bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomic, ecological and morphological diversity of Ponto-Caspian gammaridean amphipods: a review
Authors: Copilaș-Ciocianu Denis , Sidorov Dmitry 
Published: January 2021

AbstractThanks to its dynamic geological history the Ponto-Caspian region harbors a unique and unusually adaptable fauna, notorious for its invasive species. Gammarid amphipods attained considerable diversity, becoming the world’s second most speciose ancient-lake amphipod radiation. Nonetheless, apart from a few invasive species, this group remains poorly studied. Herein, we review and quantify the taxonomic, morphological and ecological diversity, as well as phylogenetic context of Ponto-Caspian gammarids within the adaptive radiation framework. Published molecular phylogenies indicate that this radiation has a monophyletic mid-Miocene Paratethyan origin, and is nested within the morphologically-conserved Atlanto-Mediterranean genusEchinogammarus. We find extensive disparity in body shape, size, ornamentation and appendage length, along a broad ecological gradient from mountain springs to depths exceeding 500 m, on virtually all substrate types (including symbiosis). We propose four putative ecomorphs that appear convergent with distantly related oceanic and Baikal Lake taxa. Thus, the identified patterns support the adaptive radiation model, although extensive further research is needed. A checklist and provisional key to all known endemic species are provided to facilitate taxonomic research. Ponto-Caspian gammarids could be a potentially powerful model for studying adaptive radiations and invasive species evolution.
Effect of Highly Loaded Nanohydroxyapatite Composite Scaffolds Prepared via Melt Extrusion Additive Manufacturing on the Osteogenic Differentiation of Human Mesenchymal Stromal Cells
Authors: Cámara-Torres María , Sinha Ravi , Sanchez Alberto , Habibovic Pamela , Patelli Alessandro , Mota Carlos , Moroni Lorenzo 
Published: January 2021

AbstractThe field of bone tissue engineering seeks to mimic the bone extracellular matrix composition, balancing the organic and inorganic components. In this regard, additive manufacturing (AM) of highly loaded polymer-calcium phosphate (CaP) composites holds great promise towards the design of bioactive scaffolds. Yet, the biological performance of such scaffolds is still poorly characterized. In this study, melt extrusion AM (ME-AM) was used to fabricate poly(ethylene oxide terephthalate)/poly(butylene terephthalate) (PEOT/PBT)-nanohydroxyapatite (nHA) scaffolds with up to 45 wt% nHA, which presented significantly enhanced compressive mechanical properties, to evaluate theirin vitroosteogenic potential as a function of nHA content. While osteogenic gene upregulation and matrix mineralization were observed on all scaffold types when cultured in osteogenic media, human mesenchymal stromal cells did not present an explicitly clear osteogenic phenotype, within the evaluated timeframe, in basic media cultures (i.e. without osteogenic factors). Yet, due to the adsorption of calcium and inorganic phosphate ions from cell culture media and simulated body fluid, the formation of a CaP layer was observed on PEOT/PBT-nHA 45 wt% scaffolds, which is hypothesized to account for their osteoinductivity in the long termin vitro,and osteoconductivityin vivo.
Synaptic inhibition in the lateral habenula shapes reward anticipation
Authors: Lalive Arnaud L. , Congiu Mauro , Clerke Joseph A. , Tchenio Anna , Ge Yuan , Mameli Manuel 
Published: January 2021

AbstractThe nervous system can associate neutral cues with rewards to promote appetitive adaptive behaviors. The lateral habenula (LHb) contributes to such behaviors as rewards and reward-predictive cues inhibit this structure and engage LHb-to-dopamine circuits. However, the mechanistic understanding of reward encoding within the LHb remains unknown. We report that, in mice, acquisition of anticipatory licking in a reward-conditioning task potentiates postsynaptic GABAergic transmission, leaving excitatory synapses unaffected. Conversely, LHb-targeted manipulations of postsynaptic GABAergic function via pharmacological blockade or impairment of GABAAreceptor trafficking decrease anticipatory licking. Hence, inhibitory signaling within LHb enables the expression of appetitive behaviors.
Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems
Authors: Hill Virginia , Akarsu Hatice , Barbarroja Rubén Sánchez , Cippà Valentina , Heller Martin , Falquet Laurent , Heller Manfred , Stoffel Michael H. , Labroussaa Fabien , Jores Joerg 
Published: January 2021

