bluuebunny/crossref_metadata_2025 huggingface dataset:
Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia
Authors: Senn Savanah , Pangell Kelly , Bowerman Adrianna L.
Published: January 2022

The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10−5), Bradyhizobium (p = 1 × 10−8), and Paenibacillus (p = 1.46 × 10−6). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10−3) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.
Caregiver Burden and Quality of Life in Late Stage Parkinson’s Disease
Authors: Rosqvist Kristina , Schrag Anette , Odin Per ,   the CLaSP Consortium
Published: January 2022

Parkinson’s disease (PD) is a chronic, progressive, neurodegenerative disease involving both motor and non-motor symptoms (NMS). In the late stage of the disease, Hoehn and Yahr (HY) stages IV-V, the symptomatology is often severe and patients become increasingly dependent on help in their daily life, resulting in an increased burden for the informal caregivers. To assess the implications of the caregiver burden, caregiver quality of life (QoL) was assessed in 74 informal caregivers to patients in late stage PD, by the Alzheimer’s Patient Partners Life Impact Questionnaire (APPLIQue), which has been found useful also in PD. The majority of caregivers were the spouse/partner. Individual items provided information on which aspects of caregiver burden were the most common, i.e., items: “feel guilty if not there” (71% affirmed), “situation wears me down” (65% affirmed) and “always on my mind” (61% affirmed). In simple linear regression analyses, female patient gender (p = 0.007), better cognition (p = 0.004), lower NMS burden (p = 0.012) and not being the partner (p = 0.022) were associated with better caregiver QoL. Multivariable linear regression analyses identified better cognition (p = 0.004) and female patient gender (p = 0.035) as independently associated with better informal caregiver QoL. Identifying and treating NMS as well as recognizing and alleviating caregiver burden seem essential to enhance QoL for both patients and caregivers in late stage PD.
Therapeutic Effects of a Newly Developed 3D Magnetic Finger Rehabilitation Device in Subacute Stroke Patients: A Pilot Study
Authors: Kim Sung-Hoon , Ji Dong-Min , Kim Chan-Yong , Choi Sung-Bok , Joo Min-Cheol , Kim Min-Su
Published: January 2022

We developed a magnetic-force-based three-dimensional (3D) rehabilitation device that can perform motor rehabilitation treatment for paralyzed fingers, regardless of upper extremity movement and position, and investigated the therapeutic effects of the device. An end-effector type rehabilitation device that can generate magnetic fields in three directions was developed using electromagnets and permanent magnetics. A double-blinded randomized controlled pilot study was conducted with a total of 12 patients. The intervention group had rehabilitation treatment using the developed magnetic finger rehabilitation device for 30 min a day for four weeks. The control group underwent exercise rehabilitation treatment. The control group received conventional occupational therapy on the upper limbs, including hands, from an occupational therapist, for the same amount of time. Adverse effects were monitored, and the patient’s sensory or proprioceptive deficits were examined before the intervention. No participants reported safety concerns while the intervention was conducted. The Wolf Motor Function Test (WMFT) scores were significantly improved in the intervention group (from 13.4 ± 3.6 to 20.9 ± 4.0 points) compared to the control group (from 13.1 ± 4.0 to 15.2 ± 3.8 points) (p = 0.016). The patients in the intervention group (from 88 ± 12 to 67 ± 13 s) showed greater improvement of WMFT times compared to the control group (from 89 ± 10 to 73 ± 11 s) (p = 0.042). The Manual Function Test and the upper limb score of the Fugl-Meyer Assessment were significantly improved in the intervention group compared with the control group (p = 0.038 and p = 0.042). The patients in the intervention group also showed significantly greater enhancement of the Korean version of the modified Barthel Index than the control group (p = 0.042). Rehabilitation treatment using the 3D magnetic-force-driven finger rehabilitation device helped improve finger motor function and activities of daily living in subacute stroke patients.
Validating EEG, MEG and Combined MEG and EEG Beamforming for an Estimation of the Epileptogenic Zone in Focal Cortical Dysplasia
Authors: Neugebauer Frank , Antonakakis Marios , Unnwongse Kanjana , Parpaley Yaroslav , Wellmer Jörg , Rampp Stefan , Wolters Carsten H.
Published: January 2022

