Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly

Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model β-nearest taxon index (βNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level βNTI (βNTIfeat), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using βNTIfeat, we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that βNTIfeat can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate βNTIfeat values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family Geobacteraceae were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that βNTIfeat offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types.
Discerning the Putative U and V Chromosomes of Saccharina japonica (Phaeophyta) by Cytogenetic Mapping of Sex-Linked Molecular Markers

Saccharina japonica, an importantly industrial species in brown seaweeds, has a typical alternate life history of heteromorphic generations and UV sex determination system. But up to now, the sex chromosomes, U and V, in this kelp remain to be evidenced cytologically. In the present study, the female-linked (SJ-f_000170 and MSj68-58-2) and male-linked (SJ-13_001840 and MSj68-16-2) molecular markers developed on the basis of Ectocarpus sex-determining regions (SDRs) were selected after PCR amplification and Southern blotting analysis. Mono-color fluorescence in situ hybridization (FISH) to the kelp metaphase chromosomes with each of these confirmed sex-linked markers as a probe indicated that the hybridization signals were confined to either female or male gametophytes exclusively. The shape and size of hybridized chromosomes and the relative location of these sex-linked markers on them suggested that the marked chromosomes in a sex were the same, which was further confirmed by dual-color FISH observations. SJ-f_000170 and SJ-13_001840, corresponding to each sex, were therefore used to map the sporophyte metaphase chromosomes by dual-color FISH technique, and they were hybridized on different chromosomes as expected. The sporophyte metaphase chromosomes as hybridized by SJ-f_000170 and SJ-13_001840 resembled those in either female or male gametophytes, suggesting that they were the putative U and V, respectively, chromosomes in S. japonica. To further demonstrate the reliability of this inference, genomic information of the screened bacterial artificial chromosome (BAC) clones carrying two female-linked markers, for example, from the constructed BAC libraries of the kelp female gametophytes was provided. The insert sequencing of two selected BAC clones revealed that repetitive elements were rich whereas gene density was poor, which was characterized as non-recombining SDR sequences in brown seaweed Ectocarpus sp. and liverwort Marchantia polymorpha. The present study laid a solid foundation for unveiling the mystery of S. japonica sex chromosomes.
Methanogen Productivity and Microbial Community Composition Varies With Iron Oxide Mineralogy

Quantifying the flux of methane from terrestrial environments remains challenging, owing to considerable spatial and temporal variability in emissions. Amongst a myriad of factors, variation in the composition of electron acceptors, including metal (oxyhydr)oxides, may impart controls on methane emission. The purpose of this research is to understand how iron (oxyhydr)oxide minerals with varied physicochemical properties influence microbial methane production and subsequent microbial community development. Incubation experiments, using lake sediment as an inoculum and acetate as a carbon source, were used to understand the influence of one poorly crystalline iron oxide mineral, ferrihydrite, and two well-crystalline minerals, hematite and goethite, on methane production. Iron speciation, headspace methane, and 16S-rRNA sequencing microbial community data were measured over time. Substantial iron reduction only occurred in the presence of ferrihydrite while hematite and goethite had little effect on methane production throughout the incubations. In ferrihydrite experiments the time taken to reach the maximum methane production rate was slower than under other conditions, but methane production, eventually occurred in the presence of ferrihydrite. We suggest that this is due to ferrihydrite transformation into more stable minerals like magnetite and goethite or surface passivation by Fe(II). While all experimental conditions enriched for Methanosarcina, only the presence of ferrihydrite enriched for iron reducing bacteria Geobacter. Additionally, the presence of ferrihydrite continued to influence microbial community development after the onset of methanogenesis, with the dissimilarity between communities growing in ferrihydrite compared to no-Fe-added controls increasing over time. This work improves our understanding of how the presence of different iron oxides influences microbial community composition and methane production in soils and sediments.
What Are the Most Effective Neighborhood Ranges for Social Comparison to Improve Water Use Efficiency?

It is commonly recognized in the field of water demand management that social comparison of water usage among people with a similar background is an effective measure to promote water efficiency. Many studies have used “neighborhood” to represent group similarity, but it is unclear how much geographic proximity is appropriate for defining a neighborhood. Therefore, the aim of this study is to clarify what neighborhood range is the most effective for promoting residential water use efficiency. We conducted a field experiment on social comparison feedback using two neighborhood ranges: narrow (condominium complex level) and wide (prefecture level), and analyzed changes in the water usage of 114 households residing in a condominium in the Tokyo metropolitan area, based on daily household water consumption data and an emoticon-based feedback system. As a result of classification of water consumption trend patterns using the K-means clustering method, it was suggested that those with low-consumption reduced their consumption as a result of the intervention, irrespective of neighborhood range. Despite the limited amount of data, the results provide insights into designing and implementing more effective feedback methods outside the US and European regions, especially in the context of residential water efficiency.
Knowledge Co-creation and Sustainable Education in the Labor Market-Driven University–Business Environment

