bluuebunny/crossref_metadata_2025 huggingface dataset:
Climatic Hazards: High Importance but Low Severity to Coastal Rural Fishing Communities
Authors: Koomson Daniel , Davies-Vollum Katherine Sian , Raha Debadayita
Published: July 2022

This study examines the relative importance and severity of climate change in the context of multiple socio-economic stressors in rural coastal fishing communities in Ghana. Although climate change poses significant threats to these communities, it is yet unclear where it fits in the range of stressors that shape the vulnerability of such communities. Without an understanding of how vulnerability is experienced by the fishing communities, it is difficult to appreciate what adaptation to climate change means to them and which adaptation options are realistic. Household surveys, interviews, gender and age-group disaggregated focus group discussions and participatory risk mapping were used to assess type, importance and severity of climatic and socio-economic stressors that impinge on the lives and livelihood of the fishing communities. Climatic stressors include erratic rainfall, increased storminess, flooding and high temperatures. Socio-economic stressors include infrastructural (e.g., water and energy insecurity), socio-cultural (e.g., conflicts and land insecurity), occupational (e.g., exploitation, power asymmetries, illegal fishing), and environmental (e.g., plastic waste pollution) factors. The participatory risk maps showed that climatic stressors generally rank higher than all others in importance due to their direct impact on fishing and fish processing activities. However, socio-economic stressors were more severely felt, especially in major fishing seasons. The study therefore highlights socio-economic stressors as realistic focus for adaptation priorities that can safeguard the lives, livelihood and wellbeing of rural coastal-small scale fishing communities.
Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2
Authors: Mohsen Attayeb , Chen Yi-An , Allendes Osorio Rodolfo S. , Higuchi Chihiro , Mizuguchi Kenji
Published: July 2022

Optimizing and automating a protocol for 16S microbiome data analysis with QIIME2 is a challenging task. It involves a multi-step process, and multiple parameters and options that need to be tested and determined. In this article, we describe Snaq, a snakemake pipeline that helps automate and optimize 16S data analysis using QIIME2. Snaq offers an informative file naming system and automatically performs the analysis of a data set by downloading and installing the required databases and classifiers, all through a single command-line instruction. It works natively on Linux and Mac and on Windows through the use of containers, and is potentially extendable by adding new rules. This pipeline will substantially reduce the efforts in sending commands and prevent the confusion caused by the accumulation of analysis results due to testing multiple parameters.
Path Planning Optimization of Intelligent Vehicle Based on Improved Genetic and Ant Colony Hybrid Algorithm
Authors: Shi Kangjing , Huang Li , Jiang Du , Sun Ying , Tong Xiliang , Xie Yuanming , Fang Zifan
Published: July 2022

Intelligent vehicles were widely used in logistics handling, agriculture, medical service, industrial production, and other industries, but they were often not smooth enough in planning the path, and the number of turns was large, resulting in high energy consumption. Aiming at the unsmooth path planning problem of four-wheel intelligent vehicle path planning algorithm, this article proposed an improved genetic and ant colony hybrid algorithm, and the physical model of intelligent vehicle was established. This article first improved ant colony optimization algorithm about heuristic function with the adaptive change of evaporation factor. Then, it improved the genetic algorithm on fitness function, adaptive adjustment of crossover factor, and mutation factor. Last, this article proposed the improved hybrid algorithm with the addition of a deletion operator, adoption of an elite retention strategy, and addition of suboptimal solutions obtained from the improved ant colony algorithm to improved genetic algorithm to obtain optimized new populations. The simulation environment for this article is windows 10, the processor is Intel Core i5-5257U, the running memory is 4GB, the compilation environment is MATLAB2018b, the number of ant samples is 50, the maximum number of iterations is 100, the initial population size of the genetic algorithm is 200, and the maximum number of iterations is 50. Simulation and physical experiments show that the improved hybrid algorithm is effective. Compared with the traditional hybrid algorithm, the improved hybrid algorithm reduced by 46% in the average number of iterations and 75% in the average number of turns in a simple grid. The improved hybrid algorithm reduced by 47% in the average number of iterations and 21% in the average number of turns in a complex grid. The improved hybrid algorithm works better to reduce the number of turns in simple maps.
Full-Scale of a Compost Process Using Swine Manure, Human Feces, and Rice Straw as Feedstock
Authors: Gao Yi , Zhang Chunxue , Tan Lu , Wei Xiaocheng , Li Qian , Zheng Xiangqun , Liu Fang , Wang Jiarui , Xu Yan
Published: July 2022