MEG and EEG source analysis is frequently used for the presurgical evaluation of pharmacoresistant epilepsy patients. The source localization of the epileptogenic zone depends, among other aspects, on the selected inverse and forward approaches and their respective parameter choices. In this validation study, we compare the standard dipole scanning method with two beamformer approaches for the inverse problem, and we investigate the influence of the covariance estimation method and the strength of regularization on the localization performance for EEG, MEG, and combined EEG and MEG. For forward modelling, we investigate the difference between calibrated six-compartment and standard three-compartment head modelling. In a retrospective study, two patients with focal epilepsy due to focal cortical dysplasia type IIb and seizure freedom following lesionectomy or radiofrequency-guided thermocoagulation (RFTC) used the distance of the localization of interictal epileptic spikes to the resection cavity resp. RFTC lesion as reference for good localization. We found that beamformer localization can be sensitive to the choice of the regularization parameter, which has to be individually optimized. Estimation of the covariance matrix with averaged spike data yielded more robust results across the modalities. MEG was the dominant modality and provided a good localization in one case, while it was EEG for the other. When combining the modalities, the good results of the dominant modality were mostly not spoiled by the weaker modality. For appropriate regularization parameter choices, the beamformer localized better than the standard dipole scan. Compared to the importance of an appropriate regularization, the sensitivity of the localization to the head modelling was smaller, due to similar skull conductivity modelling and the fixed source space without orientation constraint.
An AI/ML-Based Strategy for Disaster Response and Evacuation of Victims in Aged Care Facilities in the Hawkesbury-Nepean Valley: A Perspective
Authors: Munawar Hafiz Suliman , Mojtahedi Mohammad , Hammad Ahmed W. A. , Ostwald Michael J. , Waller S. Travis
Published: January 2022

The Hawkesbury-Nepean Valley, Australia’s longest coastal catchment, is spanned by a river system of more than 470 km, that runs from Goulburn to Broken Bay, covering a total area of over 2.2 million hectares. This region has remained prone to flood events, with considerable mortalities, economic impacts and infrastructural losses occurring quite regularly. The topography, naturally variable climatic conditions and the ‘bathtub’ effect in the region are responsible for the frequent flood events. In response, the Government at the national/federal, state and local level has focused on the design of efficient flood risk management strategies with appropriate evacuation plans for vulnerable communities from hospitals, schools, childcare and aged care facilities during a flood event. Despite these overarching plans, specialized response and evacuation plans for aged care facilities are critical to reducing the loss incurred by flood events in the region. This is the focus of this present paper, which reviews the history of flood events and responses to them, before examining the utilization of artificial intelligence (AI) techniques during flood events to overcome the flood risks. An early flood warning system, based on AI/Machine Learning (ML) strategy is being suggested for a timely decision, enhanced disaster prediction, assessment and response necessary to overcome the flood risks associated with aged care facilities within the Hawkesbury-Nepean region. A framework entailing AI/ML methods for identifying the safest route to the destination using UAV and path planning has been proposed for timely disaster response and evacuation of the residents of aged care facilities.
Therapeutic Potential of Naturally Occurring Small Molecules to Target the Wnt/β-Catenin Signaling Pathway in Colorectal Cancer
Authors: Oliveira Luiz F. S. , Predes Danilo , Borges Helena L. , Abreu Jose G.
Published: January 2022

