Miracle-dz/UniFAR-FTUs huggingface dataset:
Glucocorticoid receptor expression and cortisol level in cord blood of term infants

Objective. To examine the expression levels of glucocorticoid receptor (GR) isoforms in peripheral blood mononuclear cells (PBMCs) and serum cortisol levels in cord blood from term infants. Methods. The study population consisted of 172 term infants who were delivered from healthy pregnant women. GRalpha and GRbeta expression levels, and serum cortisol level in cord blood were determined by real-time PCR and ELISA, respectively. Results. Detection rates of GRalpha, GRbeta, and GAPDH were 100%, 63.4%, and 100%, respectively. The expression level of GRalpha was about 200 times that of GRbeta. There were no associations between GR expression level and clinical variables. There were significant associations of low UmApH, maternal gravidity or parity, and vaginal delivery with a high cortisol level; however, there were no correlations between GR expression levels and cortisol level. Conclusions. It is considered that glucocorticoid effects could be expected from the fetal period to the neonatal period, because GRalpha expression level was not related to perinatal factors, GRbeta expression level, and cortisol level in term infants. Further studies of larger populations including very preterm and small for gestational age infants are necessary to determine the balance of expression between GRalpha and GRbeta, and cortisol level.
Effects of Sulfur Levels in Fermented Total Mixed Ration Containing Fresh Cassava Root on Feed Utilization, Rumen Characteristics, Microbial Protein Synthesis, and Blood Metabolites in Thai Native Beef Cattle

Simple Summary Feeding of fresh cassava root to animals is restricted because it contains hydrocyanic acid at a high level, which is the origin for poisoning. High levels of hydrocyanic acid from fresh cassava root could be detoxified by sulfur addition to become nontoxic to cattle. The addition of 2% sulfur in a fermented total mixed ration containing fresh cassava root and ensiling for 7 days could improve dry matter digestibility, efficiency of microbial protein synthesis, and concentrations of total volatile fatty acid, propionic acid, and blood thiocyanate. Abstract The influence of sulfur included in fermented total mixed ration (FTMR) containing fresh cassava root on rumen characteristics, microbial protein synthesis, and blood metabolites in cattle was evaluated. Four Thai native beef cattle were randomly assigned according to a 2 × 2 factorial in a 4 × 4 Latin square design, and dietary treatments were as follows: factor A included a level of sulfur at 1% and 2% in total mixed ration, and factor B featured ensiling times at zero and 7 days. Digestibility of dry matter was increased when FTMR was supplemented with 2% sulfur. Blood thiocyanate increased by 69.5% when ensiling time was 7 days compared to no ensiling (p < 0.01). Bacterial populations were significantly different in the FTMR containing sulfur at 2% and 7 days of ensiling. Furthermore, microbial crude protein and efficiency of microbial protein synthesis were higher in the FTMR containing 2% sulfur and 7 days of ensiling (p < 0.01). Thus, high levels of hydrocyanic acid from fresh cassava root could be detoxified by a sulfur addition with an ensiling process to become nontoxic to cattle.
Genomic, Antimicrobial Resistance, and Public Health Insights into Enterococcus spp. from Australian Chickens

Due to Australia’s management of antimicrobial use in poultry, particularly the discontinued use of avoparcin for nearly 20 years, it is hypothesized that vancomycin-resistant enterococci associated with human disease are not derived from poultry isolates. ABSTRACT Due to Australia’s management of antimicrobial use in poultry, particularly the discontinued use of avoparcin for nearly 20 years, it is hypothesized that vancomycin-resistant enterococci associated with human disease are not derived from poultry isolates. This study evaluated antimicrobial resistance (AMR) of five enterococcal species isolated from Australian meat chickens, genomic features of Enterococcus faecium and Enterococcus faecalis, and the phylogenetic relationship of the poultry-derived E. faecium with isolates from human sepsis cases. All enterococcal isolates from chicken ceca were subjected to antimicrobial susceptibility testing. E. faecium and E. faecalis underwent whole-genome sequencing. E. faecium was compared at the core genome level to a collection of human isolates (n = 677) obtained from cases of sepsis over a 2-year period spanning 2015 to 2016. Overall, 205 enterococci were isolated consisting of five different species. E. faecium was the most frequently isolated species (37.6%), followed by E. durans (29.7%), E. faecalis (20%), E. hirae (12.2%), and E. gallinarum (0.5%). All isolates were susceptible to vancomycin and gentamicin, while one isolate was linezolid resistant (MIC 16 mg/liter). Core genome analysis of the E. faecium demonstrated two clades consisting predominantly of human or chicken isolates in each clade, with minimal overlap. Principal component analysis for total gene content revealed three clusters comprised of vanA-positive, vanB-positive, and both vanA- and vanB-negative E. faecium populations. The results of this study provide strong evidence that Australian chicken E. faecium isolates are unlikely to be precursor strains to the currently circulating vancomycin-resistant strains being isolated in Australian hospitals.
Nectar traits differ between pollination syndromes in Balsaminaceae

