bluuebunny/crossref_metadata_2025 huggingface dataset:
Coordinated Cut and Bypass: Replication of Interstrand Crosslink-Containing DNA
Authors: Li Qiuzhen , Dudás Kata , Tick Gabriella , Haracska Lajos
Published: June 2021

DNA interstrand crosslinks (ICLs) are covalently bound DNA lesions, which are commonly induced by chemotherapeutic drugs, such as cisplatin and mitomycin C or endogenous byproducts of metabolic processes. This type of DNA lesion can block ongoing RNA transcription and DNA replication and thus cause genome instability and cancer. Several cellular defense mechanism, such as the Fanconi anemia pathway have developed to ensure accurate repair and DNA replication when ICLs are present. Various structure-specific nucleases and translesion synthesis (TLS) polymerases have come into focus in relation to ICL bypass. Current models propose that a structure-specific nuclease incision is needed to unhook the ICL from the replication fork, followed by the activity of a low-fidelity TLS polymerase enabling replication through the unhooked ICL adduct. This review focuses on how, in parallel with the Fanconi anemia pathway, PCNA interactions and ICL-induced PCNA ubiquitylation regulate the recruitment, substrate specificity, activity, and coordinated action of certain nucleases and TLS polymerases in the execution of stalled replication fork rescue via ICL bypass.
Key Role for CRB2 in the Maintenance of Apicobasal Polarity in Retinal Pigment Epithelial Cells
Authors: Paniagua Antonio E. , Segurado Alicia , Dolón Jorge F. , Esteve-Rudd Julián , Velasco Almudena , Williams David S. , Lillo Concepción
Published: June 2021

Apicobasal polarity is essential for epithelial cell function, yet the roles of different proteins in its completion is not fully understood. Here, we have studied the role of the polarity protein, CRB2, in human retinal pigment epithelial (RPE) cells during polarizationin vitro, and in mature murine RPE cellsin vivo. After establishing a simplified protocol for the culture of human fetal RPE cells, we studied the temporal sequence of the expression and localization of polarity and cell junction proteins during polarization in these epithelial cells. We found that CRB2 plays a key role in tight junction maintenance as well as in cell cycle arrest. In addition, our studiesin vivoshow that the knockdown of CRB2 in the RPE affects to the distribution of different apical polarity proteins and results in perturbed retinal homeostasis, manifested by the invasion of activated microglial cells into the subretinal space. Together our results demonstrate that CRB2 is a key protein for the development and maintenance of a polarized epithelium.
Block Copolymer Synthesis by the Combination of Living Cationic Polymerization and Other Polymerization Methods
Authors: Dey Asmita , Haldar Ujjal , De Priyadarsi
Published: June 2021

The foremost limitation of block copolymer synthesis is to polymerize two or more different types of monomers with different reactivity profiles using a single polymerization technique. Controlled living polymerization techniques play a vital role in the preparation of wide range of block copolymers, thus are revolutionary techniques for polymer industry. Polymers with good control over molecular weight, molecular weight distribution, chain-end functionality and architectures can be prepared by these processes. In order to improve the existing applications and create new opportunities to design a new block copolymer system with improved physical and chemical properties, the combination of two different polymerization techniques have tremendous scope. Such kinds of macromolecules may be attended by combination of homopolymerization of different monomers by post-modification techniques using a macroinitiator or by using a dual initiator which allows the combination of two mechanistically distinct techniques. This review focuses on recent advances in synthesis of block copolymers by combination of living cationic polymerization with other polymerization techniques and click chemistry.
Binding Between Cyclohexanohemicucurbit[n]urils and Polar Organic Guests
Authors: Ustrnul Lukas , Burankova Tatsiana , Öeren Mario , Juhhimenko Kristina , Ilmarinen Jenni , Siilak Kristjan , Mishra Kamini A. , Aav Riina
Published: June 2021

Inherently chiral, barrel-shaped, macrocyclic hosts such as cyclohexanohemicucurbit[n]urils (cycHC[n]) bind zinc porphyrins and trifluoroacetic acid externally in halogenated solvents. In the current study, we tested a set of eighteen organic guests with various functional groups and polarity, namely, thiophenols, phenols, and carboxylic and sulfonic acids, to identify a preference toward hydrogen bond–donating molecules for homologous cycHC[6] and cycHC[8]. Guests were characterized by Hirshfeld partial charges on acidic hydrogens and their binding by 1H and 19F NMR titrations. Evaluation of association constants revealed the complexity of the system and indirectly proved an external binding with stoichiometry over 2:1 for both homologs. It was found that overall binding strength is influenced by the stoichiometry of the formed complexes, the partial atomic charge on the hydrogen atom of the hydrogen bond donor, and the bulkiness of the guest. Additionally, a study on the formation of complexes with halogen anions (Cl− and Br−) in methanol and chloroform, analyzed by 1H NMR, did not confirm complexation. The current study widens the scope of potential applications for host molecules by demonstrating the formation of hydrogen-bonded complexes with multisite hydrogen bond acceptors such as cycHC[6] and cycHC[8].
The Transcription Factor PfAP2-O Influences Virulence Gene Transcription and Sexual Development in Plasmodium falciparum
Authors: Cubillos Eliana F. G. , Prata Isadora Oliveira , Fotoran Wesley Luzetti , Ranford-Cartwright Lisa , Wunderlich Gerhard
Published: June 2021