Colorectal cancer (CRC) ranks second in the number of cancer deaths worldwide, mainly due to late diagnoses, which restrict treatment in the potentially curable stages and decrease patient survival. The treatment of CRC involves surgery to remove the tumor tissue, in addition to radiotherapy and systemic chemotherapy sessions. However, almost half of patients are resistant to these treatments, especially in metastatic cases, where the 5-year survival rate is only 12%. This factor may be related to the intratumoral heterogeneity, tumor microenvironment (TME), and the presence of cancer stem cells (CSCs), which is impossible to resolve with the standard approaches currently available in clinical practice. CSCs are APC-deficient, and the search for alternative therapeutic agents such as small molecules from natural sources is a promising strategy, as these substances have several antitumor properties. Many of those interfere with the regulation of signaling pathways at the central core of CRC development, such as the Wnt/β-catenin, which plays a crucial role in the cell proliferation and stemness in the tumor. This review will discuss the use of naturally occurring small molecules inhibiting the Wnt/β-catenin pathway in experimental CRC models over the past decade, highlighting the molecular targets in the Wnt/β-catenin pathway and the mechanisms through which these molecules perform their antitumor activities.
The Role of the Extracellular Matrix and Tumor-Infiltrating Immune Cells in the Prognostication of High-Grade Serous Ovarian Cancer
Authors: Belotti Yuri , Lim Elaine , Lim Chwee
Published: January 2022

Ovarian cancer is the eighth global leading cause of cancer-related death among women. The most common form is the high-grade serous ovarian carcinoma (HGSOC). No further improvements in the 5-year overall survival have been seen over the last 40 years since the adoption of platinum- and taxane-based chemotherapy. Hence, a better understanding of the mechanisms governing this aggressive phenotype would help identify better therapeutic strategies. Recent research linked onset, progression, and response to treatment with dysregulated components of the tumor microenvironment (TME) in many types of cancer. In this study, using bioinformatic approaches, we identified a 19-gene TME-related HGSOC prognostic genetic panel (PLXNB2, HMCN2, NDNF, NTN1, TGFBI, CHAD, CLEC5A, PLXNA1, CST9, LOXL4, MMP17, PI3, PRSS1, SERPINA10, TLL1, CBLN2, IL26, NRG4, and WNT9A) by assessing the RNA sequencing data of 342 tumors available in the TCGA database. Using machine learning, we found that specific patterns of infiltrating immune cells characterized each risk group. Furthermore, we demonstrated the predictive potential of our risk score across different platforms and its improved prognostic performance compared with other gene panels.
High-Sensitive TRBC1-Based Flow Cytometric Assessment of T-Cell Clonality in Tαβ-Large Granular Lymphocytic Leukemia
Authors: Muñoz-García Noemí , Morán-Plata F. , Villamor Neus , Lima Margarida , Barrena Susana , Mateos Sheila , Caldas Carolina , van Dongen Jacques , Orfao Alberto , Almeida Julia
Published: January 2022

Flow cytometric (FCM) analysis of the constant region 1 of the T-cell receptor β chain (TRBC1) expression for assessing Tαβ-cell clonality has been recently validated. However, its utility for the diagnosis of clonality of T-large granular lymphocytic leukemia (T-LGLL) needs to be confirmed, since more mature Tαβ cells (i.e., T-LGL normal-counterpart) show broader TRBC1+/TRBC1− ratios vs. total Tαβ cells. We compared the distribution and absolute counts of TRBC1+ and TRBC1− Tαβ-LGL in blood containing polyclonal (n = 25) vs. clonal (n = 29) LGL. Overall, polyclonal TRBC1+ or TRBC1− Tαβ-LGL ranged between 0.36 and 571 cells/μL (3.2–91% TRBC1+ cells), whereas the clonal LGL cases showed between 51 and 11,678 cells/μL (<0.9% or >96% TRBC1+ cells). Among the distinct TCRVβ families, the CD28− effector-memory and terminal-effector polyclonal Tαβ cells ranged between 0 and 25 TRBC1+ or TRBC1− cells/μL and between 0 and 100% TRBC1+ cells, while clonal LGL ranged between 32 and 5515 TRBC1+ or TRBC1− cells/μL, representing <1.6% or >98% TRBC1+ cells. Our data support the utility of the TRBC1-FCM assay for detecting T-cell clonality in expansions of Tαβ-LGL suspected of T-LGLL based on altered percentages of TRBC1+ Tαβ cells. However, in the absence of lymphocytosis or in the case of TαβCD4-LGL expansion, the detection of increased absolute cell counts by the TRBC1-FCM assay for more accurately defined subpopulations of Tαβ-LGL-expressing individual TCRVβ families, allows the detection of T-cell clonality, even in the absence of phenotypic aberrations.
The Effect of Fatty Acids on Ciprofloxacin Cytotoxic Activity in Prostate Cancer Cell Lines—Does Lipid Component Enhance Anticancer Ciprofloxacin Potential?
Authors: Chrzanowska Alicja , Olejarz Wioletta , Kubiak-Tomaszewska Grażyna , Ciechanowicz Andrzej K. , Struga Marta
Published: January 2022

