Miracle-dz/UniFAR-FTUs huggingface dataset:
Geographical, Temporal and Host-Species Distribution of Potentially Human-Pathogenic Group B Streptococcus in Aquaculture Species in Southeast Asia

Group B Streptococcus (GBS) is a major pathogen of humans and aquatic species. Fish have recently been recognized as the source of severe invasive foodborne GBS disease, caused by sequence type (ST) 283, in otherwise healthy adults in Southeast Asia. Thailand and Vietnam are among the major aquaculture producers in Southeast Asia, with GBS disease reported in fish as well as frogs in both countries. Still, the distribution of potentially human-pathogenic GBS in aquaculture species is poorly known. Using 35 GBS isolates from aquatic species in Thailand collected from 2007 to 2019 and 43 isolates from tilapia collected in Vietnam in 2018 and 2019, we have demonstrated that the temporal, geographical, and host-species distribution of GBS ST283 is broader than previously known, whereas the distribution of ST7 and the poikilothermic lineage of GBS are geographically restricted. The gene encoding the human GBS virulence factor C5a peptidase, scpB, was detected in aquatic ST283 from Thailand but not in ST283 from Vietnam or in ST7 from either country, mirroring current reports of GBS strains associated with human sepsis. The observed distribution of strains and virulence genes is likely to reflect a combination of spill-over, host adaptation through the gain and loss of mobile genetic elements, and current biosecurity practices. The plastic nature of the GBS genome and its importance as a human, aquatic, and potentially foodborne pathogen suggests that active surveillance of GBS presence and its evolution in aquaculture systems may be justified.
Growth and Leaf Gas Exchange Upregulation by Elevated [CO2] Is Light Dependent in Coffee Plants

Coffee (Coffea arabica L.) plants have been assorted as highly suitable to growth at elevated [CO2] (eCa), although such suitability is hypothesized to decrease under severe shade. We herein examined how the combination of eCa and contrasting irradiance affects growth and photosynthetic performance. Coffee plants were grown in open-top chambers under relatively high light (HL) or low light (LL) (9 or 1 mol photons m−2 day−1, respectively), and aCa or eCa (437 or 705 μmol mol–1, respectively). Most traits were affected by light and CO2, and by their interaction. Relative to aCa, our main findings were (i) a greater stomatal conductance (gs) (only at HL) with decreased diffusive limitations to photosynthesis, (ii) greater gs during HL-to-LL transitions, whereas gs was unresponsive to the LL-to-HL transitions irrespective of [CO2], (iii) greater leaf nitrogen pools (only at HL) and higher photosynthetic nitrogen-use efficiency irrespective of light, (iv) lack of photosynthetic acclimation, and (v) greater biomass partitioning to roots and earlier branching. In summary, eCa improved plant growth and photosynthetic performance. Our novel and timely findings suggest that coffee plants are highly suited for a changing climate characterized by a progressive elevation of [CO2], especially if the light is nonlimiting.
Errors in parametrizations of convective boundary‐layer turbulent momentum mixing

The structure of the wind profiles in the convective boundary layer is examined, through large‐eddy simulation, across a wide parameter space. The stability and baroclinicity are varied independently, for cases with roughness lengths appropriate to both land and sea, and the impact of entrainment is isolated by comparing with simulations which do not permit fluxes through the boundary‐layer top.
Using Data Augmentation and Markov Chain Monte Carlo for the Estimation of Unfolding Response Models

Unfolding response models, a class of item response theory (IRT) models that assume a unimodal item response function (IRF), are often used for the measurement of attitudes. Verhelst and Verstralen (1993)and Andrich and Luo (1993) independently developed unfolding response models by relating the observed responses to a more common monotone IRT model using a latent response model (LRM; Maris, 1995). This article generalizes their approach, and suggests a data augmentation scheme for the estimation of any unfolding response model. The article introduces two Markov chain Monte Carlo (MCMC) estimation procedures for the Bayesian estimation of unfolding model parameters; one is a direct implementation of MCMC, and the second utilizes the data augmentation method. We use the estimation procedure to analyze three data sets, one simulated, and two from real attitudinal surveys.
The Contribution of Environmental Science to Mental Health Research: A Scoping Review

