Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions between Environmental Factors and Glutathione S-Transferase (GST) Genes with Respect to Detectable Blood Aluminum Concentrations in Jamaican Children

Aluminum (Al) is a metallic toxicant at high concentrations following natural or unnatural exposures. Dietary intake is considered as the main source of aluminum exposure in children. We used data from 366 typically developing (TD) children (ages 2–8 years) who participated as controls in an age- and sex-matched case–control study in Jamaica. We investigated additive and interactive associations among environmental factors and children’s genotypes for glutathione S-transferase (GST) genes (GSTT1, GSTM1, GSTP1), in relation to having a detectable blood aluminum concentration (BAlC) of >5.0 μg/L, using multivariable logistic regression models. Findings from interactive models revealed that the odds of having a detectable BAlC was significantly higher among children who ate string beans (p ≤ 0.01), whereas about 40% lower odds of having a detectable BAlC was observed in children with higher parental education level, (p = 0.02). A significant interaction between consumption of saltwater fish and GSTP1 in relation to having a detectable BAlC using either co-dominant or dominant genetic models (overall interaction p = 0.02 for both models) indicated that consumption of saltwater fish was associated with higher odds of having a detectable BAlC only among children with the GSTP1 Ile105Val Ile/Ile genotype using either co-dominant or dominant models [OR (95% CI) = 2.73 (1.07, 6.96), p = 0.04; and OR (95% CI) = 2.74 (1.08, 6.99), p = 0.03]. Since this is the first study from Jamaica that reports such findings, replication in other populations is warranted.
Multilocus Phylogeography and Population Genetic Analyses of Opsariichthys hainanensis Reveal Pleistocene Isolation Followed by High Gene Flow around the Gulf of Tonkin

The ichthyofauna of continental islands is characterized by immigration through a land bridge due to fluctuating sea levels. Hainan Island is adjacent to the southern margin of mainland China and provides opportunities for understanding the origin and diversification of freshwater fishes. The aim of our study was to evaluate the level of genetic variation and phylogeographic structure of Opsariichthys hainanensis on Hainan Island and mainland China, using mtDNA cyt b gene (1140 bp) and D-loop (926 bp), nuclear RAG1 gene (1506 bp), and 12 microsatellite loci. Mitochondrial phylogenetic analysis identified five major lineages according to the geographical distribution from different populations. We suggested that two dispersal events occurred: the population in the Changhua River migrated to the Red River (Lineage B), and the populations in the South Hainan region moved northwards to the North Hainan region. However, populations in Northwest Hainan Island dispersed to the populations around the Gulf of Tonkin (Lineage A1) and populations in Northeast Hainan Island dispersed to the populations in mainland China (Lineage A2). Our results indicated that the populations of O. hainanensis suffered a bottleneck event followed by a recent population expansion supported by the ABC analysis. We suggest that O. hainanensis populations were found mostly in the lowlands and a lack of suitable freshwater habitat in southern mainland China and Hainan during the Last Interglacial period, and then expansion occurred during the Last Glacial Maximum.
Universal vs tailored internal models in semiclassical robust output regulation for linear hybrid systems

Output regulation for hybrid systems requires very complex input signals, whose generation in general cannot be based only on the knowledge of the exosystem (or its state, in the full information case); however, for a special class of hybrid systems semiclassical solutions are possible, such that the hybrid steady state motions required for output regulation can be generated by control inputs which are simple functions of the exosystem (or its state). Even in the semiclassical case, the complexity of the internal models required for robust output regulation motivates the search for simpler solutions, which is investigated in this paper.
Phylogenetic Characterization of HIV-1 Sub-Subtype A1 in Karachi, Pakistan

