bluuebunny/crossref_metadata_2025 huggingface dataset:
Semi-MsST-GAN: A Semi-Supervised Segmentation Method for Corneal Ulcer Segmentation in Slit-Lamp Images
Authors: Wang Tingting , Wang Meng , Zhu Weifang , Wang Lianyu , Chen Zhongyue , Peng Yuanyuan , Shi Fei , Zhou Yi , Yao Chenpu , Chen Xinjian
Published: January 2022

Corneal ulcer is a common leading cause of corneal blindness. It is difficult to accurately segment corneal ulcers due to the following problems: large differences in the pathological shapes between point-flaky and flaky corneal ulcers, blurred boundary, noise interference, and the lack of sufficient slit-lamp images with ground truth. To address these problems, in this paper, we proposed a novel semi-supervised multi-scale self-transformer generative adversarial network (Semi-MsST-GAN) that can leverage unlabeled images to improve the performance of corneal ulcer segmentation in fluorescein staining of slit-lamp images. Firstly, to improve the performance of segmenting the corneal ulcer regions with complex pathological features, we proposed a novel multi-scale self-transformer network (MsSTNet) as the MsST-GAN generator, which can guide the model to aggregate the low-level weak semantic features with the high-level strong semantic information and adaptively learn the spatial correlation in feature maps. Then, to further improve the segmentation performance by leveraging unlabeled data, the semi-supervised approach based on the proposed MsST-GAN was explored to solve the problem of the lack of slit-lamp images with corresponding ground truth. The proposed Semi-MsST-GAN was comprehensively evaluated on the public SUSTech-SYSU dataset, which contains 354 labeled and 358 unlabeled fluorescein staining slit-lamp images. The results showed that, compared with other state-of-the-art methods, our proposed method achieves better performance with comparable efficiency.
Event-Related Potentials in Women on the Pill: Neural Correlates of Positive and Erotic Stimulus Processing in Oral Contraceptive Users
Authors: Schmidt Norina M. , Hennig Juergen , Munk Aisha J. L.
Published: January 2022

Background/Aims: Exposure toward positive emotional cues with – and without – reproductive significance plays a crucial role in daily life and regarding well-being as well as mental health. While possible adverse effects of oral contraceptive (OC) use on female mental and sexual health are widely discussed, neural processing of positive emotional stimuli has not been systematically investigated in association with OC use. Considering reported effects on mood, well-being and sexual function, and proposed associations with depression, it was hypothesized that OC users showed reduced neural reactivity toward positive and erotic emotional stimuli during early as well as later stages of emotional processing and also rated these stimuli as less pleasant and less arousing compared to naturally cycling (NC) women.

Method: Sixty-two female subjects (29 NC and 33 OC) were assessed at three time points across the natural menstrual cycle and corresponding time points of the OC regimen. Early (early posterior negativity, EPN) and late (late positive potential, LPP) event-related potentials in reaction to positive, erotic and neutral stimuli were collected during an Emotional Picture Stroop Paradigm (EPSP). At each appointment, subjects provided saliva samples for analysis of gonadal steroid concentration. Valence and arousal ratings were collected at the last appointment.

Results: Oral contraceptive users had significantly lower endogenous estradiol and progesterone concentrations compared to NC women. No significant group differences in either subjective stimulus evaluations or neural reactivity toward positive and erotic emotional stimuli were observed. For the OC group, LPP amplitudes in reaction to erotic vs. neutral pictures differed significantly between measurement times across the OC regimen.

Discussion: In this study, no evidence regarding alterations of neural reactivity toward positive and erotic stimuli in OC users compared to NC was found. Possible confounding factors and lines for future research are elaborated and discussed.
Modeling Somatic Mutations Associated With Neurodevelopmental Disorders in Human Brain Organoids
Authors: Deb Bipan K. , Bateup Helen S.
Published: January 2022

Neurodevelopmental disorders (NDDs) are a collection of diseases with early life onset that often present with developmental delay, cognitive deficits, and behavioral conditions. In some cases, severe outcomes such as brain malformations and intractable epilepsy can occur. The mutations underlying NDDs may be inherited or de novo, can be gain- or loss-of-function, and can affect one or more genes. Recent evidence indicates that brain somatic mutations contribute to several NDDs, in particular malformations of cortical development. While advances in sequencing technologies have enabled the detection of these somatic mutations, the mechanisms by which they alter brain development and function are not well understood due to limited model systems that recapitulate these events. Human brain organoids have emerged as powerful models to study the early developmental events of the human brain. Brain organoids capture the developmental progression of the human brain and contain human-enriched progenitor cell types. Advances in human stem cell and genome engineering provide an opportunity to model NDD-associated somatic mutations in brain organoids. These organoids can be tracked throughout development to understand the impact of somatic mutations on early human brain development and function. In this review, we discuss recent evidence that somatic mutations occur in the developing human brain, that they can lead to NDDs, and discuss how they could be modeled using human brain organoids.
Disrupted Association of Sensory Neurons With Enveloping Satellite Glial Cells in Fragile X Mouse Model
Authors: Avraham Oshri , Deng Pan-Yue , Maschi Dario , Klyachko Vitaly A. , Cavalli Valeria
Published: January 2022