Mental health is influenced by multiple complex and interacting genetic, psychological, social, and environmental factors. As such, developing state-of-the-art mental health knowledge requires collaboration across academic disciplines, including environmental science. To assess the current contribution of environmental science to this field, a scoping review of the literature on environmental influences on mental health (including conditions of cognitive development and decline) was conducted. The review protocol was developed in consultation with experts working across mental health and environmental science. The scoping review included 202 English-language papers, published between 2010 and 2020 (prior to the COVID-19 pandemic), on environmental themes that had not already been the subject of recent systematic reviews; 26 reviews on climate change, flooding, air pollution, and urban green space were additionally considered. Studies largely focused on populations in the USA, China, or Europe and involved limited environmental science input. Environmental science research methods are primarily focused on quantitative approaches utilising secondary datasets or field data. Mental health measurement was dominated by the use of self-report psychometric scales. Measures of environmental states or exposures were often lacking in specificity (e.g., limited to the presence or absence of an environmental state). Based on the scoping review findings and our synthesis of the recent reviews, a research agenda for environmental science’s future contribution to mental health scholarship is set out. This includes recommendations to expand the geographical scope and broaden the representation of different environmental science areas, improve measurement of environmental exposure, prioritise experimental and longitudinal research designs, and giving greater consideration to variation between and within communities and the mediating pathways by which environment influences mental health. There is also considerable opportunity to increase interdisciplinarity within the field via the integration of conceptual models, the inclusion of mixed methods and qualitative approaches, as well as further consideration of the socio-political context and the environmental states that can help support good mental health. The findings were used to propose a conceptual model to parse contributions and connections between environmental science and mental health to inform future studies.
Paediatric Major Trauma: A Retrospective Observational Comparison of Mortality in Prehospital Bypass and Secondary Transfer in the East of England

Background More than half of seriously injured children are not initially treated at a major trauma centre (MTC). Children may be transported by private vehicle to a trauma unit (TU). Children may also be transported by emergency medical services (EMS) to the nearest TU with approximately one in five of these undergoing secondary transfer to an MTC. Most trauma networks permit TU bypass to an MTC. However, the evidence on outcomes between transfer and bypass is limited. This study aimed to evaluate the use of the trauma network by comparing outcomes between paediatric major trauma patients by the method of presentation. Methods In this retrospective observational study, a consecutive sample of paediatric (<16 years old) major trauma patients transported to the regional MTC (Cambridge University Hospitals NHS Foundation Trust (CUH)) between 1st January 2015 and 31st December 2020 was included. Patients were excluded if they arrived at the MTC >24 hours post-injury or were transported to the MTC as the nearest hospital. Patients were divided into four groups: self-presented to MTC, MTC as nearest hospital, bypass and secondary transfer. Results A total of 315 patients (28 ‘self-presented’, 55 ‘nearest’, 58 ‘bypass’ and 174 ‘secondary transfers’) were included. The median age was 9.4 [3.7-13.6] years, and n=209 (66.3%) were male. The median Injury Severity Score (ISS) was 16.0 [9.0-25.0] and n=190 (60.3%) had an ISS >15. There was no difference in 30-day mortality between the ‘bypass’ and ‘secondary transfer’ groups. There was a significantly longer hospital and intensive care unit length of stay (LOS) in the bypass group compared to other groups, both p<0.001. The median time to definitive care was five hours greater in the secondary transfer group compared to ‘bypass’ (bypass 117.6 minutes [100.8-136.6], secondary transfer 418.8 minutes [315.6-529.8]). Conclusion There was no significant difference in 30-day mortality of paediatric major trauma patients who underwent secondary transfer compared to those transported directly from the scene to the MTC, despite significant time delays in reaching definitive care.
New exact integrable spin-1 quantum chains