Abstract Background and Aims The attractiveness of nectar rewards depends both on the quantity of nectar produced and on its chemical composition. It is known that nectar quantity and chemical composition can differ in plant species depending on the main pollinator associated with the species. The main aims of this study were to test formally whether nectar traits are adapted to pollination syndromes in the speciose Balsaminaceae and, if so, whether a combination of nectar traits mirrors pollination syndromes. Methods Comparative methods based on Ornstein–Uhlenbeck models were used to test whether nectar volume, nectar sucrose proportion, sugar and amino acid concentration and amino acid composition had evolved as a function of pollination syndromes in 57 species of Balsaminaceae. Cluster analysis and ordination were performed to derive clusters of species resembling each other in nectar composition. Key Results Evolutionary models for nectar volume and nectar sucrose proportion performed best when including information on pollination syndrome, while including such information improve model fit neither for sugar and amino acid concentration nor for amino acid composition. A significant relationship emerged between pollination syndrome and the combined nectar traits. Conclusions Our results show that nectar volume and nectar sucrose proportion evolve rapidly towards optimal values associated with different pollination syndromes. The detection of a signal indicating that nectar traits in combination are to a certain extent able to predict pollination syndromes in Balsaminaceae suggests that a holistic approach including the whole set of nectar traits helps us to better understand evolution of nectar composition in response to pollinators.
Resource Reasoning and Labelled Separation Logic

This thesis develops resource reasoning with separation lo gic in the areas of modular program specification, program optimization, and concurrency veri fication for heap-manipulating programs. In the first part, we investigate the resources that are requi r d for modular and complete program specifications. Since the safety footprints of a program (th e resources required for safe execution) do not always yield complete specifications, we first ch aracterize the notion of the r levance footprint. We show that the relevance footprints are the only elements ssential for a complete specification, and also identify the conditions for sufficie n y. We then introduce a novel semantic model of heaps which establishes the correspondence betwee n safety and relevance footprints, and we identify a general condition that guarantees this corres pondence in arbitrary resource models. In the second part, we present labelled separation logicfor introducing optimizations such as automatic parallelization in heap manipulating programs. In order to detect dependences between distant statements in a program, we annotate spatial conjun cts i separation logic formulae with the labels of accessing commands, and propagate these label s through program proofs. We also identify the notion of ‘allocation dependences’ which, in a ddition to standard stack and heap dependences, are needed to ensure the safety of optimizatio ns. In the final part, we address the analysis of resource ownersh ip transfers in concurrent programs, and present an algorithm for automating concurrent separat ion logic proofs. This is based on a form of labelled separation logic in which ownership constr aints are tracked through a proof and ownership is inferred from heap accesses at arbitrary progr am points. Unlike previous methods, the algorithm presented here does not require user annotati ons about ownership distribution, and we demonstrate how it can verify programs that could not be ha ndled by previous methods.
Cyclohexane, naphthalene, and diesel fuel increase oxidative stress, CYP153, sodA, and recA gene expression in Rhodococcus erythropolis

In this study, we compared the expression of CYP153, sodA, sodC, and recA genes and ROS generation in hydrocarbon‐degrading Rhodococcus erythropolis in the presence of cyclohexane, naphthalene, and diesel fuel. The expression of cytochrome P450, sodA (encoding Fe/Mn superoxide dismutase), recA, and superoxide anion radical generation rate increased after the addition of all studied hydrocarbons. The peak of CYP153, sodA, and recA gene expression was registered in the presence of naphthalene. The same substrate upregulated the Cu/Zn superoxide dismutase gene, sodC. Cyclohexane generated the highest level of superoxide anion radical production. Hydrogen peroxide accumulated in the medium enriched with diesel fuel. Taken together, hydrocarbon biotransformation leads to oxidative stress and upregulation of antioxidant enzymes and CYP153 genes, and increases DNA reparation levels in R. erythropolis cells.
Immunophenotype of pediatric‐onset mastocytosis does not correlate with clinical course

Pediatric mastocytosis differs from adult mastocytosis in its presentation and clinical course. However, the data regarding the immunophenotypic characterization of mast cells in children are limited. Our objective was to evaluate the immunophenotype of mast cells in pediatric mastocytosis and correlate it with the clinical course.
Empirical Model of Optical Sensing via Spectral Shift of Circular Bragg Phenomenon

