The ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. Here we evaluate the microbial biota in healthy mule deer (Odocoileus hemionus) by analyses of lymph node meta-transcriptomes. cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Protein-coding and 16S ribosomal RNA (rRNA) sequences were taxonomically profiled using protein and rRNA specific databases. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Residents of skin and rumen, and those ubiquitous in mule deer habitat dominated classifiable bacterial species. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. Among viruses, a novel gamma retrovirus and other members of the Poxviridae and Retroviridae were identified. We additionally evaluated bacterial diversity by amplicon sequencing the hypervariable V6 region of 16S rRNA and demonstrate that overall taxonomic diversity is higher with the meta-transcriptomic approach. These data provide the most complete picture to date of the microbial diversity within a wildlife host. Our research advances the use of meta-transcriptomics to study microbiota in wildlife tissues, which will facilitate detection of novel organisms with pathogenic potential to human and animals.

Soybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is also an excellent model for studying evolution of duplicated genes. However, relative to the model plants Arabidopsis and rice, the present knowledge about soybean transcriptome is quite limited.

Despite similar components, the heterogeneity of skin characteristics across the human body is enormous. It is classically believed that site-specific fibroblasts in the dermis control postnatal skin identity by modulating the behavior of the surface-overlying keratinocytes in the epidermis. To begin testing this hypothesis, we characterized the gene expression differences between volar (ventral; palmoplantar) and nonvolar (dorsal) human skin. We show that KERATIN 9 (KRT9) is the most uniquely enriched transcript in volar skin, consistent with its etiology in genetic diseases of the palms and soles. In addition, ectopic KRT9 expression is selectively activated by volar fibroblasts. However, KRT9 expression occurs in the absence of all fibroblasts, although not to the maximal levels induced by fibroblasts. Through gain-of-function and loss-of-function experiments, we demonstrate that the mechanism is through overlapping paracrine or autocrine canonical WNT-β-catenin signaling in each respective context. Finally, as an in vivo example of ectopic expression of KRT9 independent of volar fibroblasts, we demonstrate that in the human skin disease lichen simplex chronicus, WNT5a and KRT9 are robustly activated outside of volar sites. These results highlight the complexities of site-specific gene expression and its disruption in skin disease.

The space of metastable materials offers promising new design opportunities for next-generation technological materials, such as complex oxides, semiconductors, pharmaceuticals, steels, and beyond. Although metastable phases are ubiquitous in both nature and technology, only a heuristic understanding of their underlying thermodynamics exists. We report a large-scale data-mining study of the Materials Project, a high-throughput database of density functional theory-calculated energetics of Inorganic Crystal Structure Database structures, to explicitly quantify the thermodynamic scale of metastability for 29,902 observed inorganic crystalline phases. We reveal the influence of chemistry and composition on the accessible thermodynamic range of crystalline metastability for polymorphic and phase-separating compounds, yielding new physical insights that can guide the design of novel metastable materials. We further assert that not all low-energy metastable compounds can necessarily be synthesized, and propose a principle of 'remnant metastability'-that observable metastable crystalline phases are generally remnants of thermodynamic conditions where they were once the lowest free-energy phase.

Rheological disorders of red blood cells (RBC) and decreased RBC deformability have been involved in the development of diabetic microangiopathy. However, few studies have evaluated the association of RBC count with microvascular complications in patients with type 2 diabetes mellitus (T2DM). The purpose of this study was to investigate the association of RBC count with microvascular complications in patients with T2DM.

Lindera glauca fruit with high quality and quantity of oil has emerged as a novel potential source of biodiesel in China, but the molecular regulatory mechanism of carbon flux and energy source for oil biosynthesis in developing fruits is still unknown. To better develop fruit oils of L. glauca as woody biodiesel, a combination of two different sequencing platforms (454 and Illumina) and qRT-PCR analysis was used to define a minimal reference transcriptome of developing L. glauca fruits, and to construct carbon and energy metabolic model for regulation of carbon partitioning and energy supply for FA biosynthesis and oil accumulation.

Systematic, automated methods for monitoring physician performance are necessary if outlying behavior is to be detected promptly and acted on. In the Michigan Urological Surgery Improvement Collaborative (MUSIC), we evaluated several statistical process control (SPC) methods to determine the sensitivity and ease of interpretation for assessing adherence to imaging guidelines for patients with newly diagnosed prostate cancer.

