Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of phylogenetic scale on the relationships of taxonomic and phylogenetic turnovers with environment for angiosperms in China

Abstract We aim to assess the influence of phylogenetic scale on the relationships of taxonomic and phylogenetic turnovers with environment for angiosperms in China. Specifically, we quantify the effects of contemporary climate on β‐diversity at different phylogenetic scales representing different evolutionary depths of angiosperms. We sampled a latitudinal gradient and a longitudinal gradient of angiosperm assemblages across China (each ≥3400 km). Species composition in each assemblage was documented. Three metrics of β‐diversity (βsim.tax measuring taxonomic β‐diversity; βsim.phy and Dpw measuring tip‐ and basal‐weighted phylogenetic β‐diversity, respectively) were quantified among assemblages at sequential depths in the evolutionary history of angiosperms from the tips to deeper branches. This was done by slicing the angiosperm phylogenetic tree at six evolutionary depths (0, 15, 30, 45, 60, and 75 million years ago). β‐diversity at each evolutionary depth was related to geographic and climatic distances between assemblages. In general, the relationship between β‐diversity and climatic distance decreased from shallow to deep evolutionary time slice for all the three metrics. The slopes of the decreasing trends for βsim. tax and βsim. phy were much steeper for the latitudinal gradient than for the longitudinal gradient. The decreasing trend of the strength of the relationship was monotonic in all cases except for Dpw across the longitudinal gradient. Geographic distance between assemblages explained little variation in β‐diversity that was not explained by climatic distance. Our study shows that the strength of the relationship between β‐diversity and climatic distance decreases conspicuously from shallow to deep evolutionary depth for the latitudinal gradient, but this decreasing trend is less steep for the longitudinal gradient than for the latitudinal gradient, which likely reflects the influence of historical processes (e.g., the collision of the Indian plate with the Eurasian plate) on β‐diversity.
Protective Effects of the Wenfei Buqi Tongluo Formula on the Inflammation in Idiopathic Pulmonary Fibrosis through Inhibiting the TLR4/MyD88/NF-κB Pathway

Background Idiopathic pulmonary fibrosis (IPF) is a progressive disease with high mortality and poor prognosis. The prognostic signatures related to conventional therapy response remain limited. The Wenfei Buqi Tongluo (WBT) formula, a traditional Chinese medicine (TCM) formula, has been widely utilized to treat respiratory diseases in China, which is particularly effective in promoting inflammatory absorption. In this study, we aim to explore the mechanism of the WBT formula in the inhibition of inflammatory response during IPF, based on network pharmacology and in vivo experiments. Methods Network pharmacology was applied to predict the changes of biological processes and potential pathways for the WBT formula against IPF. Histopathological changes, inflammatory factors (IL-6, IL-1β, and TNF-α), and the proteins of the TLR4/MyD88/NF-κB pathway in bleomycin- (BLM-) induced mice model were examined by hematoxylin-eosin (H&E), Masson or immunohistochemistry staining, Western blot, and enzyme-linked immunosorbent assay analysis. Results A total of 163 possible components and 167 potential targets between the WBT formula and IPF were obtained. The enrichments of network pharmacology showed that inflammation response, TNF, and NF-κB pathways were involved in the treatment of WBT against IPF. The in vivo experiments indicated that the WBT formula could ameliorate inflammatory exudation and collagen deposition at a histopathology level in the BLM-induced mice model. The levels of IL-6, IL-1β, and TNF-α were reduced after the WBT formula treatment. Moreover, the expressions of phosphorylated-NF-κB p65, TLR4, and MyD88 were significantly downregulated by the WBT formula, compared with the BLM-induced group. Conclusion These results indicated that the WBT formula can suppress BLM-induced IPF in a mouse model by inhibiting the inflammation via the TLR4/MyD88/NF-κB pathway. This study provides a new insight into the molecular mechanisms of the WBT formula in the application at the clinic.
Pedestrians’ and bicyclists’ route choice during winter conditions

