Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Germline Genetics on Tacrolimus Pharmacokinetics and Pharmacodynamics in Allogeneic Hematopoietic Stem Cell Transplant Patients

Tacrolimus exhibits high inter-patient pharmacokinetics (PK) variability, as well as a narrow therapeutic index, and therefore requires therapeutic drug monitoring. Germline mutations in cytochrome P450 isoforms 4 and 5 genes (CYP3A4/5) and the ATP-binding cassette B1 gene (ABCB1) may contribute to interindividual tacrolimus PK variability, which may impact clinical outcomes among allogeneic hematopoietic stem cell transplantation (HSCT) patients. In this study, 252 adult patients who received tacrolimus for acute graft versus host disease (aGVHD) prophylaxis after allogeneic HSCT were genotyped to evaluate if germline genetic variants associated with tacrolimus PK and pharmacodynamic (PD) variability. Significant associations were detected between germline variants in CYP3A4/5 and ABCB1 and PK endpoints (e.g., median steady-state tacrolimus concentrations and time to goal tacrolimus concentration). However, significant associations were not observed between CYP3A4/5 or ABCB1 germline variants and PD endpoints (e.g., aGVHD and treatment-emergent nephrotoxicity). Decreased age and CYP3A5*1/*1 genotype were independently associated with subtherapeutic tacrolimus trough concentrations while CYP3A5*1*3 or CYP3A5*3/*3 genotypes, myeloablative allogeneic HSCT conditioning regimen (MAC) and increased weight were independently associated with supratherapeutic tacrolimus trough concentrations. Future lines of prospective research inquiry are warranted to use both germline genetic and clinical data to develop precision dosing tools that will optimize both tacrolimus dosing and clinical outcomes among adult HSCT patients.
Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald

Leaf scald (caused by Xanthomonas albilineans) is an important bacterial disease affecting sugarcane in most sugarcane growing countries, including China. High genetic diversity exists among strains of X. albilineans from diverse geographic regions. To highlight the genomic features associated with X. albilineans from China, we sequenced the complete genome of a representative strain (Xa-FJ1) of this pathogen using the PacBio and Illumina platforms. The complete genome of strain Xa-FJ1 consists of a circular chromosome of 3,724,581 bp and a plasmid of 31,536 bp. Average nucleotide identity analysis revealed that Xa-FJ1 was closest to five strains from the French West Indies and the USA, particularly to the strain GPE PC73 from Guadeloupe. Comparative genomic analysis between Xa-FJ1 and GPE PC73 revealed prophage integration, homologous recombination, transposable elements, and a clustered regulatory interspaced short palindromic repeats (CRISPR) system that were linked with 16 insertions/deletions (InDels). Ten and 82 specific genes were found in Xa-FJ1 and GPE PC73, respectively, and some of these genes were subjected to phage-related proteins, zona occludens toxin, and DNA methyltransferases. Our findings highlight intra-species genetic variability of the leaf scald pathogen and provide additional genomic resources to investigate its fitness and virulence.
Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability

Landscape permeability is often explored spatially, but may also vary temporally. Landscape permeability, including partial barriers, influences migratory animals that move across the landscape. Partial barriers are common in rivers where barrier passage varies with streamflow. We explore the influence of partial barriers on the spatial and temporal distribution of migration‐linked genotypes of Oncorhynchus mykiss, a salmonid fish with co‐occurring resident and migratory forms, in tributaries to the South Fork Eel River, California, USA, Elder and Fox Creeks. We genotyped >4,000 individuals using RAD‐capture and classified individuals as resident, heterozygous or migratory genotypes using life history‐associated loci. Across four years of study (2014–2017), the permeability of partial barriers varied across dry and wet years. In Elder Creek, the largest waterfall was passable for adults migrating up‐river 4–39 days each year. In this stream, the overall spatial pattern, with fewer migratory genotypes above the waterfall, remained true across dry and wet years (67%–76% of migratory alleles were downstream of the waterfall). We also observed a strong relationship between distance upstream and proportion of migratory alleles. In Fox Creek, the primary barrier is at the mouth, and we found that the migratory allele frequency varied with the annual timing of high flow events. In years when rain events occurred during the peak breeding season, migratory allele frequency was high (60%–68%), but otherwise it was low (30% in two years). We highlight that partial barriers and landscape permeability can be temporally dynamic, and this effect can be observed through changing genotype frequencies in migratory animals.
Adding noise to Markov cohort state-transition models

