bluuebunny/crossref_metadata_2025 huggingface dataset:
Characteristic MicroRNAs Linked to Dysregulated Metabolic Pathways in Qatari Adult Subjects With Obesity and Metabolic Syndrome
Authors: Mir Fayaz Ahmad , Mall Raghvendra , Iskandarani Ahmad , Ullah Ehsan , Samra Tareq A. , Cyprian Farhan , Parray Aijaz , Alkasem Meis , Abdalhakam Ibrahem , Farooq Faisal , Abou-Samra Abdul-Badi
Published: July 2022

Background

Obesity-associated dysglycemia is associated with metabolic disorders. MicroRNAs (miRNAs) are known regulators of metabolic homeostasis. We aimed to assess the relationship of circulating miRNAs with clinical features in obese Qatari individuals.

Methods

We analyzed a dataset of 39 age-matched patients that includes 18 subjects with obesity only (OBO) and 21 subjects with obesity and metabolic syndrome (OBM). We measured 754 well-characterized human microRNAs (miRNAs) and identified differentially expressed miRNAs along with their significant associations with clinical markers in these patients.

Results

A total of 64 miRNAs were differentially expressed between metabolically healthy obese (OBO) versus metabolically unhealthy obese (OBM) patients. Thirteen out of 64 miRNAs significantly correlated with at least one clinical trait of the metabolic syndrome. Six out of the thirteen demonstrated significant association with HbA1c levels; miR-331-3p, miR-452-3p, and miR-485-5p were over-expressed, whereas miR-153-3p, miR-182-5p, and miR-433-3p were under-expressed in the OBM patients with elevated HbA1c levels. We also identified, miR-106b-3p, miR-652-3p, and miR-93-5p that showed a significant association with creatinine; miR-130b-5p, miR-363-3p, and miR-636 were significantly associated with cholesterol, whereas miR-130a-3p was significantly associated with LDL. Additionally, miR-652-3p’s differential expression correlated significantly with HDL and creatinine.

Conclusions

MicroRNAs associated with metabolic syndrome in obese subjects may have a pathophysiologic role and can serve as markers for obese individuals predisposed to various metabolic diseases like diabetes.
In silico integrative analysis of multi-omics reveals regulatory layers for diurnal gene expression in mouse liver
Authors: Jiang Chunjie , Liu Panpan , La Cam Mong , Guan Dongyin
Published: July 2022

Diurnal oscillation persists throughout the body and plays an essential role in maintaining physiological homeostasis. Disruption of diurnal rhythm contributes to many diseases including type 2 diabetes. The regulatory mechanism of the transcription-translation feedback loop (TTFL) of core clock genes is well-established, while a systematic study across all regulatory layers of gene expression, including gene transcription, RNA translation, and DNA binding protein (DBP) activities, is still lacking. We comprehensively bioinformatics analyzed the rhythmicity of gene transcription, mature RNA abundance, protein abundance and DBP activity using publicly available omic-datasets from mouse livers. We found that the core clock genes, Bmal1 and Rev-erbα, persistently retained rhythmicity in all stages, which supported the essential rhythmic function along with the TTFL. Interestingly, there were many layer-specific rhythmic genes playing layer-specific rhythmic functions. The systematic analysis of gene transcription rate, RNA translation efficiency, and post-translation modification of DBP were incorporated to determine the potential mechanisms for layer-specific rhythmic genes. We observed the gene with rhythmic expression in both mature RNA and protein layers were largely due to relatively consistent translation rate. In addition, rhythmic translation rate induced the rhythms of protein whose mature RNA levels were not rhythmic. Further analysis revealed a phosphorylation-mediated and an enhancer RNA-mediated cycling regulation between the corresponding layers. This study presents a global view of the oscillating genes in multiple layers via a systematical analysis and indicates the complexity of regulatory mechanisms across different layers for further functional study.
Association Between the Neutrophil-To-Lymphocyte Ratio and Diabetes Secondary to Exocrine Pancreatic Disorders
Authors: Chen Guanhua , Tan Chunlu , Liu Xubao , Chen Yonghua
Published: July 2022

Background

Diabetes mellitus among patients with exocrine pancreatic disorders is commonly known to be associated with chronic inflammation, including chronic pancreatitis and pancreatic ductal adenocarcinoma (PDAC). The neutrophil-to-lymphocyte ratio (NLR) is a novel marker that indicates the presence of various chronic inflammatory diseases, including type 2 diabetes (T2DM). However, no studies have examined the relationship between the NLR value and diabetes secondary to exocrine pancreatic disorders.

Aim

To determine whether the NLR value is associated with diabetes secondary to exocrine pancreatic disorders.

Methods

The medical data of subjects with confirmed pancreatic disease who were admitted to the Department of Pancreatic Surgery of our institution from August 2017 to October 2021 were obtained from the database and retrospectively analyzed. Anthropometric measures, laboratory data, including HbA1c, fasting insulin, and fasting C-peptide levels and the inflammatory index (white blood cell count, NLR, platelet-to-lymphocyte ration, monocyte-to-lymphocyte ratio) were recorded. The NLR is the ratio of neutrophils to lymphocytes. A homeostasis model (HOMA-B and HOMA-IR) was used to measure beta-cell dysfunction and insulin resistance.

