Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.

As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing

Co-infusion of haplo-identical CD19-chimeric antigen receptor T cells and stem cells achieved full donor engraftment in refractory acute lymphoblastic leukemia

Abstract Background Elderly patients with relapsed and refractory acute lymphoblastic leukemia (ALL) have poor prognosis. Autologous CD19 chimeric antigen receptor-modified T (CAR-T) cells have potentials to cure patients with B cell ALL; however, safety and efficacy of allogeneic CD19 CAR-T cells are still undetermined. Case presentation We treated a 71-year-old female with relapsed and refractory ALL who received co-infusion of haplo-identical donor-derived CD19-directed CAR-T cells and mobilized peripheral blood stem cells (PBSC) following induction chemotherapy. Undetectable minimal residual disease by flow cytometry was achieved, and full donor cell engraftment was established. The transient release of cytokines and mild fever were detected. Significantly elevated serum lactate dehydrogenase, alanine transaminase, bilirubin and glutamic-oxalacetic transaminase were observed from days 14 to 18, all of which were reversible after immunosuppressive therapy. Conclusions Our preliminary results suggest that co-infusion of haplo-identical donor-derived CAR-T cells and mobilized PBSCs may induce full donor engraftment in relapsed and refractory ALL including elderly patients, but complications related to donor cell infusions should still be cautioned. Trial registration Allogeneic CART-19 for Elderly Relapsed/Refractory CD19+ ALL. NCT0279955

Time-Dependent Behavior of Full-Scale Recycled Aggregate Concrete Beams under Long-Term Loading

Sixteen full-scale recycled aggregate concrete (RAC) beams were cast and tested to study their time-dependent behavior under long-term loading. The test parameters include the replacement rate of the recycled coarse aggregates (RCAs), the replacement rate of the recycled fine aggregates (RFAs), the concrete strength, and the stress ratio. The influence of the above variables on the deflection and stiffness is discussed. The results show that the RCAs will increase the deflection of the specimen at a low stress ratio; at a high stress ratio, the beams will experience nonlinear creep, and the deflection of the specimen will be affected by the RCAs and the stress ratio. The RFAs have a substantial influence on the time-dependent behavior of the specimen, and the deflection of the specimen with 100% replacement of recycled aggregates can increase by 30%; the strength of the concrete does not have a substantial influence on the time-dependent behavior of the specimen; and the stress ratio has an influence on the initial deflection of the specimen. A deflection calculation formula is established based on the stress–strain relationship of the beam under long-term loading and the characteristics of the RAC. The calculation results are in good agreement with the test results

Changes of Reference Evapotranspiration and Its Relationship to Dry/Wet Conditions Based on the Aridity Index in the Songnen Grassland, Northeast China

Reference evapotranspiration (ET0) plays an important role in regional dry/wet conditions. Based on the Food and Agriculture Organization of the United (FAO) Penman-Monteith method and daily climate variables, ET0 was calculated for 21 stations in and around the Songnen Grassland, northeast China, during 1960–2014. The temporal and spatial variations of ET0 and precipitation (P) were analyzed in the annual, seasonal, and growing season (from April to October) time series using the Mann-Kendall test, Sen’s slope estimator, and linear regression coupled with a break trend analysis. A sensitivity analysis was used to detect the key climate parameter contributing to ET0 change. By linear regression analysis on the relationship between ET0, P, and the aridity index (AI), the role of ET0 in determining regional wet/dry conditions was analyzed. Results show a higher ET0 in the southwest and a lower ET0 in the northeast, but P was opposite to that of ET0. Evident decreasing trends of ET0 in the annual, seasonal, and growing season time series were detected in almost the entire region by the trend analysis methods. For the entire region, the decreasing trend of ET0 can be linked to the relative humidity and maximum air temperature. The positive contribution of increasing temperature to ET0 was offset by the effect of the significantly decreasing relative humidity, wind speed, and sunshine duration at the 0.05 level during 1960–2014. In addition, the value of ET0 was higher in drought years and lower in wet years

Wireless LC Conformal Temperature Sensor Based on Ag Film (9912-K FL) for Bearing Temperature Measurement

As the key component of aero-engines and industrial gas turbines, a bearing’s working temperature at high speed is close to 300 ℃. The measurement of an engine bearing’s temperature is of great significance to ensure flight safety. In this study, we present a wireless LC conformal temperature sensor for bearing temperatures, which integrates silver on the bearing surface in situ through a screen-printing process. This process makes Ag film (9912-K FL) firmly adhere to the bearing surface and realizes wireless measurements for bearing temperatures in situ. A high-temperature holding experiment of the prepared sensor was conducted, and the results showed that the sensor can work stably for 10 h at 300 ℃. We tested the designed wireless LC conformal temperature sensor at 20–270 ℃. The results showed that the proposed temperature sensor attained as good accuracy and stability in the temperature range 20–270 ℃. The sensitivity of the temperature measurements was 20.81 KHz/℃  when the bearing rotateds, the maximum repeatability was 0.039%, the maximum uncertainty was 0.081%, and the relative error was stable within  0.08%

Late Quaternary tectonic activity and strong earthquake generation mechanism around the boundary zone of the Ordos active-tectonic block, central China

