bluuebunny/crossref_metadata_2025 huggingface dataset:
The critical BMI hypothesis for puberty initiation and the gender prevalence difference: Evidence from an epidemiological survey in Beijing, China
Authors: Liu Meijuan , Cao Bingyan , Luo Qipeng , Wang Qiao , Liu Min , Liang Xuejun , Wu Di , Li Wenjing , Su Chang , Chen Jiajia , Gong Chunxiu
Published: October 2022

Background

Although previous studies suggested that there is a certain level of body fat mass before puberty can be initiated, most studies have focused on girls.

Objective

To investigate the relationship between precocious puberty and physical growth in school-aged children in Beijing, China.

Methods

7590 Chinese children (3591 girls and 3999 boys) aged 6–11 years were recruited in Beijing, China. Body mass index (BMI) categories were defined by WHO Child Growth Standards and central obesity were defined by sex-specific waist-to-height ratio cut-offs (≥0.46 for girls, ≥0.48 for boys). Sexual development was assessed using Tanner criteria.

Results

The prevalence of general obesity and central obesity among boys was higher than that in girls. Girls had a significantly higher precocious puberty rate than boys (5.93% vs. 0.87%), particularly in those aged 7 years old (9.20%). Children in the general obesity and central obesity groups have a higher prevalence of precocious puberty and earlier median ages for the attainment of Tanner B2/T2. For girls with Tanner stages≥II at 6-year-old and 7-year-old, the mean BMI was equivalent to the 50th centile of a normal 9.9-year-old and 11.9-year-old girl, respectively. The mean BMI of boys with Tanner stages≥II at 7-year-old and 8-year-old was correspondent to the 50th centile of a normal 14-year-old and 15.3-year-old boy, respectively. For girls, general obesity appears to contribute to the risk of the development of precocious puberty to a greater extent than central obesity does. For boys, central obesity, but not general obesity, was an independent risk factor for precocious puberty.

Conclusions

The prevalence of childhood obesity and precocious puberty was high in China. Precocious puberty was correlated with a large BMI. Boys had a higher threshold of BMI for puberty development than girls. Children with precocious puberty, particularly those with central obesity, should be aware of adverse cardiovascular events.
Pet cats, the better sentinels for indoor organic pollutants
Authors: Ma Tingting , Wu Peng , Ding Zhengman , Wang Tiantian , Luo Yongming
Published: October 2022

Pets are the most intimate companions of humans, as pets and people share most of their lives indoors. Based on the connections between pet animals, humans, and the environment, pet cats and dogs are often recommended as sentinels for the detection of environmental contaminants and for comorbidity tracking. However, their suitability as sentinels is yet to be established. Persistent organic pollutants and environmental hormones have replaced particulate matter (PM2.5) and volatile organic compounds (VOCs) in causing indoor air pollution. This review summarises the differences in the types and concentrations of indoor organic environmental pollutants detected in pet dogs and cats. This includes an analysis of the main exposure routes of different types of pollutants. To identify which of the two pet species are better sentinels, cats and dogs were compared based on their metabolic capacities of various indoor organic pollutants. In addition to PM2.5, a range of organic compounds including polychlorinated biphenyls, polybrominated diphenyl ethers (PBDEs), bromophenols, perfluoroalkyl substances, organochlorine pesticides, fungicides, polycyclic aromatic hydrocarbons, phthalic acid esters, organophosphate pesticides, organophosphorus flame retardants, and melamine have been detected in both dogs and cats. Pets often accumulate PBDEs from dust; however, traces of PBDEs are present in their diet. The indoor pollutant contamination levels in internal cats were generally higher than those in dogs. Cats accumulate organic pollutants associated with indoor environments, but they are sensitive to their toxicity because, unlike dogs, cats cannot metabolise most of the accumulated pollutants. Moreover, cats share similar clinical symptoms of thyroid diseases in humans. Based on the above observations of detection of indoor organic pollutants, it could be said that cats are better sentinels than dogs.
Causes of the interdecadal transition in interannual variability of summertime intraseasonal rainfall over Southern China
Authors: Lu Wei , Zhu Yimin , Hu Yijia , Zhong Zhong , Ha Yao
Published: October 2022

This paper studies the interdecadal transition of interannual variability of summertime intraseasonal rainfall (SIR) over South China (SC). It is found that after the mid-1990s (1995/96), the interannual oscillation of SIR over SC has significantly enhanced. The inner connection and possible physical processes associated with the atmospheric intraseasonal oscillation (ISO) involved in the interdecadal transition of the interannual variability of SIR over SC are discussed. The results show that the “Silk Road” teleconnection wave trains distributed zonally across Eurasia from western Europe to northeastern China in the mid-to-high latitudes and the intraseasonal component of the western Pacific subtropical high (WPSH) are two major factors that control the increase of SIR interannual oscillation over SC after 1996. In the period after 1996, the low-frequency perturbation kinetic energy of the wave activity flux associated with the “Silk Road” teleconnection converges more significantly over SC. At the same time, note that the positive SIR anomaly years tend to be in the El Niño decaying phase, the eastward-propagating Kelvin waves triggered by the warm Indian ocean can promote the development of the western Pacific anticyclonic anomaly, which subsequently strengthens the WPSH effectively. The interannual variability of the WPSH east-west movement increases the low-level intraseasonal change of atmospheric circulation over SC. Low-level circulation anomalies in the low latitudes combined with the dispersion of Rossby wave energy in the mid-to-high latitudes eventually lead to an increased interannual variability of SIR over SC.
Effect of environmental tax reform on corporate green technology innovation
Authors: Zhang Chuan , Zou Cai Feng , Luo Wenbo , Liao Lamei
Published: October 2022