Among most prevalent deficits in individuals with Fragile X syndrome (FXS) is hypersensitivity to sensory stimuli and somatosensory alterations. Whether dysfunction in peripheral sensory system contributes to these deficits remains poorly understood. Satellite glial cells (SGCs), which envelop sensory neuron soma, play critical roles in regulating neuronal function and excitability. The potential contributions of SGCs to sensory deficits in FXS remain unexplored. Here we found major structural defects in sensory neuron-SGC association in the dorsal root ganglia (DRG), manifested by aberrant covering of the neuron and gaps between SGCs and the neuron along their contact surface. Single-cell RNAseq analyses demonstrated transcriptional changes in both neurons and SGCs, indicative of defects in neuronal maturation and altered SGC vesicular secretion. We validated these changes using fluorescence microscopy, qPCR, and high-resolution transmission electron microscopy (TEM) in combination with computational analyses using deep learning networks. These results revealed a disrupted neuron-glia association at the structural and functional levels. Given the well-established role for SGCs in regulating sensory neuron function, altered neuron-glia association may contribute to sensory deficits in FXS.
Novel Millet-Based Flavored Yogurt Enriched With Superoxide Dismutase
Authors: Fan Xiankang , Li Xiefei , Zhang Tao , Guo Yuxing , Shi Zihang , Wu Zhen , Zeng Xiaoqun , Pan Daodong
Published: January 2022

Superoxide dismutase (SOD) is an important antioxidant enzyme with different physiological functions, which can be used as a nutritional fortifier in food. Cereal-based fermented products are becoming popular worldwide. In this study, novel millet-based flavored yogurt enriched with SOD was developed. Lactiplantibacillus plantarum subsp. plantarum was screened, which manufactured SOD activity of 2476.21 ± 1.52 U g−1. The SOD content of millet yogurt was 19.827 ± 0.323 U mL−1, which was 63.01, 50.11, and 146.79% higher than that of Bright Dairy Yogurt 1911, Junlebao and Nanjing Weigang, respectively. Fifty-four volatile flavor substances and 22,571 non-volatile flavor substances were found in yogurt. Compared to traditional fermented yogurt, 37 non-volatile metabolites in yogurt with millet enzymatic fermentation broth were significantly upregulated, including 2-phenyl ethanol, hesperidin, N-acetylornithine and L-methionine, which were upregulated by 3169.6, 228.36, 271.22, and 55.67 times, respectively, thereby enriching the sensory and nutritional value of yogurt. Moreover, the manufacture of unpleasant volatile flavor substances was masked, making the product more compatible with consumers' tastes.
FAPI PET/CT in the Diagnosis of Abdominal and Pelvic Tumors
Authors: Yang Tianshuo , Ma Long , Hou Haodong , Gao Feng , Tao Weijing
Published: January 2022

Positron emission tomography/computed tomography (PET/CT) with 18F-fluorodeoxyglucose (18F-FDG) is currently a standard imaging examination used in clinical practice, and plays an essential role in preoperative systemic evaluation and tumor staging in patients with tumors. However, 18F-FDG PET/CT has certain limitations in imaging of some tumors, like gastric mucus adenocarcinoma, highly differentiated hepatocellular carcinoma, renal cell carcinoma, and peritoneal metastasis. Therefore, to search for new tumor diagnosis methods has always been an important topic in radiographic imaging research. Fibroblast activation protein (FAP) is highly expressed in many epithelial carcinomas, and various isotope-labelled fibroblast activation protein inhibitors (FAPI) show lower uptake in the brain and abdominal tissues than in tumor, thus achieving high image contrast and good tumor delineation. In addition to primary tumors, FAPI PET/CT is better than FDG PET/CT for detecting lymph nodes and metastases. Additionally, the highly selective tumor uptake of FAPI may open up new application areas for the non-invasive characterization, staging of tumors, as well as monitoring tumor treatment efficacy. This review focuses on the recent research progress of FAPI PET/CT in the application to abdominal and pelvic tumors, with the aim of providing new insights for diagnostic strategies for tumor patients, especially those with metastases.
circHIPK3 Exacerbates Folic Acid-Induced Renal Tubulointerstitial Fibrosis by Sponging miR-30a
Authors: Wu Yan , Luan Junjun , Jiao Congcong , Zhang Shiwen , Ma Cong , Zhang Yixiao , Fu Jingqi , Lai En Yin , Kopp Jeffrey B. , Pi Jingbo , Zhou Hua
Published: January 2022

