bluuebunny/crossref_metadata_2025 huggingface dataset:
Next-Generation and Single-Cell Sequencing Approaches to Study Atherosclerosis and Vascular Inflammation Pathophysiology: A Systematic Review
Authors: McQueen Liam W. , Ladak Shameem S. , Abbasciano Riccardo , George Sarah J. , Suleiman M-Saadeh , Angelini Gianni D. , Murphy Gavin J. , Zakkar Mustafa
Published: March 2022

Background and Aims

Atherosclerosis is a chronic inflammatory disease that remains the leading cause of morbidity and mortality worldwide. Despite decades of research into the development and progression of this disease, current management and treatment approaches remain unsatisfactory and further studies are required to understand the exact pathophysiology. This review aims to provide a comprehensive assessment of currently published data utilizing single-cell and next-generation sequencing techniques to identify key cellular and molecular contributions to atherosclerosis and vascular inflammation.

Methods

Electronic searches of Cochrane Central Register of Controlled Trials, MEDLINE, and EMBASE databases were undertaken from inception until February 2022. A narrative synthesis of all included studies was performed for all included studies. Quality assessment and risk of bias analysis was evaluated using the ARRIVE and SYRCLE checklist tools.

Results

Thirty-four studies were eligible for narrative synthesis, with 16 articles utilizing single-cell exclusively, 10 utilizing next-generation sequencing and 8 using a combination of these approaches. Studies investigated numerous targets, ranging from exploratory tissue and plaque analysis, cell phenotype investigation and physiological/hemodynamic contributions to disease progression at both the single-cell and whole genome level. A significant area of focus was placed on smooth muscle cell, macrophage, and stem/progenitor contributions to disease, with little focus placed on contributions of other cell types including lymphocytes and endothelial cells. A significant level of heterogeneity exists in the outcomes from single-cell sequencing of similar samples, leading to inter-sample and inter-study variation.

Conclusions

Single-cell and next-generation sequencing methodologies offer novel means of elucidating atherosclerosis with significantly higher resolution than previous methodologies. These approaches also show significant potential for translatability into other vascular disease states, by facilitating cell-specific gene expression profiles between disease states. Implementation of these technologies may offer novel approaches to understanding the disease pathophysiology and improving disease prevention, management, and treatment.

Systematic Review Registration:https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021229960, identifier: CRD42021229960.
PHREND®—A Real-World Data-Driven Tool Supporting Clinical Decisions to Optimize Treatment in Relapsing-Remitting Multiple Sclerosis
Authors: Braune Stefan , Stuehler Elisabeth , Heer Yanic , van Hoevell Philip , Bergmann Arnfin ,   NeuroTransData Study Group
Published: March 2022

Background

With increasing availability of disease-modifying therapies (DMTs), treatment decisions in relapsing-remitting multiple sclerosis (RRMS) have become complex. Data-driven algorithms based on real-world outcomes may help clinicians optimize control of disease activity in routine praxis.

Objectives

We previously introduced the PHREND® (Predictive-Healthcare-with-Real-World-Evidence-for-Neurological-Disorders) algorithm based on data from 2018 and now follow up on its robustness and utility to predict freedom of relapse and 3-months confirmed disability progression (3mCDP) during 1.5 years of clinical practice.

Methods

The impact of quarterly data updates on model robustness was investigated based on the model's C-index and credible intervals for coefficients. Model predictions were compared with results from randomized clinical trials (RCTs). Clinical relevance was evaluated by comparing outcomes of patients for whom model recommendations were followed with those choosing other treatments.

Results

Model robustness improved with the addition of 1.5 years of data. Comparison with RCTs revealed differences <10% of the model-based predictions in almost all trials. Treatment with the highest-ranked (by PHREND®) or the first-or-second-highest ranked DMT led to significantly fewer relapses (p < 0.001 and p < 0.001, respectively) and 3mCDP events (p = 0.007 and p = 0.035, respectively) compared to non-recommended DMTs.

Conclusion

These results further support usefulness of PHREND® in a shared treatment-decision process between physicians and patients.
Widespread Grylloblattid Insects After the End-Permian Mass Extinction
Authors: Zhang Qianqi , Jarzembowski Edmund A. , Wang Bo
Published: March 2022

The end-Permian mass extinction (EPME) led to a severe terrestrial ecosystem collapse. However, the ecological response of insects to the EPME remains poorly understood. Here, we report a new species assigned to Chauliodites, Chauliodites tongchuanensis sp. nov. (Grylloblattida: Chaulioditidae), from the Middle Triassic Tongchuan Formation of Shaanxi, northwestern China, and redescribe Chauliodites fuyuanensis (Lin, 1978) from the Lower Triassic Kayitou Formation of Yunnan and Chauliodites nanshenghuensis (Lin, 1978) comb. nov. from the Middle Triassic of Guizhou, southwestern China. Our results show that Chauliodites widely distributed after the EPME is probably related to the rise of isoetalean-dominated low-productivity terrestrial ecosystems.
Exploration and Petrogenesis of Corundum-Bearing Pegmatites: A Case Study in Migif-Hafafit Area, Egypt
Authors: Khaleal Farrage M. , Saleh Gehad M. , Lasheen El Saeed R. , Alzahrani Abdullah M. , Kamh Samir Z.
Published: March 2022

