DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct ...taxonomic names and clearly annotated specimen data has never been greater. Furthermore, the growing number of molecular ecology projects employing high-throughput sequencing require fast and effective methods for en masse species assignments. In this paper we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer (ITS) region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated, public database at the National Center for Biotechnology Information (NCBI), RefSeq Targeted Loci (RTL), and will be visible during routine BLAST searches with NR prefixed accession numbers. A set of standards and protocols is proposed in order to improve the data quality of new sequences and we suggest how type and other reference sequences can be used to improve identification of Fungi.
A rod-shaped, facultatively aerobic bacterium, designated strain S2-27
T
, was isolated from a mangrove soil sample, and a polyphasic approach was employed to determine its taxonomic position. ...Phylogenetic analysis of the 16S rRNA gene sequence indicated the closest relationship between strain S2-27
T
and
Caldimonas brevitalea
ATCC 53080
T
, which was further supported by phylogenetic analysis based on the core genes of genomic sequences. Digital DNA-DNA hybridization (dDDH) and the average nucleotide identity analyses (ANI) further supported the identification of strain S2-27
T
as a novel species of the genus
Caldimonas
. Q-8 was detected as its only ubiquinone. The major fatty acids were C
16:0
and C
16:1
ω
7c
/C
16:1
ω
6c
. Polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, glycolipid, and several uncharacterized polar lipids and phospholipids. Biosynthetic gene cluster and pan-genome analyses strongly indicated that
Caldimonas
members held a great potential, displaying diverse biological functions and metabolic activities. Here, we propose a novel species of the genus
Caldimonas
,
Caldimonas mangrovi
sp. nov. with the type strain S2-27
T
(=CGMCC 4.7715
T
= JCM 34532
T
).
OBJECTIVETo analyze the causes of the esophagogastric junction outlet obstruction (EGJOO) patients, to discuss the differences of the clinical manifestation and esophageal motility characteristics ...between the anatomic EGJOO (A-EGJOO) and functional EGJOO (F-EGJOO) subgroups, and to search the diagnostic values of the specific metrics for differentiating the subgroups of EGJOO patients. METHODSFor the current retrospective study, all the patients who underwent the esophageal high resonance manometry test were retrospectively analyzed from Jan 2012 to Oct 2018 in Peking University Third Hospital. The EGJOO patients were enrolled in the following research. The clinical characteristics, such as symptoms and causes of the patients were studied. Then the patients were divided into two subgroups as A-EGJOO subgroup and F-EGJOO subgroup. The clinical symptoms and the main manometry metrics were compared between these two subgroups. The significant different metrics between the two groups were selected to draw receive
Endoscopic spray cryoablation is a novel approach for the treatment of Barrett's esophagus. However, few studies have reported its efficacy, especially with the use of carbon dioxide (CO (2)). The ...aim of the current study was to evaluate the short term efficacy and complications using CO (2) in endoscopic cryoablation of Barrett's esophagus.
Patients diagnosed with Barrett's esophagus underwent monthly stepwise cryoablation with pressurized CO (2) gas, with follow-up esophageal biopsies until complete histological reversal was achieved. Responses were analyzed with an intention-to-treat analysis according to complete response for intestinal metaplasia (CR-IM), which was defined as the elimination of all intestinal metaplasia including specialized intestinal metaplasia (SIM), subsquamous SIM, and dysplasia with intestinal metaplasia in the biopsies under narrow-band imaging (NBI).
In total, 22 patients were enrolled, 20 of whom completed the treatment. Two patients declined further ablation after the first cryotherapy session. A total of 44 sessions were performed; a median of 2 sessions per patient (range 1 - 3 sessions) were needed to complete the ablation of Barrett's esophagus. No severe complications occurred. Follow-up endoscopies were performed in 20 patients (90.9 %). Two patients (9.1 %) were lost to follow-up. Median follow-up was 10 months (range 6 - 18 months). After cryotherapy, 20 patients (90.9 %) reached CR-IM of Barrett's esophagus. Patients underwent a median number of 3 follow-up endoscopies (range 2 - 4) with biopsies. At 6 months, recurrence was evident in three patients (13.6 % of the overall population, 15.0 % of the CR-IM population). One of the three patients developed intestinal metaplasia but no dysplastic change and the other two developed subsquamous SIM.