Renal tubulointerstitial fibrosis is a common pathological feature of progressive chronic kidney disease (CKD), and current treatment has limited efficacy. The circular RNA circHIPK3 is reported to participate in the pathogenesis of various human diseases. However, the role of circHIPK3 in renal fibrosis has not been examined. In this study, we aimed to determine whether and how circHIPK3 might participate in the pathogenesis of renal fibrosis. Mice received a peritoneal injection of folic acid (250 mg/kg). Of note, 30 days later, renal fibrosis was present on periodic acid–Schiff (PAS) and Masson staining, and mRNA and protein of profibrotic genes encoding fibronectin (FN) and collagen 1 (COL1) were increased. Renal circHIPK3 was upregulated, while miR-30a was downregulated, assessed by quantitative PCR (qPCR) and fluorescence in situ hybridization (FISH). The expression of transforming growth factor beta-1 (TGF-β1) was increased by qPCR analysis, immunoblotting, and immunofluorescence. Renal circHIPK3 negatively correlated with miR-30a, and kidney miR-30a negatively correlated with TGF-β1. Target Scan and miRanda algorithms predicted three perfect binding sites between circHIPK3 and miR-30a. We found that circHIPK3, miR-30a, and TGF-β1 colocalized in the cytoplasm of human tubular epithelial cells (HK-2 cells) on FISH and immunofluorescence staining. We transfected circHIPK3 and a scrambled RNA into HK-2 cells; miR-30a was downregulated, and the profibrotic genes such as TGF-β1, FN, and COL1 were upregulated and assessed by qPCR, immunoblotting, and immunofluorescence staining. Third, the upregulation of circHIPK3, downregulation of miR-30a, and overproduction of profibrotic FN and COL1 were also observed in HK-2 cells exposed to TGF-β1. Finally, renal biopsies from patients with chronic tubulointerstitial nephritis manifested similar expression patterns of circHIPK3, miR-30a, and profibrotic proteins, such as TGF-β1, FN, and COL1 as observed in the experimental model. A feed-forward cycle was observed among circHIPK3, miR-30a, and TGF-β1. Our results suggest that circHIPK3 may contribute to progressive renal fibrosis by sponging miR-30a. circHIPK3 may be a novel therapeutic target for slowing CKD progression.
The Brain-Nose Interface: A Potential Cerebrospinal Fluid Clearance Site in Humans
Authors: Mehta Neel H. , Sherbansky Jonah , Kamer Angela R. , Carare Roxana O. , Butler Tracy , Rusinek Henry , Chiang Gloria C. , Li Yi , Strauss Sara , Saint-Louis L. A. , Theise Neil D. , Suss Richard A. , Blennow Kaj , Kaplitt Michael , de Leon Mony J.
Published: January 2022

The human brain functions at the center of a network of systems aimed at providing a structural and immunological layer of protection. The cerebrospinal fluid (CSF) maintains a physiological homeostasis that is of paramount importance to proper neurological activity. CSF is largely produced in the choroid plexus where it is continuous with the brain extracellular fluid and circulates through the ventricles. CSF movement through the central nervous system has been extensively explored. Across numerous animal species, the involvement of various drainage pathways in CSF, including arachnoid granulations, cranial nerves, perivascular pathways, and meningeal lymphatics, has been studied. Among these, there is a proposed CSF clearance route spanning the olfactory nerve and exiting the brain at the cribriform plate and entering lymphatics. While this pathway has been demonstrated in multiple animal species, evidence of a similar CSF egress mechanism involving the nasal cavity in humans remains poorly consolidated. This review will synthesize contemporary evidence surrounding CSF clearance at the nose-brain interface, examining across species this anatomical pathway, and its possible significance to human neurodegenerative disease. Our discussion of a bidirectional nasal pathway includes examination of the immune surveillance in the olfactory region protecting the brain. Overall, we expect that an expanded discussion of the brain-nose pathway and interactions with the environment will contribute to an improved understanding of neurodegenerative and infectious diseases, and potentially to novel prevention and treatment considerations.
Can Time-Lapse Incubation and Monitoring Be Beneficial to Assisted Reproduction Technology Outcomes? A Randomized Controlled Trial Using Day 3 Double Embryo Transfer
Authors: Guo Yu-han , Liu Yan , Qi Lin , Song Wen-yan , Jin Hai-xia
Published: January 2022

Objective: To determine if the application of time-lapse incubation and monitoring can be beneficial to clinical outcomes in assisted reproductive technology.

Methods: A total of 600 patients were equally randomized to three groups, namely, conventional embryo culture and standard morphological selection (CM group), time-lapse culture and standard morphological selection (TLM group), and time-lapse culture and morphokinetic selection (TLA group). Notably, 424 undergoing fresh autologous in vitro fertilization cycles were analyzed, 132 patients in the CM group, 158 in the TLM group, and 134 in the TLA group. Main outcomes included clinical outcomes, embryo development rates, and perinatal outcomes.

Results: Clinical pregnancy rates in the time-lapse groups were significantly higher than in the CM group (CM 65.2% vs. TLM 77.2% vs. TLA 81.3%). Implantation rates and live birth rates were significantly higher for the TLA group (59.7 and 70.9%) compared with the CM group (47.7 and 56.1%) but not compared with the TLM group (55.4 and 67.1%). There was no statistical difference in miscarriage and ectopic pregnancy rates among the three groups. Overall, birth weight was significantly higher in the time-lapse groups (CM 2,731.7 ± 644.8 g vs. TLM 3,066.5 ± 595.4 g vs. TLA 2,967.4 ± 590.0 g). The birth height of newborns in the TLM group was significantly longer than that of the CM group and TLA group (CM 48.3± 4.4 cm vs. TLM 49.8± 2.3 cm vs. TLA 48.5± 2.7 cm).

Conclusion: Time-lapse incubation and monitoring have a significant benefit on clinical pregnancy rates and on overall birth weights while morphokinetic analysis is not necessary.