ABSTRACT This study investigates the association between surface conditions and pedestrians’ and bicyclists’ route choices during winter. We analyzed responses from two surveys in which pedestrians and bicyclists answered questions regarding their route choices in winter environments. We also conducted an experimental study to investigate the association between surface conditions and route choice. The results indicate that surface conditions have a significant impact on pedestrians’ and bicyclists’ route choice. Specifically, pedestrians avoid slippery surfaces in general, while bicyclists avoid surfaces with a build-up of loose snow on the pavement. When bare pavement is available, some pedestrians change their route from snow- or slush-covered surfaces to walk on a bare surface, even when the amount of snow or slush is minimal. On the other hand, based on the experimental results, a partly ice-covered surface did not deter pedestrians, indicating that a correspondence between actual surface conditions and pedestrians’ visual perceptions is an important factor in their informed decision-making. Decision makers can use the results to gain an understanding of which winter maintenance measures are the most important for implementation in order to provide an acceptable service level that promotes walking and cycling in a winter environment.
Parental decision-making for a baby room in daycare centres: conceptions, motivations and influential factors

ABSTRACT This exploratory study aims to explore and analyse the process of parental decision-making for baby rooms in daycare centres, within the Portuguese context of early childhood education and care. The theoretical framework is based on the accommodation model. Methodologically, the research is based on a qualitative and interpretative approach involving data collection through a focus group discussion, with seven parents who decided to enrol their babies, in baby rooms of seven non-profit daycare settings. The findings and discussion show that parental decision-making for a baby room in daycare is a complex and multidimensional process that involves opportunities, constraints, and preferences concerning pragmatic, personal, family, contextual and baby-centred factors. The need to provide parents with better information on what matters in daycare contexts is also a significant finding. The article ends by presenting some conclusions and recommendations addressed to all stakeholders, especially educators, to support the parental decision-making process for baby rooms in daycare.
Inovasi Strategi Pendidikan Karakter Berbasis Masyarakat pada Satuan Pendidikan Dasar

Permasalahan dalam penguatan pendidikan karakter (PPK) berbasis masyarakat. Permasalahan antara lain adanya perbedaan pandangan dan konsep tentang pendidikan karakter antara sekolah, keluarga, dan masyarakat. Tujuan penelitian ini menganalisis inovasi strategi PPK berbasis masyarakat di satuan pendidikan dasar. Jenis penelitian deskriptif kualitatif. Penelitian didesain dalam tiga tahapan persiapan (koordinasi, penyusunan materi dan instrumen), pelaksanaan (penyegaran konsep PPK berbasis masyarakat, forum grup diskusi, pengisian google form, analisis dan validasi data), dan pelaporan (penyusunan laporan seminar hasil penelitian). Subjek penelitian terdiri dari dua kepala sekolah dan 37 guru. Metode pengumpulan data dengan wawancara, forum grup diskusi, dan dokumentasi. Instrumen penelitian list pertanyaan dan google form. Teknik analisis data reduksi data, klasifikasi data, display data, dan penyimpulan. Hasil penelitian, inovasi strategi penguatan pendidikan karakter berbasis masyarakat oleh satuan pendidikan dasar di kapanewon Galur Kulon Proggo adalah menjalin komunikasi secara luring maupun daring dengan semua stakeholder (orang tua, komite sekolah, unit-unit pemerintah maupun swasta dilingkungan sekolah), penandatanganan MOU dengan stakeholder sebagai sumber belajar, implementasi buku Pantauan Kegiatan Penguatan Nilai-nilai Karakter Siswa, dan memberdayakan stakeholder sebagai sumber belajar peserta didik,. Komunikasi secara virtual tetap dilaksanakan, meskipun kadang-kadang ditemukan beberapa kendala di dalamnya.
Power-law Inflation in the f(R) Gravity

