A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes.

Predicting phenotypes from genotypes is a fundamental task in quantitative genetics. With technological advances, it is now possible to measure multiple phenotypes in large samples. Multiple phenotypes can share their genetic component; therefore, modeling these phenotypes jointly may improve prediction accuracy by leveraging effects that are shared across phenotypes. However, effects can be shared across phenotypes in a variety of ways, so computationally efficient statistical methods are needed that can accurately and flexibly capture patterns of effect sharing. Here, we describe new Bayesian multivariate, multiple regression methods that, by using flexible priors, are able to model and adapt to different patterns of effect sharing and specificity across phenotypes. Simulation results show that these new methods are fast and improve prediction accuracy compared with existing methods in a wide range of settings where effects are shared. Further, in settings where effects are not shared, our methods still perform competitively with state-of-the-art methods. In real data analyses of expression data in the Genotype Tissue Expression (GTEx) project, our methods improve prediction performance on average for all tissues, with the greatest gains in tissues where effects are strongly shared, and in the tissues with smaller sample sizes. While we use gene expression prediction to illustrate our methods, the methods are generally applicable to any multi-phenotype applications, including prediction of polygenic scores and breeding values. Thus, our methods have the potential to provide improvements across fields and organisms.

Ultrathin Bronchoscopy Without Virtual Navigation for Diagnosis of Peripheral Lung Lesions.

BACKGROUND: The increasing incidence of encountering lung nodules necessitates an ongoing search for improved diagnostic procedures. Various bronchoscopic technologies have been introduced or are in development, but further studies are needed to define a method that fits best in clinical practice and health care systems. RESEARCH QUESTION: How do basic bronchoscopic tools including a combination of thin (outer diameter 4.2 mm) and ultrathin bronchoscopes (outer diameter 3.0 mm), radial endobronchial ultrasound (rEBUS) and fluoroscopy perform in peripheral pulmonary lesion diagnosis? STUDY DESIGN AND METHODS: This is a retrospective review of the performance of peripheral bronchoscopy using thin and ultrathin bronchoscopy with rEBUS and 2D fluoroscopy without a navigational system for evaluating peripheral lung lesions in a single academic medical center from 11/2015 to 1/2021. We used a strict definition for diagnostic yield and assessed the impact of different variables on diagnostic yield, specifically after employment of the ultrathin bronchoscope. Logistic regression models were employed to assess the independent associations of the most impactful variables. RESULTS: A total of 322 patients were included in this study. The median of the long axis diameter was 2.2 cm and the median distance of the center of the lesion from the visceral pleural surface was 1.9 cm. Overall diagnostic yield was 81.3% after employment of the ultrathin bronchoscope, with more detection of concentric rEBUS views (93% vs. 78%, p < 0.001). Sensitivity for detecting malignancy also increased from 60.5% to 74.7% (p = 0.033) after incorporating the ultrathin scope into practice, while bronchus sign and peripheral location of the lesion were not found to affect diagnostic yield. Concentric rEBUS view, solid appearance, upper/middle lobe location and larger size of the nodules were found to be independent predictors of successful achievement of diagnosis at bronchoscopy. INTERPRETATION: This study demonstrates a high diagnostic yield of biopsy of lung lesions achieved by utilization of thin and ultrathin bronchoscopes. Direct visualization of small peripheral airways with simultaneous rEBUS confirmation increased localization rate of small lesions in a conventional bronchoscopy setting without virtual navigational planning.

Glial Cells Response in Stroke.

As the second-leading cause of death, stroke faces several challenges in terms of treatment because of the limited therapeutic interventions available. Previous studies primarily focused on metabolic and blood flow properties as a target for treating stroke, including recombinant tissue plasminogen activator and mechanical thrombectomy, which are the only USFDA approved therapies. These interventions have the limitation of a narrow therapeutic time window, the possibility of hemorrhagic complications, and the expertise required for performing these interventions. Thus, it is important to identify the contributing factors that exacerbate the ischemic outcome and to develop therapies targeting them for regulating cellular homeostasis, mainly neuronal survival and regeneration. Glial cells, primarily microglia, astrocytes, and oligodendrocytes, have been shown to have a crucial role in the prognosis of ischemic brain injury, contributing to inflammatory responses. They play a dual role in both the onset as well as resolution of the inflammatory responses. Understanding the different mechanisms driving these effects can aid in the development of therapeutic targets and further mitigate the damage caused. In this review, we summarize the functions of various glial cells and their contribution to stroke pathology. The review highlights the therapeutic options currently being explored and developed that primarily target glial cells and can be used as neuroprotective agents for the treatment of ischemic stroke.