The human malaria parasite Plasmodium falciparum expresses variant PfEMP1 proteins on the infected erythrocyte, which function as ligands for endothelial receptors in capillary vessels, leading to erythrocyte sequestration and severe malaria. The factors that orchestrate the mono-allelic expression of the 45–90 PfEMP1-encoding var genes within each parasite genome are still not fully identified. Here, we show that the transcription factor PfAP2-O influences the transcription of var genes. The temporary knockdown of PfAP2-O leads to a complete loss of var transcriptional memory and a decrease in cytoadherence in CD36 adherent parasites. AP2-O-knocked-down parasites exhibited also significant reductions in transmission through Anopheles mosquitoes. We propose that PfAP2-O is, beside its role in transmission stages, also one of the virulence gene transcriptional regulators and may therefore be exploited as an important target to disrupt severe malaria and block parasite transmission.
Serum Sphingolipids Aiding the Diagnosis of Adult HIV-Negative Patients with Talaromyces marneffei Infection
Authors: Li Zheng-Tu , Yau Lee-Fong , Qiu Ye , Li Shao-Qiang , Zhan Yang-Qing , Chan Wai-Him , Chen Zhao-Ming , Li Zhun , Li Yongming , Lin Ye , Cheng Jing , Zhang Jian-Quan , Jiang Zhi-Hong , Wang Jing-Rong , Ye Feng
Published: June 2021

Increasing attention has been directed toTalaromyces marneffei(T. marneffei) infection in HIV-negative patients due to its high mortality rate. However, nonspecific symptoms and biological characteristics similar to those of other common pathogenic fungi complicate the rapid and accurate diagnosis ofT. marneffeiinfection. Sphingolipids (SPLs) are bioactive lipids involved in the regulation of various physiological and pathological processes and have been identified as serum biomarkers for several diseases. This study employed a sphingolipidomic approach established in our previous work to explore the use of serum SPLs in the diagnosis of HIV-negative patients withT. marneffeiinfection. Additional clinical cohorts of patients infected with other microorganisms were also recruited. We found that sphinganine (Sa) (d16:0) exhibited obvious depletion after infection; moreover, its level in patients withT. marneffeiinfection was significantly lower than that in patients infected with other microorganisms. Therefore, Sa (d16:0) was considered a specific diagnostic biomarker forT. marneffeiinfection, and 302.71 nM was selected as the optimal cutoff value with a diagnostic sensitivity of 87.5% and specificity of 100%. These results suggested that determination of serum Sa (d16:0) levels can be used as a new alternative tool for the rapid diagnosis ofT. marneffeiinfection in HIV-negative patients.
Tiger Becomes Termite Hill: Soliga/Solega Perceptions of Wildlife Interactions and Ecological Change
Authors: Agnihotri Samira , Madegowda C. , Si Aung
Published: June 2021

The Solega community living in the Biligiri Rangan Hills (B. R. Hills) of Karnataka State, southern India, have noticed significant changes to the ecosystem of their forest homeland over the last four or five decades. Originally hunter-gatherers, who carried out swidden agriculture at a subsistence level, they were forced to abandon the semi-nomadic ways of their ancestors, and settle in permanent villages when these forests were first declared a wildlife sanctuary in 1974. In this paper, we present the views of Solega elders on the ecological changes that have taken place in the B. R. Hills, along with the subsequent changes in their interactions with the animals that also inhabit this landscape. The Solega way of life is accustomed to co-existing with wildlife, and they worship several animal deities. Their folklore and traditional ecological knowledge are also replete with ways of avoiding dangerous encounters with wildlife. Many of the detrimental ecological changes observed by Solega people are ascribed by them to the halting of their traditional litter fire regime, and the subsequent rampant growth of the exotic invasive plant Lantana camara, which now dominates the understorey in large swathes of the forest. These factors combine, according to Solega elders, to negatively impact the well-being of both animals as well as their own people. We hope to demonstrate how a deeper understanding of Solega language and culture, both essential facets of everyday life, as well as of their traditional ecological knowledge—can allow a full appreciation of the interactions between small Indigenous communities, such as the Solega, and the natural environment. We argue for a greater appreciation of, and engagement with, Indigenous knowledge in conservation efforts in countries such as India, where the protection of charismatic species, such as tigers, is often perceived to be at odds with the rights of small minority groups, such as the Solega.
Acute Myocardial Infarction Detection Using Deep Learning-Enabled Electrocardiograms
Authors: Chen Xiehui , Guo Wenqin , Zhao Lingyue , Huang Weichao , Wang Lili , Sun Aimei , Li Lang , Mo Fanrui
Published: June 2021

Background: Acute myocardial infarction (AMI) is associated with a poor prognosis. Therefore, accurate diagnosis and early intervention of the culprit lesion are of extreme importance. Therefore, we developed a neural network algorithm in this study to automatically diagnose AMI from 12-lead electrocardiograms (ECGs).

Methods: We used the open-source PTB-XL database as the training and validation sets, with a 7:3 sample size ratio. Twenty-One thousand, eight hundred thirty-seven clinical 12-lead ECGs from the PTB-XL dataset were available for training and validation (15,285 were used in the training set and 6,552 in the validation set). Additionally, we randomly selected 205 ECGs from a dataset built by Chapman University, CA, USA and Shaoxing People's Hospital, China, as the testing set. We used a residual network for training and validation. The model performance was experimentally verified in terms of area under the curve (AUC), precision, sensitivity, specificity, and F1 score.

