bluuebunny/crossref_metadata_2025 huggingface dataset:
Modflow-setup: Robust automation of groundwater model construction
Authors: Leaf Andrew T. , Fienen Michael N.
Published: September 2022

In an age of both big data and increasing strain on water resources, sound management decisions often rely on numerical models. Numerical models provide a physics-based framework for assimilating and making sense of information that by itself only provides a limited description of the hydrologic system. Often, numerical models are the best option for quantifying even intuitively obvious connections between human activities and water resource impacts. However, despite many recent advances in model data assimilation and uncertainty quantification, the process of constructing numerical models remains laborious, expensive, and opaque, often precluding their use in decision making. Modflow-setup aims to provide rapid and consistent construction of MODFLOW groundwater models through robust and repeatable automation. Common model construction tasks are distilled in an open-source, online code base that is tested and extensible through collaborative version control. Input to Modflow-setup consists of a single configuration file that summarizes the workflow for building a model, including source data, construction options, and output packages. Source data providing model structure and parameter information including shapefiles, rasters, NetCDF files, tables, and other (geolocated) sources to MODFLOW models are read in and mapped to the model discretization, using Flopy and other general open-source scientific Python libraries. In a few minutes, an external array-based MODFLOW model amenable to parameter estimation and uncertainty quantification is produced. This paper describes the core functionality of Modflow-setup, including a worked example of a MODFLOW 6 model for evaluating pumping impacts to a lake in central Wisconsin, United States.
Evolution Characteristics of the Flows Around the Tibetan Plateau and the Relationship with the Climate in China in Winter
Authors: Zhang Yongli , Zuo Hongchao , Gao Xiaoqing , Fan Guangzhou , Lv Shihua , Hua Wei , Dong Longxiang
Published: September 2022

During the winter half-year (previous October–April), the mid-latitude westerlies flows around the Tibetan Plateau (TP) and generate a dynamic low-pressure trough on its south side and a high-pressure ridge on its north side. In this study, we define the vorticity perturbation as the difference between local vorticity and the meridionally-averaged vorticity. Then, the difference of averaged vorticity perturbation at 600 hPa in the two key areas where the trough and ridge are located is used to represent the intensity of the flows around the Tibetan Plateau (FAT). The evolution characteristics of FAT in the winter half-year, as well as in autumn, winter and spring, are analyzed. Moreover, under global warming, in winter the relationship of FAT to the precipitation and temperature in China are discussed. The results show that FAT steadily exists on both sides of TP during the winter half-year. With the north-south migration of the mid-latitude westerlies, the FAT gradually strengthens in autumn, with the strongest intensity and the widest range in winter, and begins to weaken in spring. The intensity of FAT (IFAT) has a decreasing trend and a quasi-4a period variation on the interannual scale in all the time, both of which are closely related to the mid-latitude westerlies upstream of TP. Represented by the winter when IFAT is strongest, the IFAT is significantly correlated to the change of precipitation and temperature in most parts of China under global warming, especially in the convergence area over central-eastern China. There is also a significant correlation between IFAT and the precipitation and temperature anomalies in Northwest China, TP, and Northeast China. This relationship between the FAT anomaly and the climate anomaly in China in winter can be well explained by analyzing the anomalies of large-scale circulation, outgoing longwave radiation and water vapor flux divergence. The FAT anomaly maybe one of the reasons for the climate extreme events in China in winter.
A geothermal heat flow model of Africa based on random forest regression
Authors: Al-Aghbary M. , Sobh M. , Gerhards C.
Published: September 2022

Geothermal heat flow (GHF) data measured directly from boreholes are sparse. Purely physics-based models for geothermal heat flow prediction require various simplifications and are feasible only for few geophysical observables. Thus, data-driven multi-observable approaches need to be explored for continental-scale models. In this study, we generate a geothermal heat flow model over Africa using random forest regression, originally based on sixteen different geophysical and geological quantities. Due to an intrinsic importance ranking of the observables, the number of observables used for the final GHF model has been reduced to eleven (among them are Moho depth, Curie temperature depth, gravity anomalies, topography, and seismic wave velocities). The training of the random forest is based on direct heat flow measurements collected in the compilation of (Lucazeau et al., Geochem. Geophys. Geosyst. 2019, 20, 4001–4024). The final model reveals structures that are consistent with existing regional geothermal heat flow information. It is interpreted with respect to the tectonic setup of Africa, and the influence of the selection of training data and observables is discussed.
Deciphering metasomatic events beneath Mindszentkálla (Bakony-Balaton Highland Volcanic Field, western Pannonian Basin) revealed by single-lithology and composite upper mantle xenoliths
Authors: Patkó Levente , Kovács Zoltán , Liptai Nóra , Aradi László E. , Berkesi Márta , Ciazela Jakub , Hidas Károly , Garrido Carlos J. , Kovács István J. , Szabó Csaba
Published: September 2022