We investigate a form of f(R)=R1+δ/Rcδ and study the viability of the model for inflation in the Jordan and the Einstein frames. We have extended this form to f(R)=R+R1+δ/Rcδ in an attempt to solve the problems of the former model. This model is further analyzed by using the power spectrum indices of inflation and the reheating temperature. During the inflationary evolution, the model predicts a value of the δ parameter very close to one (δ = 0.98), while the reheating temperature Tre∼1016 GeV at δ = 0.98 is consistent with the standard approach to inflation and observations. We calculate the slow roll parameters for the minimally coupled scalar field within the framework of our models. It is found that the values of the scalar spectral index and tensor-to-scalar ratio are very close to the recent observational data, including those released by Planck. Further, we find the scalar spectral index and the tensor-to-scalar ratio are exactly the same in the first model because the Jordan and the Einstein frames are conformally equivalent. We also attempt to provide a constraint through the non-Gaussianity parameter.
Elemental Abundances in M31: Gradients in the Giant Stellar Stream

We analyze existing measurements of [Fe/H] and [α/Fe] for individual red giant branch (RGB) stars in the Giant Stellar Stream (GSS) of M31 to determine whether spatial abundance gradients are present. These measurements were obtained from low- (R ∼ 3000) and moderate- (R ∼ 6000) resolution Keck/DEIMOS spectroscopy using spectral synthesis techniques as part of the Elemental Abundances in M31 survey. From a sample of 62 RGB stars spanning the GSS at 17, 22, and 33 projected kpc, we measure a [Fe/H] gradient of −0.018 ± 0.003 dex kpc−1 and negligible [α/Fe] gradient with M31-centric radius. We investigate GSS abundance patterns in the outer halo using additional [Fe/H] and [α/Fe] measurements for six RGB stars located along the stream at 45 and 58 projected kpc. These abundances provide tentative evidence that the trends in [Fe/H] and [α/Fe] beyond 40 kpc in the GSS are consistent with those within 33 kpc. We also compare the GSS abundances to 65 RGB stars located along the possibly related Southeast (SE) shelf substructure at 12 and 18 projected kpc. The abundances of the GSS and SE shelf are consistent, supporting a common origin hypothesis, although this interpretation may be complicated by the presence of [Fe/H] gradients in the GSS. We discuss the abundance patterns in the context of photometric studies from the literature and explore implications for the properties of the GSS progenitor, suggesting that the high 〈[α/Fe]〉 of the GSS (+0.40 ± 0.05 dex) favors a major merger scenario for its formation.
No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study

Abstract Motivation The biases in CoDing Sequence (CDS) prediction tools, which have been based on historic genomic annotations from model organisms, impact our understanding of novel genomes and metagenomes. This hinders the discovery of new genomic information as it results in predictions being biased towards existing knowledge. To date, users have lacked a systematic and replicable approach to identify the strengths and weaknesses of any CDS prediction tool and allow them to choose the right tool for their analysis. Results We present an evaluation framework (ORForise) based on a comprehensive set of 12 primary and 60 secondary metrics that facilitate the assessment of the performance of CDS prediction tools. This makes it possible to identify which performs better for specific use-cases. We use this to assess 15 ab initio- and model-based tools representing those most widely used (historically and currently) to generate the knowledge in genomic databases. We find that the performance of any tool is dependent on the genome being analysed, and no individual tool ranked as the most accurate across all genomes or metrics analysed. Even the top-ranked tools produced conflicting gene collections, which could not be resolved by aggregation. The ORForise evaluation framework provides users with a replicable, data-led approach to make informed tool choices for novel genome annotations and for refining historical annotations. Availability and implementation Code and datasets for reproduction and customisation are available at https://github.com/NickJD/ORForise. Supplementary information Supplementary data are available at Bioinformatics online.
Antecedents and outcomes of work-family conflict: A mega-meta path analysis

