A leading hypothesis for the role of bacteria in inflammatory bowel diseases is that an imbalance in normal gut flora is a prerequisite for inflammation. Testing this hypothesis requires comparisons ...between the microbiota compositions of ulcerative colitis and Crohn's disease patients and those of healthy individuals. In this study, we obtained biopsy samples from patients with Crohn's disease and ulcerative colitis and from healthy controls. Bacterial DNA was extracted from the tissue samples, amplified using universal bacterial 16S rRNA gene primers, and cloned into a plasmid vector. Insert-containing colonies were picked for high-throughput sequencing, and sequence data were analyzed, yielding species-level phylogenetic data. The clone libraries yielded 3,305 sequenced clones, representing 151 operational taxonomical units. There was no significant difference between floras from inflamed and healthy tissues from within the same individual. Proteobacteria were significantly (P = 0.0007) increased in Crohn's disease patients, as were Bacteroidetes (P < 0.0001), while Clostridia were decreased in that group (P < 0.0001) in comparison with the healthy and ulcerative colitis groups, which displayed no significant differences. Thus, the bacterial flora composition of Crohn's patients appears to be significantly altered from that of healthy controls, unlike that of ulcerative colitis patients. Imbalance in flora in Crohn's disease is probably not sufficient to cause inflammation, since microbiotas from inflamed and noninflamed tissues were of similar compositions within the same individual.
As quantum coherence times of superconducting circuits have increased from nanoseconds to hundreds of microseconds, they are currently one of the leading platforms for quantum information processing. ...However, coherence needs to further improve by orders of magnitude to reduce the prohibitive hardware overhead of current error correction schemes. Reaching this goal hinges on reducing the density of broken Cooper pairs, so-called quasiparticles. Here, we show that environmental radioactivity is a significant source of nonequilibrium quasiparticles. Moreover, ionizing radiation introduces time-correlated quasiparticle bursts in resonators on the same chip, further complicating quantum error correction. Operating in a deep-underground lead-shielded cryostat decreases the quasiparticle burst rate by a factor thirty and reduces dissipation up to a factor four, showcasing the importance of radiation abatement in future solid-state quantum hardware.
ROCR is a package for evaluating and visualizing the performance of scoring classifiers in the statistical language R. It features over 25 performance measures that can be freely combined to create ...two-dimensional performance curves. Standard methods for investigating trade-offs between specific performance measures are available within a uniform framework, including receiver operating characteristic (ROC) graphs, precision/recall plots, lift charts and cost curves. ROCR integrates tightly with R's powerful graphics capabilities, thus allowing for highly adjustable plots. Being equipped with only three commands and reasonable default values for optional parameters, ROCR combines flexibility with ease of usage. Availability: http://rocr.bioinf.mpi-sb.mpg.de. ROCR can be used under the terms of the GNU General Public License. Running within R, it is platform-independent. Contact: tobias.sing@mpi-sb.mpg.de
Modern physics experiments often utilize field-programmable gate array (FPGA)-based systems for real-time data acquisition (DAQ). Integrated analog electronics demand for complex calibration ...routines. Furthermore, versatile configuration and control of the whole system are key requirements. Besides a low-level register interface to the FPGA, also, access to I 2 C and SPI buses is often needed to configure the complete system. Calibration through an FPGA is inflexible and yields a complex hardware implementation. On the contrary, calibration through a remote system is possible but considerably slower due to repetitive network accesses. By using system-on-chip (SoC)-FPGA solutions with a microprocessor, more sophisticated configuration and calibration solutions, as well as standard remote access protocols, can be efficiently integrated into the software. Based on Xilinx Zynq US+ SoC-FPGAs, we implemented a versatile control framework. This software framework offers convenient access to the hardware and a flexible abstraction via remote-procedure calls (RPCs). Based on the open-source RPC library gRPC, functionality with low-latency control flow, complex algorithms, data conversions and processing, and configuration via external buses can be provided to a client via Ethernet. Furthermore, client interfaces for various programming languages can be generated automatically, which eases collaboration among different working groups and integration into existing software. This contribution presents the framework and benchmarks regarding latency and data throughput.
Abstract
More than one-quarter of the world’s greenhouse gas emissions come from agriculture, forestry, and land-use change. As with other sectors of the economy, agriculture should also contribute ...to meeting countries’ emission reduction targets. Transformation of agriculture to low-carbon food systems requires much larger investments in low emission development options from global climate finance, domestic budgets, and the private sector. Innovative financing mechanisms and instruments that integrate climate finance, agriculture development budgets, and private sector investment can improve and increase farmers’ and other value chain actors’ access to finance while delivering environmental, economic, and social benefits. Investment cases assessed in this study provide rich information to design and implement mitigation options in agriculture through unlocking additional sources of public and private capital, strengthening the links between financial institutions, farmers, and agribusiness, and coordination of actions across multiple stakeholders. These investment cases expand support for existing agricultural best practices, integrate forestry and agricultural actions to avoid land-use change, and support the transition to market-based solutions.
