Miracle-dz/UniFAR-FTUs huggingface dataset:
How Does a Historical System of Meaning Weigh on the Present? Social Representations of Confucianism and Their Role in Young Chinese Lives in the People’s Republic of China

The present study focuses on a new type of social representation: the historical system of meaning embodied by the philosophy and lifeways of Confucianism. Eighteen young and educated Chinese were interviewed face-to-face. Thematic analyses of their transcripts showed that Confucianism representations contained two subthemes, figures (Confucius and Mencius) and thoughts (e.g., propriety and benevolence, etc.). These representations were transmitted by formal education from school and informal education from family, and the influence of Confucianism was often implicit, as evidenced by two subthemes: self-cultivation and social norms. The analyses also showed that almost everything mentioned about Confucianism was more than 2,000 years old and more recent developments were ignored. These results provide insight into how a historically central system of meaning is represented today, when it has lost its institutional bases. It is argued that the social representation of Confucianism is fragmented rather than hegemonic and lacks the systematic coherence that characterises a historical charter. Contributions to social representations theory and implications for how Confucianism could function in the modern world are discussed.
Hyphodermella aurantiaca sp. nova (Polyporales, Basidiomycota) as Evidenced by Morphological Characters and Phylogenetic Analyses

Hyphodermella aurantiaca C.L. Zhao sp. nova (Polyporales, Basidiomycota) is described based on morphological and molecular evidence. The species has an annual growth habit, resupinate basidiomata with saffron to orange hymenial surface, a monomitic hyphal system with generative hyphae bearing simple septa, IKI–, CB–, and ellipsoid, hyaline, thin-walled, smooth, IKI–, CB– basidiospores. In phylogenetic analyses based on molecular data of ITS + nLSU and nLSU sequences H. aurantiaca formed a monophyletic lineage with a strong support (100% BS, 100% BP, 1.00 BPP) and grouped with H. corrugata, H. poroides and H. rosae.
Extraction of nitric acid, uranyl nitrate, and bismuth nitrate from aqueous nitric acid solutions with CMPO

DOE sponsored development of the transuranium extraction (TRUEX) process for removing actinides from radioactive wastes. The solvent is a mixture of CMPO and TBP. Since the extraction characteristics of CMPO are not as well understood as those of TBP, the extraction of nitric acid, uranyl nitrate, and bismuth nitrate with CMPO (dissolved in n-dodecane) were studied. Results indicate that CMPO extracts nitric acid with a 1:1 stoichiometry; equilibrium constant is 2. 660{plus_minus}0.092 at 25 C, and extraction enthalpy is -5. 46{plus_minus}0.46 kcal/mol. Slope analysis indicates that uranyl nitrate extracts with a mixed equilibria of 1:1 and 2:1 stoichiometries in nearly equal proportion. Equil. constant of the 2: 1 extraction was 1.213 {times} 10{sup 6}{plus_minus}3.56 {times} 10{sup 4} at 25 C; reaction enthalpy was -9.610{plus_minus}0.594 kcal/mol. Nitration complexation constant is 8.412{plus_minus}0.579, with an enthalpy of -10.72{plus_minus}1.87 kcal/mol. Bismuth nitrate also extracts with a mixed equilibria of (perhaps) 1:1 and 2:1 stoichiometries. A 2:1 extraction equilibrium and a nitrate complexation adequately model the data. Kinetics and enthalpies were also measured.
Use of an Improved Chemiluminescence Assay for Non-Intrusive Measurement of Hydroxyl Radicals in a Biomimetic Pulp Bleaching Model System

Summary A chemiluminescence assay was used to measure the production of hydroxyl radicals (·OH) in aqueous solutions of hydrogen peroxide and iron-containing catalysts. Preliminary experiments evaluating assay sensitivity revealed that one of the required reagents, phthalhydrazide (PtH), interfered with the studied reactions. In addition, undesirable degradation of the chemiluminescent form of PtH was observed. By removing PtH from reaction solutions and modifying the published procedures, a successful non-intrusive method for measurement of ·OH was obtained. The modified assay was used to compare the rate of ·OH generation in solutions of H2O2, either FeSO4 or Fe-EDTA and a substrate, lignosulfonate. This “biomimetic” pulp bleaching system is meant to simulate naturally occurring biological reactions utilized for degradation of lignins by wood-degrading fungi. Results from these experiments show that FeSO4 produced more ·OH than Fe-EDTA. The improved non-intrusive chemiluminescence assay has proven to be an excellent tool for investigating the role of the ·OH in biomimetic pulp bleaching and potentially other systems.
Validation andapplication of dual-energy x-ray absorptiometry to measurebonemassandbody composition insmallinfants1@

