bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential of immune-related genes as promising biomarkers for premature coronary heart disease through high throughput sequencing and integrated bioinformatics analysis
Authors: Wang Haiming , Shao Junjie , Lu Xuechun , Jiang Min , Li Xin , Liu Zifan , Zhao Yunzhang , Zhou Jingjing , Lin Lejian , Wang Lin , Xu Qiang , Chen Yundai , Zhang Ran
Published: August 2022

Background

Coronary heart disease (CHD) is the most common progressive disease that is difficult to diagnose and predict in the young asymptomatic period. Our study explored a mechanistic understanding of the genetic effects of premature CHD (PCHD) and provided potential biomarkers and treatment targets for further research through high throughput sequencing and integrated bioinformatics analysis.

Methods

High throughput sequencing was performed among recruited patients with PCHD and young healthy individuals, and CHD-related microarray datasets were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified by using R software. Enrichment analysis and CIBERSORT were performed to explore the enriched pathways of DEGs and the characteristics of infiltrating immune cells. Hub genes identified by protein–protein interaction (PPI) networks were used to construct the competitive endogenous RNA (ceRNA) networks. Potential drugs were predicted by using the Drug Gene Interaction Database (DGIdb).

Results

A total of 35 DEGs were identified from the sequencing dataset and GEO database by the Venn Diagram. Enrichment analysis indicated that DEGs are mostly enriched in excessive immune activation pathways and signal transduction. CIBERSORT exhibited that resting memory CD4 T cells and neutrophils were more abundant, and M2 macrophages, CD8 T cells, and naïve CD4 T cells were relatively scarce in patients with PCHD. After the identification of 10 hub gens, three ceRNA networks of CD83, CXCL8, and NR4A2 were constructed by data retrieval and validation. In addition, CXCL8 might interact most with multiple chemical compounds mainly consisting of anti-inflammatory drugs.

Conclusions

The immune dysfunction mainly contributes to the pathogenesis of PCHD, and three ceRNA networks of CD83, CXCL8, and NR4A2 may be potential candidate biomarkers for early diagnosis and treatment targets of PCHD.
Case report: Short-long-short mechanism triggering sustained ventricular tachycardia in a patient with a single-chamber ICD but inhibiting antitachycardia therapy
Authors: Schernthaner Christiana , Topf Albert , Motloch Lukas J. , Kraus Johannes , Hauptmann Laurenz , Hoppe Uta C. , Strohmer Bernhard
Published: August 2022

Introduction

Short-long-short (SLS) sequences are an important cause of ICD pro-arrhythmia and can initiate both polymorphic and monomorphic ventricular tachycardias (VT). Depending on the programming of a single-chamber ICD, the interplay between SLS sequences and combined VT detection criteria can be responsible for withholding adequate anti-tachycardia pacing (ATP) or shock therapy.

Methods

A 78-year-old patient with ICD was admitted to our emergency department after external cardioversion of a long-lasting VT with hemodynamic compromise. The interrogation of the ICD revealed an SLS sequence initiating a monomorphic VT at a rate of 171 bpm (350 ms). The VT discrimination of the implanted single-chamber ICD was based on the onset and stability criteria as the patient had a history of paroxysmal atrial fibrillation. The ICD was programmed that both criteria had to be met for VT detection and initiation of anti-tachycardia therapy.

Results

Due to the SLS sequence in combination with the programmed VT detection interval, the onset threshold was not fulfilled and inhibited adequate therapy. Some relatively slow VT beats following the SLS sequence resulted finally in a considerable delay in the declaration of the episode onset. As a first step, the threshold for VT detection was programmed to 150 instead of 160 bpm. To avoid SLS sequences and pause-dependent ventricular tachyarrhythmias, VVI backup stimulation was increased from 35 to 55 ppm. Besides, a device-specific algorithm called rate smoothing was activated as a potential preventive feature. On the 3-month follow-up, all sustained VT episodes were detected adequately by the reprogrammed device, resulting in appropriate anti-tachycardia pacing. After further refinement and less aggressive programming of rate smoothing, the patient remained free of symptoms and arrhythmias over a follow-up of more than 2.5 years, particularly since progression to permanent atrial fibrillation and pacing at a lower rate of 60 ppm.

Conclusions

SLS sequences may initiate or trigger VT episodes. Misclassification of the true onset may occur in some ICD devices due to specific programming of VT detection criteria. If both criteria “Onset and Stability” have to be fulfilled, ICD therapy is not delivered despite ongoing VT. Anti-bradycardia backup pacing at a very low stimulation rate may facilitate SLS sequences in patients with ICD resembling a potential pro-arrhythmic mechanism. In case of gradual VT onset with some intervals slower than the programmed VT threshold, the detection rate has to be adjusted down to guarantee appropriate identification of the onset.
Zircon U–Pb Dating of Tuff Layers in the Middle–Upper Triassic Strata of Successions and Sedimentation of Chang 7 Member in the Ordos Basin, China
Authors: Lu Gang , Gou Mingxing , Liu Guanglin , Wang Changcheng , Shi Zhiqiang
Published: August 2022