AbstractMycoplasmas are minute bacteria controlled by very small genomes ranging from 0.6 to 1.4 Mbp. They lack a cell wall and have been suggested to have progressed through reductive evolution from phylogenetically closely related Clostridia. They are known to colonize the respiratory tract or the urogenital tract among other organs and can cause chronic and subclinical diseases associated with long persistence of the causative agent. Toxin-antitoxin systems (TAS) are genetic elements that have been described for several respiratory and urogenital pathogens as well as for Clostridia, but never for pathogenic mycoplasmas. Here we describe for the first-time different types of TAS in aMycoplasmapathogen, namelyM. mycoidessubsp.capri. We identified candidate TASin silicovia TASmania database. Two candidate TAS identifiedin silicoand another candidate TAS suggested in a minimal cell based on transposon mutagenesis were systematically tested for their functionality in hosts with different phylogenetic distance using heterologous expression. Phylogenetic distance of the host used for heterologous expression influenced the outcome of the functional testing. We corroborated functionality of the three candidate TAS inMycoplasma capricolumsubsp.capricolum. Moreover, we confirmed transcription and translation of molecules of the TAS investigated duringin vitrogrowth. We sequence analyzed 15 genomes ofM. mycoidessubsp.capriand revealed an unequal distribution of the TAS studied pointing towards dynamic gain and loss of TAS within the species.Author summaryMycoplasmas have a minimal genome and have never been shown to possess TAS. In this work we showed the presence of different functional TAS systems inMycoplasma mycoidessubsp.capri, a caprine pathogen for the first time. Sequence analysis of a number ofMycoplasma mycoidessubsp.capristrains revealed a plasticity of the genome with respect to TAS carriage. This work paves the way to investigate the biological role of TAS (e.g. persistence, stress tolerance) during infection using mycoplasmas as a simple model organism. Since most mycoplasmas lack classical virulence factors such as exotoxins and go into a kind of stealth mode to evade the immune system, TAS are likely to contribute to the parasitic lifestyle of mycoplasmas and should be investigated in that respect. The availability of synthetic genomics tools to modify a range ofMycoplasmapathogens and well-established challenge models for the latter mycoplasmas will foster future research on TAS in mycoplasmas.
Decomposing the admixture statistic, D, suggests a negligible contribution due to archaic introgression into humans
Authors: Amos William 
Published: January 2021

AbstractIt is widely accepted that non-African humans carry a few percent of Neanderthal DNA due to historical inter-breeding. However, methods used to infer a legacy all assume that mutation rate is constant and that back-mutations can be ignored. Here I decompose the widely used admixture statistic, D, in a way that allows the overall signal to be apportioned to different classes of contributing site. I explore three main characteristics: whether the putative Neanderthal allele is likely derived or ancestral; whether an allele is fixed in one of the two human populations; and the type of mutation that created the polymorphism, defined by the base that mutated and immediately flanking bases. The entire signal used to infer introgression can be attributed to a subset of sites where the putative Neanderthal base is common in Africans and fixed in non-Africans. Moreover, the four triplets containing highly mutable CpG motifs alone contribute 29%. In contrast, sites expected to dominate the signal if introgression has occurred, where the putative Neanderthal allele is absent from Africa and rare outside Africa, contribute negligibly. Together, these observations show that D does not capture a signal due to introgression but instead they support an alternative model in which a higher mutation rate in Africa drives increased divergence from the ancestral state.
Glycoproteomics ofHaloferax volcaniireveals an extensive glycoproteome and concurrence of differentN-glycosylation pathways
Authors: Schulze Stefan , Pfeiffer Friedhelm , Garcia Benjamin A. , Pohlschroder Mechthild 
Published: January 2021