Single-lithology and composite xenoliths from Mindszentkálla (Bakony-Balaton Highland Volcanic Field) in the Carpathian-Pannonian region record geochemical evolution of the subcontinental lithospheric mantle. The dominant single-lithology xenoliths are orthopyroxene-rich (22 vol% on average) harzburgites. Three composite xenoliths contain either two or more domains including dunite, olivine-orthopyroxenite, orthopyroxenite, apatite-bearing websterite and amphibole-phlogopite-bearing vein. The presence of different lithologies is a result of at least two metasomatic events that affected the lithospheric mantle. The first event resulted in orthopyroxene enrichment thus formed harzburgitic mantle volumes (Group I xenoliths). Major- and trace element distributions of the bulk harzburgites differ from the geochemical trends expected in residues of mantle melting. In contrast, petrographic and geochemical attributes suggest that the harzburgite was formed by silica-rich melt - peridotitic wall rock interactions in a supra-subduction zone. Within the Group I xenoliths, two subgroups were identified based on the presence or lack of enrichment in U, Pb and Sr. Since these elements are fluid mobile, their enrichment in certain Group I xenoliths indicate reaction with a subduction-related fluid, subsequent to the harzburgite formation. The effect of a second event overprints the features of the Group I xenoliths and is evidenced in all domains of two composite xenoliths (Group II xenoliths). The general geochemical character involves enrichment of basaltic major and minor elements (Fe, Mn, Ti, Ca) in the rock-forming minerals and convex-upward rare earth element (REE) patterns in clinopyroxenes. We suggest that the different domains represent reaction products with variably evolved basaltic melts of a single magmatic event. The tectonic background to the formation of Group I xenoliths is likely linked to the subduction of oceanic crust during the Mesozoic–Paleogene. This happened far from the current position of Mindszentkálla, to where the lithosphere, including the metasomatized mantle volume, was transferred via plate extrusion. The Group II xenoliths appear to bear the geochemical signature of a younger (Neogene) basaltic magmatic event, likely the same that produced the host basalt transporting the xenoliths to the surface.
Identification and validation of a signature involving voltage-gated chloride ion channel genes for prediction of prostate cancer recurrence
Authors: Luo Yong , Liu Xiaopeng , Li Xiaoxiao , Zhong Weide , Lin Jingbo , Chen Qingbiao
Published: September 2022

Voltage-gated chloride ion channels (CLCs) are transmembrane proteins that maintain chloride ion homeostasis in various cells. Accumulating studies indicated CLCs were related to cell growth, proliferation, and cell cycle. Nevertheless, the role of CLCs in prostate cancer (PCa) has not been systematically profiled. The purpose of this study was to investigate the expression profiles and biofunctions of CLCs genes, and construct a novel risk signature to predict biochemical recurrence (BCR) of PCa patients. We identified five differentially expressed CLCs genes in our cohort and then constructed a signature composed of CLCN2 and CLCN6 through Lasso-Cox regression analysis in the training cohort from the Cancer Genome Atlas (TCGA). The testing and entire cohorts from TCGA and the GSE21034 from the Gene Expression Omnibus (GEO) were used as internal and independent external validation datasets. This signature could divide PCa patients into the high and low risk groups with different prognoses, was apparently correlated with clinical features, and was an independent excellent prognostic indicator. Enrichment analysis indicated our signature was primarily concentrated in cellular process and metabolic process. The expression patterns of CLCN2 and CLCN6 were detected in our own cohort based immunohistochemistry staining, and we found CLCN2 and CLCN6 were highly expressed in PCa tissues compared with benign tissues and positively associated with higher Gleason score and shorter BCR-free time. Functional experiments revealed that CLCN2 and CLCN6 downregulation inhibited cell proliferation, colony formation, invasion, and migration, but prolonged cell cycle and promoted apoptosis. Furthermore, Seahorse assay showed that silencing CLCN2 or CLCN6 exerted potential inhibitory effects on energy metabolism in PCa. Collectively, our signature could provide a novel and robust strategy for the prognostic evaluation and improve treatment decision making for PCa patients.
Metabolic effects of prolactin and the role of dopamine agonists: A review
Authors: Kirsch Polly , Kunadia Jessica , Shah Shruti , Agrawal Nidhi
Published: September 2022

Prolactin is a polypeptide hormone that is well known for its role in reproductive physiology. Recent studies highlight its role in neurohormonal appetite regulation and metabolism. Elevated prolactin levels are widely associated with worsening metabolic disease, but it appears that low prolactin levels could also be metabolically unfavorable. This review discusses the pathophysiology of prolactin related metabolic changes, and the less commonly recognized effects of prolactin on adipose tissue, pancreas, liver, and small bowel. Furthermore, the effect of dopamine agonists on the metabolic profiles of patients with hyperprolactinemia are discussed as well.
Complement receptor C5aR1 on osteoblasts regulates osteoclastogenesis in experimental postmenopausal osteoporosis
Authors: Bülow Jasmin Maria , Renz Nikolai , Haffner-Luntzer Melanie , Fischer Verena , Schoppa Astrid , Tuckermann Jan , Köhl Jörg , Huber-Lang Markus , Ignatius Anita
Published: September 2022