Purpose: To assess cytotoxic effect of ciprofloxacin conjugates with fatty acids on prostate cancer cells (LNCaP and DU-145) with different hormone sensitivity, based on previous promising results from the PC3 cells. Methods: Cytotoxicity were estimated using MTT and LDH tests, whereas its mechanisms were estimated by apoptosis and IL-6 assays. The intensity of proteins involved in lipid metabolism was determined using ML-CS assay. Results: The hormone insensitive DU-145 cells were more vulnerable than the hormone sensitive LNCaP cells. The IC50 values for oleic (4), elaidic (5) and docosahexaenoic acid (8) conjugates were 20.2 µM, 17.8 µM and 16.5 µM, respectively, in DU-145 cells, whereas in LNCaP cells IC50 exceeded 20 µM. The strong conjugate cytotoxicity was confirmed in the LDH test, the highest (70.8%) for compound (5) and 64.2% for compound (8) in DU-145 cells. This effect was weaker for LNCaP cells (around 60%). The cytotoxic effect of unconjugated ciprofloxacin and fatty acids was weaker. The early apoptosis was predominant in LNCaP while in DU-145 cells both early and late apoptosis was induced. The tested conjugates decreased IL-6 release in both cancer cell lines by almost 50%. Proteomic analysis indicated influence of the ciprofloxacin conjugates on lipid metabolic proteins in prostatic cancer. Conclusion: Our findings suggested the cytotoxic potential of ciprofloxacin conjugates with reduction in proteins involved in prostate cancer progress.
HIF-1 and NRF2; Key Molecules for Malignant Phenotypes of Pancreatic Cancer
Authors: Hamada Shin , Matsumoto Ryotaro , Masamune Atsushi
Published: January 2022

Pancreatic cancer is intractable due to early progression and resistance to conventional therapy. Dense fibrotic stroma, known as desmoplasia, is a characteristic feature of pancreatic cancer, and develops through the interactions between pancreatic cancer cells and stromal cells, including pancreatic stellate cells. Dense stroma forms harsh tumor microenvironments characterized by hypoxia, few nutrients, and oxidative stress. Pancreatic cancer cells as well as pancreatic stellate cells survive in the harsh microenvironments through the altered expression of signaling molecules, transporters, and metabolic enzymes governed by various stress response mechanisms. Hypoxia inducible factor-1 and KEAP1-NRF2, stress response mechanisms for hypoxia and oxidative stress, respectively, contribute to the aggressive behaviors of pancreatic cancer. These key molecules for stress response mechanisms are activated, both in pancreatic cancer cells and in pancreatic stellate cells. Both factors are involved in the mutual activation of cancer cells and stellate cells, by inducing cancer-promoting signals and their mediators. Therapeutic interventions targeting these pathways are promising approaches for novel therapies. In this review, we summarize the roles of stress response mechanisms, focusing on hypoxia inducible factor-1 and KEAP1-NRF2, in pancreatic cancer. In addition, we discuss the potential of targeting these molecules for the treatment of pancreatic cancer.
Introduction of Mutant GNAQ into Endothelial Cells Induces a Vascular Malformation Phenotype with Therapeutic Response to Imatinib
Authors: Sasaki Maiko , Jung Yoonhee , North Paula , Elsey Justin , Choate Keith , Toussaint Michael Andrew , Huang Christina , Radi Rakan , Perricone Adam J. , Corces Victor G. , Arbiser Jack L.
Published: January 2022

