Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project.

Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants was developed in the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, but the known indels in the known-positive set were limited. This project sought to provide an enriched set of known indels that would be more translationally relevant by focusing on additional cancer related regions. A thorough manual review process completed by 42 reviewers, two advisors, and a judging panel of three researchers significantly enriched the known indel set by an additional 516 indels. The extended benchmarking indel set has a large range of variant allele frequencies (VAFs), with 87% of them having a VAF below 20% in reference Sample A. The reference Sample A and the indel set can be used for comprehensive benchmarking of indel calling across a wider range of VAF values in the lower range. Indel length was also variable, but the majority were under 10 base pairs (bps). Most of the indels were within coding regions, with the remainder in the gene regulatory regions. Although high confidence can be derived from the robust study design and meticulous human review, this extensive indel set has not undergone orthogonal validation. The extended benchmarking indel set, along with the indels in the previously published known-positive set, was the truth set used to benchmark indel calling pipelines in a community challenge hosted on the precisionFDA platform. This benchmarking indel set and reference samples can be utilized for a comprehensive evaluation of indel calling pipelines. Additionally, the insights and solutions obtained during the manual review process can aid in improving the performance of these pipelines.

Voting by mouth: media attention and environmental governance.

External regulation is crucial for environmental protection. This study investigates the impact of media attention on corporate environmental governance from 2011 to 2021, using China's public companies as our samples. The empirical results indicate that media attention consistently and significantly enhances corporate environmental governance. This effect remains robust across endogeneity considerations and alternative tests. Additionally, in regions with higher marketization and stronger rule of law frameworks, the efficacy of media attention in improving corporate environmental performance becomes remarkably pronounced. Further analysis unveils that media attention positively impacts environmental governance by elevating public awareness, refining internal management efficiency, and fostering innovative strategies for minimizing environmental impact. These results offer empirical backing for the reinforcement of external oversight and corporate governance practices.

Rapid screening of pharmaceutical products for elemental impurities by a high-resolution portable energy dispersive X-ray fluorescence spectrometer using an efficient fundamental parameter method.

In this study, a rapid screening method for elemental impurities in pharmaceutical products has been established by portable energy dispersive X-ray fluorescence (EDXRF) spectroscopy combined with the efficient fundamental parameter method. The proposed method has been used for the screening of 22 elemental impurities (i.e., Cd, Pb, As, Hg, Co, V, Ni, Tl, Au, Pd, Ir, Os, Rh, Ru, Se, Ag, Pt, Sb, Mo, Cu, Sn, and Cr) in the International Conference on Harmonization (ICH) Q3D guideline. The verification of results could meet the acceptance criteria for accuracy, precision and linearity in the United States Pharmacopoeia 〈233〉. On the other hand, the limit of quantitation of the proposed EDXRF method for the screening of 22 elemental impurities in pharmaceutical products could meet the concentration limits of each element at 10 g maximum daily intake based on the established permitted daily exposure to oral drugs in the ICH Q3D guideline. Our findings open up new possibilities in the rapid screening of pharmaceutical products for the detection of elemental impurities by EDXRF, which can be expected to provide a novel, nondestructive, high-throughput, portable, and sensitive platform for the process control of elemental impurities to ensure the quality and safety of drugs.

Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples.

BACKGROUND: Clinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targeted therapy. To understand the technical error due to FFPE processing, a robustly characterized diploid cell line was used to create FFPE samples with four different pre-tissue processing formalin fixation times. A total of 96 FFPE sections were then distributed to different laboratories for targeted sequencing analysis by four oncopanels, and variants resulting from technical error were identified. RESULTS: Tissue sections that fail more frequently show low cellularity, lower than recommended library preparation DNA input, or target sequencing depth. Importantly, sections from block surfaces are more likely to show FFPE-specific errors, akin to "edge effects" seen in histology, while the inner samples display no quality degradation related to fixation time. CONCLUSIONS: To assure reliable results, we recommend avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence.

Promotion incentives and air pollution: From the political promotion tournament to the environment tournament.