Following its introduction over thirty years ago, the Markov cohort model state-transition has been used extensively to model population trajectories over time (Markov trace) in decision modeling and cost-effectiveness studies. We recently showed that a cohort model represents the average of a continuous-time stochastic process on a multidimensional integer lattice governed by a master equation (ME), which represents the time-evolution of the probability function of an integer-valued random vector. Leveraging this theoretical connection, this study introduces an alternative modeling method using a stochastic differential equation (SDE) approach which captures not only the mean behavior but also the variance of the process. The SDE method constitutes the time-evolution of a random vector of population counts. We show the derivation of an SDE model from first principles by postulating the expected change in the distribution of population across states in a small time step. We then describe an algorithm to construct an SDE and solve the SDE via simulation for use in practice. We show the applications of SDE in two case studies. The first example demonstrates that the population trajectories, and their mean and variance, from the SDE and other commonly-used methods match. The second example shows that users can readily apply the SDE method in their existing works without the need for additional inputs beyond those required for constructing a conventional cohort model. In addition, the second example demonstrates that the SDE model is superior to a microsimulation model in terms of computational speed. In summary, an SDE model provides an alternative modeling framework which includes information on variance, can accommodate for time-varying parameters, and is computationally less expensive than microsimulation for a typical modeling problem in cost-effectiveness and decision analyses.
Design and Modeling of Light Emitting Nano-Pixel Structure (LENS) for High Resolution Display (HRD) in a Visible Range

LENS (Light Emitting Nano-pixel Structure), a new nano-metric device, was designed, simulated, and modeled for feasibility analysis, with the challenge of combining high resolution and high brightness for display, essentially adapted for Augmented Reality (AR) and Virtual Reality. The device is made of two parts: The first one is a reflective nano-cone Light Emitting Device (LED) structure to reduce the Total Internal Reflection effects (TIR), and to enable improved light extraction efficiency. The second part is a Compound Parabolic Concentrator (CPC) above the nano-LED to narrow the outgoing light angular distribution so most of the light would be “accepted” by an imaging system. Such a way is drastically limiting any unnecessary light loss. Our simulations show that the total light intensity gain generated by each part of the pixel is at least 3800% when compared to a typical flat LED. It means that, for the same electrical power consumption, the battery life duration is increased by 38. Furthermore, this improvement significantly decreases the display thermal radiation by at least 300%. Since pixel resolution is critical to offer advanced applications, an extensive feasibility study was performed, using the LightTools software package for ray tracing optimization. In addition to the simulation results, an analytical model was developed. This new device holds the potential to change the efficiency for military, professional and consumer applications, and can serve as a game changer.
A Bayesian nonparametric testing procedure for paired samples

We propose a Bayesian hypothesis testing procedure for comparing the distributions of paired samples. The procedure is based on a flexible model for the joint distribution of both samples. The flexibility is given by a mixture of Dirichlet processes. Our proposal uses a spike‐slab prior specification for the base measure of the Dirichlet process and a particular parametrization for the kernel of the mixture in order to facilitate comparisons and posterior inference. The joint model allows us to derive the marginal distributions and test whether they differ or not. The procedure exploits the correlation between samples, relaxes the parametric assumptions, and detects possible differences throughout the entire distributions. A Monte Carlo simulation study comparing the performance of this strategy to other traditional alternatives is provided. Finally, we apply the proposed approach to spirometry data collected in the United States to investigate changes in pulmonary function in children and adolescents in response to air polluting factors.
Identification of New Peptides from Fermented Milk Showing Antioxidant Properties: Mechanism of Action

Due to their beneficial properties, fermented foods are considered important constituents of the human diet. They also contain bioactive peptides, health-promoting compounds studied for a wide range of effects. In this work, several antioxidant peptides extracted from fermented milk proteins were investigated. First, enriched peptide fractions were purified and analysed for their antioxidant capacity in vitro and in a cellular model. Subsequently, from the most active fractions, 23 peptides were identified by mass spectrometry MS/MS), synthesized and tested. Peptides N-15-M, E-11-F, Q-14-R and A-17-E were selected for their antioxidant effects on Caco-2 cells both in the protection against oxidative stress and inhibition of ROS production. To define their action mechanism, the activation of the Kelch-like ECH-associated protein 1/nuclear factor erythroid 2-related factor 2(Keap1/Nrf2) pathway was studied evaluating the translocation of Nrf2 from cytosol to nucleus. In cells treated with N-15-M, Q-14-R and A-17-E, a higher amount of Nrf2 was found in the nucleus with respect to the control. In addition, the three active peptides, through the activation of Keap1/Nrf2 pathway, led to overexpression and increased activity of antioxidant enzymes. Molecular docking analysis confirmed the potential ability of N-15-M, Q-14-R and A-17-E to bind Keap1, showing their destabilizing effect on Keap1/Nrf2 interaction.
A clustering approach for autistic trait classification