China has recently taken several measures to counter the environmental pollution caused by the crude model of past economic development. Among them, taxation has proved especially efficient. We take the Environmental Protection Tax Law, implemented on 1 January 2018, as a quasi-natural experiment to study the effect of environmental protection tax reform on corporate green technology innovation. We analyze data on Shanghai and Shenzhen A-share listed companies for 2013–2020. We find that raising the tax levy significantly promotes green innovation among enterprises. The promotion effect is more significant in state-owned enterprises, heavily polluting enterprises, and the eastern region. The findings of the full sample and subsample still hold after replacing the explanatory variables for stability testing. The effects vary significantly based on property rights, geography, and level of industry pollution. Nevertheless, environmental tax reform is an effective initiative toward environmental protection, even if the complexity of China’s economic environment reveals some variation in the effects of this policy reform. We make suggestions to address these differences for future studies.
Effects of drought and salt stress on seed germination of ephemeral plants in desert of northwest China
Authors: Lu Yuting , Liu Huiliang , Chen Yanfeng , Zhang Lan , Kudusi Kawushaer , Song Jihu
Published: October 2022

Seed germination is the most sensitive stage of plant life history. Studying its response to drought and salinity can analysis the response and adaptation characteristics of desert plants to the environment. In this experiment, the seeds of four common desert ephemeral plants in Xinjiang (Ixiolirion tataricum, Nepeta micrantha, Lepidium apetalum, and Plantago minuta) were used as materials. To study the germination characteristics of seeds under drought, we used salt stress, and coupled salt-drought stress under treatments and explored the germination recovery ability of rehydrated seeds after salt and drought stress treatments. The results showed that: (1) Under salt stress, the germination ability of four plant seeds was inhibited in different degrees. Overall, the degree of inhibition was proportional to the concentration of NaCl solution. (2) Drought stress slowed the seed germination process, and the greater the degree of stress, the more pronounced the slowdown; PEG treatment showed no significant effect on the germination of the four seeds at low concentrations and significant inhibition at medium and high concentrations. (3) The coupled salt-drought treatment significantly alleviated the stress effect of one factor and improved the germination characteristics of seeds. (4) Seeds that did not germinate under different concentrations of salt stress, drought stress, and coupled stresses rapidly recover germination when the stress was relieved or lifted. Ephemeral plants are sensitive to environmental changes, and this study aims to provide a reference basis for vegetation restoration and ecological rehabilitation in arid and semi-arid areas.
Forecasting wildfires in major forest types of India
Authors: Kale Manish P. , Mishra Asima , Pardeshi Satish , Ghosh Suddhasheel , Pai D. S. , Roy Parth Sarathi
Published: October 2022

Severity of wildfires witnessed in different parts of the world in the recent times has posed a significant challenge to fire control authorities. Even when the different fire early warning systems have been developed to provide the quickest warnings about the possible wildfire location, severity, and danger, often it is difficult to deploy the resources quickly to contain the wildfire at a short notice. Response time is further delayed when the terrain is complex. Early warning systems based on physics-based models, such as WRF-FIRE/SFIRE, are computationally intensive and require high performance computing resources and significant data related to fuel properties and climate to generate forecasts at short intervals of time (i.e., hourly basis). It is therefore that when the objective is to develop monthly and yearly forecasts, time series models seem to be useful as they require lesser computation power and limited data (as compared to physics-based models). Long duration forecasts are useful in preparing an efficient fire management plan for optimal deployment of resources in the event of forest fire. The present research is aimed at forecasting the number of fires in different forest types of India on a monthly basis using “Autoregressive Integrated Moving Average” time series models (both univariate and with regressors) at 25 km × 25 km spatial resolution (grid) and developing the fire susceptibility maps using Geographical Information System. The performance of models was validated based on the autocorrelation function (ACF), partial ACF, cumulative periodogram, and Portmanteau (L-Jung Box) test. Both the univariate- and regressor-based models performed equally well; however, the univariate model was preferred due to parsimony. The R software package was used to run and test the model. The forecasted active fire counts were tested against the original 3 years monthly forecasts from 2015 to 2017. The variation in coefficient of determination from 0.94 (for year 1 forecast) to 0.64 (when all the 3-year forecasts were considered together) was observed for tropical dry deciduous forests. These values varied from 0.98 to 0.89 for tropical moist deciduous forest and from 0.97 to 0.88 for the tropical evergreen forests. The forecasted active fire counts were used to estimate the future forest fire frequency ratio, which has been used as an indicator of forest fire susceptibility.
The types of tumor infiltrating lymphocytes are valuable for the diagnosis and prognosis of breast cancer
Authors: Sun Ying , Zhang Chunyan
Published: October 2022