Cardio-cerebrovascular disease is one of the three major causes of mortality in humans and constitutes a major socioeconomic burden. Carotid atherosclerosis (CAS) is a very common lesion of the arterial walls, which leads to narrowing of the arteries, in some cases occluding them entirely, increasing the risk of cardiovascular events. The aim of the present study was to evaluate a cynomolgus monkey model of carotid atherosclerosis (CAS) induced by puncturing and scratching combined with a high-fat diet. A total of 12 cynomolgus monkeys were randomly divided into four groups: A, puncturing and scratching carotid artery intimas + high-fat diet (n=3); B, puncturing and scratching carotid artery intimas + regular diet (n=3); C, high-fat diet only (n=3); and D, regular diet only (n=3). Blood was harvested at weeks 4, 6 and 8 and plasma lipid levels were assessed. At week 8, monkeys were sacrificed and carotid arteries were harvested for hematoxylin and eosin (H&E) staining to observe pathological changes. The results revealed that a high-fat diet led to increased plasma lipid levels and accelerated plaque formation. Carotid color Doppler ultrasonography was performed and, along with H&E staining, revealed plaque formation in group A. In summary, the results of the present study suggest that a cynomolgus monkey model of CAS model may be successfully constructed by puncturing and scratching of the carotid artery intimas in combination with a high-fat diet.

Viral myocarditis (VMC) is a common cardiac disease, however, there still lacks an effective therapeutic strategy for VMC. Astragalus mongholicus (Fisch.) Bge (AB), a Chinese herb with some functional metabolites, may have some pharmacological effects on VMC. AB ingredients were measured by a full-scan LCQ mass spectrum. We aimed to explore the effects of AB on the VMC children by investigating peripheral Treg cell homeostasis. A total of 68 VMC children were random and evenly assigned into an AG group (received 10-mL AB oral liquid daily), and a CG group (received placebo daily). Peripheral blood mononuclear cells (PBMC) were obtained from peripheral blood and Treg cells were isolated. The levels of miR-146b, miR-155, Treg immunity activity and myocarditis biomarkers were measured in Treg cells. There were four main components (sucrose, calycosin, Astragaloside IV and calycosin-7-glucoside) in AB. The cases sinus tachycardia, frequent premature ventricular contractions, and supraventricular tachycardia were significantly reduced in the AG group (P < 0.05). Meanwhile, the myocardial enzymes and cardiac function indexes were improved in the AG group when compared with the CG group (P < 0.05). The time of electrocardiogram recovery, symptom duration and hospital stay was shorter in the AG group than in the CG group (P < 0.05). The levels of miR-146b and miR-155 were higher in the CG group than in the AG group (P < 0.05). The levels of ROR-γt (retinoic acid receptor-related orphan nuclear receptor gamma), FoxP3 (forkhead transcription factor), IL-10 (interleukin-11) and TGF-β (transforming growth factor beta) were lower in the CG group than in the AG group (P < 0.05). In contrast, the levels of IL-17, IL-21, CK-MB (creatine kinase-MB), cTnI (cardiac troponin I), GrB (granzyme B), sFasL (soluble fas ligand) and caspase-3 were higher in the CG group than in the AG group (P < 0.05). Furthermore, the levels of ROR-γt, FoxP3, IL-10, and TGF-β were positively, whereas the levels of IL-17, IL-21, CK-MB, cTnI, GrB, sFasL and caspase-3 were negatively, associated with the levels of miR-146b and miR-155 (P < 0.05). AB treatment improved cardiac functions, peripheral Treg cell immunity imbalance in the children with VMC by reducing the levels of miR-146b and miR-155.

The improvement of ferromagnetic properties is critical for the practical application of multiferroic materials, to be exact, BiFeO₃ (BFO). Herein, we have investigated the evolution in the structure and morphology of Ho or/and Mn-doped thin films and the related diversification in ferromagnetic behavior. BFO, Bi0.95Ho0.05FeO₃ (BHFO), BiFe0.95Mn0.05O₃ (BFMO) and Bi0.95Ho0.05Fe0.95Mn0.05O₃ (BHFMO) thin films are synthesized via the conventional sol-gel method. Density, size and phase structure are crucial to optimize the ferromagnetic properties. Specifically, under the applied magnetic field of 10 kOe, BHFO and BFMO thin films can produce obvious magnetic properties during magnetization and, additionally, doping with Ho and Mn (BHFMO) can achieve better magnetic properties. This enhancement is attributed to the lattice distortions caused by the ionic sizes difference between the doping agent and the host, the generation of the new exchange interactions and the inhibition of the antiferromagnetic spiral modulated spin structure. This study provides key insights of understanding the tunable ferromagnetic properties of co-doped BFO.