Clinical Trial Registration: [www.ClinicalTrials.gov], identifier [NCT02974517].
Immune Aging and How It Works for Inflammation and Fibrosis
Authors: Nishiura Hiroshi , Imasaka Mai , Yamanegi Koji , Fujimoto Jiro , Ohmuraya Masaki
Published: January 2022

Almost all mature cells that undergo apoptosis in an age-dependent or an accidental manner are completely recovered in tissue-specific microenvironments without any physiological changes. After peripheral blood leukocytes are released into the local region, fibroblast cells and new blood vessels commonly proliferate during wound healing. Inducible repair tools mainly supplied from blood vessels are cleared by peripheral blood phagocytic macrophages. Finally, hematopoietic stem cell (HSC)-derived precursor cells migrate from bone marrow (BM) to the microenvironment to rebuild damaged tissues (the mature immune system). In contrast to the mature immune system, the effects of aging on HSCs (long-term HSCs) and peripheral blood lymphocytes (long-term PBLs) are not clearly understood in the BM and thymus niches with tissue-specific microenvironments with some physiological changes (the aged BM niche) for incomplete rebuilding of damaged tissues (the aged immune system). In this review, the roles of the aged immune system in both a delay of acute inflammation and the development of chronic inflammation or fibrosis are discussed.
Druggable Lipid Binding Sites in Pentameric Ligand-Gated Ion Channels and Transient Receptor Potential Channels
Authors: Cheng Wayland W. L. , Arcario Mark J. , Petroff John T.
Published: January 2022

Lipids modulate the function of many ion channels, possibly through direct lipid-protein interactions. The recent outpouring of ion channel structures by cryo-EM has revealed many lipid binding sites. Whether these sites mediate lipid modulation of ion channel function is not firmly established in most cases. However, it is intriguing that many of these lipid binding sites are also known sites for other allosteric modulators or drugs, supporting the notion that lipids act as endogenous allosteric modulators through these sites. Here, we review such lipid-drug binding sites, focusing on pentameric ligand-gated ion channels and transient receptor potential channels. Notable examples include sites for phospholipids and sterols that are shared by anesthetics and vanilloids. We discuss some implications of lipid binding at these sites including the possibility that lipids can alter drug potency or that understanding protein-lipid interactions can guide drug design. Structures are only the first step toward understanding the mechanism of lipid modulation at these sites. Looking forward, we identify knowledge gaps in the field and approaches to address them. These include defining the effects of lipids on channel function in reconstituted systems using asymmetric membranes and measuring lipid binding affinities at specific sites using native mass spectrometry, fluorescence binding assays, and computational approaches.
Expanding the Gap: An Updated Look Into Sex Differences in Running Performance
Authors: Hallam Lydia C. , Amorim Fabiano T.
Published: January 2022

Males consistently outperform females in athletic endeavors, including running events of standard Olympic distances (100 m to Marathon). The magnitude of this percentage sex difference, i.e., the sex gap, has evolved over time. Two clear trends in sex gap evolution are evident; a narrowing of the gap during the 20th century, followed by a period of stability thereafter. However, an updated perspective on the average sex gap from top 20 athlete performances over the past two decades reveals nuanced trends over time, indicating the sex gap is not fixed. Additionally, the sex gap varies with performance level; the difference in absolute running performance between males and females is lowest for world record/world lead performances and increases in lower-ranked elite athletes. This observation of an increased sex gap with world rank is evident in events 400 m and longer and indicates a lower depth in female competitive standards. Explanations for the sex difference in absolute performance and competition depth include physical (physiological, anatomical, neuromuscular, biomechanical), sociocultural, psychological, and sport-specific factors. It is apparent that females are the disadvantaged sex in sport; therefore, measures should be taken to reduce this discrepancy and enable both sexes to reach their biological performance potential. There is scope to narrow the sex performance gap by addressing inequalities between the sexes in opportunities, provisions, incentives, attitudes/perceptions, research, and media representation.
A Proof-of-Principle Study of Non-invasive Identification of Peanut Genotypes and Nematode Resistance Using Raman Spectroscopy
Authors: Payne William Z. , Dou Tianyi , Cason John M. , Simpson Charles E. , McCutchen Bill , Burow Mark D. , Kurouski Dmitry
Published: January 2022

Identification of peanut cultivars for distinct phenotypic or genotypic traits whether using visual characterization or laboratory analysis requires substantial expertise, time, and resources. A less subjective and more precise method is needed for identification of peanut germplasm throughout the value chain. In this proof-of-principle study, the accuracy of Raman spectroscopy (RS), a non-invasive, non-destructive technique, in peanut phenotyping and identification is explored. We show that RS can be used for highly accurate peanut phenotyping via surface scans of peanut leaves and the resulting chemometric analysis: On average 94% accuracy in identification of peanut cultivars and breeding lines was achieved. Our results also suggest that RS can be used for highly accurate determination of nematode resistance and susceptibility of those breeding lines and cultivars. Specifically, nematode-resistant peanut cultivars can be identified with 92% accuracy, whereas susceptible breeding lines were identified with 81% accuracy. Finally, RS revealed substantial differences in biochemical composition between resistant and susceptible peanut cultivars. We found that resistant cultivars exhibit substantially higher carotenoid content compared to the susceptible breeding lines. The results of this study show that RS can be used for quick, accurate, and non-invasive identification of genotype, nematode resistance, and nutrient content. Armed with this knowledge, the peanut industry can utilize Raman spectroscopy for expedited breeding to increase yields, nutrition, and maintaining purity levels of cultivars following release.
Stress-Responsive cis-Regulatory Elements Underline Podophyllotoxin Biosynthesis and Better Performance of Sinopodophyllum hexandrum Under Water Deficit Conditions
Authors: Kumari Anita , Dogra Vivek , Joshi Rohit , Kumar Sanjay
Published: January 2022

