Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain Activation-based Filtering: a Scholarly Journal Recommendation Model for Human Neuroimaging Studies

The development of noninvasive neuroimaging techniques such as functional magnetic resonance imaging was followed by a large volume of human neuroimaging studies of mental processes, mechanisms, and diseases. Due to the high volume of studies and the large number of journals, it is increasingly challenging for neuroscientists to review existing scholarly journals and find the most suitable journal to publish their studies. Therefore, this paper proposes a scholarly journal recommendation model for human neuroimaging studies called brain activation-based filtering (BAF). Based on the collective matrix factorization technique, BAF recommends journals relevant to the activated brain regions that are described in a given neuroimaging study. For instance, if ‘social brain’ regions such as the dorsomedial prefrontal cortex, precuneus, and temporoparietal junction are activated in a study, BAF recommends relevant social neuroscience journals (e.g., Social Cognitive and Affective Neuroscience). Five-fold cross-validation shows that BAF predicts journals with a reliable area under the curve score of 0.855. Furthermore, an interactive Google Colab notebook is offered to recommend relevant journals for a novel human neuroimaging study (https://github.com/JunsolKim/brain-activation-based-filtering).
Scaffolded Learning of Bipedal Walkers: Bootstrapping Ontogenetic Development

Bipedal locomotion has several key challenges, such as balancing, foot placement, and gait optimization. We reach optimality from a very early age by using natural supports, such as our parent’s hands, chairs, and training wheels, and bootstrap a new knowledge from the recently acquired one. In this paper, we propose a scaffolded learning method from an evolutionary robotics perspective, where a biped creature achieves stable and independent bipedal walking while exploiting the natural scaffold of its changing morphology to create a third limb. Hence, we compare three conditions of scaffolded learning to reach bipedalism, and we prove that a performance-based scaffold is the most conducive to accelerate the learning of ontogenetic bipedal walking. Beyond a pedagogical experiment, this work presents a powerful tool to accelerate learning on robots.
Purification and Characterization of an Extracellular Acidic Protease of Pediococcus pentosaceus Isolated from Fermented Fish

Protease from lactic acid bacteria is of great importance to flavor and texture quality of fermented foods. An acidic protease from Pediococcus pentosaceus 220 was purified to homogeneity with a 11.5-fold increase in specific activity and 13.4% of recovery by precipitation with ammonium sulfate (20 _ 60%, w/v), DEAE-Sepharose CL-6B ionic exchange chromatography, and Sephadex G-75 gel filtration chromatography. The molecular weight of the purified protease was estimated to be 37 kDa by Sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The optimum pH and temperature for protease activities were around pH4.0 and 35°C, respectively. The enzyme was stable at 20 _ 40°C and showed pH stability between 4.0 and 7.0. The protease was activated by Ca, but inhibited by Zn, Mg and Fe. The enzyme activity was also strongly inhibited by Sodium dodecyl sulfate and EDTA. It could be deduced that the purified enzyme was an acidic metalloprotease.
Academics as play and the social as discipline: school readiness in Denmark

ABSTRACT Denmark has a tradition of kindergarten pedagogy focused on children’s play, sociality and individual interests. Political emphasis on global competition, however, has led to reforms in early childhood education and care (ECEC) since 2004. Based on ethnographic fieldwork at three kindergartens, we analyse how the ECEC-reforms have affected the priorities of parents and pedagogues regarding school readiness. To understand how this is negotiated, we draw upon Lareau’s distinction between childrearing as ‘concerted cultivation’ or as ‘the accomplishment of natural growth’ (Lareau, A. 2003. Unequal Childhoods. Class, Race and Family Life. London: University of California Press). We show that parents and staff consider the social as the most important thing for kindergarten children to learn and as something that the adults must cultivate – often in a disciplinary manner. Meanwhile, parents and pedagogues state that academic competences are not important to cultivate because an interest in academics will naturally grow. Adults just have to support academic activities through play when the children choose to engage in them. However, academic competences are actively cultivated in practice.
Benchmarking Non-Targeted Metabolomics Using Yeast-Derived Libraries