During the Late Triassic, the southern margin of the Ordos Basin was influenced by the Indosinian Movement, in response to closure of the Paleo-Tethys Ocean. Thinly bedded tuff layers are exposed near the base of the Middle–Upper Triassic formations (Chang 8/7/6 members) in the Ordos Basin. Tuff samples from drilling core (well An-35) and outcrop (Motiangou section) samples in the Yanchang Formation were studied by the detailed field work. Igneous zircon crystals were picked and analyzed by the instruments of cathodoluminescence and laser ablation inductively coupled plasma mass spectrometery (LA-ICP-MS). The timing of volcanic activity was determined by means of high-precision zircon age. Combining tectonic setting and paleogeographic reconstruct, the ages of tuff layers indicate that volcanic activities occurred at three peaks (241.6 ± 1.1 Ma, 240.2 ± 1.1 Ma, and 233.5 ± 1.2 Ma) from the top of Chang 8 Member to the Chang 7 Member. The results implied that the volcanic activities lasted from Ladinian to Carnian, as well as define the sedimentary duration of the Chang 7 Member with a deposition rate of 1.34 cm/ka.
Vertically layered flow structure at confluence of a reservoir and tributary carrying high sediment loads
Authors: Sun Yining , Li Ji , Cao Zhixian , Borthwick Alistair G.L.
Published: August 2022

Enhanced understanding of flow structure at a river confluence is essential for predictions of sediment transport and morphological evolution. To date, however, the confluent flow structure of a reservoir and tributary carrying high sediment loads has remained poorly understood, and may be vertically layered sharply, featuring subaqueous sediment-laden flow, i.e., turbidity currents underneath subaerial clear water. Here a recently established 2D double layer-averaged model, able to resolve the formation, propagation, and recession of turbidity currents, is used to investigate a series of idealized laboratory-scale cases and a prototype case study of the Guxian Reservoir on the Yellow River, China. Four primary patterns of the stable, vertically layered flow structure at a reservoir-tributary confluence are identified: 1) single layers of sediment-laden inflow in both the main channel and tributary, sustained by sufficient vertical mixing; 2) a double layer in the main channel and a single layer of sediment-laden inflow in the tributary, when the sediment-laden flow in the tributary suffices to block intrusion of flow in the main channel; 3) a single layer of sediment-laden inflow in the main channel and a double layer in the tributary, induced by the intrusion of sediment-laden flow from the main channel into clear-water flow with small discharge in the tributary; and 4) double layers in both the main channel and tributary, which may be further divided into three subpatterns, as turbidity current exists in both the main channel and tributary, or in the main channel (tributary) intruding into the tributary (main channel). In response to unsteady discharge and sediment inputs from upstream, the vertically layered flow structure evolves in time, and may fall into one of the patterns identified above. Although bed deformation in the long term may modify the confluent flow, the vertically layered flow pattern remains so far as the present cases are concerned. The findings have implications for sediment transport and morphological evolution at a reservoir–tributary confluence, for which further studies are suggested to inform the optimization of reservoir operation schemes to mitigate capacity loss caused by sedimentation.
Comprehensive analysis of the stability of tailings-geotextile composite—Iron Mine Tailings Dam in Gushan, Anhui, China
Authors: Zhou Yuxin , Ji Jinzhi , Hu Xuelong , Hu Shengsong , Wu Xiaogang , Yuan Canming , Zhu Tianqiang
Published: August 2022

The application of tailings-geotextile composites can effectively reduce tailings dam safety accidents. In this paper, the tailings dam of the Gushan Iron Mine is the research background. The construction of tailings-geotextile composites was briefly studied. Based on the existing experimental data, the permeability and physical properties of the composite material were analyzed, and the model of the composite material was generalized. The seepage characteristics of the composite were analyzed by using the numerical simulation method of the seepage field. Finally, the overall stability of the composite during the construction and storage phases was investigated. The conclusions are as follows: 1) In the early stage of stacking, the permeability coefficient of the composite body increases with the increase in filling tension; in the later stage, under the action of excess pore pressure, the composite body still exhibits strong permeability; 2) In the early stage of stacking, the height of the composite body is low, and the relative position of the saturated zone is relatively high; as the composite continues to rise or the stacking time increases, the lower part of the composite is gradually consolidated, and the position of the saturated zone is gradually raised; when the stacking is stopped, the saturated zone gradually decreases until it is close to the original position; 3) With the increase in the stacking height of the composite, the safety factor decreases rapidly; when the stacking height is 22.0 m, it decreases to the minimum; with time, the stability of the composite will gradually increase. This study helps people understand tailings-geotextile composites, and it has significant reference value for practical engineering.
Low-latitude climate change linked to high-latitude glaciation during the late paleozoic ice age: Evidence from terrigenous detrital kaolinite
Authors: Zhang Peixin , Yang Minfang , Lu Jing , Shao Longyi , Wang Ziwei , Hilton Jason
Published: August 2022