Anion Storage Chemistry of Organic Cathodes for High-Energy and High-Power Density Divalent Metal Batteries.

Multivalent batteries show promising prospects for next-generation sustainable energy storage applications. Herein, we report a polytriphenylamine (PTPAn) composite cathode capable of highly reversible storage of tetrakis(hexafluoroisopropyloxy) borate [B(hfip)4 ] anions in both Magnesium (Mg) and calcium (Ca) battery systems. Spectroscopic and computational studies reveal the redox reaction mechanism of the PTPAn cathode material. The Mg and Ca cells exhibit a cell voltage >3 V, a high-power density of ∼∼3000 W kg-1 and a high-energy density of ∼∼300 Wh kg-1 , respectively. Moreover, the combination of the PTPAn cathode with a calcium-tin (Ca-Sn) alloy anode could enable a long battery-life of 3000 cycles with a capacity retention of 60 %. The anion storage chemistry associated with dual-ion electrochemical concept demonstrates a new feasible pathway towards high-performance divalent ion batteries.

Discovery and characterization of variance QTLs in human induced pluripotent stem cells.

Quantification of gene expression levels at the single cell level has revealed that gene expression can vary substantially even across a population of homogeneous cells. However, it is currently unclear what genomic features control variation in gene expression levels, and whether common genetic variants may impact gene expression variation. Here, we take a genome-wide approach to identify expression variance quantitative trait loci (vQTLs). To this end, we generated single cell RNA-seq (scRNA-seq) data from induced pluripotent stem cells (iPSCs) derived from 53 Yoruba individuals. We collected data for a median of 95 cells per individual and a total of 5,447 single cells, and identified 235 mean expression QTLs (eQTLs) at 10% FDR, of which 79% replicate in bulk RNA-seq data from the same individuals. We further identified 5 vQTLs at 10% FDR, but demonstrate that these can also be explained as effects on mean expression. Our study suggests that dispersion QTLs (dQTLs) which could alter the variance of expression independently of the mean can have larger fold changes, but explain less phenotypic variance than eQTLs. We estimate 4,015 individuals as a lower bound to achieve 80% power to detect the strongest dQTLs in iPSCs. These results will guide the design of future studies on understanding the genetic control of gene expression variance.

Structural and Magnetic Properties of BaFeO2.667 Synthesized by Oxidizing BaFeO2.5 Obtained via Nebulized Spray Pyrolysis.

A vacancy-ordered perovskite-type compound Ba3Fe3O8 (BaFeO2.667) was prepared by oxidizing BaFeO2.5 (P21/c) with the latter compound obtained by a spray pyrolysis technique. The structure of Ba3Fe3O8 was found to be isotypic to Ba3Fe3O7F (P21/m) and can be written as Ba3Fe3+2Fe4+1O8. Mössbauer spectroscopy and ab initio calculations were used to confirm mixed iron oxidation states, showing allocation of the tetravalent iron species on the tetrahedral site, and octahedral as well as square pyramidal coordination for the trivalent species within a G-type antiferromagnetic ordering. The uptake and release of oxygen were investigated over a broad temperature range from room temperature to 1100 °C under pure oxygen and ambient atmosphere via a combination of DTA/TG and variable temperature diffraction measurements. The compound exhibited a strong lattice enthalpy driven reduction to monoclinic and cubic BaFeO2.5 at elevated temperatures.

Integrative analysis of 111 reference human epigenomes.

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

A simple new approach to variable selection in regression, with application to genetic fine mapping.