This study examines the mediating role of work-to-family conflict and family-to-work conflict between the Big Five personality traits and mental health thereby enhancing theoretical development based upon empirical evidence. Integrating Conservation of Resources theory with the self-medication hypothesis, we conducted a mega-meta analytic path analysis examining the relationships among employees’ Big Five traits, work-to-family conflict and family-to-work conflict, anxiety and depression, and substance use. We produced a ten-by-ten synthetic correlation matrix from existing meta-analytic bivariate relationships to test our sequential mediation model. Results from our path analysis model showed that agreeableness and conscientiousness predicted substance use via mediated paths through both work-to-family conflict and family-to-work conflict and sequentially through depression as well as through family-to-work conflict followed by anxiety. Extroversion and openness-to-experience had relatively weaker influences on substance use through work-to-family conflict, anxiety, and depression. Neuroticism was the strongest driver of the two forms of conflict, the two mental health conditions, and substance use. From this model it can be inferred that work-to-family conflict and family-to-work conflict may be generative mechanisms by which the impact of personality is transmitted to mental health outcomes and then to substance use when analyzed via a Conservation of Resources theory lens.
Ontogeny of osmoregulation of the Asian shore crab Hemigrapsus sanguineus at an invaded site of Europe

Abstract We studied the ontogeny of osmoregulation of the Asian shore crab Hemigrapsus sanguineus at an invaded area in the North Sea. H. sanguineus is native to Japan and China but has successfully invaded the Atlantic coast of North America and Europe. In the invaded areas, H. sanguineus is becoming a keystone species as driver of community structure and the adults compete with the shore crab Carcinus maenas. Strong osmoregulatory abilities may confer the potential to use and invade coastal areas already earlier in the life cycle. We reared larvae and first juveniles at 24°C in seawater from hatching to intermoult of each developmental stage (zoea I-V, megalopa, crab I). We exposed each stage to a range of salinities (0–39 ppt) for 24 h, and then we quantified haemolymph osmolality, using nano-osmometry. In addition, we quantified osmolality in field-collected adults after acclimation to the test salinities for 6 days. Larvae of H. sanguineus were able to hyper-osmoregulate at low salinities (15 and 20 ppt) over the complete larval development, although the capacity was reduced at the zoeal stage V; at higher salinities (25–39 ppt), all larval stages were osmoconformers. The capacity to slightly hypo-regulate at high salinity appeared in the first juvenile. Adults were able to hyper-osmoregulate at low salinities and hypo-regulate at concentrated seawater (39 ppt). H. sanguineus showed a strong capacity to osmoregulate as compared to its native competitor C. maenas, which only hyper-regulates at the first and last larval stages and does not hypo-regulate at the juvenile-adult stages. The capacity of H. sanguineus to osmoregulate over most of the life cycle should underpin the potential to invade empty niches in the coastal zone (characterized by low salinity and high temperatures). Osmoregulation abilities over the whole life cycle also constitute a strong competitive advantage over C. maenas.
Analysis of Eukaryotic lincRNA Sequences Indicates Signatures of Hindered Translation Linked to Selection Pressure

Abstract Long intergenic noncoding RNAs (lincRNAs) represent a large fraction of transcribed loci in eukaryotic genomes. Although classified as noncoding, most lincRNAs contain open reading frames (ORFs), and it remains unclear why cytoplasmic lincRNAs are not or very inefficiently translated. Here, we analyzed signatures of hindered translation in lincRNA sequences from five eukaryotes, covering a range of natural selection pressures. In fission yeast and Caenorhabditis elegans, that is, species under strong selection, we detected significantly shorter ORFs, a suboptimal sequence context around start codons for translation initiation, and trinucleotides (“codons”) corresponding to less abundant tRNAs than for neutrally evolving control sequences, likely impeding translation elongation. For human, we detected signatures for cell-type-specific hindrance of lincRNA translation, in particular codons in abundant cytoplasmic lincRNAs corresponding to lower expressed tRNAs than control codons, in three out of five human cell lines. We verified that varying tRNA expression levels between cell lines are reflected in the amount of ribosomes bound to cytoplasmic lincRNAs in each cell line. We further propose that codons at ORF starts are particularly important for reducing ribosome-binding to cytoplasmic lincRNA ORFs. Altogether, our analyses indicate that in species under stronger selection lincRNAs evolved sequence features generally hindering translation and support cell-type-specific hindrance of translation efficiency in human lincRNAs. The sequence signatures we have identified may improve predicting peptide-coding and genuine noncoding lincRNAs in a cell type.
Traveling wave of inflammatory response to regulate the expansion or shrinkage of skin erythema