The Late Paleozoic Ice Age (LPIA; ca. 335–260 million years ago) was one of the most significant glacial events in Earth’s history. It records cycles of ice advance and retreat in southern high-latitude Gondwana and provides a deep-time perspective for climate–glaciation coevolution. However, climate records using clay mineral proxies from the LIPA are poorly developed in low latitudes, particularly in the North China Plate (NCP) on the eastern Paleo-Tethys. We address this through a detailed mineralogical study of the marine–continental sedimentary succession in the Yuzhou Coalfield from the southern NCP. We apply biostratigraphy and high-resolution clay mineral composition to reconstruct the latest Carboniferous to early Permian chronostratigraphy and climate change. The Benxi, Taiyuan, and Shanxi formations in the study area are assigned to the Gzhelian, Asselian–Artinskian, and Kungurian-Roadian stages, respectively, and the Carboniferous and Permian lithostratigraphic units across the NCP recognized as widely diachronous. Under scanning electron microscopy, the detrital micromorphology of kaolinite is mostly found as irregular fragments with sizes of 1–5 μm. Illite crystallization varies from 0.22 to 1.88 ∆°/2θ (x̄ = 0.49 ∆°/2θ) and indicates changes in kaolinite content to be a robust proxy for paleoclimate reconstruction. Kaolinite data show alternating warm-humid and cool-humid climate conditions that are roughly consistent with the calibrated glaciations and nonglacial interval successions recognized in high-latitude Gondwana. These include the Asselian-early Sakmarian and late Sakmarian-early Artinskian glacials and the climatic transition to glacial P3 during the Roadian. Our results indicate a comparatively cool-humid and warm-humid climate mode in low-latitude NCP during glacial and nonglacial periods, respectively. This is a significant step toward connecting climate change in low-latitude to high-latitude glaciation during the LPIA in eastern Paleo-Tethys.
Middle Miocene (Serravallian) rhodoliths and coralline algal debris in carbonate ramps (Betic Cordillera, S Spain)
Authors: Aguirre Julio , Braga Juan C.
Published: August 2022

Serravallian (middle Miocene) coralline algal assemblages at the southern margin of the Guadalquivir Basin (southern Spain) occur as rhodoliths preservedin situor very close to their growth habitats (autochthonous–parautochthonous assemblages) and also as reworked remains (allochthonous assemblages). The former assemblages consist of spherical rhodoliths built up by encrusting to warty plants and also of large fragments of branches, whereas the latter are mostly unrecognizable small fragments occurring in channeled packstone–grainstone beds. In both cases, the most abundant components are members of the order Hapalidiales (Mesophyllum roveretoi,Mesophyllumsp.,Lithothamnion ramosissimum, and less frequentlyPhymatolithongroupcalcareumandLithothamniongroupcorallioides). Laminar growths ofLithoporella minusand branches ofSpongitesgroupfruticulosusandSporolithonsp. occur very rarely. There are also anecdotal records ofSubterraniphyllum thomasii, extending its upper stratigraphic range up to the Serravallian in the western Tethys. The autochthonous–parautochthonous coralline algal assemblages formed in a middle ramp, at several tens of meters of water depth, as suggested by the dominance of Hapalidiales. The allochthonous assemblages represent fragments of coralline algae derived from the middle ramp and redeposited in deeper settings, most likely the outer ramp, due to storm-generated currents.
Comparative effectiveness of a low-calorie diet combined with acupuncture, cognitive behavioral therapy, meal replacements, or exercise for obesity over different intervention periods: A systematic review and network meta-analysis
Authors: Kim Seo-Young , Shin In-Soo , Park Young-Jae
Published: August 2022

Objective

The aim of this study was to evaluate the comparative effectiveness of a low-calorie diet (LCD) combined with acupuncture, cognitive behavioral therapy (CBT), meal replacements (MR), and exercise on weight loss.

Methods

The electronic databases MEDLINE, EMBASE, CENTRAL, CNKI, RISS, and KISS were searched systematically. Randomized controlled trials (RCTs) that directly compared the effect of a low-calorie diet (LCD)-combined acupuncture, CBT, and exercise and an MR-based diet on weight loss with LCD-alone for adults with simple obesity (body mass index [BMI] > 25) published before August 2021 were included in the study. Two investigators extracted and coded the data using a template. Any disagreements between investigators were resolved through discussion. Changes in BMI or weight were transformed to Hedges’ g values with a 95% CI, and network meta-analyses using a Bayesian random-effects model were conducted.

Results

A total of thirty-two trials involving 3,364 patients were finally included in the study. The effect sizes of four interventions were medium, in the order of acupuncture (Hedges’ g = 0.48, 95% CI = 0.25 - 0.71), CBT (Hedges’ g = 0.42, 95% CI = 0.20 - 0.63), MR (Hedges’ g = 0.32, 95% CI = 0.19 - 0.45), and exercise (Hedges’ g = 0.27, 95% CI = 0.06 - 0.46).

In terms of intervention period, acupuncture was effective in the short period (≤ 12 weeks, Hedges’ g = 0.39, 95% CI = 0.12 - 0.67) and the long period (>12 weeks, Hedges’ g = 0.89, 95% CI = 0.37 - 1.40), whereas CBT (Hedges’ g = 0.51, 95% CI = 0.26 - 0.76) and exercise (Hedges’ g = 0.37, 95% CI = 0.12 - 0.59) were effective only in the long period. MR was effective only in the short period (Hedges’ g = 0.35, 95% CI = 0.18 - 0.53).

