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1.	Beal, Jacob, et al. (author) Robust estimation of bacterial cell count from optical density 2020 In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1 Journal article (peer-reviewed)abstract Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
2.	Geng, Xin, et al. (author) Challenges and Strategies on Interphasial Regulation for Aqueous Rechargeable Batteries 2024 In: Advanced Energy Materials. - : Wiley-VCH Verlagsgesellschaft. - 1614-6832 .- 1614-6840. ; 14:12 Research review (peer-reviewed)abstract The practical application of aqueous rechargeable batteries faces several challenges due to the limited stability window of electrolytes and parasitic side reactions, such as corrosion, passivation, gas evolution, and co-intercalations. The solid electrolyte interphase (SEI) formed at the electrode/electrolyte interface plays a critical role in determining interfacial properties and battery performance. Efforts are being made to develop effective SEIs, functionalize interphase layers, and explore various aqueous hybrid electrolytes that facilitate SEI formation. This review highlights the role of interphasial structures in aqueous batteries. First, common issues encountered by aqueous batteries and specific characteristics of aqueous lithium-ion, sodium-ion, zinc-ion, and aluminum-ion batteries are outlined. Then the tactics used to improve cycle stability of aqueous batteries are introduced and compared and the working principles and key parameters from the context of interphasial modification are discussed. Finally, constructive insights and suggestions for developing high-performance batteries are offered, with a focus on SEI formation and interphase layer design.
3.	Jin, Ying-Hui, et al. (author) Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version) 2020 In: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1 Journal article (peer-reviewed)abstract The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
4.	Zhou, Lihua, et al. (author) Perceived professional benefits and their associated factors among Chinese registered nurses caring for women diagnosed with gynecological cancer 2023 In: European Journal of Oncology Nursing. - : Elsevier. - 1462-3889 .- 1532-2122. ; 66 Journal article (peer-reviewed)abstract ProposeRegistered nurses (RNs) are considered to be a major source of professional supportive care for women diagnosed with gynecological cancer (GC). This study described the level of perceived professional benefits and explored association between perceived professional benefits, sense of coherence (SOC), and coping strategies in Chinese RNs caring for women diagnosed with GC.MethodA cross-sectional survey was employed to collect data using the Nurses' Perceived Professional Benefits Questionnaire (NPPBQ), Sense of coherence scale (SOC-13), and Brief Coping Orientation to Problems Experienced (Brief COPE). The questionnaires were administered to 250 RNs in China. The correlations between NPPBQ, SOC-13, and Brief COPE were evaluated with Pearson's correlation coefficient. Multiple regression analysis was performed to assess the relative contribution of each possible factor in explaining variance in the increased NPPBQ.ResultsTotal score for NPPBQ was 142.4 (range 33.0–165.0). SOC, dysfunctional coping strategies, and problem-focused coping strategies were recognized as predictors of RNs' perceived professional benefit, while, emotion-focused coping strategies were not significantly associated with RNs’ perceived professional benefits.ConclusionsThe findings indicate that RNs who have high levels of SOC, dysfunctional coping strategies, and problem-focused coping strategies tend to experience more perceived professional benefit. These findings propose new perspectives for nursing managers to promote RNs' perceived professional benefit by helping RNs to find meaningfulness when caring for women diagnosed with GC, increasing RNs’ communication skills to improve their relationship with patients, and training RNs to use coping strategies effectively.