Sinopodophyllum hexandrum is an endangered medicinal herb known for its bioactive lignan podophyllotoxin (PTOX), which is used for the preparation of anticancer drugs. In its natural habitat, S. hexandrum is exposed to a multitude of adversities, such as fluctuating temperatures, water deficit, and high UV radiations. Transcriptional regulation of genes, which is regulated by the condition-specific binding of transcriptional factors to precise motifs in the promoter region, underlines responses to an environmental cue. Therefore, analysis of promoter sequences could ascertain the spatio-temporal expression of genes and overall stress responses. Unavailability of genomic information does not permit such analysis in S. hexandrum, especially on regulation of PTOX pathway. Accordingly, this study describes isolation and in silico analysis of 5′-upstream regions of ShPLR (PINORESINOL-LARICIRESINOL REDUCTASE) and ShSLD (SECOISOLARICIRESINOL DEHYDROGENASE), the two key genes of the PTOX biosynthetic pathway. Data showed a range of motifs related to basal transcription, stress-responsive elements, such as those for drought, low temperature, and light, suggesting that the expression of these genes and resulting PTOX accumulation would be affected by, at least, these environmental cues. While the impact of temperature and light on PTOX accumulation is well studied, the effect of water deficit on the physiology of S. hexandrum and PTOX accumulation remains obscure. Given the presence of drought-responsive elements in the promoters of the key genes, the impact of water deficit on growth and development and PTOX accumulation was studied. The results showed decline in relative water content and net photosynthetic rate, and increase in relative electrolyte leakage with stress progression. Plants under stress exhibited a reduction in transpiration rate and chlorophyll content, with a gradual increase in osmoprotectant content. Besides, stressed plants showed an increase in the expression of genes involved in the phenylpropanoid pathway and PTOX biosynthesis, and an increase in PTOX accumulation. Upon re-watering, non-irrigated plants showed a significant improvement in biochemical and physiological parameters. Summarily, our results demonstrated the importance of osmoprotectants during water deficit and the revival capacity of the species from water deficit, wherein PTOX synthesis was also modulated. Moreover, isolated promoter sequences could be employed in genetic transformation to mediate the expression of stress-induced genes in other plant systems.
Highly Conserved Evolution of Aquaporin PIPs and TIPs Confers Their Crucial Contribution to Flowering Process in Plants
Authors: Li Qi , Tong Tao , Jiang Wei , Cheng Jianhui , Deng Fenglin , Wu Xiaojian , Chen Zhong-Hua , Ouyang Younan , Zeng Fanrong
Published: January 2022

Flowering is the key process for the sexual reproduction in seed plants. In gramineous crops, the process of flowering, which includes the actions of both glume opening and glume closing, is directly driven by the swelling and withering of lodicules due to the water flow into and out of lodicule cells. All these processes are considered to be controlled by aquaporins, which are the essential transmembrane proteins that facilitate the transport of water and other small molecules across the biological membranes. In the present study, the evolution of aquaporins and their contribution to flowering process in plants were investigated via an integration of genome-wide analysis and gene expression profiling. Across the barley genome, we found that HvTIP1;1, HvTIP1;2, HvTIP2;3, and HvPIP2;1 were the predominant aquaporin genes in lodicules and significantly upregulated in responding to glume opening and closing, suggesting the importance of them in the flowering process of barley. Likewise, the putative homologs of the above four aquaporin genes were also abundantly expressed in lodicules of the other monocots like rice and maize and in petals of eudicots like cotton, tobacco, and tomato. Furthermore, all of them were mostly upregulated in responding to the process of floret opening, indicating a conserved function of these aquaporin proteins in plant flowering. The phylogenetic analysis based on the OneKP database revealed that the homologs of TIP1;1, TIP1;2, TIP2;3, and PIP2;1 were highly conserved during the evolution, especially in the angiosperm species, in line with their conserved function in controlling the flowering process. Taken together, it could be concluded that the highly evolutionary conservation of TIP1;1, TIP1;2, TIP2;3 and PIP2;1 plays important roles in the flowering process for both monocots and eudicots.
Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications
Authors: Hu Yanting , Wu Xiaopei , Jin Guihua , Peng Junchu , Leng Rong , Li Ling , Gui Daping , Fan Chuanzhu , Zhang Chengjun
Published: January 2022