Chinese officials play an important role in air pollution control. This paper used a sample of 282 prefecture-level cities in China to discuss the impact of promotion incentives of officials on air pollution from the perspectives of heterogeneity, mechanism and spatial effects. We found that the promotion incentives of officials reduced air pollution, and GDP per capita had positive moderating effects. The effects of promotion incentives were more significant in cities with less air pollution, in the central and western regions, for officials with higher education levels, or years after 2007. The promotion incentives could promote the development of green finance and green technology innovation, both of which were conducive to mitigating air pollution. Using the dynamic spatial Durbin model (DSDM), we found that the promotion incentives had negative spatial spillover effects. The promotion incentives in surrounding cities reduced air pollution in the local city; however, it had only short-run effects and no long-run effects.

Method Improving for Isolation and Characterization of Allergy-Inducing Polymer Impurities in Cefotaxime Sodium Medicines Available From Pharmaceutical Industry.

Objective: To prepare and validate the chemical structure of the cefotaxime dimer and cefotaxime trimer impurities available from pharmaceutical industry. Methods: A polymer stock solution of cefotaxime sodium was obtained using a concentrated solution degradation method. The cefotaxime dimer and trimer impurities were separated and purified by preparative reversed-high-performance liquid chromatograph (RP-HPLC), and the pure cefotaxime dimer and trimer were obtained by a freeze-drying method. The two impurities were characterized by infrared (IR) spectroscopy, ultraviolet (UV) spectroscopy, mass spectroscopy, and nuclear magnetic resonance (NMR, including one-dimensional and two-dimensional NMR). The groups corresponding to the characteristic absorption peaks in the UV and IR spectra were analyzed, and the 1H and 13C NMR signals were assigned. Results: The cefotaxime dimer was isolated and purified from the actual sample of industrial medicines, and chemical structure of the dimer is the same as in the dimers investigated earlier. The polymerization sites and stereoscopic configuration of trimer impurity was validated for the first time. Conclusion: This study is of great significance for the study of the structures and quality control of polymer impurities in cephalosporin drugs. Promoting the polymerization sites study and providing a technical basis for allergic study of polymer impurities.

Trace Level Quantification of 4-Methyl-1-nitrosopiperazin in Rifampicin Capsules by LC-MS/MS.

Rifampicin is a first-line anti-tuberculosis drug. However, in August 2020, the presence of 1-methyl-4-nitrosopiperazine (MNP), a nitrosamine impurity, was detected by the United Stated Food and Drug Administration (US FDA) in rifampicin capsules. Consequently, the development of efficient methods for the detection of MNP is an important objective. In this study, the MNP present in rifampicin capsules was detected using LC-MS/MS. A total of 27 batches from nine manufacturers in the Chinese market were tested, with MNP (0.33-2.36 ppm) being detected in all samples at levels exceeding the maximum acceptable intake limit of 0.16 ppm initially set by the FDA. However, after considering the associated benefits and risks, the FDA-approved limit was revised to 5 ppm; hence, all the samples examined herein exhibited MNP levels well below the required limit. Furthermore, the results of forced degradation experiments suggest that MNP is formed by the thermal degradation of rifampicin.

A novel method for determining relative response factors using high-performance liquid chromatography with photodiode array detector and evaporative light scattering detection.

OBJECTIVES: Because the purity of the two impurities reference standard (RS) of cefathiamidine is not easy to obtain, HPLC-PDA-ELSD were used to determin the RRFs of cefathiamidine impurities. METHODS: Peak area correction was applied to calculate RRFs to eliminate the influence of different responses caused by the difference in pH between the two mobile phases of HPLC-PDA and HPLC-PDA-ELSD. The resulting RRF values have been verified by qNMR. CONCLUSION: The new calcution method described in this article provides a reliable research idea for determintion the RRFs by HPLC-PDA-ELSD, especially when the purity of RS is unknown and the mobile phase of HPLC-PDA and HPLC-PDA-ELSD have difference. This method can be mutually verified with qNMR to ensure the accuracy of RRFs. It is also promingsing replace determination RRF by qNMR becausing economical, simple and low cost.

A strategy for population pharmaceutical quality assessment based on quality by design.