ABSTRACT Machine learning (ML) techniques can be utilized by physicians, clinicians, as well as other users, to discover Autism Spectrum Disorder (ASD) symptoms based on historical cases and controls to enhance autism screening efficiency and accuracy. The aim of this study is to improve the performance of detecting ASD traits by reducing data dimensionality and eliminating redundancy in the autism dataset. To achieve this, a new semi-supervised ML framework approach called Clustering-based Autistic Trait Classification (CATC) is proposed that uses a clustering technique and that validates classifiers using classification techniques. The proposed method identifies potential autism cases based on their similarity traits as opposed to a scoring function used by many ASD screening tools. Empirical results on different datasets involving children, adolescents, and adults were verified and compared to other common machine learning classification techniques. The results showed that CATC offers classifiers with higher predictive accuracy, sensitivity, and specificity rates than those of other intelligent classification approaches such as Artificial Neural Network (ANN), Random Forest, Random Trees, and Rule Induction. These classifiers are useful as they are exploited by diagnosticians and other stakeholders involved in ASD screening.
Adult weight change and premenopausal breast cancer risk: A prospective pooled analysis of data from 628,463 women

Early‐adulthood body size is strongly inversely associated with risk of premenopausal breast cancer. It is unclear whether subsequent changes in weight affect risk. We pooled individual‐level data from 17 prospective studies to investigate the association of weight change with premenopausal breast cancer risk, considering strata of initial weight, timing of weight change, other breast cancer risk factors and breast cancer subtype. Hazard ratios (HR) and 95% confidence intervals (CI) were obtained using Cox regression. Among 628,463 women, 10,886 were diagnosed with breast cancer before menopause. Models adjusted for initial weight at ages 18–24 years and other breast cancer risk factors showed that weight gain from ages 18–24 to 35–44 or to 45–54 years was inversely associated with breast cancer overall (e.g., HR per 5 kg to ages 45–54: 0.96, 95% CI: 0.95–0.98) and with oestrogen‐receptor(ER)‐positive breast cancer (HR per 5 kg to ages 45–54: 0.96, 95% CI: 0.94–0.98). Weight gain from ages 25–34 was inversely associated with ER‐positive breast cancer only and weight gain from ages 35–44 was not associated with risk. None of these weight gains were associated with ER‐negative breast cancer. Weight loss was not consistently associated with overall or ER‐specific risk after adjusting for initial weight. Weight increase from early‐adulthood to ages 45–54 years is associated with a reduced premenopausal breast cancer risk independently of early‐adulthood weight. Biological explanations are needed to account for these two separate factors.
Regulation of hypoxia‐inducible factor functions in the nucleus by sphingosine‐1‐phosphate

Sphingosine kinase 2 (SphK2) is known to phosphorylate the nuclear sphingolipid metabolite to generate sphingosine‐1‐phosphate (S1P). Nuclear S1P is involved in epigenetic regulation of gene expression; however, the underlying mechanisms are not well understood. In this work, we have identified the role of nuclear S1P and SphK2 in regulating hypoxia‐responsive master transcription factors hypoxia‐inducible factor (HIF)‐1α/2α, and their functions in breast cancer, with a focus on triple‐negative breast cancer (TNBC). We have shown SphK2 is associated with HIF‐1α in protein complexes, and is enriched at the promoters of HIF target genes, including vascular endothelial growth factor (VEGF), where it enhances local histone H3 acetylation and transcription. S1P specifically binds to the PAS domains of HIF‐1α. SphK2, and HIF‐1α expression levels are elevated in metastatic estrogen receptor‐positive (ER+) and TNBC clinical tissue specimens compared to healthy breast tissue samples. To determine if S1P formation in the nucleus by SphK2 is a key regulator of HIF functions, we found using a preclinical TNBC xenograft mouse model, and an existing selective SphK2 inhibitor K‐145, that nuclear S1P, histone acetylation, HIF‐1α expression, and TNBC tumor growth were all reduced in vivo. Our results suggest that S1P and SphK2 in the nucleus are linked to the regulation of HIF‐1α/2α functions associated with breast cancer progression, and may provide potential therapeutic targets.
Neutrophil Adaptations upon Recruitment to the Lung: New Concepts and Implications for Homeostasis and Disease