Retrotransposons are the most abundant group of transposable elements (TEs) in plants, providing an extraordinarily versatile source of genetic variation. Thlaspi arvense, a close relative of the model plant Arabidopsis thaliana with worldwide distribution, thrives from sea level to above 4,000 m elevation in the Qinghai-Tibet Plateau (QTP), China. Its strong adaptability renders it an ideal model system for studying plant adaptation in extreme environments. However, how the retrotransposons affect the T. arvense genome evolution and adaptation is largely unknown. We report a high-quality chromosome-scale genome assembly of T. arvense with a scaffold N50 of 59.10 Mb. Long terminal repeat retrotransposons (LTR-RTs) account for 56.94% of the genome assembly, and the Gypsy superfamily is the most abundant TEs. The amplification of LTR-RTs in the last six million years primarily contributed to the genome size expansion in T. arvense. We identified 351 retrogenes and 303 genes flanked by LTRs, respectively. A comparative analysis showed that orthogroups containing those retrogenes and genes flanked by LTRs have a higher percentage of significantly expanded orthogroups (SEOs), and these SEOs possess more recent tandem duplicated genes. All present results indicate that RNA-based gene duplication (retroduplication) accelerated the subsequent tandem duplication of homologous genes resulting in family expansions, and these expanded gene families were implicated in plant growth, development, and stress responses, which were one of the pivotal factors for T. arvense’s adaptation to the harsh environment in the QTP regions. In conclusion, the high-quality assembly of the T. arvense genome provides insights into the retroduplication mediated mechanism of plant adaptation to extreme environments.
Genome-Wide Prediction, Functional Divergence, and Characterization of Stress-Responsive BZR Transcription Factors in B. napus
Authors: Sarwar Rehman , Geng Rui , Li Lei , Shan Yue , Zhu Ke-Ming , Wang Jin , Tan Xiao-Li
Published: January 2022

BRASSINAZOLE RESISTANT (BZR) are transcriptional factors that bind to the DNA of targeted genes to regulate several plant growth and physiological processes in response to abiotic and biotic stresses. However, information on such genes in Brassica napus is minimal. Furthermore, the new reference Brassica napus genome offers an excellent opportunity to systematically characterize this gene family in B. napus. In our study, 21 BnaBZR genes were distributed across 19 chromosomes of B. napus and clustered into four subgroups based on Arabidopsis thaliana orthologs. Functional divergence analysis among these groups evident the shifting of evolutionary rate after the duplication events. In terms of structural analysis, the BnaBZR genes within each subgroup are highly conserved but are distinctive within groups. Organ-specific expression analyses of BnaBZR genes using RNA-seq data and quantitative real-time polymerase chain reaction (qRT-PCR) revealed complex expression patterns in plant tissues during stress conditions. In which genes belonging to subgroups III and IV were identified to play central roles in plant tolerance to salt, drought, and Sclerotinia sclerotiorum stress. The insights from this study enrich our understanding of the B. napus BZR gene family and lay a foundation for future research in improving rape seed environmental adaptability.
Investigating Constraints Along the Plant Secretory Pathway to Improve Production of a SARS-CoV-2 Spike Vaccine Candidate
Authors: Margolin Emmanuel , Verbeek Matthew , de Moor Warren , Chapman Ros , Meyers Ann , Schäfer Georgia , Williamson Anna-Lise , Rybicki Edward
Published: January 2022

Given the complex maturation requirements of viral glycoproteins and the challenge they often pose for expression in plants, the identification of host constraints precluding their efficient production is a priority for the molecular farming of vaccines. Building on previous work to improve viral glycoprotein production in plants, we investigated the production of a soluble SARS-CoV-2 spike comprising the ectopic portion of the glycoprotein. This was successfully transiently expressed in N. benthamiana by co-expressing the human lectin-binding chaperone calreticulin, which substantially increased the accumulation of the glycoprotein. The spike was mostly unprocessed unless the protease furin was co-expressed which resulted in highly efficient processing of the glycoprotein. Co-expression of several broad-spectrum protease inhibitors did not improve accumulation of the protein any further. The protein was successfully purified by affinity chromatography and gel filtration, although the purified product was heterogenous and the yields were low. Immunogenicity of the antigen was tested in BALB/c mice, and cellular and antibody responses were elicited after low dose inoculation with the adjuvanted protein. This work constitutes an important proof-of-concept for host plant engineering in the context of rapid vaccine development for SARS-CoV-2 and other emerging viruses.
Pepper Fruit Elongation Is Controlled by Capsicum annuum Ovate Family Protein 20
Authors: Borovsky Yelena , Raz Amit , Doron-Faigenboim Adi , Zemach Hanita , Karavani Eldad , Paran Ilan
Published: January 2022

Fruit shape is one of the most important quality traits of pepper (Capsicum spp.) and is used as a major attribute for the classification of fruit types. Wide natural variation in fruit shape exists among the major cultivated species Capsicum annuum, allowing the identification of several QTLs controlling the trait. However, to date, no genes underlying fruit shape QTLs have been conclusively identified, nor has their function been verified in pepper. We constructed a mapping population from a cross of round- and elongated-fruited C. annuum parents and identified a single major QTL on chromosome 10, termed fs10, explaining 68 and 70% of the phenotypic variation for fruit shape index and for distal fruit end angle, respectively. The QTL was mapped in several generations and was localized to a 5 Mbp region containing the ortholog of SlOFP20 that suppresses fruit elongation in tomato. Virus-induced gene silencing of the pepper ortholog CaOFP20 resulted in increased fruit elongation on two independent backgrounds. Furthermore, CaOFP20 exhibited differential expression in fs10 near-isogenic lines, as well as in an association panel of elongated- and round-fruited accessions. A 42-bp deletion in the upstream region of CaOFP20 was most strongly associated with fruit shape variation within the locus. Histological observations in ovaries and fruit pericarps indicated that fs10 exerts its effect on fruit elongation by controlling cell expansion and replication. Our results indicate that CaOFP20 functions as a suppressor of fruit elongation in C. annuum and is the most likely candidate gene underlying fs10.
Disruption Leads to Methodological and Analytic Innovation in Developmental Sciences: Recommendations for Remote Administration and Dealing With Messy Data
Authors: Krogh-Jespersen Sheila , MacNeill Leigha A. , Anderson Erica L. , Stroup Hannah E. , Harriott Emily M. , Gut Ewa , Blum Abigail , Fareedi Elveena , Fredian Kaitlyn M. , Wert Stephanie L. , Wakschlag Lauren S. , Norton Elizabeth S.
Published: January 2022

