bluuebunny/crossref_metadata_2025 huggingface dataset:
Associations between epigenetic aging and childhood peer victimization, depression, and suicidal ideation in adolescence and adulthood: A study of two population-based samples
Authors: Perret L. C. , Geoffroy M-C. , Barr E. , Parnet F. , Provencal N. , Boivin M. , O’Donnell K. J. , Suderman M. , Power C. , Turecki G. , Ouellet-Morin I.
Published: January 2023

Background: Prior studies indicate that peer victimization (including bullying) is associated with higher risk for depression and suicidal ideation across the life course. However, molecular mechanisms underlying these associations remain unclear. This two-cohort study proposes to test whether epigenetic aging and pace of aging, as well as a DNA methylation marker of responsive to glucocorticoids, are associated to childhood peer victimization and later depressive symptoms, or suicidal ideation.

Methods: Cohort 1: Epigenome-wide DNA methylation (EPIC array) was measured in saliva collected when participants were 10.47 years (standard deviation = 0.35) in a subsample of the Quebec Longitudinal Study of Child Development (QLSCD, n = 149 participants), with self-reported peer victimization at 6–8 years, depressive symptoms (mean symptoms, and dichotomized top 30% symptoms) and suicidal ideation at 15–17 years. Cohort 2: Epigenome-wide DNA methylation (EPIC array) was measured in blood collected from participants aged 45.13 years (standard deviation = 0.37) in a subsample of the 1958 British Birth cohort (1958BBC, n = 238 participants) with information on mother-reported peer victimization at 7–11 years, self-reported depressive symptoms at 50 years, and suicidal ideation at 45 years. Five epigenetic indices were derived: three indicators of epigenetic aging [Horvath’s pan-tissue (Horvath1), Horvath’s Skin-and-Blood (Horvath2), Pediatric-Buccal-Epigenetic age (PedBE)], pace of aging (DunedinPACE), and stress response reactivity (Epistress).

Results: Peer victimization was not associated with the epigenetic indices in either cohort. In the QLSCD, higher PedBE epigenetic aging and a slower pace of aging as measured by DunedinPACE predicted higher depressive symptoms scores. In contrast, neither the Horvath1, or Horvath2 epigenetic age estimates, nor the Epistress score were associated with depressive symptoms in either cohort, and none of the epigenetic indices predicted suicidal ideation.

Conclusion: The findings are consistent with epigenome-wide and candidate gene studies suggesting that these epigenetic indices did not relate to peer victimization, challenging the hypothesis that cumulative epigenetic aging indices could translate vulnerability to depressive symptoms and suicidal ideation following peer victimization. Since some indices of epigenetic aging and pace of aging signaled higher risk for depressive symptoms, future studies should pursue this investigation to further evaluate the robustness and generalization of these preliminary findings.
Intense femtosecond optical pulse shaping approaches to spatiotemporal control
Authors: Goswami Debabrata
Published: January 2023

For studying any event, measurement can never be enough; “control” is required. This means mere passive tracking of the event is insufficient and being able to manipulate it is necessary. To maximize this capability to exert control and manipulate, both spatial and temporal domains need to be jointly accounted for, which has remained an intractable problem at microscopic scales. Simultaneous control of dynamics and position of an observable event requires a holistic combination of spatial and temporal control principles, which gives rise to the field of spatiotemporal control. For this, we present a novel femtosecond pulse-shaping approach. We explain how to achieve spatiotemporal control by spatially manipulating the system through trapping and subsequently or simultaneously exerting temporal control using shaped femtosecond pulses. By leveraging ultrafast femtosecond lasers, the prospect of having temporal control of molecular dynamics increases, and it becomes possible to circumvent the relaxation processes at microscopic timescales. Optical trapping is an exemplary demonstration of spatial control that results in the immobilization of microscopic objects with radiation pressure from a tightly focused laser beam. Conventional single-beam optical tweezers use continuous-wave (CW) lasers for achieving spatial control through photon fluxes, but these lack temporal control knobs. We use a femtosecond high repetition rate (HRR) pulsed laser to bypass this lack of dynamical control in the time domain for optical trapping studies. From a technological viewpoint, the high photon flux requirement of stable optical tweezers necessitates femtosecond pulse shaping at HRR, which has been a barrier until the recent Megahertz pulse shaping developments. Finally, recognizing the theoretical distinction between tweezers with femtosecond pulses and CW lasers is of paramount interest. Non-linear optical (NLO) interactions must be included prima facie to understand pulsed laser tweezers in areas where they excel, like the two-photon-fluorescence-based detection. We show that our theoretical model can holistically address the common drawback of all tweezers. We are able to mitigate the effects of laser-induced heating by balancing this with femtosecond laser-induced NLO effects. An interesting side-product of HRR femtosecond-laser-induced thermal lens is the development of femtosecond thermal lens spectroscopy (FTLS) and its ability to provide sensitive molecular detection.
Development of a novel loop-mediated isothermal amplification assay for ß-lactamase gene identification using clinical isolates of Gram-negative bacteria
Authors: Kim Eun Jin , Lee Jiwon , Yoon Youngbae , Lee Donghyun , Baek Yeongjun , Takano Chika , Sakai Jun , Iijima Takahiro , Kanamori Dai , Gardner Humphrey , McLaughlin Robert E. , Kilgore Paul E. , Nakamura Akihiro , Ogihara Takashi , Hayakawa Satoshi , Hoshino Tomonori , Kim Dong Wook , Seki Mitsuko
Published: January 2023