Conclusions

This study suggests that acupuncture, CBT, MR, and exercise for simple obesity show a medium effect size, and their effectiveness differs according to the intervention period.
A novel cloud-edge collaboration based short-term load forecasting method for smart grid
Authors: Wang Ai-Xia , Li Jing-Jiao
Published: August 2022

With the increasing development of smart grid technology, short-term load forecasting becomes particularly important in power system operation. However, the design of accurate and reliable short-term load forecasting methods and models is challenging due to the volatility and intermittency of renewable energy sources, as well as the privacy and individual characteristics of electricity consumption data from user data. To overcome this issue, in this paper, a novel cloud-edge collaboration short-term load forecasting method is proposed for smart grid. In order to reduce the computational load of edge nodes and improve the accuracy of node prediction, we use the method of building a model pre-training pool to train multiple pre-training models in the cloud layer at the same time. Then we use edge nodes to retrain the pre-trained model, select the optimal model and update the model parameters to achieve short-term load forecasting. To assure the validity of the model and the confidentiality of private data, we utilize the model pre-training pool to minimize edge node training difficulty and employ the approach of secondary edge node training. Finally, extensive experiments confirm the efficacy of our proposed method.
Phosphorus forms by depth in sediments from the Qu’Appelle lakes, Saskatchewan, Canada
Authors: Wauchope-Thompson Michelle S. , Cade-Menun Barbara J. , Baulch Helen M.
Published: August 2022

Understanding sediment phosphorus (P) compounds is essential to managing P in lake sediments because P speciation will determine bioavailability and reactivity. Little is known about organic P (Po) in hardwater eutrophic lakes in the North American Great Plains, or the role of metals in Po cycling. Sediment cores (0–12 cm deep) collected from four lakes from the Qu’Appelle chain in Saskatchewan, Canada, were sectioned by depth and analyzed by solution P nuclear magnetic resonance spectroscopy to characterize P forms. Concentrations and pools of calcium (Ca), magnesium (Mg), iron (Fe), manganese (Mn), and aluminum (Al) were also determined. A range of P compounds was detected with significant interactions between lakes and depth for orthophosphate, phytate and DNA, and significant differences among lakes or with depth for polyphosphates and phosphonates. The main class of Po compounds identified in all lakes was orthophosphate diesters, including phospholipids and DNA, typical of living biota, suggesting that P immobilized by microbes and algae is an important pool in the sediments of these lakes. There were significant differences in metal concentrations among the lakes. In three lakes, Ca concentrations were high, and P was tightly bound with Ca compounds of low solubility. In the fourth lake with lower Ca concentrations, P appeared to be loosely bound to Al and Fe compounds. Our study indicates that there were significant differences in P compounds and the factors controlling their cycling among these four lakes in the same chain, which has implications for P management and water quality control.
Surface deformation simulation for InSAR detection using a machine learning approach on the hantangang river volcanic field: A case study on the orisan mountain
Authors: Fadhillah Muhammad Fulki , Hakim Wahyu Luqmanul , Park Sungjae , Kim Daewoo , Park Yu-Chul , Kim Chang-Hwan , Lee Chang-Wook
Published: August 2022

Recent developments in remote sensing research have resulted in a large amount of variability in the data provided by researchers. Synthetic aperture radar (SAR) is a tool used to measure surface deformation and assess changes in the Earth’s surface. Here, we consider the usefulness of Interferometric Synthetic Aperture Radar (InSAR) in assessing past volcanic activity as a key to learning the characteristics of the deformation around a volcano. The Hantangang River volcanic field (HRVF) is a geoheritage site in the Korean Peninsula that has interesting geological characteristics. This volcanic field has formed along 110 km of the paleochannel of the Hantangang River. Since the eruptions occurred from 0.15 to 0.51 Ma, the source is limited, which has raised interest in the assessment of volcanic landforms. The recent integration of machine learning and InSAR processing has shown promising results for many purposes, such as classifying, modeling, and detecting surface deformation. To examine the future impact based on information from the past, we utilized a synthetic interferogram with the Okada model and transferred it to a machine learning algorithm. The synthetic interferogram was formed based on Sentinel-1 C-band satellite data to simulate the deformation phases. The orbital errors, the topographical data errors, and the atmospheric effect were also simulated and added to the synthetic interferogram to enrich the learning input. A convolutional neural network (CNN) trained with the unwrapped simulated interferogram data and its performance was evaluated. Our proposed method exhibits the capability to detect volcanic activity’s deformation patterns with synthetic interferogram data. The results show that an overall accuracy of more than 80% was achieved using the CNN algorithms on the validation dataset. This study is the first to use machine learning approaches for detecting prehistorical volcanic deformation and demonstrates potential techniques for developing an approach based on satellite imagery. In addition, this study has introduced the possibility of developing a rapid detection of surface deformation using InSAR data based on a machine learning approach.
Health risk analysis of microplastics in soil in the 21st century: A scientometrics review
Authors: Sun Yitao , Yang Chao , Liang Huajun , Zhang Siqi , Zhang Ruifang , Dong Yongli , Tanveer Sikander Khan , Hai Jiangbo
Published: August 2022

Microplastics (MPs) in soil cause severe damage to the ecological environment and organisms, and research on their health risks has received extensive attention, but there is no comprehensive review of this research. From the perspective of bibliometrics, this paper systematically and comprehensively describes the progress, trends, and hotspots of health risks of MPs in soil based on the Web of Science Core Collection, Pubmed, and Scopus databases. Since 2016, people’s research on the health risks of MPs in soil has increased yearly; MPs in soil mainly come from Plastic mulch, Plastic waste, Sludge and sewage, and Organic fertilizer. China has the most publications on the health risks of MPs on soil, and more than half of the top 10 institutions with active publications in this field are from China. This paper systematically expounds on the health risks of MPs to organisms (plants, humans, and microorganisms) and control measures. Cooperation between different countries/institutions and fields/disciplines on the health risk analysis of MPs in soil and research on more efficient, green, and environmentally friendly methods and technologies for reducing soil MPs content will become the frontier trends of future development which provide valuable reference and help for future researchers.
Wheat straw- and maize straw-derived biochar effects on the soil cadmium fractions and bioaccumulation in the wheat–maize rotation system
Authors: Dun Yu , Wu Chao , Zhou Ming , Tian Xia , Wu Guoqing
Published: August 2022