Precision and validity of dual-energy x-ray ab sorptiometry (DXA) for analysis of whole-body composition in infants were assessed by 1) scanning piglets in triplicate to cal culate CVs, and 2) comparing DXA estimates with chemical analysis of whole carcass. The mean CVs for all DXA measures in small piglets and large piglets were < 2.5%, except for fat mass, which were 6.3% and 3.5%, respectively. In large piglets DXA provided reasonable estimates of chemical analysis for bone mineral content (BMC), lean body mass, and fat mass, but only for lean body mass in small piglets. DXA overestimated fat by twofold and underestimated BMC by a third in small piglets. Scans of prematurely born infants (n = i7) at term and at 3, 6, and i2 mo corrected age demonstrated that changes in BMC, lean body mass, and fat mass can be quantitated by DXA. How ever, further refinement of DXA technology is necessary before reliable measures of BMC and fat mass in small infants are at tainable. Am J Cli,, Nutr i993;58:839â€"45.
Demonstration of local adaptation of maize landraces by reciprocal transplantation

Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican highland and lowland common gardens and collected phenotypes relevant to fitness, as well as reported highland-adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparison between phenotypic patterns and population genetic structure. We found phenotypic patterns consistent with local adaptation, though these patterns differ between the Mexican and South American populations. While population genetic structure largely recapitulates drift during post-domestication dispersal, landrace phenotypes reflect adaptations to native elevation. Quantitative trait QST was greater than neutral FST for many traits, signaling divergent directional selection between pairs of populations. All populations exhibited higher fitness metric values when grown at their native elevation, and Mexican landraces had higher fitness than South American landraces when grown in our Mexican sites. Highland populations expressed generally higher anthocyanin pigmentation than lowland populations, and more so in the highland site than in the lowland site. Macrohair density was largely non-plastic, and Mexican landraces and highland landraces were generally more pilose. Analysis of δ13C indicated that lowland populations may have lower WUE. Each population demonstrated garden-specific correlations between highland trait expression and fitness, with stronger positive correlations in the highland site. These results give substance to the long-held presumption of local adaptation of New World maize landraces to elevation and other environmental variables across North and South America.
A simple micropreparative gel electrophoresis technique for purification of proteins, nucleic acids, and bioconjugates

The biochemical and biomedical fields hinge on the ability to effectively separate and purify biological macromolecules. Though this need is largely addressed with a variety of chromatographic and electrophoretic purification techniques, such techniques are usually laborious, time-consuming, and often require complex and costly instalments that are inaccessible to most laboratories. In this work, we introduce a simple micro-preparative (MP) method based on polyacrylamide gel electrophoresis (PAGE) to purify biological samples containing proteins, nucleic acids, and complex bioconjugates. Using a conventional vertical slab system, we demonstrate the extraction of purified DNA, proteins, and DNA-protein bioconjugates from their respective mixtures using MP-PAGE. We apply this system to recover DNA from a ladder mixture with yields of up to 90%, compared to the 58% yield obtained using specialized commercial devices. We also demonstrate the purification of folded enhanced yellow fluorescence protein (EYFP) from crude cell extract with 90% purity, comparable to purities achieved using a two-step size exclusion and immobilized metal-ion affinity chromatography purification procedure. Finally, we demonstrate the successful isolation of an EYFP-DNA bioconjugate sample that otherwise could not be processed using the two-step chromatography procedure. MP-PAGE thus offers a rapid and versatile means of purifying a variety of biomolecules without the need for specialized equipment.
Epidemiological dynamics of viral infection in a marine picoeukaryote

