bluuebunny/crossref_metadata_2025 huggingface dataset:
Health Conditions and Long Working Hours in Europe: A Retrospective Study
Authors: Korošec Darja , Vrbnjak Dominika , Štiglic Gregor
Published: September 2022

Studies have shown that working conditions and employee health are related; therefore, this study aimed to determine the relationships between working long hours per week with health outcomes in different European countries. We analyzed data derived from the Survey of Health, Ageing, and Retirement in Europe. The sample included 12.099 participants aged ≥ 50 from 16 European countries. We analyzed self-reported working hours, health outcomes of blood cholesterol, heart attack, diabetes, and hypertension, as well as a longitudinal analysis of health outcomes among healthcare workers and workers in 13 other industries. Statistical analyses identified that men are working longer hours per week compared with women in all included countries, and different levels of increase in health conditions in different industries. We also observed a slower increase in the prevalence of health conditions for healthcare workers compared with workers in other industries, especially diabetes and hypertension. The largest increase in prevalence of observed health conditions was reported for cholesterol, which increased for 17.14% among healthcare workers and for 21.70% in other industries over the observed nine-year period. Although the data point to a potentially high level of awareness in the field of preventive health among healthcare workers, more preventive health activities should be included in workplaces to strengthen employees’ health.
The Perception of Overweight and Obesity among South African Adults: Implications for Intervention Strategies
Authors: Manafe Mashudu , Chelule Paul Kiprono , Madiba Sphiwe
Published: September 2022

Obesity is a public health problem, affecting more than half of the global population. Perceptions and beliefs play a significant role in preventing and managing overweight and obesity. Thus, the paper explores own perception of overweight and obesity on personal health among South African adults. This was a qualitative study in which the participants (n = 24) were interviewed in-depth on their perception of obesity and health. Thematic analysis was used in data assessment. The results revealed four main themes: perceived causes of obesity, self-perception of being obese, perception of obesity, health, and cultural beliefs. Environmental and personal factors were perceived as the leading cause of overweight and obesity. The findings further showed that body weight preference was personal and differed from individual to individual. The study provided insight into perceptions of obesity from individuals’ perspectives. The misperceptions of overweight and obesity are helpful in the design of impactful intervention programmes that can be used to prevent and manage obesity in South Africa.
Physical Characteristics of Elite Male Bandy Players
Authors: Petré Henrik , Ovendal Alexander , Westblad Niklas , Ten Siethoff Lasse , Psilander Niklas
Published: September 2022

Physical characteristics of elite male bandy players have not been studied for the last 30 years. Therefore, the purpose of this study was to evaluate the physical characteristics of elite male bandy players with respect to playing positions. A cross-sectional study was performed that included 25 male bandy players from one of the highest-ranked bandy leagues in the world. Body weight, length, isometric mid-thigh pull, countermovement jump, squat jump, unilateral long jump, bilateral long jump, 15- and 30-m sprint, 15-m flying sprint, and VO2max were tested. Players were divided into forwards, midfielders, and defenders. Forwards had significantly (p = 0.012) higher relative VO2max than defenders (59.8 ± 4.3 compared to 53.0 ± 5.6 mL/kg/min). No significant differences for any of the other measurements were observed between positions. This is the first study to present the physical characteristics between playing positions in off- and on-ice tests for male bandy players competing at the highest level. Today’s bandy players are heavier and have lower relative VO2max compared with players in the early 1990s. However, their work capacities have increased since their absolute VO2max is higher. These results provide benchmark values that can serve as a foundation for strength and conditioning professionals when designing future training programs.
ICD: VHR-Oriented Interactive Change-Detection Algorithm
Authors: Jiang Zhuoran , Zhou Xinxin , Cao Wei , Sun Zaihong , Wu Changbin
Published: September 2022

In recent years, deep learning has become the mainstream development direction in the change-detection field, and its accuracy and speed have also reached a high level. However, the change-detection method based on deep learning cannot predict all the change areas accurately, and its application is limited due to local prediction defects. For this reason, we propose an interactive change-detection network (ICD) for very high resolution (VHR) based on a deep convolution neural network. The network integrates positive- and negative-click information in the distance layer of the change-detection network, and users can correct the prediction defects by adding clicks. We carried out experiments on the open source dataset WHU and LEVIR-CD. By adding clicks, their F1-scores can reach 0.920 and 0.912, respectively, which are 4.3% and 4.2% higher than the original network. To better evaluate the correction ability of clicks, we propose a set of evaluation indices—click-correction ranges, which is suitable for evaluating clicks, and we carry out experiments on the above models. The results show that the method of adding clicks can effectively correct the prediction defects and improve the result accuracy.
Modeling of DNA Damage Repair and Cell Response in Relation to p53 System Exposed to Ionizing Radiation
Authors: Hu Ankang , Zhou Wanyi , Wu Zhen , Zhang Hui , Li Junli , Qiu Rui
Published: September 2022