The electron capture in
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Holmium (ECHo) experiment seeks to achieve sub-eV sensitivity of the electron neutrino mass through calorimetric decay spectroscopy of
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Ho in large arrays of cryogenic ...magnetic microcalorimeters (MMCs). Microwave SQUID multiplexing serves to efficiently increase the number of readout channels, thus calorimeters per array and ultimately per cryostat. A corresponding frequency multiplexing room temperature software-defined radio (SDR) system is in development to enable the readout of this increased number of MMCs per cable. The SDR consists of a custom FPGA platform that provides signal generation and analysis capabilities, as well as tailored signal conversion and analog conditioning front end electronics that enable the room-temperature-to-cryogenic interface. Ultimately, the system will read out 400 multiplexer channels with double pixel detectors through a bandwidth of 4 GHz (IEEE C band). As high-resolution data converters are limited in sample rate, the C-band is split into five sub-bands using a two-stage mixing method. In this contribution, a prototype of the heterodyne RF design is presented. It comprises one of the five 800 MHz sub-bands for a target frequency range between 4 and 8 GHz. Furthermore, the second version of the A/D converter stage is presented, capable of generating and digitizing up to five complex basebands using 1 GSs
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converters, the reference clocks and a flux-ramp signal. We will show first results of their single and combined characterization in the lab. The current state of the prototype hardware enables preliminary measurements, only limited in bandwidth and with slightly higher noise. Potential improvements could be derived and will be implemented in the full bandwidth, 5-sub-band RF PCB design.
Abstract
Hydraulic stress in plants occurs under conditions of low water availability (soil moisture; θ) and/or high atmospheric demand for water (vapor pressure deficit; D). Different species are ...adapted to respond to hydraulic stress by functioning along a continuum where, on one hand, they close stomata to maintain a constant leaf water potential (ΨL) (isohydric species), and on the other hand, they allow ΨL to decline (anisohydric species). Differences in water-use along this continuum are most notable during hydrologic stress, often characterized by low θ and high D; however, θ and D are often, but not necessarily, coupled at time scales of weeks or longer, and uncertainty remains about the sensitivity of different water-use strategies to these variables. We quantified the effects of both θ and D on canopy conductance (Gc) among widely distributed canopy-dominant species along the isohydric–anisohydric spectrum growing along a hydroclimatological gradient. Tree-level Gc was estimated using hourly sap flow observations from three sites in the eastern United States: a mesic forest in western North Carolina and two xeric forests in southern Indiana and Missouri. Each site experienced at least 1 year of substantial drought conditions. Our results suggest that sensitivity of Gc to θ varies across sites and species, with Gc sensitivity being greater in dry than in wet sites, and greater for isohydric compared with anisohydric species. However, once θ limitations are accounted for, sensitivity of Gc to D remains relatively constant across sites and species. While D limitations to Gc were similar across sites and species, ranging from 16 to 34% reductions, θ limitations to Gc ranged from 0 to 40%. The similarity in species sensitivity to D is encouraging from a modeling perspective, though it implies that substantial reduction to Gc will be experienced by all species in a future characterized by higher D.
Many individuals experience lower gastrointestinal tract symptoms, most commonly attributable to functional conditions. These individuals are frequently diagnosed with irritable bowel syndrome (IBS) ...based on their symptoms; however, some may require additional testing or referral to specialists before this diagnosis is made.
To systematically review the literature of the accuracy of individual symptoms and combinations of findings in diagnosing IBS.
Search of MEDLINE and EMBASE (up to June 2008) for prospective studies reporting on unselected cohorts of adult patients with lower gastrointestinal tract symptoms recorded before investigation.
Studies prospectively evaluating accuracy of individual symptoms or combinations of findings compared with results from investigations of the lower gastrointestinal tract.
Two authors independently assessed studies and extracted data to estimate likelihood ratios (LRs) of individual symptoms and combinations of findings in diagnosing IBS.
Ten studies evaluating 2355 patients were identified, with a summary prevalence of IBS following investigation of 57%. Individual symptom items yielded positive LRs from 1.2 (95% confidence interval CI, 0.93-1.6) for passage of mucus per rectum to 2.1 (95% CI, 1.4-3.0) for looser stools at onset of abdominal pain and negative LRs from 0.29 (95% CI, 0.12-0.72) for no lower abdominal pain to 0.88 (95% CI, 0.72-1.1) for no passage of mucus per rectum in diagnosing IBS. The Manning criteria had a summary positive LR of 2.9 (95% CI, 1.3-6.4) and a summary negative LR of 0.29 (95% CI, 0.12-0.71). The Rome I criteria had a positive LR of 4.8 (95% CI, 3.6-6.5) and a negative LR of 0.34 (95% CI, 0.29-0.41). The Kruis scoring system provided a summary positive LR of 8.6 (95% CI, 2.9-26.0) and a summary negative LR of 0.26 (95% CI, 0.17-0.41). The Rome II and III criteria have not been studied.
Individual symptoms have limited accuracy for diagnosing IBS in patients referred with lower gastrointestinal tract symptoms. The accuracy of the Manning criteria and Kruis scoring system were only modest. Despite strong advocacy for use of the Rome criteria, only the Rome I classification has been validated. Future research should concentrate on validating existing diagnostic criteria or developing more accurate ways of predicting a diagnosis of IBS without the need for investigation of the lower gastrointestinal tract.
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