A net of pegmatite veins crosscut gneiss and dismembered ophiolitic ultramafic rocks are abundant in the Migif-Hafafit culmination area, South Eastern Desert, Egypt. Some of these pegmatites are corundum-bearing. Corundum-bearing pegmatites are studied in eight localities around the Migif-Hafafit complex. The present study aims to integrate field investigation, whole rock and corundum chemistry, remote sensing studies, and the conventional methods to detect the corundum-bearing pegmatites, which led to finding out the genesis of the corundum mineralization. In addition, the tectonic regime has been detected using bulk rock geochemistry. False-color composite (FCCs), band ratio (BR), principal component analysis (PCA), minimum noise fraction (MNF), decorrelation stretch (DS), and the constrained energy minimization (CEM) image processing algorithms were proposed and applied on Landsat-8 OLI, and Sentinel-2A data to discriminate the exposed lithological units and to detect the corundum-bearing pegmatites in the study area. These detected pegmatites are structurally controlled following the NW-SE direction. The ultramafic rocks are the host of six areas and the gneisses are the host rocks of the two others. Gneisses and pegmatites are characterized by a steep slope of LREEs relative to HREEs with week Eu negative anomaly. The studied pegmatites have both plumasite and marundite. On the other hand, the studied corundum has Al2O3 content up to 99.72 wt% in pegmatite-gneiss and up to 100 wt.% in pegmatite-ultramafics. Corundum is ascribed to metamorphic/metasomatic type according to its chromosphere. Desilication in pegmatites led to the excess of alumina content in the residual melt producing corundum mineralization.
Impact of Microbially Enhanced Coalbed Methane on the Pore Structure of Coal
Authors: Gao Di , Guo Huiling , Guo Bianqing , Tan Kaili , Ren Hengxing
Published: March 2022

Microbially enhanced coalbed methane (MECBM) has important theoretical and practical significance for reforming coal reservoir structure, alleviating greenhouse effects and energy crises and developing new sources of clean energy. In this study, No. 3 coal seams in Qinshui Basin were taken as research objects to analyze the pore structure characteristics after microbial treatment by means of low-temperature nitrogen adsorption (LTNA), mercury porosimetry (MP), and isothermal adsorption/desorption experiments. The results showed that after bioconversion, the specific surface area and pore volume increased from 1.79 m2/g and 0.0018 cm3/g to 4.01 m2/g and 0.0051 cm3/g respectively under liquid nitrogen testing; however, the specific surface area was reduced from 5.398 m2/g to 5.246 m2/g and the pore volume was increased from 0.053 cm3/g to 0.0626 cm3/g under MP. The fractal dimension based on the LTNA data indicated that the fractal dimension of micropores and minipores was increased from 2.73 to 2.60 to 2.89 and 2.81, however the fractal dimension of meso-macropores was decreased from 2.90 to 2.85. The volatile matter and fixed carbon were both reduced from 6.68% to 78.63%–5.09% to 75.63%, and the Langmuir volume and Langmuir pressure were increased from 34.84 cm3/g and 2.73 MPa to 36.34 cm3/g and 3.28 MPa, respectively. This result indicated that microorganism participated in the degradation of coal reservoir and promoted the production of methane gas, the meso-macropores were more obviously modified by microorganism, so that the pore diameter stabilized, the pores became smoother, the specific surface area decreased, and the pore volume increased. These are more beneficial to the adsorption and production of coalbed methane (CBM) after microbial treatment.
A Numerical Experiment of Full Waveform Inversion of Complex Structures Concealed Around a Horizontal Hydraulic Fracturing Well Using Perforation Seismic Data
Authors: Qian Guang , Yu Jiashun , Yuan Jianlong , Fu Xiaobo
Published: March 2022

It is difficult to image the details of complex structures concealed around a horizontal hydraulic fracturing well using seismic data from the ground surface. In this paper, an approach is proposed to solve this problem by non-linear full waveform inversion (FWI) using perforation seismic data. The feasibility of the approach was investigated using numerical modeling based on an experimental model built from the well-known SEG/EAGE overthrust model, which contains complex geological structures with faults. First, seismic modeling was performed to produce experimental synthetic data, including three sets of perforation seismic data recorded by different acquisition systems deployed in observation wells and on the ground surface, and another set of conventional seismic reflection data with both sources and receivers deployed on the ground surface. Then, FWI was performed separately on each data set using an initial velocity model which was heavily smoothed to remove the target structures. The inversion results show that the concealed complex structures around the well were successfully recovered by FWI using perforation data, while the benchmark image from the FWI using conventional seismic data was poor. Particularly, the experiments also demonstrated that FWI using perforation seismic data can image the faults around a horizontal hydraulic fracturing well, while this is unable to achieve using conventional ground surface seismic data. This conclusion was also proved to be valid for noisy data deteriorated either by synthetic Gaussian or field noises. Further experiments demonstrated that FWI using perforation data recorded from wells outperformed that of surface data in terms of structure imaging accuracy characterized by quantitative errors.
Influence Evaluation of Sensor Coordinate Error on Microseismic Source Location
Authors: Li Tao , Chen Bing-Rui , Wang Qing , Zhu Xin-Hao , Wang Xu , Xie Ming-Xing
Published: March 2022

