Nanoscale magnetometry using a single spin system in diamond

We propose a protocol to estimate magnetic fields using a single nitrogen-vacancy (N-V) center in diamond, where the estimate precision scales inversely with time, ~1/T$, rather than the square-root of time. The method is based on converting the task of magnetometry into phase estimation, performing quantum phase estimation on a single N-V nuclear spin using either adaptive or nonadaptive feedback control, and the recently demonstrated capability to perform single-shot readout within the N-V [P. Neumann et. al., Science 329, 542 (2010)]. We present numerical simulations to show that our method provides an estimate whose precision scales close to ~1/T (T is the total estimation time), and moreover will give an unambiguous estimate of the static magnetic field experienced by the N-V. By combining this protocol with recent proposals for scanning magnetometry using an N-V, our protocol will provide a significant decrease in signal acquisition time while providing an unambiguous spatial map of the magnetic field.Comment: 8 pages and 5 figure

Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine

Background: The upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small intestine microbiome have been implicated in various human diseases, such as non-alcoholic steatohepatitis and inflammatory bowel conditions. Yet, the physiological and functional roles of the small intestine microbiota in humans remain poorly characterized because of the complexities associated with its sampling. Rodent models are used extensively in microbiome research and enable the spatial, temporal, compositional, and functional interrogation of the gastrointestinal microbiota and its effects on the host physiology and disease phenotype. Classical, culture-based studies have documented that fecal microbial self-reinoculation (via coprophagy) affects the composition and abundance of microbes in the murine proximal gastrointestinal tract. This pervasive self-reinoculation behavior could be a particularly relevant study factor when investigating small intestine microbiota. Modern microbiome studies either do not take self-reinoculation into account, or assume that approaches such as single housing mice or housing on wire mesh floors eliminate it. These assumptions have not been rigorously tested with modern tools. Here, we used quantitative 16S rRNA gene amplicon sequencing, quantitative microbial functional gene content inference, and metabolomic analyses of bile acids to evaluate the effects of self-reinoculation on microbial loads, composition, and function in the murine upper gastrointestinal tract. Results: In coprophagic mice, continuous self-exposure to the fecal flora had substantial quantitative and qualitative effects on the upper gastrointestinal microbiome. These differences in microbial abundance and community composition were associated with an altered profile of the small intestine bile acid pool, and, importantly, could not be inferred from analyzing large intestine or stool samples. Overall, the patterns observed in the small intestine of non-coprophagic mice (reduced total microbial load, low abundance of anaerobic microbiota, and bile acids predominantly in the conjugated form) resemble those typically seen in the human small intestine. Conclusions: Future studies need to take self-reinoculation into account when using mouse models to evaluate gastrointestinal microbial colonization and function in relation to xenobiotic transformation and pharmacokinetics or in the context of physiological states and diseases linked to small intestine microbiome and to small intestine dysbiosis

On How to Extend the NIR Tully-Fisher Relation to be Truly All-Sky

Dust extinction and stellar confusion by the Milky Way reduce the efficiency of detecting galaxies at low Galactic latitudes, creating the so-called Zone of Avoidance. This stands as a stumbling block in charting the distribution of galaxies and cosmic flow fields, and therewith our understanding of the local dynamics in the Universe (CMB dipole, convergence radius of bulk flows). For instance, ZoA galaxies are generally excluded from the whole-sky Tully-Fisher Surveys ($|b| \leq 5^\circ$) even if catalogued. We show here that by fine-tuning the near-infrared TF relation, there is no reason not to extend peculiar velocity surveys deeper into the ZoA. Accurate axial ratios ($b/a$) are crucial to both the TF sample selection and the resulting TF distances. We simulate the effect of dust extinction on the geometrical properties of galaxies. As expected, galaxies appear rounder with increasing obscuration level, even affecting existing TF samples. We derive correction models and demonstrate that we can reliably reproduce the intrinsic axial ratio from the observed value up to extinction level of about $A_J\simeq3$ mag ($A_V\sim11$ mag), we also recover a fair fraction of galaxies that otherwise would fall out of an uncorrected inclination limited galaxy sample. We present a re-calibration of the 2MTF relation in the NIR $J$, $H$, and $K_s$-bands for isophotal rather than total magnitudes, using their same calibration sample. Both TF relations exhibit similar scatter at high Galactic latitudes. However, the isophotal TF relation results in a significant improvement in the scatter for galaxies in the ZoA, and low surface brightness galaxies in general, because isophotal apertures are more robust in the face of significant stellar confusion.Comment: 12 pages, 10 figures, 4 tables, accepted for publication in MNRA