New exactly integrable quantum spin-1 chains are derived. These new quantum Hamiltonians, like the XXZ chain, have a free parameter (anisotropy) and commute with the z-component of the total magnetization. The eigenvalues and eigenvectors are obtained directly by imposing a generalized coordinate Bethe ansatz. The derived Bethe ansatz equations have an unusual form and the associated R-matrix, has a dependence with the spectral parameter that is not of difference form, like the Hubbard quantum chain.
Genomic Identification of CCCH-Type Zinc Finger Protein Genes Reveals the Role of HuTZF3 in Tolerance of Heat and Salt Stress of Pitaya (Hylocereus polyrhizus)

Pitaya (Hylocereus polyrhizus) is cultivated in a broad ecological range, due to its tolerance to drought, heat, and poor soil. The zinc finger proteins regulate gene expression at the transcriptional and post-transcriptional levels, by interacting with DNA, RNA, and proteins, to play roles in plant growth and development, and stress response. Here, a total of 81 CCCH-type zinc finger protein genes were identified from the pitaya genome. Transcriptomic analysis showed that nine of them, including HuTZF3, responded to both salt and heat stress. RT-qPCR results showed that HuTZF3 is expressed in all tested organs of pitaya, with a high level in the roots and stems, and confirmed that expression of HuTZF3 is induced by salt and heat stress. Subcellular localization showed that HuTZF3 is targeted in the processing bodies (PBs) and stress granules (SGs). Heterologous expression of HuTZF3 could improve both salt and heat tolerance in Arabidopsis, reduce oxidative stress, and improve the activity of catalase and peroxidase. Therefore, HuTZF3 may be involved in post-transcriptional regulation via localizing to PBs and SGs, contributing to both salt and heat tolerance in pitaya.
The effect of microwave radiation (2450 MHz) on the morphology and chromosomes of lymphocytes

Effects of microwave radiation have been examined on blood lymphocytes from Chinese hamsters that were irradiated 15 minutes each day during five consecutive days by 2450-MHz (CW) energy at power densities from zero to 45 mW/cm2. Measurements of absorbed energy were accomplished by twin-well calorimetry. One hour after sham or microwave radiation, blood was obtained by orbital hemorrhage and was cultured for one day if unstimulated or for three days if stimulated with phytohemagglutinin (PHA) to induce mitosis. Cultures were terminated with a brief colchicine treatment to arrest cells in metaphase; lymphocytes were then processed for morphological and cytogenetic analyses. Microwave radiation caused a transient, reversible and dose-dependent (albeit curvilinearly related) change in rate of blastic transformation of unstimulated lymphocytes. Rate of transformation was maximum at a power density of 30 mW/cm2, which is associated with a post-radiation body temperature of 39.3 °C. However, frequency of mitoses from PHA stimulation was reduced in irradiated samples. Both the enhancement of transformation and the inhibition of mitosis were evident at 5 mW/cm2. Autoradiography of cells labelled with 3H-thymidine showed no evidence of radiation-related DNA repair. Cytogenetic analysis demonstrated no difference in chromosomal aberrations in irradiated and control samples.
Sun-Exposed versus Sun-Protected Cutaneous Basal Cell Carcinoma: Clinico-Pathological Profile and p16 Immunostaining