Rapid evaluation of antimicrobial susceptibility is important in the treatment of nosocomial infections by Gram-negative bacteria, which increasingly carry carbapenemases and metallo-β-lactamases. We developed loop-mediated isothermal amplification (LAMP)-based assays for four β-lactamase genes (blaKPC, blaNDM-1, blaIMP-1 group, and blaVIM). The assays were evaluated using eight reference bacterial strains (Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter bereziniae) harboring six β-lactamase genes. A total of 55 Gram-negative bacterial strains, including 47 clinical P. aeruginosa isolates, fully characterized by next-generation sequencing (NGS), were used to evaluate the LAMP assays. The results were compared to those of conventional PCR. The LAMP assays were able to detect as few as 10 to 100 copies of a gene, compared to 10 to 104 copies for conventional PCR. The LAMP assay detected four β-lactamase genes with a sensitivity similar to that using purified DNA as the template in DNA-spiked urine, sputum, and blood specimens. By contrast, the sensitivity of PCR was 1- to 100-fold lower with DNA-spiked clinical specimens. Therefore, the LAMP assays were proved to be an appropriate tool for the detection of four β-lactamases.
Cardiac regeneration: Options for repairing the injured heart
Authors: Wang Jun , An Meilin , Haubner Bernhard Johannes , Penninger Josef M.
Published: January 2023

Cardiac regeneration is one of the grand challenges in repairing injured human hearts. Numerous studies of signaling pathways and metabolism on cardiac development and disease pave the way for endogenous cardiomyocyte regeneration. New drug delivery approaches, high-throughput screening, as well as novel therapeutic compounds combined with gene editing will facilitate the development of potential cell-free therapeutics. In parallel, progress has been made in the field of cell-based therapies. Transplantation of human pluripotent stem cell (hPSC)-derived cardiomyocytes (hPSC-CMs) can partially rescue the myocardial defects caused by cardiomyocyte loss in large animals. In this review, we summarize current cell-based and cell-free regenerative therapies, discuss the importance of cardiomyocyte maturation in cardiac regenerative medicine, and envision new ways of regeneration for the injured heart.
Two large squirrels (Rodentia, Mammalia) from the Junggar Basin of northwestern China demonstrate early radiation among squirrels and suggest forested paleoenvironment in the late Eocene of Central Asia
Authors: Li Qiang , Ni Xijun , Stidham Thomas A. , Qin Chao , Gong Hao , Zhang Limin
Published: January 2023

Fossil evidence is indispensable for studying the derivation, divergence, and dispersal of squirrels as they responded to global Cenozoic climatic and paleoenvironmental change. Among these fossil records, the earliest known definitive fossil squirrels in Eurasia occur after the Eocene/Oligocene Boundary and are slightly younger than the oldest records in North America. Here, we report the discovery of two new extinct large squirrel species from the late Eocene of the Junggar Basin in northwestern China. The dental morphologies of these new taxa represent tree and flying morphotypes, and their estimated body masses are approximately 1.2 kg and 2.6 kg, respectively. In addition, these extinct lineages push the age of the first appearance of Sciuridae in northern Asia into the late Eocene. Together with Douglassciurus and Oligospermophilus from North America, these two new squirrels from the Junggar Basin are the earliest records of sciurids, and analysis of their teeth clearly demonstrates that the three principle morphotypes of sciurids (flying, ground, and tree squirrels) had diverged from one another by the late Eocene. That proposed late Eocene divergence among the major groupings of sciurids is consistent with some molecular clock analyses and helps to document that macroevolutionary timing and pattern. Comparison with modern squirrel analogs for body masses over 1 kg points to these early Chinese species as having occupied forested habitats, and that hypothesis is congruent with published palynological studies. Furthermore, these two new squirrel taxa from Jeminay provide new data to evaluate the examination of the long-term aridification of Central Asia.
The impact of green finance on the transformation of energy consumption structure: Evidence based on China
Authors: Gu Xiao , Qin Lingui , Zhang Mei
Published: January 2023