Non-targeted analysis by high-resolution mass spectrometry (HRMS) is the essential discovery tool in metabolomics. Up to date, standardization and validation remain a challenge. Community wide accepted, cost-effective benchmark materials are lacking. In this work, we propose yeast (Pichia pastoris) extracts, derived from fully controlled fermentations for this purpose. We established an open-source metabolite library of > 200 metabolites, reproducibly recovered in ethanolic extracts by orthogonal LCHRMS methods, different fermentations (over three years) and different laboratories. More specifically, compound identification was based on accurate mass, matching retention times, and MS/MS spectra as compared to authentic standards and internal databases. The library includes metabolites from the classes of 1) organic acids and derivatives (2) nucleosides, nucleotides and analogues, (3) lipids and lipid-like molecules, (4) organic oxygen compounds, (5) organoheterocyclic compounds, (6) organic nitrogen compounds and (7) benzoids at expected concentrations ranges of sub-nM to µM. As yeast is a eukaryotic organism, key regulatory elements are highly conserved between yeast and all annotated metabolites were also reported in the Human metabolome data base (HMDB). A large fraction of metabolites was found to be stable for several years when stored at −80°C. Thus, the yeast benchmark material enabled not only to test for the chemical space and coverage upon method implementation and developments, but enabled in-house routines for instrumental performance tests. Finally, the benchmark material opens new avenues for batch to batch corrections in large scale non-targeted metabolomics studies.
Sequence- and structure-selective mRNA m5C methylation by NSUN6 in animals

mRNA m5C, which has recently been implicated in the regulation of mRNA mobility, metabolism, and translation, plays important regulatory roles in various biological events. Two types of m5C sites are found in mRNAs. Type I m5C sites, which contain a downstream G-rich triplet motif and are computationally predicted to locate in the 5’ end of putative hairpin structures, are methylated by NSUN2. Type II m5C sites contain a downstream UCCA motif and are computationally predicted to locate in the loops of putative hairpin structures. However, their biogenesis remains unknown. Here we identified NSUN6, a methyltransferase that is known to methylate C72 of tRNAThr and tRNACys, as an mRNA methyltransferase that targets Type II m5C sites. Combining the RNA secondary structure prediction, miCLIP, and results from a high-throughput mutagenesis analysis, we determined the RNA sequence and structural features governing the specificity of NSUN6-mediated mRNA methylation. Integrating these features into an NSUN6-RNA structural model, we identified an NSUN6 variant that largely loses tRNA methylation but retains mRNA methylation ability. Finally, we revealed a negative correlation between m5C methylation and translation efficiency. Our findings uncover that mRNA m5C is tightly controlled by an elaborate two-enzyme system, and the protein-RNA structure analysis strategy established may be applied to other RNA modification writers to distinguish the functions of different RNA substrates of a writer protein.
Misic, a general deep learning-based method for the high-throughput cell segmentation of complex bacterial communities

Studies of microbial communities by live imaging require new tools for the robust identification of bacterial cells in dense and often inter-species populations, sometimes over very large scales. Here, we developed MiSiC, a general deep-learning-based segmentation method that automatically segments a wide range of spatially structured bacterial communities with very little parameter adjustment, independent of the imaging modality. Using a bacterial predator-prey interaction model, we demonstrate that MiSiC enables the analysis of interspecies interactions, resolving processes at subcellular scales and discriminating between species in millimeter size datasets. The simple implementation of MiSiC and the relatively low need in computing power make its use broadly accessible to fields interested in bacterial interactions and cell biology.
Representational drift in the mouse visual cortex