5.	Cheng, Hong, et al. (author) Home environment exposure and sick building syndrome (SBS) symptoms among adults in southern China : Health associations in 2010 and 2019 2024 In: Building and Environment. - : Elsevier. - 0360-1323 .- 1873-684X. ; 248 Journal article (peer-reviewed)abstract We studied time trends in home environment and sick building syndrome (SBS) symptoms in a repeat study in five cities in southern China. Moreover, we studied associations between home environment exposure and SBS symptoms. Parents from randomly selected day care centers were invited. One parent per family answered a questionnaire on the home environment and their own SBS symptoms. Data collection was performed in two surveys in 2010 and 2019 (27,292 participants in 2010 and 32,073 in 2019). We used two-level logistic regression to analyze health associations. Asthma decreased from 1.7% to 1.5% (P < 0.05) but allergic rhinitis increased from 6.5% to 16.4% (P < 0.001). All SBS symptoms decreased from 2010 to 2019 (all P < 0.001). Most aspects of the home environment improved from 2010 to 2019 but there were less cleaning, more cats, dogs, and urbanization in 2019. Redecoration, new furniture, and pests were associated with most types of SBS symptoms, similarly in 2010 and 2019. Environmental tobacco smoke (ETS) was associated with SBS symptoms in 2019 only. In conclusion, prevalence of SBS symptoms among young parents in southern China decreased from 2010 to 2019 but allergic rhinitis increased. Cockroaches, rats, mice, mosquitoes or flies can be consistent biological risk factors for SBS symptoms. Redecoration, buying new furniture and traffic air pollution are other risk factors for SBS symptoms. Daily cleaning, frequently putting bedding to sunshine, and having a fan in the bathroom can be protective factors. ETS is an emerging risk factor for SBS symptoms.
6.	Conti, David, V, et al. (author) Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction 2021 In: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 53:1, s. 65-75 Journal article (peer-reviewed)abstract Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84-5.29) for men of European ancestry to 3.74 (95% CI, 3.36-4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14-2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71-0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction. A meta-analysis of genome-wide association studies across different populations highlights new risk loci and provides a genetic risk score that can stratify prostate cancer risk across ancestries.
7.	Ding, Long Hua, et al. (author) Nanozymes regulated by nitrogen element: Mechanism, design, and application 2024 In: Advanced Powder Materials. - 2772-834X. ; 3:4 Research review (peer-reviewed)abstract Nanozymes, a category of nanomaterials endowed with enzyme-mimicking capabilities, have exhibited considerable potential across diverse application domains. This comprehensive review delves into the intricacies of regulating nanozymes through N elements, elucidating the mechanisms governing N element control in the design and application of these nanomaterials. The initial sections introduce the foundational background and significance of nanozymes. Subsequent exploration delves into the detailed discussion of N element regulation mechanisms on nanozymes, encompassing N vacancies, N doping, N coordination, and nitride. These regulatory pathways play an instrumental role in fine-tuning the catalytic activity and specificity of nanozymes. The review further scrutinizes practical applications of N element regulation on nanozymes, spanning sensing detection, infection therapy, tumor therapy, and pollutant degradation. In conclusion, it succinctly summarizes the current research findings and proposes future directions for development. This thorough investigation into the regulation of nanozymes by N elements anticipates precise control over their performance, thereby advancing the extensive utilization of nanozymes in the realms of biomedical and environmental applications.
8.	Du, Mulong, et al. (author) Cyp2a6 activity and cigarette consumption interact in smoking-related lung cancer susceptibility 2024 In: Cancer Research. - : American Association For Cancer Research (AACR). - 0008-5472 .- 1538-7445. ; 84:4, s. 616-625 Journal article (peer-reviewed)abstract Cigarette smoke, containing both nicotine and carcinogens, causes lung cancer. However, not all smokers develop lung cancer, highlighting the importance of the interaction between host susceptibility and environmental exposure in tumorigenesis. Here, we aimed to delineate the interaction between metabolizing ability of tobacco carcinogens and smoking intensity in mediating genetic susceptibility to smoking-related lung tumorigenesis. Single-variant and gene-based associations of 43 tobacco carcinogen–metabolizing genes with lung cancer were analyzed using summary statistics and individual-level genetic data, followed by causal inference of Mendelian randomization, mediation analysis, and structural equation modeling. Cigarette smoke–exposed cell models were used to detect gene expression patterns in relation to specific alleles. Data from the International Lung Cancer Consortium (29,266 cases and 56,450 controls) and UK Biobank (2,155 cases and 376,329 controls) indicated that the genetic variant rs56113850 C>T located in intron 4 of CYP2A6 was significantly associated with decreased lung cancer risk among smokers (OR = 0.88, 95% confidence interval = 0.85–0.91, P = 2.18 X 10-16), which might interact (Pinteraction = 0.028) with and partially be mediated (ORindirect = 0.987) by smoking status. Smoking intensity accounted for 82.3% of the effect of CYP2A6 activity on lung cancer risk but entirely mediated the genetic effect of rs56113850. Mechanistically, the rs56113850 T allele rescued the downregulation of CYP2A6 caused by cigarette smoke exposure, potentially through preferential recruitment of transcription factor helicase-like transcription factor. Together, this study provides additional insights into the interplay between host susceptibility and carcinogen exposure in smoking-related lung tumorigenesis.
