Analytical performance of an immunoprofiling assay based on RNA models

As immuno-oncology drugs grow more popular in the treatment of cancer, better methods are needed to quantify the tumor immune cell component to determine which patients are most likely to benefit from treatment. Methods such as flow cytometry can accurately assess the composition of infiltrating immune cells; however, they show limited use in formalin-fixed, paraffin-embedded (FFPE) specimens. This article describes a novel hybrid-capture RNA sequencing assay, ImmunoPrism, that estimates the relative percentage abundance of eight immune cell types in FFPE solid tumors. Immune health expression models were generated using machine learning methods and used to uniquely identify each immune cell type using the most discriminatively expressed genes. The analytical performance of the assay was assessed using 101 libraries from 40 FFPE and 32 fresh-frozen samples. With defined samples, ImmunoPrism had a precision of ±2.72%, a total error of 2.75%, and a strong correlation (

Genomic analysis of a large set of currently—and historically—important human adenovirus pathogens

Human adenoviruses (HAdVs) are uniquely important “model organisms” as they have been used to elucidate fundamental biological processes, are recognized as complex pathogens, and are used as remedies for human health. As pathogens, HAdVs may effect asymptomatic or mild and severe symptomatic disease upon their infection of respiratory, ocular, gastrointestinal, and genitourinary systems. High-resolution genomic data have enhanced the understanding of HAdV epidemiology, with recombination recognized as an important and major pathway in the molecular evolution and genesis of emergent HAdV pathogens. To support this view and to actualize an algorithm for identifying, characterizing, and typing novel HAdVs, we determined the DNA sequence of 95 isolates from archives containing historically important pathogens and collections housing currently circulating strains to be sequenced. Of the 85 samples that were completely sequenced, 18 novel recombinants within species HAdV-B and D were identified. Two HAdV-D genomes were found to contain novel penton base and fiber genes with significant divergence from known molecular types. In this data set, we found additional isolates of HAdV-D53 and HAdV-D58, two novel genotypes recognized recently using genomics. This supports the thesis that novel HAdV genotypes are not limited to “one-time” appearances of the prototype but are of importance in HAdV epidemiology. These data underscore the significance of lateral genomic transfer in HAdV evolution and reinforce the potential public health impact of novel genotypes of HAdVs emerging in the population

Development of a prototype visualization approach for next-generation sequencing technologies using genome navigator framework

The advent of next-generation sequencing (NGS) technologies has greatly accelerated the development of the genome analysis. Sequencing efficiency has improved significantly in last decade after the sequencing of the human genome was completed. A large number of NGS platforms have been developed with incredibly lower cost and higher throughputs. Terabyte of data are generated every day along with the NGS workstation, but the pace of analyzing these data is still not satisfactory. The lag between the available data and the interpretation tools will ultimately slow the progress of NGS. In this work, I aimed to add functionality to the display of NGS data in an existing genomic visualization tool - Genome Navigator (GN). By adding new features especially for the display of NGS data, the prototype GN can be used in various sequencing projects and help researchers visualize and interpret sequencing data, while exploring interested genomic region, and validating their hypotheses. After updates, the prototype GN is able to handle large amounts of sequencing data and display thousands of read at the same time. It supports several display modes such as stacked view, condensed view, and complex view. At different zoom levels, different amounts of details are shown to the users. Moreover, several utility tools have been developed to support GN when dealing with different input formats. Several new server interface features are designed for interaction with the user. I used the real sequencing data, tested the functionalities of the improvements, and had several positive results. I expect that GN will also be useful in other NGS applications and play an important role in today’s NGS research.M.S.Includes bibliographical referencesby Tiange Cu

Stomatal Ratio Showing No Response to Light Intensity in <i>Oryza</i>

Stomata control carbon and water exchange between the leaves and the ambient. However, the plasticity responses of stomatal traits to growth conditions are still unclear, especially for monocot leaves. The current study investigated the leaf anatomical traits, stomatal morphological traits on both adaxial and abaxial leaf surfaces, and photosynthetic traits of Oryza leaves developed in two different growth conditions. Substantial variation exists across the Oryza species in leaf anatomy, stomatal traits, photosynthetic rate, and stomatal conductance. The abaxial stomatal density was higher than the adaxial stomatal density in all the species, and the stomatal ratios ranged from 0.35 to 0.46 across species in two growth environments. However, no difference in the stomatal ratio was observed between plants in the growth chamber and outdoors for a given species. Photosynthetic capacity, stomatal conductance, leaf width, major vein thickness, minor vein thickness, inter-vein distance, and stomatal pore width values for leaves grown outdoors were higher than those for plants grown in the growth chamber. Our results indicate that a broad set of leaf anatomical, stomatal, and photosynthetic traits of Oryza tend to shift together during plasticity to diverse growing conditions, but the previously projected sensitive trait, stomatal ratio, does not shape growth conditions

