bluuebunny/crossref_metadata_2025 huggingface dataset:
A Flexible Approach for Assessing Heterogeneity of Causal Treatment Effects on Patient Survival Using Large Datasets with Clustered Observations
Authors: Hu Liangyuan , Ji Jiayi , Liu Hao , Ennis Ronald
Published: November 2022

Personalized medicine requires an understanding of treatment effect heterogeneity. Evolving toward causal evidence for scenarios not studied in randomized trials necessitates a methodology using real-world evidence. Herein, we demonstrate a methodology that generates causal effects, assesses the heterogeneity of the effects and adjusts for the clustered nature of the data. This study uses a state-of-the-art machine learning survival model, riAFT-BART, to draw causal inferences about individual survival treatment effects, while accounting for the variability in institutional effects; further, it proposes a data-driven approach to agnostically (as opposed to a priori hypotheses) ascertain which subgroups exhibit an enhanced treatment effect from which intervention, relative to global evidence—average treatment effects measured at the population level. Comprehensive simulations show the advantages of the proposed method in terms of bias, efficiency and precision in estimating heterogeneous causal effects. The empirically validated method was then used to analyze the National Cancer Database.
Negotiating Complexity: Challenges to Implementing Community-Led Nature-Based Solutions in England Pre- and Post-COVID-19
Authors: He Yichao , Jorgensen Anna , Sun Qian , Corcoran Amy , Alfaro-Simmonds Maria Jesus
Published: November 2022

Nature-based solutions (NbS), including green social prescribing (GSP), are sustainable ways to address health and wellbeing, especially since the COVID-19 pandemic exacerbated the strain on healthcare. NbS require national and local cross-sector coordination across complex, interrelated systems, but little is known about the specific challenges this poses for community-led NbS. We carried out a traditional literature review to establish the context and knowledge base for this study and interviewed 26 stakeholders. These came from environment, health and social care sectors at national and local levels, with local-level stakeholders from Bradford and Walsall: English cities significantly affected by the pandemic, with high levels of deprivation and health inequality. The interviews explored experiences of implementing NbS, both pre- and post-pandemic and the resulting renewed interest in the salutogenic effects of engaging with natural environments. We coded the interview transcriptions using NVivo to identify the challenges existing in the systems within which these stakeholders operate to create and manage NbS. By synthesizing what is known about the challenges from existing literature with findings from the interviews, we developed eight categories of challenges (perception and knowledge, political, financial, access to natural spaces, engagement, institutional and organisational, coordination, GSP referral and services) faced by multiple sectors in implementing community-led NbS in England. Furthermore, this study highlights the new challenges related to the pandemic. Identifying these challenges helps stakeholders in existing complex systems recognise what is needed to support and mainstream NbS in England.
Isothiocyanate-Rich Extracts from Cauliflower (Brassica oleracea Var. Botrytis) and Radish (Raphanus sativus) Inhibited Metabolic Activity and Induced ROS in Selected Human HCT116 and HT-29 Colorectal Cancer Cells
Authors: Cuellar-Nuñez Mardey Liceth , Luzardo-Ocampo Ivan , Lee-Martínez Sarah , Larrauri-Rodríguez Michelle , Zaldívar-Lelo de Larrea Guadalupe , Pérez-Serrano Rosa Martha , Camacho-Calderón Nicolás
Published: November 2022

Cruciferous vegetables such as cauliflower and radish contain isothiocyanates exhibiting chemoprotective effects in vitro and in vivo. This research aimed to assess the impact of cauliflower (CIE) and radish (RIE) isothiocyanate extracts on the metabolic activity, intracellular reactive oxygen species (ROS), and LDH production of selected human colorectal adenocarcinoma cells (HCT116 and HT-29 for early and late colon cancer development, respectively). Non-cancerous colon cells (CCD-33Co) were used as a cytotoxicity control. The CIE samples displayed the highest allyl isothiocyanate (AITC: 12.55 µg/g) contents, whereas RIE was the most abundant in benzyl isothiocyanate (BITC: 15.35 µg/g). Both extracts effectively inhibited HCT116 and HT-29 metabolic activity, but the CIE impact was higher than that of RIE on HCT116 (IC50: 0.56 mg/mL). Assays using the half-inhibitory concentrations (IC50) of all treatments, including AITC and BITC, displayed increased (p < 0.05) LDH (absorbance: 0.25–0.40 nm) and ROS release (1190–1697 relative fluorescence units) in both cell lines. BITC showed the highest in silico binding affinity with all the tested colorectal cancer molecular markers (NF-kB, β-catenin, and NRF2-NFE2). The theoretical evaluation of AITC and BITC bioavailability showed high values for both compounds. The results indicate that CIE and RIE extracts display chemopreventive effects in vitro, but additional experiments are needed to validate their effects.
Evaluating the Performance of Ball-Milled Silk Fibroin Films for Simultaneous Adsorption of Eight Pharmaceuticals from Water
Authors: Kgomo Hlobsile , Dube Simiso , Nindi Mathew Muzi
Published: November 2022

