically disordered, glutamine-rich region modulates phase separation by forming transient alpha helical structures that promote the assembly of dilute phase oligomers. These oligomers detour Whi3 proteins from condensates, thereby impacting the driving forces for phase separation, the protein-to-RNA ratio in condensates, and the material properties of condensates. Our findings show how nanoscale conformational and oligomerization equilibria can influence mesoscale phase equilibria.