Regarding the composting of rural waste, numerous studies either addressed the composting of a single waste component or were conducted at a laboratory/pilot scale. However, far less is known about the mixed composting effect of multi-component rural waste on a large scale. Here, we examined nutrient transformation, maturity degree of decomposition, and succession of microbial communities in large-scale (1,000 kg mixed waste) compost of multi-component wastes previously optimized by response models. The results showed that multi-component compost can achieve the requirement of maturity and exhibit a higher nutritional value in actual compost. It is worth noting that the mixed compost effectively removed pathogenic fungi, in which almost no pathogenic fungi were detected, and only two pathogenic bacteria regrown in the cooling and maturation stages. Structural equation models revealed that the maturity (germination index and the ratio of ammonium to nitrate) of the product was directly influenced by compost properties (electrical conductivity, pH, total organic carbon, moisture, temperature, and total nitrogen) compared with enzymes (cellulase, urease, and polyphenol oxidase) and microbial communities. Moreover, higher contents of total phosphorus, nitrate-nitrogen, and total potassium were conducive to improving compost maturity, whereas relatively lower values of moisture and pH were more advantageous. In addition, compost properties manifested a remarkable indirect effect on maturity by affecting the fungal community (Penicillium and Mycothermus). Collectively, this evidence implies that mixed compost of multi-component rural waste is feasible, and its efficacy can be applied in practical applications. This study provides a solution for the comprehensive treatment and utilization of rural waste.
Surface Defect Segmentation Algorithm of Steel Plate Based on Geometric Median Filter Pruning
Authors: Hao Zhiqiang , Wang Zhigang , Bai Dongxu , Tong Xiliang
Published: July 2022

Problems such as redundancy of detection model parameters make it difficult to apply to factory embedded device applications. This paper focuses on the analysis of different existing deep learning model compression algorithms and proposes a model pruning algorithm based on geometric median filtering for structured pruning and compression of defect segmentation detection networks on the basis of structured pruning. Through experimental comparisons and optimizations, the proposed optimization algorithm can greatly reduce the network parameters and computational effort to achieve effective pruning of the defect detection algorithm for steel plate surfaces.
Hybrid Reconnaissance Mission to the 30 October 2020 Aegean Sea Earthquake and Tsunami (Izmir, Turkey & Samos, Greece): Description of Data Collection Methods and Damage
Authors: Aktas Yasemin D. , Ioannou Ioanna , Malcioglu Fatma Sevil , Kontoe Maria , Parammal Vatteri Ahsana , Baiguera Marco , Black Jacob , Kosker Anil , Dermanis Panagiotis , Esabalioglou Martha , Cabuk Eser , Donmez Kokcan , Ercolino Marianna , Asinari Mariana , Verrucci Enrica , Putrino Valentina , Durmaz Bahar , Kazantzidou-Firtinidou Danai , Cotton Dave , O’Kane Aisling , Ozden Ali Tolga , Contreras Diana , Cels Jonas , Free Matthew , Burton Paul , Wilkinson Sean , Rostami Rohollah , D’Ayala Dina
Published: July 2022

On 30 October 2020, an earthquake of Mw 6.9 hit the Aegean coasts of Turkey and Greece. The epicentre was some 14 km northeast of Avlakia on Samos Island, and 25 km southwest of Seferihisar, Turkey, triggering also a tsunami. The event has been followed by >4,000 aftershocks up to Mw 5.2 The Earthquake Engineering Field Investigation Team (EEFIT) has immediately gathered a team to conduct a hybrid reconnaissance study, bringing together remote and field investigation techniques. The mission took place between 16 November and 17 December, inclusive of three sets of field study carried out by the field crews for building damage assessment in the affected areas in Turkey and Greece under the coordination of the remote team. The mission also aimed to assess the viability of alternative data sources for an appraisal of the future viability of hybrid missions. This paper summarises the mission setup and findings, and discusses the benefits of and difficulties encountered during this hybrid reconnaissance activity.
NF-κB Regulation by Gut Microbiota Decides Homeostasis or Disease Outcome During Ageing
Authors: Zhang Shuning , Paul Soumyajeet , Kundu Parag
Published: July 2022

Human beings and their indigenous microbial communities have coexisted for centuries, which led to the development of co-evolutionary mechanisms of communication and cooperation. Such communication machineries are governed by sophisticated multi-step feedback loops, which typically begin with the recognition of microbes by pattern recognition receptors (PRRs), followed by a host transcriptional response leading to the release of effector molecules. Our gastrointestinal tract being the main platform for this interaction, a variety of host intestinal cells tightly regulate these loops to establish tolerance towards the microbial communities of the gut and maintain homeostasis. The transcription factor, nuclear factor kappa B (NF-κB) is an integral component of such a communication apparatus, which plays a critical role in determining the state of homeostasis or inflammation associated with dysbiosis in the host. Here we outline the crucial role of NF-κB in host response to microbial cues in the context of ageing and associated diseases.
Macrophages Break Interneuromast Cell Quiescence by Intervening in the Inhibition of Schwann Cells in the Zebrafish Lateral Line
Authors: Lin Meng-Ju , Lee Chia-Ming , Hsu Wei-Lin , Chen Bi-Chang , Lee Shyh-Jye
Published: July 2022

In the zebrafish lateral line system, interneuromast cells (INCs) between neuromasts are kept quiescent by underlying Schwann cells (SWCs). Upon severe injuries that cause the complete loss of an entire neuromast, INCs can occasionally differentiate into neuromasts but how they escape from the inhibition by SWCs is still unclear. Using a genetic/chemical method to ablate a neuromast precisely, we found that a small portion of larvae can regenerate a new neuromast. However, the residual regeneration capacity was hindered by inhibiting macrophages. Using in toto imaging, we further discovered heterogeneities in macrophage behavior and distribution along the lateral line. We witnessed the crawling of macrophages between the injured lateral line and SWCs during regeneration and between the second primordium and the first mature lateral line during development. It implies that macrophages may physically alleviate the nerve inhibition to break the dormancy of INCs during regeneration and development in the zebrafish lateral line.
Utility of Biogenic Iron and Its Bimetallic Nanocomposites for Biomedical Applications: A Review
Authors: Abedini Ali , Rostami Mojtaba , Banafshe Hamid Reza , Rahimi-Nasrabadi Mehdi , SobhaniNasab Ali , Ganjali Mohammad Reza
Published: July 2022