Wheat–maize rotation is one of the most popular systems and successful intensification cropping systems in Northern China, while soils in some of this area are contaminated by cadmium (Cd). However, few studies have performed experiments on the reduction of Cd accumulation in the wheat–maize rotation system. In this study, wheat- and maize-derived biochars are applied to the Cd-contaminated soil to reduce the Cd accumulation in the wheat and maize plants. The results showed that soil biochar applications can significantly decrease DTPA-extracted Cd concentrations by 12.7–26.0% and 13.1–20.5% by wheat- and maize-derived biochars, respectively. Sequential extractions showed that biochar applications significantly reduced the Cd mobility and bioavailability in soils and changed the exchangeable and carbonate-bound fractions of Cd to organic material-bound and residual fractions. The biochar applications increased the plant growth, yield, and quality of both wheat and maize, especially a significant increase in high dosages. The biochar applications also improved the antioxidant enzyme activities and reduced the reduction of MDA in both wheat and maize roots. The Cd concentrations in wheat grains were reduced by 38.1–91.5% and 65.9–80%, and maize grain Cd concentrations were reduced by 20.9–54.2% and 30.8–44% by wheat- and maize-derived biochar applications, respectively, and the Cd concentrations in the root, stem, and leaf were also significantly reduced. The wheat-derived biochar was more effective on the Cd reduction in soil bioavailable fractions and Cd accumulation in crop plants.
Microplastics in soil induce a new microbial habitat, with consequences for bulk soil microbiomes
Authors: Kublik Susanne , Gschwendtner Silvia , Magritsch Tobias , Radl Viviane , Rillig Matthias C. , Schloter Michael
Published: August 2022

Microplastic (MP) pollution poses a threat to agricultural soils and may induce a significant loss of the soil quality and services provided by these ecosystems. Studies in marine environments suggest that this impact is mediated by shifts in the microbiome. However, studies on the mode of action of MP materials on the soil microbiome are rare, particularly when comparing the effects of different MP materials. In this study, we characterized the microbiota colonizing two different MP materials, granules made of polypropylene (PP) and expanded polystyrene (ePS), introduced into arable soil and incubated for 8 weeks using a molecular barcoding approach. We further assessed the consequences on the microbiome of bulk soil. The complexity of the bacterial communities colonizing MP materials was significantly higher on ePS compared to PP. Many of the detected genera colonizing the MP materials belonged to taxa, that are known to degrade polymeric substances, including TM7a, Phenylobacterium, Nocardia, Arthrobacter and Streptomyces. Interestingly, in bulk soil samples amended with MP materials, microbial diversity was higher after 8 weeks compared to the control soil, which was incubated without MP materials. The composition of bacterial communities colonizing the MP materials and bulk soil differed. Mainly Acidobacteria were mostly found in bulk soil, whereas they were rare colonizers of the MP materials. Differences in diversity and community composition between the MP affected bulk soil samples were not found. Overall, our data indicate that MP materials form a new niche for microbes in soil, with a specific community composition depending on the materials used, strongly influencing the bulk soil microbiota in the short term. Long-term consequences for the soil microbiome and associated functions including different soils need to be further elaborated in the future for a proper risk assessment of the mode of action of MP materials in terrestrial ecosystems.
Molecular evolution of vision-related genes may contribute to marsupial photic niche adaptations
Authors: Tian Ran , Guo Han , Jin Zhihong , Zhang Fan , Zhao Junpeng , Seim Inge
Published: August 2022

Vision plays an essential role in the life of many animals. While most mammals are night-active (nocturnal), many have adapted to novel light environments. This includes diurnal (day-active) and crepuscular (twilight-active) species. Here, we used integrative approaches to investigate the molecular evolution of 112 vision-related genes across 19 genomes representing most marsupial orders. We found that four genes (GUCA1B, GUCY2F, RGR, and SWS2) involved in retinal phototransduction likely became functionally redundant in the ancestor of marsupials, a group of largely obligate nocturnal mammals. We also show evidence of rapid evolution and positive selection of bright-light vision genes in the common ancestor of Macropus (kangaroos, wallaroos, and wallabies). Macropus-specific amino acid substitutions in opsin genes (LWS and SWS1), in particular, may be an adaptation for crepuscular vision in this genus via opsin spectral sensitivity tuning. Our study set the stage for functional genetics studies and provides a stepping stone to future research efforts that fully capture the visual repertoire of marsupials.
Present and prospects for multi-aged silviculture in Chilean temperate forests: Targeting secondary forests in transition and partially harvested old-growth forests
Authors: Donoso Pablo J. , Soto Daniel P. , Salas-Eljatib Christian , Riquelme-Buitano Tomás R.
Published: August 2022