In recent years, evidence has accumulated that the complement system, an integral part of innate immunity, may be involved in the regulation of bone homeostasis as well as inflammatory bone loss, for example, in rheumatoid arthritis and periodontitis. Complement may also contribute to osteoporosis development, but investigation of the mechanism is limited. Using mice with a conditional deletion of the complement anaphylatoxin receptor C5aR1, we here demonstrated that C5aR1 in osteoblasts (C5aR1Runx2-Cre mice) or osteoclasts (C5aR1LysM-Cre mice) did not affect physiological bone turnover or age-related bone loss in either sex, as confirmed by micro-computed tomography, histomorphometry, and biomechanical analyses of the bone and by the measurement of bone turnover markers in the blood serum. When female mice were subjected to ovariectomy (OVX), a common model for postmenopausal osteoporosis, significant bone loss was induced in C5aR1fl/fl and C5aR1LysM-Cre mice, as demonstrated by a significantly reduced bone volume fraction, trabecular number and thickness as well as an increased trabecular separation in the trabecular bone compartment. Confirming this, the osteoclast number and the receptor activator of nuclear factor k-B (RANK) ligand (RANKL) serum level were significantly elevated in these mouse lines. By contrast, C5aR1Runx2-Cre mice were protected from bone loss after OVX and the serum RANKL concentration was not increased after OVX. These data suggested that bone cell-specific C5aR1 may be redundant in bone homeostasis regulation under physiological conditions. However, C5aR1 on osteoblasts was crucial for the induction of bone resorption under osteoporotic conditions by stimulating RANKL release, whereas C5aR1 on osteoclasts did not regulate OVX-induced bone loss. Therefore, our results implicate C5aR1 on osteoblasts as a potential target for treating postmenopausal osteoporosis.
Gut microbiome and metabolic activity in type 1 diabetes: An analysis based on the presence of GADA
Authors: Luo Sihui , Yue Tong , Liu Ziyu , Yang Daizhi , Xu Mengyun , Ding Yu , Jiang Weiwei , Xu Wen , Yan Jinhua , Weng Jianping , Zheng Xueying
Published: September 2022

Objective

Type 1 diabetes (T1D) progression is affected by circulating glutamic acid decarboxylase antibody (GADA) that persist for many years. This study aimed at investigating whether and how the gut microbiome and its correlated metabolites change in T1D with the presence of GADA.

Methods

We used a radiobinding assay to measure GADA titers and identify the 49 T1D patients with GADA+ and 52 T1D patients with GADA-. The fresh feces and serum were analyzed using 16S rRNA gene sequencing and GC/MS. Then gut microbiome and serum metabolites were compared between the GADA+ patients and the GADA- patients. The association between gut microbial community and metabolites was assessed using the Spearman’s rank correlation.

Results

The gut microbiome in diversity, composition, and function differed between these two groups. The abundance of genus Alistipes, Ruminococcus significantly increased in patients with GADA+ compared to that observed in the samples of GADA-. There were 54 significantly altered serum metabolites associated with tryptophan metabolism, phenylalanine, and tyrosine biosynthesis in individuals with GADA+ compared with those of GADA-For the serum metabolites, compared with those of GADA-, there were 54 significantly different metabolites with tryptophan metabolism, phenylalanine, and tyrosine and tryptophan biosynthesis decreased in individuals with GADA+. The abundance of Alistipes was positively correlated with altered metabolites involved in tryptophan metabolism.

Conclusion

We demonstrate that T1D patients with GADA+ are characterised by aberrant profiles of gut microbiota and serum metabolites. The abundance of Alistipes disturbances may participate in the development of T1D patients with GADA by modulating the host’s tryptophan metabolism. These findings extend our insights into the association between the gut microbiota and tryptophan metabolism and GADA and might be targeted for preventing the development of T1D.
Elevated triglyceride-glucose (TyG) index predicts impaired islet β-cell function: A hospital-based cross-sectional study
Authors: Chen Zi , Wen Jie
Published: September 2022

Objective

To explore the relationship between the TyG index and the insulin secretion function of pancreatic β-cells, and to determine the possibility of the TyG index in predicting β-cell dysfunction and the development of diabetes.

Methods

A cross-sectional study was performed among 914 participants who took their annual health checkups at the Third Xiangya Hospital. The early- and late-phase pancreatic β-cell secretion was assessed based on the results of the oral glucose tolerance test (OGTT). In addition to anthropometric parameters and laboratory parameters, information about health-related habits and disease histories was obtained from the National Physical Examination Questionnaire. Partial correlation analysis was used to study the relationship between the TyG index and pancreatic β-cell function. The receiver operating characteristic (ROC) curve was used to calculate the cut-off points of the TyG index in predicting β-cell dysfunction. According to the OGTT results and medical history, the participants were categorized into three groups: the normal glucose tolerance group (NGT, n=276), the impaired glucose regulation group (IGT, n=323), and the diabetes group (DM, n=315). The correlation between the TyG index and β-cell function among the three groups and the association between the TyG index and glucose metabolic conditions were further explored.

Results

The TyG index was negatively correlated with the indexes that reflect the early and late secretory function of β-cells, not only in the NGT group but also in the IGT and DM group. The minimum cut-off values for the TyG index to identify the risk of early- and late-phase β-cell dysfunction are 9.08 and 9.2 respectively. The TyG indexes of the IGT and DM group were higher than that of the NGT group, and with the growth of the TyG index, the risk of prediabetes and diabetes increased significantly.