This study aimed at constructing a diagnostic immune risk score (dIRS) system and a prognostic immune risk score (pIRS) system for diagnose and prognosis of breast cancer (BC). The gene expression data of BC were downloaded from TCGA dataset (training set), and from GSE65194, GSE29044, GSE42568, and GSE20685 (validation sets). Then, the immune cell type proportions in each dataset were assessed using EPIC tool, and the dIRS system was built based on the SVM-RFE and RF-VIMP algorithms. Subsequently, the pIRS system and the nomogram survival model were established separately using penalized and rms packages. Finally, the differential expressed genes (DEGs) between low and high pIRS groups were screened, and submitted for functional analysis. The dIRS system consisted of B cells, CD8 + T cells, endothelial cells, NK cells, and other cells had high accuracy in distinguishing BC patients from the healthy controls (AUROC >0.7). Subsequently, the pIRS system with the five prognosis-associated immune-infiltrating cell was constructed, and Kaplan-Meier analysis demonstrated that the survival rate of low pIRS group was significantly higher than that of high pIRS group (p < 0.05). Based on age, pathologic stage and the pIRS values, the nomogram survival model was built. The AUROC value, Specificity value, Sensitivity value and C-index of the nomogram survival model were higher than 0.7000, and had a good predictive ability for BC. Finally, a total of 539 DEGs were identified, and significantly enriched in six pathways. The dIRS system and the pIRS system composed of immune cells might be critical for the diagnosis and prognosis of BC patients.
Immunogenic cell death mediation patterns reveal novel paradigm for characterizing the immune microenvironment and immunotherapeutic responses in bladder cancer
Authors: Fu Jialei , Zhang Wei , Jiang Tao
Published: October 2022

Background: Immunogenic cell death (ICD) plays an important role in several malignancies. However, the role of ICD-mediated patterns in bladder cancer (BCA) remains unknown.

Methods: For assessing the ICD-mediated patterns based on the expression of IRGs, 4 large BCA cohorts were obtained. The ICD-mediated patterns of individual samples were quantified as an ICD score by principal component analysis. The correlations of the ICD-mediated patterns with the tumor immune microenvironment (TIME) and responses to immunotherapy were comprehensively evaluated. The IRGs with predictive prognostic values were further validated by in vitro loss of function assays.

Results: Two distinct ICD-mediated patterns were established, showing distinct clinical features and immune microenvironment features. Although ICD cluster A was associated with a poor prognosis with a high ICD score, it showed an immune activation state with a more favorable response to immunotherapy and treatment that induced ICD. The ICD-related gene, CALR, was significantly upregulated in the T24 BCA cell line relative to the control SV-HUC-1 cells. Knocking down CALR suppressed T24 cell viability and caused ER stress.

Conclusion: We identified the existence of distinct ICD-mediated patterns in BCA closely associated with the remodeling of the TIME. Further in-depth examination of ICD-related features is warranted to obtain a broader prospect for therapeutic innovations and improved prognosis of BCA.
Comparison of pulmonary lesions using lung ultrasound and high-resolution computed tomography in adult patients with primary humoral immunodeficiencies
Authors: Ziętkiewicz Marcin , Buda Natalia , Więsik-Szewczyk Ewa , Piskunowicz Maciej , Grzegowska Dominika , Jahnz-Różyk Karina , Zdrojewski Zbigniew
Published: October 2022

Pulmonary involvement is the most common complication in patients with predominantly antibody deficiencies (PADs). Therefore, patients require repeated imaging tests. Unlike high-resolution computed tomography (HRCT), lung ultrasonography (LUS) does not expose patients to X-rays or contrast agents, and can be performed even at the bedside. This study aimed to evaluate lung lesions using simultaneous LUS and HRCT in a group of patients with PADs. Twenty-nine adult patients (13 women and 16 men) diagnosed with PADs according to the ESID criteria (23 Common variable immunodeficiency, 2 X-linked agammaglobulinemia, 2 IgG subclass deficiencies, and 2 Unspecified hypogammaglobulinemia) were included in the study. The mean age was 39.0 ± 11.9 years. The mean time elapsed between the first symptoms of PADs and the examination was 15.4 ± 10.1 years. Lung ultrasonography and high-resolution computed tomography were performed simultaneously according to a defined protocol during the clinic visits. In both examinations, lesions were compared in the same 12 regions: for each lung in the upper, middle, and lower parts, separately, front and back. A total of 435 lesions were described on LUS, whereas 209 lesions were described on HRCT. The frequencies of lesions in the lung regions were similar between LUS and HRCT. In both examinations, lesions in the lower parts of the lungs were most often reported (LUS 60.9% vs. HRCT 55.5%) and least often in the upper parts of the lungs (LUS 12.7% vs. HRCT 12.0%). The most frequently described lesions were LUS consolidations (99; 22.8%) and HRCT fibrosis (74; 16.5%). A statistically significant relationship was found in the detection of fibrosis in 11 of the 12 regions (phi = 0.4−1.0). Maximum values of the phi coefficient for the upper part of the left lung were recorded. Compared with HRCT, LUS is an effective alternative for evaluating and monitoring pulmonary lesions in adult patients with PADs, especially for pulmonary fibrosis.
H11-induced immunoprotection is predominantly linked to N-glycan moieties during Haemonchus contortus infection
Authors: Wang Chunqun , Liu Lu , Wang Tianjiao , Liu Xin , Peng Wenjie , Srivastav Ratnesh Kumar , Zhu Xing-Quan , Gupta Nishith , Gasser Robin B. , Hu Min
Published: October 2022

