Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of ...bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.
We present a near-infrared optical parametric chirped-pulse amplifier (OPCPA) and soft X-ray (SXR) high-harmonic generation system. The OPCPA produces few-cycle pulses at a center wavelength of 800 ...nm and operates at a high repetition rate of 100 kHz. It is seeded by fully programmable amplitude and phase controlled ultra-broadband pulses from a Ti:sapphire oscillator. The output from the OPCPA system was compressed to near-transform-limited 9.3-fs pulses. Fully characterized pulse compression was recorded for an average power of 22.5 W, demonstrating pulses with a peak power greater than 21 GW. Without full temporal characterization, high-power operation was achieved up to 35 W. We demonstrate that at such high repetition rates, spatiotemporally flattened pump pulses can be achieved through a cascaded second-harmonic generation approach with an efficiency of more than 70%. This combination provides a compelling OPCPA architecture for scaling the peak power of high-repetition-rate ultra-broadband systems in the near-infrared. The output of this 800-nm OPCPA system was used to generate SXR radiation reaching 190 eV photon energy through high-harmonic generation in helium.
A rotationally hindered and thus stereogenic biaryl axis is the structurally and stereochemically decisive element of a steadily growing number of natural products, chiral auxiliaries, and catalysts. ...Thus, it is not surprising that significant advances have been made in the asymmetric synthesis of axially chiral biaryl compounds over the past decade. In addition to the classic approach (direct stereoselective aryl–aryl coupling), innovative concepts have been developed in which the asymmetric information is introduced into a preformed, but achiral—that is, symmetric or configurationally labile—biaryl compound, or in which an arylC single bond is stereoselectively transformed into an axis. This Review classifies these strategies according to their underlying concepts and critically evaluates their scope and limitations with reference to selected model reactions and applications. Furthermore, the preconditions required for the existence of axial chirality in biaryl compounds are discussed.
Not only classic, atroposelective biaryl couplings lead to stereochemically pure, axially chiral biaryl compounds (see scheme); recently, novel, highly original strategies have also emerged. The authors present a discussion of the structural preconditions of axial chirality and the most successful and innovative of these strategies.
Samarium hexaboride (SmB
) is a Kondo insulator, with a narrow gap due to hybridization between localized and conduction electrons. Despite being an insulator, many samples show metal-like ...properties. Rare-earth purification is exceedingly difficult, and nominally pure samples may contain 2% or more of impurities. Here to determine the effects of rare-earth doping on SmB
, we synthesized and probed a series of gadolinium-doped samples. We found a relationship between specific heat and impurity moment screening which scales systematically. Consistent with this finding, our neutron scattering experiments of a high purity sample of doubly isotopic
Sm
B
show no intrinsic excitations below the well-established 13 meV spin-exciton. The result of introducing impurities into a Kondo insulator is incompletely understood, but it is clear from our measurements that there is a systematic relationship between rare-earth impurities and metal-like properties in SmB
.
Coherent soft x-ray (SXR) sources enable fundamental studies in the important water window spectral region. Until now, such sources have been limited to repetition rates of 1 kHz or less, which ...restricts count rates and signal-to-noise ratio for a variety of experiments. SXR generation at high repetition rate has remained challenging because of the missing high-power infrared laser sources to drive the high-harmonic generation (HHG) process. Here we present an optical parametric chirped pulse amplifier (OPCPA) centered at a wavelength of 2.2 µm and generating 16.5 fs pulses (2.2 oscillation cycles of the carrier wave) with 25 W of average power and a peak power exceeding 14 GW at 100 kHz pulse repetition rate. This corresponds to the highest reported peak power for high-repetition-rate long-wavelength laser systems. The output of this 2.2 µm OPCPA system was used to generate a coherent SXR radiation extending beyond 0.6 keV through HHG in a high-pressure gas cell.
Background
The Chicago Classification (CC) of esophageal motility disorders, utilizing an algorithmic scheme to analyze clinical high‐resolution manometry (HRM) studies, has gained acceptance ...worldwide.
Methods
This 2014 update, CC v3.0, developed by the International HRM Working Group, incorporated the extensive clinical experience and interval publications since the prior (2011) version.
Key Results
Chicago Classification v3.0 utilizes a hierarchical approach, sequentially prioritizing: (i) disorders of esophagogastric junction (EGJ) outflow (achalasia subtypes I‐III and EGJ outflow obstruction), (ii) major disorders of peristalsis (absent contractility, distal esophageal spasm, hypercontractile esophagus), and (iii) minor disorders of peristalsis characterized by impaired bolus transit. EGJ morphology, characterized by the degree of overlap between the lower esophageal sphincter and the crural diaphragm and baseline EGJ contractility are also part of CC v3.0. Compared to the previous CC version, the key metrics of interpretation, the integrated relaxation pressure (IRP), the distal contractile integral (DCI), and the distal latency (DL) remain unchanged, albeit with much more emphasis on DCI for defining both hypo‐ and hypercontractility. New in CC v3.0 are: (i) the evaluation of the EGJ at rest defined in terms of morphology and contractility, (ii) ‘fragmented’ contractions (large breaks in the 20‐mmHg isobaric contour), (iii) ineffective esophageal motility (IEM), and (iv) several minor adjustments in nomenclature and defining criteria. Absent in CC v3.0 are contractile front velocity and small breaks in the 20‐mmHg isobaric contour as defining characteristics.