Conclusion

Increased TyG index is associated with impaired β-cell function regardless of the glucose metabolic conditions. The TyG index is an alternative indicator for predicting β-cell dysfunction.
Developmental exposure to indoor flame retardants and hypothalamic molecular signatures: Sex-dependent reprogramming of lipid homeostasis
Authors: Kozlova Elena V. , Denys Maximillian E. , Benedum Jonathan , Valdez Matthew C. , Enriquez Dave , Bishay Anthony E. , Chinthirla Bhuvaneswari D. , Truong Edward , Krum Julia M. , DiPatrizio Nicholas V. , Deol Poonamjot , Martins-Green Manuela , Curras-Collazo Margarita C.
Published: September 2022

Polybrominated diphenyl ethers (PBDEs) are a class of flame-retardant organohalogen pollutants that act as endocrine/neuroendocrine disrupting chemicals (EDCs). In humans, exposure to brominated flame retardants (BFR) or other environmentally persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) and novel organophosphate flame retardants has been associated with increasing trends of diabetes and metabolic disease. However, the effects of PBDEs on metabolic processes and their associated sex-dependent features are poorly understood. The metabolic-disrupting effects of perinatal exposure to industrial penta-PBDE mixture, DE-71, on male and female progeny of C57BL/6N mouse dams were examined in adulthood. Dams were exposed to environmentally relevant doses of PBDEs daily for 10 weeks (p.o.): 0.1 (L-DE-71) and 0.4 mg/kg/d (H-DE-71) and offspring parameters were compared to corn oil vehicle controls (VEH/CON). The following lipid metabolism indices were measured: plasma cholesterol, triglycerides, adiponectin, leptin, and liver lipids. L-DE-71 female offspring were particularly affected, showing hypercholesterolemia, elevated liver lipids and fasting plasma leptin as compared to same-sex VEH/CON, while L- and H-DE-71 male F1 only showed reduced plasma adiponectin. Using the quantitative Folch method, we found that mean liver lipid content was significantly elevated in L-DE-71 female offspring compared to controls. Oil Red O staining revealed fatty liver in female offspring and dams. General measures of adiposity, body weight, white and brown adipose tissue (BAT), and lean and fat mass were weighed or measured using EchoMRI. DE-71 did not produce abnormal adiposity, but decreased BAT depots in L-DE-71 females and males relative to same-sex VEH/CON. To begin to address potential central mechanisms of deregulated lipid metabolism, we used RT-qPCR to quantitate expression of hypothalamic genes in energy-regulating circuits that control lipid homeostasis. Both doses of DE-71 sex-dependently downregulated hypothalamic expression of Lepr, Stat3, Mc4r, Agrp, Gshr in female offspring while H-DE-71 downregulated Npy in exposed females relative to VEH/CON. In contrast, exposed male offspring displayed upregulated Stat3 and Mc4r. Intestinal barrier integrity was measured using FITC-dextran since it can lead to systemic inflammation that leads to liver damage and metabolic disease, but was not affected by DE-71 exposure. These findings indicate that maternal transfer of PBDEs disproportionately endangers female offspring to lipid metabolic reprogramming that may exaggerate risk for adult metabolic disease.
Investigation on distribution of electro-thermal coupling fields influenced by HVDC bushing insulation properties
Authors: Teng Chenyuan , Ding Yichao , Zhang Youbing , Zhang Yunxiao , Huang Meng , Zhan Zhenyu
Published: September 2022

Bushing is an indispensable component in high voltage direct current (HVDC) transmission project. As the main insulating material possesses poor thermal conductivity and negative temperature coefficient (NTC) electrical resistivity, HVDC bushing suffers from the distortion of electro-thermal-coupled fields. Therefore, it is urgent to reveal the influence of electrical resistivity-temperature characteristic and thermal conductivity on the DC electric field distribution within bushing insulation, guiding the design and application advanced insulating materials. Here, the simulation of temperature and DC electric field distribution within a 400 kV bushing are carried out. The results show that the optimization of NTC effect and thermal conductivity of an insulating material is able to obtain a more uniform electric field distribution through homogenizing the electric resistivity distribution within bushing insulation. The activation energy of the insulating material has a similar variation trend with the maximum electric field within bushing insulation, which has a potential to represent the temperature dependence of electrical resistivity of insulating materials. It also shows that the reduction of DC electric field by increasing the thermal conductivity has a saturation feature. As a result, the suppression of the NTC effect should be considered together to obtain a smaller electric field within HVDC bushing. The research study provides a new idea to regulate the DC electric field distribution, which is beneficial to the design of advanced insulating materials.
Economic-environmental dispatch for the integrated energy system considering off-design conditions
Authors: Xu Yurui , Deng Youjun , Guo Xiangwei , Wang Jiarui , Zhang Jiajun
Published: September 2022