GNAQ is mutated in vascular and melanocytic lesions, including vascular malformations and nevi. No in vivo model of GNAQ activation in endothelial cells has previously been described. We introduce mutant GNAQ into a murine endothelial cell line, MS1. The resultant transduced cells exhibit a novel phenotype in vivo, with extensive vasoformative endothelial cells forming aberrant lumens similar to those seen in vascular malformations. ATAC-seq analysis reveals activation of c-Kit in the novel vascular malformations. We demonstrate that c-Kit is expressed in authentic human Sturge–Weber vascular malformations, indicating a novel druggable target for Sturge–Weber syndrome. Since c-Kit is targeted by the FDA-approved drug imatinib, we tested the ability of imatinib on the phenotype of the vascular malformations in vivo. Imatinib treated vascular malformations are significantly smaller and have decreased supporting stromal cells surrounding the lumen. Imatinib may be useful in the treatment of human vascular malformations that express c-Kit, including Sturge–Weber syndrome.
Longitudinal Associations of Adherence to the World Cancer Research Fund/American Institute for Cancer Research (WCRF/AICR) Lifestyle Recommendations with Quality of Life and Symptoms in Colorectal Cancer Survivors up to 24 Months Post-Treatment
Authors: Kenkhuis Marlou-Floor , Mols Floortje , van Roekel Eline H. , Breedveld-Peters José J. L. , Breukink Stéphanie O. , Janssen-Heijnen Maryska L. G. , Keulen Eric T. P. , van Duijnhoven Fränzel J. B. , Weijenberg Matty P. , Bours Martijn J. L.
Published: January 2022

Post-treatment adherence to the World Cancer Research Fund/American Institute for Cancer Research (WCRF/AICR) lifestyle recommendations were associated with health-related quality of life (HRQoL), fatigue, and chemotherapy-induced peripheral neuropathy (CIPN) in colorectal cancer (CRC) survivors. In a prospective cohort among CRC survivors (n = 459), repeated home-visits were performed at 6 weeks, 6, 12, and 24 months post-treatment. Dietary intake, body composition, sedentary behaviour, and physical activity were assessed to construct a lifestyle score based on adherence to seven 2018 WCRF/AICR recommendations. Longitudinal associations of the lifestyle score with HRQoL, fatigue, and CIPN were analysed by confounder-adjusted linear mixed models. A higher lifestyle score was associated with better physical functioning and less activity-related fatigue, but not with CIPN. Adjustment for physical activity substantially attenuated observed associations, indicating its importance in the lifestyle score with regards to HRQoL. In contrast, adjustment for body composition and alcohol inflated observed associations, indicating that both recommendations had a counteractive influence within the lifestyle score. Our findings suggest that CRC survivors benefit from an overall adherence to the WCRF/AICR lifestyle recommendations in terms of HRQoL and fatigue, but not CIPN. Specific recommendations have a varying influence on these associations, complicating the interpretation and requiring further study.
Risk for Pelvic Metastasis and Role of Pelvic Lymphadenectomy in Node-Positive Vulvar Cancer-Results from the AGO-VOP.2 QS Vulva Study
Authors: Woelber Linn , Hampl Monika , Eulenburg Christine zu , Prieske Katharina , Hambrecht Johanna , Fuerst Sophie , Klapdor Ruediger , Heublein Sabine , Gass Paul , Rohner Annika , Canzler Ulrich , Becker Sven , Bommert Mareike , Bauerschlag Dirk , Denecke Agnieszka , Hanker Lars , Runnebaumn Ingo , Forner Dirk M. , Schochter Fabienne , Klar Maximilian , Schwab Roxana , Koepke Melitta , Kalder Matthias , Hantschmann Peer , Ratiu Dominik , Denschlag Dominik , Schroeder Willibald , Tuschy Benjamin , Baumann Klaus , Mustea Alexander , Soergel Philipp , Bronger Holger , Bauerschmitz Gerd , Kosse Jens , Koch Martin C. , Ignatov Atanas , Sehouli Jalid , Dannecker Christian , Mahner Sven , Jaeger Anna
Published: January 2022