Repair of DNA damage induced by ionizing radiation plays an important role in the cell response to ionizing radiation. Radiation-induced DNA damage also activates the p53 system, which determines the fate of cells. The kinetics of repair, which is affected by the cell itself and the complexity of DNA damage, influences the cell response and fate via affecting the p53 system. To mechanistically study the influences of the cell response to different LET radiations, we introduce a new repair module and a p53 system model with NASIC, a Monte Carlo track structure code. The factors determining the kinetics of the double-strand break (DSB) repair are modeled, including the chromosome environment and complexity of DSB. The kinetics of DSB repair is modeled considering the resection-dependent and resection-independent compartments. The p53 system is modeled by simulating the interactions among genes and proteins. With this model, the cell responses to low- and high-LET irradiation are simulated, respectively. It is found that the kinetics of DSB repair greatly affects the cell fate and later biological effects. A large number of DSBs and a slow repair process lead to severe biological consequences. High-LET radiation induces more complex DSBs, which can be repaired by slow processes, subsequently resulting in a longer cycle arrest and, furthermore, apoptosis and more secreting of TGFβ. The Monte Carlo track structure simulation with a more realistic repair module and the p53 system model developed in this study can expand the functions of the NASIC code in simulating mechanical radiobiological effects.
Cytokine Imbalance as a Biomarker of Treatment-Resistant Schizophrenia
Authors: Shnayder Natalia A. , Khasanova Aiperi K. , Strelnik Anna I. , Al-Zamil Mustafa , Otmakhov Andrey P. , Neznanov Nikolay G. , Shipulin German A. , Petrova Marina M. , Garganeeva Natalia P. , Nasyrova Regina F.
Published: September 2022

Treatment-resistant schizophrenia (TRS) is an important and unresolved problem in biological and clinical psychiatry. Approximately 30% of cases of schizophrenia (Sch) are TRS, which may be due to the fact that some patients with TRS may suffer from pathogenetically “non-dopamine” Sch, in the development of which neuroinflammation is supposed to play an important role. The purpose of this narrative review is an attempt to summarize the data characterizing the patterns of production of pro-inflammatory and anti-inflammatory cytokines during the development of therapeutic resistance to APs and their pathogenetic and prognostic significance of cytokine imbalance as TRS biomarkers. This narrative review demonstrates that the problem of evaluating the contribution of pro-inflammatory and anti-inflammatory cytokines to maintaining or changing the cytokine balance can become a new key in unlocking the mystery of “non-dopamine” Sch and developing new therapeutic strategies for the treatment of TRS and psychosis in the setting of acute and chronic neuroinflammation. In addition, the inconsistency of the results of previous studies on the role of pro-inflammatory and anti-inflammatory cytokines indicates that the TRS biomarker, most likely, is not the serum level of one or more cytokines, but the cytokine balance. We have confirmed the hypothesis that cytokine imbalance is one of the most important TRS biomarkers. This hypothesis is partially supported by the variable response to immunomodulators in patients with TRS, which were prescribed without taking into account the cytokine balance of the relation between serum levels of the most important pro-inflammatory and anti-inflammatory cytokines for TRS.
The Receptor Binding Domain of SARS-CoV-2 Lambda Variant Has a Better Chance Than the Delta Variant in Evading BNT162b2 COVID-19 mRNA Vaccine-Induced Humoral Immunity
Authors: Liu Haolin , Wei Pengcheng , Aviszus Katja , Zhang Qianqian , Linderberger Jared , Yang John , Liu Junfeng , Chen Zhongzhou , Waheed Hassan , Reynoso Lyndon , Downey Gregory P. , Frankel Stephen K. , Kappler John W. , Marrack Philippa , Zhang Gongyi
Published: September 2022

The SARS-CoV-2 Delta and Lambda variants had been named variants of concern (VOC) and variants of interest (VOI), respectively, by the World Health Organization (WHO). Both variants have two mutations in the spike receptor binding domain (RBD) region, with L452R and T478K mutations in the Delta variant, and L452Q and F490S mutations in the Lambda variant. We used surface plasmon resonance (SPR)-based technology to evaluate the effect of these mutations on human angiotensin-converting enzyme 2 (ACE2) and Bamlanivimab binding. The affinity for the RBD ligand, ACE2, of the Delta RBD is approximately twice as strong as that of the wild type RBD, an increase that accounts for the increased infectivity of the Delta variant. On the other hand, in spite of its amino acid changes, the Lambda RBD has similar affinity to ACE2 as the wild type RBD. The protective anti-wild type RBD antibody Bamlanivimab binds very poorly to the Delta RBD and not at all to the Lambda RBD. Nevertheless, serum antibodies from individuals immunized with the BNT162b2 vaccine were found to bind well to the Delta RBD, but less efficiently to the Lambda RBD in contrast. As a result, the blocking ability of ACE2 binding by serum antibodies was decreased more by the Lambda than the Delta RBD. Titers of sera from BNT162b2 mRNA vaccinated individuals dropped 3-fold within six months of vaccination regardless of whether the target RBD was wild type, Delta or Lambda. This may account partially for the fall off with time in the protective effect of vaccines against any variant.
Sox6 Differentially Regulates Inherited Myogenic Abilities and Muscle Fiber Types of Satellite Cells Derived from Fast- and Slow-Type Muscles
Authors: Zhang Zihao , Lin Shudai , Luo Wen , Ren Tuanhui , Huang Xing , Li Wangyu , Zhang Xiquan
Published: September 2022

Adult skeletal muscle is primarily divided into fast and slow-type muscles, which have distinct capacities for regeneration, metabolism and contractibility. Satellite cells plays an important role in adult skeletal muscle. However, the underlying mechanisms of satellite cell myogenesis are poorly understood. We previously found that Sox6 was highly expressed in adult fast-type muscle. Therefore, we aimed to validate the satellite cell myogenesis from different muscle fiber types and investigate the regulation of Sox6 on satellite cell myogenesis. First, we isolated satellite cells from fast- and slow-type muscles individually. We found that satellite cells derived from different muscle fiber types generated myotubes similar to their origin types. Further, we observed that cells derived from fast muscles had a higher efficiency to proliferate but lower potential to self-renew compared to the cells derived from slow muscles. Then we demonstrated that Sox6 facilitated the development of satellite cells-derived myotubes toward their inherent muscle fiber types. We revealed that higher expression of Nfix during the differentiation of fast-type muscle-derived myogenic cells inhibited the transcription of slow-type isoforms (MyH7B, Tnnc1) by binding to Sox6. On the other hand, Sox6 activated Mef2C to promote the slow fiber formation in slow-type muscle-derived myogenic cells with Nfix low expression, showing a different effect of Sox6 on the regulation of satellite cell development. Our findings demonstrated that satellite cells, the myogenic progenitor cells, tend to develop towards the fiber type similar to where they originated. The expression of Sox6 and Nfix partially explain the developmental differences of myogenic cells derived from fast- and slow-type muscles.
RB49-like Bacteriophages Recognize O Antigens as One of the Alternative Primary Receptors
Authors: Efimov Alexandr D. , Golomidova Alla K. , Kulikov Eugene E. , Belalov Ilya S. , Ivanov Pavel A. , Letarov Andrey V.
Published: September 2022