9.	Farnocchia, Davide, et al. (author) International Asteroid Warning Network Timing Campaign: 2019 XS 2022 In: The Planetary Science Journal. - : Institute of Physics Publishing (IOPP). - 2632-3338. ; 3:7 Journal article (peer-reviewed)abstract As part of the International Asteroid Warning Network's observational exercises, we conducted a campaign to observe near-Earth asteroid 2019 XS around its close approach to Earth on 2021 November 9. The goal of the campaign was to characterize errors in the observation times reported to the Minor Planet Center, which become an increasingly important consideration as astrometric accuracy improves and more fast-moving asteroids are observed. As part of the exercise, a total of 957 astrometric observations of 2019 XS during the encounter were reported and subsequently were analyzed to obtain the corresponding residuals. While the timing errors are typically smaller than 1 s, the reported times appear to be negatively biased, i.e., they are generally earlier than they should be. We also compared the observer-provided position uncertainty with the cross-track residuals, which are independent of timing errors. A large fraction of the estimated uncertainties appear to be optimistic, especially when <0 2. We compiled individual reports for each observer to help identify and remove the root cause of any possible timing error and improve the uncertainty quantification process. We suggest possible sources of timing errors and describe a simple procedure to derive reliable, conservative position uncertainties.
10.	Fu, Xi, et al. (author) Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms 2020 In: mSystems. - : AMER SOC MICROBIOLOGY. - 2379-5077. ; 5:3 Journal article (peer-reviewed)abstract Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome composition and the associated environmental characteristics have not been characterized in hotel environments. We presented here the first continental-scale microbiome study of hotel rooms (n = 68) spanning Asia and Europe. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified in the same sequencing depth, but most fungal taxa showed a restricted distribution compared to bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for -80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbiome and 16 indoor and outdoor environmental characteristics. Fungal composition and absolute quantity showed concordant associations with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea, and visible mold, while fungal richness was negatively associated with heavy traffic (95% confidence interval [CI] = -127.05 to -0.25) and wall-to-wall carpet (95% CI = -47.60 to -3.82). Bacterial compositional variation was associated with latitude, quality of the interior, and floor type, while bacterial richness was negatively associated with recent redecoration (95% CI -179.00 to -44.55) and mechanical ventilation (95% CI = -136.71 to -5.12). IMPORTANCE This is the first microbiome study to characterize the microbiome data and associated environmental characteristics in hotel environments. In this study, we found concordant variation between fungal compositional variation and absolute quantity and discordant variation between community variation/quantity and richness. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.
11.	Guo, Jiawei, et al. (author) Bimetallic Sulfides with Vacancy Modulation Exhibit Enhanced Electrochemical Performance 2024 In: Advanced Functional Materials. - 1616-3028 .- 1616-301X. ; In Press Journal article (peer-reviewed)abstract Transition bimetallic sulfides show significant promise for energy-related applications because of their plentiful active sites and synergistic redox activity. However, limited pore size and low-conductivity issues hinder their application. The structure of NiCo-S with rich sulfur vacancies is first predicted by density functional theory (DFT) calculations. Different sulfur vacancy concentrations are modeled by DFT calculations, and the results confirm that sulfur vacancies enhance the conductivity of the electrode material and are more beneficial for the adsorption of OH* species. It is verified by the differential charge density that the electric field formed on the surface of the electrode can lead to strong interfacial interactions by electron aggregation, which promotes electron/ion transfer kinetics. Furthermore, NiCo-S nanosheets are prepared on carbon cloth enriched with different concentrations of sulfur vacancies (denoted as NiCo-Sv-x, with x representing the concentration of sulfur vacancies) by sulfide etching NiCo-MOF and annealing under H2/Ar atmosphere. The NiCo-Sv-x electrodes obtained are applied to the cathode of supercapacitors and the anode of the oxygen evolution reaction. Through combining experimental and theoretical analysis, the effect of vacancy defect engineering on the electrochemical performance of the electrode materials is further confirmed. This work constructs transition metal sulfides with different sulfur vacancy concentrations through DFT model prediction and experimental validation, further confirming the effect of vacancy defect engineering on the electrochemical performance of electrode materials. Therefore, this modulation of sulfur vacancy concentration by vacancy defects contributes to the construction of electrode materials with excellent performance for energy applications.