Results: The AUC of the training, validation, and testing sets were 0.964 [95% confidence interval (CI): 0.961–0.966], 0.944 (95% CI: 0.939–0.949), and 0.977 (95% CI: 0.961–0.991), respectively. The precision, sensitivity, specificity, and F1 score of the deep learning model for AMI diagnosis from ECGs were 0.827, 0.824, 0.950, and 0.825, respectively, in the training set, 0.789, 0.818, 0.913, and 0.803, respectively, in the validation set, and 0.830, 0.951, 0.951, and 0.886, respectively, in the testing set. The AUC for automatic AMI location diagnosis of LMI, IMI, ASMI, AMI, ALMI were 0.969 (95% CI: 0.959–0.979), 0.973 (95% CI: 0.962–0.978), 0.987 (95% CI: 0.963–0.989), 0.961 (95% CI: 0.956–0.989), and 0.996 (95% CI: 0.957–0.997), respectively.

Conclusions: The residual network-based algorithm can effectively automatically diagnose AMI and MI location from 12-lead ECGs.
Development and Validation of a Random Forest Diagnostic Model of Acute Myocardial Infarction Based on Ferroptosis-Related Genes in Circulating Endothelial Cells
Authors: Yifan Chen , Jianfeng Shi , Jun Pu
Published: June 2021

The high incidence and mortality of acute myocardial infarction (MI) drastically threaten human life and health. In the past few decades, the rise of reperfusion therapy has significantly reduced the mortality rate, but the MI diagnosis is still by means of the identification of myocardial injury markers without highly specific biomarkers of microcirculation disorders. Ferroptosis is a novel reported type of programmed cell death, which plays an important role in cancer development. Maintaining iron homeostasis in cells is essential for heart function, and its role in the pathological process of ischemic organ damages remains unclear. Being quickly detected through blood tests, circulating endothelial cells (CECs) have the potential for early judgment of early microcirculation disorders. In order to explore the role of ferroptosis-related genes in the early diagnosis of acute MI, we relied on two data sets from the GEO database to first detect eight ferroptosis-related genes differentially expressed in CECs between the MI and healthy groups in this study. After comparing different supervised learning algorithms, we constructed a random forest diagnosis model for acute MI based on these ferroptosis-related genes with a compelling diagnostic performance in both the validation (AUC = 0.8550) and test set (AUC = 0.7308), respectively. These results suggest that the ferroptosis-related genes might play an important role in the early stage of MI and have the potential as specific diagnostic biomarkers for MI.
The Cardiac Mineralocorticoid Receptor (MR): A Therapeutic Target Against Ventricular Arrhythmias
Authors: Rossier Michel F.
Published: June 2021

Mineralocorticoid antagonists have been shown to be useful in the treatment of severe heart failure and may even save lives in this context. However, the reason for the beneficial action of these drugs, as well as the physiological role played by the cardiac mineralocorticoid receptor (MR), are still poorly understood. While the proinflammatory action of aldosterone on the heart and the resulting fibrosis partly explain the improvement due to the anti-mineralocorticoid therapy, the reduction in sudden death is probably related to a lower occurrence of ventricular arrhythmias. In this review, the author explains the physiological mechanism linking the positive chronotropic response induced by aldosterone observed in vitro with isolated ventricular cardiomyocytes and the increased risk of ventricular arrhythmias reported in vivo in hyperaldosteronism. He describes the molecular steps involved between MR activation and acceleration of spontaneous myocyte contractions, including expression of a specific micro RNA (miR204), down-regulation of a silencing transcription factor (NRSF), and re-expression of a fetal gene encoding a low threshold voltage-gated calcium channel (CaV3.2). Finally, he provides evidence suggesting aldosterone-independent and redox-sensitive mechanisms of MR activation in cardiac myocytes. Taken together, this information suggests that the use of anti-mineralocorticoid therapy could benefit the heart by preventing ventricular arrhythmias, not only in established hyperaldosteronism, but also in various pathological situations such as Cushing’s disease, oxidative stress, or even diabetes mellitus.
Transgenerational Effects of Parental Diet on Offspring Development and Disease Resistance in Flies
Authors: Dinh Hue , Nguyen Binh , Morimoto Juliano , Lundback Ida , Kumar Sheemal S. , Ponton Fleur
Published: June 2021

The environmental conditions experienced by parents influence next generations, with the parental nutritional status playing an important role in shaping offspring phenotypes. Our understanding of transgenerational effects of parental diet on offspring pathogen resistance is, however, poorly documented. We manipulated the quality of parental diet (i.e., mother, father, or both) and measured effects on offspring development and survival after an immune challenge by septic infection. We used Bactrocera tryoni as host model infected with the pathogenic bacterium, Serratia marcescens. Our results showed no significant effect of maternal, or paternal, diet on offspring resistance. Interestingly, when the diet of both parents was manipulated, sons from parents fed either carbohydrate- or protein-biased diets had higher survival upon pathogen infection than sons from parents fed balanced diets. The quality of the parental diet had no effect on offspring developmental traits with the exception of egg hatching percentage which decreased when mothers were fed a protein-biased diet. Our results emphasised the complexity of nutritional transgenerational effects on offspring pathogen resistance and development.
TeaTime4Schools: Using Data Mining Techniques to Model Litter Decomposition in Austrian Urban School Soils
Authors: Sandén Taru , Wawra Anna , Berthold Helene , Miloczki Julia , Schweinzer Agnes , Gschmeidler Brigitte , Spiegel Heide , Debeljak Marko , Trajanov Aneta
Published: June 2021