The power of most of the enterobacterial O antigen types to provide robust protection against direct recognition of the cell surface by bacteriophage receptor-recognition proteins (RBP) has been recently recognized. The bacteriophages infecting O antigen producing strains of E. coli employ various strategies to tackle this nonspecific protection. T-even related phages, including RB49-like viruses, often have wide host ranges, being considered good candidates for use in phage therapy. However, the mechanisms by which these phages overcome the O antigen barrier remain unknown. We demonstrate here that RB49 and related phages Cognac49 and Whisky49 directly use certain types of O antigen as their primary receptors recognized by the virus long tail fibers (LTF) RBP gp38, so the O antigen becomes an attractant instead of an obstacle. Simultaneously to recognize multiple O antigen types, LTFs of each of these phages can bind to additional receptors, such as OmpA protein, enabling them to infect some rough strains of E. coli. We speculate that the mechanical force of the deployment of the short tail fibers (STF) triggered by the LTF binding to the O antigen or underneath of it, allows the receptor binding domains of STF to break through the O polysaccharide layer.
Safeguarding DNA Replication: A Golden Touch of MiDAS and Other Mechanisms
Authors: Al Ahmad Nachar Baraah , Rosselli Filippo
Published: September 2022

DNA replication is a tightly regulated fundamental process allowing the correct duplication and transfer of the genetic information from the parental cell to the progeny. It involves the coordinated assembly of several proteins and protein complexes resulting in replication fork licensing, firing and progression. However, the DNA replication pathway is strewn with hurdles that affect replication fork progression during S phase. As a result, cells have adapted several mechanisms ensuring replication completion before entry into mitosis and segregating chromosomes with minimal, if any, abnormalities. In this review, we describe the possible obstacles that a replication fork might encounter and how the cell manages to protect DNA replication from S to the next G1.
Association of Hypomagnesemia and Liver Injury, Role of Gut-Barrier Dysfunction and Inflammation: Efficacy of Abstinence, and 2-Week Medical Management in Alcohol Use Disorder Patients
Authors: Winrich Evan J. , Gala Khushboo S. , Rajhans Abhas , Rios-Perez Christian D. , Royer Amor J. , Zamani Zarlakhta , Parthasarathy Ranganathan , Marsano-Obando Luis S. , Barve Ashutosh J. , Schwandt Melanie L. , Vatsalya Vatsalya
Published: September 2022

(1) We investigated the involvement of serum magnesium level in early alcoholic liver disease (ALD), gut barrier dysfunction, and inflammation in alcohol use disorder (AUD) patients; and lastly, the efficacy of 2-week abstinence and medical management to alleviate hypomagnesemia. (2) Forty-eight heavy drinking AUD patients (34 males (M)/14 females (F)) participated in this study. Patients were grouped by serum alanine aminotransferase (ALT) level (a marker of liver injury) as group 1 (Group 1 (Gr.1); ALT ≤ 40 U/L, 7M/8F, without any indication of early-stage ALD) and group 2 (Group 2 (Gr.2); ALT > 40 U/L, 27M/6F or early-stage ALD). These patients were sub-divided within each group into patients with normal magnesium (0.85 and more mmol/L) and deficient magnesium (less than 0.85 mmol/L) levels. All participants were assessed at baseline (BL) and received standard medical management for 2 weeks with reassessment at the treatment end (2w). (3) Female participants of this study showed a significantly lower baseline level of magnesium than their male counterparts. Gr.2 patients showed a greater propensity in the necrotic type of liver cell death, who reported higher chronic and recent heavy drinking. Magnesium level improved to the normal range in Gr.2 post-treatment, especially in the hypomagnesemia sub-group (0.77 ± 0.06 mmol/L (BL) vs. 0.85 ± 0.05 mmol/L (2w), p = 0.02). In Gr.2, both apoptotic (K18M30) and necrotic (K18M65) responses were significantly and independently associated with inflammasome activity comprising of LBP (Lipopolysaccharide binding-protein) and TNFα (Tumor necrosis factor -α), along with serum magnesium. (4) In AUD patients with liver injury, 2-week medical management seems to improve magnesium to a normal level. This group exhibited inflammatory activity (LBP and TNFα) contributing to clinically significant hypomagnesemia. In this group, the level of magnesium, along with the unique inflammatory activity, seems to significantly predict apoptotic and necrotic types of hepatocyte death.
In Planta, In Vitro and In Silico Studies of Chiral N6-Benzyladenine Derivatives: Discovery of Receptor-Specific S-Enantiomers with Cytokinin or Anticytokinin Activities
Authors: Savelieva Ekaterina M. , Zenchenko Anastasia A. , Drenichev Mikhail S. , Kozlova Anna A. , Kurochkin Nikolay N. , Arkhipov Dmitry V. , Chizhov Alexander O. , Oslovsky Vladimir E. , Romanov Georgy A.
Published: September 2022