12.	He, Li, et al. (author) Evolutionary origin and establishment of a dioecious diploid-tetraploid complex 2023 In: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 32:11, s. 2732-2749 Journal article (peer-reviewed)abstract Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants. Here we test the hypothesis that a stable sex-determination system and spatial/ecological isolation facilitate the establishment of dioecious polyploids. We determined the ploidy levels of 351 individuals from 28 populations of the dioecious species Salix polyclona, and resequenced 190 individuals of S. polyclona and related taxa for genomic diversity analyses. The ploidy survey revealed a frequency 52% of tetraploids in S. polyclona, and genomic k-mer spectra analyses suggested an autopolyploid origin for them. Comparisons of diploid male and female genomes identified a female heterogametic sex-determining factor on chromosome 15, which probably also acts in the dioecious tetraploids. Phylogenetic analyses revealed two diploid clades and a separate clade/grade of tetraploids with a distinct geographic distribution confined to western and central China, where complex mountain systems create higher levels of environmental heterogeneity. Fossil-calibrated phylogenies showed that the polyploids emerged during 7.6–2.3 million years ago, and population demographic histories largely matched the geological and climatic history of the region. Our results suggest that inheritance of the sex-determining system from the diploid progenitor as intrinsic factor and spatial isolation as extrinsic factor may have facilitated the preservation and establishment of polyploid dioecious populations.
13.	Hu, Jiwen, et al. (author) Rapid detection of mercury (II) ions and water content by a new rhodamine B-based fluorescent chemosensor 2020 In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy. - : PERGAMON-ELSEVIER SCIENCE LTD. - 1386-1425 .- 1873-3557. ; 241 Journal article (peer-reviewed)abstract A rhodamine B-based sensor (RS) was designed and synthesized by a combination of the spirolacton rhodamine B (fluorophore) and multidentate chelates (ionophore) with high affinity towards Hg2+. In the presence of Hg2+, the resulting red-orange fluorescence (under UV light) and naked eye red color of IDS are supposed to be used for quantitative and qualitative measurement of Hg2+. Further fluorescent titration and analysis demonstrate that RS can selectively detect Hg2+ within 1 s with a low limit of detection (LOD) of 16 nM in acetonitrile media, meanwhile, the association constant (K-a) was calculated to be 0.32 x 10(5) M-1. More importantly, the resultant complex (RSHg) of RS and Hg2+ has also been successfully applied to detect limited water content in acetonitrile solution. (C) 2020 Published by Elsevier B.V.
14.	Hu, Jiwen, et al. (author) Selective colorimetric detection of copper (II) by a protein-based nanoprobe 2021 In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy. - : PERGAMON-ELSEVIER SCIENCE LTD. - 1386-1425 .- 1873-3557. ; 252 Journal article (peer-reviewed)abstract In this work, we report a novel protein-based nanoprobe (PNP) that can be employed for quantitative analysis of Cu2+ in pure water medium and real samples. Structurally, the proposed nanoprobe comprises a biofriendly protein (hen egg-white lysozyme (HEWL)) and a Cu2+-specific chromogenic agent, where HEWL acts as a nanocarrier encapsulating a structurally tailored rhodamine B derivate. The resulting PNP exhibits a hydrodynamic diameter of similar to 106 nm and efficiently disperses in water, enabling the detection of Cu2+ in pure aqueous systems without the aid of any organic co-solvents. The high sensitivity and selectivity of PNP allow the colorimetric detection of Cu2+ in the presence of other metal interferents with a low detection limit of 160 nM. The satisfying recovery of trace level Cu2+ in environmental samples demonstrate the great potential of employing PNP for the determination of Cu2+ in actual applications. Most importantly, the simple co-grinding method employing proteins and chromogenic agents provides a novel strategy to generate sensing systems that are useful detection of pollutants in aqueous samples. (C) 2021 Elsevier B.V. All rights reserved.
