Miracle-dz/UniFAR-FTUs huggingface dataset:
The POU-er of gene nomenclature

The pluripotency factor POU5F1 (OCT4) is well known as a key regulator of stem cell fate. Homologues of POU5F1 exist throughout vertebrates, but the evolutionary and functional relationships between the various family members have been unclear. The level to which function has been conserved within this family provides insight into the evolution of early embryonic potency. Here, we seek to clarify the relationship between POU5F1 homologues in the vertebrate lineage, both phylogenetically and functionally. We resolve the confusion over the identity of the zebrafish gene, which was originally named pou2, then changed to pou5f1 and again, more recently, to pou5f3. We argue that the use of correct nomenclature is crucial when discussing the degree to which the networks regulating early embryonic differentiation are conserved.
Developmental profiles of SUMOylation pathway proteins in rat cerebrum and cerebellum

Protein SUMOylation regulates multiple processes involved in the differentiation and maturation of cells and tissues during development. Despite this, relatively little is known about the spatial and temporal regulation of proteins that mediate SUMOylation and deSUMOylation in the CNS. Here we monitor the expression of key SUMO pathway proteins and levels of substrate protein SUMOylation in the forebrain and cerebellum of Wistar rats during development. Overall, the SUMOylation machinery is more highly-expressed at E18 and decreases thereafter, as previously described. All of the proteins investigated are less abundant in adult than in embryonic brain. Furthermore, we show for first time that the profiles differ between cerebellum and cerebrum, indicating differential regional regulation of some of the proteins analysed. These data provide further basic observation that may open a new perspective of research about the role of SUMOylation in the development of different brain regions.
Microbial diversity involved in iron and cryptic sulfur cycling in the ferruginous, low-sulfate waters of Lake Pavin

Both iron- and sulfur- reducing bacteria strongly impact the mineralogy of iron, but their activity has long been thought to be spatially and temporally segregated based on the higher thermodynamic yields of iron over sulfate reduction. However, recent evidence suggests that sulfur cycling can predominate even under ferruginous conditions. In this study, we investigated the potential for bacterial iron and sulfur metabolisms in the iron-rich (1.2 mM dissolved Fe2+), sulfate-poor (< 20 μM) Lake Pavin which is expected to host large populations of iron-reducing and iron-oxidizing microorganisms influencing the mineralogy of iron precipitates in its permanently anoxic bottom waters and sediments. 16S rRNA gene amplicon libraries from at and below the oxycline revealed that highly diverse populations of sulfur/sulfate-reducing (SRB) and sulfur/sulfide-oxidizing bacteria represented up to 10% and 5% of the total recovered sequences in situ, respectively, which together was roughly equivalent to the fraction of putative iron cycling bacteria. In enrichment cultures amended with key iron phases identified in situ (ferric iron phosphate, ferrihydrite) or with soluble iron (Fe2+), SRB were the most competitive microorganisms, both in the presence and absence of added sulfate. The large fraction of Sulfurospirillum, which are known to reduce thiosulfate and sulfur but not sulfate, present in all cultures was likely supported by Fe(III)-driven sulfide oxidation. These results support the hypothesis that an active cryptic sulfur cycle interacts with iron cycling in the lake. Analyses of mineral phases showed that ferric phosphate in cultures dominated by SRB was transformed to vivianite with concomitant precipitation of iron sulfides. As colloidal FeS and vivianite have been reported in the monimolimnion, we suggest that SRB along with iron-reducing bacteria strongly influence iron mineralogy in the water column and sediments of Lake Pavin.
Auxin represses stomatal development in dark-grown seedlings via Aux/IAA proteins

