Learning Raw Image Denoising with Bayer Pattern Unification and Bayer Preserving Augmentation

In this paper, we present new data pre-processing and augmentation techniques for DNN-based raw image denoising. Compared with traditional RGB image denoising, performing this task on direct camera sensor readings presents new challenges such as how to effectively handle various Bayer patterns from different data sources, and subsequently how to perform valid data augmentation with raw images. To address the first problem, we propose a Bayer pattern unification (BayerUnify) method to unify different Bayer patterns. This allows us to fully utilize a heterogeneous dataset to train a single denoising model instead of training one model for each pattern. Furthermore, while it is essential to augment the dataset to improve model generalization and performance, we discovered that it is error-prone to modify raw images by adapting augmentation methods designed for RGB images. Towards this end, we present a Bayer preserving augmentation (BayerAug) method as an effective approach for raw image augmentation. Combining these data processing technqiues with a modified U-Net, our method achieves a PSNR of 52.11 and a SSIM of 0.9969 in NTIRE 2019 Real Image Denoising Challenge, demonstrating the state-of-the-art performance. Our code is available at https://github.com/Jiaming-Liu/BayerUnifyAug.Comment: Accepted by CVPRW 201

DeePMD-kit v2: A software package for Deep Potential models

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments.Comment: 51 pages, 2 figure

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Serum MiRNA Biomarkers serve as a Fingerprint for Proliferative Diabetic Retinopathy

Background: Diabetic retinopathy (DR) is a retinopathy resulting from diabetes mellitus (DM) which was classified into non-proliferative DR (NPDR) and proliferative DR (PDR). Without an early screening and effective diagnosis, patients with PDR will develop serious complications. Therefore, we sought to identify special serum microRNAs (miRNAs) that can serve as a novel non-invasive screening signature of PDR and test its specificity and sensitivity in the early diagnosis of PDR. Methods: In total, we obtained serum samples from 90 PDR cases, 90 matched NPDR patients and 20 controls. An initial screening of miRNA expression was performed through TaqMan Low Density Array (TLDA). The candidate miRNAs were validated by individual reverse transcription quantitative real-time PCR (RT-qPCR) arranged in an initial and a two-stage validation sets. Moreover, additional double-blind testing was performed in 20 patients clinically suspected of having DR to evaluate the diagnostic value and accuracy of the serum miRNA profiling system in predicting PDR. Results: Three miRNAs were significantly increased in patients with PDR compared with NPDR after the multiple stages. The areas under the receiver operating characteristic (ROC) curves of the validated three-serum miRNAs signature were 0.830, 0.803 and 0.873 in the initial and two validation sets, respectively. Combination of miR-21, miR-181c, and miR-1179 possessed a moderate ability to discrimination between PDR and NPDR with an area under ROC value of 0.89. The accuracy rate of the three-miRNA profile as PDR signature was 82.6%. Conclusions: These data provide evidence that serum miRNAs have the potential to be sensitive, cost-effective biomarkers for the early detection of PDR. These biomarkers could serve as a dynamic monitoring factor for detecting the progression of PDR from NPDR

Performance of multigene testing in cytologically indeterminate thyroid nodules and molecular risk stratification

Objective Thyroid cancer is the third most prevalent cancer among females. Genetic testing based on next-generation sequencing may provide an auxiliary diagnosis to reduce cytologically diagnostic uncertainty. However, commercial multigene tests are not widely available and are not well-tested in the Chinese population. Methods In this study, we designed a multigene testing panel and evaluated its performance in 529 cytologically indeterminate thyroid nodules (Bethesda III, IV and V). The molecular data of the DNA mutations and RNA fusions of fine needle aspiration samples were reviewed in conjunction with a clinical diagnosis, pathological reports, and definitive surgery for retrospective analysis. Then, the molecular risk stratification was investigated for its accuracy in malignant risk prediction. Results The overall combined consistency revealed substantial agreement (Kappa = 0.726) with the sensitivity, specificity, positive predictive value, and negative predictive values of 97.80%, 82.14%, 98.99%, and 67.65%, respectively. The most common aberration was BRAFV600E (82.59%), followed by NRAS mutants (4.07%), RET fusions (3.70%), and KRAS mutants (3.15%). Two cases (0.44%) were categorized into a high-risk group, 426 cases (94.67%) were categorized into a BRAF-like group with totally histopathologic papillary patterned tumors, and 22 cases (4.89%) were categorized into a RAS-like group with 14 papillary and eight follicular patterned tumors when the cohort concurrent aberrations were excluded. Potentially aggressive features may be related to concurrent molecular alterations of BRAFV600E with TERTQ302R, and AKT1L52R, NRASG12C, NRASQ61R, and CCDC6-RET fusions. Conclusions This study provided a multigene panel for identifying benign nodules from cytologically indeterminate thyroid nodules to avoid unnecessary surgery. We provide further evidence for using molecular risk stratification as a promising predictor of disease outcomes. The results of this study may be limited by the extremely high prevalence of cancer in the cohort for clinical reference

The PK–PD Relationship and Resistance Development of Danofloxacin against Mycoplasma gallisepticum in An In Vivo Infection Model