Nematodes are one of the largest groups of animals on the planet. Many of them are major pathogens of humans, animals and plants, and cause destructive diseases and socioeconomic losses worldwide. Despite their adverse impacts on human health and agriculture, nematodes can be challenging to control, because anthelmintic treatments do not prevent re-infection, and excessive treatment has led to widespread drug resistance in nematode populations. Indeed, many nematode species of livestock animals have become resistant to almost all classes of anthelmintics used. Most efforts to develop commercial anti-nematode vaccines (native or recombinant) for use in animals and humans have not succeeded, although one effective (dead) vaccine (Barbervax) has been developed to protect animals against one of the most pathogenic parasites of livestock animals –Haemonchus contortus(the barber’s pole worm). This vaccine contains native molecules, called H11 and H-Gal-GP, derived from the intestine of this blood-feeding worm. In its native form, H11 alone consistently induces high levels (75-95%) of immunoprotection in animals against disease (haemonchosis), but recombinant forms thereof do not. Here, to test the hypothesis that post-translational modification (glycosylation) of H11 plays a crucial role in achieving such high immunoprotection, we explored the N-glycoproteome and N-glycome of H11 using the high-resolution mass spectrometry and assessed the roles of N-glycosylation in protective immunity againstH. contortus. Our results showed conclusively that N-glycan moieties on H11 are the dominant immunogens, which induce high IgG serum antibody levels in immunised animals, and that anti-H11 IgG antibodies can confer specific, passive immunity in naïve animals. This work provides the first detailed account of the relevance and role of protein glycosylation in protective immunity against a parasitic nematode, with important implications for the design of vaccines against metazoan parasites.
B cells from anti-thyroid antibody positive, infertile women show hyper-reactivity to BCR stimulation
Authors: Serény-Litvai Timea , Bajnok Anna , Temesfoi Viktoria , Nörenberg Jasper , Pham-Dobor Greta , Kaposi Ambrus , Varnagy Akos , Kovacs Kalman , Pentek Sandor , Koszegi Tamas , Mezosi Emese , Berki Timea
Published: October 2022

Anti-thyroid antibody (ATA) positivity affects 1 out of 9 women in childbearing age and presents a significant risk for infertility. Emerging evidence indicates that alterations in the B cell receptor induced calcium (Ca2+) signaling could be key in the development of autoimmunity. We aimed to investigate the Ca2+flux response of B lymphocyte subsets to BCR stimulation in Hashimoto’s thyroiditis and related infertility. We collected peripheral blood samples from ATA+, infertile, euthyroid patients (HIE), hypothyroid, ATA+ patients before (H1) and after levothyroxine treatment (H2), and age-matched healthy controls (HC). All B cell subsets of ATA+, infertile, euthyroid patients showed elevated basal Ca2+level and hyper-responsivity to BCR ligation compared to the other groups, which could reflect altered systemic immune function. The Ca2+flux of hypothyroid patients was similar to healthy controls. The levothyroxine-treated patients had decreased prevalence of CD25+B cells and lower basal Ca2+level compared to pre-treatment. Our results support the role of altered Ca2+flux of B cells in the early phase of thyroid autoimmunity and infertility.
Single-cell mechanistic studies of radiation-mediated bystander effects
Authors: Han Xueqiong , Chen Yixuan , Zhang Nan , Huang Chengyu , He Guangyao , Li Ting , Wei Mengxin , Song Qiong , Mo Shaowen , Lv Yufeng
Published: October 2022

Ionizing radiation (IR) has been widely used in the diagnosis and treatment of clinical diseases, with radiation therapy (RT) being particularly rapid, but it can induce “bystander effects” that lead to biological responses in non-target cells after their neighboring cells have been irradiated. To help clarify how radiotherapy induces these effects, To help clarify how radiotherapy induces these effects, we analyzed single-cell RNA sequencing data from irradiated intestinal tissues on day 1 (T1 state), day 3 (T3 state), day 7 (T7 state), and day 14 (T14 state) after irradiation, as well as from healthy intestinal tissues (T0 state), to reveal the cellular level, molecular level, and involvement of different time irradiated mouse intestinal tissues in biological signaling pathways. In addition, changes in immune cell subpopulations and myeloid cell subpopulations after different radiation times were further explored, and gene regulatory networks (GRNs) of these cell subpopulations were constructed. Cellular communication between radiation-specific immune cells was explored by cell-to-cell communication events. The results suggest that radiotherapy trigger changes in immune cell subsets, which then reprogram the immune ecosystem and mediate systemic bystander effects. These radiation-specific immune cells participate in a wide range of cell-to-cell communication events. In particular, radiation-specific CD8+T cells appear to be at the core of communication and appear to persist in the body after recovery from radiotherapy, with enrichment analysis showing that radiation-specific CD8+ T cells are associated with ferroptosis. Thus, radiation-specific CD8+ T cells may be involved in cellular ferroptosis-mediated adverse effects caused by RT.
Fully understanding the efficacy profile of the COVID-19 vaccination and its associated factors in multiple real-world settings
Authors: Panahi Yunes , Einollahi Behzad , Beiraghdar Fatemeh , Darvishi Mohammad , Fathi Saeid , Javanbakht Mohammad , Shafiee Sepehr , Akhavan-Sigari Reza
Published: October 2022