The integrated energy system (IES) is recognized as a promising energy utilization approach enabled to both improve the energy efficiency and reduce pollutant emissions. Although the economic-environmental dispatch (EED) problem of the IES has been widely studied, the fact that the IES is operated under off-design conditions, having a significant influence on the efficiency of energy devices, is neglected usually, resulting in the scheduled operations, for the IES could not be accurate enough in many actual situations. This study investigates the EED problem of the IES under off-design conditions. Technically, by integrating an efficiency correction process into the traditional energy hub (EH) model, a dynamic energy hub (DEH) model is first formulated for adapting itself to variable energy conversion efficiencies. Then, a deep neural network (DNN)-based efficiency correction method is proposed to predict and correct the time-varying efficiency of energy devices based on three main off-design conditions including the load rate, air temperature, and pressure. A multi-objective EED model is finally formulated for the IES, with the framework of the DEH model, aiming at establishing a trade-off between operational cost and emitted pollutants. Case studies show that the proposed approach helps in enhancing the accuracy of IES dispatch while having a good performance in both the operational cost and pollutant emission reduction.
Multi-layer state of health balancing control for a battery-based energy storage system to extend cycle life based on active equalization circuits
Authors: Li Xiaohang , Yin Xin , Tian Zhongbei , Jiang Xinyu , Jiang Lin , Smith Jeremy
Published: September 2022

State of health (SoH) imbalance causes capacity waste and cycle life reduction of the battery-based energy storage systems (BESS), which demands SoH balancing control of the parallel-connected packs and the series-connected cells of the BESS. This study proposed a multi-layer SoH balancing control to extend the cycle life of the BESS. For the series-connected battery cells, active equalization circuits based on the fly-back converter are used to exchange energy between cells and control the depth of discharge (DoD) of cells to achieve the SoH balance. For the parallel-connected packs, SoH is equalized by distributing the output power based on the SoH balancing principle and the minimum power distribution constraints of packs caused by the bidirectional balancing current among the series-connected cells are considered. Because the proposed method achieves the SoH balancing by utilizing the active equalization circuits to transfer the energy between the cells with different SoH, it can achieve higher capacity and energy utilization efficiency and lower heat release compared with the passive equalization typology that dissipates the energy. The effectiveness of the proposed method is verified by a case study based on a 3-packs-15-cells BESS. Simulation results show that this method can prolong the cycle life of BESS by about 52.9% compared with the active SoC balancing method using the same fly-back converter and 18.3% with a passive multi-layer SoH balancing method, respectively.
Integument carotenoid-based colouration reflects contamination to perfluoroalkyl substances, but not mercury, in arctic black-legged kittiwakes
Authors: Costantini David , Blévin Pierre , Bustnes Jan Ove , Esteve Valérie , Gabrielsen Geir Wing , Herzke Dorte , Humann-Guilleminot Ségolène , Moe Børge , Parenteau Charline , Récapet Charlotte , Bustamante Paco , Chastel Olivier
Published: September 2022

Anthropogenic activities are introducing multiple chemical contaminants into ecosystems that act as stressors for wildlife. Perfluoroalkyl substances (PFAS) and mercury (Hg) are two relevant contaminants that may cause detrimental effects on the fitness of many aquatic organisms. However, there is a lack of information on their impact on the expression of secondary sexual signals that animals use for mate choice. We have explored the correlations between integument carotenoid-based colourations, blood levels of carotenoids, and blood levels of seven PFAS and of total Hg (THg) in 50 adult male black-legged kittiwakes (Rissa tridactyla) from the Norwegian Arctic during the pre-laying period, while controlling for other colouration influencing variables such as testosterone and body condition. Kittiwakes with elevated blood concentrations of PFAS (PFOSlin, PFNA, PFDcA, PFUnA, or PFDoA) had less chromatic but brighter bills, and brighter gape and tongue; PFOSlin was the pollutant with the strongest association with bill colourations. Conversely, plasma testosterone was the only significant correlate of hue and chroma of both gape and tongue, and of hue of the bill. Kittiwakes with higher concentrations of any PFAS, but not of THg, tended to have significantly higher plasma concentrations of the carotenoids astaxanthin, zeaxanthin, lutein, and cryptoxanthin. Our work provides the first correlative evidence that PFAS exposure might interfere with the carotenoid metabolism and the expression of integument carotenoid-based colourations in a free-living bird species. This outcome may be a direct effect of PFAS exposure or be indirectly caused by components of diet that also correlate with elevated PFAS concentrations (e.g., proteins). It also suggests that there might be no additive effect of THg co-exposure with PFAS on the expression of colourations. These results call for further work on the possible interference of PFAS with the expression of colourations used in mate choice.
Vegetation complexity and pool size predict species richness of forest birds
Authors: Remeš Vladimír , Harmáčková Lenka , Matysioková Beata , Rubáčová Lucia , Remešová Eva
Published: September 2022