Valdivian Temperate Rainforests in Chile have a global conservation value, but nowadays many correspond to secondary forests following regeneration in agricultural and burned lands, and to high-graded old-growth due to mismanagement, especially at mid to low elevations. Perspectives for increasing old-growth attributes in these productive forests through silviculture are high considering the diverse demands of ecosystem services and the high timber value of tree species. In the Llancahue experimental forest (40°S Lat) we implemented three ecological silviculture approaches: variable-density thinning in a Nothofagus dombeyi secondary forest (NDS), irregular shelterwood in a mature N. dombeyi forest (NDM), and single-tree selection cutting in a partially harvested old-growth forest (OG). Based upon an old-growth index (OGI) that includes density, basal area (BA), BA of the trees >80 cm in diameter, ba of shade-tolerant species, and the Gini coefficient, and aims to estimate how close a given forest is to a typical old-growth forest, these forests had a 22, 22, and 62% OGI before management. The OGI remained similar or declined following management, but 7–10 years after management it increased in NDS and NDM and declined in the OG (significant changes only in NDM and OG). We discuss these results considering that managed forests should target for an OGI ≈70% rather than maximum values. These managed forests contribute to halt degradation, mitigate climate change (carbon stores in the forest and in timber), and may have greater adaptive capacity to disturbances. We discuss perspectives for the potential scale-up of implementing these approaches.
LncRNA RP11-59J16.2 aggravates apoptosis and increases tau phosphorylation by targeting MCM2 in AD
Authors: Guan Fulin , Gao Qichang , Dai Xinghua , Li Lei , Bao Rui , Gu Jiaao
Published: August 2022

Alzheimer’s disease (AD) is a degenerative disease of central nervous system with unclear pathogenesis, accounting for 60%–70% of dementia cases. Long noncoding RNAs (LncRNAs) play an important function in the development of AD. This study aims to explore the role of differentially expressed lncRNAs in AD patients’ serum in the pathogenesis of AD. Microarray analysis was performed in the serum of AD patients and healthy controls to establish lncRNAs and mRNAs expression profiles. GO analysis and KEGG pathway analysis revealed that G1/S transition of mitotic cell cycle might be involved in the development of AD. The result showed that RP11-59J16.2 was up-regulated and MCM2 was down-regulated in serum of AD patients. SH-SY5Y cells were treated with Aβ 1–42 to establish AD cell model. Dual luciferase reporter gene analysis verified that RP11-59J16.2 could directly interact with 3′UTR of MCM2 and further regulate the expression of MCM2. Inhibition of RP11-59J16.2 or overexpression of MCM2, CCK-8 assay and Annexin V FITC/PI apoptosis assay kit results showed that RP11-59J16.2 could reduce cell viability, aggravate apoptosis and increase Tau phosphorylation in AD cell model by inhibiting MCM2. In short, our study revealed a novel lncRNA RP11-59J16.2 that could promote neuronal apoptosis and increase Tau phosphorylation by regulating MCM2 in AD model, and indicated that lncRNA RP11-59J16.2 might be a potential target molecule for AD development.
Detection of a Cryptic 25 bp Deletion and a 269 Kb Microduplication by Nanopore Sequencing in a Seemingly Balanced Translocation Involving the LMLN and LOC105378102 Genes
Authors: Wang Yanan , Zhao Zhenhua , Fu Xinyu , Li Shufang , Zhang Qiuyan , Kong Xiangdong
Published: August 2022

Preimplantation genetic testing plays a critical role in enabling a balanced translocation carrier to obtain the normal embryo. Identifying the precise breakpoints for the carriers with phenotypic abnormity, allows us to reveal disrupted genes. In this study, a seemingly balanced translocation 46, XX, t (3; 6) (q29; q26) was first detected using conventional karyotype analysis. To locate the precise breakpoints, whole genomes of DNA were sequenced based on the nanopore GridION platform, and bioinformatic analyses were further confirmed by polymerase-chain-reaction (PCR) and copy number variation (CNV). Nanopore sequencing results were consistent with the karyotype analysis. Meanwhile, two breakpoints were successfully validated using polymerase-chain-reaction and Sanger Sequencing. LOC105378102 and LMLN genes were disrupted at the breakpoint junctions. Notably, observations found that seemingly balanced translocation was unbalanced due to a cryptic 269 kilobases (Kb) microduplication and a 25 bp deletion at the breakpoints of chromosome (chr) 6 and chr 3, respectively. Furthermore, 269 Kb microduplication was also confirmed by copy number variation analyses. In summary, nanopore sequencing was a rapid and direct method for identifying the precise breakpoints of a balanced translocation despite low coverage (3.8×). In addition, cryptic deletion and duplication were able to be detected at the single-nucleotide level.
Pancancer analysis of a potential gene mutation model in the prediction of immunotherapy outcomes
Authors: Yu Lishan , Gong Caifeng
Published: August 2022

Background: Immune checkpoint blockade (ICB) represents a promising treatment for cancer, but predictive biomarkers are needed. We aimed to develop a cost-effective signature to predict immunotherapy benefits across cancers.

Methods: We proposed a study framework to construct the signature. Specifically, we built a multivariate Cox proportional hazards regression model with LASSO using 80% of an ICB-treated cohort (n = 1661) from MSKCC. The desired signature named SIGP was the risk score of the model and was validated in the remaining 20% of patients and an external ICB-treated cohort (n = 249) from DFCI.

Results: SIGP was based on 18 candidate genes (NOTCH3, CREBBP, RNF43, PTPRD, FAM46C, SETD2, PTPRT, TERT, TET1, ROS1, NTRK3, PAK7, BRAF, LATS1, IL7R, VHL, TP53, and STK11), and we classified patients into SIGP high (SIGP-H), SIGP low (SIGP-L) and SIGP wild type (SIGP-WT) groups according to the SIGP score. A multicohort validation demonstrated that patients in SIGP-L had significantly longer overall survival (OS) in the context of ICB therapy than those in SIGP-WT and SIGP-H (44.00 months versus 13.00 months and 14.00 months, p < 0.001 in the test set). The survival of patients grouped by SIGP in non-ICB-treated cohorts was different, and SIGP-WT performed better than the other groups. In addition, SIGP-L + TMB-L (approximately 15% of patients) had similar survivals to TMB-H, and patients with both SIGP-L and TMB-H had better survival. Further analysis on tumor-infiltrating lymphocytes demonstrated that the SIGP-L group had significantly increased abundances of CD8+ T cells.