Realizing the growing number of possible or hypothesized metastable crystalline materials is extremely challenging. There is no rigorous metric to identify which compounds can or cannot be synthesized. We present a thermodynamic upper limit on the energy scale, above which the laboratory synthesis of a polymorph is highly unlikely. The limit is defined on the basis of the amorphous state, and we validate its utility by effectively classifying more than 700 polymorphs in 41 common inorganic material systems in the Materials Project for synthesizability. The amorphous limit is highly chemistry-dependent and is found to be in complete agreement with our knowledge of existing polymorphs in these 41 systems, whether made by the nature or in a laboratory. Quantifying the limits of metastability for realizable compounds, the approach is expected to find major applications in materials discovery.

While surgical excision remains the principal management strategy for clinical T1 renal masses (cT1RMs), the rates of noninterventional approaches are not well known. Most single-institution and population-based series suggest rates below 10%.

Renal mass biopsy (RMB) has had limited and varied utilization to guide management of renal masses (RM).

A broad collection of technologies, including e.g. drug metabolism, biofuel combustion, photochemical decontamination of water, and interfacial passivation in energy production/storage systems rely on chemical processes that involve bond-breaking molecular reactions. In this context, a fundamental thermodynamic property of interest is the bond dissociation energy (BDE) which measures the strength of a chemical bond. Fast and accurate prediction of BDEs for arbitrary molecules would lay the groundwork for data-driven projections of complex reaction cascades and hence a deeper understanding of these critical chemical processes and, ultimately, how to reverse design them. In this paper, we propose a chemically inspired graph neural network machine learning model, BonDNet, for the rapid and accurate prediction of BDEs. BonDNet maps the difference between the molecular representations of the reactants and products to the reaction BDE. Because of the use of this difference representation and the introduction of global features, including molecular charge, it is the first machine learning model capable of predicting both homolytic and heterolytic BDEs for molecules of any charge. To test the model, we have constructed a dataset of both homolytic and heterolytic BDEs for neutral and charged (-1 and +1) molecules. BonDNet achieves a mean absolute error (MAE) of 0.022 eV for unseen test data, significantly below chemical accuracy (0.043 eV). Besides the ability to handle complex bond dissociation reactions that no previous model could consider, BonDNet distinguishes itself even in only predicting homolytic BDEs for neutral molecules; it achieves an MAE of 0.020 eV on the PubChem BDE dataset, a 20% improvement over the previous best performing model. We gain additional insight into the model's predictions by analyzing the patterns in the features representing the molecules and the bond dissociation reactions, which are qualitatively consistent with chemical rules and intuition. BonDNet is just one application of our general approach to representing and learning chemical reactivity, and it could be easily extended to the prediction of other reaction properties in the future.

Fabaceae is a large family of angiosperms with high biodiversity that contains a variety of economically important crops and model plants for the study of biological nitrogen fixation. Polyploidization events have been extensively studied in some Fabaceae plants, but the occurrence of new genes is still concealed, owing to a lack of genomic information on certain species of the basal clade of Fabaceae. Cercis chinensis (Cercidoideae) is one such species; it diverged earliest from Fabaceae and is essential for phylogenomic studies and new gene predictions in Fabaceae. To facilitate genomic studies on Fabaceae, we performed genome sequencing of C. chinensis and obtained a 352.84 Mb genome, which was further assembled into seven pseudochromosomes with 30 612 predicted protein-coding genes. Compared with other legume genomes, that of C. chinensis exhibits no lineage-specific polyploidization event. Further phylogenomic analyses of 22 legumes and 11 other angiosperms revealed that many gene families are lineage specific before and after the diversification of Fabaceae. Among them, dozens of genes are candidates for new genes that have evolved from intergenic regions and are thus regarded as de novo-originated genes. They differ significantly from established genes in coding sequence length, exon number, guanine-cytosine content, and expression patterns among tissues. Functional analysis revealed that many new genes are related to asparagine metabolism. This study represents an important advance in understanding the evolutionary pattern of new genes in legumes and provides a valuable resource for plant phylogenomic studies.