Neutrophils have a prominent role in all human immune responses against any type of pathogen or stimulus. The lungs are a major neutrophil reservoir and neutrophilic inflammation is a primary response to both infectious and non-infectious challenges. While neutrophils are well known for their essential role in clearance of bacteria, they are also equipped with specific mechanisms to counter viruses and fungi. When these defense mechanisms become aberrantly activated in the absence of infection, this commonly results in debilitating chronic lung inflammation. Clearance of bacteria by phagocytosis is the hallmark role of neutrophils and has been studied extensively. New studies on neutrophil biology have revealed that this leukocyte subset is highly adaptable and fulfills diverse roles. Of special interest is how these adaptations can impact the outcome of an immune response in the lungs due to their potent capacity for clearing infection and causing damage to host tissue. The adaptability of neutrophils and their propensity to influence the outcome of immune responses implicates them as a much-needed target of future immunomodulatory therapies. This review highlights the recent advances elucidating the mechanisms of neutrophilic inflammation, with a focus on the lung environment due to the immense and growing public health burden of chronic lung diseases such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD), and acute lung inflammatory diseases such as transfusion-related acute lung injury (TRALI).
Potentilla rugulosa Nakai Extract Attenuates Bisphenol A-, S- and F-Induced ROS Production and Differentiation of 3T3-L1 Preadipocytes in the Absence of Dexamethasone

Endocrine disrupting chemicals (EDCs) disrupt the physiological metabolism, thus playing an important role in the development of obesity. EDCs, the so-called ‘obesogens’, might predispose some individuals to gain weight. This study investigated the effects of bisphenol A (BPA) and its alternatives (BPS and BPF) on adipocyte differentiation and the effects of the leaves of Potentilla rugulosa Nakai extract (LPE) as a functional food ingredient on obesogen-induced lipid production and adipogenesis in 3T3-L1 cells. The results showed that LPE has high total phenolic and flavonoid contents (77.58 ± 0.57 mg gallic acid equivalents (GAE)/g and 57.31 ± 1.72 mg quercetin equivalents (QE)/g, respectively). In addition, LPE exerted significant antioxidant effects in terms of DPPH radical scavenging activity, reducing power, ferric-ion reducing antioxidant power, and oxygen radical absorbance capacity. BPA, BPS, and BPF increased lipid accumulation, protein expressions of adipogenic transcription factors (PPAR-γ, C/EBP-α, and aP2), and reactive oxygen species (ROS) production in 3T3-L1 cells. However, LPE suppressed the BPA-, BPS-, and BPF-induced effects on adipogenesis. Therefore, LPE has potential as a functional food supplement that can prevent bisphenol-induced lipid metabolism disorders.
Phenotypic expansion of autosomal dominant retinitis pigmentosa associated with the D477G mutation in RPE65

Mutations in the gene RPE65 (OMIM: 180069) are recessively inherited and known to cause Leber congenital amaurosis. Recently, the mutation D477G in RPE65 has been identified as a cause of autosomal dominant retinitis pigmentosa (RP). Variable expressivity of this disease has been reported, as carrier individuals can present with mild, nonpenetrant, or, most commonly, a severe chorioretinal phenotype that resembles choroideremia. We report the case of a 57-yr-old male who presented to our clinic with nyctalopia and decreasing visual acuity for 1 yr. Dilated fundus examination revealed retinal atrophy and peripheral mottling of the retinal pigment epithelium (RPE). SW-AF revealed patchy hypoautofluorescence throughout the posterior pole with separate lacunae-like areas in the macula of severe RPE atrophy along with foveal sparing. Full-field electroretinogram suggested a rod–cone dystrophy. Whole-exome sequencing revealed the heterozygous mutation c.1430A > G (p.D477G) in the RPE65 gene. This phenotype of peripheral RPE mottling and severe macular lacunae-like atrophy has not been previously reported with RPE65 autosomal dominant RP, supporting the variable expressivity of the disease and expanding the known phenotypic presentations.
High-throughput quantitative microscopy-based half-life measurements of intravenously injected agents

Significance The effectiveness of systemically delivered therapeutics is dependent on their residence time in circulation, as this parameter influences the frequency of interaction with intended target sites prior to elimination from the body. Consequently, measurements of circulation half-life in relevant animal models of disease can be essential to therapeutic design. We designed a high-throughput quantitative microscopy-based approach to accurately measure the blood concentration and circulation half-life of intravenously administered fluorescently labeled agents using only a small amount of blood volume. This platform can be used to analyze large sample volumes from multivariable studies without the need for specialized equipment or extensive sample processing and has the potential to significantly accelerate preclinical therapeutic screening. Accurate analysis of blood concentration and circulation half-life is an important consideration for any intravenously administered agent in preclinical development or for therapeutic application. However, the currently available tools to measure these parameters are laborious, expensive, and inefficient for handling multiple samples from complex multivariable experiments. Here we describe a robust high-throughput quantitative microscopy-based method to measure the blood concentration and circulation half-life of any fluorescently labeled agent using only a small (2 µL) amount of blood volume, enabling additional end-point measurements to be assessed in the same subject. To validate this method, we demonstrate its use to measure the circulation half-life in mice of two types of fluorescently labeled polymeric nanoparticles of different sizes and surface chemistries and of a much smaller fluorescently labeled monoclonal antibody. Furthermore, we demonstrate the improved accuracy of this method compared to previously described methods.