We introduce a simple new approach to variable selection in linear regression, with a particular focus on quantifying uncertainty in which variables should be selected. The approach is based on a new model - the "Sum of Single Effects" (SuSiE) model - which comes from writing the sparse vector of regression coefficients as a sum of "single-effect" vectors, each with one non-zero element. We also introduce a corresponding new fitting procedure - Iterative Bayesian Stepwise Selection (IBSS) - which is a Bayesian analogue of stepwise selection methods. IBSS shares the computational simplicity and speed of traditional stepwise methods, but instead of selecting a single variable at each step, IBSS computes a distribution on variables that captures uncertainty in which variable to select. We provide a formal justification of this intuitive algorithm by showing that it optimizes a variational approximation to the posterior distribution under the SuSiE model. Further, this approximate posterior distribution naturally yields convenient novel summaries of uncertainty in variable selection, providing a Credible Set of variables for each selection. Our methods are particularly well-suited to settings where variables are highly correlated and detectable effects are sparse, both of which are characteristics of genetic fine-mapping applications. We demonstrate through numerical experiments that our methods outperform existing methods for this task, and illustrate their application to fine-mapping genetic variants influencing alternative splicing in human cell-lines. We also discuss the potential and challenges for applying these methods to generic variable selection problems.

Genetic analysis of complex traits in the emerging Collaborative Cross.

The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipient strains reveals high genetic diversity, balanced allele frequencies, and dense, evenly distributed recombination sites-all ideal qualities for a systems genetics resource. We map discrete, complex, and biomolecular traits and contrast two quantitative trait locus (QTL) mapping approaches. Analysis based on inferred haplotypes improves power, reduces false discovery, and provides information to identify and prioritize candidate genes that is unique to multifounder crosses like the CC. The number of expression QTLs discovered here exceeds all previous efforts at eQTL mapping in mice, and we map local eQTL at 1-Mb resolution. We demonstrate that the genetic diversity of the CC, which derives from random mixing of eight founder strains, results in high phenotypic diversity and enhances our ability to map causative loci underlying complex disease-related traits.

Bronchoscopic deployment and implantation of Diffusing alpha-emitters Radiation Therapy into the lung and mediastinum for treatment of lung cancer: a pre-clinical safety and feasibility study.

Background: Radiotherapy is a standard treatment modality in cancer therapy, particularly for lung cancer. Diffusing alpha-emitters Radiation Therapy sources (hereafter, "Alpha DaRTs") are fixed with Ra-244 (half-life =3.6 days) that releases alpha-emitting atoms into the tumor tissue to an effective range of a few millimeters. Methods: The feasibility, usability, and safety of Alpha DaRTs deployment and implantation via bronchoscopy into the lung parenchyma and mediastinum in a big animal model of healthy swine was studied in two phases: (I) inert and (II) active Alpha DaRTs deployment. The Alpha DaRTs were inserted in both individual and cluster patterns based on a predefined plan. Swine health was monitored throughout the study. The usability of bronchoscopic deployment and implantation was evaluated using a user questionnaire. The movement and migration of the Alpha DaRTs were assessed. Necropsy was performed, and lungs were evaluated via gross pathology and histopathology. Results: A total of 158 Alpha DaRTs were inserted successfully in the lung parenchyma and mediastinum of five swine in two phases. It was possible to deliver and place the Alpha DaRTs in clusters of no more than 4 mm distance between the Alpha DaRTs. No adverse event or change in the health and general condition of animals was observed. Hematologic evaluation did not show any clinically significant abnormality related to the Alpha DaRTs. Histopathology demonstrated local mild inflammatory changes, minimal fibrosis, and dystrophic mineralization with giant cells. Minimal movement and no migration of Alpha DaRTs were observed. Conclusions: Bronchoscopic deployment of Alpha DaRTs in the lung parenchyma and mediastinum of the porcine animal is feasible, precise, and safe.

APDDM mixed with i-PRF as a graft material for bone regeneration - A case report.

Demineralized dentine matrix (DDM) has both osteoconductive and osteoinductive properties, and has porous structure which helps in cell and blood vessel penetration and the release of various growth factors from the dentinal tubules. The first human dentine autograft case was done in 2002 in Japan for maxillary sinus lifting. In this clinical report, we use a hand-operated order made stainless steel apparatus to crush the tooth and prepare the DDM chair side. Chemical treatment of DDM particulate was done for demineralization and sterilisation purpose, and used immediately as a graft material for socket preservation. Dentascan after 4 month showed remarkable bone at the site of grafting and implant was placed. The patient was restored successfully with their own DDM and implant-supported prosthesis.

Utility and Safety of Bronchoscopic Cryotechniques-A Comprehensive Review.