Litter decomposition plays a pivotal role in the global carbon cycle, but is difficult to measure on a global scale, especially by citizen scientists. Here, citizen scientists, i.e., school students with their teachers, used the globally applied and standardized Tea Bag Index (TBI) method to collect data on litter decomposition in urban areas in Austria. They also sampled soils to investigate the linkages between litter decomposition and soil attributes. For this study, 54 sites were selected from the school experiments and assembled into a TBI dataset comprising litter decomposition rates (k), stabilization factors (S), as well as soil and environmental attributes. An extensive pre-processing procedure was applied to the dataset, including attribute selection and discretization of the decomposition rates and stabilization factors into three categories each. Data mining analyses of the TBI data helped reveal trends in litter decomposition. We generated predictive models (classification trees) that identified the soil attributes governing litter decomposition. Classification trees were developed for both of the litter decomposition parameters: decomposition rate (k) and stabilization factor (S). The main governing factor for both decomposition rate (k) and stabilization factor (S) was the sand content of the soils. The data mining models achieved an accuracy of 54.0 and 66.7% for decomposition rates and stabilization factors, respectively. The data mining results enhance our knowledge about the driving forces of litter decomposition in urban soils, which are underrepresented in soil monitoring schemes. The models are very informative for understanding and describing litter decomposition in urban settings in general. This approach may also further encourage participatory researcher-teacher-student interactions and thus help create an enabling environment for cooperation for further citizen science research in urban school settings.
Functional miR-142a-3p Induces Apoptosis and Macrophage Polarization by Targeting tnfaip2 and glut3 in Grass Carp (Ctenopharyngodon idella)
Authors: Tao Lizhu , Pang Yifan , Wang Anqi , Li Lisen , Shen Yubang , Xu Xiaoyan , Li Jiale
Published: June 2021

In the process of microbial invasion, the inflammation reaction is induced to eliminate the pathogen. However, un-controlled or un-resolved inflammation can lead to tissue damage and death of the host. MicroRNAs (miRNAs) are the signaling regulators that prevent the uncontrolled progress of an inflammatory response. Our previous work strongly indicated that miR-142a-3p is related to the immune regulation in grass carp. In the present study, we found that the expression of miR-142a-3p was down-regulated after infection by Aeromonas hydrophila. tnfaip2 and glut3 were confirmed as be the target genes of miR-142a-3p, which were confirmed by expression correlation analysis, gene overexpression, and dual luciferase reporter assay. The miR-142a-3p can reduce cell viability and stimulate cell apoptosis by targeting tnfaip2 and glut3. In addition, miR-142a-3p also regulates macrophage polarization induced by A. hydrophila. Our results suggest that miR-142a-3p has multiple functions in host antibacterial immune response. Our research provides further understanding of the molecular mechanisms between miRNAs and their target genes, and provides a new insights for the development of pro-resolution strategies for the treatment of complex inflammatory diseases in fish.
P18 (SRS35/TgSAG4) Plays a Role in the Invasion and Virulence of Toxoplasma gondii
Authors: Hamie Maguy , Tawil Nadim , El Hajj Rana , Najm Rania , Moodad Sara , Hleihel Rita , Karam Martin , El Sayyed Sana , Besteiro Sébastien , El-Sabban Marwan , Dubremetz Jean-Francois , Lebrun Maryse , El Hajj Hiba
Published: June 2021

Toxoplasmosis is a prevalent parasitic disease caused byToxoplasma gondii(T. gondii). Under the control of the host immune system,T. gondiipersists as latent bradyzoite cysts. Immunosuppression leads to their reactivation, a potentially life-threatening condition. Interferon-gamma (IFN-γ) controls the different stages of toxoplasmosis. Here, we addressed the role of the parasite surface antigen P18, belonging to the Surface-Antigen 1 (SAG-1) Related Sequence (SRS) family, in a cyst-forming strain. Deletion ofP18gene (KOP18) impaired the invasion of parasites in macrophages and IFN-γ-mediated activation of macrophages further reduced the invasion capacity of this KO, as compared to WT strain. Mice infected by KOP18, showed a marked decrease in virulence during acute toxoplasmosis. This was consequent to less parasitemia, accompanied by a substantial recruitment of dendritic cells, macrophages and natural killer cells (NK). Furthermore, KOP18resulted in a higher number of bradyzoite cysts, and a stronger inflammatory response. A prolonged survival of mice was observed upon immunosuppression of KOP18infected BALB/c mice or upon oral infection of Severe Combined Immunodeficiency (SCID) mice, with intact macrophages and natural killer (NK) cells. In stark contrast, oral infection of NSG (NOD/Shi-scid/IL-2Rγnull) mice, defective in macrophages and NK cells, withKO P18, was as lethal as that of the control strain showing that the conversion from bradyzoites to tachyzoites is intact and, suggesting a role of P18 in the response to host IFN-γ. Collectively, these data demonstrate a role for P18 surface antigen in the invasion of macrophages and in the virulence of the parasite, during acute and chronic toxoplasmosis.
Association Between Prospective Registration and Quality of Systematic Reviews in Type 2 Diabetes Mellitus: A Meta-epidemiological Study
Authors: Zheng Qiuyi , Lai Fenghua , Li Bin , Xu Jia , Long Jianyan , Peng Sui , Li Yanbing , Liu Yihao , Xiao Haipeng
Published: June 2021

Background: We sought to investigate the methodological and reporting quality of published systematic reviews describing randomized controlled trials in type 2 diabetes mellitus and analyze their association with status of protocol registration.

Methods: We searched the PubMed database and identified non-Cochrane systematic reviews, with or without meta-analysis, reporting on type 2 diabetes mellitus and published between 2005 and 2018. We then randomly selected 20% of these reviews in each year, and performed methodological and reporting quality assessment using the Assessment of Multiple Systematic Review 2 (AMSTAR-2) checklist and Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement. We also conducted regression analyses to explore the association between characteristics of systematic reviews and AMSTAR-2 or PRISMA scores.