Ostreococcus tauri is a ubiquitous marine pico-eukaryote that is susceptible to lysis upon infection by its species specific Ostreococcus tauri viruses (OtVs). In natural populations of O. tauri, costs of resistance are usually invoked to explain the persistence or reappearance of susceptible individuals in resistant populations. Given the low costs of resistance measured in laboratory experiments with the O. tauri/OtV system to date, the question remains of why susceptible individuals persist in the wild at all. Epidemiological models of host and pathogen population dynamics are one useful approach to understand the conditions that can allow the coexistence of susceptible and resistant hosts. We used a SIR (Susceptible-Infected-Resistant) model to investigate epidemiological dynamics under different laboratory culturing regimes that are commonly used in the O.tauri/OtV system. When taking into account serial transfer (i.e. batchcycle lengths) and dilution rates as well as different resistance costs, our model predicts that no susceptible cells should be detected under any of the simulated conditions – this is consistent with laboratory findings. We thus considered an alternative model that is not used in laboratory experiments, but which incorporates one key process in natural populations: host populations are periodically re-seeded with new infective viruses. In this model, susceptible individuals re-occurred in the population, despite low costs of resistance. This suggests that periodic attack by new viruses, rather than (or in addition to) costs of resistance, may explain the high proportion of susceptible hosts in natural populations, and underlie the discrepancy between laboratory studies and observations of fresh isolates. Importance In natural samples of Ostreococcus sp. and its associated viruses, susceptible hosts are common. However, in laboratory experiments, fully resistant host populations readily and irreversibly evolve. Laboratory experiments are powerful methods for studying process because they offer a stripped-down simplification of a complex system, but this simplification may be an oversimplification for some questions. For example, laboratory and field systems of marine microbes and their viruses differ in population sizes and dynamics, mixing or migration rates, and species diversity, all of which can dramatically alter process outcomes. We demonstrate the utility of using epidemiological models to explore experimental design and to understand mechanisms underlying host-virus population dynamics. We highlight that such models can be used to form strong, testable hypotheses about which key elements of natural systems need to be included in laboratory systems to make them simplified, rather than oversimplified, versions of the processes we use them to study.
Electrophysiological and Transcriptomic Features Reveal a Circular Taxonomy of Cortical Neurons

The complete understanding of the mammalian brain requires exact knowledge of the function of each of the neurons composing its parts. To achieve this goal, an exhaustive, precise, reproducible, and robust neuronal taxonomy should be defined. In this paper, a new circular taxonomy based on transcriptomic features and novel electrophysiological features is proposed. The approach is validated by analysing more than 1850 electrophysiological signals of different mouse visual cortex neurons proceeding from the Allen Cell Types Database. The study is conducted on two different levels: neurons and their cell-type aggregation into Cre Lines. At the neuronal level, electrophysiological features have been extracted with a promising model that has already proved its worth in neuronal dynamics. At the Cre Line level, electrophysiological and transcriptomic features are joined on cell types with available genetic information. A taxonomy with a circular order is revealed by a simple transformation of the first two principal components that allow the characterization of the different Cre Lines. Moreover, the proposed methodology locates other Cre Lines in the taxonomy that do not have transcriptomic features available. Finally, the taxonomy is validated by Machine Learning methods which are able to discriminate the different neuron types with the proposed electrophysiological features.
A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs

Background The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Results Here we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 Mb and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb of the genome in which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. Conclusions The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
Sysrev: A FAIR Platform for Data Curation and Systematic Evidence Review

Abstract Well-curated datasets are essential to evidence based decision making and to the integration of artificial intelligence with human reasoning across disciplines. However, many sources of data remain siloed, unstructured, and/or unavailable for complementary and secondary research. Sysrev was developed to address these issues. First, Sysrev was built to aid in systematic evidence reviews (SER), where digital documents are evaluated according to a well defined process, and where Sysrev provides an easy to access, publicly available and free platform for collaborating in SER projects. Secondly, Sysrev addresses the issue of unstructured, siloed, and inaccessible data in the context of generalized data extraction, where human and machine learning algorithms are combined to extract insights and evidence for better decision making across disciplines. Sysrev uses FAIR - Findability, Accessibility, Interoperability, and Reuse of digital assets - as primary principles in design. Sysrev was developed primarily because of an observed need to reduce redundancy, reduce inefficient use of human time and increase the impact of evidence based decision making. This publication is an introduction to Sysrev as a novel technology, with an overview of the features, motivations and use cases of the tool. Methods Sysrev.com is a FAIR motivated web platform for data curation and SER. Sysrev allows users to create data curation projects called “sysrevs” wherein users upload documents, define review tasks, recruit reviewers, perform review tasks, and automate review tasks. Conclusion Sysrev is a web application designed to facilitate data curation and SERs. Thousands of publicly accessible Sysrev projects have been created, accommodating research in a wide variety of disciplines. Described use cases include data curation, managed reviews, and SERs.
The role of the Andean uplift as an asymmetrical barrier to gene flow in the Neotropical leaf-cutting ant Atta cephalotes