In microseismic (MS) source localization, it is usually assumed that the sensor coordinates are accurate. However, there are generally measurement errors for the sensor coordinates in practical engineering, which severely affect the location accuracy of the MS sources. Therefore, based on the least square linear inversion equation, the theoretical analysis shows that the location error is proportional to the sensor coordinate error. To reduce the systematic error of the MS source location, a calculation method for the sensor coordinate error threshold is proposed. First, the theoretical arrival time of each sensor is calculated. Then, the sensor coordinate error is added and combined with the original sensor coordinate for location. Finally, the sensor coordinate error threshold that makes the location results reach the source location accuracy is obtained. Furthermore, based on this method and assuming that the sensor coordinate error is in a normal distribution, a comprehensive evaluation index of the sensor coordinates is proposed to evaluate the influence of the sensor coordinates on the MS source location. The application results of the Beiminghe Iron Mine in Hebei Province show that the farther the source is from the sensor array, the smaller the sensor coordinate error threshold is. The sensor coordinate error threshold in the sensor array is larger than that outside the sensor array. The sensor coordinate error threshold decreases rapidly in the sensor array and slowly outside the sensor array. After removing sensor No. 201, which has the greatest influence on MS source location and has a large measurement error, the average location accuracy of blasting test events is improved by 25.74%. The research results have a certain guiding significance for the sensor coordinate measurement.
Effectiveness of Panretinal Photocoagulation Plus Intravitreal Anti-VEGF Treatment Against PRP Alone for Diabetic Retinopathy: A Systematic Review With Meta-Analysis
Authors: Zhang Wuyue , Geng Jinsong , Sang Aimin
Published: March 2022

Objective

To compare the efficacy and safety of panretinal photocoagulation (PRP) combined with intravitreal anti-vascular endothelial growth factor (anti-VEGF) against PRP monotherapy for diabetic retinopathy (DR).

Methods

We searched Pubmed, Cochrane Library, Web of Science, Embase, and Science Direct Register of Controlled Trials from April 2011 to January 2021 to identify the randomized trials that compared the efficacy and safety between PRP combined with intravitreal anti-VEGF and PRP monotherapy for DR. We searched in the following databases between April 2011 and January 2021: Pubmed, Cochrane Library, Web of Science, Embase, and Science Direct without any restriction of countries or article type. The outcome measures were the best-corrected visual acuity (BCVA), neovascularization on the disc (NVD), neovascularization elsewhere (NVE), central macula thickness (CMT), and total retinal volume over time (FAS), and we also observed the adverse events (AEs) between the two groups.

Results

A total of 351 studies were identified, of which 11 studies were included in this meta-analysis (N = 1,182 eyes). Compared with PRP monotherapy, PRP plus anti-VEGF combination treatment produced a mean reduction in BCVA in units of logMAR of -0.23 [95% CI -0.32, -0.15] or a mean improvement in BCVA in units of letters of 4.99 [95% CI 3.79, 6.19], and also yielded a mean reduction in NVD of -28.41 [95% CI -30.30, -26.52], in NVE of -1.33 [95% CI -1.52, -1.14], in CMT of -1.33 [95% CI -1.52, -1.14], or in total FAS. No significant difference was observed on the risk of AEs as vitreous hemorrhage, elevation in intraocular pressure, and cataract between the two different treatments.

Conclusion

PRP with anti-VEGF combination treatment can achieve the ideal efficacy on DR by improving BCVA and NV regression, with no potential increased incidence of AEs, which proves that the combination therapy is an efficient therapeutic strategy that could improve the management of patients with DR.
Intraoperative Neuromonitoring: Evaluating the Role of Continuous IONM and IONM Techniques for Emerging Surgical and Percutaneous Procedures
Authors: McManus Catherine , Kuo Jennifer Hong
Published: March 2022

Intraoperative nerve monitoring (IONM) is a tool used during thyroid surgery to assist in the identification of the recurrent laryngeal nerve (RLN). Multiple IONM systems that exist for thyroidectomy require intubation with an endotracheal tube. Given that one of the advantages of thermal ablation procedures, such as radiofrequency ablation, is that they can be done safely without the use of general anesthesia, nerve monitoring systems that utilize cutaneous surface electrodes have been developed, though are not widely available in the United States. This article will review the use of IONM for RFA including the cutaneous surface electrode system.
Methylome Analysis in Nonfunctioning and GH-Secreting Pituitary Adenomas
Authors: Giuffrida Giuseppe , D’Argenio Valeria , Ferraù Francesco , Lasorsa Vito Alessandro , Polito Francesca , Aliquò Federica , Ragonese Marta , Cotta Oana Ruxandra , Alessi Ylenia , Oteri Rosaria , Di Maggio Federica , Asmundo Alessio , Romeo Petronilla Daniela , Spagnolo Federica , Pastore Lucio , Angileri Filippo Flavio , Capasso Mario , Cannavò Salvatore , Aguennouz M’Hammed
Published: March 2022

Pituitary adenomas (PAs), usually benign lesions, can sometimes present with “aggressive” features (rapid growth, local invasiveness, scarce response to conventional treatments). Despite the fact that a few genetic alterations have been associated to this clinical behavior, the role of epigenetic modifications, mainly methylation and miRNAs activity, is now opening new frontiers in this field. We evaluated the methylation profile of 21 PA (11 GH-omas, 10 nonfunctioning tumors—NFPAs) samples from TNS surgery and 5 normal pituitaries, collected at our neurosurgery between 2015 and 2017. DNA was extracted and sequenced, selecting 184,841 target regions. Moreover, methylation profiles were correlated with demographic, radiological, and clinicopathological features. NFPAs showed higher methylation levels vs. GH-omas, with 178 differentially methylated regions (DMRs) mainly consisting of noncoding and intronic sequences, and mostly localized in the open sea regions. We also found three hypermethylated genes (C7orf50, GNG7, and BAHCC1) involved in tumorigenesis processes and potentially influencing pituitary tumor pathophysiology. Among the clinicopathological features, only the maximum diameter resulted significantly higher in NFPAs. Our data provide further evidence of the complex epigenetic background of pituitary tumors. In line with the current literature, we confirmed a significant prevalence of hypermethylation in NFPAs vs. GH-omas, whose pathophysiological consequence is yet to be defined.
Immune Cell Regulation of White Adipose Progenitor Cell Fate
Authors: Altun Irem , Yan Xiaocheng , Ussar Siegfried
Published: March 2022