Footwear, carpet, automotive interiors, and multilayer packaging are examples of products manufactured from several types of polymers whose inextricability poses substantial challenges for recycling at the end of life. Here, we show that chemical circularity in mixed-polymer recycling becomes possible by controlling the rates of depolymerization of polydiketoenamines (PDK) over several orders of magnitude through molecular engineering. Stepwise deconstruction of mixed-PDK composites, laminates, and assemblies is chemospecific, allowing a prescribed subset of monomers, fillers, and additives to be recovered under pristine condition at each stage of the recycling process. We provide a theoretical framework to understand PDK depolymerization via acid-catalyzed hydrolysis and experimentally validate trends predicted for the rate-limiting step. The control achieved by PDK resins in managing chemical and material entropy points to wide-ranging opportunities for pairing circular design with sustainable manufacturing.

Spinal cord injury (SCI) is often accompanied by rapid and extensive bone mineral loss below the lesion level, and there is currently no gold standard for treatment. Evidence suggests that polydatin (PLD) may help promote osteogenic differentiation and exhibit anti-osteoporotic activity. However, whether PLD could reverse substantial bone loss in SCI patients, especially those with protracted injury, and the underlying regulatory mechanism have not been investigated.

Chemiluminescence (CL) imaging, as an excitation-free technique, exhibits a markedly improved signal-to-noise ratio (SNR) owing to the absence of an excitation light source and autofluorescence interference. However, conventional chemiluminescence imaging generally focuses on the visible and first near-infrared (NIR-I) regions, which hinders high-performance biological imaging due to strong tissue scattering and absorption. To address the issue, self-luminescent NIR-II CL nanoprobes with a second near-infrared (NIR-II) luminescence in the presence of hydrogen peroxide are rationally designed. A cascade energy transfer, including chemiluminescence resonance energy transfer (CRET) from the chemiluminescent substrate to NIR-I organic molecules and Förster resonance energy transfer (FRET) from NIR-I organic molecules to NIR-II organic molecules, occurs in the nanoprobes, contributing to NIR-II light with great efficiency and good tissue penetration depth. Based on excellent selectivity, high sensitivity to hydrogen peroxide, and long-lasting luminescence performance, the NIR-II CL nanoprobes are applied to detect inflammation in mice, showing a 7.4-fold enhancement in SNR compared with that of fluorescence.

Assessment of the microbial diversity residing in arthropod vectors of medical importance is crucial for monitoring endemic infections, for surveillance of newly emerging zoonotic pathogens, and for unraveling the associated bacteria within its host. The tick Ixodes ricinus is recognized as the primary European vector of disease-causing bacteria in humans. Despite I. ricinus being of great public health relevance, its microbial communities remain largely unexplored to date. Here we evaluate the pathogen-load and the microbiome in single adult I. ricinus by using 454- and Illumina-based metagenomic approaches. Genomic DNA-derived sequences were taxonomically profiled using a computational approach based on the BWA algorithm, allowing for the identification of known tick-borne pathogens at the strain level and the putative tick core microbiome. Additionally, we assessed and compared the bacterial taxonomic profile in nymphal and adult I. ricinus pools collected from two distinct geographic regions in Northern Italy by means of V6-16S rRNA amplicon pyrosequencing and community based ecological analysis. A total of 108 genera belonging to representatives of all bacterial phyla were detected and a rapid qualitative assessment for pathogenic bacteria, such as Borrelia, Rickettsia and Candidatus Neoehrlichia, and for other bacteria with mutualistic relationship or undetermined function, such as Wolbachia and Rickettsiella, was possible. Interestingly, the ecological analysis revealed that the bacterial community structure differed between the examined geographic regions and tick life stages. This finding suggests that the environmental context (abiotic and biotic factors) and host-selection behaviors affect their microbiome.Our data provide the most complete picture to date of the bacterial communities present within I. ricinus under natural conditions by using high-throughput sequencing technologies. This study further demonstrates a novel detection strategy for the microbiomes of arthropod vectors in the context of epidemiological and ecological studies.

Although attempts have been made to reveal the relationships between bacteria and human health, little is known about the species and function of the microbial community associated with oral diseases. In this study, we report the sequencing of 16 metagenomic samples collected from dental swabs and plaques representing four periodontal states. Insights into the microbial community structure and the metabolic variation associated with periodontal health and disease were obtained. We observed a strong correlation between community structure and disease status, and described a core disease-associated community. A number of functional genes and metabolic pathways including bacterial chemotaxis and glycan biosynthesis were over-represented in the microbiomes of periodontal disease. A significant amount of novel species and genes were identified in the metagenomic assemblies. Our study enriches the understanding of the oral microbiome and sheds light on the contribution of microorganisms to the formation and succession of dental plaques and oral diseases.