Stomatal development is tightly regulated through internal and external factors that are integrated by a complex signalling network. Light represents an external factor that strongly promotes stomata formation. Here, we show that auxin-resistant aux/iaa mutants, e.g. axr3-1, exhibit a de-repression of stomata differentiation in dark-grown seedlings. The higher stomatal index in dark-grown axr3-1 mutants when compared with the wild type is due to increased cell division in the stomatal lineage. Excessive stomata in dark-grown seedlings were also observed in mutants defective in auxin biosynthesis or auxin perception and in seedlings treated with the polar auxin transport inhibitor NPA. Consistent with these findings, exogenous auxin repressed stomata formation in light-grown seedlings. Taken together, these results indicate that auxin is a negative regulator of stomatal development in dark-grown seedlings. Epistasis analysis revealed that axr3-1 acts genetically upstream of the bHLH transcription factors SPCH, MUTE and FAMA, as well as the YDA MAP kinase cascade, but in parallel with the repressor of photomorphogenesis COP1 and the receptor-like protein TMM. The effect of exogenous auxin required the ER family of leucine-rich repeat receptor-like kinases, suggesting that auxin acts at least in part through the ER family. Expression of axr3-1 in the stomatal lineage was insufficient to alter the stomatal index, implying that cell-cell communication is necessary to mediate the effect of auxin. In summary, our results show that auxin signalling contributes to the suppression of stomatal differentiation observed in dark-grown seedlings.
High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry ∼60–70% of the genes. Identifying sequence and/or chromosome features affecting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed fine-scale mapping of COs and revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length. We used 774 SNPs to genotype 180 varieties representative of the Asian and European genetic pools and a segregating population of 1270 F6 lines. We observed a common location for ancestral COs (predicted through linkage disequilibrium) and the COs derived from the segregating population. We delineated 73 small intervals (<26 kb) on chromosome 3B that contained 252 COs. We observed a significant association of COs with genic features (73 and 54% in recombinant and nonrecombinant intervals, respectively) and with those expressed during meiosis (67% in recombinant intervals and 48% in nonrecombinant intervals). Moreover, while the recombinant intervals contained similar amounts of retrotransposons and DNA transposons (42 and 53%), nonrecombinant intervals had a higher level of retrotransposons (63%) and lower levels of DNA transposons (28%). Consistent with this, we observed a higher frequency of a DNA motif specific to the TIR-Mariner DNA transposon in recombinant intervals.
Aerosol vaccination with Bacille Calmette-Guerin induces a trained innate immune phenotype in calves

Mycobacterium bovis Bacillus Calmette-Guérin (BCG) is a live attenuated vaccine for use against tuberculosis (TB); however, it is known to reduce childhood mortality from infections other than TB. The unspecific protection induced by BCG vaccination has been associated with the induction of memory-like traits of the innate immune system identified as ‘trained’ immunity. In humans and mouse models, in vitro and in vivo BCG training leads to enhanced production of monocyte-derived proinflammatory cytokines in response to secondary unrelated bacterial and fungal pathogens. While BCG has been studied extensively for its ability to induce innate training in humans and mouse models, BCG’s nonspecific protective effects have not been defined in agricultural species. Here, we show that in vitro BCG training induces a functional change in bovine monocytes, characterized by increased transcription of proinflammatory cytokines upon restimulation with the toll-like receptor agonists. Importantly, in vivo, aerosol BCG vaccination in young calves also induced a ‘trained’ phenotype in circulating peripheral blood mononuclear cells (PBMCs), that lead to a significantly enhanced TLR-induced proinflammatory cytokine response and changes in cellular metabolism compared to PBMCs from unvaccinated control calves. Similar to the long-term training effects of BCG reported in humans, our results suggest that in young calves, the effects of BCG induced innate training can last for at least 3 months in circulating immune populations. Interestingly, however, aerosol BCG vaccination did not ‘train’ the innate immune response at the mucosal level, as alveolar macrophages from aerosol BCG vaccinated calves did not mount an enhanced inflammatory response to secondary stimulation, compared to cells isolated from control calves. Together, our results suggest that, like mice and humans, the innate immune system of calves can be ‘trained’; and that BCG vaccination could be used as an immunomodulatory strategy to reduce disease burden in juvenile food animals before the adaptive immune system has fully matured.
Coordination of Double Strand Break Repair and Meiotic Progression in Yeast by a Mek1-Ndt80 Negative Feedback Loop