Pollutants mainly exist as multicomponent mixtures in the environment. Therefore, it is necessary to synthesize low-cost adsorbents that can simultaneously adsorb multiple compounds. This work presents the prospect of the adsorption of multiclass pharmaceuticals from the aqueous environment using an adsorbent derived from silk fibroin of the wild silkworm Argema mimosae. The adsorbent was prepared by dissolving degummed silk fibroin and the resultant solution was cast to obtain films that were ball-milled to powder. FTIR results revealed bands corresponding to N-H and C=O stretching vibrations. Particle size distribution data generally showed two size groups in the range of 50–90 nm and 250–625 nm. The study focused on the adsorptive removal of multiple compounds consisting of eight pharmaceuticals representing various classes including a β-blocker (pindolol), anesthetic (lidocaine), stimulant (caffeine), antiviral (nevirapine), steroid (estriol), anti-epileptic (carbamazepine), and a non-steroidal anti-inflammatory drug (naproxen). The adsorption process was best fitted to the pseudo-second-order isotherm and an overall match to the Freundlich model. Thermodynamic parameters suggested that the process was mainly exothermic and more spontaneous at lower temperatures. The performance of the adsorbent was further evaluated using environmental waters and the adsorbent demonstrated good potential for simultaneous adsorption of multicomponent pharmaceuticals.
The Chinese Mandarin Version of the Esophageal-Atresia-Quality-of-Life Questionnaires for Children and Adolescents: Evaluation of Linguistic and Content Validity
Authors: Li Siqi , Dellenmark-Blom Michaela , Zhao Yong , Gu Yichao , Li Shuangshuang , Yang Shen , Quitmann Julia H. , Huang Jinshi
Published: November 2022

Background: After repair of esophageal atresia (EA), children risk digestive and respiratory morbidity, but knowledge of their health-related quality of life (HRQOL) in China is lacking. The EA-QOL questionnaires were developed in Sweden and Germany to evaluate condition-specific HRQOL in children with EA aged 2–7 and 8–17. This study aimed to evaluate the linguistic and content validity of the Chinese Mandarin version of the EA-QOL questionnaires. Methods: The procedure was conducted in compliance with international standards, including a forward-backward translation procedure, expert reviews, and cognitive debriefing interviews with 14 Chinese families of children with EA (parents of 8 children aged 2–7/6 children aged 8–17 and their parents). Results: Following forward-backward translation, minor issues were identified and solved. In interviews, all participants rated all EA-QOL items easy to understand, none expressed negative emotions about them and most described them comprehensive and relevant for EA. Leading from cognitive debriefing, three EA-QOL items in the questionnaire version for children aged 2–7 and three EA-QOL items in the questionnaire version for children aged 8–17 were modified in the Chinese language to improve cultural appropriateness and/or clarity. Conclusion: The Chinese Mandarin version of the EA-QOL questionnaires achieved satisfactory linguistic and content validity. This can help increase focus of HRQOL in research and clinical practice of children with EA in China.
The Relationship between Intolerance of Uncertainty and Problematic Social Media Use during the COVID-19 Pandemic: A Serial Mediation Model
Authors: Sun Chaoran , Li Yumei , Kwok Sylvia Y. C. L. , Mu Wenlong
Published: November 2022

The COVID-19 pandemic has brought significant interruptions to life certainty, and there has been a lack of research on the influence of uncertainty. The present research aimed to explore how intolerance of uncertainty, maladaptive coping strategies, and fear of missing out affect social media use in a Chinese community sample (N = 311) during the pandemic. Serial mediation analysis was applied, integrating the mediating role of maladaptive coping strategy and fear of missing out. Intolerance of uncertainty, maladaptive coping strategies, and fear of missing out was positively related to PSMU. Based on the mediation analysis, when age and gender were controlled, the direct effect of intolerance of uncertainty on PSMU was significant. The total indirect effect was also significant. The effect of intolerance of uncertainty on PSMU was mediated by maladaptive coping strategies and fear of missing out. Taken together, maladaptive coping strategies and fear of missing out played a serial mediating role between intolerance of uncertainty and PSMU. The findings imply that strategies to improve the tolerance of uncertainty, reduce fear of missing out, and relevant coping strategies could be potentially helpful in mitigating problematic social media use, especially during the COVID-19 pandemic.
Challenges and Actions of IAQ under COVID-19: A Survey of Taiwanese People’s Perception of Epidemic Prevention and Indoor Places Certification
Authors: Hu Chih-Pei , Cheng Jen-Hsiung
Published: November 2022

COVID-19 is still spreading around the world, and the pandemic has awakened the public’s attention to environmental cleanliness. This article used an online survey for people living in Taiwan, and a total of 1206 valid questionnaires were collected in October 2021. According to the survey results of Taiwanese people’s awareness of and needs for epidemic prevention and IAQ, 94.4% of the respondents agreed that maintaining IAQ during the COVID-19 pandemic is very important for prevention. In addition, 95.4% of them also pointed out that the “Clean and Safe” mark certification should be promoted in public places. Finally, this article also uses hierarchical regression to analyze public perceptions of seven indoor places, including elevators, restaurants, dwellings, offices, gyms, kindergartens, and long-term care centers. The results found that: (1) from the perspective of epidemic prevention, improving IAQ through ventilation strategies could prevent the spread of the COVID-19 pandemic, and (2) from the perspective of promotion certification, the elevators, restaurants and offices could establish strengthened IAQ, dwellings, gyms and long-term care centers should emphasize the display of IAQ information in entrances and exits, and kindergartens should focus on increasing safety and reducing infection.
Acute Effects of Sprint Interval Training and Chronic Effects of Polarized Training (Sprint Interval Training, High Intensity Interval Training, and Endurance Training) on Choice Reaction Time in Mountain Bike Cyclists
Authors: Hebisz Paulina , Cortis Cristina , Hebisz Rafal
Published: November 2022