Conclusion: Our proposed model of the SIGP signature based on 18-gene mutations has good predictive value for the clinical benefit of ICB in pancancer patients. Additional patients without TMB-H were identified by SIGP as potential candidates for ICB, and the combination of both signatures showed better performance than the single signature.
Ferroptosis-related lncRNAs signature to predict the survival and immune evasion for lung squamous cell carcinoma
Authors: Zhang Rusi , Zhang Xuewen , Yang Han , Lin Yongbin , Wen Yingsheng , Zhao Dechang , Chen Lianjuan , Lin Peng , Zhang Lanjun
Published: August 2022

Introduction: the investigation on the interactions between ferroptosis and lncRNAs for lung squamous cell carcinoma (LUSC) has been scare, and its impact on tumor immune microenvironment remained unknown. We aim to not only identify a ferroptosis-related lncRNAs signature for LUSC prognosis, but also evaluate its correlation to tumor immune evasion.

Methods: RNA sequencing data and survival information were obtained from The Cancer Genome Atlas database. A ferroptosis-related lncRNAs signature (FerRLSig) was developed and validated by univariate Cox regression, Least Absolute Shrinkage and Selection Operator regression and multivariate Cox regression. The tumor immune microenvironment and immune evasion were subsequently evaluated based on the FerRLSig stratification.

Results: the FerRLSig consisted of 10 ferroptosis-related lncRNAs and significantly associated with overall survival with satisfactory area under curve (HR = 2.240, 95% CI: 1.845–2.720, p < 0.001, 5-years AUC: 0.756). Based on the FerRLSig stratification, the high-risk group demonstrated not only significantly higher immune infiltration, but also more profound T cell dysfunction and immune evasion, which might ultimately lead to the resistance to current immune checkpoint inhibitors.

Conclusion: a robust prognostic FerRLSig for LUSC has been developed and validated, demonstrating a close association not only with tumor immune cell infiltration, but also with T cell dysfunction and immune evasion. Further investigation is warranted to better improve the survival of LUSC patients based on the FerRLSig stratification.
Global research trends on precision cancer medicine-related rashes (2008-2021): A bibliographic study
Authors: Zhao Fangmin , Yu Rui , Chen Shuyi , Zhao Shuya , Sun Lin , Xu Zeting , Zhang Yao , Dai Shuying , Zhang Gaochenxi , Shu Qijin
Published: August 2022

Background

Precision cancer medicine-related rashes are a kind of skin and mucous lesions caused by precision therapy. More and more evidences indicated that such events should not be ignored in the course of anti-tumor therapy. Since cancer treatment entered the “Precision Era”, there has been a rapid increase in this field. However, there was few bibliometric studies to provide an overall review of this field. This study aims to evaluate the literature output and trends in researches on precision cancer medicine-related rashes from a global perspective.

Methods

Collected publications on precision cancer medicine-related rashes from the Web of Science Core Collection database, which were limited to articles and reviews in English. Microsoft Excel, VOS viewer and CiteSpace V were used for quantitative and visual analysis.

Results

A total of 1,229 papers were identified. From 2008 to 2021, annual publications increased year by year. The United States published the most papers in this field (44.9%) and ranking first in citation frequency (19,854 times) and H-index (69). The University of Texas system ranks first with 98 papers published. Lacouture M.E and Robert C were the principal investigators. Cancers has the largest number of articles published, with 70 articles. In recent years, there have been research hotspots related to immunotherapy, including ipilimumab, immunotherapy, tumor microenvironment, association, checkpoint inhibitor, and cutaneous adverse event.

Conclusion

Precision cancer medicine-related rashes are a hot research topic in oncology. The number of relevant publications will increase dramatically. “Checkpoint inhibitors”, “skin adverse events”, “associations” and “tumor microenvironment” may become research hotspots in the future.
Lactate: A regulator of immune microenvironment and a clinical prognosis indicator in colorectal cancer
Authors: Zhu Daoqi , Jiang Yiping , Cao Huihui , Yang Jiabin , Shu Yuqi , Feng Haowei , Yang Xiaoyu , Sun Xiaomin , Shao Meng
Published: August 2022