Adipose tissue is essential for energy storage and endocrine regulation of metabolism. Imbalance in energy intake and expenditure result in obesity causing adipose tissue dysfunction. This alters cellular composition of the stromal cell populations and their function. Moreover, the individual cellular composition of each adipose tissue depot, regulated by environmental factors and genetics, determines the ability of the depots to expand and maintain its endocrine and storage function. Thus, stromal cells modulate adipocyte function and vice versa. In this mini-review we discuss heterogeneity in terms of composition and fate of adipose progenitor subtypes and their interactions with and regulation by different immune cell populations. Immune cells are the most diverse cell populations in adipose tissue and play essential roles in regulating adipose tissue function via interaction with adipocytes but also with adipocyte progenitors. We specifically discuss the role of macrophages, mast cells, innate lymphoid cells and T cells in the regulation of adipocyte progenitor proliferation, differentiation and lineage commitment. Understanding the factors and cellular interactions regulating preadipocyte expansion and fate decision will allow the identification of novel mechanisms and therapeutic strategies to promote healthy adipose tissue expansion without systemic metabolic impairment.
Energy Security and Energy Poverty in Emerging Economies: A Step Towards Sustainable Energy Efficiency
Authors: Nasir Muhammad Hamid , Wen Jun , Nassani Abdelmohsen A. , Haffar Mohamed , Igharo Amechi Endurance , Musibau Hammed Oluwaseyi , Waqas Muhammad
Published: March 2022

This paper presents the energy security, energy poverty, and mediating role of environmental tax policy. The environmental tax policy affects energy consumption and energy poverty. The research applied multiple, comprehensive, and relevant sets of indicators to measure energy security, energy poverty, and environmental consideration of energy poverty through environmental tax. The study used a mathematical composite indicator and an econometric estimation to conduct an empirical estimation. The study used annual data from 1990 to 2018 and concluded that long-run associations between energy security, energy poverty, and environmental tax have been characterized by the linear and asymmetric association to specify hidden cointegration behavior among the trilemma. The results show how policymakers have clouded the decision to implement appropriate energy security to mitigate energy poverty in Vietnam through environmental tax.Results show that from 2001 to 2016 in Vietnam, energy security was low and energy poverty was high, but after 2016, it can be seen that there is a dramatic change in energy security and energy poverty. The year 2018 shows the highest energy security index score (0.92) and the lowest energy poverty index score (0.12). Since 2017, Vietnam’s rural electrification plan has provided electricity to 100% of Vietnam’s population. The plan provides electricity access to 82 million people who traditionally have no grid access.
Characterisation of Two Wood-Waste and Coffee Bean Husk Biochars for the Removal of Micropollutants from Water
Authors: Van Limbergen Thessa , Roegiers Inez Henriette , Bonné Robin , Mare Federica , Haeldermans Tom , Joos Bjorn , Nouwen Olivier , Manca Jean V. , Vangronsveld Jaco , Thijs Sofie
Published: March 2022

The inclusion of bioaugmented low-cost biochar in current wastewater treatment technologies is a promising way to enhance the removal and degradation of emerging contaminants. In this paper, the properties of two wood waste biochars (wood waste mix - AB, and date palm fiber wood - PDF), and coffee bean husks (COF), produced at four temperatures (350, 450, 500, 550°C) were compared, and investigated in the presence of Geobacter sulfurreducens or a mixed freshwater stream bacterial culture to understand their potential for the adsorption and biotransformation of two types of pesticides (thiacloprid, pirimicarb), and two pharmaceuticals (ibuprofen, diclofenac). Biochar yield was similar for all three biochars and ranged between 30 and 35%. The ash content of PDF and COF was significantly higher than AB. pH and electrical conductivity (EC) were initially high for COF (pH: 7.4–8; EC: 3–4.27 mS/cm) and PDF (pH: 7.7–10.1; EC: 4–6.24 mS/cm) after 24 h, but stabilized at neutral pH and <0.5 mS/cm EC after additional washes. COF and AB did not leach high concentrations of chloride (<10 mg/L), nitrate (<1 mg/L), nor sulphate (<76 mg/L), this in contrast to date palm fiber wood (PDF) with 1760 mg/L Cl− (550°C), and 846 mg/L sulphate (350°C). Lower pyrolysis temperatures reduced leachable anions. The biochars were highly (ultra)microporous with little meso- and macroporosity. The adsorption experiments showed that AB and COF biochars were both suited to sorb more than 90% of the initially spiked 10 ppm pirimicarb, AB removed 50.2% of the initial diclofenac concentration compared to only 5% for the no-biochar control, and both biochars could remove about 55% of the initially spiked thiacloprid, and 40% of the ibuprofen. In the presence of a mixed culture, on average 30% more thiacloprid and ibuprofen was removed from the supernatant by AB and COF than the sterile control. This work shows that selected wood-waste feedstocks and low pyrolysis temperature can produce environmentally-safe biochars that have suitable characteristics to sorb emergent pollutants from water. These materials could be further studied in multi-pollution sorption/competition experiments, and in larger environmental wastewater treatment systems.
On-Farm Relationships Between Agricultural Practices and Annual Changes in Organic Carbon Content at a Regional Scale
Authors: Dupla Xavier , Lemaître Téo , Grand Stéphanie , Gondret Karine , Charles Raphaël , Verrecchia Eric , Boivin Pascal
Published: March 2022