From a regulatory perspective, drug quality consistency evaluation must concern different processes used for the same drug. In this study, an assessment strategy based on quality by design (QbD) was developed for population pharmaceutical quality evaluation. A descriptive analysis method based on QbD concept was first established to characterize the process by critical evaluation attributes (CEAs). Then quantitative analysis method based on an improved statistical process control (SPC) method was established to investigate the process indicators (PIs) in the process population, such as mean distribution, batch-to-batch difference and abnormal quality probability. After that rules for risk assessment were established based on the SPC limitations and parameters. Both the SPC parameters of the CEAs and the risk of PIs were visualized according to the interaction test results to obtain a better understanding of the population pharmaceutical quality. Finally, an assessment strategy was built and applied to generic drug consistency assessment, process risk assessment and quality trend tracking. The strategy demonstrated in this study could help reveal quality consistency from the perspective of process control and process risk, and further show the recent development status of domestic pharmaceutical production processes. In addition, a process risk assessment and population quality trend tracking provide data-based information for approval. Not only can this information serve as a further basis for decision-making by the regulatory authority regarding early warnings, but it can also reduce some avoidable adverse reactions. With continuous addition of data, dynamic population pharmaceutical quality is meaningful for emergencies and decision-making regarding drug regulation.

Multi-residue method for the detection of 40 ß-lactam-antibiotics in vaccines by LC-MS/MS.

Antibiotics are widely used to treat bacterial infections during the process of vaccine production and storage resulting in antibiotic residues that can cause serious harm. A simple and sensitive method for residue analysis of 40 ß-lactam antibiotics was developed and validated for vaccines including inactivated enterovirus 71 vaccine (Vero cells), recombinant hepatitis B vaccine (Saccharomyces cerevisiae), and live attenuated varicella vaccine using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI- MS/MS). Samples were prepared with acetonitrile as the protein precipitant. LC separation was performed on a C18 column. These analytes were determined by LC-MS/MS operating multiple-reaction monitoring (MRM) scans in positive mode. The ranges for limits of detection (LOD) and quantification (LOQ) were as follows: 0.02-4 ng/dose (S/N ≥ 3) and 0.04-10 ng/dose in inactivated enterovirus 71 vaccine (Vero cells) and recombinant hepatitis B vaccine (Saccharomyces cerevisiae), 0.04-16 ng/dose and 0.2-20 ng/dose in live attenuated varicella vaccine. The ranges of recoveries of all antibiotics were 84.5%-108.2% in inactivated enterovirus 71 vaccine (Vero cells), 73%-108% in recombinant hepatitis B vaccine (Saccharomyces cerevisiae), and mostly 68.2%-107.8% in live attenuated varicella vaccine. This method simultaneously offers qualitative and quantitative analysis of multi-antibiotics in vaccines, which improves vaccine safety.

A colorimetric aptasensor for the simple and rapid detection of human papillomavirus type 16 L1 proteins.

In this study, a novel colorimetric aptasensor was developed for the rapid detection and visual screening of HPV16 L1 proteins using gold nanoparticles (AuNPs) and an RNA aptamer against HPV16 L1 protein (APTHPV16 L1). The AuNP-APTHPV16 L1 conjugates could be aggregated by the addition of a salt in the presence of HPV16 L1 proteins at the ppb level. At the same time, the surface plasma resonance absorption peaks of AuNPs shifted to a short wavelength, and an observable change in color from red to blue occurred. The relative absorbance (Ablank - Asample/Ablank) at 520 nm exhibited a stable response to HPV16 L1 proteins over a concentration range from 9.6 to 201.6 ng mL-1. The visual detection limit of HPV16 L1 proteins was found to be 9.6 ng mL-1. Finally, the proposed colorimetric aptasensor was successfully applied for the rapid and effective detection of HPV16 L1 proteins in clinical samples and vaccine samples. The validity and reliability of the proposed colorimetric aptasensor were verified by the enzyme-linked immunosorbent assay method. The proposed colorimetric aptasensor provided a promising indicator for screening and quantitative detection of HPV16 L1 proteins in clinical samples.

Identification of Multi-Class Drugs Based on Near Infrared Spectroscopy and Bidirectional Generative Adversarial Networks.