Reducing the use of traditional fossil energy and optimizing the energy consumption structure is an important starting point for China to balance sustainable and stable economic development, dual carbon goals and energy security. Green finance can help improve the energy consumption structure through providing financial support for green development. Based on this, taking the proportions of coal consumption as the index of energy consumption structure, this paper uses panel data for 30 provinces in China from 2009 to 2019, and analyzes the impact of green finance on energy consumption structure and its mechanism. The results show that the development of green finance in China has significantly improved the energy consumption structure, when considering the endogenous and robustness, the conclusion is still valid. In the mid-western region, green finance plays a greater role in improving the energy consumption structure. With the help of the quantile regression model, it is found that the higher the proportion of coal consumption, the greater the improvement effect of green finance on energy consumption structure. With the help of the threshold model, it is found that when exceeding the threshold value, the improvement effect of green finance on energy consumption structure will decline. Both the market and the government can enhance the role of green finance in optimizing the energy consumption structure. According to the research conclusion, the suggestions for improving the energy consumption structure of green finance are given from the aspects of developing green finance, formulating differentiated green finance development strategies, and encouraging green innovation.
Review of deep fluids in sedimentary basins and their influence on resources, with a focus on oil and geothermal exploitation
Authors: Lu Jia , Li Chuanming , Wang Maoyun , Zhang Chengju
Published: January 2023

Deep fluid activity is widespread in large oil-gas basins around the world. Deep fluids, as the links between internal and external factors of a basin, run in the way of organic-inorganic interactions through the oil-gas formation and aggregation. Herein, the identification characteristics of deep fluids in sedimentary basins as well as their influence on oil-gas reservoir formation and geothermal resource are summarized. The deep fluids of sedimentary basins are identified from three aspects, including mineral composition, fluid inclusions, and geochemical characteristics. The effects of deep fluid activities on oil-gas reservoir formation are manifested in two key aspects of matter and energy. As for the matter effects, deep fluids can improve the primary productivity of sedimentary basins and carry abundant inorganic hydrogen, which contributes to improving the hydrocarbon productivity through hydrogenation. As for the energy effects, the heat energy of deep fluids can promote the mature evolution from organic matter to oil and gas. During this process, the heating of deep fluids will cause the oil-generation window depth of the hydrocarbon source rocks to become thinner, and it will also generate very high pressure, which will promote the discharge of abundant hydrocarbons formed by the hydrocarbon source rocks. Furthermore, deep fluids can directly form volcanic rock oil-gas reservoirs. And another manifestation of deep fluid energy is geothermal. And the thermal energy of deep fluids can directly form hot dry rocks, which is the most important existing form of geothermal resources. The geological exploration of hot dry rocks should be supported by further geochemical and geophysical research.
English language teachers’ conceptions of assessment
Authors: Muianga Felizardo
Published: January 2023

Conceptions of assessment are critical to implementing new assessment policies since they influence how teachers understand, interpret, and implement new policies. This small-scale qualitative study investigated 12 secondary school English language teachers’ views about the current secondary school assessment policy and their conceptions of assessment. The data were collected through in-depth interviews in Maputo, Mozambique. The findings suggest that most participants are unfamiliar with the current assessment policy. The participants conceive of assessment as extrinsically motivating students, improving teaching and learning, holding students accountable, reporting, compliance, and irrelevant. Some participants reported pure conceptions of assessment (either improvement or student accountability), while others reported mixed conceptions (either mixed school and student accountability and improvement and mixed student accountability and irrelevant). The emerging profiles of teachers’ conceptions of assessment are expected to provide a starting point for a discussion about designing effective professional development programs in assessment literacy in Mozambique.
Growth in girls with Turner syndrome
Authors: Isojima Tsuyoshi , Yokoya Susumu
Published: January 2023

Turner syndrome (TS) is a chromosomal disorder affecting females characterized by short stature and gonadal dysgenesis. Untreated girls with TS reportedly are approximately 20-cm shorter than normal girls within their respective populations. The growth patterns of girls with TS also differ from those of the general population. They are born a little smaller than the normal population possibly due to a mild developmental delay in the uterus. After birth, their growth velocity declines sharply until 2 years of age, then continues to decline gradually until the pubertal age of normal children and then drops drastically around the pubertal period of normal children because of the lack of a pubertal spurt. After puberty, their growth velocity increases a little because of the lack of epiphyseal closure. A secular trend in height growth has been observed in girls with TS so growth in excess of the secular trend should be used wherever available in evaluating the growth in these girls. Growth hormone (GH) has been used to accelerate growth and is known to increase adult height. Estrogen replacement treatment is also necessary for most girls with TS because of hypergonadotropic hypogonadism. Therefore, both GH therapy and estrogen replacement treatment are essential in girls with TS. An optimal treatment should be determined considering both GH treatment and age-appropriate induction of puberty. In this review, we discuss the growth in girls with TS, including overall growth, pubertal growth, the secular trend, growth-promoting treatment, and sex hormone replacement treatment.
Quantification of lumbar vertebral fat deposition: Correlation with menopausal status, non-alcoholic fatty liver disease and subcutaneous adipose tissue
Authors: Zheng Chu-Shan , Wen Hui-Quan , Lin Wu-Sheng , Luo Xiao-Wen , Shen Li-Shan , Zhou Xiang , Zou Feng-Yun , Li Qing-Ling , Hu Hui-Jun , Guo Ruo-Mi
Published: January 2023

Purpose

To assess abdominal fat deposition and lumbar vertebra with iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL-IQ) and investigate their correlation with menopausal status.