Both soil quality degradation and climate change mitigation issues emphasize the need to increase, or at least stabilize, the topsoil organic carbon content (wt%) in arable land. This on-farm study aimed at measuring the impact of agricultural practices on changes in soil organic carbon (SOC) content over 10 years. A total of 120 fields belonging to 120 farms representative of the cropping systems and soil properties in Western Switzerland (Lake Geneva region) was randomly selected. The field 0–20 cm topsoil was sampled at a 10-years interval, and the corresponding cropping practices were gathered using farmer’s interviews and the mandatory records of yearly practices at field level in Swiss-farms. Only 1) organic matter inputs and 2) cover-crop intensity were significantly correlated to SOC increase while 3) the soil tillage intensity and 4) the soil saturation in carbon expressed as a SOC to clay content ratio were correlated to SOC decrease. Among others, temporary meadows were not correlated to changes in SOC content mainly due to increased tillage and decreased cover-crops between meadows. Organic farming did not correlate either with SOC changes due to the large tillage intensity applied for weed control. The observed SOC content changes ranged from −56‰ to +74‰ and were well explained by a linear regression model with additive effect of the four identified SOC change factors. The additivity of these factors means that farmers can emphasize the methods of their choice when regenerating their soils. This study advocates that strict no-till is not required at low carbon saturation level (small SOC:Clay ratio). However, as carbon saturation increases, conservation tillage and then no-till practices become necessary to further increase SOC contents. These findings are in accordance with previous studies showing that since 2015 SOC is increasing at more than +4‰ on average in the region and provide practical insights to further manage the transition of farming systems towards soil regeneration.
Search Foraging Strategies of Migratory Raptors Under Different Environmental Conditions
Authors: Vidal-Mateo Javier , Benavent-Corai José , López-López Pascual , García-Ripollés Clara , Mellone Ugo , De la Puente Javier , Bermejo Ana , Urios Vicente
Published: March 2022

Several studies have shown in different organisms how their movements can be fitted to different patterns to optimize search of food resources. According to abundance and availability of resources, different strategies will be optimal, such as Lévy and Brownian random search. We analyze the movement patterns of four species of migratory raptors with different degrees of ecological specialization in diet during the breeding and wintering periods to evaluate the differences according to species and season: the Egyptian Vulture, the Short-toed Snake Eagle, the Booted Eagle, and the Red Kite. From GPS locations, we obtained a set of segments and lengths that were analyzed to verify their fitting to the functions of Lévy and Brownian strategies. Egyptian Vulture’s trajectories fitted to both patterns during the breeding period, whereas during the wintering period most trajectories fitted a Brownian pattern. In the case of the Short-toed Eagle, fit was greater to a Lévy strategy throughout the year, while Booted Eagles and Red Kites exhibited a combination of search patterns. These differences could be accounted for different feeding strategies and environmental context over the annual cycle. In species with a specialized diet (i.e., Short-toed Eagle) the Lévy pattern would maximize the encounters with scarce and unpredictable resources, whereas for species with a broad trophic niche (i.e., Booted Eagle and Red Kite), movements could be adapted to exploit different resources according to their abundance. Scavengers like the Egyptian Vulture shift also between search strategies according to the distribution of carrion. Therefore, the analysis of food search patterns can be used as an indirect indicator to track changes in food availability across a broad range of environmental conditions. This is particularly important under the current context of global change which is largely expected to affect migratory species that spend their vital cycle in distant areas.
Ethnoichthyology and Ethnotaxonomy of the Kichwa Indigenous People of Arawanu (Arajuno), in the Ecuadorian Amazon
Authors: Tobes Ibon , Carrillo-Moreno Carolina , Guarderas-Flores Lida , Jácome-Negrete Iván , Velázquez-Cárdenas Yetlanezi
Published: March 2022