Objective: The university-business partnership plays a particularly important role in society, allowing a symbiosis between socio-economic stakeholders and the university. This symbiosis is based on co-creating and sharing knowledge, creating collaborative projects, valorizing research, implementing SD principles, and on good governance. The aim of this research is to identify groups of francophone socio-economic organizations willing to engage in co-creating knowledge with universities to adapt the academic curriculum to the dynamic requirements of the labor market, supporting entrepreneurship, whilst implementing SDG principles, and ensuring sustainable education. We base our approach on the two-step cluster analysis, data being collected via questionnaires among representatives of francophone organizations in an emerging market. This allows the identification of two clusters of francophone organizations according to the extent to which they contribute to strengthening their relationship with the university by co-creating knowledge, implementing SDG principles, and supporting sustainable education. Findings: The first cluster is represented by francophone organizations reluctant to co-create knowledge and innovate with universities. These organizations have a rather unclear long-term vision and are not actively involved in supporting SDG education or understanding the universities’ training needs. The second cluster is represented by francophone organizations willing to strengthen the relationship with universities and to co-create value, developing students’ entrepreneurial skills and cooperating on the adaptation of the academic curriculum to labor market requirements. Originality/Implications: The originality of this paper consists in conducting exhaustive research among francophone organizations in Romania, with significant practical and social implications for strengthening the strategic university-business environment partnership and identifying solutions to improve knowledge co-creation and sustainable education within a proper university governance.
The Sexual Dimorphic Synapse: From Spine Density to Molecular Composition

A synaptic sexual dimorphism is relevant in the context of multiple neurodevelopmental, neurodegenerative, and neuropsychiatric disorders. Many of these disorders show a different prevalence and progression in woman and man. A similar variance is also present in corresponding animal models. To understand and characterize this dimorphism in pathologies it is important to first understand sex differences in unaffected individuals. Therefore, sexual differences have been studied since 1788, first focusing on brain weight, size, and volume. But as these measures are not directly related to brain function, the investigation of sexual dimorphism also expanded to other organizational levels of the brain. This review is focused on sexual dimorphism at the synaptic level, as these specialized structures are the smallest functional units of the brain, determining cell communication, connectivity, and plasticity. Multiple differences between males and females can be found on the levels of spine density, synaptic morphology, and molecular synapse composition. These differences support the importance of sex-disaggregated data. The specificity of changes to a particular brain region or circuit might support the idea of a mosaic brain, in which each tile individually lies on a continuum from masculinization to feminization. Moreover, synapses can be seen as the smallest tiles of the mosaic determining the classification of larger areas.
Knowledge of, and Attitudes Toward, Concussion in Japanese Male Collegiate Athletes

Japan has no streamlined concussion education for collegiate athletes, and guidelines vary by sport. In particular, research on knowledge of, and attitudes toward, concussion is necessary for the establishment of concussion education for Japanese collegiate athletes. The aim of the present study was to assess the knowledge of, and attitudes toward, concussion in Japanese male collegiate athletes and to investigate their experiences with suspected concussion symptoms. An online questionnaire was administered to 390 collegiate athletes participating in the following five sports with a high incidence of concussion: rugby union, soccer, basketball, American football, and judo. Of the 121 valid responses, 91 (77.1%) indicated that they had experienced suspected concussion symptoms at least once and 46 of these 91 respondents had not reported their symptoms of suspected concussion at least once. Athletes who had never experienced concussion symptoms were significantly less likely to recognize the symptoms of concussion (p < 0.001). Most athletes recognized headache and dizziness as suspected concussion symptoms. However, the recognition rate for several symptoms was lower than the prevalence of these symptoms as shown in previous studies. This suggests that educational initiatives might be important to bridge the gap between athletes' knowledge and understanding of frequently occurring concussion symptoms and to improve reporting behavior.
Trophectoderm Biopsy Differentially Influences the Level of Serum β-Human Chorionic Gonadotropin With Different Embryonic Trophectoderm Scores in Early Pregnancy From 7847 Single-Blastocyst Transfer Cycles