Results

The NLR values of the diabetes secondary to exocrine pancreatic disorders group were significantly higher than those of the nondiabetic group (P=0.001). In multivariate logistic regression, after adjusting for covariates, high NLR values were found to be an independent risk factor for diabetes secondary to exocrine pancreatic disorders (OR: 1.37, 95% CI: 1.138-1.649, P=0.001). According to Spearman correlation analysis, the NLR was significantly correlated with fasting plasma glucose levels (P<0.0001) and HOMA2-IR values (P=0.02).

Conclusion

The NLR inflammation marker was significantly higher in subjects with diabetes secondary to exocrine pancreatic disorders and was associated with insulin resistance. NLR values may be reliable predictive markers for diabetes among patients with exocrine pancreatic disorders.
An Improved Dual-Loop Feedforward Control Method for the Enhancing Stability of Grid-Connected PV and Energy Storage System Under Weak Grids
Authors: Li Chunxu , Liu Xinrui , Wang Rui , Zhang Yi , Zhang Li
Published: July 2022

Although the stability of the grid-connected photovoltaics (PV) and energy storage systems under weak grids has been widely researched, the classical improvement methods focus more on suppressing the harmonics introduced by the phase-locked loop (PLL). Furthermore, the current distortion caused by the DC voltage loop is difficult to be eliminated. In this study, based on the hybrid energy storage system of battery-supercapacitor, a dual-loop compensation method is proposed. First, the small-signal model and output impedance matrix are built in d-q axis. Second, for different disturbance loops, a DC voltage loop disturbance compensation method based on power feedforward is proposed to suppress the harmonics caused by the DC voltage controller (DVC). In addition, a voltage feedforward PLL disturbance compensation method is proposed, which can reduce the PLL perturbations and revise the output impedance to improve system stability. Finally, the output impedance frequency characteristic analysis and the hardware-in-the-loop (HIL) simulation results show that the proposed control method can effectively improve the stability of the system under weak grids.
Distributed low-carbon energy management method for port microgrid based on we-energies under polymorphic network
Authors: Teng Fei , Wang Jianyuan , Luo Hanguang , Zhang Qing , Shen Congqi
Published: July 2022

In order to reduce port pollution and carbon emissions and improve the utilization rate of clean energy, a port microgrid based on we-energies (WEs) and its polymorphic distributed low-carbon energy management method is proposed. First, this study considers a variety of heterogeneous Wes, such as ship we-energies (SWEs), to establish a polymorphic energy management system for port microgrids and to achieve reliable information exchange between WEs under different communication networks. Second, considering the bidirectional energy transmission characteristic of the port WEs, the operating cost function of heterogeneous WEs is established. In addition, with the objective of economic and low-carbon operation of port microgrids, the energy management model of a port microgrid is constructed, and the optimal solution is obtained based on distributed optimization theory. Finally, simulation cases are performed to verify the effectiveness of the proposed method.
Research on generation scheduling mechanism of interconnected power system based on runoff forecast
Authors: Jiang Shiming , wu Ping , Peng Xuhong , Tang Yibo
Published: July 2022

In order to reduce power energy consumption and ensure the sustainable development of resources, a research on the generation scheduling mechanism of interconnected power systems based on runoff forecasting is proposed. First, by studying energy-saving power generation scheduling and using the average distribution method, there will be a lot of energy consumption and pollution emissions, so it is necessary to formulate a reasonable power generation scheduling plan; secondly, the medium and long-term runoff forecasting method is analyzed, and artificial neural networks are used to select appropriate hidden nodes Finally, the economic characteristics of the two-stage power generation of the hydropower station are explored, and the marginal benefit of the water level storage capacity and the total power generation is obtained by combining the current operating status and forecast information of the reservoir. Through experiments, it is proved that the method in this paper can better predict the power generation scheduling mechanism of hydropower stations, and the annual power generation of the optimized scheduling is 1.92% higher than that of conventional scheduling, which has significant advantages, ensuring the reasonable distribution of power resources and preventing unnecessary waste.
A relaxed support vector data description algorithm based fault detection in distribution systems
Authors: Chu Fei , Lu Zhenlin , Jin Shuowei , Liu Xin , Yu Ziyang
Published: July 2022

The power detection of the distribution network is essential for reliable and secure distribution. In this paper, a flexible dual-threshold SVDD fault warning algorithm with fault samples is proposed to deal with problems concerning complex network topology, accessible data, and missing fault data in the power grid. For the problems of complicated network topology and a wide variety of signal types, we propose to combine wavelet packet energy features with Spearman to extract electric signal features, and finally achieve accurate feature extraction of multiple signal types. In the case of the problems of untimely judgement and low accuracy of the original SVDD, a relaxed SVDD fault warning algorithm with fault samples is correspondingly proposed. We turn the original SVDD boundary into a double-layer boundary, and divides the hypersphere space into three regions to increase the sensitivity to the fault samples and lessen the risk of missed detection. Besides, an adaptive update strategy is developed, which reduces the computational effort of the model and is proven more applicable to the distribution. Finally, the method is applied to numerical examples and fault detection experiments, and the experimental results in turn verified its effectiveness and superiority.
Relative viability proxy of airborne prokaryotic microorganisms at the Southeastern Mediterranean coastal Sea
Authors: Rahav E. , Paytan A. , Herut B.
Published: July 2022