Drug detection and identification technology are of great significance in drug supervision and management. To determine the exact source of drugs, it is often necessary to directly identify multiple varieties of drugs produced by multiple manufacturers. Near-infrared spectroscopy (NIR) combined with chemometrics is generally used in these cases. However, existing NIR classification modeling methods have great limitations in dealing with a large number of categories and spectra, especially under the premise of insufficient samples, unbalanced samples, and sensitive identification error cost. Therefore, this paper proposes a NIR multi-classification modeling method based on a modified Bidirectional Generative Adversarial Networks (Bi-GAN). It makes full utilization of the powerful feature extraction ability and good sample generation quality of Bi-GAN and uses the generated samples with obvious features, an equal number between classes, and a sufficient number within classes to replace the unbalanced and insufficient real samples in the courses of spectral classification. 1721 samples of four kinds of drugs produced by 29 manufacturers were used as experimental materials, and the results demonstrate that this method is superior to other comparative methods in drug NIR classification scenarios, and the optimal accuracy rate is even more than 99% under ideal conditions.

A strategy for population pharmaceutical quality assessment based on quality by design / 药物分析学报

From a regulatory perspective,drug quality consistency evaluation must concern different processes used for the same drug.In this study,an assessment strategy based on quality by design(QbD)was developed for population pharmaceutical quality evaluation.A descriptive analysis method based on QbD concept was first established to characterize the process by critical evaluation attributes(CEAs).Then quantitative analysis method based on an improved statistical process control(SPC)method was established to investigate the process indicators(PIs)in the process population,such as mean distri-bution,batch-to-batch difference and abnormal quality probability.After that rules for risk assessment were established based on the SPC limitations and parameters.Both the SPC parameters of the CEAs and the risk of PIs were visualized according to the interaction test results to obtain a better understanding of the population pharmaceutical quality.Finally,an assessment strategy was built and applied to generic drug consistency assessment,process risk assessment and quality trend tracking.The strategy demon-strated in this study could help reveal quality consistency from the perspective of process control and process risk,and further show the recent development status of domestic pharmaceutical production processes.In addition,a process risk assessment and population quality trend tracking provide data-based information for approval.Not only can this information serve as a further basis for decision-making by the regulatory authority regarding early warnings,but it can also reduce some avoidable adverse reactions.With continuous addition of data,dynamic population pharmaceutical quality is meaningful for emergencies and decision-making regarding drug regulation.

Water-soluble fluorescent sensor for Zn2+ with high selectivity and sensitivity imaging in living cells.

A new water-soluble 4-amino-1, 8-naphthalimide based fluorescent sensor, with iminoacetic acid and iminoethoxyacetic acid as receptor contained two different arms, was developed. Under physiological pH conditions, it demonstrates good water solubility, high selectivity and sensitivity for sensing Zn2+ with about 20-fold enhancement in aqueous solution, with a characteristic emission band of 4-amino-1, 8-naphthalimide with a green color centered at 550 nm. It was applied successfully to detect Zn2+ in living cells.

Competitive adsorption on gold nanoparticles for human papillomavirus 16 L1 protein detection by LDI-MS.

The detection of the HPV L1 protein provides information about the infection status of the virus, reflects the replication status of the HPV virus in cervical cells, and helps understand the regression and progress of cervical lesions. Herein, we report a novel laser desorption ionization mass spectrometry (LDI MS) method for the sensitive detection of the HPV 16 L1 protein, based on non-covalent competitive adsorption between the HPV 16 L1 aptamer and melamine on gold nanoparticles (AuNPs). The intensity of the MS signal corresponding to the mass tag shows a linear relationship with the HPV 16 L1 concentration in the range 2-80 ng mL-1, with a limit of detection (LOD) of 58.8 pg mL-1. Using this method, the HPV 16 L1 protein is quantitatively analyzed in both clinical and vaccine samples. The described method is simple and has high sensitivity and good reliability.

Mass Spectrometry Genotyping of Human Papillomavirus Based on High-Efficiency Selective Enrichment of Nanoparticles.

This work developed a novel spermine-modified nanodiamonds (SP-NDs)-based method to selectively enrich oligonucleotides for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of human papillomavirus (HPV) virus. Our results showed that SP-NDs can effectively extract and enrich DNA oligonucleotides from sodium dodecyl sulfonate and urea solution. In addition, SP-NDs can also selectively extract oligonucleotides from enzymes digestion products of polymerase chain reaction-restriction fragment mass polymorphism (PCR-RFMP) of HPV virus. Then, the extract can be detected by MALDI-TOF MS directly without further purification. According to the MS results, the HPV genotyping can be achieved. More importantly, with SP-NDs extraction, clinical samples infected with HPV genotype 16 and 18 can be identified. The described method shows great advantages of simplicity, high selectivity, and good reliability in real clinical samples. Due to our methods improvement on DNA enrichment, extraction and purification, the PCR-based MALDI-TOF MS for the analysis of oligonucleotides maybe become more rapid, sensitive, and high-throughput, is promising for analysis for DNA methylation, single-nucleotide polymorphisms, and other virus typing.