The Amazon Basin is home to a great number of Indigenous nationalities that have coevolved with aquatic habitats and fish resulting in a precise traditional ecological knowledge. Nevertheless, this biocultural heritage is threatened by the degradation of rivers and fisheries, and cultural erosion. This research was designed and carried out in the community ofArawanu(Arajuno in Spanish), in the Ecuadorian Amazon, and was requested by the local Kichwa people looking for guidance to gather, systematize and disseminate their ethnoichthyological knowledge. Data collection was carried out through participatory workshops using the pile sorting technique in group dynamics, to identify, name and classify local fish and compile biocultural information about them. From the Linnaean taxonomic perspective, 86 taxa were identified, included in 26 families, and corresponded with 16 Kichwa ethnofamilies and 58 ethnospecies. Five classification levels were identified: (I)Aycha: unique beginner–Animalia kingdom; (II)Yaku Aycha: life form–Pisces superclass; (III)Ayllukuna: ethnofamilies–Linnaean families; (IV) Ethnogenera–Linnaean genus; and (V) Ethnospecies–Linnaean species. A one-to-one correspondence was registered between 35 Kichwa ethnospecies and Linnean species, along with one case of over-differentiation and 21 cases of subdifferentiation (Type A: 7; Type B: 14). The Kichwa ethnoichthyological classification is multidimensional and considers attributes like skin and scales, fishbones and spines, meat quality, body shape, diet, and salience. Of the 58 ethnospecies, 38 were valued for consumption, while medicinal and spiritual uses were mentioned for 40 of them. The participatory work created a forum to discuss the value and threats to ichthyofauna and freshwater systems, enabled the dissemination of their biocultural heritage, and highlighted the cultural relevance of hydro-social ecosystems in their livelihood. The collected information may be critical to adapt local education systems to the Kichwa worldview and to pass down traditional ecological knowledge to future generations, fostering a respectful, careful and conscious relationship between humans and nature. Our results offer a solid and novel information compilation and practical guidance for participatory ethnobiological surveys. Additionally, the ethnobiological and the ethnotaxonomical information establishes the basis to develop sustainable fishing strategies and promote conservation of the local ichthyofauna.
Comparative Adult Mortality and Relative Attractiveness of Spotted-Wing Drosophila (Diptera: Drosophilidae) to Novel Attract-and-Kill (ACTTRA SWD) Formulations Mixed With Different Insecticides
Authors: Babu Arun , Rodriguez-Saona Cesar , Sial Ashfaq A.
Published: March 2022

Since its first appearance in California in 2008 and subsequent spread across the continental United States, the spotted-wing drosophila,Drosophila suzukiiMatsumura, has become an economically damaging pest of multiple stone and soft-skinned fruits in the United States. The adjuvant ACTTRA SWD, when mixed with a suitable insecticide, constitutes an innovative attract-and-kill tactic that can be applied as a sprayable bait to manageD. suzukii. As an adjuvant, growers can mix ACTTRA SWD with any insecticide recommended forD. suzukiimanagement in a specific crop; however, to achieve this, the efficacy of this adjuvant incorporated with various insecticides needs testing. This research aims to test the suitability of nine insecticides added to two ACTTRA SWD formulations (named OR1 and TD) to maintain the formulation’s attractiveness toD. suzukiiadults and in resulting mortality. We conducted a series of two-choice bioassays to test the relative attraction ofD. suzukiito ACTTRA SWD formulations prepared with and without a specific insecticide. Additionally, we tested the efficacy of ACTTRA SWD formulations mixed with insecticides in managingD. suzukiiby using no-choice efficacy bioassays. Adding Mustang Maxx (zeta-cypermethrin) to ACTTRA SWD OR1 significantly improvedD. suzukiiadult attraction to the formulation, while Azera (azadirachtin + pyrethrins) significantly reduced attraction to both ACTTRA SWD formulations. Among the insecticides tested, we identified Danitol (fenpropathrin), Exirel (cyantraniliprole), Malathion (malathion), Mustang Maxx, and Entrust (spinosad) as suitable insecticide additives for both ACTTRA SWD formulations. The results from this study will assist growers in selecting proper insecticide components when preparing attract-and-kill formulations of the new adjuvant ACTTRA SWD.
Transcription Factor KLF7 Promotes Osteoclast Differentiation by Suppressing HO-1
Authors: Chen Changhong , Hu Fei , Miao Shichang , Sun Liping , Jiao Yajun , Xu Mingwei , Huang Xin , Yang Ying , Zhou Rongkui
Published: March 2022

Background: Osteoporosis is a common orthopedic disease with high prevalence in patients older than 50 years. Osteoporosis is often detected only after the fracture and is hard to treat. Therefore, it is of great significance to explore the molecular mechanism of the occurrence of osteoporosis.

Methods: The expression of Heme oxygenase-1 (HO-1) in people with different bone mineral density (BMD) was analyzed based on public databases. GenHacncer and JASPAR databases were adopted to search and verify the upstream transcription factor of HO-1. qRT-PCR, western blot and tartrate-resistant acid phosphatase assays were performed to explore the impact of HO-1 and Kruppel-like factor 7 (KLF7) on osteoclast differentiation. Chromatin immunoprecipitation (ChIP) assay confirmed the binding relationship between KLF7 and HO-1. Finally, Hemin, the agonist of HO-1, was applied in rescue assays, thereby verifying the mechanism of KLF7 modulating osteoclast differentiation by HO-1.

Results: Bioinformatics analysis revealed that HO-1 was highly-expressed while KLF7 lowly-expressed in people with high BMD. Besides, a potential binding site of KLF7 was found on the promoter region of HO-1. ChIP assay further manifested the targeting relationship between HO-1 and KLF7. Western blot and TRAP staining unveiled that osteoclast differentiation was suppressed by HO-1, while facilitated by KLF7. Rescue experiments indicated that over-expressed HO-1 could reverse of the promoting effect of KLF7 on osteoclast differentiation.

Conclusion: The study confirmed that osteoclast differentiation was promoted by KLF7 constraining HO-1, thereby facilitating osteoporosis. The cognation of the pathogenesis of osteoporosis was further enriched. New treatment could be developed on this basis.
F2RL3 Methylation in the Peripheral Blood as a Potential Marker for the Detection of Coronary Heart Disease: A Case-Control Study
Authors: Zhao Xiaojing , Zhu Liya , Yin Qiming , Xu Zhenguo , Jia Qian , Yang Rongxi , He Kunlun
Published: March 2022

Background and Aims: Previous work has shown the association between blood-based methylation of coagulation factor II receptor-like 3 gene (F2RL3) and cardiovascular mortality in Caucasians. However, the diagnostic value of F2RL3 methylation for CHD is still unknown. The aim of our study was to evaluate the association between blood-based F2RL3 methylation and the risk of CHD in the Chinese population.