This study evaluated the acute effects of sprint interval training and chronic effects of polarized training on choice reaction time in cyclists. Twenty-six mountain bike cyclists participated in the study and were divided into experimental (E) and control (C) groups. The cyclists trained for 9-weeks and performed five training sessions each week. Types of training sessions: (1) sprint interval training (SIT) which consisted of 8–16, 30 s repetitions at maximal intensity, (2) high-intensity interval training (HIIT) included 5 to 7, 5-min efforts at an intensity of 85–95% maximal aerobic power (Pmax), and (3) endurance training (ET) performed at an intensity of 55–60% Pmax, lasting 120–-180 min. In each week the cyclists performed: in group E a polarized training program, which included 2 × SIT, 1 × HIIT and 2 × ET, while in group C 2 × HIIT and 3 × ET. Before (acute effects) and after the 9-week training period (chronic effects) participants performed laboratory sprint interval testing protocol (SITP), which consisted of 12 maximal repetitions lasting 30 s. During SITP maximal and mean anaerobic power, as well as lactate ion concentration and blood pH were measured. Choice reaction time (RT) was measured 4-times: before and immediately after the SITP test—before and after the 9-week training period. Evaluated the average choice RT, minimal choice RT (shortest reaction), maximal choice RT (longest reaction), and the number of incorrect reactions. Before the training period as acute effects of SITP, it was observed: a shorter average choice RT (F = 13.61; p = 0.001; η2 = 0.362) and maximal choice RT (F = 4.71; p = 0.040; η2 = 0.164), and a decrease the number of incorrect reactions (F = 53.72; p = 0.000; η2 = 0.691), for E and C groups. After the 9-week training period, chronic effects showed that choice RT did not change in any of the cyclists’ groups. Only in the E group after the polarized training period, the number of incorrect reactions decreased (F = 49.03; p = 0.000; η2 = 0.671), average anaerobic power increased (F = 8.70; p = 0.007; η2 = 0.274) and blood pH decreased (F = 27.20; p = 0.000; η2 = 0.531), compared to the value before the training period. In conclusion, a shorter choice RT and a decrease in the number of incorrect reactions as acute effects of SITP, and a decrease in the number of incorrect reactions and higher average power as chronic effects of the polarized training program are beneficial for mountain bike cyclists.
Co-Benefits of Energy Structure Transformation and Pollution Control for Air Quality and Public Health until 2050 in Guangdong, China
Authors: Mo Haihua , Jiang Kejun , Wang Peng , Shao Min , Wang Xuemei
Published: November 2022

In order to mitigate global warming and improve air quality, the transformation of regional energy structures is the most important development pathway. China, as a major global consumer of fossil fuels, will face great pressure in this regard. Aiming toward achieving the global 2 °C warming target in China, this study takes one of the most developed regions of China, Guangdong Province, as the research area in order to explore a future development pathway and potential air quality attainment until 2050, by developing two energy structure scenarios (BAU_Energy and 2Deg_Energy) and three end-of-pipe scenarios (NFC, CLE, and MTFR), and simulating future air quality and related health impacts for the different scenarios using the WRF-Chem model. The results show that under the energy transformation scenario, total energy consumption in Guangdong rises from 296 Mtce (million tons of coal equivalent) in 2015 to 329 Mtce in 2050, with electricity and clean energy accounting for 45% and 35%. In 2050, the transformation of the energy structure leads to 64%, 75%, and 46% reductions in the emissions of CO2, NOx, and SO2 compared with those in 2015. Together with the most stringent end-of-pipe control measures, the emissions of VOCs and primary PM2.5 are effectively reduced by 66% and 78%. The annual average PM2.5 and MDA8 (daily maximum 8 h O3) concentrations in Guangdong are 33.8 and 85.9 μg/m3 in 2015, with 63.4 thousand premature deaths (95% CI: 57.1–70.8) due to environmental exposure. Under the baseline scenario, no improvement is gained in air quality or public health by 2050. In contrast, the PM2.5 and MDA8 concentrations decline to 21.7 and 75.5 μg/m3 under the scenario with energy structure transformation, and total premature deaths are reduced to 35.5 thousand (31.9–39.5). When further combined with the most stringent end-of-pipe control measures, the PM2.5 concentrations decrease to 16.5 μg/m3, but there is no significant improvement for ozone, with premature deaths declining to 20.6 thousand (18.5–23.0). This study demonstrates that the transformation of energy structure toward climate goals could be effective in mitigating air pollution in Guangdong and would bring significant health benefits. Compared with the end-of-pipe control policies, transformation of the energy structure is a more effective way to improve regional air quality in the long term, and synergistic promotion of both is crucial for regional development.
Correlations of Accelerometer-Measured Physical Activity with Body Image and Quality of Life among Young and Older Adults: A Pilot Study
Authors: Dana Amir , Ranjbari Sheida , Mosazadeh Hasan , Maliszewski Wojciech Jan , Błachnio Aleksandra
Published: November 2022