Materials and Methods

Two hundred forty women who underwent routine abdominal MRI and IDEAL-IQ between January 2016 and April 2021 were divided into two cohorts (first cohort: 120 pre- or postmenopausal women with severe fatty livers or without fatty livers; second cohort: 120 pre- or postmenopausal women who were obese or normal weight). The fat fraction (FF) values of the liver (FFliver) and lumbar vertebra (FFlumbar) in the first group and the FF values of subcutaneous adipose tissue (SAT) (FFSAT) and FFlumbar in the second group were measured and compared using IDEAL-IQ.

Results

Two hundred forty women were evaluated. FFlumbar was significantly higher in both pre- and postmenopausal women with severe fatty liver than in patients without fatty livers (premenopausal women: p < 0.001, postmenopausal women: p < 0.001). No significant difference in the FFlumbar was observed between obese patients and normal-weight patients among pre- and postmenopausal women (premenopausal women: p = 0.113, postmenopausal women: p = 0.092). Significantly greater lumbar fat deposition was observed in postmenopausal women than in premenopausal women with or without fatty liver and obesity (p < 0.001 for each group). A high correlation was detected between FFliver and FFlumbar in women with severe fatty liver (premenopausal women: r=0.76, p<0.01; postmenopausal women: r=0.82, p<0.01).

Conclusion

Fat deposition in the vertebral marrow was significantly associated with liver fat deposition in postmenopausal women.
Case report: Diabetic muscle infarction with diabetic ketoacidosis: A rare complication of diabetes
Authors: Tang Jun , Sun Li , Huang Qi , Wu Yu-Wen , Li Xin , Deng Hao-Hua , Sun Jia-Zhong , Dai Zhe , Xu Yan-Cheng
Published: January 2023

Background

Diabetic muscle infarction (DMI), which is also referred to as diabetic myonecrosis, is a rare and long-term complication of poorly controlled diabetes mellitus, while we found that acute diabetes decompensation, such as diabetic ketoacidosis (DKA), could also stimulate the occurrence and development of DMI.

Case presentation

A 23-year-old woman with type 1 diabetes presented with a 10-day history of nausea, vomiting, pain, and swelling of her left leg. Her urine ketone test was positive. The 3-beta-hydroxybutyrate and leukocyte counts and creatine kinase levels were elevated. Magnetic resonance imaging of the left thigh revealed extensive deep tissue oedema and an increase in the T2 signal in the involved muscles. Once the diagnosis of DMI was made, she was managed with rest, celecoxib, clopidogrel and aggressive insulin therapy. Three months after treatment, the patient reported complete resolution of symptoms.

Conclusion

DMI is a rare DM complication with a high recurrence rate, commonly presenting with chronic complications, while our case report shows that acute diabetes decompensation, such as DKA, can stimulate the occurrence and development of DMI. Timely diagnosis and appropriate treatment could shorten the recovery time.
Muscle plays a more superior role than fat in bone homeostasis: A cross-sectional study of old Asian people
Authors: Liu Chaoran , Wong Pui Yan , Tong Xin , Chow Simon Kwoon-Ho , Hung Vivian Wing-Yin , Cheung Wing-Hoi , Qin Ling , Law Sheung Wai , Wong Ronald Man Yeung
Published: January 2023

Objectives

The aim of this study was to discover the role of fat and muscle in bone structures, as well as the relationship between obesity and sarcopenia on age-related osteoporosis.

Methods

A total of 400 participants (65.0 ± 8.2 years old, 42.3% women) were recruited. Fat, muscle, bone parameters, basic demographics, medical history, physical performance and activity, and calcium intake of participants were obtained from datasets. The diagnosis of osteoporosis, sarcopenia, and obesity was based on current recommendations. Pearson correlation, non-linear regression models, and decision tree analyses were performed to study the relationship between fat, muscle, and bone. Logistic regression analyses were used to explore the risk of osteoporosis in old people with obesity or sarcopenia via Model 1 (unadjusted) and Model 2 (adjusted by age, physical activity, and calcium intake).

Results

Correlation analysis showed that limb muscle mass and index, and age were best related to bone mineral density (BMD) (|r| = 0.386–0.632, p < 0.001). On the contrary, body mass index (BMI) and increased body fat percentage (BF%) were harmful for bone health. An increase of BMI and fat mass index slowed the increase of BMD in the spine, while skeletal muscle mass index accelerated the increase. People with sarcopenia had low muscle mass and strength. When separating subjects into sarcopenia and non-sarcopenia status, sarcopenia was independently related to higher risks of osteoporosis in both models (OR > 1, p < 0.05). BMI-defined obesity in Model 1 as well as BF%-defined obesity in both models did not reduce the risk of osteoporosis in both models (p > 0.05). The decision tree classification (85% accuracy) showed that greater body weight and larger lower limb muscle performance were negatively related to osteoporosis, while fat mass and percentage did not play roles in this prediction.