Methods: The methylation level of F2RL3 was quantified by mass spectrometry in a case-control study with 180 CHD cases and 184 controls. The association between F2RL3 methylation intensity and CHD was assessed by logistic regression models, controlling confounding factors.

Results: The hypomethylation in F2RL3_A amplicon was significantly associated with CHD (odds ratio (ORs) per -10% methylation: 1.22–1.42, p < 0.035 for six out of seven CpG loci). Specifically, this significant association was observed in elderly CHD patients (≥60 years), myocardial infarction (MI) patients, heart failure patients and the patients with minor to medium cardiac function impairment (NYHA Ⅰ&Ⅱ CHD cases) (ORs per -10% methylation: 1.35–1.58, 1.32–2.00, 1.29–1.43, 1.25–1.44; p < 0.024, 0.033, 0.035, 0.025, respectively). However, F2RL3_B CpG sites showed no or very weak association with CHD. The combination of F2RL3_A_CpG_1 and F2RL3_A_CpG_3 methylation levels could efficiently discriminate CHD, MI, heart failure, NYHA I&II CHD, and elderly CHD patients from controls (area under curve (AUC) = 0.75, 0.79, 0.75, 0.76, and 0.82, respectively).

Conclusion: We propose blood-based F2RL3 methylation as a potential biomarker for CHD, especially for people with older age or with the status of MI. The combination of F2RL3 methylation and conventional risk factors might be an approach to evaluate CHD at early stage.
A Mendelian Randomization Study of the Effect of Tea Intake on Type 2 Diabetes
Authors: Zhang Yanan , Wang Ruiqing , Tang Xinhua , Wang Yanjun , Guo Ping , Wang Shukang , Liu Jing
Published: March 2022

Background: The association reported between tea intake and type 2 diabetes (T2D) is inconsistent in previous studies and remains controversial. We aimed to explore the causal relationship between tea intake, T2D, and glycemic traits including hemoglobin A1c (HbA1c), fasting plasma glucose (FPG), fasting serum insulin (FSI), and homeostasis model of insulin resistance (HOMA-IR) levels.

Methods: A 2-sample Mendelian randomization (MR) was performed using summary statistics from large-scale genome-wide association studies of tea intake from the UK Biobank, T2D from the DIAGRAM consortium, and glycemic traits from the Magic consortium. The findings were verified through sensitivity analyses using various MR methods with different model assumptions and by comprehensively evaluating the influence of pleiotropy effects and outliers.

Results: With the use of a two-sample MR with inverse variance-weighted method, the odds ratio per unit SD change of tea intake (SD: 2.85 cups/day) for T2D, HbA1c, FPG, FSI, and HOMA-IR levels was 0.949 (95% CI 0.844–1.067, p = 0.383), 0.994 (95% CI 0.975–1.013, p = 0.554), 0.996 (95% CI 0.978–1.015, p = 0.703), 0.968 (95% CI 0.948–0.986, p = 0.001), and 0.953 (95% CI 0.900–1.009, p = 0.102), respectively. The results were consistent with those of the other six methods that we used with different model assumptions, suggesting that the findings were robust and convincing. We also performed various sensitivity analyses for outlier removal, pleiotropy detection, and leave-one-out analysis.

Conclusion: Our MR results did not support the causal effect of tea intake on T2D and crucial glycemic traits. These findings suggest that previous observational studies may have been confounded.
Case Report: Identification of a De novo C19orf12 Variant in a Patient With Mitochondrial Membrane Protein–Associated Neurodegeneration
Authors: Yang Yue , Zhang Shijie , Yang Wenming , Wei Taohua , Hao Wenjie , Cheng Ting , Wang Jiuxiang , Dong Wei , Qian Nannan
Published: March 2022

Background: Mitochondrial membrane protein–associated neurodegeneration (MPAN) mostly arises as an autosomal recessive disease and is caused by variants in the chromosome 19 open reading frame 12 (C19orf12) gene. However, a few C19orf12 monoallelic truncating de novo variants have been reported and segregated as autosomal dominant traits in some cases.

Methods: We performed whole-exome sequencing and analyzed genes related to neurodegeneration associated with brain iron accumulation for pathogenic variants. The identified variants were confirmed by Sanger sequencing and tested using in silico tools.

Results: The patient had an onset of depression at the age of 22 years, which rapidly progressed to severe dystonia, dementia, and bladder and bowel incontinence. Neuroimaging showed hypointensity in the substantia nigra and the globus pallidum, with additional frontotemporal atrophy. Genetic analysis revealed a single complex de novo variant [c.336_338delinsCACA (p.Trp112CysfsTer40)] in the C19orf12 gene.

Conclusion: This study enriches the genetic spectrum and clinical features of C19orf12 variants and provides additional evidence of the variable inheritance pattern of MPAN.
Construction and Bioinformatics Analysis of circRNA-miRNA-mRNA Network in Acute Myocardial Infarction
Authors: Zhou Jin , He Shaolin , Wang Boyuan , Yang Wenling , Zheng Yuqi , Jiang Shijiu , Li Dazhu , Lin Jibin
Published: March 2022

Background: Acute myocardial infarction (AMI) is one of the main fatal diseases of cardiovascular diseases. Circular RNA (circRNA) is a non-coding RNA (ncRNA), which plays a role in cardiovascular disease as a competitive endogenous RNA (ceRNA). However, their role in AMI has not been fully clarified. This study aims to explore the mechanism of circRNA-related ceRNA network in AMI, and to identify the corresponding immune infiltration characteristics.