The need for pelvic treatment in patients with node-positive vulvar cancer (VSCC) and the value of pelvic lymphadenectomy (LAE) as a staging procedure to plan adjuvant radiotherapy (RT) is controversial. In this retrospective, multicenter analysis, 306 patients with primary node-positive VSCC treated at 33 gynecologic oncology centers in Germany between 2017 and 2019 were analyzed. All patients received surgical staging of the groins; nodal status was as follows: 23.9% (73/306) pN1a, 23.5% (72/306) pN1b, 20.4% (62/306) pN2a/b, and 31.9% (97/306) pN2c/pN3. A total of 35.6% (109/306) received pelvic LAE; pelvic nodal involvement was observed in 18.5%. None of the patients with nodal status pN1a or pN1b and pelvic LAE showed pelvic nodal involvement. Taking only patients with nodal status ≥pN2a into account, the rate of pelvic involvement was 25%. In total, adjuvant RT was applied in 64.4% (197/306). Only half of the pelvic node-positive (N+) patients received adjuvant RT to the pelvis (50%, 10/20 patients); 41.9% (122/291 patients) experienced recurrent disease or died. In patients with histologically-confirmed pelvic metastases after LAE, distant recurrences were most frequently observed (7/20 recurrences). Conclusions: A relevant risk regarding pelvic nodal involvement was observed from nodal status pN2a and higher. Our data support the omission of pelvic treatment in patients with nodal status pN1a and pN1b.
Identification and Functional Analysis of a Novel CTNNB1 Mutation in Pediatric Medulloblastoma
Authors: Alaña Lide , Nunes-Xavier Caroline E. , Zaldumbide Laura , Martin-Guerrero Idoia , Mosteiro Lorena , Alba-Pavón Piedad , Villate Olatz , García-Obregón Susana , González-García Hermenegildo , Herraiz Raquel , Astigarraga Itziar , Pulido Rafael , García-Ariza Miguel
Published: January 2022

Medulloblastoma is the primary malignant tumor of the Central Nervous System (CNS) most common in pediatrics. We present here, the histological, molecular, and functional analysis of a cohort of 88 pediatric medulloblastoma tumor samples. The WNT-activated subgroup comprised 10% of our cohort, and all WNT-activated patients had exon 3 CTNNB1 mutations and were immunostained for nuclear β-catenin. One novel heterozygous CTNNB1 mutation was found, which resulted in the deletion of β-catenin Ser37 residue (ΔS37). The ΔS37 β-catenin variant ectopically expressed in U2OS human osteosarcoma cells displayed higher protein expression levels than wild-type β-catenin, and functional analysis disclosed gain-of-function properties in terms of elevated TCF/LEF transcriptional activity in cells. Our results suggest that the stabilization and nuclear accumulation of ΔS37 β-catenin contributed to early medulloblastoma tumorigenesis.
Application of Raw and Chemically Modified Biomasses for Heterogeneous Cu-Catalysed Conversion of Aryl boronic Acids to Phenols Derivatives
Authors: Torres Fernanda Guimarães , Teodoro Filipe Simões , Gurgel Leandro Vinícius Alves , Bourdreux Flavien , Zayene Olfa , Gaucher Anne , Gil Laurent Frédéric , Prim Damien
Published: January 2022