We performed a review study according to recent COVID-19 vaccines’ real-world data to provide comparisons between COVID-19 vaccines regarding their relative efficacy. Although most vaccine platforms showed comparable effectiveness and efficacy, we highlight critical points and recent developments generated in studies that might affect vaccine efficacy including population-dependent effects of the vaccine (transplantation, adiposity, and specific comorbidities, as well as older age, male sex, ethnicity, and prior infection), vaccine type, variants of concern (VOC), and an extended vaccine schedule. Owing to these factors, community-based trials can be of great importance in determining vaccine effectiveness in a systematic manner; thus, uncertainty remains regarding vaccine efficacy. Long immune protection of vaccination with BNT162b2 or ChAdOx1 nCoV-19 has been demonstrated to be up to 61 months and 5–12 months after the previous infection, and boosting infection-acquired immunity for both the first and second doses of the BNT162b2 and ChAdOx1 nCoV-19 vaccines was correlated with high and durable protection. However, large cohort and longitudinal studies are required for the evaluation of immunity dynamics and longevity in unvaccinated, vaccinated, and infected individuals, as well as vaccinated convalescent individuals in real-world settings. Regarding the likelihood of vaccine escape variants evolving, an ongoing examination of the protection conferred against an evolving virus (new variant) by an extended schedule can be crucial.
The anti-aging effects of Renshen Guben on thyrotoxicosis mice: Improving immunosenescence, hypoproteinemia, lipotoxicity, and intestinal flora
Authors: Feng Qin , Li Guangyan , Xia Wenkai , Dai Guoxin , Zhou Jidong , Xu Yan , Liu Deshan , Zhang Guimin
Published: October 2022

With the rapid aging of the population, the control of age-related disease susceptibility and prognosis faces greater challenges. There is an urgent need for a strategy to maintain the vitality of elderly people. In this study, the effect of Renshen Guben (RSGB) oral liquid was investigated on an accelerated aging mice model of thyrotoxicosis by conventional detection methods combined with multiomics technology. The results showed that RSGB increased the number of neutrophils and lymphocytes, enhanced the function of lymphocytes, and increased the levels of complement and antimicrobial peptides, which indicated that RSGB improved the immunity of thyrotoxicosis mice at the cellular and molecular levels. RSGB corrected malnutrition in thyrotoxicosis mice by improving anemia, hypoalbuminemia, ion transporters, and vitamin-binding proteins. RSGB significantly reduced the lipotoxicity by reducing the level of fatty acids, triglyceride, sphingolipids, and glucocorticoids, thus increasing the level of docosapentaenoic acid (DPA) and bile acids, which contributed to improve immunosenescence. The intestinal defense ability of thyrotoxicosis mice was enhanced with the increase of bile acids and lactic acid bacteria by the RSGB treatment. The plant metabolomics analysis showed that there were various active components in RSGB oral liquid and medicated serum, including terpenoids, phenolic acids, flavonoids, tannin, alkaloids, organic acids, phenolamines, amino acids, and others. They have antioxidant, immune regulation, and anti-aging effects, which was the material basis of RSGB. Totally, RSGB protected the thyrotoxicosis mice against aging by improving immunosenescence, hypoproteinemia, lipotoxicity, and the intestinal flora. It will be beneficial for improving the disease susceptibility and prognosis of the elderly.
Mesozooplankton biodiversity, vertical assemblages, and diel migration in the western tropical Pacific Ocean revealed by eDNA metabarcoding and morphological methods
Authors: Feng Yunzhi , Sun Dong , Shao Qianwen , Fang Chen , Wang Chunsheng
Published: October 2022

Zooplankton plays a crucial role in marine ecosystems. However, due to issues with morphological identification and sampling methods, knowledge of their biodiversity and community structure in the vast pelagic zone of the western tropical Pacific Ocean is still limited compared with other areas in the North Pacific Ocean. In this study, we used environmental DNA (eDNA) metabarcoding and morphological identification approaches to investigate mesozooplankton’s biodiversity and vertical assemblages in the western tropical Pacific Ocean from the surface to 1000 m deep. Two different barcodes were used in metabarcoding: mitochondrial cytochrome oxidase I (COI) and small subunit ribosomal RNA genes (18S). Our results showed that eDNA metabarcoding revealed 2-4 times more medusae taxa than morphological processing. Both methods detected that small copepod species were dominant in the community and six of the top-10 most abundant copepod genera overlapped. Morphological results showed that mesozooplankton communities were classified into three groups: epipelagic (0–200 m), upper mesopelagic (200-500 m), and lower mesopelagic (500–1000 m). And eDNA results showed distinct vertical variations of mesozooplankton communities within the epipelagic. Both methods showed that the dominant genera Clausocalanus, Paracalanus, and Calocalanus exhibited diel patterns in relative abundance, demonstrating that the eDNA method can capture diel vertical migration (DVM) signals of copepods. Overall, our results indicate that eDNA metabarcoding is an effective and efficient tool for the study and monitoring of mesozooplankton diversity and vertical assemblages in the open sea.
Rhodolith beds and their onshore transport in Fuerteventura Island (Canary Archipelago, Spain)
Authors: Rebelo Ana Cristina , Martín-González Esther , Melo Carlos S. , Johnson Markes E. , González-Rodríguez Alberto , Galindo Inés , Quartau Rui , Baptista Lara , Ávila Sérgio P. , Rasser Michael W.
Published: October 2022