Nanotechnology mainly deals with the production and application of compounds with dimensions in nanoscale. Given their dimensions, these materials have considerable surface/volume ratios, and hence, specific characteristics. Nowadays, environmentally friendly procedures are being proposed for fabrication of Fe nanoparticles because a large amount of poisonous chemicals and unfavorable conditions are needed to prepare them. This work includes an inclusive overview on the economical and green procedures for the preparation of such nanoparticles (flower, fruits, tea, carbohydrates, and leaves). Pure and bimetallic iron nanoparticles, for instance, offer a high bandwidth and excitation binding energy and are applicable in different areas ranging from antibacterial, anticancer, and bioimaging agents to drug delivery systems. Preparation of nano-sized particles, such as those of Fe, requires the application of high quantities of toxic materials and harsh conditions, and naturally, there is a tendency to develop more facile and even green pathways (Sultana, Journal of Materials Science & Technology, 2013, 29, 795–800; Bushra et al., Journal of hazardous materials, 2014, 264, 481–489; Khan et al., Ind. Eng. Chem. Res., 2015, 54, 76–82). This article tends to provide an overview on the reports describing green and biological methods for the synthesis of Fe nanoparticles. The present review mainly highlights selenium nanoparticles in the biomedical domain. Specifically, this review will present detailed information on drug delivery, bioimaging, antibacterial, and anticancer activity. It will also focus on procedures for their green synthesis methods and properties that make them potential candidates for various biomedical applications. Finally, we provide a detailed future outlook.
Non-Palladium-Catalyzed Oxidative Coupling Reactions Using Hypervalent Iodine Reagents
Authors: Shetgaonkar Samata E. , Raju Aleena , China Hideyasu , Takenaga Naoko , Dohi Toshifumi , Singh Fateh V.
Published: July 2022

Transition metal-catalyzed direct oxidative coupling reactions via C–H bond activation have emerged as a straightforward strategy for the construction of complex molecules in organic synthesis. The direct transformation of C–H bonds into carbon–carbon and carbon–heteroatom bonds renders the requirement of prefunctionalization of starting materials and, therefore, represents a more efficient alternative to the traditional cross-coupling reactions. The key to the unprecedented progress made in this area has been the identification of an appropriate oxidant that facilitates oxidation and provides heteroatom ligands at the metal center. In this context, hypervalent iodine compounds have evolved as mainstream reagents particularly because of their excellent oxidizing nature, high electrophilicity, and versatile reactivity. They are environmentally benign reagents, stable, non-toxic, and relatively cheaper than inorganic oxidants. For many years, palladium catalysis has dominated these oxidative coupling reactions, but eventually, other transition metal catalysts such as gold, copper, platinum, iron, etc. were found to be promising alternate catalysts for facilitating such reactions. This review article critically summarizes the recent developments in non-palladium-catalyzed oxidative coupling reactions mediated by hypervalent iodine (III) reagents with significant emphasis on understanding the mechanistic aspects in detail.
Design of a Novel Series of Hetero-Binuclear Superhalogen Anions MM′X4− (M = Li, Na; M′ = Be, Mg, Ca; X = Cl, Br)
Authors: Yang Hui , He Hui-Min , Li Ning , Jiang Shang , Pang Min-Jun , Li Ying , Zhao Jian-Guo
Published: July 2022

A series of hetero-binuclear superatom motifs involving chloride/bromide ligands, that is, MM′X4− (M = Li, Na; M′ = Be, Mg, Ca; X = Cl, Br) anions, have been characterized by using many-body perturbation theory calculations. Large vertical electron detachment energies (VDEs, 5.470–6.799 eV) confirm the superhalogen identity of these anions. A larger VDE value can be obtained by introducing small M or large M′ central atoms and small halogen ligand atoms. Thus, one isomer of LiCaCl4− possesses the largest VDE value. Besides, when the extra electron is shared by all ligand atoms or three bridging ligand atoms, the isomers have relatively larger VDE values.
Interaction Between Autophagy and Porphyromonas gingivalis-Induced Inflammation
Authors: Kang Sen , Dai Anna , Wang Huiming , Ding Pei-Hui
Published: July 2022

Autophagy is an immune homeostasis process induced by multiple intracellular and extracellular signals. Inflammation is a protective response to harmful stimuli such as pathogen microbial infection and body tissue damage. Porphyromonas gingivalis infection elicits both autophagy and inflammation, and dysregulation of autophagy and inflammation promotes pathology. This review focuses on the interaction between autophagy and inflammation caused by Porphyromonas gingivalis infection, aiming to elaborate on the possible mechanism involved in the interaction.
Methylene Blue–Mediated Antimicrobial ​Photodynamic Therapy Against Clinical Isolates of Extensively Drug Resistant ​Gram-Negative Bacteria Causing Nosocomial Infections in Thailand, An In Vitro Study
Authors: Songsantiphap Chankiat , Vanichanan Jakapat , Chatsuwan Tanittha , Asawanonda Pravit , Boontaveeyuwat Einapak
Published: July 2022

Background/Purpose

Some multidrug-resistant gram-negative bacteria as a global threat have been recently prioritized for research and development of new treatments. We studied the efficacy of methylene blue–mediated antimicrobial photodynamic therapy (MB-aPDT) for the reduction of extensively drug-resistant Acinetobacter baumannii (XDR-AB) and Pseudomonas aeruginosa (XDR-PS) and multidrug-resistant Klebsiella pneumoniae (MDR-KP) isolated in a university hospital setting in Thailand.