Disentangling regional and local drivers of species richness in communities is a long-term focus of ecology. Regional species pools affect local communities by providing their constituent species. Additionally, the amount and variety of resources enhance diversity locally. Here, we investigated whether the same ecological factor (vegetation complexity) shapes both regional and local species richness and thus drives local diversity both indirectly (via pool size) and directly (via facilitating the coexistence of species). We studied passerine birds of woodlands and forests in eastern Australia. We quantified regional species pool size and sampled local bird communities at 63 transects spanning 3,000 km. We estimated canopy height both regionally using satellite imagery and locally using vegetation sampling in the field. We studied how species pool size changed with regional canopy height and water availability, and how local species richness changed with pool size and local canopy height. Local species richness increased with both local canopy height and the size of the regional species pool. Pool size, in turn, increased with regional canopy height, which itself increased with water availability. Moreover, local species richness expressed as a proportion of the regional pool also increased with local canopy height. In sum, vegetation complexity indexed by canopy height had a doubly positive effect on local species richness: indirectly by promoting a large regional species pool and directly by facilitating the coexistence of disproportionately many species locally. Regional pools were larger in tall forests probably due to the legacy of extensive moist forests that once covered most of Australia, thus providing a sizeable potential for speciation, diversification, and species persistence. Local species richness was greater in tall, more productive forests with more vegetation layers likely due to more and varied resources (i.e., more potential niches), allowing the coexistence of more individuals and species of consumers.
Taxon-specific ultraconserved element probe design for phylogenetic analyses of scale insects (Hemiptera: Sternorrhyncha: Coccoidea)
Authors: Liu Dajun , Niu Minmin , Lu Yunyun , Wei Jiufeng , Zhang Hufang
Published: September 2022

Scale insects (Coccoidea) are morphologically specialized members of the order Hemiptera, with 56 families recognized to date. However, the phylogenetic relationships within and among families are poorly resolved. In this study, to further characterize the phylogenetic relationships among scale insects, an ultraconserved element (UCE) probe set was designed specifically for Coccoidea based on three low-coverage whole genome sequences along with three publicly available genomes. An in silico test including eight additional genomes was performed to evaluate the effectiveness of the probe set. Most scale insect lineages were recovered by the phylogenetic analysis. This study recovered the monophyly of neococcoids. The newly developed UCE probe set has the potential to reshape and improve our understanding of the phylogenetic relationships within and among families of scale insects at the genome level.
A new CCCH-type zinc finger-related lncRNA signature predicts the prognosis of clear cell renal cell carcinoma patients
Authors: Shen Cheng , Chen Zhan , Jiang Jie , Zhang Yong , Xu Wei , Peng Rui , Zuo Wenjing , Jiang Qian , Fan Yihui , Fang Xingxing , Zheng Bing
Published: September 2022

Background: Clear cell renal cell carcinoma (ccRCC) is the main component of renal cell carcinoma (RCC), and advanced ccRCC frequently indicates a poor prognosis. The significance of the CCCH-type zinc finger (CTZF) gene in cancer has been increasingly demonstrated during the past few years. According to studies, targeted radical therapy for cancer treatment may be a revolutionary therapeutic approach. Both lncRNAs and CCCH-type zinc finger genes are essential in ccRCC. However, the predictive role of long non-coding RNA (lncRNA) associated with the CCCH-type zinc finger gene in ccRCC needs further elucidation. This study aims to predict patient prognosis and investigate the immunological profile of ccRCC patients using CCCH-type zinc finger-associated lncRNAs (CTZFLs).

Methods: From the Cancer Genome Atlas database, RNA-seq and corresponding clinical and prognostic data of ccRCC patients were downloaded. Univariate and multivariate Cox regression analyses were conducted to acquire CTZFLs for constructing prediction models. The risk model was verified using receiver operating characteristic curve analysis. The Kaplan-Meier method was used to analyze the overall survival (OS) of high-risk and low-risk groups. Multivariate Cox and stratified analyses were used to assess the prognostic value of the predictive feature in the entire cohort and different subgroups. In addition, the relationship between risk scores, immunological status, and treatment response was studied.

Results: We constructed a signature consisting of eight CTZFLs (LINC02100, AC002451.1, DBH-AS1, AC105105.3, AL357140.2, LINC00460, DLGAP1-AS2, AL162377.1). The results demonstrated that the prognosis of ccRCC patients was independently predicted by CTZFLs signature and that the prognosis of high-risk groups was poorer than that of the lower group. CTZFLs markers had the highest diagnostic adequacy compared to single clinicopathologic factors, and their AUC (area under the receiver operating characteristic curve) was 0.806. The overall survival of high-risk groups was shorter than that of low-risk groups when patients were divided into groups based on several clinicopathologic factors. There were substantial differences in immunological function, immune cell score, and immune checkpoint expression between high- and low-risk groups. Additionally, Four agents, including ABT737, WIKI4, afuresertib, and GNE 317, were more sensitive in the high-risk group.

Conclusion: The Eight-CTZFLs prognostic signature may be a helpful prognostic indicator and may help with medication selection for clear cell renal cell carcinoma.
Genetic and immune crosstalk between severe burns and blunt trauma: A study of transcriptomic data
Authors: Chen Xiaoming , Wang Kuan , Li Dazhuang , Zhao Mingyue , Huang Biao , Su Wenxing , Yu Daojiang
Published: September 2022

Background:Severe burns and blunt trauma can lead to multiple organ dysfunction syndrome, the leading cause of death in intensive care units. In addition to infection, the degree of immune inflammatory response also affects prognosis. However, the characteristics and clinical relevance of the common mechanisms of these major diseases are still underexplored.

Methods:In the present study, we performed microarray data analysis to identify immune-related differentially expressed genes (DEGs) involved in both disease progression in burns and blunt trauma. Six analyses were subsequently performed, including gene enrichment analysis, protein‐protein interaction (PPI) network construction, immune cell infiltration analysis, core gene identification, co-expression network analysis, and clinical correlation analysis.