AbstractGlycosylation is one of the most complex post-translational protein modifications. Its importance has been established not only for eukaryotes but also for a variety of prokaryotic cellular processes, such as biofilm formation, motility and mating. However, comprehensive glycoproteomic analyses are largely missing in prokaryotes. Here we extend the phenotypic characterisation ofN-glycosylation pathway mutants inHaloferax volcaniiand provide a detailed glycoproteome for this model archaeon through the mass spectrometric analysis of intact glycopeptides. Using in-depth glycoproteomic datasets generated for the wild-type and mutant strains as well as a reanalysis of datasets within the Archaeal Proteome Project, we identify the largest archaeal glycoproteome described so far. We further show that differentN-glycosylation pathways can modify the same glycosites under the same culture conditions. The extent and complexity of theHfx. volcanii N-glycoproteome revealed here provides new insights into the roles ofN-glycosylation in archaeal cell biology.
4D chromosome reconstruction elucidates the spatial reorganization of the mammalian X-chromosome
Authors: Lappala Anna , Wang Chen-Yu , Kriz Andrea , Michalk Hunter , Tan Kevin , Lee Jeannie T. , Sanbonmatsu Karissa Y. 
Published: January 2021

AbstractChromosomes are segmented into domains and compartments; yet, how these structures are spatially related in 3D is unclear. Here, by directly integrating Hi-C capture experiments and 3D modeling, we use X-inactivation as a model to examine the time evolution of 3D chromosome architecture during substantial changes in gene expression. First, we show that gene expression A/B compartments are consistent with phase separation in 3D space. Second, we show that residuals of smaller scale structures persist through transitions, despite further large-scale reorganization into the final inactive configuration, comprising two “megadomains”. Interestingly, these previously hidden residual structures were not detectable in 2D Hi-C maps or principal component analyses. Third, time-dependent reaction-diffusion simulations reveal how Xist RNA particles diffuse across the 3D X-superstructure as it reorganizes. Our 4DHiC pipeline helps satisfy the growing demand for methodologies that produce 3D chromosome reconstructions directly from 2D datasets, which are consistent with the empirical data.
Increased ventromedial prefrontal cortex activity in adolescence benefits prosocial reinforcement learning
Authors: Westhoff Bianca , Blankenstein Neeltje E. , Schreuders Elisabeth , Crone Eveline A. , van Duijvenvoorde Anna C. K. 
Published: January 2021

AbstractLearning which of our behaviors benefit others contributes to social bonding and being liked by others. An important period for the development of (pro)social behavior is adolescence, in which peers become more salient and relationships intensify. It is, however, unknown how learning to benefit others develops across adolescence and what the underlying cognitive and neural mechanisms are. In this functional neuroimaging study, we assessed learning for self and others (i.e., prosocial learning) and the concurring neural tracking of prediction errors across adolescence (ages 9-21, N=74). Participants performed a two-choice probabilistic reinforcement learning task in which outcomes resulted in monetary consequences for themselves, an unknown other, or no one. Participants from all ages were able to learn for themselves and others, but learning for others showed a more protracted developmental trajectory. Prediction errors for self were observed in the ventral striatum and showed no age-related differences. However, prediction error coding for others was specifically observed in the ventromedial prefrontal cortex and showed age-related increases. These results reveal insights into the computational mechanisms of learning for others across adolescence, and highlight that learning for self and others show different age-related patterns.
Spatiotemporal manipulation of the mismatch repair system ofPseudomonas putidaaccelerates phenotype emergence
Authors: Fernández-Cabezón Lorena , Cros Antonin , Nikel Pablo I. 
Published: January 2021