Pre-clinical Evidence: Berberine as a Promising Cardioprotective Candidate for Myocardial Ischemia/Reperfusion Injury, a Systematic Review, and Meta-Analysis

Objective: Myocardial ischemia/reperfusion (I/R) injury is one of the causes of most cardiomyocyte injuries and deaths. Berberine (BBR) has been suggested a potential to exert protective effects against myocardial I/R injury. This systematic review aims to determine the intrinsic mechanisms of BBR's protective effects in myocardial I/R injury.Methods: Seven databases were searched for studies performed from inception to July 2020. Methodological quality was assessed by SYRCLE's-RoB tool.Results: Ten studies including a total of 270 animals were included in this study. The methodology quality scores of the included studies ranged from 5 to 7 points. The meta-analysis we conducted demonstrated that BBR significantly reduced myocardial infarct size and the incidence of ventricular arrhythmia, compared to control groups (P &lt; 0.00001). Cardiac function of animals in the BBR treatment group was also markedly increased (P &lt; 0.00001). The index of myocardial apoptosis and the levels of biomarkers of myocardial infarction (LDH and CK) were also decreased in the BBR treatment groups compared to the control groups (P &lt; 0.00001).Conclusions: The pre-clinical evidence, according to our study, showed that BBR is a promising therapeutic agent for myocardial I/R injury. However, this conclusion should be further investigated in clinical studies

Impact of Precursor Concentration on Perovskite Crystallization for Efficient Wide-Bandgap Solar Cells

High-crystalline-quality wide-bandgap metal halide perovskite materials that achieve superior performance in perovskite solar cells (PSCs) have been widely explored. Precursor concentration plays a crucial role in the wide-bandgap perovskite crystallization process. Herein, we investigated the influence of precursor concentration on the morphology, crystallinity, optical property, and defect density of perovskite materials and the photoelectric performance of solar cells. We found that the precursor concentration was the key factor for accurately controlling the nucleation and crystal growth process, which determines the crystallization of perovskite materials. The precursor concentration based on Cs0.05FA0.8MA0.15Pb(I0.84Br0.16)3 perovskite was controlled from 0.8 M to 2.3 M. The perovskite grains grow larger with the increase in concentration, while the grain boundary and bulk defect decrease. After regulation and optimization, the champion PSC with the 2.0 M precursor concentration exhibits a power conversion efficiency (PCE) of 21.13%. The management of precursor concentration provides an effective way for obtaining high-crystalline-quality wide-bandgap perovskite materials and high-performance PSCs

CEPC Technical Design Report -- Accelerator

International audienceThe Circular Electron Positron Collider (CEPC) is a large scientific project initiated and hosted by China, fostered through extensive collaboration with international partners. The complex comprises four accelerators: a 30 GeV Linac, a 1.1 GeV Damping Ring, a Booster capable of achieving energies up to 180 GeV, and a Collider operating at varying energy modes (Z, W, H, and ttbar). The Linac and Damping Ring are situated on the surface, while the Booster and Collider are housed in a 100 km circumference underground tunnel, strategically accommodating future expansion with provisions for a Super Proton Proton Collider (SPPC). The CEPC primarily serves as a Higgs factory. In its baseline design with synchrotron radiation (SR) power of 30 MW per beam, it can achieve a luminosity of 5e34 /cm^2/s^1, resulting in an integrated luminosity of 13 /ab for two interaction points over a decade, producing 2.6 million Higgs bosons. Increasing the SR power to 50 MW per beam expands the CEPC's capability to generate 4.3 million Higgs bosons, facilitating precise measurements of Higgs coupling at sub-percent levels, exceeding the precision expected from the HL-LHC by an order of magnitude. This Technical Design Report (TDR) follows the Preliminary Conceptual Design Report (Pre-CDR, 2015) and the Conceptual Design Report (CDR, 2018), comprehensively detailing the machine's layout and performance, physical design and analysis, technical systems design, R&D and prototyping efforts, and associated civil engineering aspects. Additionally, it includes a cost estimate and a preliminary construction timeline, establishing a framework for forthcoming engineering design phase and site selection procedures. Construction is anticipated to begin around 2027-2028, pending government approval, with an estimated duration of 8 years. The commencement of experiments could potentially initiate in the mid-2030s