Setting up an empirical model of optical sensing to exploit the circular Bragg phenomenon displayed by chiral sculptured thin films (CSTFs), we considered a CSTF with and without a central twist defect of ¿/2 rad. The circular Bragg phenomenon of the defect-free CSTF and the spectral hole in the copolarized reflectance spectrum of the CSTF with the twist defect were both found to be acutely sensitive to the refractive index of a fluid that infiltrates the void regions of the CSTF. These findings bode well for the deployment of CSTFs as optical sensors.
Opportunities for improved surveillance and control of dengue from age-specific case data

One of the challenges faced by global disease surveillance efforts is the lack of comparability across systems. Reporting commonly focuses on overall incidence, despite differences in surveillance quality between and within countries. For most immunizing infections, the age distribution of incident cases provides a more robust picture of trends in transmission. We present a framework to estimate transmission intensity for dengue virus from age-specific incidence data, and apply it to 359 administrative units in Thailand, Colombia, Brazil and Mexico. Our estimates correlate well with those derived from seroprevalence data (the gold standard), capture the expected spatial heterogeneity in risk, and correlate with known environmental drivers of transmission. We show how this approach could be used to guide the implementation of control strategies such as vaccination. Since age-specific counts are routinely collected by masany surveillance systems, they represent a unique opportunity to further our understanding of disease burden and risk for many diseases.
A Sensitive Piezoresistive Tactile Sensor Combining Two Microstructures

A tactile sensor is an indispensable component for electronic skin, mimicking the sensing function of organism skin. Various sensing materials and microstructures have been adopted in the fabrication of tactile sensors. Herein, we propose a highly sensitive flexible tactile sensor composed of nanocomposites with pyramid and irregularly rough microstructures and implement a comparison of piezoresistive properties of nanocomposites with varying weight proportions of multi-wall nanotubes and carbon black particles. In addition to the simple and low-cost fabrication method, the tactile sensor can reach high sensitivity of 3.2 kPa−1 in the range of <1 kPa and fast dynamic response of 217 ms (loading) and 81 ms (recovery) at 40 kPa pressure. Moreover, body movement monitoring applications have been carried out utilizing the flexible tactile sensor. A sound monitoring application further indicates the potential for applications in electronic skin, human–computer interaction, and physiological detection.
Preserved extrastriate visual network in a monkey with substantial, naturally occurring damage to primary visual cortex

Lesions of primary visual cortex (V1) lead to loss of conscious visual perception with significant impact on human patients. Understanding the neural consequences of such damage may aid the development of rehabilitation methods. In this rare case of a Rhesus macaque (monkey S), likely born without V1, the animal’s in-group behaviour was unremarkable, but visual task training was impaired. With multi-modal magnetic resonance imaging, visual structures outside of the lesion appeared normal. Visual stimulation under anaesthesia with checkerboards activated lateral geniculate nucleus of monkey S, while full-field moving dots activated pulvinar. Visual cortical activation was sparse but included face patches. Consistently across lesion and control monkeys, functional connectivity analysis revealed an intact network of bilateral dorsal visual areas temporally correlated with V5/MT activation, even without V1. Despite robust subcortical responses to visual stimulation, we found little evidence for strengthened subcortical input to V5/MT supporting residual visual function or blindsight-like phenomena.
Primary cilia defects causing mitral valve prolapse

Genetic variations in primary cilia genes cause defects during valve morphogenesis that can progress to mitral valve prolapse in the adult. DZIPping along to diagnosis Mitral valve prolapse is a common congenital abnormality that can cause severe complications. By combining studies of mitral valve development in mice with human genetic data, Toomer et al. found that mitral valve prolapse can be caused by abnormal cilia function. The authors tracked mitral valve development in mice from fetal life to adulthood and also performed genetic analysis of human patients with mitral valve prolapse, particularly one family with an inherited form of the disease. The affected members of this family had a mutation in DZIP1, a gene that regulates ciliogenesis, and mice with this mutation also developed mitral valve prolapse, supporting its pathogenic nature. Mitral valve prolapse (MVP) affects 1 in 40 people and is the most common indication for mitral valve surgery. MVP can cause arrhythmias, heart failure, and sudden cardiac death, and to date, the causes of this disease are poorly understood. We now demonstrate that defects in primary cilia genes and their regulated pathways can cause MVP in familial and sporadic nonsyndromic MVP cases. Our expression studies and genetic ablation experiments confirmed a role for primary cilia in regulating ECM deposition during cardiac development. Loss of primary cilia during development resulted in progressive myxomatous degeneration and profound mitral valve pathology in the adult setting. Analysis of a large family with inherited, autosomal dominant nonsyndromic MVP identified a deleterious missense mutation in a cilia gene, DZIP1. A mouse model harboring this variant confirmed the pathogenicity of this mutation and revealed impaired ciliogenesis during development, which progressed to adult myxomatous valve disease and functional MVP. Relevance of primary cilia in common forms of MVP was tested using pathway enrichment in a large population of patients with MVP and controls from previously generated genome-wide association studies (GWAS), which confirmed the involvement of primary cilia genes in MVP. Together, our studies establish a developmental basis for MVP through altered cilia-dependent regulation of ECM and suggest that defects in primary cilia genes can be causative to disease phenotype in some patients with MVP.
Mechanism of CK2.3, a Novel Mimetic Peptide of Bone Morphogenetic Protein Receptor Type IA, Mediated Osteogenesis

