Supervised Learning and Model Analysis with Compositional Data

The compositionality and sparsity of high-throughput sequencing data poses a challenge for regression and classification. However, in microbiome research in particular, conditional modeling is an essential tool to investigate relationships between phenotypes and the microbiome. Existing techniques are often inadequate: they either rely on extensions of the linear log-contrast model (which adjusts for compositionality, but is often unable to capture useful signals), or they are based on black-box machine learning methods (which may capture useful signals, but ignore compositionality in downstream analyses). We propose KernelBiome, a kernel-based nonparametric regression and classification framework for compositional data. It is tailored to sparse compositional data and is able to incorporate prior knowledge, such as phylogenetic structure. KernelBiome captures complex signals, including in the zero-structure, while automatically adapting model complexity. We demonstrate on par or improved predictive performance compared with state-of-the-art machine learning methods. Additionally, our framework provides two key advantages: (i) We propose two novel quantities to interpret contributions of individual components and prove that they consistently estimate average perturbation effects of the conditional mean, extending the interpretability of linear log-contrast models to nonparametric models. (ii) We show that the connection between kernels and distances aids interpretability and provides a data-driven embedding that can augment further analysis. Finally, we apply the KernelBiome framework to two public microbiome studies and illustrate the proposed model analysis. KernelBiome is available as an open-source Python package at https://github.com/shimenghuang/KernelBiome

Soil Disturbance by Invertebrates in a Semi-arid Eucalypt Woodland: Effects of Grazing Exclusion, Faunal Reintroductions, Landscape and Patch Characteristics

Soil disturbing invertebrates are common elements of arid and semi-arid landscapes. Disturbances such as burrows, nest entrances, emergence holes and mounds of ejecta soil have large, but often poorly understood, effects on ecosystem properties and processes as broad as pedogenesis, soil movement and water infiltration. We examined disturbances created by a range of invertebrates in a semi-arid eucalypt woodland in eastern Australia in relation to three levels of disturbance varying from areas currently grazed by domestic herbivores to those where domestic herbivores have been removed, with and without the reintroduction of locally-extinct omnivorous native mammals. Overall, the tunnels and ejecta soil from ant nests comprised 80% of all invertebrate disturbances across all sites and treatments. There were significantly more invertebrate disturbances at sites where domestic herbivores had been excluded, more disturbances on dunes and in the swales than on plains, and more under shrubs than under trees. The cover of disturbances by invertebrates tended to increase with increasing cover of disturbance by native vertebrates, but only under exclosure where no locally-extinct native mammals had been reintroduced. Our results indicate that invertebrate-created disturbances are a common feature of semi-arid woodland soils, and that management activities, such as grazing and the reintroduction of locally-extinct vertebrates, will affect their density, potentially influencing a range of ecosystem processes

Soil Disturbance by Invertebrates in a Semi-arid Eucalypt Woodland: Effects of Grazing Exclusion, Faunal Reintroductions, Landscape and Patch Characteristics

. Soil disturbance by invertebrates in a semiarid eucalypt woodland: effects of grazing exclusion, faunal reintroductions, landscape and patch characteristics. Proceedings of the Linnean Society of New South Wales 134, A11-A18. Soil disturbing invertebrates are common elements of arid and semi-arid landscapes. Disturbances such as burrows, nest entrances, emergence holes and mounds of ejecta soil have large, but often poorly understood, effects on ecosystem properties and processes as broad as pedogenesis, soil movement and water infi ltration. We examined disturbances created by a range of invertebrates in a semi-arid eucalypt woodland in eastern Australia in relation to three levels of disturbance varying from areas currently grazed by domestic herbivores to those where domestic herbivores have been removed, with and without the reintroduction of locally-extinct omnivorous native mammals. Overall, the tunnels and ejecta soil from ant nests comprised 80% of all invertebrate disturbances across all sites and treatments. There were signifi cantly more invertebrate disturbances at sites where domestic herbivores had been excluded, more disturbances on dunes and in the swales than on plains, and more under shrubs than under trees. The cover of disturbances by invertebrates tended to increase with increasing cover of disturbance by native vertebrates, but only under exclosure where no locally-extinct native mammals had been reintroduced. Our results indicate that invertebrate-created disturbances are a common feature of semi-arid woodland soils, and that management activities, such as grazing and the reintroduction of locally-extinct vertebrates, will affect their density, potentially infl uencing a range of ecosystem processes

Opini Komunitas Warga Sekitar Tentang Maraknya Pedagang Kaki Lima (PKL) (Studi Deskriptif Analitis Tentang Opini Komunitas Warga Sekitar Pkl – Tamansari, Kepatihan, dan Dalem Kaum – Kota Bandung)