Cytokinins, classical phytohormones, affect all stages of plant ontogenesis, but their application in agriculture is limited because of the lack of appropriate ligands, including those specific for individual cytokinin receptors. In this work, a series of chiral N6-benzyladenine derivatives were studied as potential cytokinins or anticytokinins. All compounds contained a methyl group at the α-carbon atom of the benzyl moiety, making them R- or S-enantiomers. Four pairs of chiral nucleobases and corresponding ribonucleosides containing various substituents at the C2 position of adenine heterocycle were synthesized. A nucleophilic substitution reaction by secondary optically active amines was used. A strong influence of the chirality of studied compounds on their interaction with individual cytokinin receptors of Arabidopsis thaliana was uncovered in in vivo and in vitro assays. The AHK2 and CRE1/AHK4 receptors were shown to have low affinity for the studied S-nucleobases while the AHK3 receptor exhibited significant affinity for most of them. Thereby, three synthetic AHK3-specific cytokinins were discovered: N6-((S)-α-methylbenzyl)adenine (S-MBA), 2-fluoro,N6-((S)-α-methylbenzyl)adenine (S-FMBA) and 2-chloro,N6-((S)-α-methylbenzyl)adenine (S-CMBA). Interaction patterns between individual receptors and specific enantiomers were rationalized by structure analysis and molecular docking. Two other S-enantiomers (N6-((S)-α-methylbenzyl)adenosine, 2-amino,N6-((S)-α-methylbenzyl)adenosine) were found to exhibit receptor-specific and chirality-dependent anticytokinin properties.
Efficacy and Renal Safety of Prophylactic Tenofovir Alafenamide for HBV-Infected Cancer Patients Undergoing Chemotherapy
Authors: Lee I-Cheng , Lan Keng-Hsin , Su Chien-Wei , Li Chung-Pin , Chao Yee , Lin Han-Chieh , Hou Ming-Chih , Huang Yi-Hsiang
Published: September 2022

There are no data comparing the efficacy and safety of prophylactic entecavir (ETV), tenofovir disoproxil fumarate (TDF) and tenofovir alafenamide (TAF) for HBV-infected cancer patients undergoing chemotherapy. This study aimed to compare the efficacy and renal safety of ETV, TDF and TAF in this setting. HBsAg-positive cancer patients treated with ETV (n = 582), TDF (n = 200) and TAF (n = 188) during chemotherapy were retrospectively enrolled. Antiviral efficacy and risk of renal events were evaluated. The rate of complete viral suppression at 1 year was 94.7%, 94.7% and 96.1% in ETV, TDF and TAF groups, respectively (p = 0.877). A significant proportion of patients developed renal dysfunction during chemotherapy. The incidences of acute kidney injury (AKI) and chronic kidney disease stage migration were comparable among the ETV, TDF and TAF groups. TAF was relatively safe in patients with predisposing factors of AKI, including hypoalbuminemia and cisplatin use. In patients who were switched from TDF to TAF during chemotherapy, the renal function remained stable and viral suppression was well maintained after switching. In conclusion, TAF had good renal safety and comparable efficacy with ETV and TDF for HBV-infected cancer patients receiving chemotherapy. Switching from TDF to TAF during chemotherapy is safe, without a loss of efficacy.
Preparation of Highly Crystalline Silk Nanofibrils and Their Use in the Improvement of the Mechanical Properties of Silk Films
Authors: Lee Ji Hye , Park Bo Kyung , Um In Chul
Published: September 2022

Due to their commendable biocompatibility, regenerated silk fibroin (RSF) films have attracted considerable research interest. However, the poor mechanical properties of RSF films have limited their use in various biomedical applications. In this study, a novel, highly crystalline silk fibril was successfully extracted from silk by combining degumming with ultrasonication. Ultrasonication accelerated the development of silk nanofibrils measuring 130–200 nm on the surface of the over-degummed silk fibers, which was confirmed via scanning electron microscopy. Additionally, the crystallinity index of silk fibril was found to be significantly higher (~68%) than that of conventionally degummed silk (~54%), as confirmed by the Fourier-transform infrared (FTIR) spectroscopy results. Furthermore, the breaking strength and elongation of the RSF film were increased 1.6 fold and 3.4 fold, respectively, following the addition of 15% silk nanofibrils. Thus, the mechanical properties of the RSF film were remarkably improved by the addition of the silk nanofibrils, implying that it can be used as an excellent reinforcing material for RSF films.
Interspecies Comparison of Interaction Energies between Photosynthetic Protein RuBisCO and 2CABP Ligand
Authors: Fujii Masayasu , Tanaka Shigenori
Published: September 2022

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) functions as the initial enzyme in the dark reactions of photosynthesis, catalyzing reactions that extract CO2 from the atmosphere and fix CO2 into organic compounds. RuBisCO is classified into four types (isoforms I–IV) according to sequence-based phylogenetic trees. Given its size, the computational cost of accurate quantum-chemical calculations for functional analysis of RuBisCO is high; however, recent advances in hardware performance and the use of the fragment molecular orbital (FMO) method have enabled the ab initio analyses of RuBisCO. Here, we performed FMO calculations on multiple structural datasets for various complexes with the 2′-carboxylarabinitol 1,5-bisphosphate (2CABP) ligand as a substrate analog and investigated whether phylogenetic relationships based on sequence information are physicochemically relevant as well as whether novel information unobtainable from sequence information can be revealed. We extracted features similar to the phylogenetic relationships found in sequence analysis, and in terms of singular value decomposition, we identified residues that strongly interacted with the ligand and the characteristics of the isoforms for each principal component. These results identified a strong correlation between phylogenetic relationships obtained by sequence analysis and residue interaction energies with the ligand. Notably, some important residues were located far from the ligand, making comparisons among species using only residues proximal to the ligand insufficient.
Evaluation of Circulating MicroRNAs and Adipokines in Breast Cancer Survivors with Arm Lymphedema
Authors: Yusof Khairunnisa’ Md , Groen Kira , Rosli Rozita , Abdullah Maha , Mahmud Rozi , Avery-Kiejda Kelly A.
Published: September 2022