Conclusion

Low muscle mass and function were harmful to bone health. Obesity defined by both BMI and BF% had limited protective roles in osteoporosis. The benefits for bone from increased muscle mass and function play a more superior role than increased fat mass in old people. Sarcopenia prevention and treatment instead of controlling obesity should be recommended as an approach to reduce the risks of age-related osteoporosis and fragility fracture for elderly people.
Experiments and evaluation on residual strength of X52 steel pipe with various internal defects
Authors: Qi Changchao , Li Tang , Liu Chang , Gao Jian , Du Xinjie , Ren Qingyang , Jia Wenlong
Published: January 2023

The strength of the natural gas transmission pipe is reduced due to sag deformation and corrosion defects. However, there are rare experiment data to quantitatively describe the effect of the defect’s size and position on the pipe strength. This paper designed seven groups of steel pipes with various defects to perform the hydrostatic bursting experiments, and to research the effects of the defects on the strength of the steel pipe. The experimental pipe sample is selected as the X52 material. Three types of defects were set up: concave and corrosion combinational defects, one corrosion defect, and two corrosion defects. The pipe rupture size, the strain around defects, and pipe perimeters before and after experiments are measured, finally yielding the strain-pressure curve of each steel pipe. Comparisons of experimental results show that the defect depth is the dominant factor affecting the pipe strength. Moreover, results show that the DNV-RP-F101 code tends to yield less distance beyond which two defects will not affect each other. The ASME B31G code also tends to give a lower residual strength of the pipe. However, in comparison with the PCORRC criterion, the ASME B31G formula has higher accuracy for X52 pipes. The average relative deviation between the experimental and calculated corroded pipe strength is 14.87%.
Empirical impact of China-Pak business cycle synchronization on environmental degradation in Pakistan
Authors: Huang Yongming , Xu Fan , Abbas Ali , Cong Phan The , Zhang Yuanwei , Kim Euijune
Published: January 2023

This study investigates the empirical impact of China-Pak business cycle synchronization, urbanization, foreign direct investment, exports, and imports on environmental degradation in Pakistan from 1975 to 2017. In doing so, we use the Hodrick-Prescott filter to obtain the trend component of GDP. Then the trend component is subtracted from the original series of GDP to capture the cyclical component of China and Pakistan. The business cycle synchronization index is used to estimate synchronization between the business cycles of both countries. Using the ARDL method, we investigate the existence of a long-run co-integration relationship between the variables of interest. The empirical findings indicate that all explanatory variables (except FDI) are found to be significant factors of environmental degradation in the model. Furthermore, both imports and urbanization have a positive and significant impact on environmental degradation in Pakistan. At the same time, China-Pak business cycle synchronization and exports are discovered to have negative and significant coefficients for environmental degradation in Pakistan. The negative and significant ECM value indicates model convergence and a short-run relationship. The findings of the study suggest that improvement in China-Pak business cycle synchronization may be a factor that promotes environmental sustainability in Pakistan. An increase in exports and a decrease in imports can significantly contribute to reducing environmental degradation in Pakistan. A favorable balance of payment can provide sufficient financial prosperity to take environmental preservation measures. Policymakers should create effective urban planning, which has the potential to improve the country’s environmental quality.
Determination of the cost-benefit efficient interval for sponge city construction by a multi-objective optimization model
Authors: Liang Changmei , Zhang Xiang , Liu Jie , Liu Luguang , Tao Shiyong
Published: January 2023

The cost-benefit is a key factor when selecting an appropriate sponge city construction scheme. The research of applying intelligent technology to find cost-benefit efficient planning and construction of sponge city is urgently required. This paper established a multi-objective simulation optimization framework of sponge city construction which considered minimization of runoff control rate, pollutant control rate and life-cycle cost Non-dominated sorting genetic algorithm (NSGA-II) was successfully coupled to Storm water management model to complete the simulation-optimization process. A case study in Xining, China, was conducted to demonstrate the proposed framework. The results of this research suggested that 1) different sponge city construction schemes lead to different runoff control rates and pollutant control rates although under the same investment; 2) the runoff control rate and pollutant control rate total suspended solids decreased with the increase of the rainfall return period, while the cost of sponge city construction increased with the increase of rainfall return period. Furthermore, for T = 2-year, the sponge facility exhibited the most stable control effect on runoff and pollutants among the three different return periods (T = 2-year, 5-year, 10-year); 3) sponge city construction exhibited a “cost-benefit” efficient interval. For T = 2-year, the cost-benefit high efficiency interval of sponge city construction is calculated between 1.2 billion and 1.8 billion; for T = 5-year, the interval is between 1.2 billion and 1.8 billion, while for T = 10-year, the interval is between 1.3 billion and 2.1 billion. The above observations provide reference for reasonable and effective sponge city construction in Xining, China.
Components and composition of active volatiles attract on Diorhabda tarsalis (Coleoptera: Chrysomelidae) from Glycyrrhiza uralensis (Rosales: Leguminoseae)
Authors: Chen Hong-hao , Zhang Rong , Tan Shu-qian , Wang Yan , Liu Xiao-li , Shi Wang-peng
Published: January 2023

Introduction

Perennial Chinese licorice, Glycyrrhiza uralensis, is an important medicinal plant. Diorhabda tarsalis, a leaf beetle, is a serious insect pest on the plant and cause serious yield losses every year and is attracted to healthy and pest-damaged licorice by plant volatiles.