15.	Kivipelto, Miia, et al. (author) World-Wide FINGERS Network : A global approach to risk reduction and prevention of dementia 2020 In: Alzheimer's & Dementia. - : Wiley. - 1552-5260 .- 1552-5279. ; 16:7, s. 1078-1094 Journal article (peer-reviewed)abstract Reducing the risk of dementia can halt the worldwide increase of affected people. The multifactorial and heterogeneous nature of late-onset dementia, including Alzheimer's disease (AD), indicates a potential impact of multidomain lifestyle interventions on risk reduction. The positive results of the landmark multidomain Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (FINGER) support such an approach. The World-Wide FINGERS (WW-FINGERS), launched in 2017 and including over 25 countries, is the first global network of multidomain lifestyle intervention trials for dementia risk reduction and prevention. WW-FINGERS aims to adapt, test, and optimize the FINGER model to reduce risk across the spectrum of cognitive decline-from at-risk asymptomatic states to early symptomatic stages-in different geographical, cultural, and economic settings. WW-FINGERS aims to harmonize and adapt multidomain interventions across various countries and settings, to facilitate data sharing and analysis across studies, and to promote international joint initiatives to identify globally implementable and effective preventive strategies.
16.	Li, Xin, et al. (author) Innovation of International Logistics Talent Training Mode in Applied Undergraduate Colleges and Universities Based on the ‘Belt and Road’ 2023 In: Advances in Artificial Systems for Medicine and Education VI. - Cham : Springer Nature. ; , s. 624-633 Conference paper (other academic/artistic)abstract Under the tide of world multi polarization and economic globalization, the internationalization of higher education has become the general trend. Implementing the ‘going out’ strategy and cultivating international logistics talents are the internal needs of Application-oriented Undergraduate Colleges and universities to adapt to the development trend of higher education, and also the internal needs of Application-oriented Undergraduate Colleges and universities to improve the level of running a school. At present, in terms of international logistics talent training, there are some problems in the undergraduate of application-oriented universities, such as the lack of international logistics talent training platform and funds, the lack of international teaching staff, and the imperfect teaching system of international logistics talent training. In view of these problems, this topic introduces the guiding ideology of the ‘the Belt and Road’ and builds an application-oriented undergraduate university, which can explore the cultivation of international logistics talents from the aspects of the construction of an international logistics talent training platform, giving full play to its own characteristics and advantages, improving the curriculum, teaching and evaluation system, and promoting the internationalization of professional construction, so as to continuously improve the cultivation level of international logistics talents.
17.	Liao, Hong, et al. (author) Genome-wide identification of resistance genes and response mechanism analysis of key gene knockout strain to catechol in Saccharomyces cerevisiae 2024 In: FRONTIERS IN MICROBIOLOGY. - 1664-302X. ; 15 Journal article (peer-reviewed)abstract Engineering Saccharomyces cerevisiae for biodegradation and transformation of industrial toxic substances such as catechol (CA) has received widespread attention, but the low tolerance of S. cerevisiae to CA has limited its development. The exploration and modification of genes or pathways related to CA tolerance in S. cerevisiae is an effective way to further improve the utilization efficiency of CA. This study identified 36 genes associated with CA tolerance in S. cerevisiae through genome-wide identification and bioinformatics analysis and the ERG6 knockout strain (ERG6 Delta) is the most sensitive to CA. Based on the omics analysis of ERG6 Delta under CA stress, it was found that ERG6 knockout affects pathways such as intrinsic component of membrane and pentose phosphate pathway. In addition, the study revealed that 29 genes related to the cell wall-membrane system were up-regulated by more than twice, NADPH and NADP(+) were increased by 2.48 and 4.41 times respectively, and spermidine and spermine were increased by 2.85 and 2.14 times, respectively, in ERG6 Delta. Overall, the response of cell wall-membrane system, the accumulation of spermidine and NADPH, as well as the increased levels of metabolites in pentose phosphate pathway are important findings in improving the CA resistance. This study provides a theoretical basis for improving the tolerance of strains to CA and reducing the damage caused by CA to the ecological environment and human health.