Results:A total of 117 common immune-related DEGs was selected for subsequent analyses. Functional analysis emphasizes the important role of Th17 cell differentiation, Th1 and Th2 cell differentiation, Cytokine-cytokine receptor interaction and T cell receptor signaling pathway in these two diseases. Finally, eight core DEGs were identified using cytoHubba, including CD8A, IL10, CCL5, CD28, LCK, CCL4, IL2RB, and STAT1. The correlation analysis showed that the identified core DEGs were more or less significantly associated with simultaneous dysregulation of immune cells in blunt trauma and sepsis patients. Of these, the downregulation of CD8A and CD28 had a worse prognosis.

Conclusion:Our analysis lays the groundwork for future studies to elucidate molecular mechanisms shared in burns and blunt trauma. The functional roles of identified core immune-related DEGs and dysregulated immune cell subsets warrant further in-depth study.
Case report: Difference in outcomes between two cases of Hailey-Hailey disease treated with apremilast
Authors: Yamaga Misako , Miyauchi Toshinari , Peh Jin Teng , Itamoto Sota , Mai Yosuke , Iwata Hiroaki , Nomura Toshifumi , Ujiie Hideyuki
Published: September 2022

Hailey-Hailey disease (HHD) is a rare autosomal dominant acantholytic dermatosis clinically characterized by recurrent erythematous plaques and erosions mainly on the intertriginous regions. Although HHD seriously affects quality of life, conventional treatments often fail to provide long-term relief for most patients. The effectiveness of apremilast, a phosphodiesterase-4 inhibitor, against severe HHD was first reported in 2018, and after further testing, this agent is currently expected to be established as an efficacious and safe therapeutic option. Here we report two cases of HHD treated with apremilast which showed opposite outcomes. Although the case with extremely severe symptoms showed remarkable and long-lasting improvement with apremilast used after acute treatment with oral corticosteroid, the other case, with milder symptoms treated only with apremilast, showed no improvement. Our transcriptome analysis using skin samples collected prior to apremilast administration revealed the involvement of the NF-κB signaling pathway, which is related to the responses to bacteria and other organisms. However, this pathway was more strongly activated in case 2 than in case 1, suggesting that the steroid treatment preceding apremilast may have been effective and supportive in the apremilast-responding case. One of the two cases highlights the potential of apremilast as a treatment option for HHD, but the other underlines the difficulties in managing HHD and the complexity of the disease background. The accumulation of cases and larger clinical studies are expected to precisely evaluate the safety and efficacy of apremilast, and the potential for therapies in combination with conventional treatments.
Case report: A novel missense variant in melanopsin associates with delayed sleep phenotype: Whole genome sequencing study
Authors: Smieszek Sandra P. , Polymeropoulos Christos M. , Birznieks Gunther , Polymeropoulos Mihael H.
Published: September 2022

Melanopsin (OPN4) is a blue light-sensitive opsin-type G-protein coupled receptor. It is highly expressed in photosensitive retinal ganglion cells which mediate responses to light, including regulation of sleep, circadian photoentrainment, and pupillary light response. Mutations in OPN4 were shown to affect responses to light, ultimately affecting the regulation of circadian rhythms and sleep. In this study, we describe a male carrier of the OPN4 missense variant diagnosed with delayed sleep-wake phase disorder (DSWPD), with a consistent recurrent pattern of delayed sleep onset The rs143641898 [NM_033282.4:c.502C>T p.(Arg168Cys)] variant in the OPN4 gene was shown in a functional study to render the OPN4 protein non-functional. The variant is rare and likely increases the risk of DSWPD via its direct effect on the melanopsin pathway. This study offers useful insights for the differential diagnosis and ultimately treatment of DSWPD risk in which patients carry pathogenic variants in the OPN4 gene.
Identification and characterization of extrachromosomal circular DNA in alcohol induced osteonecrosis of femoral head
Authors: Zhou Tingting , Ma Shiqiang , Zhao Yunchao , Guo Donghui , Wang Hengjun , Kuang Mingjie , Li Xiaoming
Published: September 2022

Alcohol-induced osteonecrosis of the femoral head (AIONFH) is a complicated refractory bone disease seen in the clinic. The pathogenesis of AIONFH is still controversial. Extrachromosomal circular DNA (eccDNA) elements have been indicated ubiquitously exist in eukaryotic genomes. However, the characteristics and biological functions of eccDNAs remain unclear in AIONFH. In this study, eccDNAs from AIONFH samples (n = 7) and fracture of femoral neck samples as a control (n = 7) were purified by removing linear DNA and rolling circle amplification. High-throughput sequencing and bioinformatics analysis were performed to study the characterization and biofunction of eccDNAs. We identified more than 600,000 unique eccDNAs. The number of detected eccDNAs in AIONFH was less than that in the control, and eccDNA formation may be related to transcription or other characteristics of coding genes. The eccDNA lengths are mainly distributed between 0.1 kb and 1 kb, with a major peak in 0.358 kb. The bioinformatic analysis showed that 25 significant genes were detected, including MAP3K1, ADCY1, CACNA1S, and MACF1, which contributed to regulating bone formation. GO and KEGG analyses suggested that the related genes derived from exons mainly affected metabolic processes and signal transduction, and bone metabolism-related pathways, such as the MAPK pathway and TGF-β pathway, were enriched. EccDNAs in AIONFH are common and may play an important role in pathogenesis by regulating bone metabolism.
Development and verification of a prognostic model for colon cancer on pyroptosis-related genes
Authors: Wu Zizhen , Wang Bo , Ye Yingjiang , Wang Shan , Jiang Kewei
Published: September 2022

Background: Recently, the role of pyroptosis in cancer has attracted people’s attention, but its function in colon cancer remains unclear. This study aimed to construct a pyroptosis-related model that can effectively predict the prognosis of patients with colon cancer and explore the potential functions of pyroptosis-related genes.