Cryosurgical techniques are employed for diagnostic and therapeutic bronchoscopy and serve as important tools for the management of pulmonary diseases. The diagnosis of interstitial lung disease requires multidisciplinary team discussions after a thorough assessment of history, physical exam, computed tomography, and lung-function testing. However, histological diagnosis is required in selected patients. Surgical lung biopsy has been the gold standard but this can be associated with increased morbidity and mortality. Transbronchial lung cryobiopsy is an emerging technique and multiple studies have shown that it has a high diagnostic yield with a good safety profile. There is wide procedural variability and the optimal technique for cryobiopsy is still under investigation. There is emerging data that demonstrate that cryobiopsy is safe and highly accurate in the diagnosis of thoracic malignancies. Furthermore, cryorecanalization procedures are a useful adjunct for the palliation of tumors in patients with central airway obstruction. One should keep in mind that these procedures are not free from complications and should be carried out in a specialized center by a trained and experienced bronchoscopy team. We present a review of the literature on the diagnostic and therapeutic utility of bronchoscopy-guided cryosurgical procedures and their safety profile.

Digital Tomosynthesis: Review of Current Literature and Its Impact on Diagnostic Bronchoscopy.

Bronchoscopy has garnered increased popularity in the biopsy of peripheral lung lesions. The development of navigational guided bronchoscopy systems along with radial endobronchial ultrasound (REBUS) allows clinicians to access and sample peripheral lesions. The development of robotic bronchoscopy improved localization of targets and diagnostic accuracy. Despite such technological advancements, published diagnostic yield remains lower compared to computer tomography (CT)-guided biopsy. The discordance between the real-time location of peripheral lesions and anticipated location from preplanned navigation software is often cited as the main variable impacting accurate biopsies. The utilization of cone beam CT (CBCT) with navigation-based bronchoscopy has been shown to assist with localizing targets in real-time and improving biopsy success. The resources, costs, and radiation associated with CBCT remains a hindrance in its wider adoption. Recently, digital tomosynthesis (DT) platforms have been developed as an alternative for real-time imaging guidance in peripheral lung lesions. In North America, there are several commercial platforms with distinct features and adaptation of DT. Early studies show the potential improvement in peripheral lesion sampling with DT. Despite the results of early observational studies, the true impact of DT-based imaging devices for peripheral lesion sampling cannot be determined without further prospective randomized trials and meta-analyses.

Direct Visualization of Homogeneous Chemical Distribution in Functional Polyradical Microspheres.

It is demonstrated that the postfunctionalization of solid polymeric microspheres can generate fully and throughout functionalized materials, contrary to the expectation that core-shell structures are generated. The full functionalization is illustrated on the example of photochemically generated microspheres, which are subsequently transformed into polyradical systems. Given the all-organic nature of the functionalized microspheres, characterization methods with high analytical sensitivity and spatial resolution are pioneered by directly visualizing the inner chemical distribution of the postfunctionalized microspheres based on characteristic electron energy loss signals in transmission electron microscopy (TEM). Specifically, ultrasonic ultramicrotomy is combined successfully with electron energy loss spectroscopy (EELS) and electron spectroscopic imaging (ESI) during TEM. These findings open a key avenue for analyzing all-organic low-contrast soft-matter material structures, while the specifically investigated system concomitantly holds promise as an all-radical solid-state functional material.

GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership.

Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.

GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership.

Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.

A New Class of Cluster-Matrix Nanocomposite Made of Fully Miscible Components.

Nanocomposite materials, consisting of two or more phases, at least one of which has a nanoscale dimension, play a distinctive role in materials science because of the multiple possibilities for tailoring their structural properties and, consequently, their functionalities. In addition to the challenges of controlling the size, size distribution, and volume fraction of nanometer phases, thermodynamic stability conditions limit the choice of constituent materials. This study goes beyond this limitation by showing the possibility of achieving nanocomposites from a bimetallic system, which exhibits complete miscibility under equilibrium conditions. A series of nanocomposite samples with different compositions are synthesized by the co-deposition of 2000-atom Ni-clusters and a flux of Cu-atoms using a novel cluster ion beam deposition system. The retention of the metastable nanostructure is ascertained from atom probe tomography (APT), magnetometry, and magnetotransport studies. APT confirms the presence of nanoscale regions with ≈100 at% Ni. Magnetometry and magnetotransport studies reveal superparamagnetic behavior and magnetoresistance stemming from the single-domain ferromagnetic Ni-clusters embedded in the Cu-matrix. Essentially, the magnetic properties of the nanocomposites can be tailored by the precise control of the Ni concentration. The initial results offer a promising direction for future research on nanocomposites consisting of fully miscible elements.