Neuronal representations in the hippocampus and related structures gradually change over time despite no changes in the environment or behavior. The extent to which such ‘representational drift’ occurs in sensory cortical areas and whether the hierarchy of information flow across areas affects neural-code stability have remained elusive. Here, we address these questions by analyzing large-scale optical and electrophysiological recordings from six visual cortical areas in behaving mice that were repeatedly presented with the same natural movies. We found representational drift over timescales spanning minutes to days across multiple visual areas. The drift was driven mostly by changes in individual cells’ activity rates, while their tuning changed to a lesser extent. Despite these changes, the structure of relationships between the population activity patterns remained stable and stereotypic, allowing robust maintenance of information over time. Such population-level organization may underlie stable visual perception in the face of continuous changes in neuronal responses.
Two independent approaches converge to the cloning of a new Leptosphaeria maculans avirulence effector gene, AvrLmS‐Lep2

Leptosphaeria maculans, the causal agent of blackleg disease, interacts with Brassica napus (oilseed rape, canola) in a gene-for-gene manner. The avirulence genes AvrLmS and AvrLep2 were described to be perceived by the resistance genes RlmS and LepR2, respectively, present in the cultivar Surpass 400. Here we report cloning of AvrLmS and AvrLep2 using two independent methods. AvrLmS was cloned using combined in vitro crossing between avirulent and virulent isolates with sequencing of DNA bulks from avirulent or virulent progeny (Bulked-Segregant-Sequencing) to rapidly identify one candidate avirulence gene present in the effector repertoire of L. maculans. AvrLep2 was cloned using a bi-parental cross of avirulent and virulent L. maculans isolates and a classical map-based cloning approach. Taking these two approaches independently, we found that AvrLmS and AvrLep2 are the same gene. Complementation of virulent isolates with this gene confirmed its role in inducing resistance on Surpass 400 and Topas-LepR2. The gene renamed AvrLmS-Lep2 encodes for a small cysteine-rich protein of unknown function with an N-terminal secretory signal peptide, which are common features of the majority of effectors from extracellular fungal plant pathogens. The AvrLmS-Lep2 / LepR2 interaction phenotype was found to vary from a typical hypersensitive response to intermediate resistance sometimes at the edge of, or evolving toward, susceptibility depending on the inoculation conditions. AvrLmS-Lep2 was nevertheless sufficient to significantly reduce the stem lesion size on plant genotypes with LepR2, indicating the potential efficiency of this resistance to control the disease in the field.
Alleviation of Osmotic Stress on Seed Germination and Seedling Growth of Cotton, Pea and Wheat by Proline

HEIKAL M. M. D. & SHADDAD M. A. 1982: Alleviation of osmotic stress on seed germination and seedling growth of cotton, pea and wheat by proline. — Phyton (Austria) 22 (2): 275 — 287, with 8 figures. — English with German summary. The rate of water uptake, rate of germination, final germination percentage, as well as seedling growth were considerably lowered with the rise of osmotic stress levels using NaCl or polyethylene glycol 6000 (0 — 8 bars). More considerable reduction was obtained under polyethylene glycol than under NaCl, presumably due to the greater water stress caused by the former osmotic substrate. The addition of exogenous proline was very effective in counteracting the effect of osmotic stress on seed germination and seedling growth of the tested species. Zusammenfassung
Connectivity for Rapid Synchronization in a Neural Pacemaker Network

Synchronization is a fundamental property of biological neural networks, playing a mechanistic role in both healthy and disease brain states. The medullary pacemaker nucleus of the weakly electric fish is a synchronized network of high-frequency neurons, weakly coupled via gap junctions. Synchrony in the pacemaker is behaviourally modulated on millisecond timescales, but how gap junctional connectivity enables such rapid resynchronization speeds is poorly understood. Here, we use a computational model of the pacemaker, along with graph theory and predictive analyses, to investigate how network properties, such as randomness and the directionality of coupling (bidirectional/non-rectifying versus directional/rectifying gap junctions) characterize the fast synchronization of the pacemaker network. Our results provide predictions about connectivity in the pacemaker and insight into the relationship between structural network properties and synchronization dynamics in neural systems more generally.
A global database of photosynthesis model parameters, and modelled photosynthetic responses from every major terrestrial plant clade