Many skin diseases show circular red lesions on the skin, called erythema. Erythema is characterized by the expansion of its circular area solely from local stimulation. A pathological inflammatory response caused by the stimulation persistently increases inflammatory mediators in the dermis, whereas a normal inflammatory response transiently increases mediators, resulting in the shrinkage of the erythema. Although the diffusion of mediators theoretically reproduces the expansion, how the inflammatory response expands or shrinks the erythema remains unknown. A possibility is positive feedback, which affects mediator production and can generate two distinct stable states (i.e., inflamed and noninflamed), referred to as bistability. Bistability causes a state transition either from the noninflamed to inflamed state or the reverse direction by suprathreshold stimulation. Additionally, the diffusion selectively causes state transition in either direction, resulting in spatial spread of the transited state, known as the traveling wave. Therefore, we hypothesize that the traveling wave of the inflammatory response can account for both the expansion and shrinkage. Using a reaction-diffusion model with bistability, we theoretically show a possible mechanism in which the circular inflamed area expands via the traveling wave from the noninflamed to the inflamed state. During the expansion, the boundary between the inflamed and noninflamed areas moves at a constant velocity while maintaining its concentration gradient. Moreover, when the positive feedback is weak, the traveling wave selectively occurs from the inflamed to noninflamed state, shrinking the inflamed area. Whether the inflamed area expands or shrinks is mainly controlled by the balance of mediator concentration between the noninflamed and inflamed states, relative to the threshold. The traveling wave of the inflammatory response provides an experimentally testable framework for erythema expansion and shrinkage, thereby contributing to the development of effective treatments, including probiotics.
Users’ polarisation in dynamic discussion networks: The case of refugee crisis in Sweden

This paper presents a study on the dynamics of sentiment polarisation in the active online discussion communities formed around a controversial topic—immigration. Using a collection of tweets in the Swedish language from 2012 to 2019, we track the development of the communities and their sentiment polarisation trajectories over time and in the context of an exogenous shock represented by the European refugee crisis in 2015. To achieve the goal of the study, we apply methods of network and sentiment analysis to map users’ interactions in the network communities and quantify users’ sentiment polarities. The results of the analysis give little evidence for users’ polarisation in the network and its communities, as well as suggest that the crisis had a limited effect on the polarisation dynamics on this social media platform. Yet, we notice a shift towards more negative tonality of users’ sentiments after the crisis and discuss possible explanations for the above-mentioned observations.
Plasma neutrophil gelatinase-associated lipocalin and kidney graft outcome

ABSTRACT Background Plasma neutrophil gelatinase-associated lipocalin (pNGAL) has been investigated extensively in acute kidney injury. This study investigated its pathophysiological significance and utility as marker for graft failure and mortality in stable kidney transplant recipients (KTR). Methods Baseline pNGAL was measured in 698 KTR (58% male, age 53 ± 13 years, estimated glomerular filtration rate 52.4 ± 20.4 mL/min/1.73 m2) at median 5.4 (interquartile range 1.8–12.0) years after transplantation, enrolled in the prospective TransplantLines Food and Nutrition Biobank and Cohort Study. Results pNGAL concentrations were higher in males, younger patients, patients with a deceased-donor kidney and higher serum creatinine. Independent of these, pNGAL was positively associated with urinary protein excretion, systemic inflammation parameters and calcineurin inhibitor use. During median follow-up of 5.3 (4.5–6.0) years, death-censored graft failure rates were 3.9%, 7.3% and 25.0% across increasing tertiles of pNGAL (Plog-rank < 0.001). Cox-regression analyses showed no independent associations of pNGAL with mortality, but strong associations with graft failure (hazard ratio, per doubling 4.16; 95% confidence interval 3.03–5.71; P < 0.001), which remained independent of adjustment for confounders. These associations were present only in patients with pre-existent proteinuria and poor kidney function. Conclusions pNGAL is associated with parameters of kidney graft damage and with graft failure. The latter association is particularly present in KTR with pre-existent poor kidney function and proteinuria. Trial Registration: ClinicalTrials.gov NCT02811835.