Method

Two isolates of each selected bacterium were collected, XDR-AB1 and AB2, XDR- PS1 and PS2, and MDR-KP1 and KP2. Three triplicate experiments using various MB concentrations alone, various red light fluences alone, as well as the selected non-toxic doses of MB and fluences of red light combined as MB-aPDT were applied on each selected isolate. The colonies were counted [colony forming units (CFU)/ml]. Estimation of the lethal treatment dose defined as reduction of > 2 log10 in CFU/ml compared with untreated bacteria.

Result

There were generally negligible changes in the viable counts of the bacterial suspensions treated with all the MB concentrations (p > 0.05). In the second experiment with the only red light treatments, at fluences higher than 2 J/cm, reduction trend in viable counts across all the isolates was observed. Only for MDR-KP1, however, the lethal dose was achieved with the highest fluence of red light (80 J/cm). With the concentration of MB, 50 and 150 mg/L in the third experiment (MB-aPDT), the greater bacterial reduction was observed in all clinical isolates leading to their lethal viable cell reduction when escalating the light fluence to 80 J/cm.

Conclusions

MB-aPDT evidently killed the selected XDR and MDR-gram negative bacteria. In highly drug-resistant crisis era, MB-aPDT could be a promising option, particularly for local infections and infection complicating chronic wounds.
Rigor Me This: What Are the Basic Criteria for a Rigorous, Transparent, and Reproducible Scientific Study?
Authors: Sansbury Brian E. , Nystoriak Matthew A. , Uchida Shizuka , Wysoczynski Marcin , Moore Joseph B.
Published: July 2022

Scientific advancement is predicated upon the ability of a novel discovery to be independently reproduced and substantiated by others. Despite this inherent necessity, the research community is awash in published studies that cannot be replicated resulting in widespread confusion within the field and waning trust from the general public. In many cases, irreproducibility is the unavoidable consequence of a study that is conducted without the appropriate degree of rigor, typified by fundamental flaws in approach, design, execution, analysis, interpretation, and reporting. Combatting the irreproducibility pandemic in preclinical research is of urgent concern and is the primary responsibility of individual investigators, however there are important roles to be played by institutions, journals, government entities, and funding agencies as well. Herein, we provide an updated review of established rigor criteria pertaining to both in vitro and in vivo studies compiled from multiple sources across the research enterprise and present a practical checklist as a straightforward reference guide. It is our hope that this review may serve as an approachable resource for early career and experienced investigators alike, as they strive to improve all aspects of their scientific endeavors.
Atrial Cardiomyopathy Predicts Worse Outcome in Patients With Lung Cancer
Authors: Ren Mengdi , Ma Yuyan , Wei Meng , Ning Yuye , Liu Hui , Shi Xue , Yao Yu , Guo Fengwei
Published: July 2022

Background

Reports of the clinical outcomes associated with the co-occurrence of atrial cardiomyopathy (ACM) and lung cancer (LC) are limited.

Objectives

This study aims to investigate the influence of ACM on the prognosis of LC patients and related clinical determinants.

Methods

Newly diagnosed LC patients from January 1st, 2015, to December 31st, 2020, were retrospectively enrolled at the First Affiliated Hospital of Xi’an Jiaotong University. The demographics and overall survival (OS) of the patients with or without ACM were compared. The survival rate was analyzed using the Kaplan–Meier method and multivariate Cox regression analysis. Binary logistic regression analysis was used to determine the risk factors for ACM.

Results

A total of 306 patients (65.04 ± 10.30 years of age, 72.88% male) were analyzed. The prevalence of ACM in the non-small cell lung cancer (241, 78.76%) and small cell lung cancer (65, 21.24%) population was not statistically different. Overall, 53 (17.32%) LC patients had coexisting ACM. ACM patients were older (69 vs. 64, p = 0.0013) and had higher D-dimer levels (1.0 vs. 0.6, p = 0.001), lower serum calcium levels (2.23 vs. 2.31, p = 0.001), lower left ventricular ejection fraction (LVEF) values (67% vs. 69%, p = 0.036) and had more frequent coronary comorbidity disease (16.98% vs. 8.82%, p = 0.031). The median OS for patients with or without ACM was 15 months and 25 months, respectively (p = 0.018). Coexisting ACM compared to non-ACM was associated with worse OS in patients with LC (HR = 1.543, 95% CI: 1.042–2.283, p = 0.030).