Materials and Methods: The circRNA (GSE160717), miRNA (GSE24548), and mRNA (GSE60993) microarray datasets of AMI were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed circRNAs (DEcircRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) were identified by the “limma” package. After integrating the circRNA, miRNA and mRNA interaction, we constructed a circRNA-miRNA-mRNA network. The “clusterProfiler” package and String database were used for functional enrichment analysis and protein-protein interaction (PPI) analysis, respectively. After that, we constructed a circRNA-miRNA-hub gene network and validated the circRNAs and mRNAs using an independent dataset (GSE61144) as well as qRT-PCR. Finally, we used CIBERSORTx database to analyze the immune infiltration characteristics of AMI and the correlation between hub genes and immune cells.

Results: Using the “limma” package of the R, 83 DEcircRNAs, 54 DEmiRNAs, and 754 DEmRNAs were identified in the microarray datasets of AMI. Among 83 DEcircRNAs, there are 55 exonic DEcircRNAs. Then, a circRNA-miRNA-mRNA network consists of 21 DEcircRNAs, 11 DEmiRNAs, and 106 DEmRNAs were predicted by the database. After that, 10 hub genes from the PPI network were identified. Then, a new circRNA-miRNA-hub gene network consists of 14 DEcircRNAs, 7 DEmiRNAs, and 9 DEmRNAs was constructed. After that, three key circRNAs (hsa_circ_0009018, hsa_circ_0030569 and hsa_circ_0031017) and three hub genes (BCL6, PTGS2 and PTEN) were identified from the network by qRT-PCR. Finally, immune infiltration analysis showed that hub genes were significantly positively correlated with up-regulated immune cells (neutrophils, macrophages and plasma cells) in AMI.

Conclusion: Our study constructed a circRNA-related ceRNA networks in AMI, consists of hsa_circ_0031017/hsa-miR-142-5p/PTEN axis, hsa_circ_0030569/hsa-miR-545/PTGS2 axis and hsa_circ_0009018/hsa-miR-139-3p/BCL6 axis. These three hub genes were significantly positively correlated with up-regulated immune cells (neutrophils, macrophages and plasma cells) in AMI. It helps improve understanding of AMI mechanism and provides future potential therapeutic targets.
pitpβ_w Encoding Phosphatidylinositol Transfer Protein Is Involved in Female Differentiation of Chinese Tongue Sole, Cynoglossus semilaevis
Authors: Sun Yuxuan , Zhang Mengqian , Cheng Peng , Gong Zhihong , Li Xihong , Wang Na , Wei Min , Xu Xiaodong , Xu Wenteng
Published: March 2022

Phosphatidylinositol transfer protein (pitp) plays an important role in phospholipid transfer in animals. A pitp variant (pitpβ_w) in Chinese tongue sole was identified by transcriptomic analysis for its female-biased expression. The coding sequence of pitpβ_w was 816 bp, encoding a 371-amino-acid protein. pitpβ_w showed female-biased expression and was relatively high in brain, muscle, and ovary tissues. In different developmental stages of the ovary, pitpβ_w could be detected from 40 days until 3 years post hatching, and the highest expression was observed at 90 days. In situ hybridization revealed that pitpβ_w was predominantly localized in early-stage oocytes (I–III stages). After siRNA-mediated knockdown of pitpβ_w in an ovarian cell line, the expression of sox9a was reduced, while that of figla_tv1 and sox9b was significantly increased. Our findings suggest that pitpβ_w might be involved in female differentiation and early oogenesis.
An Integrated Platform for Serological Detection and Vaccination of COVID-19
Authors: Wei Sung-Chan , Hsu Wei-Ting , Chiu Chun-Hsiang , Chang Feng-Yee , Lo Huei-Ru , Liao Chuan-Yu , Yang Hwai-I , Chou Yu-Chi , Tsai Chih-Hsuan , Chao Yu-Chan
Published: March 2022

Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is an ongoing pandemic. Detection and vaccination are essential for disease control, but they are distinct and complex operations that require significant improvements. Here, we developed an integrated detection and vaccination system to greatly simplify these efforts. We constructed recombinant baculoviruses to separately display the nucleocapsid (N) and spike (S) proteins of SARS-CoV-2. Insect cells infected by the recombinant baculoviruses were used to generate a cell-based system to accurately detect patient serum. Notably, although well-recognized by our newly developed detection system in which S-displaying insect cells acted as antigen, anti-S antibodies from many patients were barely detectable by Western blot, evidencing that COVID-19 patients primarily produce conformation-dependent anti-S antibodies. Furthermore, the same baculovirus constructs can display N (N-Bac) or S (S-Bac) on the baculovirus envelope and serve as vector vaccines. Animal experiments show that S-Bac or N-Bac immunization in mice elicited a strong and specific antibody response, and S-Bac in particular stimulated effective neutralizing antibodies without the need for adjuvant. Our integrated system maintains antigen conformation and membrane structure to facilitate serum detection and antibody stimulation. Thus, compared with currently available technologies, our system represents a simplified and efficient platform for better SARS-CoV-2 detection and vaccination.