Objective To evaluate whether trophectoderm (TE) biopsy differentially influence the level of serum β-human chorionic gonadotropin (β-hCG) with different TE-scored blastocysts transferred in early pregnancy. Methods This retrospective cohort study contained 7847 single-blastocyst transfer cycles executed between January 2019 and June 2020, including 2657 preimplantation genetic testing (PGT) cycles and 5190 in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) cycles. All cycles were classified into biopsy and control groups, and further stratified based on the TE morphological scores into three subgroups: grades A, B, and C for TE scores, respectively. Intra-group and inter-group analyses were performed on serum β-hCG levels on the 12th day after blastocyst transfer (HCG12), and obstetric and neonatal outcomes. Results For cycles with a live birth, in grade A TE score subgroups, the HCG12 level did not exhibit statistical significance between the control and biopsy groups after adjustment (769 mIU/mL vs. 753 mIU/mL, P=0.631). In contrast, in grade B and C TE score subgroups, the control group showed a significantly higher level of HCG12 relative to the biopsy group (690 mIU/mL vs. 649 mIU/mL, P=0.001; 586 mIU/mL vs. 509 mIU/mL, P<0.001, respectively). We observed no statistically significant differences in obvious adverse obstetric and neonatal outcomes between the same TE-score subgroups of the biopsy group and control group. Conclusions While blastocysts with higher TE grades produced higher serum β-hCG levels in early pregnancy, TE biopsy might exert a negative impact on serum β-hCG levels by blastocysts with a grade-B TE score and below. TE biopsy did not increase the risk for adverse obstetric and neonatal outcomes.
Insights Into the Cultivable Bacterial Fraction of Sediments From the Red Sea Mangroves and Physiological, Chemotaxonomic, and Genomic Characterization of Mangrovibacillus cuniculi gen. nov., sp. nov., a Novel Member of the Bacillaceae Family

Mangrove forests are dynamic and productive ecosystems rich in microbial diversity; it has been estimated that microbial cells in the mangrove sediments constitute up to 91% of the total living biomass of these ecosystems. Despite in this ecosystem many of the ecological functions and services are supported and/or carried out by microorganisms (e.g., nutrient cycling and eukaryotic-host adaptation), their diversity and function are overlooked and poorly explored, especially for the oligotrophic mangrove of the Red Sea coast. Here, we investigated the cultivable fraction of bacteria associated with the sediments of Saudi Arabian Red Sea mangrove forest by applying the diffusion-chamber-based approach in combination with oligotrophic medium and long incubation time to allow the growth of bacteria in their natural environment. Cultivation resulted in the isolation of numerous representatives of Isoptericola (n = 51) and Marinobacter (n = 38), along with several less abundant and poorly study taxa (n = 25) distributed across ten genera. Within the latest group, we isolated R1DC41T, a novel member of the Bacillaceae family in the Firmicutes phylum. It showed 16S rRNA gene similarity of 94.59–97.36% with closest relatives of Rossellomorea (which was formerly in the Bacillus genus), Domibacillus, Bacillus, and Jeotgalibacillus genera. Based on the multilocus sequence analysis (MLSA), R1DC41T strain formed a separated branch from the listed genera, representing a novel species of a new genus for which the name Mangrovibacillus cuniculi gen. nov., sp. nov. is proposed. Genomic, morphological, and physiological characterizations revealed that R1DC41T is an aerobic, Gram-stain-variable, rod-shaped, non-motile, endospore-forming bacterium. A reduced genome and the presence of numerous transporters used to import the components necessary for its growth and resistance to the stresses imposed by the oligotrophic and salty mangrove sediments make R1DC41T extremely adapted to its environment of origin and to the competitive conditions present within.
Cuprizone Intoxication Results in Myelin Vacuole Formation

Myelin damage is a histopathological hallmark of multiple sclerosis lesions. Results of post mortem studies suggest that impaired myelin-axon interaction characterized by focal myelin detachments is an early event during lesion genesis. In this study, we investigated the ultrastructural changes of the axon-myelin interface in the cuprizone model using serial block face scanning electron microscopy and immunohistochemistry. We show that non-inflammatory injury of oligodendrocytes by cuprizone intoxication results in myelin vacuole formation and axonal swellings, paralleled by early alterations of the node of Ranvier cytoarchitecture. This remarkable resemblance of ultrastructural myelin characteristics in multiple sclerosis and the cuprizone animal model suggests that the cuprizone model is a valuable tool to study early pathologies during lesion formation.
Corneal and Epidermal Nerve Quantification in Chemotherapy Induced Peripheral Neuropathy