Rhodoliths occur extensively around the shores of Fuerteventura Island in the Canary Archipelago, with Lithothamnion cf. corallioides being the most prominent species. A large number of rhodoliths end up washed onshore, the debris from which contributes to the formation of sediments constituting modern beaches. In a previous study by one of the co-authors (MEJ), the northern coast of Fuerteventura was shown to comprise various types of rhodolith deposits such as beach, platform overwash, tidal pools, coastal dunes, and others. An extraordinary example of stranded rhodoliths is located near Caleta del Bajo de Mejillones, approximately 3 km west of Corralejo, on the north coast of the island. The deposit forms a supratidal beach 120 m long and 10 m wide that sits above the landward termination of an extensive wave-cut platform eroded in basalt and exposed at low tide to a width of 130 m perpendicular to shore. Here, rhodoliths are very small (<3 cm) resembling popcorn, and the locality is known as the “Popcorn Beach”. Other examples are berms up to 150 m long and 9 m wide at Caleta del Bajo de Mejillones, or an exposed beach at Playa del Hierro with an area of more than 1500 m2 covered entirely of very coarse rhodolith sand. Extensive living rhodolith beds were found at a water depth of 22 m.
Pharmacogenes that demonstrate high association evidence according to CPIC, DPWG, and PharmGKB
Authors: Alshabeeb Mohammad A. , Alyabsi Mesnad , Aziz Mohammad A. , Abohelaika Salah
Published: October 2022

Background

Different levels of evidence related to the variable responses of individuals to drug treatment have been reported in various pharmacogenomic (PGx) databases. Identification of gene-drug pairs with strong association evidence can be helpful in prioritizing the implementation of PGx guidelines and focusing on a gene panel. This study aimed to determine the pharmacogenes with the highest evidence-based association and to indicate their involvement in drug-gene interactions.

Methodology

The publicly available datasets CPIC, DPWG, and PharmGKB were selected to determine the pharmacogenes with the highest drug outcome associations. The upper two levels of evidence rated by the three scoring methods were specified (levels A–B in CPIC, 3–4 in DPWG, or 1–2 levels in PharmGKB). The identified pharmacogenes were further ranked in this study based on the number of medications they interacted with.

Results

Fifty pharmacogenes, with high to moderately high evidence of associations with drug response alterations, with potential influence on the therapeutic and/or toxicity outcomes of 152 drugs were identified. CYP2D6, CYP2C9, CYP2C19, G6PD, HLA-B, SLCO1B1, CACNA1S, RYR1, MT-RNR1, and IFNL4 are the top 10 pharmacogenes, where each is predicted to impact patients' responses to ≥5 drugs.

Conclusion

This study identified the most important pharmacogenes based on the highest-ranked association evidence and their frequency of involvement in affecting multiple drugs. The obtained data is useful for customizing a gene panel for PGx testing. Identifying the strength of scientific evidence supporting drug-gene interactions aids drug prescribers in making the best clinical decision.
One-stage laparoscopy combined with resectoscope in the treatment of huge bladder diverticulum, multiple stones in diverticulum, multiple stones in bladder and benign prostatic hyperplasia: A case report
Authors: Zhengqiang Wan , Yinglei Wang , Cheng Li , Dongbing Zheng
Published: October 2022

Background

Bladder diverticulum is due to the abnormal arrangement of congenital bladder wall muscle fibers, weak limitations, combined with lower urinary tract obstruction, increased intravesical pressure, and protruding between the self-separated detrusor muscle bundles of the bladder wall. Giant bladder diverticulum refers to 10*8 cm or diverticulum over 150 ml in volume.

Case summary

An 80-year-old male patient was admitted to our hospital on August 14, 2020, the preoperative diagnosis was: bladder diverticulum, bladder diverticulum calculi, multiple bladder stones and prostatic hyperplasia. On August 18, 2020, one-stage laparoscopic bladder diverticulectomy + diverticulum neck incision for stone removal + cystopuncture fistula + transurethral bladder stone removal + transurethral resection of the prostate (TURP) under general anesthesia. First, the bladder diverticulum was separated under laparoscopy, the diverticulum was incised, the diverticulum calculi were taken out, and then the diverticulum was completely removed, and the neck of the diverticulum was extended by 1.5 cm, and the large calculus of about 2.7*3.6 cm was completely removed, and then cystostomy + transurethral Bladder stone removal + TURP. There was no bleeding from the bladder suture during the operation. 200 ml of urine was drained from the extraperitoneal drainage tube, and 20 ml of urine was drained from the abdominal drainage tube during the operation, the urination is smooth, and the general condition can be discharged. The patient’s general condition is good after follow-up.

Conclusion

One-stage laparoscopic treatment of bladder diverticulectomy + diverticulum neck incision for stone extraction + cystopuncture fistula + transurethral bladder stone extraction + TURP surgery. There is no report at home and abroad, which can provide diagnosis and treatment ideas and surgical methods for urological colleagues to deal with such diseases.
Age-dependent changes in fat- and water-soluble vitamins—National Health and Nutrition Examination Surveys study
Authors: Tomasiuk Ryszard , Zubrzycki Igor Z. , Wiacek Magdalena
Published: October 2022