Breast cancer-related lymphedema (BCRL) is a form of secondary lymphedema that is characterized by abnormal swelling of one or both arms due to the accumulation of lymph fluid in the interstitial tissue spaces, resulting from obstruction of the lymphatic vessels due to surgery insults, radiotherapy, or chemotherapy. Due to the multifactorial nature of this condition, the pathogenesis of secondary lymphedema remains unclear and the search for molecular factors associated with the condition is ongoing. This study aimed to identify serum microRNAs and adipokines associated with BCRL. Blood was collected from 113 breast cancer survivors and processed to obtain serum for small RNA-sequencing (BCRL vs. non-BCRL, n = 7 per group). MicroRNAs that were differentially expressed (fold change >1.5, p < 0.05) between lymphedema cases and those without lymphedema were further quantified in a validation cohort through quantitative reverse transcription PCR (BCRL n = 16, non-BCRL, n = 83). Leptin and adiponectin levels were measured in a combined cohort (BCRL n = 23, non-BCRL n = 90) using enzyme-linked immunosorbent assays. Two of the most significantly upregulated microRNAs, miR-199a-3p and miR-151a-3p, were strongly correlated with the onset of lymphedema and diabetes mellitus in the BCRL group. Leptin levels were higher in the BCRL cohort compared to the non-BCRL cohort (p < 0.05). A metabolic syndrome biomarker, the adiponectin/leptin ratio, was found to be lower in the BCRL group than in the non-BCRL group (median: 0.28 vs. 0.41, p < 0.05). Extensive studies on the mechanisms of the identified microRNAs and association of leptin with arm lymphedema may provide new insights on the potential biomarkers for lymphedema that should be followed up in a prospective cohort study.
Spatial Structure of NanoFAST in the Apo State and in Complex with its Fluorogen HBR-DOM2
Authors: Lushpa Vladislav A. , Baleeva Nadezhda S. , Goncharuk Sergey A. , Goncharuk Marina V. , Arseniev Alexander S. , Baranov Mikhail S. , Mineev Konstantin S.
Published: September 2022

NanoFAST is a fluorogen-activating protein and can be considered one of the smallest encodable fluorescent tags. Being a shortened variant of another fluorescent tag, FAST, nanoFAST works nicely only with one out of all known FAST ligands. This substantially limits the applicability of this protein. To find the reason for such a behavior, we investigated the spatial structure and dynamics of nanoFAST, both in the apo state and in the complex with its fluorogen molecule, using the solution NMR spectroscopy. We showed that the truncation of FAST did not affect the structure of the remaining part of the protein. Our data suggest that the deleted N-terminus of FAST destabilizes the C-terminal domain in the apo state. While it does not contact the fluorogen directly, it serves as a free energy reservoir that enhances the ligand binding propensity of the protein. The structure of nanoFAST/HBR-DOM2 complex reveals the atomistic details of nanoFAST interactions with the rhodanine-based ligands and explains the ligand specificity. NanoFAST selects ligands with the lowest dissociation constants, 2,5-disubstituted 4-hydroxybenzyldienerhodainines, which allow the non-canonical intermolecular CH–N hydrogen bonding and provide the optimal packing of the ligand within the hydrophobic cavity of the protein.
Evaluating the Safety and Quality of Life of Colorectal Cancer Patients Treated by Autologous Immune Enhancement Therapy (AIET) in Vinmec International Hospitals
Authors: Nguyen Hoang-Phuong , Pham Duc-Anh Dao , Dinh Nguyen Duy , Nguyen Phong Van , Bui Viet-Anh , Hoang My-Nhung Thi , Nguyen Liem Thanh
Published: September 2022

(1) Colorectal cancer (CRC) is an increasingly prevalent disease with a high mortality rate in recent years. Immune cell-based therapies have received massive attention among scientists, as they have been proven effective as low-toxicity treatments. This study evaluated the safety and effectiveness of autologous immune enhancement therapy (AIET) for CRC. (2) An open-label, single-group study, including twelve patients diagnosed with stages III and IV CRC, was conducted from January 2016 to December 2021. Twelve CRC patients received one to seven infusions of natural killer (NK)-cell and cytotoxic T-lymphocyte (CTL). Multivariate modelling was used to identify factors associated with health-related quality-of-life (HRQoL) scores. (3) After 20–21 days of culture, the NK cells increased 3535-fold, accounting for 85% of the cultured cell population. Likewise, CTLs accounted for 62.4% of the cultured cell population, which was a 1220-fold increase. Furthermore, the QoL improved with increased EORTC QLQ-C30 scores, decreased symptom severity, and reduced impairment in daily living caused by these symptoms (MDASI-GI report). Finally, a 14.3 ± 14.1-month increase in mean survival time was observed at study completion. (4) AIET demonstrated safety and improved survival time and HRQoL for CRC patients in Vietnam.
Challenges and Future Trends of Hepatocellular Carcinoma Immunotherapy
Authors: Rizzo Alessandro , Ricci Angela Dalia
Published: September 2022

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide [...]
Lysyl Oxidases: Orchestrators of Cellular Behavior and ECM Remodeling and Homeostasis
Authors: Zaffryar-Eilot Shelly , Hasson Peleg
Published: September 2022