The pressurized CO (2) spray cryotherapy is a relatively effective and safe endoscopic treatment for Barrett's esophagus.
To explore the mechanism of Doublecortin-like kinase 1 (DCLK1) in promoting cell migration, invasion and proliferation in pancreatic cancer.
The correlation between DCLK1 and Hippo pathway was ...analyzed using TCGA and GTEx databases and confirmed by fluorescence staining of pancreatic cancer tissue microarrays. At the cellular level, immunofluorescence staining of cell crawls and western blot assays were performed to clarify whether DCLK1 regulates yes associated protein1 (YAP1), a downstream effector of the Hippo pathway. Reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) was used to analyze the expressions of YAP1 binding transcription factor TEA-DNA binding proteins (TEAD) and downstream malignant behavior-promoting molecules CYR61, EDN1, AREG, and CTGF. Transwell test of the DCLK1-overexpressing cells treated with the Hippo pathway inhibitor Verteporfin was used to examine whether the malignant behavior-promoting ability was blocked. Analysis of changes in the proliferation in
Positron Annihilation Lifetime (PAL) spectroscopyis widely applied in material and biomedical science. The conventional analog PAL spectrometer built by multiple Nuclear Instrumentation Modules ...gradually shows deficiencies in performance. Most digital PAL spectrometers strongly rely on the advanced Analog-to-Digital Converter (ADC) or oscilloscope with an ultra-high-speed sampling rate. In this paper, we developed a prototype system of the digital PAL spectrometer based on ordinary Time-to-Digital Converter (TDC) and ADC. Benefiting from the high-performance digitization devices and digital signal processing algorithms accomplished by Field-Programmable Gate Array (FPGA), the system achieves remarkable energy and lifetime resolution in a simple structure and at a much lower cost. Electronic test results show that the time resolution of the TDC reaches 67 ps and the Effective Number Of Bits of ADC is better than 10.77 bit. The energy resolution of 511 keV photopeak is 4.1% and the Full Width at Half Maximum of the lifetime spectrum reaches 210.6 ps when using Hamamatsu H3378-50 Photomultiplier Tubes with LaBr3:5% Ce3+ scintillators as detectors.
Many previous studies have shown that multiangle, multispectral polarimetric remote sensing can provide valuable information on aerosol microphysical and optical properties, in which the aerosol ...layer height (ALH) is an important parameter but with less studies, especially in the near-ultraviolet (near-UV) and visible (VIS) wavelength bands. Based on the optimal estimation (OE) theory and information content analysis method, we focus on the sensitivity study of ALH with the synthetic data in the near-UV and VIS wavelength in the range of 410–865 nm, and further to assess the capability of multiangle intensity and polarization measurements for the retrieval of ALH. Unified Linearized Vector Radiative Transfer Model (UNL-VRTM) has been used as the forward model to simulate the intensity and polarized radiance at the top of atmosphere (TOA), as well as the Jacobians of TOA results with respective to corresponding parameters. The degree of freedom for signal (DFS) and a posteriori error are introduced to quantity the information content of ALH from the intensity and polarization measurements, respectively. By assuming the surface type, aerosol model, aerosol loads, prior errors and observation geometries, the sensitivity of ALH has been preliminarily investigated. The sensitivity study results show that the near-UV and polarization measurements are the important source of information content for the aerosol height retrieval in satellite remote sensing.