The atmosphere plays a fundamental role in transporting airborne prokaryotes across the oceans and land. Despite the harsh atmospheric conditions, a considerable fraction of the airborne prokaryotic microorganisms survive the journey and remain viable upon deposition, and can affect the receiving environment. Here, we provide the first estimate of potential viability proxy for airborne prokaryotic cells at the Southeastern Mediterranean coast in 22 events during 2015, representing marine and terrestrial air-mass trajectories and a significant dust storm event. This was assessed using sequence amplicons of the small subunit ribosomal RNA gene (SSU rRNA) jointly with other complementary measurements. To estimate the relative viability in our dataset we used the ratio between the abundance of the bacterial SSU rRNA transcripts in a given sampling date and the lowest measured value (23.7.2015) as a measure of a relative viability proxy. The abundance of prokaryotes SSU rRNA transcripts ranged from ∼500 to 11,000 copies m3, with ∼2-fold higher relative viability proxy in marine-origin aerosols than predominantly terrestrial atmospheric trajectories. The relative viability proxy of prokaryotes was low during the peak of an intense and prolonged dust storm, and increased by ∼1.5-fold in the subsequent days representing background conditions (<1700 ng Al m−3). Furthermore, we show that anthropogenic/toxic trace-metals (Cu/Al, Pb/Al) negatively correlates with potentially viable airborne prokaryotes in marine trajectory aerosols, whereas mineral dust load (Al, Fe proxy) positively affect their potential viability proxy. This may suggest that airborne prokaryotes associated to marine trajectories benefit from a particle-associate lifestyle, enabling relatively higher humidity and supply of nutrients attributed to mineral dust particles.
Exploring the Role of Shared Mobility in Alleviating Private Car Dependence and On-Road Carbon Emissions in the Context of COVID-19
Authors: Zhang Xiaoyu , Shao Chunfu , Wang Bobin , Huang Shichen , Mi Xueyu , Zhuang Yan
Published: July 2022

Shared mobility is becoming increasingly popular worldwide, and travelers show more complex choice preferences during the post-pandemic era. This study explored the role of shared mobility in the context of coronavirus disease (COVID-19) by comparing the travel mode choice behavior with and without shared mobility. Considering the shared mobility services of ride-hailing, ride-sharing, car-sharing, and bike-sharing, the stated preference survey was designed, and the mixed logit model with panel data was applied. The results show that if shared mobility is absent, approximately 50% of motorized mobility users and 84.62% of bike-sharing adopters will switch to using private car and public transport, respectively. The perceived pandemic severity positively affects the usage of car-sharing and bike-sharing, while it negatively affects the ride-sharing usage. Under different pandemic severity levels, the average probabilities of private car choice with and without shared mobility are 38.70 and 57.77%, respectively; thus, shared mobility would alleviate the dependence on private car in post-pandemic future. It also helps to decrease the on-road carbon emissions when the pandemic severity is lower than 53. These findings suggest policymakers to maintain the shared mobility ridership and simultaneously contain the pandemic. Additionally, pricing discount and safety enhancement are more effective than reducing detour time to protect ride-sharing against COVID-19.
Co- and Post-seismic Deformation Mechanisms of the 2020 Mw6.0 Jiashi Earthquake in Xinjiang (China), Revealed by Sentinel-1 InSAR Observations
Authors: Wang T. , Zhu S. N. , Yang C. S. , Wei Y. J. , Zhao C.Y. , Hou H.C.
Published: July 2022

On 19 January 2020, an Mw6.0 earthquake occurred in Jiashi County, Xinjiang, China. This earthquake is a strong earthquake that occurred in the Kepingtage Belt. The monitoring and inversion of the co-seismic and post-earthquake will help further understand the geometry and movement properties of this tectonic belt. In this study, Sentinel-1A images were used to analyze the deformation of co-seismic and post-seismic events. The Okada elastic dislocation model was used to invert the geometric parameters of the fault and co-seismic slip distribution. The results showed that the maximum uplift and maximum subsidence deformations from the ascending images were 55 and 45 mm, respectively. The maximum uplift and subsidence deformations from the descending images were 62 and 28 mm, respectively. The inversion results show that the earthquake was induced by a fault with a length of 23.5 km, width of 4.7 km, and depth of 7.2 km. This earthquake was a typical dip-slip event. The distributed inversion results of post-earthquake deformation show that the maximum co-seismic slip and maximum post-seismic slip are located on the same fault plane, mainly distributed on the edge of the co-seismic fault, between the two faults.
How Does Risk Management Improve Farmers’ Green Production Level? Organic Fertilizer as an Example
Authors: Wang Xiaohuan , Ma Yifei , Li Hua , Xue Caixia
Published: July 2022