Significant evidence suggests that regular physical activity (PA) is correlated with numerous psychological benefits in adults such as improving body image and quality of life. However, this issue has not been differentiated between young and older adults. In addition, most previous studies used a self-reported questionnaire for measuring PA, the objectivity of which is limited in several ways. Hence, by using accelerometer technology for monitoring PA, this study was designed to examine the correlations of PA with body image and quality of life in young and older adults. In this cross-sectional study, we used objective actigraphy and survey data from 147 young and older adults, including 77 young and 70 older adults from Tehran, Iran. To examine our variables and hypothesis, the following instruments were implemented: the Persian version of the Multidimensional Body-Self Relations Questionnaire (MBSRQ), the Persian version of the Quality-of-Life Questionnaire (WHOQOL-BREF), and the ActiGraph wGT3X-BT for measuring PA. An independent t-test and a multivariate regression analysis were used to analyze the data. The weekly PA of both young and older adults was found to be lower than the recommended amount. Young adults engaged in significantly more weekly PA than older adults. For young adults, PA (including MPA, VPA, and MVPA) was generally found to be significantly correlated with body image and quality of life. For older adults, however, we found only significant correlations between VPA and quality of life. These findings indicated that PA is a critical concern in adults, particularly older adults. Accordingly, it is necessary to adopt appropriate strategies to promote an active lifestyle among adults.
Recent Progress in Research on Mechanisms of Action of Natural Products against Alzheimer’s Disease: Dietary Plant Polyphenols
Authors: Wang Yi , Wang Kaiyue , Yan Junyuan , Zhou Qian , Wang Xiaoying
Published: November 2022

Alzheimer’s disease (AD) is an incurable degenerative disease of the central nervous system and the most common type of dementia in the elderly. Despite years of extensive research efforts, our understanding of the etiology and pathogenesis of AD is still highly limited. Nevertheless, several hypotheses related to risk factors for AD have been proposed. Moreover, plant-derived dietary polyphenols were also shown to exert protective effects against neurodegenerative diseases such as AD. In this review, we summarize the regulatory effects of the most well-known plant-derived dietary polyphenols on several AD-related molecular mechanisms, such as amelioration of oxidative stress injury, inhibition of aberrant glial cell activation to alleviate neuroinflammation, inhibition of the generation and promotion of the clearance of toxic amyloid-β (Aβ) plaques, inhibition of cholinesterase enzyme activity, and increase in acetylcholine levels in the brain. We also discuss the issue of bioavailability and the potential for improvement in this regard. This review is expected to encourage further research on the role of natural dietary plant polyphenols in the treatment of AD.
Fission Yeast Rho1p-GEFs: From Polarity and Cell Wall Synthesis to Genome Stability
Authors: García Patricia , Celador Rubén , Pérez-Parrilla Jorge , Sánchez Yolanda
Published: November 2022

Rho1p is a membrane-associated protein that belongs to the Rho family of small GTPases. These proteins coordinate processes such as actin remodelling and polarised secretion to maintain the shape and homeostasis of yeast cells. In response to extracellular stimuli, Rho1p undergoes conformational switching between a guanosine triphosphate (GTP)-bound active state and a guanosine diphosphate (GDP)-bound inactive state. Cycling is improved with guanine nucleotide exchange factor (GEF) activity necessary to activate signalling and GTPase activating protein (GAP) activity required for subsequent signal depletion. This review focuses on fission yeast Rho1p GEFs, Rgf1p, Rgf2p, and Rgf3p that belong to the family of DH-PH domain-containing Dbl-related GEFs. They are multi-domain proteins that detect biological signals that induce or inhibit their catalytic activity over Rho1p. Each of them activates Rho1p in different places and times. Rgf1p acts preferentially during polarised growth. Rgf2p is required for sporulation, and Rgf3p plays an essential function in septum synthesis. In addition, we outline the noncanonical roles of Rho1p-GEFs in genomic instability.
Zona Pellucida like Domain Protein 1 (ZPLD1) Polymerization Is Regulated by Two Distinguished Hydrophobic Motifs
Authors: Knepper Marie Isabell , Dernedde Jens
Published: November 2022

Zona Pellucida Like Domain 1 Protein (ZPLD1) is a main component of the cupula, a gelatinous structure located in the labyrinth organ of the inner ear and involved in vestibular function. The N-glycosylated protein is likely able to organize high-molecular-weight polymers via its zona pellucida (ZP) module, which is common for many extracellular proteins that self-assemble into matrices. In this work, we confirmed that ZPLD1 can form multimers while setting up a cellular model leveraging Madin–Darby canine kidney (MDCK) cells to study protein polymerization. We identified two motifs within ZPLD1 which regulate its polymerization and follow previously published conserved regions, identified across ZP proteins. Mutational depletion of either one of these modules led to diminished or abnormal polymer formation outside of the cells, likely due to altered processing at the plasma membrane. Further, intracellular polymer formation was observed. Proteolytic cleavage during secretion, separating the regulatory motif located distinct of the ZP module from the mature monomer, seems to be necessary to enable polymerization. While the molecular interactions of the identified motifs remain to be proven, our findings suggest that ZPLD1 is a polymer forming ZP protein following an orchestrated mechanism of protein polymerization to finally build up a gelatinous hydrogel.
The Renin–Angiotensin-Aldosterone System, Nitric Oxide, and Hydrogen Sulfide at the Crossroads of Hypertension and COVID-19: Racial Disparities and Outcomes
Authors: Ranjbar Tara , Oza Palak P. , Kashfi Khosrow
Published: November 2022