Conclusion

Coexisting ACM is associated with undesirable survival outcomes in patients with LC. These findings could help us to better understand the cardiac burden in these patients and provide additional risk stratification for them.
The Main Builders of Mediterranean Coralligenous: 2D and 3D Quantitative Approaches for its Identification
Authors: Bracchi Valentina Alice , Bazzicalupo Pietro , Fallati Luca , Varzi Andrea Giulia , Savini Alessandra , Negri Mauro Pietro , Rosso Antonietta , Sanfilippo Rossana , Guido Adriano , Bertolino Marco , Costa Gabriele , De Ponti Elena , Leonardi Riccardo , Muzzupappa Maurizio , Basso Daniela
Published: July 2022

Along the Mediterranean Sea shelf, algal reefs made of crustose coralline algae and Peyssonneliales are known as Coralligenous. It ranks among the most important ecosystems in the Mediterranean Sea because of its extent, complexity, and heterogeneity, supporting very high levels of biodiversity. Descriptive approaches for monitoring purposes are often aimed at assessing the surficial ephemeral canopy, which is sustained and controlled by the occurrence of the long-lasting rigid structure at the base. This practice led to the non-univocal definition of Coralligenous, sometimes indicated as “animal Coralligenous” because of the surficial dominance of these components. The quantitative assessment of the builders that actively build up the persistent structure through geological time is therefore a fundamental topic. We collected two discrete coralligenous samples in front of Marzamemi village (Sicily, Ionian Sea), the first from an area of a dense coralligenous cover (- 37 m) and the second one from an area with sparse build-ups (- 36 m). By using image analysis and computerized axial tomography, we distinguished and quantified the different components both on the surface and inside the framework. In both cases, our results confirm the primary role of crustose coralline algae as major builders of the Mediterranean Coralligenous, this aspect matching with the evidence from the Quaternary fossil record. We suggest that the role of encrusting calcareous red algae in the Coralligenous should be considered in conservation and management policies.
Sex Discrepancy Observed for Gestational Metabolic Syndrome Parameters and Polygenic Risk Associated With Preschoolers’ BMI Growth Trajectory: The Ma’anshan Birth Cohort Study
Authors: Zhu Bei-bei , Gao Hui , Geng Meng-long , Wu Xiulong , Tong Juan , Deng Fen , Zhang Si-ying , Wu Li-hong , Huang Kun , Wu Xiao-yan , Gan Hong , Zhu Peng , Tao Fang-biao
Published: July 2022

Background

Few studies have investigated the associations of childhood growth trajectories with the prenatal metabolic risks of mothers and their interaction with children’s genetic susceptibility.

Objective

To investigate the effects of gestational metabolic syndrome (GMS) risks and children’s polygenic risk scores (PRSs), and their interaction effect on the BMI trajectory and obesity risk of offspring from birth to 6 years of age.

Methods

A total of 2,603 mother-child pairs were recruited from the Ma’anshan birth cohort (Anhui Province of China) study. Data on maternal prepregnancy obesity, gestational weight gain (GWG), gestational diabetes mellitus (GDM), and hypertensive disorders of pregnancy (HDP) were used to evaluate maternal GMS risk. In addition, 1,482 cord blood samples were used to genotype 11 candidate single-nucleotide polymorphisms (SNPs) to calculate children’s PRSs. The latent class growth model using the longitudinal BMI-for-age z scores (BMIz) was applied to validly capture the BMIz growth trajectory.

Results

Maternal GMS status was associated with higher BMIz scores and with an increased risk of overweight/obesity. Positive relationships were revealed between PRS and the risk of overweight/obesity among girls. Additionally, maternal GMS significantly interacted with the child’s PRS on BMIz scores and the risk of overweight/obesity among girls. Hierarchical BMI trajectory graphs by different exposure groups showed consistent findings, and both boys’ and girls’ BMIz trajectories were divided into three groups. Among girls, the higher the GMS risk or PRS they had, the higher the probability of being in the high BMIz trajectory group.

Conclusions

Maternal GMS status increased BMIz scores and the risk of obesity in both boys and girls and elevated the child’s BMI trajectory from birth to 6 years of age among girls. PRSs were significantly associated with children’s BMI trajectory and the risk of obesity and modified the associations between maternal GMS status and obesity biomarkers only among girls. Thus, regarding childhood obesity, steps should be taken to decrease maternal metabolic risks before and during pregnancy, and sex discrepancies should be noted to identify high-risk populations after birth to hierarchically manage them.
Rs864745 in JAZF1, an Islet Function Associated Variant, Correlates With Plasma Lipid Levels in Both Type 1 and Type 2 Diabetes Status, but Not Healthy Subjects
Authors: Dai Hao , Qian Yu , Lv Hui , Jiang Liying , Jiang Hemin , Shen Min , Chen Heng , Chen Yang , Zheng Shuai , Fu Qi , Yang Tao , Xu Kuanfeng
Published: July 2022

Objective

This study aims to reveal the association between JAZF1 rs864745 A>G variant and type 2 diabetes (T2D), type 1 diabetes (T1D) risk, and their correlation with clinical features, including islet function, islet autoimmunity, and plasma lipid levels.

Methods

We included 2505 healthy controls based on oral glucose tolerance test (OGTT), 1736 unrelated T2D, and 1003 unrelated autoantibody-positive T1D individuals. Binary logistic regression was performed to evaluate the relationships between rs864745 in JAZF1 and T2D, T1D, and islet-specific autoantibody status under the additive model, while multiple linear regression was used to assess its effect on glycemic-related quantitative traits and plasma lipid levels.