ABSTRACTDeveloping complex phenotypes in industrially-relevant bacteria is a major goal of metabolic engineering, which encompasses the implementation of both rational and random approaches. In the latter case, several tools have been developed towards increasing mutation frequencies—yet the precise spatiotemporal control of mutagenesis processes continues to represent a significant technical challenge.Pseudomonasspecies are endowed with one of the most efficient DNA mismatch repair (MMR) systems found in bacteria. Here, we investigated if the endogenous MMR system could be manipulated as a general strategy to artificially alter mutation rates inPseudomonasspecies. To bestow a conditional mutator phenotype in the platform bacteriumPseudomonas putida, we constructed inducible mutator devices to modulate the expression of the dominant-negativemutLE36Kallele. Regulatable overexpression ofmutLE36Kin a broad-host-range, easy-to-cure plasmid format resulted in a transitory inhibition of the MMR machinery, leading to a significant increase (up to 438-fold) in mutation frequencies and a heritable fixation of genome mutations. Following such accelerated mutagenesis-followed-by selection approach, three phenotypes were successfully evolved: resistance to antibiotics streptomycin and rifampicin and reversion of a synthetic uracil auxotrophy. Thus, these mutator devices could be applied to accelerate evolution of metabolic pathways in long-term evolutionary experiments, alternating cycles of (inducible) mutagenesis coupled to selection schemes.
Finnish teachers’ views on co‐teaching
Authors: Kokko Marjut , Takala Marjatta , Pihlaja Päivi 
Published: January 2021

Co‐teaching has become a well‐known way of working among Finnish teachers in recent years. Teachers’ collaboration is becoming increasingly important in light of the rising number of diverse students in regular classes. In an ideal co‐teaching context, teachers collaborate as equals, recognise and respect each other’s skills and competencies, and strengthen and support each other. In this study, we examine teachers’ views on co‐teaching and investigate which background factors explain teachers’ views concerning the benefits and the challenges of co‐teaching. The data obtained from Finnish basic education teachers’ (N = 694) responses to an online questionnaire are analysed quantitatively. The results show some differences among the teachers’ views. Subject teachers perceive more challenges in co‐teaching than class and special education teachers. Class teachers perceive the fewest challenges. Although teachers are generally interested in co‐teaching and some of them co‐teach regularly, they also report several barriers to its application. The explanatory factors concerning the differences in teachers’ views are gender, teachers’ co‐teaching experiences, the amount of co‐teaching per week and working as a class teacher.
How is the client‐dietitian relationship embedded in the professional education of dietitians? An analysis of curriculum documentation and program coordinators' perspectives in Australia
Authors: Nagy Annaliese , McMahon Anne , Tapsell Linda , Deane Frank 
Published: January 2021

AbstractAimHow dietitians are trained to develop relationships with clients is not clearly articulated despite its importance being well‐documented. This study aimed to describe how this relationship is expressed and addressed in curriculum documents of Australian dietetics education programs, and to explore program coordinators' perspectives of this description and how relationship development is actually taught.MethodsData extracted from subject outlines included subject descriptions, learning outcomes, assessments, readings and the mode of delivery (eg, lectures). Guided by a pre‐existing coding framework, deductive thematic analysis was utilised to explore qualitative themes from subject outline data. Semi‐structured telephone interviews were conducted with 10 program coordinators and analysed using inductive thematic analysis.ResultsSubject outlines for 122 subjects across all 21 accredited Australian programs were analysed. The over‐arching theme was the wide “variability” in the ways that the client‐dietitian relationship was expressed across subject outlines. Program coordinators perceived that findings from the analysis of subject outlines made sense, however, acknowledged limitations of analysing data from curriculum documents. The relationship appeared ambiguously defined amongst programs and was described as occurring mostly in communication, counselling and medical nutrition therapy subjects and through theoretical and practical learning.ConclusionThe client‐dietitian relationship appears inconsistently embedded in the curriculum of Australian dietetics education programs despite widespread acceptance of its importance to practice. Further research is needed to investigate if training programs should embed more consistent language around therapeutic relationships, and how this might be achieved to reflect current competency standards.
Interleukin‐37 improves T‐cell‐mediated immunity and chimeric antigen receptor T‐cell therapy in aged backgrounds
Authors: Hamilton Jamie A. G. , Lee Miyoung Y. , Hunter Rae , Ank Raira S. , Story Jamie Y. , Talekar Ganesh , Sisroe Talia , Ballak Dov B. , Fedanov Andrew , Porter Christopher C. , Eisenmesser Elan Z. , Dinarello Charles A. , Raikar Sunil S. , DeGregori James , Henry Curtis J. 
Published: January 2021