Plant photosynthesis is a major part of the global carbon cycle and climate system. Carbon capture by C3 plants is most often modelled using the Farquhar-von-Caemmerer-Berry (FvCB) equations. We undertook a global synthesis of all parameters required to solve the FvCB model. The publicly available dataset we assembled includes 3663 observations from 336 different C3 plant species among 96 taxonomic families coming from every major vascular plant clade (lycophytes, ferns, gymnosperms, magnoliids, eudicots and monocots). Geographically, the species in the database have distributions that span the majority of the globe. We used the model to predict photosynthetic rates for a hypothetical average plant in each major terrestrial plant clade and find that generally plants have dramatically increased their photosynthetic abilities through evolutionary time, with the average monocot (the youngest clade) achieving maximum rates of photosynthesis almost double that of the average lycophyte (the oldest clade). We also solved the model for different hypothetical average plant functional types (PFTs) and find that herbaceous species generally have much higher rates of photosynthesis compared to woody plants. Indeed, the maximum photosynthetic rate of graminoids is almost three times the rate of the average tree. The resulting functional responses to increasing CO2 in average hypothetical PFTs would suggest that most groups are already at or near their maximum rate of photosynthesis. However, phylogenetic analysis showed that there was no evidence of niche conservatism with most variance occurring within, rather than among clades (K=0.357, p=0.001). This high within-group variability suggests that average PFTs may obscure important plant responses to increasing CO2. Indeed, when we solved the model for each of the 3663 individual observations, we found that, contrary to the predictions of hypothetical average PFTs, that most plants are predicted to be able to increase their photosynthetic rates. These results suggest that global models should seek to incorporate high within-group variability to accurately predict plant photosynthesis in response to a changing climate.
The restricted nature of protein glycosylation in the mammalian brain

Glycosylation is essential to brain development and function, though prior studies have often been limited to a single analytical technique. Using several methodologies, we analyzed Asn-linked (N-glycans) and Ser/Thr/Tyr-linked (O-glycans) protein glycosylation between brain regions and sexes in mice. Brain N-glycans were surprisingly less complex in sequence and variety compared to other tissues, consisting predominantly of high-mannose precursors and fucosylated/bisected structures. Most brain O-glycans were unbranched, sialylated O-GalNAc and O-mannose structures. A consistent pattern was observed between regions, and sex differences were minimal compared to those observed in plasma. Brain glycans correlate with RNA expression of their synthetic enzymes, and analysis of all glycosylation genes in humans showed a global downregulation in the brain compared to other tissues. We hypothesize that the restricted repertoire of protein glycans arises from their tight regulation in the brain. These results provide a roadmap for future studies of glycosylation in neurodevelopment and disease.
Dimerization of a membrane transporter is driven by differential energetics of lipid solvation of dissociated and associated states

Over two-thirds of membrane proteins of known structure assemble into oligomers. Yet, the forces that drive the association of these proteins in the membrane remain to be delineated, as the lipid bilayer is a solvent environment that is both structurally and chemically complex. In this study we reveal how the lipid solvent defines the dimerization equilibrium of the CLC-ec1 Cl-/H+ antiporter. Integrating experimental and computational approaches, we show that monomers associate to avoid an energetic penalty for solvating a thinned-membrane defect caused by their exposed dimerization interfaces. Supporting this theory, we demonstrate that this penalty is drastically reduced with minimal amounts of short-chain lipids, which stabilize the monomeric state by preferentially solvating the defect rather than altering the physical state of the membrane. We thus posit that the energy differentials for local lipid-solvation define membrane-protein association equilibria, and describe a molecular-level physical mechanism for lipid regulation of such processes in biological conditions.
Glyoxal fixation facilitates transcriptome analysis after antigen staining and cell sorting by flow cytometry