Coronavirus disease 2019 is caused by SARS-CoV-2 and is more severe in the elderly, racial minorities, and those with comorbidities such as hypertension and diabetes. These pathologies are often controlled with medications involving the renin–angiotensin–aldosterone system (RAAS). RAAS is an endocrine system involved in maintaining blood pressure and blood volume through components of the system. SARS-CoV-2 enters the cells through ACE2, a membrane-bound protein related to RAAS. Therefore, the use of RAAS inhibitors could worsen the severity of COVID-19’s symptoms, especially amongst those with pre-existing comorbidities. Although a vaccine is currently available to prevent and reduce the symptom severity of COVID-19, other options, such as nitric oxide and hydrogen sulfide, may also have utility to prevent and treat this virus.
Indirect Immobilised Jagged-1 Enhances Matrisome Proteins Associated with Osteogenic Differentiation of Human Dental Pulp Stem Cells: A Proteomic Study
Authors: Chansaenroj Ajjima , Kornsuthisopon Chatvadee , Roytrakul Sittiruk , Phothichailert Suphalak , Rochanavibhata Sunisa , Fournier Benjamin P. J. , Srithanyarat Supreda Suphanantachat , Nowwarote Nunthawan , Osathanon Thanaphum
Published: November 2022

The indirect immobilisation of Jagged-1 (Jagged-1) promoted osteogenic differentiation of human dental pulp cells (hDPs). Furthermore, the analysis of the Reactome pathway of RNA sequencing data indicates the upregulated genes involved with the extracellular matrix (ECM). Hence, our objective was to investigate the effects of Jagged-1 on proteomic profiles of human dental pulp stem cells (hDPSC). hDPSCs were cultured on the surface coated with human IgG Fc fragment (hFc) and the surface coated with rhJagged1/Fc recombinant protein-coated surface. Cells were differentiated to the osteogenic lineage using an osteogenic differentiation medium (OM) for 14 days, and cells cultured in a growth medium were used as a control. The protein component of the cultured cells was extracted into the cytosol, membrane, nucleus, and cytoskeletal compartment. Subsequently, the proteomic analysis was performed using liquid chromatography–tandem mass spectrometry (LC-MS). Metascape gene list analysis reported that Jagged-1 stimulated the expression of the membrane trafficking protein (DOP1B), which can indirectly improve osteogenic differentiation. hDPSCs cultured on Jagged-1 surface under OM condition expressed COL27A1, MXRA5, COL7A1, and MMP16, which played an important role in osteogenic differentiation. Furthermore, common matrisome proteins of all cellular components were related to osteogenesis/osteogenic differentiation. Additionally, the gene ontology categorised by the biological process of cytosol, membrane, and cytoskeleton compartments was associated with the biomineralisation process. The gene ontology of different culture conditions in each cellular component showed several unique gene ontologies. Remarkably, the Jagged-1_OM culture condition showed the biological process related to odontogenesis in the membrane compartment. In conclusion, the Jagged-1 induces osteogenic differentiation could, mainly through the regulation of protein in the membrane compartment.
Detergent-Assisted Protein Digestion—On the Way to Avoid the Key Bottleneck of Shotgun Bottom-Up Proteomics
Authors: Danko Katerina , Lukasheva Elena , Zhukov Vladimir A. , Zgoda Viktor , Frolov Andrej
Published: November 2022

Gel-free bottom-up shotgun proteomics is the principal methodological platform for the state-of-the-art proteome research. This methodology assumes quantitative isolation of the total protein fraction from a complex biological sample, its limited proteolysis with site-specific proteases, analysis of the resulted peptides with nanoscaled reversed-phase high-performance liquid chromatography-(tandem) mass spectrometry (nanoRP-HPLC-MS and MS/MS), protein identification by sequence database search and peptide-based quantitative analysis. The most critical steps of this workflow are protein reconstitution and digestion; therefore, detergents and chaotropic agents are strongly mandatory to ensure complete solubilization of complex protein isolates and to achieve accessibility of all protease cleavage sites. However, detergents are incompatible with both RP separation and electrospray ionization (ESI). Therefore, to make LC-MS analysis possible, several strategies were implemented in the shotgun proteomics workflow. These techniques rely either on enzymatic digestion in centrifugal filters with subsequent evacuation of the detergent, or employment of MS-compatible surfactants, which can be degraded upon the digestion. In this review we comprehensively address all currently available strategies for the detergent-assisted proteolysis in respect of their relative efficiency when applied to different biological matrices. We critically discuss the current progress and the further perspectives of these technologies in the context of its advances and gaps.
Effects of Piptoporus betulinus Ethanolic Extract on the Proliferation and Viability of Melanoma Cells and Models of Their Cell Membranes
Authors: Bożek Justyna , Tomala Joanna , Wójcik Sylwia , Kamińska Beata , Brand Izabella , Pocheć Ewa , Szostak Elżbieta
Published: November 2022

Piptoporus betulinus is a fungus known for its medicinal properties. It possesses antimicrobial, anti-inflammatory, and anti-cancer activity. In this study, several tests were performed to evaluate the cytotoxic effect of the ethanolic extract of Piptoporus betulinus on two melanoma human cell lines, WM115 primary and A375 metastatic cell lines, as well as Hs27 human skin fibroblasts. The extract proved to affect cancer cells in a dose-dependent manner, and at the same time showed a low cytotoxicity towards the normal cells. The total phenolic content (TPC) was determined spectrophotometrically by the Folin-Ciocalteu method (F-C), and the potential antioxidant activity was measured by ferric-reducing antioxidant power (FRAP) assay. One of the active compounds in the extract is betulin. It was isolated and then its cytotoxic activity was compared to the results obtained from the Piptoporus betulinus extract. To further understand the mechanism of action of the extract’s anticancer activity, tests on model cell membranes were conducted. A model membrane of a melanoma cell was designed and consisted of 1,2-dimyristoyl-sn-glycero-3-phosphocholine, disialoganglioside-GD1a and cholesterol: DMPC:GD1a:chol (5:2:3 mole ratio). Changes in a Langmuir monolayer were observed and described based on Π-Amol isotherm and compressibility modulus changes. LB lipid bilayers were deposited on a hydrophilic gold substrate and analyzed by IR and X-ray photoelectron spectroscopy. Our study provides new data on the effect of Piptoporus betulinus extract on melanoma cells and its impact on the model of melanoma plasma membranes.
Effect of Quercetin and Fingolimod, Alone or in Combination, on the Sphingolipid Metabolism in HepG2 Cells
Authors: Momchilova Albena , Nikolaev Georgi , Pankov Stefan , Vassileva Evgenia , Krastev Nikolai , Robev Bozhil , Krastev Dimo , Pinkas Adriana , Pankov Roumen
Published: November 2022