Results

We did not find any association between rs864745 in JAZF1 and T2D, T1D, or their subgroups (All P > 0.05). For glycemic traits, we found that the G allele of this variant was significantly associated with higher 120 min insulin level, insulinogenic index (IGI), corrected insulin response (CIR), and acute insulin response (BIGTT-AIR) (P = 0.033, 0.006, 0.009, and 0.016, respectively) in healthy individuals. Similar associations were observed in newly diagnosed T2D but not T1D individuals. Although this variant had no impact on islet autoimmunity (All P > 0.05), significant associations with plasma total cholesterol (TC) and low-density lipoprotein (LDL) level stratified by JAZF1 rs864745 variant were observed in the disease status of T2D (P = 0.002 and 0.003) and T1D (P = 0.024 and 0.009), with significant heterogeneity to healthy individuals.

Conclusions

The common JAZF1 rs864745 variant contributes to islet function and lipid metabolism, which might be put into genetic risk scores to assess the risk of related clinical features.
The Essential Role of Body Weight in Adjusting Gn Dosage to Prevent High Ovarian Response for Women With PCOS During IVF: A Retrospective Study
Authors: Zeng Rujun , Chen Hanxiao , Zeng Xun , Qin Lang
Published: July 2022

Polycystic ovarian syndrome (PCOS) is the major cause of anovulatory infertility. Since women with PCOS are often accompanied by increased body weight and hyper response to controlled ovarian stimulation, individualized gonadotropin (Gn) dose is required to achieve a therapeutic effect while minimizing the risk of ovarian hyperstimulation simultaneously. We aimed to investigate the essential role of body weight in optimizing initial Gn dosage for PCOS patients during in vitro fertilization (IVF). We retrospectively included 409 infertile PCOS patients who used gonadotropin-releasing hormone (GnRH)-antagonist fixed protocol and underwent their first cycle of IVF in West China Second University Hospital from January 2019 to June 2021. Baseline characteristics controlled ovarian stimulation parameters, and reproductive outcomes were compared between patients with different body weights and different ovarian responses. Multivariable linear regression analyses were adopted to investigate the relationship between body weight and initial Gn dosage. Receiver operating characteristic (ROC) curves were drawn to find the optimal cut-off value of body weight in predicting the starting Gn dosage so as to prevent high ovarian response (HOR). We found that luteinizing hormone (LH) level and Anti-Mullerian hormone (AMH) level were lowest in the group with body weight over 70 kg and was highest in the group with body weight less than 50 kg. Increased body weight was significantly correlated to the rise of initial Gn dosage (Beta = 0.399, t = 8.921, p < 0.001). Normal ovarian response (NOR) patients had significantly less fresh cycle cancel rate and ovarian hyperstimulation syndrome (OHSS) rate which outweighed the fewer embryos compared with HOR patients. Using ROC curves, 53.25 kg (sensitivity, 84.2%; specificity, 53.8%) and 70.5 kg (sensitivity, 58.8%; specificity, 93.0%) were identified as the optimal cut-off values to predict the initial Gn dosage of no more than 150 IU and 225 IU, respectively. In conclusion, adjusting the initial Gn dosage based on body weight is crucial to preventing ovarian hyperstimulation while not influencing reproductive outcomes for PCOS patients during IVF.
Pasireotide-Induced Shrinkage in GH and ACTH Secreting Pituitary Adenoma: A Systematic Review and Meta-Analysis
Authors: Mondin Alessandro , Manara Renzo , Voltan Giacomo , Tizianel Irene , Denaro Luca , Ferrari Marco , Barbot Mattia , Scaroni Carla , Ceccato Filippo
Published: July 2022

Introduction

Pasireotide (PAS) is a novel somatostatin receptor ligands (SRL), used in controlling hormonal hypersecretion in both acromegaly and Cushing’s Disease (CD). In previous studies and meta-analysis, first-generation SRLs were reported to be able to induce significant tumor shrinkage only in somatotroph adenomas. This systematic review and meta-analysis aim to summarize the effect of PAS on the shrinkage of the pituitary adenomas in patients with acromegaly or CD.

Materials and methods

We searched the Medline database for original studies in patients with acromegaly or CD receiving PAS as monotherapy, that assessed the proportion of significant tumor shrinkage in their series. After data extraction and analysis, a random-effect model was used to estimate pooled effects. Quality assessment was performed with a modified Joanna Briggs’s Institute tool and the risk of publication bias was addressed through Egger’s regression and the three-parameter selection model.

Results

The electronic search identified 179 and 122 articles respectively for acromegaly and CD. After study selection, six studies considering patients with acromegaly and three with CD fulfilled the eligibility criteria. Overall, 37.7% (95%CI: [18.7%; 61.5%]) of acromegalic patients and 41.2% (95%CI: [22.9%; 62.3%]) of CD patients achieved significant tumor shrinkage. We identified high heterogeneity, especially in acromegaly (I2 of 90% for acromegaly and 47% for CD), according to the low number of studies included.