This work describes the application of raw and chemically modified cellulose and sugarcane bagasse for ipso-hydroxylation of aryl boronic acids in environmentally friendly reaction conditions. The catalytic efficiency of five support-[Cu] materials was compared in forming phenols from aryl boronic acids. Our investigation highlights that the CEDA-[Cu] material (6-deoxy-6-aminoethyleneamino cellulose loaded with Cu) leads to the best results under very mild reaction conditions. The optimized catalytic sequence, allowing a facile transformation of boronic acids to phenols, required the mandatory and joint presence of the support, Cu2O, and KOH at room temperature. CEDA-[Cu] was characterized using 13C solid-state NMR, ICP, and FTIR. The use of CEDA-[Cu] accounts for the efficacious synthesis of variously substituted phenol derivatives and presents very good recyclability after five catalytic cycles.
Signal Amplification in Highly Ordered Networks Is Driven by Geometry
Authors: Vanamee Éva S. , Lippner Gábor , Faustman Denise L.
Published: January 2022

Here, we hypothesize that, in biological systems such as cell surface receptors that relay external signals, clustering leads to substantial improvements in signaling efficiency. Representing cooperative signaling networks as planar graphs and applying Euler’s polyhedron formula, we can show that clustering may result in an up to a 200% boost in signaling amplitude dictated solely by the size and geometry of the network. This is a fundamental relationship that applies to all clustered systems regardless of its components. Nature has figured out a way to maximize the signaling amplitude in receptors that relay weak external signals. In addition, in cell-to-cell interactions, clustering both receptors and ligands may result in maximum efficiency and synchronization. The importance of clustering geometry in signaling efficiency goes beyond biological systems and can inform the design of amplifiers in nonbiological systems.
Nuclear Fragility in Radiation-Induced Senescence: Blebs and Tubes Visualized by 3D Electron Microscopy
Authors: Freyter Benjamin M. , Abd Al-razaq Mutaz A. , Isermann Anna , Dietz Anne , Azimzadeh Omid , Hekking Liesbeth , Gomolka Maria , Rübe Claudia E.
Published: January 2022

Irreparable DNA damage following ionizing radiation (IR) triggers prolonged DNA damage response and induces premature senescence. Cellular senescence is a permanent state of cell-cycle arrest characterized by chromatin restructuring, altered nuclear morphology and acquisition of secretory phenotype, which contributes to senescence-related inflammation. However, the mechanistic connections for radiation-induced DNA damage that trigger these senescence-associated hallmarks are poorly understood. In our in vitro model of radiation-induced senescence, mass spectrometry-based proteomics was combined with high-resolution imaging techniques to investigate the interrelations between altered chromatin compaction, nuclear envelope destabilization and nucleo-cytoplasmic chromatin blebbing. Our findings confirm the general pathophysiology of the senescence-response, with disruption of nuclear lamin organization leading to extensive chromatin restructuring and destabilization of the nuclear membrane with release of chromatin fragments into the cytosol, thereby activating cGAS-STING-dependent interferon signaling. By serial block-face scanning electron microscopy (SBF-SEM) whole-cell datasets were acquired to investigate the morphological organization of senescent fibroblasts. High-resolution 3-dimensional (3D) reconstruction of the complex nuclear shape allows us to precisely visualize the segregation of nuclear blebs from the main nucleus and their fusion with lysosomes. By multi-view 3D electron microscopy, we identified nanotubular channels formed in lamin-perturbed nuclei of senescent fibroblasts; the potential role of these nucleo-cytoplasmic nanotubes for expulsion of damaged chromatin has to be examined.
Theoretical Concepts in Magnetobiology after 40 Years of Research
Authors: Binhi Vladimir N. , Rubin Andrei B.
Published: January 2022