Combinations of anti-cancer drugs can overcome resistance to therapy and provide new more effective treatments. In this work we have analyzed the effect of the polyphenol quercetin and the anti-cancer sphingosine analog fingolimod on the sphingolipid metabolism in HepG2 cells, since sphingolipids are recognized as mediators of cell proliferation and apoptosis in cancer cells. Treatment of hepatocellular carcinoma HepG2 cells with quercetin and fingolimod, alone or in combination, induced different degrees of sphingomyelin (SM) reduction and a corresponding activation of neutral sphingomyelinase (nSMase). Western blot analysis showed that only treatments containing quercetin induced up-regulation of nSMase expression. The same treatment caused elevation of ceramide (CER) levels, whereas the observed alterations in sphingosine (SPH) content were not statistically significant. The two tested drugs induced a reduction of the pro-proliferative sphingolipid, sphingosine 1 phosphate (S1P), in the following order: quercetin, fingolimod, quercetin + fingolimod. The activity of the enzyme responsible for CER hydrolysis, alkaline ceramidase (ALCER) was down-regulated only in the incubations involving quercetin and fingolimod did not affect this activity. The enzyme, maintaining the balance between apoptosis and proliferation, sphingosine kinase 1 (SK1), was down-regulated by incubations in the following order: quercetin, fingolimod, quercetin + fingolimod. Western blot analysis showed down-regulation in SK1 expression upon quercetin but not upon fingolimod treatment. Studies on the effect of quercetin and fingolimod on the two proteins associated with apoptotic events, AKT and Bcl-2, showed that only quercetin, alone or in combination, down-regulated the activity of the two proteins. The reported observations provide information which can be useful in the search of novel anti-tumor approaches, aiming at optimization of the therapeutic effect and maximal preservation of healthy tissues.
The Intersection of Human and Veterinary Medicine—A Possible Direction towards the Improvement of Cell Therapy Protocols in the Treatment of Perianal Fistulas
Authors: Burdzinska Anna , Galanty Marek , Więcek Sabina , Dabrowski Filip A. , Lotfy Ahmed , Sadkowski Tomasz
Published: November 2022

The effective treatment of perianal fistulizing Crohn’s disease is still a challenge. Local administration of mesenchymal stromal cells (MSCs) is becoming a part of accepted treatment options. However, as a fledgling technique, it still can be optimized. A new trend in translational research, which is in line with “One Health” approach, bases on exploiting parallels between naturally occurring diseases affecting humans and companion animals. Canine anal furunculosis (AF) has been indicated as condition analogous to human perianal Crohn’s disease (pCD). This narrative review provides the first comprehensive comparative analysis of these two diseases based on the published data. The paper also outlines the molecular mechanisms of action of MSCs which are likely to have a role in modulating the perianal fistula niche in humans, and refers them to the current knowledge on the immunomodulatory properties of canine MSCs. Generally, the pathogenesis of both diseases shares main determinants such as the presence of genetic predispositions, dysregulation of immune response and the relation to intestine microbiota. However, we also identified many aspects which should be further specified, such as determining the frequency of true fistulas formation in AF patients, elucidating the role of TNF and Th17 pathway in the pathogenesis of AF, or clarifying the role of epithelial-to-mesenchymal transition phenomenon in the formation of canine fistulae. Nevertheless, the available data support the hypothesis that the results from testing cell therapies in dogs with anal furunculosis have a significant translational value in optimizing MSC transplants procedures in pCD patients.
DRPreter: Interpretable Anticancer Drug Response Prediction Using Knowledge-Guided Graph Neural Networks and Transformer
Authors: Shin Jihye , Piao Yinhua , Bang Dongmin , Kim Sun , Jo Kyuri
Published: November 2022

Some of the recent studies on drug sensitivity prediction have applied graph neural networks to leverage prior knowledge on the drug structure or gene network, and other studies have focused on the interpretability of the model to delineate the mechanism governing the drug response. However, it is crucial to make a prediction model that is both knowledge-guided and interpretable, so that the prediction accuracy is improved and practical use of the model can be enhanced. We propose an interpretable model called DRPreter (drug response predictor and interpreter) that predicts the anticancer drug response. DRPreter learns cell line and drug information with graph neural networks; the cell-line graph is further divided into multiple subgraphs with domain knowledge on biological pathways. A type-aware transformer in DRPreter helps detect relationships between pathways and a drug, highlighting important pathways that are involved in the drug response. Extensive experiments on the GDSC (Genomics of Drug Sensitivity and Cancer) dataset demonstrate that the proposed method outperforms state-of-the-art graph-based models for drug response prediction. In addition, DRPreter detected putative key genes and pathways for specific drug–cell-line pairs with supporting evidence in the literature, implying that our model can help interpret the mechanism of action of the drug.
Biochemical Targets and Molecular Mechanism of Ginsenoside Compound K in Treating Osteoporosis Based on Network Pharmacology
Authors: Zhang Sen , Shen Shihong , Ma Pei , Fan Daidi
Published: November 2022