With increases in the frequency of various natural and social risks, effectively coping with uncertainty is necessary for the sustainable development of individuals and the society, particularly smallholder farmers with vulnerable livelihoods. Using survey data from farmers in China, we constructed a risk management capability index system for farmers at the individual, collective, and government levels to empirically analyze the impact of risk management on green production behavior through the Heckman model for two-stage sample selection. The results showed that risk management is a key factor affecting green production behavior. Membership status (membership in an organization), government subsidies, and income levels significantly promote green production levels. Moreover, risk management not only directly affects the green production level but also promotes green production behavior by expanding the scale of operation, improving the sense of responsibility, and enhancing the behavioral responsibility. Additionally, the mediating effect of these factors on farmers in the low-risk perception group was more obvious. Therefore, the risk management level of farmers should be improved at the individual, collective, and government levels to promote sustainable agriculture.
Coprecipitation of Organic Matter, Phosphate With Iron: Implications for Internal Loadings of Phosphorus in Algae-Dominated and Macrophyte-Dominated Lakes
Authors: Dai JiaRu , Zhang QiaoYing , Liu JingJing , Wen ShuaiLong , Zhang YuFeng , He Ding , Du YingXun
Published: July 2022

Coprecipitation with iron (Fe) plays an essential role in the biogeochemical cycles of organic carbon (OC) and phosphorus (P) in lakes. The sources and composition of organic matter (OM) mediate its association with iron, which could thus influence the immobilization of phosphorus. In this study, water-soluble organic matter from the sediments of two typical states of shallow lakes, macrophyte-dominated zones (M-WSOM) and algae-dominated zones (A-WSOM), was extracted, and the ternary coprecipitation of WSOM, phosphate with Fe(III), was investigated. The ternary coprecipitation process was enhanced with increasing Fe(III) or decreasing pH value. It was found that pH of 6.5 was more favorable for coprecipitation than a pH of 7.5 or 8.5. At pH 6.5, the complexation between WSOM and Fe(III) occurred at the low Fe(III) inputs, while the coprecipitation of phosphate, WSOM with Fe(III) took place when Fe(III) inputs reached 40 μM. The presence of A-WSOM showed stronger inhibition on the coprecipitation of phosphate than that by M-WSOM. The formed ternary coprecipitates with A-WSOM had lower C/Fe ratios (0.13–2.78) than those with M-WSOM (1.28–4.05), which was because A-WSOM had lower aromaticity than M-WSOM. In addition, more functional groups in A-WSOM could complex with Fe(III), resulting in less immobilization of OC and P during the coprecipitation of A-WSOM, phosphate, and Fe(III). Our results demonstrated that in algae-dominated zones, more phosphorus remained soluble during the ternary coprecipitation, which could perform positive feedback on the growth of phytoplankton and provide a novel explanation for the difficulty in restoring eutrophic lakes.
How Green Organizational Strategy and Environmental CSR Affect Organizational Sustainable Performance Through Green Technology Innovation Amid COVID-19
Authors: Ye Maoran , Hao Feng , Shahzad Mohsin , Kamran Hafiz Waqas
Published: July 2022

The growth of green-oriented businesses for sustainable development (SD) is no longer optional in the current dynamic world, especially for manufacturing businesses in general. Accordingly, the present study investigates the interlinkages between green organizational strategy (GOS), environmental corporate social responsibility (ECSR), and organizational sustainable performance (OSP) by exploring the key mediating role of green technology innovation (GTI). This study uses a quantitative method to gather data from Chinese manufacturing industries, employing a well-structured questionnaire. Senior and middle-level managers were the intended respondents. From the primary survey, 264 valid responses were gathered. The final data were analyzed using SmartPLS (version 3.3.9) by adopting structural equation modeling (SEM) to examine the associations between the targeted constructs, and the results add to the recent literature by offering a cohesive model of GOS, ECSR, GTI, and OSP. The findings revealed that GOS has a strong positive effect on ECSR, GTI, and OSP. Further, ECSR has a strong positive impact on GTI and OSP. Meanwhile, GTI is a key mediating variable in these relationships, which previous studies have not explored. This study innovatively integrates the three green traits, namely, GOS, ECSR, and GTI, into a comprehensive model that is understudied in existing literature in order to help businesses improve their sustainable competitive advantage. The ultimate aim is to help businesses improve their environmental performance and achieve solid sustainability over the long term.
Vineyard Management and Its Impacts on Soil Biodiversity, Functions, and Ecosystem Services
Authors: Giffard Brice , Winter Silvia , Guidoni Silvia , Nicolai Annegret , Castaldini Maurizio , Cluzeau Daniel , Coll Patrice , Cortet Jérôme , Le Cadre Edith , d’Errico Giada , Forneck Astrid , Gagnarli Elena , Griesser Michaela , Guernion Muriel , Lagomarsino Alessandra , Landi Silvia , Bissonnais Yves Le , Mania Elena , Mocali Stefano , Preda Cristina , Priori Simone , Reineke Annette , Rusch Adrien , Schroers Hans-Josef , Simoni Sauro , Steiner Magdalena , Temneanu Elena , Bacher Sven , Costantini Edoardo A. C. , Zaller Johann , Leyer Ilona
Published: July 2022