Conclusions & Inferences
Chicago Classification v3.0 is an updated analysis scheme for clinical esophageal HRM recordings developed by the International HRM Working Group.
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The Chicago Classification (CC) of esophageal motility disorders, utilizing an algorithmic scheme to analyze clinical high‐resolution manometry (HRM) studies, has gained acceptance worldwide. This 2014 update, CC v3.0, developed by the International HRM Working Group, incorporated the extensive clinical experience and interval publications since the prior (2011) version.
•Airborne Laser Scanning (ALS) data allows bringing back past archaeological landscapes.•Automated detection of Former Field Systems (FFS) is a key goal for Historical Ecology studies.•Machine and ...Deep Learning models provide high performances when identifying various archaeological relics from ALS data.•Local Binary Patterns are effective features to measure properties of FFS.
Former field systems (FFS) are the most widespread traces of ancient activities in present European landscapes and represent significant perturbations to ecosystems. Through its ability to penetrate forest canopies and detect microlandforms, Airborne Laser Scanning data reveal archaeological relics over large areas, from periods older than the first available Historical Topographic Maps. Mapping these traces from ALS-derived data (e.g. Digital Elevation Model (DEM)) thus allows for a determination of a new temporal baseline in order to evaluate the effects of a longer history on current patterns of biodiversity. Here, we evaluate the ability of traditional machine learning (Random Forest-RF) and deep learning (Fully Connected Networks-FCN) models to detect Medieval Terraced slopes and Ridges and Furrows (RaF) from an ALS-derived DEM in the southern Vosges (1462 km2). We used a combination of Local Binary Patterns and topographical metrics to measure properties of FFS and to train detection models. We then assessed the relative performance of each model semantically and spatially. Our results demonstrated the high suitability of our approach for reproducing major trends in the landscape with a high level of similarity between the predicted and reference spatial patterns (Structural Similarity Index - SSIM > 0.75). RF outperformed FCN for Terraced Slopes, whilst minimizing the false positive rate. FCN slightly outperformed RF for the RaF dataset but showed promising abilities to survey unseen data with a low sensitivity to annotation errors. We suggest that this approach has the potential to offer new spatio-temporal possibilities in Historical Ecology studies as a means of automatically detecting past archaeological ecosystems from a landscape to a regional scale.
Due to increased cancer detection rates (CDR), breast MR (breast MRI) can reduce underdiagnosis of breast cancer compared to conventional imaging techniques, particularly in women with dense breasts. ...The purpose of this study is to report the additional breast cancer yield by breast MRI in women with dense breasts after receiving a negative screening mammogram.
For this study we invited consecutive participants of the national German breast cancer Screening program with breast density categories ACR C & D and a negative mammogram to undergo additional screening by breast MRI. Endpoints were CDR and recall rates. This study reports interim results in the first 200 patients. At a power of 80% and considering an alpha error of 5%, this preliminary population size is sufficient to demonstrate a 4/1000 improvement in CDR.
In 200 screening participants, 8 women (40/1000, 17.4–77.3/1000) were recalled due to positive breast MRI findings. Image-guided biopsy revealed 5 cancers in 4 patients (one bilateral), comprising four invasive cancers and one case of DCIS. 3 patients revealed 4 invasive cancers presenting with ACR C breast density and one patient non-calcifying DCIS in a woman with ACR D breast density, resulting in a CDR of 20/1000 (95%-CI 5.5–50.4/1000) and a PPV of 50% (95%-CI 15.7–84.3%).
Our initial results demonstrate that supplemental screening using breast MRI in women with heterogeneously dense and very dense breasts yields an additional cancer detection rate in line with a prior randomized trial on breast MRI screening of women with extremely dense breasts. These findings are highly important as the population investigated constitutes a much higher proportion of women and yielded cancers particularly in women with heterogeneously dense breasts.
We compare the generation of high-order harmonics in the water window (283-543 eV) with 0.8-µm and 2.2-µm few-cycle lasers at a pulse repetition rate of 100 kHz. Using conventional phase matching ...with the 2.2-µm driver and what we attribute to nonadiabatic self-phase-matching with the 0.8-µm driver, photons up to 0.6 keV (2 nm) are generated in both cases. Special attention is paid to the understanding of the generation mechanism with the 0.8-µm laser amplifier system. We use the same beamline and pump laser for both drivers, which allows for a direct flux comparison at the two driving wavelengths. For photon energies around 280 eV, a 10-100 times higher flux is obtained from the 2.2-µm versus the 0.8-µm laser system in helium and neon. The crossover at which the 2.2-µm yields a higher flux compared to the 0.8-µm driver is found to be as high as 0.2 keV. Our study supports the common approach of using long-wavelength lasers in a phase-matched regime for efficient generation of water-window harmonics, but also shows that the more widespread 0.8-µm wavelength can be used to generate water-window harmonics with an efficiency close to the one of a less common 2.2-µm source.
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