The COVID-19 pandemic has impacted data collection for longitudinal studies in developmental sciences to an immeasurable extent. Restrictions on conducting in-person standardized assessments have led to disruptive innovation, in which novel methods are applied to increase participant engagement. Here, we focus on remote administration of behavioral assessment. We argue that these innovations in remote assessment should become part of the new standard protocol in developmental sciences to facilitate data collection in populations that may be hard to reach or engage due to burdensome requirements (e.g., multiple in-person assessments). We present a series of adaptations to developmental assessments (e.g., Mullen) and a detailed discussion of data analytic approaches to be applied in the less-than-ideal circumstances encountered during the pandemic-related shutdown (i.e., missing or messy data). Ultimately, these remote approaches actually strengthen the ability to gain insight into developmental populations and foster pragmatic innovation that should result in enduring change.
Development and Validity Test of Social Attachment Multidimensional Scale
Authors: Yang Maosheng , Suanpong Kwanrat , Ruangkanjanases Athapol , Yu Wei , Xu Hongyu
Published: January 2022

Social attachment can explain well the bond between users and social media, but existing research lacks measures of social attachment scales. To this end, this study takes attachment theory as the basis for scale development. On the basis of the development of multidimensional scales for adult, brand, and local attachment, it combines existing relevant studies on social attachment, selects three representative social media such as TikTok, WeChat, and MicroBlog as theoretical samples, explores the concept and structure of social attachment, and develops a social attachment scale through qualitative interviews and open-ended questionnaires. This study applied SPSS 24.0 and Mplus 7.0 to test the social attachment scale. The findings reveal that social attachment consists of three constructs: social connection, social dependence and social identity, and the scale possesses high reliability and validity. This study has developed and validated a social attachment scale in the context of social software use, realizing a quantitative study of social attachment and providing a basis for future empirical research related to social attachment.
The Impact of Cognitive Biases on Professionals’ Decision-Making: A Review of Four Occupational Areas
Authors: Berthet Vincent
Published: January 2022

The author reviewed the research on the impact of cognitive biases on professionals’ decision-making in four occupational areas (management, finance, medicine, and law). Two main findings emerged. First, the literature reviewed shows that a dozen of cognitive biases has an impact on professionals’ decisions in these four areas, overconfidence being the most recurrent bias. Second, the level of evidence supporting the claim that cognitive biases impact professional decision-making differs across the areas covered. Research in finance relied primarily upon secondary data while research in medicine and law relied mainly upon primary data from vignette studies (both levels of evidence are found in management). Two research gaps are highlighted. The first one is a potential lack of ecological validity of the findings from vignette studies, which are numerous. The second is the neglect of individual differences in cognitive biases, which might lead to the false idea that all professionals are susceptible to biases, to the same extent. To address that issue, we suggest that reliable, specific measures of cognitive biases need to be improved or developed.
Heart Rate Variability Indices as Possible Biomarkers for the Severity of Post-traumatic Stress Disorder Following Pregnancy Loss
Authors: de Faria Cardoso Cláudia , Ohe Natalia Tiemi , Bader Yazan , Afify Nariman , Al-Homedi Zahrah , Alwedami Salma Malalla , O'Sullivan Siobhán , Campos Luciana Aparecida , Baltatu Ovidiu Constantin
Published: January 2022

Background: Psychological distress, such as posttraumatic stress disorder (PTSD), is commonly evaluated using subjective questionnaires, a method prone to self-report bias. The study's working hypothesis was that levels of autonomic dysfunction determined by heart rate variability (HRV) measures are associated with the severity of PTSD in women following pregnancy loss.

Methods: This was an observational prospective cohort study with 53 patients enrolled. The DSM-5 (Diagnostic and Statistical Manual of Mental Disorders) PTSD scale (PCL-5) was used to assess the severity of PTSD in women after pregnancy loss. The cardiac autonomic function was assessed using HRV measurements during a deep breathing test using an HRV scanner system with wireless ECG enabling real-time data analysis and visualization. HRV measures were: standard deviation (SD) of normal R-R wave intervals [SDNN, ms], square root of the mean of the sum of the squares of differences between adjacent normal R wave intervals [RMSSD, ms], and the number of all R-R intervals in which the change in consecutive normal sinus intervals exceeds 50 milliseconds divided by the total number of R-R intervals measured [pNN50 = (NN50/n-1)*100%] [pNN50%].