Healthy soils form the basis of sustainable viticulture, where soil characteristics have a direct impact on wine quantity and quality. Soil not only provides water and nutrients to vines, but is also a living medium containing micro- and macroorganisms that perform many ecological functions and provide ecosystem services. These organisms are involved in many processes, from decomposing organic matter to providing minerals to vine roots. They also control diseases, pests, and weeds, in addition to improving the soil structure in terms of its capacity to retain water and nutrients. Related to decomposition processes, the carbon content of vineyard soils influences fertility, erosion and biogeochemical cycles, with significant implications for the global climate. However, common agricultural practices represent strong threats to biodiversity and associated ecosystem services provided by vineyard soils. As consumers increasingly consider environmental aspects in their purchase decisions, winegrowers have to adapt their vineyard management strategies, raising the demand for sustainable pest- and weed-control methods. This article presents a comprehensive review of the impacts of vineyard practices on the soil ecosystem, biodiversity, and biodiversity-based ecosystem services, and provides future prospects for sustainable viticulture.
Provision of carbohydrate resources to support Apanteles polychrosidis, to increase parasitism of Caloptilia fraxinella in horticultural ash trees
Authors: McPike S. M. , Pain R. A. , Evenden M. L.
Published: July 2022

The provision of nutritional resources for beneficial insects that support pest control, such as parasitoid wasps, is one tactic in conservation biological control. This tactic could be an important element for the development of a biological control program to help control the ash leaf-cone roller, Caloptilia fraxinella Ely (Lepidoptera: Gracillariidae), an introduced pest of horticultural ash trees (Fraxinus) in Canadian Prairie cities, including Edmonton, AB, Canada. In the current study, we test the efficacy of carbohydrate food provision to support parasitism of C. fraxinella by its primary parasitoid, Apanteles polychrosidis Viereck (Hymenoptera: Braconidae). Laboratory experiments compared the longevity, parasitism rate and offspring fitness of wasps fed sucrose solutions at one of two concentrations (10 and 25% v/v) or flowers of buckwheat, Fagopyrum esculentum (Polygonaceae). Fed wasps lived longer than wasps with access to water only. Mated, but not unmated, males and females lived longer when fed 25% than 10% sucrose. Female A. polychrosidis had similar longevity when fed 25% sucrose or buckwheat flowers. Egg load did not change with sucrose provision. Adult longevity of fed unmated female A. polychrosidis was negatively correlated with egg load. Female A. polychrosidis fed 25% sucrose produced offspring with a slightly female-biased sex ratio and higher fecundity than offspring from female A. polychrosidis fed the 10% sucrose solution.
Stressful Daylight: Differences in Diel Rhythmicity Between Albino and Pigmented Fish
Authors: Valchářová Tereza , Slavík Ondřej , Horký Pavel , Stará Alžběta , Hrušková Iveta , Maciak Matúš , Pešta Michal , Velíšek Josef
Published: July 2022

In laboratory experiments, variously colored strains of animals, including those with albino phenotypes, are commonly used. The melanocortin theory suggests, however, that coloration phenotypes alter animal physiology and behavior. Animals with the albino phenotype show photoreceptor degradation associated with lowered visual accuracy, escape reactions, etc., presumably accompanied by prevailing nocturnal activity and lowered aggressiveness. This assumption was tested in small groups of albino and pigmented European catfish, Silurus glanis, during the diel cycle. The frequency of agonistic interactions was observed during mutual contests for shelters, and subsequently, blood plasma, brain, gill, and liver samples were collected to evaluate stress parameters. In an experimental arena with shelters, the light/dark rhythmicity of locomotor activity and aggressiveness of the two phenotypes were comparable; the peak was observed at night, and a lower peak was observed at dawn. In an experimental stream without shelters, the peak of locomotor activity occurred at night for only the pigmented phenotype. In the evaluation of 4 antioxidants and 1 oxidative stress indicator, representing a total of 15 indices, albino fish showed significant rhythmicity for 8 indices, whereas pigmented catfish showed significant rhythmicity for 5 indices. The production of blood stress parameters with the peak during the day occurred only in albino fish. A complex model was fitted with the aim of evaluating the links between behavioral and biochemical indices. Time periodicity was modeled using a sine wave and confirmed parallel courses of agonistic interactions in the catfish groups; the peak at dawn was associated with a 4.08-fold (conf. int. 3.53–4.7) increase in such interactions. The changes in glucose and superoxide dismutase concentrations varied with phenotype, while the effects of cortisol, lactate and catalase did not. In summary, the rhythmicity of locomotor activity and changes in the aggressiveness of catfish were influenced by shelter availability, and the effect of light-induced stress was more apparent in albino fish than in pigmented conspecific fish. The results suggested that laboratory-raised animals with pigmentation patterns naturally occurring in the wild show more reasonable values during experiments than those with an albino phenotype.
Decomposition of soil organic matter by ectomycorrhizal fungi: Mechanisms and consequences for organic nitrogen uptake and soil carbon stabilization
Authors: Tunlid Anders , Floudas Dimitrios , Op De Beeck Michiel , Wang Tao , Persson Per
Published: July 2022