Neotropical diversification by the Andean uplift is typically addressed on a large evolutionary scale (e.g. speciation), even though many species are still distributed in both sides of the mountains. The three parallel mountain ranges in the northern Andes (Colombia) impose a major geographical barrier to species’ migration from South to Central America. How important these barriers are for conspecific diversification of cross-Andean species such as the leaf-cutting ants remains largely unknown. To answer this question, we studied the mtCOI gene of Atta cephalotes, the most widely distributed leaf-cutting ant species. Our hierarchical analyzes evidenced substantial genetic structure among regions and populations, suggesting a more complex biogeographical history of Andean populations than previously thought. These mountains seem to isolate Central American and Western Colombian populations from the rest of A. cephalotes in South America. Population and migration modelling are consistent with the origin of this species in South America and a major role of the Eastern cordillera as a geographical barrier to historical gene flow, restricting dispersion from north to south. These findings provide insights into the role of the Andean uplift as barrier to gene flow and, eventually, implications for monitoring and designing management strategies for leaf-cutting ants.
Curvature sensing steers actin-driven cell migration

Cell migration is fundamental for the immune response, development, and morphogenesis. For navigation through complex and ever-changing environments, migrating cells require a balance between a stable leading-edge, which is necessary for directional migration, and some unstable features to enable the required dynamic behaviors. The leading edge is often composed of actin-driven protrusions including lamellipodia and ruffles with continuously changing membrane curvature. Whether their membrane topography affects the cell’s leading edge and motion persistence in complex environments remains unknown. To study this, we combined a theoretical analysis with machine learning-based segmentation for time-resolved TIRF microscopy, membrane topography analysis from electron microscopy images and microfluidics. We discovered that cell motion persistence and directionality, in both freely moving and environmentally-constrained cells, strongly depend on the curvature-sensing protein Snx33. Specifically, Snx33 promotes leading edge instabilities by locally inhibiting WAVE2-driven actin polymerization in a curvature-dependent manner. Snx33 knockout cells migrate faster and are more persistent during unobstructed migration, but fail when a change in direction is required. Thus, Snx33 is key for steering cell motility in complex environments by facilitating contact inhibition of locomotion and promoting efficient turning. These results identify cell surface topography as an organizing principle at the cell periphery that directs cell migration.
A Multiscale Immuno-Oncology on-Chip System (MIOCS) establishes that collective T cell behaviors govern tumor regression

T cell-based tumor immunotherapies such as CAR T cells or immune checkpoint inhibitors harness the cytotoxic potential of T cells to promote tumor regression. However, patient response to immunotherapy remains heterogeneous, highlighting the need to better understand the rules governing a successful T cell attack. Here, we develop a microfluidic-based method to track the outcome of T cell activity on many individual cancer spheroids simultaneously, with a high spatiotemporal resolution. By combining these parallel measurements of T cell behaviors and tumor fate with probabilistic modeling, we establish that the first recruited T cells initiate a positive feedback loop leading to an accelerated effector accumulation on the spheroid. We also provide evidence that cooperation between T cells on the spheroid during the killing phase facilitates tumor destruction. We propose that tumor destruction does not simply reflect the sum of individual T cell activities but relies instead on collective behaviors promoting both T cell accumulation and function. The possibility to track many replicates of immune-tumor interactions with such a level of detail should help delineate the mechanisms and efficacy of various immunotherapeutic strategies.
The Synergic Role of Actomyosin Architecture and Biased Detachment in Muscle Energetics: Insights in Cross Bridge Mechanism beyond the Lever-Arm Swing

Muscle energetics reflects the ability of myosin motors to convert chemical energy into mechanical energy. How this process takes place remains one of the most elusive questions in the field. Here we combined experimental measurements of in vitro sliding velocity based on DNA-origami built filaments carrying myosins with different lever arm length and simulations based on a Monte-Carlo model which accounts for three basic components: (i) the geometrical hindrance, (ii) the mechano-sensing mechanism, and (iii) the biased kinetics for stretched or compressed motors. The model simulations showed that the geometrical hindrance due to acto-myosin spatial mismatching and the preferential detachment of compressed motors are synergic in generating the rapid increase in the ATP-ase rate from isometric to moderate velocities of contraction, thus acting as an energy-conservation strategy in muscle contraction. The velocity measurements on a DNA-origami filament that preserves the motors’ distribution showed that geometrical hindrance and biased detachment generate a non-zero sliding velocity even without rotation of the myosin lever-arm, which is widely recognized as the basic event in muscle contraction. Because biased detachment is a mechanism for the rectification of thermal fluctuations, in the Brownian-ratchet framework, we predict that it requires a non-negligible amount of energy to preserve the second law of thermodynamics. Taken together, our theoretical and experimental results elucidate non-conventional components in the chemo-mechanical energy transduction in muscle.