Role of microRNA 146a on the healing of cornea alkali burn treated with mesenchymal stem cells.

The aim of the present study was to investigate the effect of microRNA 146a (miR146a) on promoting the repair of corneal alkali burn with bone marrow mesenchymal stem cells (MSCs). A total of 24 Sprague­Dawley female rats were divided into a normal group (Control), a normal MSC treatment group (Normal MSCs), an miR146a knockout MSC treatment group (miR146a­low MSCs) and an miR146a high­expression MSC treatment group (miR146a­high MSCs) according to the random number table. Quantitative polymerase chain reaction was used to evaluate the expression levels of miR146a. MTT assay was performed to measure the cell viability of mesenchymal stem cells (MSCs) and apoptosis was measured by flow cytometry. The expression levels of p65 nuclear factor (NF)­κB, proliferating cell nuclear antigen (PCNA) and Fas proteins were analyzed by western blotting. MSCs were tested for the secretion levels of vascular endothelial growth factor (VEGF), CD45, interferon (IFN)­Î³ and interleukin (IL)­10 by ELISA. The miR146a­high MSCs improved cell viability of MSCs and inhibited apoptosis of MSCs following alkali burn. miR146a­high MSCs decreased the expression levels of p65NF­κB and PCNA, and enhanced the expression level of Fas. Furthermore, miR146a­high MSCs improved the cornea opacity and enhanced the inhibition of neovascularization in the rats following alkali burn. miR146a­high MSCs inhibit the expression of VEGF, CD45, IFN­Î³, while enhanced the expression of IL­10. Therefore, miR146a promotes the repair of corneal alkali burn in rats treated with MSCs.

Advances in rapid drug detection technology.

Spurious/Falsely-labeled/Falsified/Counterfeit (SFFC)drugs have become a major threat to public health, especially in rural areas of developing countries.The goal of this review is to provide an overview of rapid detection technologies for counterfeits recently reported, such as Near Infrared Spectroscopy, Near Infrared Chemical Imaging, Raman Spectroscopy, X-Ray Fluorescence, X-RayPowder Diffraction, Ion Mobility Spectrometry, Ion MobilityMass Spectrometry,Isotope Ratio Mass Spectrometry and visual analytical methods The advantages of each of these detection methods are introduced. Examples of characterization of SFFC drugs using the detection technology mentioned are presented. In addition, new characteristics and trends of SFFC drugs are listed and the solution is discussed.

The Outcomes of Minimally Invasive versus Open Posterior Approach Spinal Fusion in Treatment of Lumbar Spondylolisthesis: The Current Evidence from Prospective Comparative Studies.

Purpose. To investigate the evidence of minimally invasive (MI) versus open (OP) posterior lumbar fusion in treatment of lumbar spondylolisthesis from current prospective literatures. Methods. The electronic literature database of Pubmed, Embase, and Cochrane library was searched at April 2016. The data of operative time, estimated blood loss and length of hospital stay, visual analog scale (VAS) of both lower back pain and leg pain, Oswestry disability index (ODI), SF-36 PCS (physical component scores) and SF-36 MCS (mental component scores), complications, fusion rate, and secondary surgery were extracted and analyzed by STATA 12.0 software. Results. Five nonrandom prospective comparative studies were included in this meta-analysis. The meta-analysis showed that the MI group had a significantly longer operative time than OP group, less blood loss, and shorter hospital stay. No significant difference was found in back pain, leg pain, ODI, SF-36 PCS, SF-36 MCS, complications, fusion rate, and secondary surgery between MI and OP groups. Conclusion. The prospective evidence suggested that MI posterior fusion for spondylolisthesis had less EBL and hospital stay than OP fusion; however it took more operative time. Both MI and OP fusion had similar results in pain and functional outcomes, complication, fusion rate, and secondary surgery.