Methods: We identified 40 differentially expressed PRGs between colon cancer and normal colon tissues. The model was established using the least absolute shrinkage and selection operator (LASSO) Cox regression method, and the patients were divided into high- and low-risk groups. Finally, we verified its biological function in vitro based on three PRGs and demonstrated discrepant expression of PRGs within colon cancer and non-tumor tissues at the protein level with immunohistochemistry.

Results: A pyroptosis-related prognosis model was constructed, which divided 446 patients with colon cancer into high- and low-risk groups. Kaplan–Meier analysis results showed that the survival of patients with colon cancer in the high-risk group was worse than that in the low-risk group. Finally, we also confirmed that this score is an independent prognostic factor for colon cancer progression.

Conclusion: In summary, the model established by three PRGs was a reliable indicator for predicting prognosis, suggesting that pyroptosis might be a noteworthy therapeutic target in CC.
Ecological niche modelling as a tool to identify candidate indigenous chicken ecotypes of Tigray (Ethiopia)
Authors: Gebru Gebreslassie , Belay Gurja , Vallejo-Trujillo Adriana , Dessie Tadelle , Gheyas Almas , Hanotte Olivier
Published: September 2022

The Tigray region is an ancient entry route for the domestic chickens into Africa. The oldest African chicken bones were found in this region at Mezber, a pre-Aksumite rural farming settlement. They were dated to around 800–400 BCE. Since then, the farming communities of the region have integrated chicken into their livelihoods. The region is also recognised for its high chicken-to-human population ratio and diverse and complex geography, ranging from 500 to 4,000 m above sea level (m.a.s.l.). More than 15 agro-ecological zones have been described. Following exotic chicken introductions, the proportion of indigenous chicken is now 70% only in the region. It calls for the characterisation of indigenous Tigrayan chicken ecotypes and their habitats. This study reports an Ecological Niche Modelling using MaxEnt to characterise the habitats of 16 indigenous village chicken populations of Tigray. A total of 34 ecological and landscape variables: climatic (22), soil (eight), vegetation, and land cover (four), were included. We applied Principal Component Analysis correlation, and MaxentVariableSelection procedures to select the most contributing and uncorrelated variables. The selected variables were three climatic (bio5 = maximum temperature of the warmest month, bio8 = mean temperature of the wettest quarter, bio13 = precipitation of the wettest month), three vegetation and land cover (grassland, forest land, and cultivated land proportional areas), and one soil (clay content). Following our analysis, we identified four main chicken agro-ecologies defining four candidates indigenous Tigrayan chicken ecotypes. The study provides baseline information for phenotypic and genetic characterisation as well as conservation interventions of indigenous Tigrayan chickens.
Genome-wide characterization and identification of cyclophilin genes associated with leaf rust resistance in bread wheat (Triticum aestivum L.)
Authors: Tyagi Sandhya , Jha Shailendra Kumar , Kumar Anuj , Saripalli Gautam , Bhurta Ramesh , Hurali Deepak T. , Sathee Lekshmy , Mallick Niharika , Mir Reyazul Rouf , Chinnusamy Viswanathan , Vinod
Published: September 2022

Cyclophilins (CYPs) are a group of highly conserved proteins involved in host-pathogen interactions in diverse plant species. However, the role of CYPs during disease resistance in wheat remains largely elusive. In the present study, the systematic genome-wide survey revealed a set of 81TaCYPgenes from three subfamilies (GI, GII, and GIII) distributed on all 21 wheat chromosomes. The gene structures ofTaCYP members were found to be highly variable, with 1–14 exons/introns and 15 conserved motifs. A network of miRNA targets withTaCYPsdemonstrated thatTaCYPswere targeted by multiple miRNAs and vice versa. Expression profiling was done in leaf rust susceptible Chinese spring (CS) and the CS-Ae. Umbellulataderived resistant IL “Transfer (TR). Three homoeologousTaCYPgenes (TaCYP24,TaCYP31, andTaCYP36) showed high expression and three homoeologousTaCYPgenes (TaCYP44,TaCYP49, andTaCYP54) showed low expression in TR relative to Chinese Spring. Most of the other TaCYPs showed comparable expression changes (down- or upregulation) in both contrasting TR and CS. Expression of 16TaCYPs showed significant association (p< 0.05) with superoxide radical and hydrogen peroxide abundance, suggesting the role ofTaCYPsin downstream signaling processes during wheat-leaf rust interaction. The differentially expressingTaCYPs may be potential targets for future validation using transgenic (overexpression, RNAi or CRISPR-CAS) approaches and for the development of leaf rust-resistant wheat genotypes.