Results: A total of 238 systematic reviews, including 33 registered and 205 non-registered articles, met the inclusion criteria and were subsequently reviewed. Analysis indicated an increase in both registered rates and quality of systematic reviews in type 2 diabetes mellitus over the recent years. With regards to methodological and reporting quality, we found higher scores in registered, relative to non-registered reviews (AMSTAR-2 mean score: 18.0 vs. 14.5, P = 0.000; PRISMA mean score: 20.4 vs. 17.6, P = 0.000). AMSTAR-2 and PRISMA scores were associated with registration status, country of the first author, and statistical results, whereas the proportion of discussing publication bias and reporting funding sources were <40% for both registered and non-registered systematic reviews.

Conclusions: Methodological and reporting quality of systematic reviews in type 2 diabetes mellitus indicates an improvement in the recent years. However, the overall quality remains low, necessitating further improvement. Future studies are expected to pay more attention to prospective registration, description of publication bias and reporting of funding sources.
Case Report: A Rehabilitation Practice Report During ICU Management for a Patient With Multiple Disabilities Due to COVID-19 Pneumonia and COPD
Authors: Kinoshita Tokio , Kouda Ken , Umemoto Yasunori , Yasuoka Yoshinori , Minoshima Yuta , Mikami Yukio , Nishimura Yukihide , Miyamoto Kyohei , Kato Seiya , Tajima Fumihiro
Published: June 2021

Patients with severe coronavirus disease (COVID-19) and admitted to the intensive care unit (ICU) are at high risk of developing ICU-acquired weakness and disuse syndrome. Although their medical management may include prolonged deep sedation for pulmonary protection and ventilator management, we aim for early mobilization of these patients with COVID-19. We present the case of a 71-year-old man with chronic obstructive pulmonary disease (COPD) and COVID-19 pneumonia. Passive range of motion training and sitting on the edge of the bed were started in the ICU while the patient was under deep sedation. His activities of daily living eventually improved to where he could independently walk to the toilet without respiratory distress. Patients with severe COVID-19 who require mechanical ventilation are at risk of muscle weakness and exercise intolerance. These patients require rehabilitation therapy, beginning in the acute phase of illness, to recover their physical function. Although validation with a larger cohort is necessary, our results suggest that patients with COPD and COVID-19 pneumonia should undergo rehabilitation concurrently with status-driven changes in respiratory management.
Peroxisomes Implicated in the Biosynthesis of Siderophores and Biotin, Cell Wall Integrity, Autophagy, and Response to Hydrogen Peroxide in the Citrus Pathogenic Fungus Alternaria alternata
Authors: Wu Pei-Ching , Chen Yu-Kun , Yago Jonar I. , Chung Kuang-Ren
Published: June 2021

Little is known about the roles of peroxisomes in the necrotrophic fungal plant pathogens. In the present study, a Pex6 gene encoding an ATPase-associated protein was characterized by analysis of functional mutations in the tangerine pathotype of Alternaria alternata, which produces a host-selective toxin. Peroxisomes were observed in fungal cells by expressing a mCherry fluorescent protein tagging with conserved tripeptides serine-lysing-leucine and transmission electron microscopy. The results indicated that Pex6 plays no roles in peroxisomal biogenesis but impacts protein import into peroxisomes. The number of peroxisomes was affected by nutritional conditions and H2O2, and their degradation was mediated by an autophagy-related machinery termed pexophagy. Pex6 was shown to be required for the formation of Woronin bodies, the biosynthesis of biotin, siderophores, and toxin, the uptake and accumulation of H2O2, growth, and virulence, as well as the Slt2 MAP kinase-mediated maintenance of cell wall integrity. Adding biotin, oleate, and iron in combination fully restored the growth of the pex6-deficient mutant (Δpex6), but failed to restore Δpex6 virulence to citrus. Adding purified toxin could only partially restore Δpex6 virulence even in the presence of biotin, oleate, and iron. Sensitivity assays revealed that Pex6 plays no roles in resistance to H2O2 and superoxide, but plays a negative role in resistance to 2-chloro-5-hydroxypyridine (a hydroxyl radical-generating compound), eosin Y and rose Bengal (singlet oxygen-generating compounds), and 2,3,5-triiodobenzoic acid (an auxin transport inhibitor). The diverse functions of Pex6 underscore the importance of peroxisomes in physiology, pathogenesis, and development in A. alternata.
IDOPS, a Profile HMM-Based Tool to Detect Pesticidal Sequences and Compare Their Genetic Context
Authors: Díaz-Valerio Stefani , Lev Hacohen Anat , Schöppe Raphael , Liesegang Heiko
Published: June 2021

Biopesticide-based crop protection is constantly challenged by insect resistance. Thus, expansion of available biopesticides is crucial for sustainable agriculture. Although Bacillus thuringiensis is the major agent for pesticide bioprotection, the number of bacteria species synthesizing proteins with biopesticidal potential is much higher. The Bacterial Pesticidal Protein Resource Center (BPPRC) offers a database of sequences for the control of insect pests, grouped in structural classes. Here we present IDOPS, a tool that detects novel biopesticidal sequences and analyzes them within their genetic environment. The backbone of the IDOPS detection unit is a curated collection of high-quality hidden Markov models that is in accordance with the BPPRC nomenclature. IDOPS was positively benchmarked with BtToxin_Digger and Cry_Processor. In addition, a scan of the UniProtKB database using the IDOPS models returned an abundance of new pesticidal protein candidates distributed across all of the structural groups. Gene expression depends on the genomic environment, therefore, IDOPS provides a comparative genomics module to investigate the genetic regions surrounding pesticidal genes. This feature enables the investigation of accessory elements and evolutionary traits relevant for optimal toxin expression and functional diversification. IDOPS contributes and expands our current arsenal of pesticidal proteins used for crop protection.
Gremlin2 Activates Fibroblasts to Promote Pulmonary Fibrosis Through the Bone Morphogenic Protein Pathway
Authors: Huan Caijuan , Xu Wangting , Liu Yaru , Ruan Kexin , Shi Yueli , Cheng Hongqiang , Zhang Xue , Ke Yuehai , Zhou Jianying
Published: June 2021

Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease causing unremitting extracellular matrix deposition. Transforming growth factor-β (TGF-β) superfamily involves bone morphogenetic proteins (BMPs) and TGF-β, and the balance between the activation of TGF-β-dependent SMADs (Smad2/3) and BMP-dependent SMADs (Smad1/5/8) is essential for fibrosis process. GREM2, initially identified as a TGF-β-inducible gene, encodes a small secreted glycoprotein belonging to a group of matricellular proteins, its role in lung fibrosis is not clear. Here, we identified Gremlin2 as a key regulator of fibroblast activation. Gremlin2 was highly expressed in the serum and lung tissues in IPF patients. Bleomycin-induced lung fibrosis model exhibited high expression of Gremlin2 in the bronchoalveolar lavage fluid (BALF) and lung tissue. Isolation of primary cells from bleomycin-induced fibrosis lung showed a good correlation of Gremlin2 and Acta2 (α-SMA) expressions. Overexpression of Gremlin2 in human fetal lung fibroblast 1 (HFL-1) cells increased its invasion and migration. Furthermore, Gremlin2 regulates fibrosis functions through mediating TGF-β/BMP signaling, in which Gremlin2 may activate TGF-β signaling and inhibit BMP signaling. Therefore, we provided in vivo and in vitro evidence to demonstrate that Gremlin2 may be a potential therapeutic target for the treatment of IPF.
The Cannabinoid Receptor 1 Reverse Agonist AM251 Ameliorates Radiation-Induced Cognitive Decrements
Authors: Parihar Vipan K. , Syage Amber , Flores Lidia , Lilagan Angelica , Allen Barrett D. , Angulo Maria C. , Song Joseph , Smith Sarah M. , Arechavala Rebecca J. , Giedzinski Erich , Limoli Charles L.
Published: June 2021

Despite advancements in the radiotherapeutic management of brain malignancies, resultant sequelae include persistent cognitive dysfunction in the majority of survivors. Defining the precise causes of normal tissue toxicity has proven challenging, but the use of preclinical rodent models has suggested that reductions in neurogenesis and microvascular integrity, impaired synaptic plasticity, increased inflammation, and alterations in neuronal structure are contributory if not causal. As such, strategies to reverse these persistent radiotherapy-induced neurological disorders represent an unmet medical need. AM251, a cannabinoid receptor 1 reverse agonist known to facilitate adult neurogenesis and synaptic plasticity, may help to ameliorate radiation-induced CNS impairments. To test this hypothesis, three treatment paradigms were used to evaluate the efficacy of AM251 to ameliorate radiation-induced learning and memory deficits along with disruptions in mood at 4 and 12 weeks postirradiation. Results demonstrated that acute (four weekly injections) and chronic (16 weekly injections) AM251 treatments (1 mg/kg) effectively alleviated cognitive and mood dysfunction in cranially irradiated mice. The beneficial effects of AM251 were exemplified by improved hippocampal- and cortical-dependent memory function on the novel object recognition and object in place tasks, while similar benefits on mood were shown by reductions in depressive- and anxiety-like behaviors on the forced swim test and elevated plus maze. The foregoing neurocognitive benefits were associated with significant increases in newly born (doublecortin+) neurons (1.7-fold), hippocampal neurogenesis (BrdU+/NeuN+mature neurons, 2.5-fold), and reduced expression of the inflammatory mediator HMGB (1.2-fold) in the hippocampus of irradiated mice. Collectively, these findings indicate that AM251 ameliorates the effects of clinically relevant cranial irradiation where overall neurological benefits in memory and mood coincided with increased hippocampal cell proliferation, neurogenesis, and reduced expression of proinflammatory markers.
An Autism-Associated Neuroligin-3 Mutation Affects Developmental Synapse Elimination in the Cerebellum
Authors: Lai Esther Suk King , Nakayama Hisako , Miyazaki Taisuke , Nakazawa Takanobu , Tabuchi Katsuhiko , Hashimoto Kouichi , Watanabe Masahiko , Kano Masanobu
Published: June 2021

Neuroligin is a postsynaptic cell-adhesion molecule that is involved in synapse formation and maturation by interacting with presynaptic neurexin. Mutations in neuroligin genes, including the arginine to cystein substitution at the 451st amino acid residue (R451C) of neuroligin-3 (NLGN3), have been identified in patients with autism spectrum disorder (ASD). Functional magnetic resonance imaging and examination of post-mortem brain in ASD patients implicate alteration of cerebellar morphology and Purkinje cell (PC) loss. In the present study, we examined possible association between the R451C mutation in NLGN3 and synaptic development and function in the mouse cerebellum. In NLGN3-R451C mutant mice, the expression of NLGN3 protein in the cerebellum was reduced to about 10% of the level of wild-type mice. Elimination of redundant climbing fiber (CF) to PC synapses was impaired from postnatal day 10–15 (P10–15) in NLGN3-R451C mutant mice, but majority of PCs became mono-innervated as in wild-type mice after P16. In NLGN3-R451C mutant mice, selective strengthening of a single CF relative to the other CFs in each PC was impaired from P16, which persisted into juvenile stage. Furthermore, the inhibition to excitation (I/E) balance of synaptic inputs to PCs was elevated, and calcium transients in the soma induced by strong and weak CF inputs were reduced in NLGN3-R451C mutant mice. These results suggest that a single point mutation in NLGN3 significantly influences the synapse development and refinement in cerebellar circuitry, which might be related to the pathogenesis of ASD.
Designing a Self-Perception Cognitive Questionnaire for Italian Multiple Sclerosis Patients (Sclerosi Multipla Autovalutazione Cognitiva, SMAC). A Preliminary Exploratory Pilot Study
Authors: Riccardi Alice , Ognibene Francesca , Mondini Sara , Nucci Massimo , Margoni Monica , Meglioranzi Ilaria , Carta Elisa , Zywicki Sofia , Miante Silvia , Perini Paola , Rinaldi Francesca , Puthenparampil Marco , Gallo Paolo
Published: June 2021