Chemotherapy-induced neurotoxicity is an increasingly recognized clinical issue in oncology. in vivo confocal microscopy (IVCM) of corneal nerves has been successfully used to diagnose peripheral neuropathies, including diabetic neuropathy. The purpose of this study was to test if the combination of corneal nerve density and morphology assessed by IVCM is useful to monitor the neurotoxic effects of chemotherapy compared to epidermal nerve quantification. Overall, 95 adult patients with different cancer types were recruited from the oncology and hematology departments of the San Raffaele Hospital. Neurological examination, including clinical Total Neuropathy Score, and in vivo corneal confocal microscopy (IVCM), were performed before and after chemotherapy. In a group of 14 patients, skin biopsy was performed at the first and last visit. In the group of 14 patients who underwent both skin biopsy and corneal nerve imaging, clinical worsening (+69%, p = 0.0018) was paralleled by corneal nerve fiber (CNF) density reduction (−22%, p = 0.0457). Clinical Total neuropathy score significantly worsened from the first to the last visit (+62%, p < 0.0001). CNF length was not significantly reduced overall. However, CNF density/tortuosity ratio significantly decreased after therapy. Correlation analysis showed that the CNF density/tortuosity ratio was also correlated with the number of chemotherapy cycles (r = −0.04790, P = 0.0009). Our data confirm that in vivo corneal confocal microscopy is a helpful, non-invasive tool which shows promise for the diagnosis of chemotherapy-induced peripheral neuropathies. IVCM could allow a rapid, reproducible and non-invasive quantification of peripheral nerve pathology in chemotherapy-associated neuropathy.
Bioanalytics for Influenza Virus-Like Particle Characterization and Process Monitoring

Virus-like particles (VLPs) are excellent platforms for the development of influenza vaccine candidates. Nonetheless, their characterization is challenging due to VLPs’ unique biophysical and biochemical properties. To cope with such complexity, multiple analytical techniques have been developed to date (e.g., single-particle analysis, thermal stability, or quantification assays), most of which are rarely used or have been successfully demonstrated for being applicable for virus particle characterization. In this study, several biophysical and biochemical methods have been evaluated for thorough characterization of monovalent and pentavalent influenza VLPs from diverse groups (A and B) and subtypes (H1 and H3) produced in insect cells using the baculovirus expression vector system (IC-BEVS). Particle size distribution and purity profiles were monitored during the purification process using two complementary technologies — nanoparticle tracking analysis (NTA) and tunable resistive pulse sensing (TRPS). VLP surface charge at the selected process pH was also assessed by this last technique. The morphology of the VLP (size, shape, and presence of hemagglutinin spikes) was evaluated using transmission electron microscopy. Circular dichroism was used to assess VLPs’ thermal stability. Total protein, DNA, and baculovirus content were also assessed. All VLPs analyzed exhibited similar size ranges (90–115 nm for NTA and 129–141 nm for TRPS), surface charges (average of −20.4 mV), and morphology (pleomorphic particles resembling influenza virus) exhibiting the presence of HA molecules (spikes) uniformly displayed on M1 protein scaffold. Our data shows that HA titers and purification efficiency in terms of impurity removal and thermal stability were observed to be particle dependent. This study shows robustness and generic applicability of the tools and methods evaluated, independent of VLP valency and group/subtype. Thus, they are most valuable to assist process development and enhance product characterization.
A Nomogram for Predicting Portal Hypertensive Gastropathy in Patients With Liver Cirrhosis: A Retrospective Analysis

Background There is an urgent need for non-invasive methods for predicting portal hypertensive gastropathy (PHG). This study aims to develop and validate a non-invasive method based on clinical parameters for predicting PHG in patients with liver cirrhosis (LC). Methods The overall survival (OS) and hepatocellular carcinoma (HCC)-free survival were evaluated in LC patients, both with and without PHG. A prediction model for PHG was then constructed based on a training dataset that contained data on 492 LC patients. The discrimination, calibration, and clinical utility of the predicting nomogram were assessed using the C-index, calibration plot, and decision curve analysis. Internal validation was conducted using a bootstrapping method, and further external validation using data on the 208 other patients. Results LC patients with PHG had a worse prognosis compared with those without PHG. A nomogram was constructed using clinical parameters, such as age, hemoglobin content, platelet count and Child-Pugh class. The C-index was 0.773 (95% CI: 0.730–0.816) in the training cohort, 0.761 after bootstrapping and 0.745 (95% CI: 0.673–0.817) in the validation cohort. The AUC values were 0.767, 0.724, and 0.756 in the training, validation and total cohorts, respectively. Well-fitted calibration curves were observed in the training and validation cohorts. Decision curve analysis demonstrated that the nomogram was clinically useful at a threshold of 15%. Conclusion The nomogram constructed to predict the risk of developing PHG was found to be clinically viable. Furthermore, PHG is an independent risk factor for OS of LC, but not for the occurrence of HCC.