Mycoplasma gallisepticum is the causative agent of chronic respiratory disease (CRD), a prevalent disease of poultry, which is responsible for significant economic losses in farms. Although several antimicrobial agents are currently recommended for the treatment and prevention of M. gallisepticum infections, investigations of M. gallisepticum have been hampered by their fastidious growth requirements and slow growth rate. As such, little work has been conducted concerning the PK/PD relationship and mechanisms of antibiotic resistance between antimicrobials against M. gallisepticum. In the present study, danofloxacin was orally administrated to the infected chickens once daily for 3 days by an established in vivo M. gallisepticum infection model. Not only the concentrations of danofloxacin in plasma and lung tissues were analyzed, but also the counting of viable cells and changes in antimicrobial susceptibility in air sac and lung were determined. The PK and PD data were fitted by WinNonlin to evaluate the PK/PD interactions of danofloxacin against M. gallisepticum. PCR amplification of quinolone resistance-determining regions (QRDRs) and DNA sequencing were performed to identify point mutations in gyrA, gyrB, parC, and parE of the selected resistant mutant strains. In addition, susceptibility of enrofloxacin, ofloxacin, levofloxacin, gatifloxacin, and norfloxacin against these mutant strains were also determined. The PK profiles indicated that danofloxacin concentration in the lung tissues was higher than plasma. Mycoplasmacidal activity was achieved when infected chickens were exposed to danofloxacin at the dose group above 2.5 mg/kg. The ratios of AUC24/MIC (the area under the concentration-time curve over 24 h divided by the MIC) for 2 log10 (CFU) and 3 log10 (CFU) reduction were 31.97 and 97.98 L h/kg, respectively. Substitutions of Ser-83→Arg or Glu-87→Gly in gyrA; Glu-84→Lys in parC were observed in the resistant mutant strains that were selected from the dose group of 1 and 2.5 mg/kg. MICs of danofloxacin, enrofloxacin, ofloxacin, levofloxacin, gatifloxacin, and norfloxacin against the resistant mutant strains with a single mutation in position-83 were higher than that with a single mutation in position-87. These findings suggested that danofloxacin may be therapeutically effective to treat M. gallisepticum infection in chickens if administered at a dosage of 5.5 mg/kg once daily for 3 days

A qualitative study of user experience， knowledge and attitude of e-cigarette use in Shanghai

ObjectiveTo understand the experience， knowledge and attitudes of e-cigarette users in Shanghai， and to provide evidence for the development of intervention programs for e-cigarette use.MethodsThe Respondent-Driven Sampling （RDS） method was used to recruit 40 e-cigarette users for qualitative interviews from November 2020 to February 2021. NVivo （11.0） software was used to code interview records， and the thematic pattern and relationship analysis were conducted.ResultsIn terms of the reasons and user experience of e-cigarette use， most respondents used e-cigarettes for the first time after recommendation of friends； The reasons for the current use of e-cigarettes focus on the subjective feelings generated by the use of e-cigarettes （easy to use， replacing traditional tobacco， and having many flavors）. Compared with traditional tobacco use， respondents said e-cigarettes tasted good and had no physical impact （they could be used all the time without making them uncomfortable）. In terms of the awareness of e-cigarette use related knowledge， the respondents' opinions on whether e-cigarettes caused health risks were mostly based on their own experience of using them， and they said it was difficult to identify real information online. As for whether they were interested in relevant knowledge， most respondents said they wanted to learn about the professional knowledge related to e-cigarettes. Regarding the attitude related to the use of e-cigarettes， most respondents believed that e-cigarettes are addictive， e-cigarettes are not a safe alternative to traditional tobacco， and e-cigarettes couldn't help them quit smoking. Three out of ten respondents said they supported including e-cigarettes in the Regulation on Smoking Control in Public.ConclusionThere are certain characteristics of e-cigarette users' feelings， related knowledge and attitude towards e-cigarette use that should be targeted to carry out publicity， education and intervention

An Aerosol Optical Module With Observation‐Constrained Black Carbon Properties for Global Climate Models

Abstract Atmospheric black carbon (BC) aerosols have been long‐lasting uncertain components in environmental and climate studies. Global climate models (GCMs) potentially overestimate BC absorption efficiency due to a lack of consideration of complex BC microphysical and mixing properties. We extract multiple BC properties from observations and develop an aerosol optical module known as Advanced Black Carbon (ABC) in the framework of the Modal Aerosol Model version 4 (MAM4). The ABC module is implemented in the Community Atmosphere Model version 6 (CAM6) and evaluated by in situ and remote sensing observations. CAM6‐ABC addresses the shortcomings of CAM6‐MAM4 in terms of BC microphysical and mixing properties, particularly their size, mixing state and optical simulations. Sensitivity simulations show that the global BC absorption aerosol optical depth at 550 nm simulated by CAM6‐ABC is reduced by ∼29% compared with that in CAM6‐MAM4. The BC absorption enhancement simulated by CAM6‐ABC is reduced from ∼2.6 of the default MAM4 to ∼1.4, which is closer to the observed values (mostly less than 1.5). With improved BC absorption estimation, the biases of aerosol single‐scattering coalbedo simulations are reduced by 18%–69% compared with global Aerosol Robotic Network observations. Moreover, the globally averaged BC direct radiative effect is reduced from 0.37 to 0.28 W/m2 at the top of the atmosphere. Our new scheme alleviates the overestimation of BC absorption in GCMs by constraining BC microphysical and mixing properties when assessing aerosol radiative and climate effects, and it can be easily implemented in most modal‐based aerosol modules of climate models