Background: Although cognition in multiple sclerosis (MS) is assessed by means of several neuropsychological tests, only a few tools exist to investigate patients' perspectives on cognitive functioning.

Objective: To develop a new questionnaire aimed at exploring patients' self-perception with respect to cognition in Italian MS patients.

Methods: A total of 120 relapsing-remitting MS (RRMS) patients and 120 matched healthy controls (HC) completed a 25-item questionnaire called the Sclerosi Multipla Autovalutazione Cognitiva (SMAC). The Symbol Digit Modalities Test (SDMT), the Delis-Kaplan Executive Function System Sorting Test (D-KEFS ST), the Beck Depression Inventory (BDI-II), and the Fatigue Scale (FSS) were also administered to the patients.

Results: Significantly higher SMAC scores were displayed by RRMS patients compared with HC (30.1 ± 16.9 vs. 23.4 ± 10.4, p = 0.003). SMAC inversely correlated with SDMT (r = −0.31, p < 0.001), D-KEFS ST FSC (r = −0.21, p = 0.017), D-KEFS ST FSD (r = −0.22, p = 0.015) and D-KEFS ST SR (r = −0.19, p = 0.035) and positively correlated with FSS (r = 0.42, p < 0.001) and BDI-II (r = 0.59, p < 0.001). Cronbach's alpha coefficient for the questionnaire was 0.94.

Conclusion: Preliminary findings suggest that SMAC is a promising patient-reported outcome to be included in MS neuropsychological evaluation and thus warrants being further tested and developed.
Saccades Matter: Reduced Need for Caloric Testing of Cochlear Implant Candidates by Joint Analysis of v-HIT Gain and Corrective Saccades
Authors: Fuentealba Bassaletti Constanza , van Esch Babette F. , Briaire Jeroen J. , van Benthem Peter Paul G. , Hensen Erik F. , Frijns Johan H. M.
Published: June 2021

Objectives: Video head impulse test (v-HIT) is a quick, non-invasive and relatively cheap test to evaluate vestibular function compared to the caloric test. The latter is, however, needed to decide on the optimal side to perform cochlear implantation to avoid the risk on inducing a bilateral vestibular areflexia. This study evaluates the effectiveness of using the v-HIT to select cochlear implant (CI) candidates who require subsequent caloric testing before implantation, in that way reducing costs and patient burden at the same time.

Study Design: Retrospective study using clinical data from 83 adult CI-candidates, between 2015 and 2020 at the Leiden University Medical Center.

Materials and Methods: We used the v-HIT mean gain, MinGain_LR, the gain asymmetry (GA) and a newly defined parameter, MGS (Minimal Gain & Saccades) as different models to detect the group of patients that would need the caloric test to decide on the ear of implantation. The continuous model MGS was defined as the MinGain_LR, except for the cases with normal gain (both sides ≥0.8) where no corrective saccades were present. In the latter case MGS was defined to be 1.0 (the ideal gain value).

Results: The receiver operating characteristics curve showed a very good diagnostic accuracy with and area under the curve (AUC) of 0.81 for the model MGS. The v-HIT mean gain, the minimal gain and GA had a lower diagnostic capacity with an AUC of 0.70, 0.72, and 0.73, respectively. Using MGS, caloric testing could be avoided in 38 cases (a reduction of 46%), with a test sensitivity of 0.9 (i.e., missing 3 of 28 cases).

Conclusions: The newly developed model MGS balances the sensitivity and specificity of the v-HIT better than the more commonly evaluated parameters such as mean gain, MinGain_LR and GA. Therefore, taking the presence of corrective saccades into account in the evaluation of the v-HIT gain can considerably reduce the proportion of CI-candidates requiring additional caloric testing.
Brain Energy Metabolism in Two States of Mind Measured by Phosphorous Magnetic Resonance Spectroscopy
Authors: Galijašević Malik , Steiger Ruth , Regodić Milovan , Waibel Michaela , Sommer Patrick Julian David , Grams Astrid Ellen , Singewald Nicolas , Gizewski Elke Ruth
Published: June 2021

Introduction:Various functional neuroimaging studies help to better understand the changes in brain activity during meditation. The purpose of this study was to investigate how brain energy metabolism changes during focused attention meditation (FAM) state, measured by phosphorous magnetic resonance spectroscopy (31P-MRS).

Methods:31P-MRS imaging was carried out in 27 participants after 7 weeks of FAM training. Metabolite ratios and the absolute values of metabolites were assessed after meditation training in two MRI measurements, by comparing effects in a FAM state with those in a distinct focused attention awake state during a backwards counting task.