Introduction: Although widespread, BCC is still relatively poorly understood in regards to pathogenesis and prognosis, particularly the lesions formed on anatomical sites away from sun exposure. With the aim of deepening our understanding of the pathogenesis and clinico-pathological correlations of BCCs, we conducted this study. Methods: Tissue blocks and data of 52 Egyptian patients diagnosed with BCC were retrieved for clinical information and inclusion criteria, then re-examined histologically; p16 immunostaining was carried out and evaluated for analysis and comparison between the two groups, i.e., sun-exposed and sun-protected. Results: Sex, age, clinical suspicion, tumor size, recurrence status, and histologic variants did not show a significant difference between the sun-protected and sun-exposed groups; however, the mean ages recorded were 67.2 vs. 62.7 for the sun-protected and sun-exposed groups, respectively. A total of 52% of BCCs were positive for p16. The sun-protected lesions showed p16 positivity in 61% of cases, whereas 49% of the sun-exposed lesions were positive with no significant difference. There was a significant difference in p16 expression between the recurrent and non-recurrent lesions. Conclusions: A significant difference was seen in the case of cancer recurrence, where all the recurrent BCCs in this study demonstrated negative p16 immunostaining of the primary lesions; however, the positively stained cases in total were 52% of BCCs. The mean patient age of the sun-protected group was much higher than in previous peer studies. We assume that the biological, prognostic, and clinical aspects of p16 protein expression in BCCs are still far from being clearly understood. Further studies are highly recommended, with more focus on its role in the pathogenesis and the prognostic factors.
Distinct Predictors of Clinical Response after Repetitive Transcranial Magnetic Stimulation between Bipolar and Unipolar Disorders

Background: Repetitive transcranial magnetic stimulation (rTMS) has been shown to be therapeutically effective for patients suffering from drug-resistant depression. The distinction between bipolar and unipolar disorders would be of great interests to better adapt their respective treatments. Methods: We aimed to identify the factors predicting clinical improvement at one month (M1) after the start of rTMS treatment for each diagnosis, which was preceded by a comparison of the patients’ clinical conditions. We used the data collected and the method employed in a previous publication on 291 patients. Results: Although the bipolar group had fewer responders, these patients seemed to better maintain their post-rTMS improvement on anxiety and perception of the severity of their illness than those in the unipolar group. For the bipolar group, young age coupled with low number of medications and high fatigue was shown to be the best combination for predicting improvement at M1. The duration of current depressive episode, which was previously demonstrated for whole group, combined with being attached was shown to favor clinical improvement among the patients in unipolar group. Conclusion: We were able to define a combination of specific factors related to each diagnosis for predicting the patients’ clinical response. This could be extremely useful to predict the efficacy of rTMS during routine clinical practice in neuromodulation services.
A meta-analysis of relationship between self-efficacy and mathematical academic achievement among primary and secondary school students in China

The discussion on the association between primary and secondary school students' self-efficacy and academic achievement in mathematics has recently caught the attention of some researchers, but this research topic needs further exploration. We selected 11 relevant studies (20,029 samples) by using a meta-analytic approach to examine the link between self-efficacy and academic achievement in mathematics and to explore how various factors moderate these links. These findings offer robust evidence for the link between self-efficacy and academic achievement in mathematics. Additionally, the average age of students, the proportion of female students, measurement instruments, and soundness moderated the association between self-efficacy and academic achievement, with average age exhibiting the strongest effect. The implications of this study deserve further discussion.
KINETIC MODEL OF DNA REPLICATION AND THE LOOPING OF SEMIFLEXIBLE POLYMERS

Biological systems are a rich source of new problems in physics, and solving them requires ideas from various fields. In this thesis, we focus on the specific biological phenomenon of DNA replication, which is tightly regulated by spatio-temporal "programs" during the cell cycle. Inspired by a formal analogy between DNA replication and one-dimensional nucleation-andgrowth processes, we extend the 1 D Kolmogorov-Johnson-Mehl-Avrami (KJMA) model to arbitrary nucleation rates I ( t ) . We then use the KJMA model to extract kinetic parameters from data taken from molecular combing experiments. The analysis developed here can help biologists to understand and compare temporal programs of DNA replication of different organisms from a unified scheme. After developing the kinetic model, we show how underlying physical properties of chromatin, in particular its intrinsic stiffness, can explain various long-standing experimental observations. These include synchrony and correlations in the initiation of replication origins, as well as determination of the origin spacings in the absence of sequence requirements in early embryos.
Identification and experimental verification of an anoikis and immune related signature in prognosis for lung adenocarcinoma