To investigate the potential of ginsenosides in treating osteoporosis, ginsenoside compound K (GCK) was selected to explore the potential targets and mechanism based on network pharmacology (NP). Based on text mining from public databases, 206 and 6590 targets were obtained for GCK and osteoporosis, respectively, in which 138 targets were identified as co-targets of GCK and osteoporosis using intersection analysis. Five central gene clusters and key genes (STAT3, PIK3R1, VEGFA, JAK2 and MAP2K1) were identified based on Molecular Complex Detection (MCODE) analysis through constructing a protein–protein interaction network using the STRING database. Gene Ontology (GO) analysis implied that phosphatidylinositol-related biological process, molecular modification and function may play an important role for GCK in the treatment of osteoporosis. Function and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that the c-Fms-mediated osteoclast differentiation pathway was one of the most important mechanisms for GCK in treating osteoporosis. Meanwhile, except for being identified as key targets based on cytoHubba analysis using Cytoscape software, MAPK and PI3K-related proteins were enriched in the downstream of the c-Fms-mediated osteoclast differentiation pathway. Molecular docking further confirmed that GCK could interact with the cavity on the surface of a c-Fms protein with the lowest binding energy (−8.27 Kcal/moL), and their complex was stabilized by hydrogen bonds (Thr578 (1.97 Å), Leu588 (2.02 Å, 2.18 Å), Ala590 (2.16 Å, 2.84 Å) and Cys 666 (1.93 Å)), van der Waals and alkyl hydrophobic interactions. Summarily, GCK could interfere with the occurrence and progress of osteoporosis through the c-Fms-mediated MAPK and PI3K signaling axis regulating osteoclast differentiation.
Predicting Dihydropyrimidine Dehydrogenase Deficiency and Related 5-Fluorouracil Toxicity: Opportunities and Challenges of DPYD Exon Sequencing and the Role of Phenotyping Assays
Authors: De Luca Ottavia , Salerno Gerardo , De Bernardini Donatella , Torre Maria Simona , Simmaco Maurizio , Lionetto Luana , Gentile Giovanna , Borro Marina
Published: November 2022

Deficiency of dihydropyrimidine dehydrogenase (DPD), encoded by the DPYD gene, is associated with severe toxicity induced by the anti-cancer drug 5-Fluorouracil (5-FU). DPYD genotyping of four recommended polymorphisms is widely used to predict toxicity, yet their prediction power is limited. Increasing availability of next generation sequencing (NGS) will allow us to screen rare variants, predicting a larger fraction of DPD deficiencies. Genotype–phenotype correlations were investigated by performing DPYD exon sequencing in 94 patients assessed for DPD deficiency by the 5-FU degradation rate (5-FUDR) assay. Association of common variants with 5-FUDR was analyzed with the SNPStats software. Functional interpretation of rare variants was performed by in-silico analysis (using the HSF system and PredictSNP) and literature review. A total of 23 rare variants and 8 common variants were detected. Among common variants, a significant association was found between homozygosity for the rs72728438 (c.1974+75A>G) and decreased 5-FUDR. Haplotype analysis did not detect significant associations with 5-FUDR. Overall, in our sample cohort, NGS exon sequencing allowed us to explain 42.5% of the total DPD deficiencies. NGS sharply improves prediction of DPD deficiencies, yet a broader collection of genotype–phenotype association data is needed to enable the clinical use of sequencing data.
Destruction of Lysozyme Amyloid Fibrils Induced by Magnetoferritin and Reconstructed Ferritin
Authors: Gombos Jan , Balejcikova Lucia , Kopcansky Peter , Batkova Marianna , Siposova Katarina , Kovac Jozef , Zolochevska Kristina , Safarik Ivo , Lokajova Alica , Garamus Vasil , Dobrota Dusan , Strbak Oliver
Published: November 2022

Neurodegenerative disorders, including Alzheimer’s disease (AD), Parkinson’s disease (PD), or systemic amyloidosis, are characterized by the specific protein transformation from the native state to stable insoluble deposits, e.g., amyloid plaques. The design of potential therapeutic agents and drugs focuses on the destabilization of the bonds in their beta-rich structures. Surprisingly, ferritin derivatives have recently been proposed to destabilize fibril structures. Using atomic force microscopy (AFM) and fluorescence spectrophotometry, we confirmed the destructive effect of reconstructed ferritin (RF) and magnetoferritin (MF) on lysosome amyloid fibrils (LAF). The presence of iron was shown to be the main factor responsible for the destruction of LAF. Moreover, we found that the interaction of RF and MF with LAF caused a significant increase in the release of potentially harmful ferrous ions. Zeta potential and UV spectroscopic measurements of LAF and ferritin derivative mixtures revealed a considerable difference in RF compared to MF. Our results contribute to a better understanding of the mechanism of fibril destabilization by ferritin-like proteins. From this point of view, ferritin derivatives seem to have a dual effect: therapeutic (fibril destruction) and adverse (oxidative stress initiated by increased Fe2+ release). Thus, ferritins may play a significant role in various future biomedical applications.
On the TPPP Protein of the Enigmatic Fungus, Olpidium—Correlation between the Incidence of p25alpha Domain and That of the Eukaryotic Flagellum
Authors: Orosz Ferenc
Published: November 2022