18.	Lin, Jianyan, et al. (author) Exploring the Limits of Transition-Metal Fluorination at High Pressures 2020 In: Angewandte Chemie - International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 59:23, s. 9155-9162 Journal article (peer-reviewed)abstract Fluorination is a proven method for challenging the limits of chemistry, both structurally and electronically. Here we explore computationally how pressures below 300 GPa affect the fluorination of several transition metals. A plethora of new structural phases are predicted along with the possibility for synthesizing four unobserved compounds: TcF7, CdF3, OsF8, and IrF8. The Ir and Os octaflourides are both predicted to be stable as quasi-molecular phases with an unusual cubic ligand coordination, and both compounds formally correspond to a high oxidation state of +8. Electronic-structure analysis reveals that otherwise unoccupied 6p levels are brought down in energy by the combined effects of pressure and a strong ligand field. The valence expansion of Os and Ir enables ligand-to-metal F 2p -> M 6p charge transfer that strengthens M-F bonds and decreases the overall bond polarity. The lower stability of IrF8, and the instability of PtF8 and several other compounds below 300 GPa, is explained by the occupation of M-F antibonding orbitals in octafluorides with a metal-valence-electron count exceeding 8.
19.	Lin, Zhipeng, et al. (author) Electrocatalyzed direct arene alkenylations without directing groups for selective late-stage drug diversification 2023 In: Nature Communications. - 2041-1723. ; 14:1 Journal article (peer-reviewed)abstract Electrochemistry has emerged as an increasingly viable tool in molecular synthesis. Here the authors realize electrocatalyzed C-H activations, with the aid of data science and artificial intelligence, towards selective alkenylations for late-stage drug diversifications. Electrooxidation has emerged as an increasingly viable platform in molecular syntheses that can avoid stoichiometric chemical redox agents. Despite major progress in electrochemical C-H activations, these arene functionalizations generally require directing groups to enable the C-H activation. The installation and removal of these directing groups call for additional synthesis steps, which jeopardizes the inherent efficacy of the electrochemical C-H activation approach, leading to undesired waste with reduced step and atom economy. In sharp contrast, herein we present palladium-electrochemical C-H olefinations of simple arenes devoid of exogenous directing groups. The robust electrocatalysis protocol proved amenable to a wide range of both electron-rich and electron-deficient arenes under exceedingly mild reaction conditions, avoiding chemical oxidants. This study points to an interesting approach of two electrochemical transformations for the success of outstanding levels of position-selectivities in direct olefinations of electron-rich anisoles. A physical organic parameter-based machine learning model was developed to predict position-selectivity in electrochemical C-H olefinations. Furthermore, late-stage functionalizations set the stage for the direct C-H olefinations of structurally complex pharmaceutically relevant compounds, thereby avoiding protection and directing group manipulations.
20.	Liu, Lin, et al. (author) Research progress in the application of MXene in bacterial detection and eradication 2024 In: Materials Today Physics. - 2542-5293. ; 43 Research review (peer-reviewed)abstract Infections stemming from pathogenic bacteria pose a notable menace to public health. Traditional strategies for bacterial detection and management frequently confront hurdles such as sensitivity constraints and antibiotic resistance. This review embarks on an exploration of the synthesis techniques and inherent structural traits of MXenes. An array of fabrication approaches spanning both top-down and bottom-up paradigms is meticulously examined. Subsequently, attention shifts to the formulation of bacterial detection sensors. Electrochemical, fluorescent, and dual-modal sensors are critically examined, elucidating how MXenes elevate the precision and sensitivity of bacterial detection. Notably, the potential for MXenes to identify chiral molecules is underscored. The segment dedicated to antibacterial mechanisms and applications dissects MXenes' effectiveness in eradicating bacterial agents. Mechanisms encompassing physical harm, photothermally-driven sterilization, and reactive oxygen species -induced sterilization are expounded upon. Additionally, the practical utilization of MXene-based nanomaterials in water purification and antibacterial interventions is succinctly outlined. Prospects on the horizon are evaluated, spotlighting the persistent trajectory of research and development in this dynamic sphere. Ultimately, at its essence, this comprehensive review offers a panoramic perspective of the substantial advancements achieved in MXene-based research for bacterial identification and eradication.