Background Both metastasis and immune resistance are huge obstacle in lung adenocarcinoma (LUAD) treatment. Multiple studies have shown that the ability of tumor cells to resist anoikis is closely related to the metastasis of tumor cells. Methods In this study, the risk prognosis signature related to anoikis and immune related genes (AIRGs) was constructed by cluster analysis and the least absolute shrinkage and selection operator (LASSO) regression by using The Cancer Genome Atlas (TCGA) Program and the Gene Expression Omnibus (GEO) database. Kaplan-Meier (K-M) curve described the prognosis in the different groups. Receiver operating characteristic (ROC) was applied to evaluate the sensitivity of this signature. Principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), independent prognostic analysis, and nomogram were utilized to assess the validity of the signature. In addition, we used multiple bioinformatic tools to analyze the function between different groups. Finally, mRNA levels were analyzed by quantitative real-time PCR (qRT-PCR). Results The K-M curve showed a worse prognosis for the high-risk group compared to that for the low-risk group. ROC, PCA, t-SNE, independent prognostic analysis and nomogram showed well predictive capabilities. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differential genes were mainly enriched in immunity, metabolism, and cell cycle. In addition, multiple immune cells and targeted drugs differed in the two risk groups. Finally, we found that the mRNA levels of AIRGs were remarkably different in normal versus cancer cells. Conclusions In short, we established a new model about anoikis and immune, which can well predict prognosis and immune response.
LTR Retroelements and Bird Adaptation to Arid Environments

TEs are known to be among the main drivers in genome evolution, leading to the generation of evolutionary advantages that favor the success of organisms. The aim of this work was to investigate the TE landscape in bird genomes to look for a possible relationship between the amount of specific TE types and environmental changes that characterized the Oligocene era in Australia. Therefore, the mobilome of 29 bird species, belonging to a total of 11 orders, was analyzed. Our results confirmed that LINE retroelements are not predominant in all species of this evolutionary lineage and highlighted an LTR retroelement dominance in species with an Australian-related evolutionary history. The bird LTR retroelement expansion might have happened in response to the Earth’s dramatic climate changes that occurred about 30 Mya, followed by a progressive aridification across most of Australian landmasses. Therefore, in birds, LTR retroelement burst might have represented an evolutionary advantage in the adaptation to arid/drought environments.
The core structure and pseudo-magnetic field of the dislocation in graphene

An analytical theory is presented for the dislocation (pentagon-heptagon pair) in graphene. In order to fully determine the nonlinear interaction which is responsible for the appearance of dislocation, a γ-potential is proposed and calculated from the electron-density functional theory. The improved dislocation equation, which takes into account the change in space between the mismatched chains, is solved by the variational principle. The strain and stress, in particular the change in the bond length and bond angle at the dislocation core, are obtained explicitly and verified by the first-principle calculation. The pseudo-magnetic field felt by electrons at the band edge is investigated including contribution from topology as well as deformation.
A theory of nonlocal mixing-length convection. II: Generalized smoothed particle hydrodynamics simulations

We simulate nonlocal mixing-length convection using a generalized smoothed particle hydrodynamics (GSPH) computer code developed especially for this problem. GSPH is a numerical representation of the Boltzmann transport picture of turbulent fluids which we developed in the first paper in this series, with each particle representing a fluid blob of some characteristic size of order the mixing length. The particle dynamics are governed by the same equations as in the earlier paper, and therefore the code simulates the same physical processes as in the earlier analytical work. The properties of the mean fluid at each point are defined by the mean of the local ensemble of particles, while the dynamics of individual particles is determined by these mean properties and by forces which arise because of velocity and temperature deviations of a fluid blob relative to the local background