A major fraction of nitrogen (N) in boreal forest soils is found in organic forms associated with soil organic matter (SOM) and mineral particles. The capacity of ectomycorrhizal (ECM) fungal symbionts to access this N is debated, considering that these fungi have lost many of the genes for decomposing organic matter that were present in their saprotrophic ancestors. To gain a molecular-level understanding of the N-mining processes in ECM fungi, we developed an experimental approach where the processes of decomposition were studied in parallel with the changes in the structure and properties of the organic matter. We showed that ECM fungi have significant capacities to assimilate organic N associated with SOM and mineral surfaces. The decomposition mechanisms differ between species, reflecting the lignocellulose decomposition mechanisms found in their saprotrophic ancestors. During N-mining, the ECM fungi processed the SOM to a material with increased adsorptive properties to iron oxide mineral particles. Two pathways contributed to these changes: Extracellular modifications of the SOM and secretion of mineral surface reactive metabolites. Some of these metabolites have iron(III)-reducing activities and can participate in extracellular Fenton reactions and redox reactions at iron oxide mineral surfaces. We conclude that the traditional framework for understanding organic N acquisition by ECM fungi from recalcitrant SOM must be extended to a framework that includes how those decomposition activities affect the stabilization and reactivity of mineral-associated SOM. The activity through these complex networks of reactions is decisive for the overall effect of ECM fungal decomposition on nutrients and C-cycling in forest ecosystems.
Transcriptional progressive patterns from mild to severe renal ischemia/reperfusion-induced kidney injury in mice
Authors: Lai Dong , Wang Lei , Li Jia-Rui , Chen Chen , Zhao Wen-Lei , Yuan Qing , Ma Xin , Zhang Xu
Published: July 2022

The renal ischemia/reperfusion (I/R)-induced acute kidney injury incidence after nephron-sparing surgery for localized renal tumors is 20%, but the biological determinant process of postoperative acute kidney injury remains unclear. Using Gene Expression Omnibus database (GSE192883) and several bioinformatics analyses (discrete time points analysis, gene set enrichment analysis, dynamic network biomarker analysis, etc), combined with the establishment of the I/R model for verification, we identified three progressive patterns involving five core pathways confirmed using gene set enrichment analysis and six key genes (S100a10, Pcna, Abat, Kmo, Acadm, and Adhfe1) verified using quantitative polymerase chain reaction The dynamic network biomarker (DNB) subnetwork composite index value is the highest in the 22-min ischemia group, suggesting the transcriptome expression level fluctuated sharply in this group, which means 22-min ischemia is an critical warning point. This study illustrates the core molecular progressive patterns from mild to severe I/R kidney injury, laying the foundation for precautionary biomarkers and molecular intervention targets for exploration. In addition, the safe renal artery blocking time of nephron-sparing surgery that we currently accept may not be safe anymore.
Public Interest in Population Genetic Screening for Cancer Risk
Authors: Roberts Megan C. , Foss Kimberly S. , Henderson Gail E. , Powell Sabrina N. , Saylor Katherine W. , Weck Karen E. , Milko Laura V.
Published: July 2022

An emerging role for DNA sequencing is to identify people at risk for an inherited cancer syndrome in order to prevent or ameliorate the manifestation of symptoms. Two cancer syndromes, Hereditary Breast and Ovarian Cancer and Lynch Syndrome meet the “Tier 1” evidence threshold established by the Centers for Disease Control and Prevention (CDC) for routine testing of patients with a personal or family history of cancer. Advancements in genomic medicine have accelerated public health pilot programs for these highly medically actionable conditions. In this brief report, we provide descriptive statistics from a survey of 746 US respondents from a Qualtrics panel about the public’s awareness of genetic testing, interest in learning about their cancer risk, and likelihood of participating in a population genetic screening (PGS) test. Approximately of half the respondents were aware of genetic testing for inherited cancer risk (n = 377/745, 50.6%) and would choose to learn about their cancer risk (n-309/635, 48.7%). Characteristics of those interested in learning about their cancer risk differed by educational attainment, age, income, insurance status, having a primary care doctor, being aware of genetic testing, and likelihood of sharing information with family (p < 0.05). A sizeable majority of the respondents who were interested in about learning their cancer risk also said that they were likely to participate in a PGS test that involved a clinical appointment and blood draw, but no out-of-pocket cost (n = 255/309, 82.5%). Reasons for not wanting to participate included not finding test results interesting or important, concerns about costs, and feeling afraid to know the results. Overall, our results suggest that engaging and educating the general population about the benefits of learning about an inherited cancer predisposition may be an important strategy to address recruitment barriers to PGS.
Clinically available testing options resulting in diagnosis in post-exome clinic at one medical center
Authors: Baker Elizabeth K. , Ulm Elizabeth A. , Belonis Alyce , Brightman Diana S. , Hallinan Barbara E. , Leslie Nancy D. , Miethke Alexander G. , Vawter-Lee Marissa , Wu Yaning , Pena Loren D. M.
Published: July 2022

Exome sequencing (ES) became clinically available in 2011 and promised an agnostic, unbiased next-generation sequencing (NGS) platform for patients with symptoms believed to have a genetic etiology. The diagnostic yield of ES has been estimated to be between 25–40% and may be higher in specific clinical scenarios. Those who remain undiagnosed may have no molecular findings of interest on ES, variants of uncertain significance in genes that are linked to human disease, or variants of uncertain significance in candidate genes that are not definitively tied to human disease. Recent evidence suggests that a post-exome evaluation consisting of clinical re-phenotyping, functional studies of candidate variants in known genes, and variant reevaluation can lead to a diagnosis in 5–15% of additional cases. In this brief research study, we present our experience on post-exome evaluations in a cohort of patients who are believed to have a genetic etiology for their symptoms. We have reached a full or partial diagnosis in approximately 18% (6/33) of cases that have completed evaluations to date. We accomplished this by utilizing NGS-based methods that are available on a clinical basis. A sample of these cases highlights the utility of ES reanalysis with updated phenotyping allowing for the discovery of new genes, re-adjudication of known variants, incorporating updated phenotypic information, utilizing functional testing such as targeted RNA sequencing, and deploying other NGS-based testing methods such as gene panels and genome sequencing to reach a diagnosis.
Community input in a genomic health implementation program: Perspectives of a community advisory group
Authors: Vidgen Miranda E. , Cutler Katrina , Bean Jessica , Bunker David , Fowles Lindsay F. , Healy Louise , Hondow Gary , Istiko Satrio Nindyo , McInerney-Leo Aideen M. , Pratt Gregory , Robins Deborah , Waddell Nicola , Evans Erin
Published: July 2022