Discussion

PAS treatment is effective in reducing tumor size, especially in acromegalic patients. This result strengthens the role of PAS treatment in pituitary adenomas, particularly in those with an invasive behavior, with progressive growth and/or extrasellar extension, with a low likelihood of surgical gross-total removal, or with large postoperative residual tissue.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022328152, identifier CRD42022328152
Projection of Precipitation Extremes and Flood Risk in the China–Pakistan Economic Corridor
Authors: Du Shixiong , Wu Ruiying , Sun Huaiwei , Yan Dong , Xue Jie , Liao Weihong , Tuo Ye , Zhang Wenxin
Published: July 2022

It is reported that the China–Pakistan Economic Corridor has been affected by extreme precipitation events. Since the 20th century, extreme weather events have occurred frequently, and the damage and loss caused by them have increased. In particular, the flood disaster caused by excessive extreme precipitation seriously hindered the development of the human society. Based on CRiteria Importance Through Intercriteria Correlation and square root of generalized cross-validation, this study used intensity–area–duration to analyze the trend of future extreme precipitation events, corrected the equidistance cumulative distribution function method deviation of different future scenario models (CESM2, CNRM-CM6-1, IPSL-CM6A-LR, and MIROC6) and evaluated the simulation ability of the revised model. The results showed that: 1) the deviation correction results of CNRM-CM6-1 in the Coupled Model Intercomparison Project Phase (CMIP) 6 could better simulate the precipitation data in the study area, and its single result could achieve the fitting effect of the CMIP5 multimodel ensemble average; 2) under CNRM-CM6-1, the frequency of extreme precipitation events under the three climate scenarios (SSP1-2.6, SSP3-7.0, and SSP5-8.5) presents interdecadal fluctuations of 3.215 times/10A, 1.215 times/10A, and 5.063 times/10A, respectively. The average impact area of extreme precipitation events would decrease in the next 30 years, while the total impact area and the extreme precipitation events in a small range would increase. Under the future scenario, the increase rate of extreme precipitation was highest in August, which increased the probability of extreme events; 3) in the next 30 years, the flood risk had an obvious expansion trend, which was mainly reflected in the expansion of the area of high-, medium-, and low-risk areas. The risk zoning results obtained by the two different flood risk assessment methods were different, but the overall risk trend was the same. This study provided more advanced research for regional flood risk, reasonable prediction for flood risk under future climate models, and useful information for flood disaster prediction in the study area and contributes to the formulation of local disaster prevention and reduction policies.
Similarities and Differences in Fish Community Composition Accessed by Electrofishing, Gill Netting, Seining, Trawling, and Water eDNA Metabarcoding in Temperate Reservoirs
Authors: Golpour Amin , Šmejkal Marek , Čech Martin , dos Santos Rômulo A. , Souza Allan T. , Jůza Tomáš , Martínez Carlos , Bartoň Daniel , Vašek Mojmír , Draštík Vladislav , Kolařík Tomáš , Kočvara Luboš , Říha Milan , Peterka Jiří , Blabolil Petr
Published: July 2022

It is difficult to understand the composition and diversity of biological communities in complex and heterogeneous environments using traditional sampling methods. Recently, developments in environmental DNA metabarcoding have emerged as a powerful, non-invasive method for comprehensive community characterization and biodiversity monitoring in different types of aquatic ecosystems. In this study, water eDNA targeting fish (wf-eDNA) and four traditional fish sampling methods (electrofishing, gill netting, seining, trawling) were compared to evaluate the reliability and efficiency of wf-eDNA (vertebrate mitochondrial 12S ribosomal RNA (rRNA) as an alternative approach to assess the diversity and composition of freshwater fish communities. The results of wf-eDNA showed a consistency between the traditional sampling methods regarding species detection. However, some fish species detected using wf-eDNA assay were not detected using traditional sampling methods and vice versa. Comparison of wf-eDNA and traditional sampling methods revealed spatial homogeneity in fish community composition in all reservoirs. Ordination analysis showed that the wf-eDNA approach covers all traditional sampling methods and occupies an intermediate position. In addition, based on the Shannon diversity index, we found that in one reservoir the wf-eDNA method yielded similar fish community diversity to traditional sampling methods. However, in other reservoirs, the calculated Shannon diversity index of the wf-eDNA method was significantly higher than traditional sampling methods. In general, significant positive correlations were found between the wf-eDNA method and almost all traditional sampling methods. We conclude that wf-eDNA seems to be a reliable and complementary approach for biomonitoring and ecosystem management of freshwater ichthyofauna.
Coastal Wetland Soil Carbon Storage at Mangrove Range Limits in Apalachicola Bay, FL: Observations and Expectations
Authors: Steinmuller Havalend E. , Breithaupt Joshua L. , Engelbert Kevin M. , Assavapanuvat Prakhin , Bianchi Thomas S.
Published: July 2022