Aim

The biologically active components of the volatiles released from G. uralensis have not been reported; the components of the volatiles that attract D. tarsalis need to be identified. Such compounds could potentially be used for monitoring and mass-trapping pests.

Methods

GC-EAD, GC-MS, EAG, Y-shaped olfactometer behavioral bioassays, and field trials were performed to identify the components and composition of active volatiles.

Results

Male and virgin female adults were generally attracted to volatiles from licorice, and volatiles from pest-infested plants were more attractive. Four compounds from licorice elicited a significant electrophysiological response (EAD) and were confirmed by EAG, including hexanal, (Z)-3-hexenal, (Z)-3-hexen-1-ol, and (E)-2-hexenal. With the exception of the (E)-2-hexenal, these molecules significantly attracted adults in individual behavioral bioassays, and a proportional mixture corresponding to beetle-damaged licorice of hexanal, (Z)-3-hexenal, (Z)-3-hexen-1-ol, and (E)-2-hexenal (8.78:15.26:57.24:18.72) was most effective for attracting D. tarsalis in the field, attracted a mean of 26 ± 7.19 beetles per trap.

Discussion

D. tarsalis was attracted to volatiles from healthy and herbivore-induced G. uralensis under both laboratory and field conditions. The aforementioned compounds show considerable potential for commercial application to monitor and control D. tarsalis populations.
Genetic variation in TBC1 domain family member 1 gene associates with the risk of lean NAFLD via high-density lipoprotein
Authors: Wu Na , Zhai Xiangyu , Yuan Fan , Li Jie , Li Dong , Wang Jianying , Zhang Lei , Shi Yi , Ji Guang , He Guang , Liu Baocheng
Published: January 2023

Objective: Non-alcoholic fatty liver disease (NAFLD) affects almost a quarter of the world’s population. Although NAFLD often co-exists with obesity, a substantial proportion of NAFLD patients are lean which is relatively unexplored. This study aimed to examine the association between genetic variation in candidate genes, e.g., TBC1D1 and the risk of lean NAFLD in the elderly Chinese Han population.

Methods: This is an extension of the research on physical examination in the Zhanjiang community center including 5387 residents, Shanghai, China, in 2017. According to the classification in adult Asian populations, participants were categorized into four groups: lean NAFLD (BMI <23, n = 106), non-lean NAFLD (BMI ≥23, n = 644), lean non-NAFLD (BMI <23, n = 216) and non-lean non-NAFLD (BMI ≥23, n = 253).116 NAFLD-related candidate genes, which cover 179 single nucleotide polymorphisms (SNPs) were included in the KEGG enrichment analysis. Independent samples t-test was adopted for the group comparison. The associations between genetic variations with the specific phenotype in five genetic models were analyzed with the “SNPassoc” R package and rechecked with logistic regression analysis. Mediation models were conducted to explore whether the certain phenotype can mediate the association between SNPs and the risk of lean NAFLD.

Results: Compared with lean non-NAFLD individuals, lean NAFLD patients had higher BMI, low-density lipoprotein and triglyceride, and lower HDL. The AMPK signaling pathway, which includes TBC1D1 and ADIPOQ genes, was the most significant (p < .001). The A allele frequency of rs2279028 in TBC1D1 (p = .006) and G allele frequency of rs17366568 in ADIPOQ (p = .038) were significantly lower in lean NAFLD. The association between rs2279028 and the risk of lean NAFLD was mediated by HDL (p = .014). No significant mediation effect was found between rs17366568 and the risk of lean NAFLD.

Conclusion: This study, for the first time, indicated that rs2279028 of TBC1D1 may contribute to the progression of lean NAFLD through HDL. This finding provides more evidence for exploring the mechanism of lean NAFLD and suggests practical solutions for the treatment of lean NAFLD.
Identification of two molecular subtypes and a novel prognostic model of lung adenocarcinoma based on a cuproptosis-associated gene signature
Authors: Zhou Jinlin , Chen Dehe , Zhang Shiguo , Wang Chunmei , Zhang Li
Published: January 2023