Consumer and community engagement (CCE) in the implementation of genomics into health services and associated research is needed to ensure that changes benefit the affected patients. Queensland Genomics was a program to implement genomics into a public health service. We describe its Community Advisory Group’s (CAG) structure and function and provide recommendations based on the CAG members’ perspectives. The CAG provided advice to the Queensland Genomics program and its projects in an advisory capacity. The CAG was also resourced to develop and lead community-focused activities. Key enablers for CAG included; diversity of CAG members’ skills and experience, adequate resourcing, and the CAG’s ability to self-determine their direction. The CAG experienced limitations due to a lack of mechanisms to implement CCE in the Program’s projects. Here, we provide insights and commentary on this CAG, which will be useful for other initiatives seeking to undertake CCE in genomic research and health care.
Insights Into miRNA-mRNA Regulatory Mechanisms of Cold Adaptation in Gymnocypris eckloni: Ubiquitin-Mediated Proteolysis Is Pivotal for Adaptive Energy Metabolism
Authors: Nie Miaomiao , Ni Weilin , Wang Lihan , Gao Qiang , Liu Dan , Tian Fei , Wang Zhenji , Zhang Cunfang , Qi Delin
Published: July 2022

This study aimed to understand cold stress adaptations mechanism in fish. Thus, the transcriptional response to cold conditions in Gymnocypris eckloni was evaluated using RNA-seq and microRNA (miRNA)-seq analyses. Low-temperature (LT) group G. eckloni was cultivated outdoors in waters cooled to 2–4°C for 3 weeks, while individuals in the control temperature (CT) group were exposed to 14–16°C. Significantly different responses were observed in both mRNA and miRNA expression profiles, with more mRNAs (1,833 and 1,869 mRNAs were up- and downregulated, respectively) and fewer miRNAs (15 and 6 were up- and downregulated, respectively) observed in the LT group individuals relative to the CT group individuals. A miRNA-mRNA network involved in the regulation of G. eckloni responses to cold stress was constructed; this network included ubiquitin-mediated proteolysis, protein processing, and oxidative phosphorylation. These results provided new insights into mechanisms of cold tolerance by fish, including decreased metabolic activity in addition to proteolysis.
WDR36 Safeguards Self-Renewal and Pluripotency of Human Extended Pluripotent Stem Cells
Authors: An Shiyu , Yao Dan , Zhang Wenyi , Sun Hao , Yu Tianyi , Jia Ruizhe , Yang Yang
Published: July 2022

Extended pluripotent stem cells (EPS cells) have unlimited self-renewal ability and the potential to differentiate into mesodermal, ectodermal, and endodermal cells. Notably, in addition to developing the embryonic (Em) lineages, it can also make an effective contribution to extraembryonic (ExEm) lineages both in vitro and in vivo. However, multiple mysteries still remain about the underlying molecular mechanism of EPS cells’ maintenance and developmental potential. WDR36 (WD Repeat Domain 36), a protein of 105 kDa with 14 WD40 repeats, which may fold into two β-propellers, participates in 18sRNA synthesis and P53 stress response. Though WDR36 safeguards mouse early embryonic development, that is, homozygous knockout of WDR36 can result in embryonic lethality, what role does WDR36 plays in self-renewal and differentiation developmental potential of human EPS cells is still a subject of concern. Here, our findings suggested that the expression of WDR36 was downregulated during human hEPS cells lost self-renewal. Through constructing inducible knockdown or overexpressing WDR36-human EPS cell lines, we found that WDR36 knockdown disrupted self-renewal but promoted the mesodermal differentiation of human EPS cells; however, overexpressing of WDR36 had little effect. Additionally, P53 inhibition could reverse the effects of WDR36 knockdown, on both self-renewal maintenance and differentiation potential of human EPS cells. These data implied that WDR36 safeguards self-renewal and pluripotency of human EPS cells, which would extend our understanding of the molecular mechanisms of human EPS cells’ self-renewal and differentiation.
Genomic Analyses for Selective Signatures and Genes Involved in Hot Adaptation Among Indigenous Chickens From Different Tropical Climate Regions
Authors: Xu Nai-Yi , Liu Zhen-Yu , Yang Qi-Meng , Bian Pei-Pei , Li Ming , Zhao Xin
Published: July 2022