Loss of the flagellum was an important step in the evolution of fungi. The flagellated fungi of the phylum Olpidiomycota are the closest relative of the non-flagellated terrestrial fungi. There are genes encoding proteins, the occurrence of which shows a strong correlation with the incidence of the flagellum. One of these gene/protein families is “TPPP-like proteins” whose main feature is the presence of the p25alpha domain. The functional link between TPPP and flagellum has also been shown. Most of the phyla of flagellated fungi have been known to contain TPPP-like proteins but Olpidiomycota was an exception. This study demonstrates that Olpidium bornovanus, similarly to some fungi of Chytridiomycota and Blastocladiomycota, has a “fungal-type” TPPP characterized by the presence of two (a complete and an incomplete) p25alpha domains.
Regulation of Metastatic Tumor Dormancy and Emerging Opportunities for Therapeutic Intervention
Authors: Tamamouna Vasilia , Pavlou Evangelia , Neophytou Christiana M. , Papageorgis Panagiotis , Costeas Paul
Published: November 2022

Cancer recurrence and metastasis, following successful treatment, constitutes a critical threat in clinical oncology and are the leading causes of death amongst cancer patients. This phenomenon is largely attributed to metastatic tumor dormancy, a rate-limiting stage during cancer progression, in which disseminated cancer cells remain in a viable, yet not proliferating state for a prolonged period. Dormant cancer cells are characterized by their entry into cell cycle arrest and survival in a quiescence state to adapt to their new microenvironment through the acquisition of mutations and epigenetic modifications, rendering them resistant to anti-cancer treatment and immune surveillance. Under favorable conditions, disseminated dormant tumor cells ‘re-awake’, resume their proliferation and thus colonize distant sites. Due to their rarity, detection of dormant cells using current diagnostic tools is challenging and, thus, therapeutic targets are hard to be identified. Therefore, unraveling the underlying mechanisms required for keeping disseminating tumor cells dormant, along with signals that stimulate their “re-awakening” are crucial for the discovery of novel pharmacological treatments. In this review, we shed light into the main mechanisms that control dormancy induction and escape as well as emerging therapeutic strategies for the eradication of metastatic dormant cells, including dormancy maintenance, direct targeting of dormant cells and re-awakening dormant cells. Studies on the ability of the metastatic cancer cells to cease proliferation and survive in a quiescent state before re-initiating proliferation and colonization years after successful treatment, will pave the way toward developing innovative therapeutic strategies against dormancy-mediated metastatic outgrowth.
Maternal Distress during Pregnancy and the Postpartum Period: Underlying Mechanisms and Child’s Developmental Outcomes—A Narrative Review
Authors: Jeličić Ljiljana , Veselinović Aleksandra , Ćirović Milica , Jakovljević Vladimir , Raičević Saša , Subotić Miško
Published: November 2022

Maternal mental health may be considered a determining factor influencing fetal and child development. An essential factor with potentially negative consequences for a child’s psychophysiological development is the presence of maternal distress during pregnancy and the postpartum period. The review is organized and presented to explore and describe the effects of anxiety, stress, and depression in pregnancy and the postpartum period on adverse child developmental outcomes. The neurobiology of maternal distress and the transmission mechanisms at the molecular level to the fetus and child are noted. In addition, the paper discusses the findings of longitudinal studies in which early child development is monitored concerning the presence of maternal distress in pregnancy and the postpartum period. This topic gained importance in the COVID-19 pandemic context, during which a higher frequency of maternal psychological disorders was observed. The need for further interdisciplinary research on the relationship between maternal mental health and fetal/child development was highlighted, especially on the biological mechanisms underlying the transmission of maternal distress to the (unborn) child, to achieve positive developmental outcomes and improve maternal and child well-being.
Mitochondrial Fatty Acid β-Oxidation Disorders: From Disease to Lipidomic Studies—A Critical Review
Authors: Guerra Inês M. S. , Ferreira Helena B. , Melo Tânia , Rocha Hugo , Moreira Sónia , Diogo Luísa , Domingues Maria Rosário , Moreira Ana S. P.
Published: November 2022

Fatty acid oxidation disorders (FAODs) are inborn errors of metabolism (IEMs) caused by defects in the fatty acid (FA) mitochondrial β-oxidation. The most common FAODs are characterized by the accumulation of medium-chain FAs and long-chain (3-hydroxy) FAs (and their carnitine derivatives), respectively. These deregulations are associated with lipotoxicity which affects several organs and potentially leads to life-threatening complications and comorbidities. Changes in the lipidome have been associated with several diseases, including some IEMs. In FAODs, the alteration of acylcarnitines (CARs) and FA profiles have been reported in patients and animal models, but changes in polar and neutral lipid profile are still scarcely studied. In this review, we present the main findings on FA and CAR profile changes associated with FAOD pathogenesis, their correlation with oxidative damage, and the consequent disturbance of mitochondrial homeostasis. Moreover, alterations in polar and neutral lipid classes and lipid species identified so far and their possible role in FAODs are discussed. We highlight the need of mass-spectrometry-based lipidomic studies to understand (epi)lipidome remodelling in FAODs, thus allowing to elucidate the pathophysiology and the identification of possible biomarkers for disease prognosis and an evaluation of therapeutic efficacy.