Lysyl oxidases have long been considered key secreted extracellular matrix modifying enzymes. As such, their activity has been associated with the crosslinking of collagens and elastin, and as a result, they have been linked to multiple developmental and pathological processes. However, numerous lines of evidence also demonstrated that members of this enzyme family are localized and are active within the cytoplasm or cell nuclei, where they regulate and participate in distinct cellular events. In this review, we focus on a few of these events and highlight the intracellular role these enzymes play. Close examination of these events, suggest that the intracellular activities of lysyl oxidases is mostly observed in processes where concomitant changes in the extracellular matrix takes place. Here, we suggest that the LOX family members act in the relay between changes in the cells’ environment and the intracellular processes that promote them or that follow.
Arrangement of Hydrogen Bonds in Aqueous Solutions of Different Globular Proteins
Authors: Titus Amber R. , Madeira Pedro P. , Ferreira Luisa A. , Belgovskiy Alexander I. , Mann Elizabeth K. , Mann Jay Adin , Meyer William V. , Smart Anthony E. , Uversky Vladimir N. , Zaslavsky Boris Y.
Published: September 2022

This work presents the first evidence that dissolved globular proteins change the arrangement of hydrogen bonds in water, with different proteins showing quantitatively different effects. Using ATR-FTIR (attenuated total reflection—Fourier transform infrared) spectroscopic analysis of OH-stretch bands, we obtain quantitative estimates of the relative amounts of the previously reported four subpopulations of water structures coexisting in a variety of aqueous solutions. Where solvatochromic dyes can measure the properties of solutions of non-ionic polymers, the results correlate well with ATR-FTIR measurements. In protein solutions to which solvatochromic dye probes cannot be applied, NMR (nuclear magnetic resonance) spectroscopy was used for the first time to estimate the hydrogen bond donor acidity of water. We found strong correlations between the solvent acidity and arrangement of hydrogen bonds in aqueous solutions for several globular proteins. Even quite similar proteins are found to change water properties in dramatically different ways.
NMDA Receptor C-Terminal Domain Signalling in Development, Maturity, and Disease
Authors: Haddow Kirsty , Kind Peter C. , Hardingham Giles E.
Published: September 2022

The NMDA receptor is a Ca2+-permeant glutamate receptor which plays key roles in health and disease. Canonical NMDARs contain two GluN2 subunits, of which 2A and 2B are predominant in the forebrain. Moreover, the relative contribution of 2A vs. 2B is controlled both developmentally and in an activity-dependent manner. The GluN2 subtype influences the biophysical properties of the receptor through difference in their N-terminal extracellular domain and transmembrane regions, but they also have large cytoplasmic Carboxyl (C)-terminal domains (CTDs) which have diverged substantially during evolution. While the CTD identity does not influence NMDAR subunit specific channel properties, it determines the nature of CTD-associated signalling molecules and has been implicated in mediating the control of subunit composition (2A vs. 2B) at the synapse. Historically, much of the research into the differential function of GluN2 CTDs has been conducted in vitro by over-expressing mutant subunits, but more recently, the generation of knock-in (KI) mouse models have allowed CTD function to be probed in vivo and in ex vivo systems without heterologous expression of GluN2 mutants. In some instances, findings involving KI mice have been in disagreement with models that were proposed based on earlier approaches. This review will examine the current research with the aim of addressing these controversies and how methodology may contribute to differences between studies. We will also discuss the outstanding questions regarding the role of GluN2 CTD sequences in regulating NMDAR subunit composition, as well as their relevance to neurodegenerative disease and neurodevelopmental disorders.
BST2, a Novel Inhibitory Receptor, Is Involved in NK Cell Cytotoxicity through Its Cytoplasmic Tail Domain
Authors: Oh Jinsoo , Yi Eunbi , Jeong Soo Kyung , Park Sehoon , Park Se-Ho
Published: September 2022

Bone Marrow Stromal Cell Antigen 2 (BST2) is a type II transmembrane protein expressed on various cell types that tethers the release of viruses. Natural killer (NK) cells express low levels of BST2 under normal conditions but exhibit increased expression of BST2 upon activation. In this study, we show for the first time that murine BST2 can control the cytotoxicity of NK cells. The cytoplasmic tail of murine BST2 contains an immunoreceptor tyrosine-based inhibitory motif (ITIM). The absence of BST2 on NK cells can enhance their cytotoxicity against tumor cells compared to wild type NK cells. NK cells isolated from NZW mice, which express ITIM-deficient BST2, also showed higher cytotoxicity than wild type NK cells. In addition, we found that galectin-8 and galectin-9 were ligands of BST2, since blocking galectin-8 or -9 with monoclonal antibodies enhanced the cytotoxicity of NK cells. These results suggested that BST2 might be a novel NK cell inhibitory receptor as it was involved in regulating NK cell cytotoxicity through its interaction with galectins.
The Association of Grain Yield and Agronomical Traits with Genes of Plant Height, Photoperiod Sensitivity and Plastid Glutamine Synthetase in Winter Bread Wheat (Triticum aestivum L.) Collection
Authors: Bazhenov Mikhail S. , Bespalova Ludmila A. , Kocheshkova Alina A. , Chernook Anastasiya G. , Puzyrnaya Olga Y. , Agaeva Elena V. , Nikitina Ekaterina A. , Igonin Vladimir N. , Bazhenova Svetlana S. , Vertikova Elena A. , Kharchenko Pyotr N. , Karlov Gennady I. , Divashuk Mikhail G.
Published: September 2022