Background: Osteoporosis is a degenerative skeletal disease with a limited number of treatment options. CK2.3, a novel peptide, may be a potential therapeutic. It induces osteogenesis and bone formation in vitro and in vivo by acting downstream of BMPRIA through releasing CK2 from the receptor. However, the detailed signaling pathways, the time frame of signaling, and genes activated remain largely unknown. Methods: Using a newly developed fluorescent CK2.3 analog, specific inhibitors for the BMP signaling pathways, Western blot, and RT-qPCR, we determined the mechanism of CK2.3 in C2C12 cells. We then confirmed the results in primary BMSCs. Results: Using these methods, we showed that CK2.3 stimulation activated OSX, ALP, and OCN. CK2.3 stimulation induced time dependent release of CK2β from BMPRIA and concurrently CK2.3 colocalized with CK2α. Furthermore, CK2.3 induced BMP signaling depends on ERK1/2 and Smad1/5/8 signaling pathways. Conclusion: CK2.3 is a novel peptide that drives osteogenesis, and we detailed the molecular sequence of events that are triggered from the stimulation of CK2.3 until the induction of mineralization. This knowledge can be applied in the development of future therapeutics for osteoporosis.
A flap motif in human serine hydroxymethyltransferase is important for structural stabilization, ligand binding, and control of product release

Human cytosolic serine hydroxymethyltransferase (hcSHMT) is a promising target for anticancer chemotherapy and contains a flexible “flap motif” whose function is yet unknown. Here, using size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering (SAXS), molecular dynamics (MD) simulations, and ligand-binding and enzyme-kinetic analyses, we studied the functional roles of the flap motif by comparing WT hcSHMT with a flap-deleted variant (hcSHMT/Δflap). We found that deletion of the flap results in a mixture of apo-dimers and holo-tetramers, whereas the WT was mostly in the tetrameric form. MD simulations indicated that the flap stabilizes structural compactness and thereby enhances oligomerization. The hcSHMT/Δflap variant exhibited different catalytic properties in (6S)-tetrahydrofolate (THF)-dependent reactions compared with the WT but had similar activity in THF-independent aldol cleavage of β-hydroxyamino acid. hcSHMT/Δflap was less sensitive to THF inhibition than the WT (Ki of 0.65 and 0.27 mm THF at pH 7.5, respectively), and the THF dissociation constant of the WT was also 3-fold lower than that of hcSHMT/Δflap, indicating that the flap is important for THF binding. hcSHMT/Δflap did not display the burst kinetics observed in the WT. These results indicate that, upon removal of the flap, product release is no longer the rate-limiting step, implying that the flap is important for controlling product release. The findings reported here improve our understanding of the functional roles of the flap motif in hcSHMT and provide fundamental insight into how a flexible loop can be involved in controlling the enzymatic reactions of hcSHMT and other enzymes.
Active tectonics and intracontinental earthquakes in China: The kinematics and geodynamics

China is a country of intense intracontinental seismicity. Most earthquakes in western China occur within the diffuse Indo-Eurasian plate-boundary zone, which extends thousands of kilometers into Asia. Earthquakes in eastern China mainly occur within the North China block, which is part of the Archean Sino-Korean craton that has been thermally rejuvenated since late Mesozoic. Here, we summarize neotectonic and geodetic results of crustal kinematics and explore their implications for geodynamics and seismicity using numerical modeling. Quaternary fault movements and global positioning system (GPS) measurements indicate a strong infl uence of the Indo-Asian collision on crustal motion in continental China. Using a spherical three-dimensional (3-D) fi nite-element model, we show that the effects of the collisional plate-boundary force are largely limited to western China, whereas gravitational spreading of the Tibetan Plateau has a broad impact on crustal deformation in much of Asia. The intense seismicity in the North China block, and the lack of seismicity in the South China block, may be explained primarily by the tectonic boundary conditions that produce high deviatoric stresses within the North China block but allow the South China block to move coherently as a rigid block. Within the North China block, seismicity is concentrated in the circum-Ordos rifts, refl ecting the control of lithospheric heterogeneity. Finally, we calculated the change of Coulomb stresses associated with 49 major (M ≥ 6.5) earthquakes in the North China block since 1303. The results show that ~80% of these events occurred in regions of increasing Coulomb stresses caused by previous events.