Penelitian dengan judul “Opini komunitas warga sekitar tentang maraknya Pedagang Kaki Lima (PKL)” ini, dilakukan oleh pengajar/dosen tetap Fakultas Ilmu Komunikasi (FIK). Permasalahan penelitian adalah tentang bagaimana opini komunitas warga sekitar PKL mengenai keamanan, ketertiban, ketenangan, Kenyamanan, keindahan, kebersihan, dan keramah-tamahan (7“K”) akibat maraknya PKL. Sasaran strategis dalam penelitian ini adalah komunitas warga di sekitar lingkungan PKL Jalan Kepatihan, Dalem Kaum, dan Tamansari.Tujuan penelitian adalah untuk mengetahui, mengkaji, dan menganalisis faktor 7“K” yang dirasakan komunitas warga sekitar, akibat maraknya PKL, sehingga tanggapan yang diekspresikan mereka dapat menjadi masukan bagi Humas Pemerintah Kota Bandung dalam upaya mensosialisasikan kebijakan pemerintah tentang PKL khususnya dalam merumuskan konsep community relations berkaitan dengan 7 “K” yang dirasakan oleh komunitas warga sekitar terhadap maraknya PKL tersebut. Kesimpulan hasil penelitian ini adalah: pada umumnya opini komunitas warga sekitar terhadap maraknya PKL, dilihat dari faktor 7“K” sangatlah bervariasi di antara opini positif dan negatif, Dalam arti, untuk responden tertentu penilaiannya sangat relatif tergantung dari persepsi masing-masing dan atas dasar pengalaman masing-masing dengan para PKL tersebut. Dengan demikian tidak sepenuhnya berada pada kecenderungan tertentu yang bersifat negatif atau positif. Oleh karena itu dari opini tersebut selanjutnya dapat berkembang untuk diyakini tentang adanya kemungkinan di antara kedua belah pihak saling membina hubungan, dan pemerintah memfasilitasi hubungan tersebut dalam kebijakan-kebijakannya

Glutamate May Be an Efferent Transmitter That Elicits Inhibition in Mouse Taste Buds

Recent studies suggest that l-glutamate may be an efferent transmitter released from axons innervating taste buds. In this report, we determined the types of ionotropic synaptic glutamate receptors present on taste cells and that underlie this postulated efferent transmission. We also studied what effect glutamate exerts on taste bud function. We isolated mouse taste buds and taste cells, conducted functional imaging using Fura 2, and used cellular biosensors to monitor taste-evoked transmitter release. The findings show that a large fraction of Presynaptic (Type III) taste bud cells (∼50%) respond to 100 µM glutamate, NMDA, or kainic acid (KA) with an increase in intracellular Ca2+. In contrast, Receptor (Type II) taste cells rarely (4%) responded to 100 µM glutamate. At this concentration and with these compounds, these agonists activate glutamatergic synaptic receptors, not glutamate taste (umami) receptors. Moreover, applying glutamate, NMDA, or KA caused taste buds to secrete 5-HT, a Presynaptic taste cell transmitter, but not ATP, a Receptor cell transmitter. Indeed, glutamate-evoked 5-HT release inhibited taste-evoked ATP secretion. The findings are consistent with a role for glutamate in taste buds as an inhibitory efferent transmitter that acts via ionotropic synaptic glutamate receptors

Hydrophilic antioxidant compounds in orange juice from different fruit cultivars: Composition and antioxidant activity evaluated by chemical and cellular based (Saccharomyces cerevisiae) assays

Antioxidant capacity was evaluated by a cellular model (Saccharomyces cerevisiae) and chemical methods (FRAP, TEAC and total phenols by Folin-Ciocalteu assay) in the hydrophilic fraction (phenolic compounds and ascorbic acid) of orange juices (OJs) from six varieties (Midknight, Delta Seedless, Rohde Red, Seedless, Early and clone Sambiasi), harvested in two seasons. The contents of phenolic compounds and ascorbic acid analyzed, respectively, by UPLC and HPLC were 370.04 76.97 mg/L and 52.05 6.69 mg/100 mL. Variety and season significantly influenced (p < 0.05) composition and antioxidant capacity. TEAC and FRAP values correlated well with individual hydrophilic compounds (R2 > 0.991) but no correlation with cellular assay was observed. An increase in survival rates between 23% and 38% was obtained, excepting for two varieties that showed no activity (Rohde Red and Seedless). Narirutin, naringin-d, ferulic acid-d2, didymin, neoeriocitrin and sinapic acid hexose and caffeic acid-d1 were the phenolic compounds which contributed to survival rates (R2 = 0.979, p < 0.01

Transcriptional Activation of Low-Density Lipoprotein Receptor Gene by DJ-1 and Effect of DJ-1 on Cholesterol Homeostasis

DJ-1 is a novel oncogene and also causative gene for familial Parkinson’s disease park7. DJ-1 has multiple functions that include transcriptional regulation, anti-oxidative reaction and chaperone and mitochondrial regulation. For transcriptional regulation, DJ-1 acts as a coactivator that binds to various transcription factors, resulting in stimulation or repression of the expression of their target genes. In this study, we found the low-density lipoprotein receptor (LDLR) gene is a transcriptional target gene for DJ-1. Reduced expression of LDLR mRNA and protein was observed in DJ-1-knockdown cells and DJ-1-knockout mice and this occurred at the transcription level. Reporter gene assays using various deletion and point mutations of the LDLR promoter showed that DJ-1 stimulated promoter activity by binding to the sterol regulatory element (SRE) with sterol regulatory element binding protein (SREBP) and that stimulating activity of DJ-1 toward LDLR promoter activity was enhanced by oxidation of DJ-1. Chromatin immunoprecipitation, gel-mobility shift and co-immunoprecipitation assays showed that DJ-1 made a complex with SREBP on the SRE. Furthermore, it was found that serum LDL cholesterol level was increased in DJ-1-knockout male, but not female, mice and that the increased serum LDL cholesterol level in DJ-1-knockout male mice was cancelled by administration with estrogen, suggesting that estrogen compensates the increased level of serum LDL cholesterol in DJ-1-knockout female mice. This is the first report that DJ-1 participates in metabolism of fatty acid synthesis through transcriptional regulation of the LDLR gene