The reduction in plant height caused by mutations in Rht-B1 or Rht-D1 (Reduced height-1) genes in combination with day-length-independent early flowering associated with the Ppd-D1 (Photoperiod-D1) gene were the main factors of the drastic yield increase in bread wheat in the 1960s. Increasing nitrogen use efficiency as well as maintaining high yields under conditions of global climate change are the modern goals of wheat breeding. The glutamine synthetase (GS) enzyme plays a key role in ammonium assimilation in plants. In previous studies, the TaGS2-A1 gene, coding the plastid isoform of GS, was shown to be connected with nitrogen use efficiency in wheat. Using the polymerase chain reaction (PCR) markers, the association of yield and agronomical traits with haplotypes of Rht-B1, Rht-D1, Ppd-D1 and TaGS2-A1 genes was studied in a diverse collection of winter bread wheat cultivars grown in Krasnodar (Russia). In the three-year experiment, semidwarfism and photoperiod insensitivity were confirmed to be highly favorable for the grain yield. The TaGS2-A1b haplotype had a tendency for increased grain yield and lodging resistance, but mainly in plants not possessing the ‘green revolution’ alleles. Thus, TaGS2-A1b may have potential in breeding wheat cultivars with alternative dwarfing genes or tall cultivars, which may be optimal for growing under certain environments.
Synthesis of M-Ag3PO4, (M = Se, Ag, Ta) Nanoparticles and Their Antibacterial and Cytotoxicity Study
Authors: Qureshi Faiza , Nawaz Muhammad , Ansari Mohammad Azam , Khan Firdos Alam , Berekaa Mahmoud M. , Abubshait Samar A. , Al-Mutairi Rayyanah , Paul Alok K. , Nissapatorn Veeranoot , de Lourdes Pereira Maria , Wilairatana Polrat
Published: September 2022

Silver Phosphate, Ag3PO4, being a highly capable clinical molecule, an ultrasonic method was employed to synthesize the M-Ag3PO4, (M = Se, Ag, Ta) nanoparticles which were evaluated for antibacterial and cytotoxicity activities post-characterization. Escherichia coli and Staphylococcus aureus were used for antibacterial testing and the effects of sonication on bacterial growth with sub-MIC values of M-Ag3PO4 nanoparticles were examined. The effect of M-Ag3PO4 nanoparticles on human colorectal carcinoma cells (HCT-116) and human cervical carcinoma cells (HeLa cells) was examined by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide) assay and DAPI (4′,6-diamidino-2-phenylindole) staining. Additionally, we analyzed the effect of nanoparticles on normal and non-cancerous human embryonic kidney cells (HEK-293). Ag-Ag3PO4 exhibited enhanced antibacterial activity followed by Ta-Ag3PO4, Ag3PO4, and Se-Ag3PO4 nanoparticles against E. coli. Whereas the order of antibacterial activity against Staphylococcus aureus was Ag3PO4 > Ag-Ag3PO4 > Ta-Ag3PO4 > Se-Ag3PO4, respectively. Percentage inhibition of E. coli was 98.27, 74.38, 100, and 94.2%, while percentage inhibition of S. aureus was 25.53, 80.28, 99.36, and 20.22% after treatment with Ag3PO4, Se-Ag3PO4, Ag-Ag3PO4, and Ta-Ag3PO4, respectively. The MTT assay shows a significant decline in the cell viability after treating with M-Ag3PO4 nanoparticles. The IC50 values for Ag3PO4, Se-Ag3PO4, Ag-Ag3PO4, and Ta-Ag3PO4 on HCT-116 were 39.44, 28.33, 60.24, 58.34 µg/mL; whereas for HeLa cells, they were 65.25, 61.27, 75.52, 72.82 µg/mL, respectively. M-Ag3PO4 nanoparticles did not inhibit HEK-293 cells. Apoptotic assay revealed that the numbers of DAPI stained cells were significantly lower in the M-Ag3PO4-treated cells versus control.
Hepatoprotective Effects of a Natural Flavanol 3,3′-Diindolylmethane against CCl4-Induced Chronic Liver Injury in Mice and TGFβ1-Induced EMT in Mouse Hepatocytes via Activation of Nrf2 Cascade
Authors: Munakarmi Suvesh , Gurau Yamuna , Shrestha Juna , Risal Prabodh , Park Ho Sung , Shin Hyun Beak , Jeong Yeon Jun
Published: September 2022

Hepatic fibrosis is a form of irregular wound-healing response with acute and chronic injury triggered by the deposition of excessive extracellular matrix. Epithelial–mesenchymal transition (EMT) is a dynamic process that plays a crucial role in the fibrogenic response and pathogenesis of liver fibrosis. In the present study, we postulated a protective role of 3,3′-diindolylmethane (DIM) against TGF-β1 mediated epithelial–mesenchymal transition (EMT) in vitro and carbon tetrachloride (CCl4)-induced liver fibrosis in mice. TGF-β1-induced AML-12 hepatocyte injury was evaluated by monitoring cell morphology, measuring reactive oxygen species (ROS) and mitochondrial membrane potential, and quantifying apoptosis, inflammatory, and EMT-related proteins. Furthermore, CCl4-induced liver fibrosis in mice was evaluated by performing liver function tests, including serum ALT and AST, total bilirubin, and albumin to assess liver injury and by performing H&E and Sirius red staining to determine the degree of liver fibrosis. Immunoblotting was performed to determine the expression levels of inflammation, apoptosis, and Nrf2/HO-1 signaling-related proteins. DIM treatment significantly restored TGF-β1-induced morphological changes, inhibited the expression of mesenchymal markers by activating E-cadherin, decreased mitochondrial membrane potential, reduced ROS intensity, and upregulated levels of Nrf2-responsive antioxidant genes. In the mouse model of CCl4-induced liver fibrosis, DIM remarkably attenuated liver injury and liver fibrosis, as reflected by the reduced ALT and AST parameters with increased serum Alb activity and fewer lesions in H&E staining. It also mitigated the fibrosis area in Sirius red and Masson staining. Taken together, our results suggest a possible molecular mechanism of DIM by suppressing TGF-β1-induced EMT in mouse hepatocytes and CCl4-induced liver fibrosis in mice.
High Performance Computing PP-Distance Algorithms to Generate X-ray Spectra from 3D Models
Authors: González César , Balocco Simone , Bosch Jaume , de Haro Juan Miguel , Paolini Maurizio , Filgueras Antonio , Álvarez Carlos , Pons Ramon
Published: September 2022