Climate change, especially weather extremes like extreme cold or extreme hot, is a major challenge for global livestock. One of the animal breeding goals for sustainable livestock production should be to breed animals with excellent climate adaptability. Indigenous livestock and poultry are well adapted to the local climate, and they are good resources to study the genetic footprints and mechanism of the resilience to weather extremes. In order to identify selection signatures and genes that might be involved in hot adaptation in indigenous chickens from different tropical climates, we conducted a genomic analysis of 65 indigenous chickens that inhabit different climates. Several important unique positively selected genes (PSGs) were identified for each local chicken group by the cross-population extended haplotype homozygosity (XP-EHH). These PSGs, verified by composite likelihood ratio, genetic differentiation index, nucleotide diversity, Tajima’s D, and decorrelated composite of multiple signals, are related to nerve regulation, vascular function, immune function, lipid metabolism, kidney development, and function, which are involved in thermoregulation and hot adaptation. However, one common PSG was detected for all three tropical groups of chickens via XP-EHH but was not confirmed by other five types of selective sweep analyses. These results suggest that the hot adaptability of indigenous chickens from different tropical climate regions has evolved in parallel by taking different pathways with different sets of genes. The results from our study have provided reasonable explanations and insights for the rapid adaptation of chickens to diverse tropical climates and provide practical values for poultry breeding.
Loss of Monoallelic Expression of IGF2 in the Adult Liver Via Alternative Promoter Usage and Chromatin Reorganization
Authors: Ahn Jinsoo , Lee Joonbum , Kim Dong-Hwan , Hwang In-Sul , Park Mi-Ryung , Cho In-Cheol , Hwang Seongsoo , Lee Kichoon
Published: July 2022

In mammals, genomic imprinting operates via gene silencing mechanisms. Although conservation of the imprinting mechanism at the H19/IGF2 locus has been generally described in pigs, tissue-specific imprinting at the transcript level, monoallelic-to-biallelic conversion, and spatio-temporal chromatin reorganization remain largely uninvestigated. Here, we delineate spatially regulated imprinting of IGF2 transcripts, age-dependent hepatic mono- to biallelic conversion, and reorganization of topologically associating domains at the porcine H19/IGF2 locus for better translation to human and animal research. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) of normal and parthenogenetic porcine embryos revealed the paternally hypermethylated H19 differentially methylated region and paternal expression of IGF2. Using a polymorphism-based approach and omics datasets from chromatin immunoprecipitation sequencing (ChIP–seq), whole-genome sequencing (WGS), RNA-seq, and Hi-C, regulation of IGF2 during development was analyzed. Regulatory elements in the liver were distinguished from those in the muscle where the porcine IGF2 transcript was monoallelically expressed. The IGF2 transcript from the liver was biallelically expressed at later developmental stages in both pigs and humans. Chromatin interaction was less frequent in the adult liver compared to the fetal liver and skeletal muscle. The duration of genomic imprinting effects within the H19/IGF2 locus might be reduced in the liver with biallelic conversion through alternative promoter usage and chromatin remodeling. Our integrative omics analyses of genome, epigenome, and transcriptome provided a comprehensive view of imprinting status at the H19/IGF2 cluster.
Cuproptosis-Related lncRNAs are Biomarkers of Prognosis and Immune Microenvironment in Head and Neck Squamous Cell Carcinoma
Authors: Yang Liuqing , Yu Jinling , Tao Lu , Huang Handan , Gao Ying , Yao Jingjing , Liu Zhihui
Published: July 2022

Background: Cuproptosis is a new type of cell death that induces protein toxic stress and eventually leads to cell death. Hence, regulating cuproptosis in tumor cells is a new therapeutic approach. However, studies on cuproptosis-related long noncoding RNA (lncRNA) in head and neck squamous cell carcinoma (HNSC) have not been found. This study aimed to explore the cuproptosis-related lncRNAs prognostic marker and their relationship to immune microenvironment in HNSC by using bioinformatics methods.

Methods: RNA sequencing, genomic mutations, and clinical data of TCGA_HNSC were downloaded from The Cancer Genome Atlas. HNSC patients were randomly assigned to either a training group or a validation cohort. The least absolute shrinkage and selection operator Cox regression and multivariate Cox regression models were used to determine the prognostic model in the training cohort, and its independent prognostic effect was further confirmed in the validation and entire cohorts.

Results: Based on previous literature, we collected 19 genes associated with cuproptosis. Afterward, 783 cuproptosis-related lncRNAs were obtained through coexpression. Cox model revealed and constructed eight cuproptosis-related lncRNAs prognostic marker (AL132800.1, AC090587.1, AC079160.1, AC011462.4, AL157888.1, GRHL3-AS1, SNHG16, and AC021148.2). Patients were divided into high- and low-risk groups based on the median risk score. The Kaplan–Meier survival curve revealed that the overall survival between the high- and low-risk groups was statistically significant. The receiver operating characteristic curve and principal component analysis demonstrated the accurate prognostic ability of the model. Univariate and multivariate Cox regression analysis showed that risk score was an independent prognostic factor. In addition, we used multivariate Cox regression to establish a nomogram of the predictive power of prognostic markers. The tumor mutation burden showed significant differences between the high- and low-risk groups. HNSC patients in the high-risk group responded better to immunotherapy than those in the low-risk group. We also found that risk scores were significantly associated with drug sensitivity in HNSC.

Conclusion: In summary, our study identified eight cuprotosis-related lncRNAs signature of HNSC as the prognostic predictor, which may be promising biomarkers for predicting the benefit of HNSC immunotherapy as well as drug sensitivity.