Globally, mangrove range limits are expanding, often at the cost of adjacent coastal ecosystems including saltmarshes, potentially leading to a change in ecosystem services such as organic carbon (OC) sequestration. Studies in the southeastern US have focused almost exclusively onAvicennia germinansrange expansion, the most cold-tolerant mangroves in North America. The Apalachicola Bay region of north Florida represents the northern range limit of mangroves in the Gulf of Mexico, and uniquely also includesRhizophora mangle. The objective of this research was to quantify soil OC density beneath both mangrove species and compare results to the soils beneath two contiguous native tidal saltmarsh species:Juncus roemerianusandSpartina alterniflorain a barrier island setting. Dominant plant taxa were not a significant predictor of soil OC density, highlighting the relative importance of site-specific environmental attributes as controls on soil properties. Soil profile δ13C compositions included a range of values reflective of C3and C4plant inputs, suggesting that shifts in plant taxa, both from marsh to mangroves and between marsh species, have been occurring at all sites in this study. These findings support much of the literature on mangrove encroachment, which indicates mangrove soil OC concentrations, densities, or stocks are less than or equal to that of co-located tidal marsh habitats. Through a systematic review, the potential of several proposed explanatory variables (climate, environmental setting, plant physiology and productivity, and duration of encroachment) were identified to evaluate how soil OC density in mangrove habitats might increase over time, which is critical to forecasting how continued mangrove expansion might affect blue C storage as these habitats evolve.
Pyroptosis-Related Gene to Construct Prognostic Signature and Explore Immune Microenvironment and Immunotherapy Biomarkers in Bladder Cancer
Authors: Zhang Xiangyu , Liang Hengzhang , Tang Qi , Chen Hongyi , Guo Fangzhou
Published: July 2022

Bladder cancer is known to be the most common malignant tumor in the urinary system and has a poor prognosis; thus, new targets for drug treatment are urgently needed. Pyroptosis is defined as programmed cell death in the inflammatory form mediated by the gasdermin protein. It has therapeutic potential due to the synergistic effect of radiotherapy and chemotherapy, can reverse chemotherapy resistance, is able to regulate the body environment to alter tumor metabolism, and may enhance the response rate of the immune checkpoint inhibitor. Accordingly, this study attempted to explore the role of pyroptosis in bladder cancer. A prognostic model based on five pyroptosis-related genes was constructed by conducting univariate Cox survival and LASSO regression analyses using The Cancer Genome Atlas (TCGA) cohort. Patients were divided into high- and low-risk groups according to the median risk score, with all five PRGs having downregulated expression in the high-risk group. The high-risk group was shown to have a worse prognosis than the low-risk group, and survival differences between the two groups were then validated in the Gene Expression Omnibus (GEO) cohort. Moreover, the ROC curves demonstrated the model’s moderate predictive ability. The univariate and multivariate Cox regression analyses indicated that risk scores were found to serve as an independent prognosis factor for OS in bladder cancer patients. In addition, the high-risk group was observed to be associated with advanced N and TNM stages. A nomogram combining risk scores and clinical features was then established, with the ROC curve indicating that the AUC of TCGA training cohort in 3 and 5 years was 0.789 and 0.775, respectively. The calibration curve exhibited a high consistency between the actual survival rate and the predicted rate. Furthermore, the GO and KEGG analyses found that antigen processing and presentation of exogenous antigen, exogenous peptide antigen, and peptide antigen were enriched in the low-risk group. A higher abundance of tumor-infiltrating immune cells and additional active immune pathways were also noted in the low-risk group. In addition, immunotherapy biomarkers, including TMB, PD1, PD-L1, CTLA4, and LAG3, were shown to have higher levels in the low-risk group. Therefore, patients in the low-risk group may be potential responders to immune checkpoint inhibitors.
D3K: The Dissimilarity-Density-Dynamic Radius K-means Clustering Algorithm for scRNA-Seq Data
Authors: Liu Guoyun , Li Manzhi , Wang Hongtao , Lin Shijun , Xu Junlin , Li Ruixi , Tang Min , Li Chun
Published: July 2022

A single-cell sequencing data set has always been a challenge for clustering because of its high dimension and multi-noise points. The traditional K-means algorithm is not suitable for this type of data. Therefore, this study proposes a Dissimilarity-Density-Dynamic Radius-K-means clustering algorithm. The algorithm adds the dynamic radius parameter to the calculation. It flexibly adjusts the active radius according to the data characteristics, which can eliminate the influence of noise points and optimize the clustering results. At the same time, the algorithm calculates the weight through the dissimilarity density of the data set, the average contrast of candidate clusters, and the dissimilarity of candidate clusters. It obtains a set of high-quality initial center points, which solves the randomness of the K-means algorithm in selecting the center points. Finally, compared with similar algorithms, this algorithm shows a better clustering effect on single-cell data. Each clustering index is higher than other single-cell clustering algorithms, which overcomes the shortcomings of the traditional K-means algorithm.
Gasdermins: New Therapeutic Targets in Host Defense, Inflammatory Diseases, and Cancer
Authors: Magnani Laura , Colantuoni Mariasilvia , Mortellaro Alessandra
Published: July 2022

Gasdermins (GSDMs) are a class of pore-forming proteins related to pyroptosis, a programmed cell death pathway that is induced by a range of inflammatory stimuli. Small-scale GSDM activation and pore formation allow the passive release of cytokines, such as IL-1β and IL-18, and alarmins, but, whenever numerous GSDM pores are assembled, osmotic lysis and cell death occur. Such GSDM-mediated pyroptosis promotes pathogen clearance and can help restore homeostasis, but recent studies have revealed that dysregulated pyroptosis is at the root of many inflammation-mediated disease conditions. Moreover, new homeostatic functions for gasdermins are beginning to be revealed. Here, we review the newly discovered mechanisms of GSDM activation and their prominent roles in host defense and human diseases associated with chronic inflammation. We also highlight the potential of targeting GSDMs as a new therapeutic approach to combat chronic inflammatory diseases and cancer and how we might overcome the current obstacles to realize this potential.