X-ray crystallography is a powerful method that has significantly contributed to our understanding of the biological function of proteins and other molecules. This method relies on the production of crystals that, however, are usually a bottleneck in the process. For some molecules, no crystallization has been achieved or insufficient crystals were obtained. Some other systems do not crystallize at all, such as nanoparticles which, because of their dimensions, cannot be treated by the usual crystallographic methods. To solve this, whole pair distribution function has been proposed to bridge the gap between Bragg and Debye scattering theories. To execute a fitting, the spectra of several different constructs, composed of millions of particles each, should be computed using a particle–pair or particle–particle (pp) distance algorithm. Using this computation as a test bench for current field-programmable gate array (FPGA) technology, we evaluate how the parallel computation capability of FPGAs can be exploited to reduce the computation time. We present two different solutions to the problem using two state-of-the-art FPGA technologies. In the first one, the main C program uses OmpSs (a high-level programming model developed at the Barcelona Supercomputing Center, that enables task offload to different high-performance computing devices) for task invocation, and kernels are built with OpenCL using reduced data sizes to save transmission time. The second approach uses task and data parallelism to operate on data locally and update data globally in a decoupled task. Benchmarks have been evaluated over an Intel D5005 Programmable Acceleration Card, computing a model of 2 million particles in 81.57 s – 24.5 billion atom pairs per second (bapps)– and over a ZU102 in 115.31 s. In our last test, over an up-to-date Alveo U200 board, the computation lasted for 34.68 s (57.67 bapps). In this study, we analyze the results in relation to the classic terms of speed-up and efficiency and give hints for future improvements focused on reducing the global job time.
RUNX1/CEBPA Mutation in Acute Myeloid Leukemia Promotes Hypermethylation and Indicates for Demethylation Therapy
Authors: Romanova Ekaterina I. , Zubritskiy Anatoliy V. , Lioznova Anna V. , Ogunleye Adewale J. , Golotin Vasily A. , Guts Anna A. , Lennartsson Andreas , Demidov Oleg N. , Medvedeva Yulia A.
Published: September 2022

Acute myeloid leukemia (AML) is a rapidly progressing heterogeneous disease with a high mortality rate, which is characterized by hyperproliferation of atypical immature myeloid cells. The number of AML patients is expected to increase in the near future, due to the old-age-associated nature of AML and increased longevity in the human population. RUNX1 and CEBPA, key transcription factors (TFs) of hematopoiesis, are frequently and independently mutated in AML. RUNX1 and CEBPA can bind TET2 demethylase and attract it to their binding sites (TFBS) in cell lines, leading to DNA demethylation of the regions nearby. Since TET2 does not have a DNA-binding domain, TFs are crucial for its guidance to target genomic locations. In this paper, we show that RUNX1 and CEBPA mutations in AML patients affect the methylation of important regulatory sites that resulted in the silencing of several RUNX1 and CEBPA target genes, most likely in a TET2-dependent manner. We demonstrated that hypermethylation of TFBS in AML cells with RUNX1 mutations was associated with resistance to anticancer chemotherapy. Demethylation therapy restored expression of the RUNX1 target gene, BIK, and increased sensitivity of AML cells to chemotherapy. If our results are confirmed, mutations in RUNX1 could be an indication for prescribing the combination of cytotoxic and demethylation therapies.
PAUF Induces Migration of Human Pancreatic Cancer Cells Exclusively via the TLR4/MyD88/NF-κB Signaling Pathway
Authors: Youn So Eun , Jiang Fen , Won Hye Yun , Hong Da Eun , Kang Tae Heung , Park Yun-Yong , Koh Sang Seok
Published: September 2022

PAUF, a tumor-promoting protein secreted by cancer cells, exerts paracrine effects on immune cells through TLR4 receptors expressed on immune cell surfaces. This study aimed to investigate if PAUF elicits autocrine effects on pancreatic cancer (PC) cells through TLR4, a receptor that is overexpressed on PC cells. In this study, TLR4 expression was detected in PC cells only, but not normal pancreatic cells. The migration of TLR4 high-expressing PC cells (i.e., BxPC-3) was reduced by a selective TLR4 inhibitor, in a dose-dependent manner. Using TLR4 overexpressed and knockout PC cell lines, we observed direct PAUF-TLR4 binding on the PC cell surfaces, and that PAUF-induced cancer migration may be mediated exclusively through the TLR4 receptor. Further experiments showed that PAUF signaling was passed down through the TLR4/MyD88 pathway without the involvement of the TLR4/TRIF pathway. TLR4 knockout also downregulated PC membrane PD-L1 expression, which was not influenced by PAUF. To the best of our knowledge, TLR4 is the first receptor identified on cancer cells that mediates PAUF’s migration-promoting effect. The results of this study enhanced our understanding of the mechanism of PAUF-induced tumor-promoting effects and suggests that TLR4 expression on cancer cells may be an important biomarker for anti-PAUF treatment.