Aging is an independent risk factor for the development of various diseases associated, among others, with detrimental blood levels of fat- and water-soluble vitamins. Thus, the objective of this study is to investigate age-related changes in blood levels of vitamin A, B12, C, D, and E. Subject serum vitamin levels were obtained from the combined National Health and Nutrition Examination Surveys (NHANES). NHANESIII and NHANES 1999–2000, 2001–2002, 2003–2004, and 2005–2006. The raw data set was stratified into five age groups G1- G5: 20 ≤ G1 < 30, 30 ≤ G2 < 40, 40 ≤ G3 < 50, 50 ≤ G4 < 60, and 60 ≤ G5 < 70 years of age. Age stratified data was cleaned using the modified Horn algorithm. The reference range for the vitamin level of a specific age group was defined as data between the first and third quartile of the subject defined by normal blood pressure and normal bone density. Age-dependent changes in serum/plasma vitamin levels were assessed using the bootstrap technique with 10,000 repeats and Bonferroni adjustment. There was a continuous increase in vitamin A, B12, D, and E levels in the blood. However, the vitamin C concentration remained virtually constant in all age groups. There was a lack of cross-correlations between lipid and water-soluble vitamin levels and blood pressure and bone health. The following reference levels for vitamin A, B12, C, D, and E in subjects older than 20 years of age were established: vitamin A: 1.32–2.8 mmol/L, vitamin B12: 257.94–498.33 pmol/L, vitamin C: 38.18–79.2 mmol/L, vitamin D: 76.33–199.36 nmol/L and vitamin E: 3.65–41.12 μmol/L.
Periodontal disease in pregnancy and adverse pregnancy outcomes: Progress in related mechanisms and management strategies
Authors: Nannan Mi , Xiaoping Lin , Ying Jin
Published: October 2022

Periodontal disease is an inflammatory and destructive disease of tissues supporting the tooth. A large number of studies have confirmed that periodontal pathogens and their metabolites can lead to adverse pregnancy outcomes in direct or indirect ways. Adverse pregnancy outcomes, such as preterm birth, low birth weight, and pre-eclampsia, have a serious impact on human reproductive health. In recent years, although the level of global medical technology has gradually improved, the incidence of adverse pregnancy outcomes has not declined and is still a global public health problem. The purpose of this review is to summarize the current data on periodontal disease in pregnancy and adverse pregnancy outcomes, including the association between periodontal disease and adverse pregnancy outcomes, the pathogenic mechanism related to this association, the efficacy of different nutrition supplements for both periodontal disease and adverse pregnancy outcomes and the effect of providing periodontal treatment on the occurrence of adverse pregnancy outcomes, to provide guidance for the prevention and treatment of adverse pregnancy outcomes in clinical practice.
Biogenic propane production by a marine Photobacterium strain isolated from the Western English Channel
Authors: Currie Felicity , Twigg Matthew S. , Huddleson Nicholas , Simons Keith E. , Marchant Roger , Banat Ibrahim M.
Published: October 2022

Propane is a major component of liquefied petroleum gas, a major energy source for off-grid communities and industry. The replacement of fossil fuel-derived propane with more sustainably derived propane is of industrial interest. One potential production route is through microbial fermentation. Here we report, for the first time, the isolation of a marine bacterium from sediment capable of natural propane biosynthesis. Propane production, both in mixed microbial cultures generated from marine sediment and in bacterial monocultures was detected and quantified by gas chromatography–flame ionization detection. Using DNA sequencing of multiple reference genes, the bacterium was shown to belong to the genus Photobacterium. We postulate that propane biosynthesis is achieved through inorganic carbonate assimilation systems. The discovery of this strain may facilitate synthetic biology routes for industrial scale production of propane via microbial fermentation.
Long-term integrated soil-crop management improves soil microbial community structure to reduce GHG emission and increase yield
Authors: Yu Ningning , Liu Jiai , Ren Baizhao , Zhao Bin , Liu Peng , Gao Zheng , Zhang Jiwang
Published: October 2022

Integrated soil-crop management (ISCM) has been shown as an effective strategy to increase efficiency and yield while its soil microbial community structure and function remain unclear. We evaluated changes in soil physicochemical factors, bacterial community structure responses, and the contributions of soil properties and bacterial communities to summer maize-winter wheat yield and GHG emissions through an ISCM experiment [T1 (local smallholder farmers practice system), T2 (improved management system), T3 (high–yield production system), and T4 (optimized management system)], which could provide scientific guidance for sustainable development of soil in summer maize-winter wheat rotation system. The results showed that the optimized ISCM could improve the soil quality, which significantly changed the soil bacterial community structure to reduce GHG emissions and increase yield. The co-occurrence network density of T3 was increased significantly. The Acidobacteria (class) and OM190 (class) were enriched in T2 and T4. The Frankiales (order) and Gaiellales (order) were enriched in T3. However, the changes in different crop growth stages were different. At the wheat jointing stage and maize mature stage, T4 could enhance carbon-related functional groups, such as aromatic hydrocarbon degradation and hydrocarbon degradation, to increase the soil organic carbon content. And at the maize tasseling stage, T4 could enhance nitrogen-related functional groups. And soil bacteria structure and function indirectly affected annual yield and GHG emission. T2 and T4 exhibited a similar soil microbial community. However, the yield and nitrogen use efficiency of T2 were reduced compared to those of T4. The yield of T3 was the highest, but the GHG emission increased and soil pH and nitrogen use efficiency decreased significantly. Therefore, T4 was a suitable management system to improve soil quality and soil bacterial community structure and function to decrease GHG emissions and increase the yield of the summer maize-winter wheat rotation system.
Microbial communities associated with thermogenic gas hydrate-bearing marine sediments in Qiongdongnan Basin, South China Sea
Authors: Liu Siwei , Yu Shan , Lu Xindi , Yang Hailin , Li Yuanyuan , Xu Xuemin , Lu Hailong , Fang Yunxin
Published: October 2022