21.	Liu, Xin, et al. (author) Plasma metabolites mediate the association of coarse grain intake with blood pressure in hypertension-free adults 2020 In: Nutrition, Metabolism and Cardiovascular Diseases. - : Elsevier BV. - 0939-4753 .- 1590-3729. ; 30:9, s. 1512-1519 Journal article (peer-reviewed)abstract Increased intake of whole/coarse grains was associated with improved blood pressure control, but concurrent metabolism alterations are less clear. We sought to identify metabolomic profiles of blood pressure, and to explore their mediation effects on the coarse grain intake-blood pressure association among young adults free of hypertension. Methods and results: Plasma metabolome of 86 participants from the Carbohydrate Alternatives and Metabolic Phenotypes study was characterized by untargeted lipidomics and metabolomics using liquid chromatography–high-resolution mass spectrometry. We identified 24 and 117 metabolites associated with systolic blood pressure (SBP) and diastolic blood pressure (DBP), respectively, using random forest modeling and partial correlation analysis. Moreover, metabolite panels for highly specific prediction of blood pressure (8 metabolites for SBP and 11 metabolites for DBP) were determined using ten-fold cross-validated ridge regression (R2 ≥ 0.70). We also observed an inverse association between metabolite panel of SBP (β ± SE = −0.02 ± 0.01, P = 0.04) or DBP (β ± SE = −0.03 ± 0.01, P = 0.02) and coarse grain intake. Furthermore, we observed significant mediating effects of metabolites, in particular, sphingolipid ceramides, on the association between coarse grain exposure and blood pressure using both bias-corrected bootstrap tests and high-dimensional mediation analysis adapted for large-scale and high-throughput omics data. Conclusions: We identified metabolomic profiles specifically associated with blood pressure in young Chinese adults without diagnosed hypertension. The inverse association between coarse grain intake and blood pressure may be mediated by sphingolipid metabolites.
22.	Lu, Yingchang, et al. (author) Identification of Novel Loci and New Risk Variant in Known Loci for Colorectal Cancer Risk in East Asians 2020 In: Cancer Epidemiology, Biomarkers and Prevention. - : American Association for Cancer Research. - 1055-9965 .- 1538-7755. ; 29:2, s. 477-486 Journal article (peer-reviewed)abstract Background: Risk variants identified so far for colorectal cancer explain only a small proportion of milial risk of this cancer, particularly in Asians.Methods: We performed a genome-wide association study (GWAS) of colorectal cancer in East Asians, cluding 23,572 colorectal cancer cases and 48,700 controls. To identify novel risk loci, we selected 60 omising risk variants for replication using data from 58,131 colorectal cancer cases and 67,347 controls European descent. To identify additional risk variants in known colorectal cancer loci, we performed nditional analyses in East Asians.Results: An indel variant, rs67052019 at 1p13.3, was found to be associated with colorectal cancer risk P = 3.9 x 10(-8) in Asians (OR per allele deletion = 1.13, 95% confidence interval = 1.08-1.18). This sociation was replicated in European descendants using a variant (rs2938616) in complete linkage sequilibrium with rs67052019 (P = 7.7 x 10(-3)). Of the remaining 59 variants, 12 showed an association P < 0.05 in the European-ancestry study, including rs11108175 and rs9634162 at P < 5 x 10(-8) and o variants with an association near the genome-wide significance level (rs60911071, P = 5.8 x 10(-8); 62558833, P = 7.5 x 10(-8)) in the combined analyses of Asian- and European-ancestry data. In addition, ing data from East Asians, we identified 13 new risk variants at 11 loci reported from previous GWAS.Conclusions: In this large GWAS, we identified three novel risk loci and two highly suggestive loci for lorectal cancer risk and provided evidence for potential roles of multiple genes and pathways in the iology of colorectal cancer. In addition, we showed that additional risk variants exist in many colorectal ncer risk loci identified previously.Impact: Our study provides novel data to improve the understanding of the genetic basis for colorectal ncer risk.