Meiotic crossovers and double strand breaks (DSBs) are required for gametogenesis, but entering meiotic divisions with broken chromosomes results in. During meiosis, homologous chromosomes are physically connected by crossovers and sister chromatid cohesion. Interhomolog crossovers are generated by the highly regulated repair of programmed double strand breaks (DSBs). The meiosis-specific kinase Mek1 is critical for this regulation. Mek1 downregulates the mitotic recombinase Rad51, indirectly promoting interhomolog strand invasion by the meiosis-specific recombinase Dmc1. Mek1 also promotes the formation of crossovers that are distributed throughout the genome by interference and is the effector kinase for a meiosis-specific checkpoint that delays entry into Meiosis I until DSBs have been repaired. The target of this checkpoint is a meiosis-specific transcription factor, Ndt80, which is necessary to express the polo-like kinase CDC5 and the cyclin CLB1 thereby allowing completion of recombination and meiotic progression. This work shows that Mek1 and Ndt80 negatively feedback on each other such that when DSB levels are high, Ndt80 is inactive due to high levels of Mek1 activity. As DSBs are repaired, chromosomes synapse and Mek1 activity is reduced below a threshold that allows activation of Ndt80. Ndt80 transcription of CDC5 results in degradation of Red1, a meiosis-specific protein required for Mek1 activation, thereby abolishing Mek1 activity completely. Elimination of Mek1 kinase activity allows Rad51-mediated repair of any remaining DSBs. In this way, cells do not enter Meiosis I until recombination is complete and all DSBs are repaired.
Dog-bite injuries in Korea and risk factors for significant dog-bite injuries: A 6-year cross-sectional study

Introduction An accurate understanding of the current status of dog-bite injuries in Korea is essential for establishing preventive strategies. There have been no national reports about dog-bite injuries in Korea. This study investigated dog-bite injuries in Korea that were registered in the nationwide injury surveillance database and analysed the risk factors for significant dog-bite injury. Methods A multicentre cross-sectional study was conducted using the emergency department (ED)-based Injury In-depth Surveillance (EDIIS) registry in Korea between 2011 and 2016. We defined significant injury as death, admission, surgery, or fracture or amputation. A multivariable logistic regression model was used to obtain the adjusted odds ratios (aORs) for the factors associated with significant dog-bite injuries. Results Among 1,537,617 injured patients, 9,966 (6.5 per 1,000 injured patients) presented to the ED for dog-bite injuries (5.6 in 2011 to 7.6 in 2016, P for trend < 0.001), and 489 (4.9%) were significant injuries. In the age-specific analysis, there were increasing trends only among teenagers (12−18 years) and adults (> 18 years). Being elderly (≥ 60 years) (aOR: 2.70, 95% CI: 2.15−3.39), having injuries to multiple anatomic sites (aOR: 4.37, 95% CI: 2.96−6.45), being bitten outdoors (aOR: 2.71, 95% CI: 2.20−3.34), and being bitten by a relative’s dog (aOR: 2.37, 95% CI: 1.09−5.17) were strongly associated with significant dog-bite injury. Conclusion Dog-bite injuries are increasing in Korea, especially in teenagers and adults. A relative’s or neighbour’s dog may be more dangerous than a stranger’s dog. Preventive strategies are needed to prevent dog-bite injuries in adults and children.
Expert opinion on metal chains and other indestructible objects as proper enrichment for intensively-farmed pigs