(1) Background: HIV-1 sub-subtype A1 is common in parts of Africa, Russia, former Soviet Union countries, and Eastern Europe. In Pakistan, sub-subtype A1 is the predominant HIV-1 subtype. Preliminary evidence suggests that distinct strains of HIV-1 sub-subtype A1 are circulating in Pakistan; however, an in-depth molecular phylogenetic characterization of HIV-1 sub-subtype A1 strains in Pakistan have not been presented. We performed a detailed characterization of the HIV-1 sub-subtype A1 epidemic in Pakistan using state-of-the-art molecular epidemiology and phylodynamics. (2) Methods: A total of 143 HIV-1 sub-subtype A1 gag sequences, including 61 sequences generated specifically for this study from PLHIVs part of our cohort, representing all sub-subtype A1 gag sequences from Pakistan, were analyzed. Maximum-likelihood phylogenetic cluster analysis was used to determine the relationship between Pakistani sub-subtype A1 strains and pandemic sub-subtype A1 strains. Furthermore, we used signature variation, charge distribution, selection pressures, and epitope prediction analyses to characterize variations unique to Pakistani HIV-1 strains and establish the association between signature variations and Gag epitope profile. (3) Results: The HIV-1 sub-subtype A1 sequences from Pakistan formed three main clusters: two that clustered with Kenyan sequences (7 and 10 sequences, respectively) and one that formed a Pakistan-specific cluster of 123 sequences that were much less related to other sub-subtype A1 sequences available in the database. The sequences in the Pakistan-specific cluster and the Kenyan reference strains exhibited several signature variations, especially at amino acid positions 312, 319, 331, 372, 373, 383, and 402. Structural protein modeling suggested that amino acid changes in these positions result in alterations of the Gag protein structure as well as in Gag-specific T-cell epitopes. (4) Conclusions: Our results suggest that the majority of the Pakistan HIV-1 sub-subtype A1 strains were unique to Pakistan and with a specific mutation pattern in Gag.
Entanglement entropy and conformal field theory

We review the conformal field theory approach to entanglement entropy in 1+1 dimensions. We show how to apply these methods to the calculation of the entanglement entropy of a single interval, and the generalization to different situations such as finite size, systems with boundaries and the case of several disjoint intervals. We discuss the behaviour away from the critical point and the spectrum of the reduced density matrix. Quantum quenches, as paradigms of non-equilibrium situations, are also considered.
Scale-dependent bias of galaxies from baryonic acoustic oscillations

Baryonic acoustic oscillations (BAOs) modulate the density ratio of baryons to dark matter across large regions of the Universe. We show that the associated variation in the mass-to-light ratio of galaxies should generate an oscillatory, scale-dependent bias of galaxies relative to the underlying distribution of dark matter. A measurement of this effect would calibrate the dependence of the characteristic mass-to-light ratio of galaxies on the baryon mass fraction in their large-scale environment. This bias, though, is unlikely to significantly affect measurements of BAO peak positions.
Future Projection of Precipitation Bioclimatic Indicators over Southeast Asia using CMIP6

Precipitation is a key meteorological component that is directly related to climate change. Quantifying the changes in the precipitation bioclimate is crucial in planning climate-change adaptation and mitigation measures. Southeast Asia (SEA), home to the world’s greatest concentration of ecological variety, needs reliable monitoring of such changes. This study utilized the global-climate models from phase 6 of coupled model intercomparison project (CMIP6) to examine the variations in eight precipitation bioclimatic variables over SEA for two shared socioeconomic pathways (SSPs). All indicators were studied for the near (2020–2059) and far (2060–2099) futures to provide a better understanding of the temporal changes and their related uncertainty compared to a historical period (1975–2014). The results showed a high geographical variability of the changes in precipitation-bioclimatic indicators in SEA. The mainland of SEA would experience more changes in the bioclimate than the maritime region. The multimodel ensemble (MME) showed an increase in mean annual rainfall of 6.0–12.4% in most of SEA except the Philippines and southern SEA. The increase will be relatively less in the wettest month (15%) and more in the driest month (20.7%) in most of SEA; however, the precipitation in the wettest quarter would increase by 2.85%, while the driest quarter would decrease by 1.0%. The precipitation would be more seasonal. In addition, the precipitation would increase over a larger area in the wettest month than in the driest month, making precipitation vary more geographically.
RNAseq Analysis of Brown Adipose Tissue and Thyroid of Newborn Lambs Subjected to Short-Term Cold Exposure Reveals Signs of Early Whitening of Adipose Tissue