High Entropy Approach to Engineer Strongly Correlated Functionalities in Manganites.

Technologically relevant strongly correlated phenomena such as colossal magnetoresistance (CMR) and metal-insulator transitions (MIT) exhibited by perovskite manganites are driven and enhanced by the coexistence of multiple competing magneto-electronic phases. Such magneto-electronic inhomogeneity is governed by the intrinsic lattice-charge-spin-orbital correlations, which, in turn, are conventionally tailored in manganites via chemical substitution, charge doping, or strain engineering. Alternately, the recently discovered high entropy oxides (HEOs), owing to the presence of multiple-principal cations on a given sub-lattice, exhibit indications of an inherent magneto-electronic phase separation encapsulated in a single crystallographic phase. Here, the high entropy (HE) concept is combined with standard property control by hole doping in a series of single-phase orthorhombic HE-manganites (HE-Mn), (Gd0.25 La0.25 Nd0.25 Sm0.25 )1- x Srx MnO3 (x = 0-0.5). High-resolution transmission microscopy reveals hitherto-unknown lattice imperfections in HEOs: twins, stacking faults, and missing planes. Magnetometry and electrical measurements infer three distinct ground states-insulating antiferromagnetic, unpercolated metallic ferromagnetic, and long-range metallic ferromagnetic-coexisting or/and competing as a result of hole doping and multi-cation complexity. Consequently, CMR ≈1550% stemming from an MIT is observed in polycrystalline pellets, matching the best-known values for bulk conventional manganites. Hence, this initial case study highlights the potential for a synergetic development of strongly correlated oxides offered by the high entropy design approach.

Strain-Driven Bidirectional Spin Orientation Control in Epitaxial High Entropy Oxide Films.

High entropy oxides (HEOs), based on the incorporation of multiple-principal cations into the crystal lattice, offer the possibility to explore previously inaccessible oxide compositions and unconventional properties. Here it is demonstrated that despite the chemical complexity of HEOs external stimuli, such as epitaxial strain, can selectively stabilize certain magneto-electronic states. Epitaxial (Co0.2 Cr0.2 Fe0.2 Mn0.2 Ni0.2 )3 O4 -HEO thin films are grown in three different strain states: tensile, compressive, and relaxed. A unique coexistence of rocksalt and spinel-HEO phases, which are fully coherent with no detectable chemical segregation, is revealed by transmission electron microscopy. This dual-phase coexistence appears as a universal phenomenon in (Co0.2 Cr0.2 Fe0.2 Mn0.2 Ni0.2 )3 O4 epitaxial films. Prominent changes in the magnetic anisotropy and domain structure highlight the strain-induced bidirectional control of magnetic properties in HEOs. When the films are relaxed, their magnetization behavior is isotropic, similar to that of bulk materials. However, under tensile strain, the hardness of the out-of-plane (OOP) axis increases significantly. On the other hand, compressive straining results in an easy OOP magnetization and a maze-like magnetic domain structure, indicating the perpendicular magnetic anisotropy. Generally, this study emphasizes the adaptability of the high entropy design strategy, which, when combined with coherent strain engineering, opens additional prospects for fine-tuning properties in oxides.

Cardiolipin-Mediated Alleviation of Mitochondrial Dysfunction Is a Neuroprotective Effect of Statin in Animal Model of Ischemic Stroke.

In clinical settings, the benefit of statin for stroke is debatable as regular statin users may suffer from myalgia, statin-associated myopathy (SAM), and rarely rhabdomyolysis. Studies suggest that patients on statin therapy show lesser vulnerability toward ischemic stroke and post-stroke frailty. Both pre- and post-treatment benefits of statin have been reported as evident by its neuroprotective effects in both cases. As mitochondrial dysfunction following stroke is the fulcrum for neuronal death, we hereby explore the role of statin in alleviating mitochondrial dysfunction by regulating the mitochondrial dynamics. In the present study, we intend to evaluate the role of statin in modulating cardiolipin-mediated mitochondrial functionality and further providing a therapeutic rationale for repurposing statins either as preventive or an adjunctive therapy for stroke.