EC Directive 2001/93 requires that all pigs have access to proper investigation and manipulation materials. Intensively farmed pigs in Europe are frequently provided with a short metal chain with or without an indestructible object attached to the chain. To date authorities are regarding this as proper enrichment, perhaps with (in)direct reference to the RICHPIG model as a justification. However, it has become increasingly clear that the chains do not provide proper enrichment, and that adding an indestructible object to the end of the chain may even reduce rather than improve pig welfare. To test this hypothesis an expert survey was conducted containing 26 more or less compound questions. On a scale from 0 to 10 experts specified their level of agreement with the hypothesis, the prevalence and welfare scores of nine indestructible enrichment materials. In total 36 experts, mostly pig-welfare scientists, responded (response rate: 39%). Indestructible objects are less prevalent in countries that provide straw (like Sweden and the UK) and outside the EU (US). They are more prevalent in the Netherlands, Belgium, France and Finland, while the prevalence seems to be low in Spain. Balls, wood and pipes were provided most frequently: hard wood especially in the UK (as specified in farm assurance); indestructible balls and pipes in Germany and the Netherlands. The experts’ score for agreement with the hypothesis was only 4.6 on average (scale 0–10; n = 25). Enrichment materials, ranked from high to low welfare score, were grouped in 5 significance levels as indicated by different superscripts based on Wilcoxon signed rank tests: Branched chains (5.1a), Chain on the floor (4.4b), Hard wood (3.7bc), Pipe (3.5c), Bare chain (3.3c), Short chain (3.1d), Small ball (2.8d), Big ball (2.5d), and Chain hanging too high (1.3e). Branched chains scored significantly better than all other indestructible materials and its welfare score (5.1 on average) was close to the pre-defined level of acceptability (5.5 on a scale from 0, worst, to 10, best). The welfare benefits of adding balls, pipes or hard wood to the metal chain were marginal, and well below what the experts considered acceptable enrichment. The branched-chains design, by contrast, appears to be the most viable alternative. It involves providing a longer chain, i.e. with the free end reaching to floor level, adding ‘branches’, i.e. several short chains ending at the nose height of the pigs, and providing more chains per pen (i.e. 1 branched chain per 5 pigs). Branched chains should be implemented widely and in the short term as a first step towards, and benchmark for, providing proper enrichment to intensively-farmed pigs.
CRISPR-cas gene-editing as plausible treatment of neuromuscular and nucleotide-repeat-expansion diseases: A systematic review

Introduction The system of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (cas) is a new technology that allows easier manipulation of the genome. Its potential to edit genes opened a new door in treatment development for incurable neurological monogenic diseases (NMGDs). The aim of this systematic review was to summarise the findings on the current development of CRISPR-cas for therapeutic purposes in the most frequent NMGDs and provide critical assessment. Methods and data acquisition We searched the MEDLINE and EMBASE databases, looking for original studies on the use of CRISPR-cas to edit pathogenic variants in models of the most frequent NMGDs, until end of 2017. We included all the studies that met the following criteria: 1. Peer-reviewed study report with explicitly described experimental designs; 2. In vitro, ex vivo, or in vivo study using human or other animal biological systems (including cells, tissues, organs, organisms); 3. focusing on CRISPR as the gene-editing method of choice; and 5. featured at least one NMGD. Results We obtained 404 papers from MEDLINE and 513 from EMBASE. After removing the duplicates, we screened 490 papers by title and abstract and assessed them for eligibility. After reading 50 full-text papers, we finally selected 42 for the review. Discussion Here we give a systematic summary on the preclinical development of CRISPR-cas for therapeutic purposes in NMGDs. Furthermore, we address the clinical interpretability of the findings, giving a comprehensive overview of the current state of the art. Duchenne’s muscular dystrophy (DMD) paves the way forward, with 26 out of 42 studies reporting different strategies on DMD gene editing in different models of the disease. Most of the strategies aimed for permanent exon skipping by deletion with CRISPR-cas. Successful silencing of the mHTT gene with CRISPR-cas led to successful reversal of the neurotoxic effects in the striatum of mouse models of Huntington’s disease. Many other strategies have been explored, including epigenetic regulation of gene expression, in cellular and animal models of: myotonic dystrophy, Fraxile X syndrome, ataxias, and other less frequent dystrophies. Still, before even considering the clinical application of CRISPR-cas, three major bottlenecks need to be addressed: efficacy, safety, and delivery of the systems. This requires a collaborative approach in the research community, while having ethical considerations in mind.
Prediction and Sampling With Local Graph Transforms for Quasi-Lossless Light Field Compression