During the early postnatal period, lambs have the ability to thermoregulate body temperature via non-shivering thermogenesis through brown adipose tissue (BAT), which soon after birth begins to transform into white adipose tissue. An RNA seq approach was used to characterize the transcriptome of BAT and thyroid tissue in newborn lambs exposed to cold conditions. Fifteen newborn Romney lambs were selected and divided into three groups: group 1 (n = 3) was a control, and groups 2 and 3 (n = 6 each) were kept indoors for two days at an ambient temperature (20–22 °C) or at a cold temperature (4 °C), respectively. Sequencing was performed using a paired-end strategy through the BGISEQ-500 platform, followed by the identification of differentially expressed genes using DESeq2 and an enrichment analysis by g:Profiler. This study provides an in-depth expression network of the main characters involved in the thermogenesis and fat-whitening mechanisms that take place in the newborn lamb. Data revealed no significant differential expression of key thermogenic factors such as uncoupling protein 1, suggesting that the heat production peak under cold exposure might occur so rapidly and in such an immediate way that it may seem undetectable in BAT by day three of life. Moreover, these changes in expression might indicate the start of the whitening process of the adipose tissue, concluding the non-shivering thermogenesis period.
Developments in FRET- and BRET-Based Biosensors

Resonance energy transfer technologies have achieved great success in the field of analysis. Particularly, fluorescence resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET) provide strategies to design tools for sensing molecules and monitoring biological processes, which promote the development of biosensors. Here, we provide an overview of recent progress on FRET- and BRET-based biosensors and their roles in biomedicine, environmental applications, and synthetic biology. This review highlights FRET- and BRET-based biosensors and gives examples of their applications with their design strategies. The limitations of their applications and the future directions of their development are also discussed.
Speaking in the first-person singular or plural

Conventionally, the professional interpreter speaks in the first-person singular. Research in corpus-based discourse analysis has reported shifts from this norm towards first-person plural becoming the most frequent pronoun shift in political institutional interpreting, possibly signalling interpreter ‘alignment with the institution’. Nonetheless, few studies have teased apart the simultaneous constraints of social, cognitive, and linguistic factors on institutional interpreters’ preference for the plural. The present research adopts the usage-based theory to consider the three types of explanations together. It extends recent multivariate methodologies based on this theory to analyse 2,438 first-person cases in parallel interpreting and comparable speech corpora. Following robust context analyses and cross-linguistic prosodic transcription, this study weighs the strengths of 33 associates regarding the three explanations through regression analyses. The results show that first-person shifts are better explained by chunking effects when interpreters process complex forms and referents in the source and target speeches, and when they process zero-subject source inputs. The institutional alignment explanation fails to account for the extensive grammaticalisation of plural constructions in the interpreted speech. When all the interactive and additive effects are considered together, institutional alignment or monofactorial paradigms have little explanatory power. This study concludes by highlighting the relevance of usage-based multifactorial designs to interpreting research.
Association between cervical length and massive intraoperative bleeding in patients with suspected placenta accreta spectrum combined with placenta previa: A retrospective cohort study