Objective  The Ordos block, with typical boundary zone activity, is located in the center of mainland China. Influenced by the remote action of the Tibetan Plateau in the southwest and the Pacific Plate in the east, each boundary zone of the Ordos Block exhibits distinct tectonic activity and deformation characteristics. This study aims to provide insights into the characteristics of strong earthquake generation and the future seismic risk along the boundaries of the Ordos active block.  Methods  This study systematically summarizes research achievements made in the study of active faults and the seismogenic mechanism of strong earthquakes around the Ordos Block over the past few decades, providing a systematic overview of the characteristics of fault activity and seismic generation mechanisms along the block' s periphery.  Conslusion  The differences in fault activity in each boundary zone determined the differences in the earthquake-breeding strong tectonic environments. In the southern section of the western boundary, the faults are mainly characterized by strike-slip, reverse strike-slip, and thrust owing to the influence of the northward compression and expansion of the Qinghai-Tibet Plateau, resulting in complex structural deformation styles within the boundary zone. In the northern section of the western boundary, the latest expansion boundary of the Qinghai-Tibet Plateau is characterized by dextral movement along the Sanguankou-Niushoushan fault. The Yinchuan Basin in the northern section of the western boundary zone is a typical fault basin with basin-controlling faults exhibiting dextral strike-slip characteristics, and earthquakes are primarily of the standard strike-slip type. The Hetao Basin on the northern boundary is controlled by normal faults on its northern side, with historical and ancient earthquakes concentrated on the northern boundary faults. The Weihe Basin on the southern boundary exhibits relatively complex structural features, comprising two sets of normal faults. Historical major earthquakes mostly occur at the southern edge of the basin, with moderate seismic activity in the central-northern part of the basin. The Shanxi Graben system on the eastern boundary comprises multiple rift-type basins. Historical major earthquakes exhibit a pattern of stronger activity in the south and weaker activity in the north. The northern basins are influenced by the Zhang-Bo tectonic belt, resulting in significant changes in basin trend and fault movement characteristics, often possessing the structural conditions necessary for earthquakes of around M 7.0. Overall, in the typical fault activity zones surrounding the Ordos active block, future strong earthquakes are more likely to occur in seismic gaps or transition zones of fault systems, where significant time has passed since the occurrence of major earthquakes or at the intersections of tectonic zones

Comparative Proteomic Profiling of Human Bile Reveals SSP411 as a Novel Biomarker of Cholangiocarcinoma

<div><h3>Background</h3><p>Cholangiocarcinoma (CC) is an intractable cancer, arising from biliary epithelial cells, which has a poor prognosis and is increasing in incidence. Early diagnosis of CC is essential as surgical resection remains the only effective therapy. The purpose of this study was to identify improved biomarkers to facilitate early diagnosis and prognostication in CC.</p> <h3>Methods</h3><p>A comparative expression profile of human bile samples from patients with cholangitis and CC was constructed using a classic 2D/MS/MS strategy and the expression of selected proteins was confirmed by Western blotting. Immunohistochemistry was performed to determine the expression levels of selected candidate biomarkers in CC and matched normal tissues. Finally, spermatogenesis associated 20 (SSP411; also named SPATA20) was quantified in serum samples using an ELISA.</p> <h3>Results</h3><p>We identified 97 differentially expressed protein spots, corresponding to 49 different genes, of which 38 were upregulated in bile from CC patients. Western blotting confirmed that phosphoglycerate mutase 1 (brain) (PGAM-1), protein disulfide isomerase family A, member 3 (PDIA3), heat shock 60 kDa protein 1 (chaperonin) (HSPD1) and SSP411 were significantly upregulated in individual bile samples from CC patients. Immunohistochemistry demonstrated these proteins were also overexpressed in CC, relative to normal tissues. SSP411 displayed value as a potential serum diagnostic biomarker for CC, with a sensitivity of 90.0% and specificity of 83.3% at a cutoff value of 0.63.</p> <h3>Conclusions</h3><p>We successfully constructed a proteomic profile of CC bile proteins, providing a valuable pool novel of candidate biomarkers. SSP411 has potential as a biomarker for the diagnosis of CC.</p> </div

Transcriptional and Functional Analysis Shows Sodium Houttuyfonate-Mediated Inhibition of Autolysis in Staphylococcus aureus

Sodium houttuyfonate (SH), an addition compound of sodium bisulfite and houttuynin, showed in vitro antibacterial activity against 21 Staphylococcus aureus (S. aureus) strains grown in planktonic cultures. Microarray results showed decreased levels of autolysin atl, sle1, cidA and lytN transcripts in the SH-treated strain as compared to the control strain, consistent with the induction of the autolytic repressors lrgAB and sarA and with the downregulation of the positive regulators agrA and RNAIII. Triton X-100-induced autolysis was significantly decreased by SH in S. aureus ATCC 25923, and quantitative bacteriolytic assays and zymographic analysis demonstrated SH-mediated reduction of extracellular murein hydrolase activity in these cells. Anti-biofilm assay showed that SH is poorly active against S. aureus grown in biofilm cultures, whereas SH diminished the amounts of extracellular DNA (eDNA) of S. aureus in a dose-dependent manner, which suggested that SH may impede biofilm formation by reducing the expression of cidA to inhibit autolysis and eDNA release in the early phase. Some of the microarray results were confirmed by real-time RT-PCR

Western blot validation of four candidate cholangiocarcinoma biomarkers in individual bile samples.

<p>Western blotting (top) and quantification (bottom) of candidate biomarker expression in equal volumes of individual bile samples from 10 cholangitis patients (benign) and 19 cholangiocarcinoma (CC) patients. (A) PGAM-1; (B) PDIA3; (C) HSPD1 (D) and SSP411.</p

Immunohistochemical analysis of PGAM-1, PDIA3, HSPD1 and SSP411 in hilar cholangiocarcinoma (HCCA).

<p>Differences in the expression of PGAM-1 (A, B), PDIA3 (C, D), HSPD1 (E, F), SSP411 (G, H) in cancerous (right) versus normal tissue specimens (left). Immunohistochemical staining profiles in intrahepatic cholangiocarcinoma (IHC) are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047476#pone.0047476.s002" target="_blank">Figure S2</a>. Bar = 20 µm.</p