Galaxy peculiar velocities in the Zone of Avoidance

Dust extinction and stellar confusion of the Milky Way hinder the detection of galaxies at low Galactic latitude, creating the so-called Zone of Avoidance (ZoA). This has hampered our understanding of the local dynamics, cosmic flow fields and the origin of the Cosmic Microwave Background dipole. The ZoA ($|b| \le 5^\circ$) is also excluded from the "whole-sky" Two Micron All-Sky Survey (2MASS) Redshift Survey (2MRS) and 2MASS Tully-Fisher Survey (2MTF). The latter aims to provide distances and peculiar velocities for all bright inclined 2MASS galaxies with $K_s^o$ \leq 11\hbox{.\!\!^{\rm m}}25. Correspondingly, knowledge about the density distribution in the ZoA remains limited to statistical interpolations. To improve on this bias we pursued two different surveys to fill in the southern and northern ZoA. These data will allow a direct measurement of galaxy peculiar velocities. In this paper we will present a newly derived optimized Tully-Fisher (TF) relation that allow accurate measures of galaxy distances and peculiar velocities for dust-obscured galaxies. We discuss further corrections for magnitudes and biases and present some preliminary results on flow fields in the southern ZoA.Comment: 6 pages, 3 figures, to appear in Proceedings of SAIP2013, the 58th Annual Conference of the South African Institute of Physics, edited by Roelf Botha and Thulani Jili (SAIP and University of Zululand, 2014). ISBN: 978-0-620-62819-

A Quantitative Sequencing Framework for Absolute Abundance Measurements of Mucosal and Lumenal Microbial Communities

A fundamental goal in microbiome studies is determining which microbes affect host physiology. Standard methods for determining changes in microbial taxa measure relative, rather than absolute abundances. Moreover, studies often analyze only stool, despite microbial diversity differing substantially among gastrointestinal (GI) locations. Here, we develop a quantitative framework to measure absolute abundances of individual bacterial taxa by combining the precision of digital PCR with the high-throughput nature of 16S rRNA gene amplicon sequencing. In a murine ketogenic-diet study, we compare microbial loads in lumenal and mucosal samples along the GI tract. Quantitative measurements of absolute (but not relative) abundances reveal decreases in total microbial loads on the ketogenic diet and enable us to determine the differential effects of diet on each taxon in stool and small-intestine mucosa samples. This rigorous quantitative microbial analysis framework, appropriate for diverse GI locations enables mapping microbial biogeography of the mammalian GI tract and more accurate analyses of changes in microbial taxa in microbiome studies

Penguatan Modal Sosial dalam Penanganan Produk Olahan Kopi pada Komunitas Petani Kopi di Kabupaten Jember

Study of social capital in coffee farmer community to diversify product has not been done. This study aimed: (1) to describe the conditions of social capital in farmer community who diversify coffee products, (2) to map the components of social capital which are still strong and which still need strengthening, (3) to formulate development strategies of product diversification on coffee products. The location of study is determined purposively in 5 (five) village in five sub districts in Jember District: Sidomulyo in Silo Sub District, Sucopangepok in Jelbuk Sub District, Rowosari in Sumberjambe Sub District, Sumbersalak in Ledokombo Sub District and Kemiri in Panti Sub District. The data were analyzed using descriptive method. The results of this study are: the strong element of social capital are: partnership, trust, norm, custom and local culture value, tolerance, local wisdom and knowledge, social leadership, community participation, independence, freedom of mobility , the ability to buy "small" and "large" commodity, household decisions, relative freedom and domination of family also economic security and contribution to family. The elements of social capital that is still weak and should be strengthened are: transaction network (sale), product processing for diversification, packaging, togetherness and involvement in a campaign or protest. Strategy to develop product diversification of coffee based on social capital are: (1) lending with approriate scheme to coffee harvest time, (2) utilizing strong social capital in diversification product of coffee as well as strengthening elements of social capital that is still weak, (3) increasing capacity of coffee farmers through training to improve skill and self-reliance in coffee processing, (4) providing machinery to apply wet coffee processing, (5) establishing program for capacity development of coffee farmers in processing, (6) strengthening farmer institutions, (7) expanding marketing network, (8) strengthening institution of cooperation to improve bargaining position of farmers (9) sustainable guidance and assistance in application of innovative technology (10) determinating regions as coffee centres by utilizing strong elements of social capital within community. Key words: social capital, community, coffee farmer

Surface Fluorescence Studies of Tissue Mitochondrial Redox State in Isolated Perfused Rat Lungs

We designed a fiber-optic-based optoelectronic fluorometer to measure emitted fluorescence from the auto-fluorescent electron carriers NADH and FAD of the mitochondrial electron transport chain (ETC). The ratio of NADH to FAD is called the redox ratio (RR = NADH/FAD) and is an indicator of the oxidoreductive state of tissue. We evaluated the fluorometer by measuring the fluorescence intensities of NADH and FAD at the surface of isolated, perfused rat lungs. Alterations of lung mitochondrial metabolic state were achieved by the addition of rotenone (complex I inhibitor), potassium cyanide (KCN, complex IV inhibitor) and/or pentachlorophenol (PCP, uncoupler) into the perfusate recirculating through the lung. Rotenone- or KCN-containing perfusate increased RR by 21 and 30%, respectively. In contrast, PCP-containing perfusate decreased RR by 27%. These changes are consistent with the established effects of rotenone, KCN, and PCP on the redox status of the ETC. Addition of blood to perfusate quenched NADH and FAD signal, but had no effect on RR. This study demonstrates the capacity of fluorometry to detect a change in mitochondrial redox state in isolated perfused lungs, and suggests the potential of fluorometry for use in in vivo experiments to extract a sensitive measure of lung tissue health in real-time