Purpose Abnormal placentation is a spectrum disorder that includes creta, increta, and percreta; the term placenta accreta spectrum (PAS) disorders is used as a broad term to describe all of these conditions. PAS can lead to life-threatening hemorrhage. The predictive value of cervical length (CL) in patients with PAS remains controversial. Thus, this study investigated the relationship between CL and the probability of major bleeding in patients with PAS and placenta previa. Methods This retrospective cohort study was conducted at a comprehensive tertiary hospital in Chongqing, China, between January 2018 and December 2020. The target independent and dependent variables were CL and intraoperative massive bleeding, respectively. The covariates included demographic, clinical, and ultrasound characteristics. Logistic regression was used to explore the association between CL and massive bleeding. Results In total, 317 participants were enrolled, in whom the prevalence of massive bleeding was 41.9% (133/317). The threshold of CL associated with massive bleeding (≥1,000 ml) was 33 mm based on a receiver operating characteristic curve. In the fully adjusted model for each additional unit of CL, the risk of massive bleeding decreased by 7% [95% confidence interval (CI), 0.88–0.98]. The risk of major bleeding was reduced by 44% in patients with a CL greater than 33 mm (95% CI, 0.33–0.97) compared with patients with a CL less than 33 mm. Conclusions CL was negatively associated with massive intraoperative bleeding in patients with PAS combined with placenta previa. When the CL was greater than 33 mm, the risk of bleeding decreased by 44%. Thus, CL can be used as a standalone parameter to identify the risk of massive intraoperative bleeding in patients with suspected PAS.
Clitocybula ellipsospora, a new species found in the Iberian Peninsula

Clitocybula ellipsospora is proposed as a new species based on morphological (macro- and microscopic) and molecular characters, as well as its distinctive habitat in Pinus sylvestris forest areas near peat bogs, in the Supramedi- terranean belt. A complete discussion comparing this taxon with closely related species is also provided
NSUN5 promotes progression and predicts poor prognosis in hepatocellular carcinoma

The 5-methylcytosine (m5C) RNA methyltransferase NOP2/Sun RNA methyltransferase 5 (NSUN5) has been reported to serve important roles in numerous diseases. However, the functions and clinical significance of NSUN5 in hepatocellular carcinoma (HCC) remain unknown. Clinical information and NSUN5 mRNA sequencing data for 374 patients with HCC were downloaded from The Cancer Genome Atlas (TCGA) database, and NSUN5 mRNA and protein expression levels in 120 patients with HCC (present study cohorts) were assessed using reverse transcription-quantitative PCR, western blotting or immunohistochemistry. The association between NSUN5 mRNA and protein expression levels and the clinical characteristics (or prognosis) of patients with HCC was analyzed using the χ2 or log-rank test. The functions of NSUN5 in HCC were evaluated using in vitro and in vivo experiments, and the mechanism by which NSUN5 affected the progression of HCC was assessed using bioinformatics analysis using LinkedOmics. NSUN5 was significantly upregulated and predicted poor prognosis in HCC according to data from both TCGA database and present study cohorts. NSUN5 significantly promoted HCC proliferation and migration in vitro and significantly induced HCC tumor growth in vivo. Bioinformatics analysis demonstrated that NSUN5 was positively correlated with genes associated with translation in HCC. It was hypothesized that overexpression of NSUN5 strengthened ribosome functions and global protein translation, which may promote the proliferation and migration of HCC. In conclusion, NSUN5 may promote the progression of HCC by enhancing translation, thus making it a potential target for HCC treatment.
The Center of the Milky Way from Radio to X-rays

We summarize basic observational results on Sagittarius~A* obtained from the radio, infrared and X-ray domain. Infrared observations have revealed that a dusty S-cluster object (DSO/G2) passes by SgrA*, the central super-massive black hole of the Milky Way. It is still expected that this event will give rise to exceptionally intense activity in the entire electromagnetic spectrum. Based on February to September 2014 SINFONI observations. The detection of spatially compact and red-shifted hydrogen recombination line emission allows a us to obtain a new estimate of the orbital parameters of the DSO. We have not detected strong pre-pericenter blue-shifted or post-pericenter red-shifted emission above the noise level at the position of SgrA* or upstream the orbit. The periapse position was reached in May 2014. Our 2004-2012 infrared polarization statistics shows that SgrA* must be a very stable system - both in terms of geometrical orientation of a jet or accretion disk and in terms of the variability spectrum which must be linked to the accretion rate. Hence polarization and variability measurements are the ideal tool to probe for any change in the system as a function of the DSO/G2 fly-by. Due to the 2014 fly-by of the DSO, increased accretion activity of SgrA* may still be upcoming. Future observations of bright flares will improve the derivation of the spin and the inclination of the SMBH from NIR/sub-mm observations.
Application of Food Mechanics and Oral Processing in Modelling First Bite of Grilled Meat