23.	Mansouri, Kamel, et al. (author) CoMPARA : Collaborative Modeling Project for Androgen Receptor Activity 2020 In: Journal of Environmental Health Perspectives. - 0091-6765 .- 1552-9924. ; 128:2, s. 1-17 Journal article (peer-reviewed)abstract BACKGROUND: Endocrine disrupting chemicals (EDCs) are xenobiotics that mimic the interaction of natural hormones and alter synthesis, transport, or metabolic pathways. The prospect of EDCs causing adverse health effects in humans and wildlife has led to the development of scientific and regulatory approaches for evaluating bioactivity. This need is being addressed using high-throughput screening (HTS) in vitro approaches and computational modeling.OBJECTIVES: In support of the Endocrine Disruptor Screening Program, the U.S. Environmental Protection Agency (EPA) led two worldwide consortiums to virtually screen chemicals for their potential estrogenic and androgenic activities. Here, we describe the Collaborative Modeling Project for Androgen Receptor Activity (CoMPARA) efforts, which follows the steps of the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP).METHODS: The CoMPARA list of screened chemicals built on CERAPP's list of 32,464 chemicals to include additional chemicals of interest, as well as simulated ToxCast (TM) metabolites, totaling 55,450 chemical structures. Computational toxicology scientists from 25 international groups contributed 91 predictive models for binding, agonist, and antagonist activity predictions. Models were underpinned by a common training set of 1,746 chemicals compiled from a combined data set of 11 ToxCast (TM)/Tox21 HTS in vitro assays.RESULTS: The resulting models were evaluated using curated literature data extracted from different sources. To overcome the limitations of single-model approaches, CoMPARA predictions were combined into consensus models that provided averaged predictive accuracy of approximately 80% for the evaluation set.DISCUSSION: The strengths and limitations of the consensus predictions were discussed with example chemicals; then, the models were implemented into the free and open-source OPERA application to enable screening of new chemicals with a defined applicability domain and accuracy assessment. This implementation was used to screen the entire EPA DSSTox database of similar to 875,000 chemicals, and their predicted AR activities have been made available on the EPA CompTox Chemicals dashboard and National Toxicology Program's Integrated Chemical Environment.
24.	Ren, Luyao, et al. (author) Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance 2023 In: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1 Journal article (peer-reviewed)abstract BACKGROUND: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome.RESULTS: We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data.CONCLUSIONS: The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
25.	Tian, Songsong, et al. (author) Continuous transfer of neural network representational similarity for incremental learning 2023 In: Neurocomputing. - Amsterdam : Elsevier. - 0925-2312 .- 1872-8286. ; 545 Journal article (peer-reviewed)abstract The incremental learning paradigm in machine learning has consistently been a focus of academic research. It is similar to the way in which biological systems learn, and reduces energy consumption by avoiding excessive retraining. Existing studies utilize the powerful feature extraction capabilities of pre-trained models to address incremental learning, but there remains a problem of insufficient utilization of neural network feature knowledge. To address this issue, this paper proposes a novel method called Pre-trained Model Knowledge Distillation (PMKD) which combines knowledge distillation of neural network representations and replay. This paper designs a loss function based on centered kernel alignment to transfer neural network representations knowledge from the pre-trained model to the incremental model layer-by-layer. Additionally, the use of memory buffer for Dark Experience Replay helps the model retain past knowledge better. Experiments show that PMKD achieved superior performance on various datasets and different buffer sizes. Compared to other methods, our class incremental learning accuracy reached the best performance. The open-source code is published athttps://github.com/TianSongS/PMKD-IL. © 2023 The Author(s)

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