Biogenic and thermogenic gas are two major contributors to gas hydrate formation. Methane hydrates from both origins may have critical impacts on the ecological properties of marine sediments. However, research on microbial diversity in thermogenic hydrate-containing sediments is limited. This study examined the prokaryotic diversity and distributions along a sediment core with a vertical distribution of thermogenic gas hydrates with different occurrences obtained from the Qiongdongnan Basin by Illumina sequencing of 16S rRNA genes as well as molecular and geochemical techniques. Here, we show that gas hydrate occurrence has substantial impacts on both microbial diversity and community composition. Compared to the hydrate-free zone, distinct microbiomes with significantly higher abundance and lower diversity were observed within the gas hydrate-containing layers. Gammaproteobacteria and Actinobacterota dominated the bacterial taxa in all collected samples, while archaeal communities shifted sharply along the vertical profile of sediment layers. A notable stratified distribution of anaerobic methanotrophs shaped by both geophysical and geochemical parameters was also determined. In addition, the hydrate-free zone hosted a large number of rare taxa that might perform a fermentative breakdown of proteins in the deep biosphere and probably respond to the hydrate formation.
Duck plague virus US3 protein kinase phosphorylates UL47 and regulates the subcellular localization of UL47
Authors: Deng Liyao , Wan Jieyu , Cheng Anchun , Wang Mingshu , Tian Bin , Wu Ying , Yang Qiao , Ou Xumin , Mao Sai , Sun Di , Zhang Shaqiu , Zhu Dekang , Jia Renyong , Chen Shun , Liu Mafeng , Zhao Xinxin , Huang Juan , Gao Qun , Yu Yanling , Zhang Ling , Pan Leichang
Published: October 2022

Duck plague virus (DPV) belongs to the alphaherpesvirinae and causes high morbidity and mortality in waterfowl. UL47 is a large abundant structural protein in DPV, which means that UL47 protein plays an important role in virus replication. US3 protein, as a viral protein kinase in alphaherpesviruses, has been reported to be critical for DPV virion assembly. In this study, we over-expressed UL47 and US3 proteins and found that DPV UL47 protein was a phosphorylated substrate of US3 protein, which interacted and co-localized with US3 protein in the cytoplasm. US3-regulated phosphorylation of UL47 was important for the cytoplasmic localization of UL47 because non-phosphorylated UL47 was localized in the nucleus. The six sites of UL47 at Thr29, Ser30, Ser42, Thr47, Ser161, and Thr775 were identified as the phosphorylation targets of US3 protein. In vivo, UL47 phosphorylation was also detected but not in ΔUS3-infected cells. US3 protein promoted the cytoplasmic localization of UL47 at the late stage of infection, and the lack of US3 protein caused a delay in UL47 translocation to the cytoplasm. These results enhance our understanding of the functions of US3 during DPV infection and provide some references for DPV assembly.
Host DNA depletion can increase the sensitivity of Mycobacterium spp. detection through shotgun metagenomics in sputum
Authors: Kok Nienke A. , Peker Nilay , Schuele Leonard , de Beer Jessica L. , Rossen John W. A. , Sinha Bhanu , Couto Natacha
Published: October 2022

Identification and phenotypic drug-susceptibility testing for mycobacteria are time-consuming and challenging but essential for managing mycobacterial infections. Next-generation sequencing (NGS) technologies can increase diagnostic speed and quality, but standardization is still lacking for many aspects (e.g., unbiased extraction, host depletion, bioinformatic analysis). Targeted PCR approaches directly on sample material are limited by the number of targets that can be included. Unbiased shotgun metagenomics on direct material is hampered by the massive amount of host DNA, which should be removed to improve the microbial detection sensitivity. For this reason, we developed a method for NGS-based diagnosis of mycobacteria directly from patient material. As a model, we used the non-tuberculous mycobacterium (NTM) Mycobacterium abscessus. We first compared the efficiency of three different DNA extraction kits for isolating DNA (quality and concentration). The two most efficient kits were then used in a follow-up study using artificial sputum. Finally, one extraction kit was selected and further evaluated for DNA isolation from a patients’ sputum mixture spiked with M. abscessus at three concentrations (final concentrations 108, 107, 106  CFU/ml). The spiked sputum samples were processed with and without saponin treatment (ST) in combination with DNAse treatment prior to bacterial DNA extraction to evaluate the recovery of bacteria and depletion of host DNA by PCR and Illumina sequencing.

While Ct values of the qPCR targeting mycobacterial ITS DNA remained rather stable, Ct values in the qPCR targeting the human β-actin gene increased by five Ct values in ST samples. In subsequent Illumina sequencing, a decrease of 89% of reads mapped to the human genome was observed in ST samples. The percentage of reads mapped to M. abscessus (108 CFU/ml) increased by 89%, and the sequencing depth increased two times when undergoing ST.

In conclusion, the sensitivity of M. abscessus detection in artificial sputum was increased using a saponin pre-treatment step. The saponin followed by the DNase I treatment approach could be efficiently applied to detect and characterize mycobacterial infections, including tuberculosis, directly from sputum.