This study analyzed the potential of modelling meat mastication by using pork and poultry meat as food with different physical properties under different grilling temperatures. For the purpose of modelling oral processing, temporal dominance of sensations and finite element methods were employed. A panel with ten subjects was trained and used for oral processing analysis and temporal dominance of sensations revealing in-mouth sensations and mastication characteristics. In parallel, the second aim was to evaluate the mechanical properties of the samples and explore the potential of simulating the first bite using the finite element method. Based on the textural parameters, a 3D model of grilled meat was created and a first-bite simulation was performed. A higher level of differences was observed comparing the number of chews for pork meat compared to poultry meat. The chewing rate showed a statistical difference with values in the range of 1.31 chews/s to 1.46 chews/s for pork meat and between 1.36 chews/s and 1.42 chews/s for poultry meat. Firmness was the predominant sensory attribute recognized by panelists at the beginning of mastication, which confirmed our approach used for first-bite modelling. Simulation results show the growth of internal stress following the jaw’s path. Presented models demonstrate that the highest values are around teeth pressure and lead to a conclusion that upon biting, the meat structure will suffer irreversible damage dividing the grilled meat into two pieces, as it happens during the first bite. The main conclusion of this study is that by combining results from oral processing and testing of mechanical properties of the grilled products, it is possible to simulate the first bite.
Influence of Graphene Sheets on Compaction and Sintering Properties of Nano-Zirconia Ceramics

The use of a nanostructured graphene-zirconia composite will allow the development of new materials with improved performance properties and a high functionality. This work covers a stepwise study related to the creation of a nanostructured composite based on ZrO2 and graphene. A composite was prepared using two suspensions: nano-zirconia obtained by sol-gel synthesis and oxygen-free graphene obtained sonochemically. The morphology of oxygen-free graphene sheets, phase composition and the morphology of a zirconia powder, and the morphology of the synthesized composite were studied. The effect of the graphene sheets on the rheological and sintering properties of a nanostructured zirconia-based composite powder has been studied. It has been found that graphene sheets in a hybrid nanostructure make it difficult to press at the elastic deformation stage, and the composite passes into the plastic region at a lower pressure than a single nano-zirconia. A sintering mechanism was proposed for a composite with a graphene content of 0.635 wt%, in which graphene is an important factor affecting the process mechanism. It has been determined that the activation energy of the composite sintering is more than two times higher than for a single nano-zirconia. Apparently, due to the van der Waals interaction, the graphene sheets partially stabilize the zirconia and prevent the disordering of the surface monolayers of its nanocrystals and premelting prior to the sintering. This leads to an increase in the activation energy of the composite sintering, and its sintering occurs, according to a mixed mechanism, in which the grain boundary diffusion predominates, in contrast to the single nano-zirconia sintering, which occurs through a viscous flow.
Excitation Wavelength and Colloids Concentration-Dependent Nonlinear Optical Properties of Silver Nanoparticles Synthesized by Laser Ablation

We reported experimental results from investigations that employed the Z-scan method to explore the dependence of silver nanoparticles’ (AgNPs) nonlinear optical properties on the excitation wavelength, AgNP concentration, and size. Using a 532 nm Nd: YAG laser beam at 100 mJ/pulse for different ablation times, AgNPs were synthesized from a silver target immersed in distilled water. UV–Vis spectroscopy and an atomic absorption spectrometer are used to characterize the optical properties of laser-synthesized AgNPs as well as their concentrations. The AgNPs’ size and shape are determined using a transmission electron microscope (TEM). The laser-synthesized AgNPs are spherical, with an average particle size of 12 to 13.2 nm. Whatever the ablation time, the AgNP colloids exhibit reversed saturable absorption and a negative nonlinear refractive index (n2). Both n2 and the nonlinear absorption coefficient (α3) increase as the AgNP concentration increases. As the excitation wavelength and average size of the AgNPs increase, n2 and α3 decrease.