Results: The PCL-5 scores had a statistically significant association with HRV indices (SDNN; RMSSD, and pNN50%). Patients with PTSD had similar mean heart rate values as compared to patients without PTSD (PCL-5), but significantly higher SDNN [median[IQR, interquartile range]: 90.1 (69.1–112.1) vs. 52.5 (36.8–65.6)], RMSSD [59.4 (37.5–74.9) vs. 31.9 (19.3 – 44.0)], and PNN50% values [25.7 (16.4–37.7) vs. 10.6 (1.5–21.9)]. The SDNN of the deep breathing test HRV was effective at distinguishing between patients with PTSD and those without, with an AUC = 0.83 +/− 0.06 (95 % CI 0.94, p = 0.0001) of the ROC model.

Conclusions: In this study, HRV indices as biomarkers of cardiac dysautonomia were found to be significantly related to the severity of PTSD symptoms in women after pregnancy loss.
Healthcare Workers' Resilience Mediates the Influence of Organizational Commitment and Anxiety Response to Viral Epidemic on Their Quality of Life in the COVID-19 Pandemic
Authors: Son Hoon Sung , Kim Kyumin , Cho Inn-Kyu , Lee Joohee , Choi Jung Mun , Kil Kwang Hyun , Kim Jiyeon , Hong Youjin , Ahn Myung Hee , Chung Seockhoon
Published: January 2022

Objective: In the COVID-19 pandemic era, healthcare workers suffer from psychological problems such as anxiety in response to the viral epidemic and it may decrease their quality of life (QoL). The aim of this study was to explore the influence of healthcare workers' stress and anxiety response to the viral epidemic and their organizational commitment on their QoL. We also explored the mediating effect of resilience on any association.

Methods: From January 28, 2021, to January 29, 2021, 389 workers responded to an online survey that included the rating scales Stress and Anxiety to Viral Epidemics-9 items (SAVE-9), Perceived Stress Scale (PSS), Brief Resilience Scale (BRS), Organizational Commitment Questionnaire (OCQ), and the WHO-5 well-being index.

Results: A better QoL (WHO well-being index top 25%) of healthcare workers during the COVID-19 pandemic era was predicted by low stress and anxiety in response to the viral epidemic [SAVE-9, adjusted odds ratio (aOR) = 0.92, 95% confidence interval (CI) 0.87–0.97], a high level of resilience (BRS, aOR = 1.26, 95%CI 1.15–1.37), and high organizational commitment (OCQ, aOR = 1.04, 95%CI 1.02–1.07). Mediation analysis showed that resilience partially mediated the effects of stress/anxiety in response to the viral epidemic and the organizational commitment on the quality of life.

Conclusion: We observed that the stress and anxiety of healthcare workers in response to the viral epidemic and organizational commitment influenced their QOL. Their resilience mediated the relationship between their psychological problems and QOL.
COVID-19 Pandemic and Maternal Psychological Wellbeing During the Malaysian Movement Control Order: A Cross-Sectional Study
Authors: Kalok Aida , Syed Anwar Aly Syarifah Aminah , Abdul Rahman Rahana , Mahdy Zaleha Abdullah , Sharip Shalisah
Published: January 2022

Background: COVID-19 pandemic had resulted in nationwide lockdown as a disease control measure. Potential harm to self and baby due to COVID-19 infection as well as uncertainties about delivery are among contributors to maternal anxiety. We aimed to assess the prevalence of psychological distress among pregnant women during the Malaysian Movement Control Order (MCO).

Methods: A cross-sectional study was conducted between May and June 2020 in a teaching hospital in Kuala Lumpur, Malaysia. A self-administered electronic questionnaire was distributed which included the following; (1) Depression, Anxiety and Stress Scale-21 (DASS 21), (2) Short Warwick Edinburgh Mental Wellbeing Scale (SWEMWBS), (3) MCO effect questionnaire, and (4) newly designed COVID-19 pregnancy-related anxiety. Chi-square test and logistic regression were performed to determine significant associations whilst mean scores comparison were conducted through Mann-Whitney-U-test.

Results: Four hundred and fifteen women were included in the final analysis. The prevalence of psychological distress among our cohort was 14.7%; with a two-fold increase of risk among the non-Malays (AOR 1.98, 95% CI 1.00–3.89) whilst a greater number of social support showed a protective effect (AOR 0.51, 95%CI 0.28–0.92). Malay ethnicity (p < 0.001) alongside greater household income (p = 0.014) were positive predictors of a higher sense of maternal wellbeing. Multiparous women and those of higher economic status experienced the more negative effect of the MCO. Around 88% of our women reported a higher level of COVID-19 pregnancy-related anxiety. Younger (p = 0.017) and first-time mothers (p = 0.039) were more likely to be anxious. Although adequate maternal knowledge on COVID-19 was associated with a greater sense of maternal wellbeing (p = 0.028), it was also linked to a higher level of COVID-19 related anxiety (AOR 3.54, 95% 1.29–9.70).

Conclusion: There was a relatively low prevalence of psychological distress among expectant mothers in Malaysia during the first wave of the COVID-19 pandemic. Expectant mothers should receive accurate and reliable information on the effect of COVID-19 on pregnancy to relieve some maternal anxiety. Maternal health screening is important to identify individuals who would benefit from extra support and mental health intervention, especially in prolonged lockdown.