AbstractAging‐associated declines in innate and adaptive immune responses are well documented and pose a risk for the growing aging population, which is predicted to comprise greater than 40 percent of the world's population by 2050. Efforts have been made to improve immunity in aged populations; however, safe and effective protocols to accomplish this goal have not been universally established. Aging‐associated chronic inflammation is postulated to compromise immunity in aged mice and humans. Interleukin‐37 (IL‐37) is a potent anti‐inflammatory cytokine, and we present data demonstrating that IL‐37 gene expression levels in human monocytes significantly decline with age. Furthermore, we demonstrate that transgenic expression of interleukin‐37 (IL‐37) in aged mice reduces or prevents aging‐associated chronic inflammation, splenomegaly, and accumulation of myeloid cells (macrophages and dendritic cells) in the bone marrow and spleen. Additionally, we show that IL‐37 expression decreases the surface expression of programmed cell death protein 1 (PD‐1) and augments cytokine production from aged T‐cells. Improved T‐cell function coincided with a youthful restoration of Pdcd1, Lat, and Stat4 gene expression levels in CD4+ T‐cells and Lat in CD8+ T‐cells when aged mice were treated with recombinant IL‐37 (rIL‐37) but not control immunoglobin (Control Ig). Importantly, IL‐37‐mediated rejuvenation of aged endogenous T‐cells was also observed in aged chimeric antigen receptor (CAR) T‐cells, where improved function significantly extended the survival of mice transplanted with leukemia cells. Collectively, these data demonstrate the potency of IL‐37 in boosting the function of aged T‐cells and highlight its therapeutic potential to overcome aging‐associated immunosenescence.
… More on the use of research templates
Authors: Faff Robert W. , Lodhia Sumit 
Published: January 2021

AbstractMotivated by Bui’s thought‐provoking analysis regarding the perceived efficacy of research templates, our paper advances the debate by reviewing Faff’s Pitching Research® framework and Lodhia’s qualitative companion. The key premises of these research templates are highlighted and potential misconceptions are addressed. We reach common ground on the underlying philosophy and use of research templates for quantitative and qualitative research; and, more generally, on the process of research. As such, we provide a pathway for reducing the schism between the two ‘rival’ research camps.
Histological observation of the reproductive system in a viviparous teleost Xenotoca eiseni Rutter 1896 (Cyprinodontiformes: Goodeidae)
Authors: Iida Atsuo , Nomura Jumpei , Hondo Eiichi 
Published: January 2021

AbstractXenotoca eiseni is a viviparous teleost belonging to the family Goodeidae. Here, we report histological observations of the reproductive organs in an adult male, an adult female, a pregnant female with intraovarian embryo and an extracted embryo of X. eiseni. High‐resolution images of haematoxylin–eosin‐stained sagittal sections revealed the detailed structure of gonads, gametes and reproductive components of the mother–embryo relationship. In the male, mature spermatozoa in the epididymis formed sperm packages. In the female, oogenesis proceeded asynchronously in the ovarian wall, and various stages of oocytes were observed in single ovary. In both sexes, genital openings were located between the anus and anal fin. Developing embryos were observed in an ovary of the pregnant female. Fine structures of components of the mother‐to‐embryo nutrient supply, ovarian septum and trophotaenia were observed in the pregnant ovary. An immature gonad prior to gamete formation was identified in the extracted embryo. With the aim of supporting the development and extension of studies on this viviparous teleost, we have shared our histological images as raw data in an open online archive, the 'NAGOYA repository (http://hdl.handle.net/2237/00032456)'. Our goal is a comprehensive understanding of the viviparous system in fish using both histological observation and molecular biology methods including genomics and proteomics.