A simple method for extraction of high quality RNA from cells that have been fixed, stained and sorted by flow cytometry would allow routine transcriptome analysis of highly purified cell populations and single cells. However, formaldehyde fixation impairs RNA extraction and inhibits RNA amplification. Here we show that good quality RNA can be readily extracted from stained and sorted mammalian cells if formaldehyde is replaced by glyoxal - a well-characterised fixative that is widely compatible with immunofluorescent staining methods. Although both formaldehyde and glyoxal efficiently form protein-protein crosslinks, glyoxal does not crosslink RNA to proteins nor form stable RNA adducts, ensuring that RNA remains accessible and amenable to enzymatic manipulation after glyoxal fixation. We find that RNA integrity is maintained through glyoxal fixation, permeabilisation with methanol or saponin, indirect immunofluorescent staining and flow sorting. RNA can then be extracted by standard methods and processed into RNA-seq libraries using commercial kits; mRNA abundances measured by poly(A)+ RNA-seq correlate well between freshly harvested cells and fixed, stained and sorted cells. We validate the applicability of this approach to flow cytometry by staining MCF-7 cells for the intracellular G2/M-specific antigen cyclin B1 (CCNB1), and show strong enrichment for G2/M-phase cells based on transcriptomic data. Switching to glyoxal fixation with RNA-compatible staining methods requires only minor adjustments of most existing staining and sorting protocols, and should facilitate routine transcriptomic analysis of sorted cells.
Altered Dynamics of Cortical Beta-Oscillations during Motor Learning in Cerebellar Ataxia

Cerebellar ataxia is associated with an implicit motor learning dysfunction, specifically, a miscalibration of internal models relating motor commands to state changes of the body. Explicit cognitive strategies could compensate for deficits in implicit calibration. Surprisingly, however, patients with cerebellar ataxia use insufficient strategies compared to healthy controls. We report a candidate physiological phenomenon of disrupted strategy use in cerebellar ataxia, reflected in an interaction of implicit and explicit learning effects on cortical beta oscillations. We recorded electroencephalography in patients with cerebellar ataxia (n=18), age-matched healthy controls (n=19), and young, healthy individuals (n=34) during a visuomotor rotation paradigm in which an aiming strategy was either explicitly instructed, or had to be discovered through learning. In young, healthy individuals, learning a strategy, but not implicit learning from sensory prediction error alone, decreased the post-movement beta rebound. Disrupted learning from sensory prediction error in patients, on the other hand, unmasked effects of explicit and implicit control that are normally balanced. Specifically, the post-movement beta rebound increased during strategy use when implicit learning was disrupted, i.e., in patients, but not controls. We conclude that a network disturbance due to cerebellar degeneration surfaces in imbalanced cortical beta oscillations normally involved in strategy learning.
Nutrient digestibility and rumen fermentation of Thai native purebred compared with Thai native x Lowline Angus crossbred beef cattle

ABSTRACT The aim of this study was to compare voluntary feed intake, nutrient digestibility, and rumen fermentation of Thai native and Thai native x Lowline Angus crossbred beef cattle fed with different diets. Three different diets consisting of ad libitum rice straw (RS), ad libitum RS supplemented with 0.5% body weight (BW) concentrate (RS+C), and ad libitum Pangola grass hay (PH). The experiment was conducted as 3 × 3 replicated Latin square design with a factorial arrangement of dietary treatment and breed. It was found that Thai native and Thai native x Lowline Angus crossbred beef cattle had comparable roughage intake, BW change, nutrient digestibility, and all parameters from rumen fluid. Cattle fed with different type of feed showed similar roughage intake, BW change, and number of protozoa and fungal zoospore in rumen fluid. However, nutrient intake and digestibility of cattle supplemented with concentrate were higher than those fed the roughage alone. Accordingly, concentration of total volatile fatty acid and proportion of propionic acid in rumen fluid of cattle received concentrate was higher than cattle fed only RS (P < .05) but not for cattle fed with PH. Moreover, the PH-fed group had a higher ammonia concentration in rumen fluid than did the RS-fed group (P < .05). Therefore, the two breeds of beef cattle showed comparable feed response while supplementation of concentrate at 0.50% BW was a useful alternative feeding pattern.