Abstract
To cope with the challenge of high hit rates in some
applications, the new-generation large-area Resistive Plate Chamber
(RPC) with 1 mm thin gap was proposed. Compared to the RPC
generation ...presently, the signal of the thin-gap RPC is much weaker
(of the order of hundreds of μV) and faster (pulse width of about
5 ns). Hence a new-generation Front-End (FE) electronics needs to
be developed for the thin-gap RPC. The FE board contains 8
independent electronic channels, each with an amplifier, a
discriminator, and a Low-Voltage Differential Signaling (LVDS)
transmitter. The amplifier is made of discrete components, with
particular emphasis on SiGe:C transistors. A simplified but stable
power system is designed for the FE board, and its status can be
monitored in real-time. The test results show that the overall
charge gain of the FE amplifier reaches 0.4 mV/fC, with very low
noise (lower than 700 μV RMS with up to 10 pF input detector
capacitance), and good linearity when the amplitude of the input
amplitude is lower than 3 mV. The -3-dB bandwidth of the
amplifier reaches 154 MHz. The jitter caused by the electronics
(including amplifier, discriminator and LVDS transmitter) is around
10 ps when the threshold voltage is higher than 20 mV. The maximum
event rate per channel exceeds 20 MHz. The cosmic ray test was
conducted with two FE boards mounted on a 1 mm thin-gap RPC of
1.4 × 0.4 m
2
area. The efficiency of the detector system
reaches 95% when the threshold voltage is 20 mV, with almost no
accidental coincidence event. The overall time resolution of the
detector system is 484 ps. The performance of our FE electronics
satisfies the requirement of the thin-gap RPC.
Fine-mode aerosol usually comes from anthropogenic emissions. The fine-mode aerosol optical depth (AODf) is an important parameter for estimating the particulate matter with an aerodynamic diameter ...little than 2.5 μm (PM2.5). Compared to the ground-based observations, AODf products from satellite remote sensing have an advantage of high spatial coverage, which is suitable for monitoring the air quality at a regional or global scale. Up to now, AODf products have been released by several sensors, such as the single-angle multi-spectral intensity sensor MODIS and multi-angle multi-spectral polarization sensor POLDER, then what’re the different performances of AODf products from them? In this study, the different spatial resolution AODf products respectively from MODIS latest Collection 6.1 (C6.1, 3 and 10 km) and POLDER latest level 2 version 1.01 (L2, 18 km) were firstly compared with each other in Beijing-Tianjin-Hebei (BTH) domains. Then those products were validated against the ground-based AERosol RObotic NETwork (AERONET) measurements, where has been suffering the severe air pollution since decades ago. The comparison of yearly averaged AODf products between MODIS and POLDER shows a good consistency on the spatial distribution, the higher spatial resolution products of MODIS show more details, both low values of AODf appeared in the northwest area with small population and industry, high values appeared in the southeast area with lots of cities, industries, and large population. However, the whole yearly AODf average values of MODIS are higher than that of POLDER. The results of validation against AERONET show that the accuracy of AODf products at 865 nm from POLDER (R = 0.94, RMSE = 0.05) is high than that at 550 nm of MODIS (3 km: R = 0.69, RMSE = 0.32; 10 km: R = 0.76, RMSE = 0.3). In this study, the performance of different spatial resolutions AODf products retrieved from the intensity (MODIS 3 and 10 km) and polarized sensors (POLDER 18 km) were evaluated. Those results not only have a great significance to provide users amore appropriate choice of the AODf products in the BTH region but also display that the accuracy and spatial resolution of MODIS and POLDER AODf products need to be improved.
Feces from cattle fed 65 different diets were used to develop near-infrared spectroscopy (NIRS) calibrations to predict fecal composition organic matter (OM), starch, nitrogen (N), neutral detergent ...fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), and ether extract (EE), and feces from cattle fed 23 different diets were used to predict digestibility dry matter (DM), OM, starch, crude protein (CP), NDF, ADF, and gross energy (GE). The predictions of these parameters in feces collected from cattle fed wheat or barley grain (89% of diet DM) with barley silage (study 1) or barley grain diets containing varying levels of barley silage (study 2) were assessed. Validations for fecal composition displayed moderate to excellent linearity (R2val ≥ 0.70) for OM, starch, N, NDF, and ADL and poor linearity for ADF and EE (R2val = 0.25). When both digestibility and feedlot data sets were combined, cross-validation for fecal composition found accurate predictions (R2CV ≥ 0.90, SECV ≤ 2.42) for all fecal constituents except EE. Accuracy of predicting digestibility was high for starch (R2CV = 0.84, SECV = 1.06), good to moderate for DM, OM, CP, and GE (R2CV ≥ 0.62, SECV ≤ 3.63) but poor for NDF and ADF (R2CV ≤ 0.33, SECV ≥ 7.86). We conclude that fecal NIRS can predict both chemical composition and digestibility of most nutrients in feedlot cattle feces.
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