Lung adenocarcinoma is the most common subtype of lung cancer clinically, with high mortality and poor prognosis. Cuproptosis present a newly discovered mode of cell death characterized by aggregation of fatty acylated proteins, depletion of iron-sulfur clusterin, triggering of HSP70, and induction of intracellular toxic oxidative stress. However, the impact of cuproptosis on lung adenocarcinoma development, prognosis, and treatment has not been elucidated. By systematically analyzing the genetic alterations of 10 cuproptosis-related genes in lung adenocarcinoma, we found that CDKN2A, DLAT, LIAS, PDHA1, FDX1, GLS, and MTF1 were differentially expressed between lung cancer tissues and adjacent tissues. Based on the expression levels of 10 cuproptosis-related genes, we classified lung adenocarcinoma patients into two molecular subtypes using the Consensus clustering method, of which subtype 2 had a worse prognosis. Differential expression genes associated with prognosis between the two subtypes were obtained by differential analysis and survival analysis, and cox lasso regression was applied to construct a cuproptosis-related prognostic model. Its survival predicting ability was validated in three extrinsic validation cohorts. The results of multivariate cox analysis indicated that cuproptosis risk score was an independent prognostic predictor, and the mixed model formed by cupproptosis prognostic model combined with stage had more robust prognostic prediction accuracy. We found the differences in cell cycle, mitosis, and p53 signaling pathways between high- and low-risk groups according to GO and KEGG enrichment analysis. The results of immune microenvironment analysis showed that the enrichment score of activated dendritic cells, mast cells, and type 2 interferon response were down-regulated in the high-risk group, while the fraction of neutrophils and M0 macrophages were upregulated in the high-risk group. Compared with the high-risk group, subjects in the low-risk group had higher Immunophenoscore and may be more sensitive to immunotherapy. We identified seven chemotherapy agents may improve the curative effect in LUAD samples with higher risk score. Overall, we discovered that cuproptosis is closely related to the occurrence, prognosis, and treatment of lung adenocarcinoma. The cuproptosis prognostic model is a potential prognostic predictor and may provide new strategies for precision therapy in lung adenocarcinoma.
Molecular characterization of divergent isolates of Citrus bent leaf viroid (CBLVd) from citrus cultivars of Punjab, Pakistan
Authors: Ali Amjad , Umar Ummad ud Din , Naqvi Syed Atif Hasan , Shakeel Muhammad Taimoor , Tahir Muhammad Nouman , Khan Muhammad Fahad , Altaf Muhammad Tanveer , Ölmez Fatih , Dababat Abdelfattah A. , Haq Zia ul , Nadeem Muhammad Azhar , Hatipoğlu Rüştü , Baloch Faheem Shehzad , Chung Yong Suk
Published: January 2023

Citrus viroid infection is emerging as a serious threat because of its efficient systemic movement within the host plant and its quick spread due to contaminated pruning tools. A survey was conducted to investigate the primary distribution and molecular characterization of Citrus bent leaf viroid (CBLVd) and its variants in different citrus cultivars. A total of 154 symptomatic citrus samples were collected and detected by RT‒PCR with newly designed specific primers with the incidence of 36.33%. During biological indexing study on Etrog citron, expressions of reduced leaf size, yellowing with a light green pattern, and bending were observed. Amplified products were sequenced and analyzed using a nucleotide BLAST search, which showed 98% homology with other CBLVd isolates. The results of the phylogenetic tree analysis showed the presence of two main groups (A and B), with the predominant variants of CBLVd, i.e., CVd-I-LSS (Citrus viroid Low Sequence Similarity) sequences, clustering in subgroup A1 along with newly detected CVd-I-LSS from Palestinian sweet lime (Citrus limettioides), which has been identified as a new host of CVd-I-LSS in Pakistan. Further analysis of the sequences in subgroup A1 showed that the variant of CVd-I-LSS infecting citrus cultivars had a close relationship with isolates reported from China, Japan, and Iran, which may have resulted from the exchange of planting material. This study also unveiled the variability in nucleotide sequences of CBLVd, which made it unable to be detected by old primers. The results of this study indicate that the widespread presence of divergent variants of CBLVd is a major concern for the citrus industry in Pakistan and other countries where virulent isolates of CBLVd are prevalent. These findings suggest the need for future research on effective management and quarantine measures to stop the spread of CBLVd.
Estimating tissue-specific peptide abundance from public RNA-Seq data
Authors: Frentzen Angela , Greenbaum Jason A. , Kim Haeuk , Peters Bjoern , Koşaloğlu-Yalçın Zeynep
Published: January 2023

Several novel MHC class I epitope prediction tools additionally incorporate the abundance levels of the peptides’ source antigens and have shown improved performance for predicting immunogenicity. Such tools require the user to input the MHC alleles and peptide sequences of interest, as well as the abundance levels of the peptides’ source proteins. However, such expression data is often not directly available to users, and retrieving the expression level of a peptide’s source antigen from public databases is not trivial. We have developed the Peptide eXpression annotator (pepX), which takes a peptide as input, identifies from which proteins the peptide can be derived, and returns an estimate of the expression level of those source proteins from selected public databases. We have also investigated how the abundance level of a peptide can be best estimated in cases when it can originate from multiple transcripts and proteins and found that summing up transcript-level expression values performs best in distinguishing ligands from decoy peptides.
ANXA2 is a potential biomarker for cancer prognosis and immune infiltration: A systematic pan-cancer analysis
Authors: Ning Yijie , Li Yufei , Wang Hongqin
Published: January 2023

Background: Annexin A2 (ANXA2) belongs to the Annexin A family and plays a role in epithelial-mesenchymal transition, fibrinolysis, and other physiological processes. Annexin A2 has been extensively implicated in tumorigenesis and development in previous studies, but its precise role in pan-cancer remains largely unknown.