Results:The results showed decreased phosphocreatine/ATP (PCr/ATP), PCr/ inorganic phosphate (Pi), and intracellular pH values in the entire brain, but especially in basal ganglia, frontal lobes, and occipital lobes, and increased Pi/ATP ratio, cerebral Mg, and Pi absolute values were found in the same areas during FAM compared to the control focused attention awake state.

Conclusions:Changes in the temporal areas and basal ganglia may be interpreted as a higher energetic state induced by meditation, whereas the frontal and occipital areas showed changes that may be related to a down-regulation in ATP turnover, energy state, and oxidative capacity.
A High Accuracy Electrographic Seizure Classifier Trained Using Semi-Supervised Labeling Applied to a Large Spectrogram Dataset
Authors: Barry Wade , Arcot Desai Sharanya , Tcheng Thomas K. , Morrell Martha J.
Published: June 2021

The objective of this study was to explore using ECoG spectrogram images for training reliable cross-patient electrographic seizure classifiers, and to characterize the classifiers’ test accuracy as a function of amount of training data. ECoG channels in ∼138,000 time-series ECoG records from 113 patients were converted to RGB spectrogram images. Using an unsupervised spectrogram image clustering technique, manual labeling of 138,000 ECoG records (each with up to 4 ECoG channels) was completed in 320 h, which is an estimated 5 times faster than manual labeling without ECoG clustering. For training supervised classifier models, five random folds of data were created; with each fold containing 72, 18, and 23 patients’ data for model training, validation and testing respectively. Five convolutional neural network (CNN) architectures, including two with residual connections, were trained. Cross-patient classification accuracies and F1 scores improved with model complexity, with the shallowest 6-layer model (with ∼1.5 million trainable parameters) producing a class-balanced seizure/non-seizure classification accuracy of 87.9% on ECoG channels and the deepest ResNet50-based model (with ∼23.5 million trainable parameters) producing a classification accuracy of 95.7%. The trained ResNet50-based model additionally had 93.5% agreement in scores with an independent expert labeller. Visual inspection of gradient-based saliency maps confirmed that the models’ classifications were based on relevant portions of the spectrogram images. Further, by repeating training experiments with data from varying number of patients, it was found that ECoG spectrogram images from just 10 patients were sufficient to train ResNet50-based models with 88% cross-patient accuracy, while at least 30 patients’ data was required to produce cross-patient classification accuracies of >90%.
Autonomic Nervous System Function in Anorexia Nervosa: A Systematic Review
Authors: Jenkins Zoe M. , Eikelis Nina , Phillipou Andrea , Castle David J. , Wilding Helen E. , Lambert Elisabeth A.
Published: June 2021

Background:Autonomic nervous system (ANS) dysfunction has been suggested to contribute to the high prevalence of cardiovascular complications in individuals with anorexia nervosa (AN), yet has not been thoroughly investigated. The current review aimed to synthesize the evidence of basal ANS function in individuals with a current diagnosis of AN and those with a previous diagnosis who had achieved weight restoration, as compared to controls.

Methods:A systematic review of nine databases was conducted and studies that were published in a peer-review journal, in English, that included at least one assessment of ANS function in individuals with a current or previous diagnosis of AN were selected. Forty-six studies were included with a total of 811 participants with a current diagnosis of AN and 123 participants with a previous diagnosis of AN.

Results:ANS function was assessed through heart rate variability (n= 27), orthostatic challenge, blood pressure variability or baroreflex sensitivity (n= 11), adrenergic activity (n= 14), skin conductance level (n= 4), and pupillometry (n= 1). Individuals with AN demonstrated increased parasympathetic activity and decreased sympathetic activity, suggestive of autonomic dysregulation. Following weight restoration, autonomic function trended toward, or was equivalent to, control levels.

Discussion:Autonomic dysregulation is indicated through a range of assessments in individuals with AN. Future investigations should utilize a variety of assessments together in order to conclusively establish the nature of autonomic dysfunction in AN, and following extended weight restoration. Moreover, investigation into the co-occurrence of ANS function and cardiovascular risk is required.
Altered Spontaneous Glutamatergic and GABAergic Activity in the Peritumoral Cortex of Low-Grade Gliomas Presenting With History of Seizures
Authors: Dey Soumil , Doddamani Ramesh Sharanappa , Banerjee Dixit Aparna , Tripathi Manjari , Sharma Meher Chand , Chandra P. Sarat , Banerjee Jyotirmoy
Published: June 2021

The peritumoral regions of WHO grade II gliomas, like astrocytoma and oligodendroglioma, have been reported to show epileptiform activities. An imbalance of glutamatergic and GABAergic mechanisms is primarily responsible for the generation of epileptiform activities. Here we have compared the electrophysiological properties of pyramidal neurons in intraoperative peritumoral specimens obtained from glioma patients with (GS) and without (GN) a history of seizures at presentation. Histology and immunohistochemistry were performed to assess the infiltration of proliferating cells at the peritumoral tissues. Whole-cell patch clamp technique was performed to measure the spontaneous glutamatergic and GABAergic activity onto pyramidal neurons in the peritumoral samples of GS (n = 11) and GN (n = 15) patients. The cytoarchitecture of the peritumoral tissues was devoid of Ki67 immuno-positive cells. We observed a higher frequency of spontaneous glutamatergic and GABAergic activities onto pyramidal neurons of the peritumoral samples of GS patients. Our findings suggest that, in spite of similar histopathological features, the pyramidal neurons in the peritumoral samples of GS and GN patients showed differences in spontaneous excitatory and inhibitory synaptic neurotransmission. An alteration in postsynaptic currents may contribute to the spontaneous epileptiform activity in GS patients.