Graph-based transforms have been shown to be powerful tools in terms of image energy compaction. However, when the size of the support increases to best capture signal dependencies, the computation of the basis functions becomes rapidly untractable. This problem is in particular compelling for high dimensional imaging data such as light fields. The use of local transforms with limited supports is a way to cope with this computational difficulty. Unfortunately, the locality of the support may not allow us to fully exploit long term signal dependencies present in both the spatial and angular dimensions of light fields. This paper describes sampling and prediction schemes with local graph-based transforms enabling to efficiently compact the signal energy and exploit dependencies beyond the local graph support. The proposed approach is investigated and is shown to be very efficient in the context of spatio-angular transforms for quasi-lossless compression of light fields.
Invading, Leading and Navigating Cells in Caenorhabditis elegans: Insights into Cell Movement in Vivo

Highly regulated cell migration events are crucial during animal tissue formation and the trafficking of cells to sites of infection and injury. Misregulation of cell movement underlies numerous human diseases, including cancer. Although originally studied primarily in two-dimensional in vitro assays, most cell migrations in vivo occur in complex three-dimensional tissue environments that are difficult to recapitulate in cell culture or ex vivo. Further, it is now known that cells can mobilize a diverse repertoire of migration modes and subcellular structures to move through and around tissues. This review provides an overview of three distinct cellular movement events in Caenorhabditis elegans—cell invasion through basement membrane, leader cell migration during organ formation, and individual cell migration around tissues—which together illustrate powerful experimental models of diverse modes of movement in vivo. We discuss new insights into migration that are emerging from these in vivo studies and important future directions toward understanding the remarkable and assorted ways that cells move in animals.
Qualitative research in computer science education

This paper discusses the suitability of the qualitative research approach to computer science education research. It is based on the following two observations: First, only a small proportion of works presented in the computer science education literature contain some experimental component (Fincher and Petre, 2004; Valentine, 2004). Second, those research works conducted in computer science education that do, usually employ a quantitative research approach. This paper focuses on the qualitative research approach, presenting its nature, discussing its relationships to the quantitative research approach and addressing its application in general and in the context of computer science education in particular.
By Land, Air, or Sea: Multi-Domain Robot Communication Via Motion

In this paper, we explore the use of motion for robot-to-human communication on three robotic platforms: the 5 degrees-of-freedom (DOF) Aqua autonomous underwater vehicle (AUV), a 3-DOF camera gimbal mounted on a Matrice 100 drone, and a 3-DOF Turtlebot2 terrestrial robot. While we previously explored the use of body language-like motion (called kinemes) versus other methods of communication for the Aqua AUV, we now extend those concepts to robots in two new and different domains. We evaluate all three platforms using a small interaction study where participants use gestures to communicate with the robot, receive information from the robot via kinemes, and then take actions based on the information. To compare the three domains we consider the accuracy of these interactions, the time it takes to complete them, and how confident users feel in the success of their interactions. The kineme systems perform with reasonable accuracy for all robots and experience gained in this study is used to form a set of prescriptions for further development of kineme systems.
Identifying Critical Regions for Motion Planning using Auto-Generated Saliency Labels with Convolutional Neural Networks

In this paper, we present a new approach to learning for motion planning (MP) where critical regions of an environment with low probability measure are learned from a given set of motion plans and used to improve performance on new problem instances. We show that a convolutional neural network (CNN) can be used to identify critical regions for motion plans. We also introduce a new sampling-based motion planner, Learn and Link (LLP). LLP leverages critical region locations identified by our CNN to overcome the limitations of uniform sampling, while still maintaining guarantees of correctness inherent to sampling-based algorithms. We evaluate our planner using an extensive suite of experiments on challenging navigation planning problems and compare its performance against planners from the Open Motion Planning Library (OMPL). We show that our approach requires the creation of far fewer states than the existing sampling-based planners.