Methods: We adopted bioinformatics methods to explore the oncogenic role of Annexin A2 using different databases, including the Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) biobank, the Human Protein Atlas (HPA), the Gene Expression Profiling Interaction Analysis (GEPIA) and cBioPortal. We analyzed the differential expression of Annexin A2 in different tumors and its relationship with cancer prognosis, immune cell infiltration, DNA methylation, tumor mutation burden (TMB), microsatellite instability (MSI) and mismatch repair (MMR). Furtherly, we conducted a Gene Set Enrichment Analysis (GSEA) to identify the Annexin A2-related pathways.

Results: Annexin A2 expression was upregulated in most cancers, except in kidney chromophobe (KICH) and prostate adenocarcinoma (PRAD). Annexin A2 showed a good diagnostic efficacy in twelve types of cancer. The high expression of Annexin A2 was significantly associated with a reduced overall survival, disease-specific survival and progression-free interval in seven cancers. The Annexin A2 expression was variably associated with infiltration of 24 types of immune cells in 32 tumor microenvironments. In addition, Annexin A2 expression was differently associated with 47 immune checkpoints, immunoregulators, DNA methylation, tumor mutation burden, microsatellite instability and mismatch repair in pan-cancer. Gene Set Enrichment Analysis revealed that Annexin A2 was significantly correlated with immune-related pathways in fifteen cancers.

Conclusion: Annexin A2 widely correlates with immune infiltration and may function as a promising prognostic biomarker in many tumors, showing its potential as a target for immunotherapy in pan-cancer.
Overview of the effect of rumen-protected limiting amino acids (methionine and lysine) and choline on the immunity, antioxidative, and inflammatory status of periparturient ruminants
Authors: Khan Muhammad Zahoor , Liu Shuai , Ma Yulin , Ma Mei , Ullah Qudrat , Khan Ibrar Muhammad , Wang Jingjun , Xiao Jianxin , Chen Tianyu , Khan Adnan , Cao Zhijun
Published: January 2023

Overproduction of reactive oxygen species (ROS) is a well-known phenomenon experienced by ruminants, especially during the transition from late gestation to successful lactation. This overproduction of ROS may lead to oxidative stress (OS), which compromises the immune and anti-inflammatory systems of animals, thus predisposing them to health issues. Besides, during the periparturient period, metabolic stress is developed due to a negative energy balance, which is followed by excessive fat mobilization and poor production performance. Excessive lipolysis causes immune suppression, abnormal regulation of inflammation, and enhanced oxidative stress. Indeed, OS plays a key role in regulating the metabolic activity of various organs and the productivity of farm animals. For example, rapid fetal growth and the production of large amounts of colostrum and milk, as well as an increase in both maternal and fetal metabolism, result in increased ROS production and an increased need for micronutrients, including antioxidants, during the last trimester of pregnancy and at the start of lactation. Oxidative stress is generally neutralized by the natural antioxidant system in the body. However, in some special phases, such as the periparturient period, the animal’s natural antioxidant system is unable to cope with the situation. The effect of rumen-protected limiting amino acids and choline on the regulation of immunity, antioxidative, and anti-inflammatory status and milk production performance, has been widely studied in ruminants. Thus, in the current review, we gathered and interpreted the data on this topic, especially during the perinatal and lactational stages.
Susceptibility identification for seasonal influenza A/H3N2 based on baseline blood transcriptome
Authors: Tang Jing , Xu Qiumei , Tang Kang , Ye Xiaoyan , Cao Zicheng , Zou Min , Zeng Jinfeng , Guan Xinyan , Han Jinglin , Wang Yihan , Yang Lan , Lin Yishan , Jiang Kaiao , Chen Xiaoliang , Zhao Yang , Tian Dechao , Li Chunwei , Shen Wei , Du Xiangjun
Published: January 2023

Introduction

Influenza susceptibility difference is a widely existing trait that has great practical significance for the accurate prevention and control of influenza.

Methods

Here, we focused on the human susceptibility to the seasonal influenza A/H3N2 of healthy adults at baseline level. Whole blood expression data for influenza A/H3N2 susceptibility from GEO were collected firstly (30 symptomatic and 19 asymptomatic). Then to explore the differences at baseline, a suite of systems biology approaches - the differential expression analysis, co-expression network analysis, and immune cell frequencies analysis were utilized.

Results

We found the baseline condition, especially immune condition between symptomatic and asymptomatic, was different. Co-expression module that is positively related to asymptomatic is also related to immune cell type of naïve B cell. Function enrichment analysis showed significantly correlation with “B cell receptor signaling pathway”, “immune response−activating cell surface receptor signaling pathway” and so on. Also, modules that are positively related to symptomatic are also correlated to immune cell type of neutrophils, with function enrichment analysis showing significantly correlations with “response to bacterium”, “inflammatory response”, “cAMP−dependent protein kinase complex” and so on. Responses of symptomatic and asymptomatic hosts after virus exposure show differences on resisting the virus, with more effective frontline defense for asymptomatic hosts. A prediction model was also built based on only baseline transcription information to differentiate symptomatic and asymptomatic population with accuracy of 0.79.

Discussion

The results not only improve our understanding of the immune system and influenza susceptibility, but also provide a new direction for precise and targeted prevention and therapy of influenza.