Lactate can play an immunosuppressive role in the tumor microenvironment and promote tumor development by recruiting and inducing the activity of immunosuppressive cells and molecules. High lactate concentrations are important for tumor cell metastasis, angiogenesis, and treatment resistance. With the in-depth studies on tumor metabolism, lactate, one of the key factors involved in glycolysis, has been increasing emerged its characteristic clinical value in colorectal cancer (CRC). In this study, lactate genes were screened based on lactate metabolism pathways. Subsequently, the lactate subtypes were determined by clustering and analysis of the subtypes at all levels, including immune checkpoints, immune infiltration, and clinical characteristics, which revealed the biological significance of lactate metabolism in CRC. Subtype-based differential gene analysis resulted in a lactate score, which stratifies the prognosis of CRC. We discovered that 27 lactate genes and 61 lactate-phenotype genes are associated with immune cell infiltration and have a significant prognostic efficacy. The CRC patients were clustered into four subtypes and five clusters, based on lactate genes and lactate-phenotype genes, respectively. There are significant differences in survival time and activities of hallmark pathways, namely immune-related signatures and chemokines, among these subtypes and clusters. Particularly, cluster 2 and subtype 1 have significantly higher lactate scores than that of the others. In conclusion, lactate score is an independent prognostic factor for cancer that can be used as a clinical guide for predicting CRC progression and as an evaluation factor for the effect of immunotherapy in CRC.
Arabinogalactan enhances Mycobacterium marinum virulence by suppressing host innate immune responses
Authors: Li Ye-yu , Liu Han-Mei , Wang Decheng , Lu Yan , Ding Cairong , Zhou Li-Shuang , Wu Xiang-Yang , Zhou Zi-Wei , Xu Shu-qin , Lin Chen , Qin Lian-Hua , Li Yao , Liu Jun , Liu Hai-Peng , Zhang Lu
Published: August 2022

Arabinogalactan (AG) participates in forming the cell wall core of mycobacteria, a structure known as the mAGP complex. Few studies have reported the virulence of inartificial AG or its interaction with the host immune system. Using clustered regularly interspaced short palindromic repeats interference gene editing technology, conditional Mycobacterium marinum mutants were constructed with a low expression of embA or glfT2 (EmbA_KD or GlfT2_KD), which are separately involved in the biosynthesis of AG arabinose and galactose domains. High-performance gel permeation chromatography and high-performance liquid chromatography assays confirmed that the EmbA_KD strain showed a remarkable decrease in AG content with fragmentary arabinose chains, and the GlfT2_KD strain displayed less reduction in content with cut-down galactose chains. Based on transmission and scanning electron microscopy observations, the cell walls of the two mutants were found to be dramatically thickened, and the boundaries of different layers were more distinct. Phenotypes including the over-secretion of extracellular substances and enhanced spreading motility with a concomitant decreased resistance to ethambutol appeared in the EmbA_KD strain. The EmbA_KD and GlfT2_KD strains displayed limited intracellular proliferation after infecting murine J774A.1 macrophages. The disease progression infected with the EmbA_KD or GlfT2_KD strain significantly slowed down in zebrafish/murine tail infection models as well. Through transcriptome profiling, macrophages infected by EmbA_KD/GlfT2_KD strains showed enhanced oxidative metabolism. The cell survival measured using the CCK8 assay of macrophages exposed to the EmbA_KD strain was upregulated and consistent with the pathway enrichment analysis of differentially expressed genes in terms of cell cycle/apoptosis. The overexpression of C/EBPβ and the increasing secretion of proinflammatory cytokines were validated in the macrophages infected by the EmbA_KD mutant. In conclusion, the AG of Mycobacterium appears to restrain the host innate immune responses to enhance intracellular proliferation by interfering with oxidative metabolism and causing macrophage death. The arabinose chains of AG influence the Mycobacterium virulence and pathogenicity to a greater extent.
A comprehensive analysis of the efficacy and effectiveness of COVID-19 vaccines
Authors: He Xiaofeng , Su Jiao , Ma Yu’nan , Zhang Wenping , Tang Shixing
Published: August 2022

It is urgently needed to update the comprehensive analysis about the efficacy or effectiveness of COVID-19 vaccines especially during the COVID-19 pandemic caused by SARS-CoV-2 Delta and Omicron variants. In general, the current COVID-19 vaccines showed a cumulative efficacy of 66.4%, 79.7%, and 93.6% to prevent SARS-CoV-2 infection, symptomatic COVID-19, and severe COVID-19, respectively, but could not prevent the asymptomatic infection of SARS-CoV-2. Furthermore, the current COVID-19 vaccines could effectively prevent COVID-19 caused by the Delta variant although the incidence of breakthrough infection of the SARS-CoV-2 Delta variant increased when the intervals post full vaccination extended, suggesting the waning effectiveness of COVID-19 vaccines. In addition, one-dose booster immunization showed an effectiveness of 74.5% to prevent COVID-19 caused by the Delta variant. However, current COVID-19 vaccines could not prevent the infection of Omicron sub-lineage BA.1.1.529 and had about 50% effectiveness to prevent COVID-19 caused by Omicron sub-lineage BA.1.1.529. Furthermore, the effectiveness was 87.6% and 90.1% to prevent severe COVID-19 and COVID-19-related death caused by Omicron sub-lineage BA.2, respectively, while one-dose booster immunization could enhance the effectiveness of COVID-19 vaccines to prevent the infection and COVID-19 caused by Omicron sub-lineage BA.1.1.529 and sub-lineage BA.2. Two-dose booster immunization showed an increased effectiveness of 81.8% against severe COVID-19 caused by the Omicron sub-lineage BA.1.1.529 variant compared with one-dose booster immunization. The effectiveness of the booster immunization with RNA-based vaccine BNT162b2 or mRNA-1273 was over 75% against severe COVID-19 more than 17 weeks after booster immunization whereas the heterogenous booster immunization showed better effectiveness than homologous booster immunization. In summary, the current COVID-19 vaccines could effectively protect COVID-19 caused by Delta and Omicron variants but was less effective against Omicron variant infection. One-dose booster immunization could enhance protection capability, and two-dose booster immunization could provide additional protection against severe COVID-19.