This review contains information on the development of magnetic biology, one of the multidisciplinary areas of biophysics. The main historical facts are presented and the general observed properties of magnetobiological phenomena are listed. The unavoidable presence of nonspecific magnetobiological effects in the everyday life of a person and society is shown. Particular attention is paid to the formation of theoretical concepts in magnetobiology and the state of the art in this area of research. Some details are provided on the molecular mechanisms of the nonspecific action of a magnetic field on organisms. The prospects of magnetobiology for the near and distant future are discussed.
The Effect of Normoxic and Hypoxic U-87 Glioblastoma Paracrine Secretion on the Modulation of Brain Endothelial Cells
Authors: Rado Mariam , Flepisi Brian , Fisher David
Published: January 2022

Background: Glioblastoma multiforme (GBM) is a highly invasive brain tumour, characterized by its ability to secrete factors promoting its virulence. Brain endothelial cells (BECs) in the GBM environment are physiologically modulated. The present study investigated the modulatory effects of normoxically and hypoxically induced glioblastoma U-87 cell secretions on BECs. Methods: Conditioned media (CM) were derived by cultivating U-87 cells under hypoxic incubation (5% O2) and normoxic incubation (21% O2). Treated bEnd.3 cells were evaluated for mitochondrial dehydrogenase activity, mitochondrial membrane potential (ΔΨm), ATP production, transendothelial electrical resistance (TEER), and endothelial tight-junction (ETJ) gene expression over 96 h. Results: The coculture of bEnd.3 cells with U-87 cells, or exposure to either hypoxic or normoxic U-87CM, was associated with low cellular viability. The ΔΨm in bEnd.3 cells was hyperpolarized after hypoxic U-87CM treatment (p < 0.0001). However, normoxic U-87CM did not affect the state of ΔΨm. BEC ATP levels were reduced after being cocultured with U-87 cells, or with hypoxic and normoxic CM (p < 0.05). Suppressed mitochondrial activity in bEnd.3 cells was associated with increased transendothelial permeability, while bEnd.3 cells significantly increased the gene expression levels of ETJs (p < 0.05) when treated with U-87CM. Conclusions: Hypoxic and normoxic glioblastoma paracrine factors differentially suppressed mitochondrial activity in BECs, increasing the BECs’ barrier permeability.
Generation and Application of Inducible Chimeric RNA ASTN2-PAPPAas Knockin Mouse Model
Authors: Luo Yichen , Du Liang , Yao Zhimeng , Liu Fan , Li Kai , Li Feifei , Zhu Jianlin , Coppes Robert P. , Zhang Dianzheng , Pan Yunlong , Gao Shegan , Zhang Hao
Published: January 2022

Chimeric RNAs (chiRNAs) play many previously unrecognized roles in different diseases including cancer. They can not only be used as biomarkers for diagnosis and prognosis of various diseases but also serve as potential therapeutic targets. In order to better understand the roles of chiRNAs in pathogenesis, we inserted human sequences into mouse genome and established a knockin mouse model of the tamoxifen-inducible expression of ASTN2-PAPPA antisense chimeric RNA (A-PaschiRNA). Mice carrying the A-PaschiRNA knockin gene do not display any apparent abnormalities in growth, fertility, histological, hematopoietic, and biochemical indices. Using this model, we dissected the role of A-PaschiRNA in chemical carcinogen 4-nitroquinoline 1-oxide (4NQO)-induced carcinogenesis of esophageal squamous cell carcinoma (ESCC). To our knowledge, we are the first to generate a chiRNA knockin mouse model using the Cre-loxP system. The model could be used to explore the roles of chiRNA in pathogenesis and potential targeted therapies.
Assessment of the Impact of Post-Thaw Stress Pathway Modulation on Cell Recovery following Cryopreservation in a Hematopoietic Progenitor Cell Model
Authors: Baust John M. , Snyder Kristi K. , Van Buskirk Robert G. , Baust John G.
Published: January 2022

The development and use of complex cell-based products in clinical and discovery science continues to grow at an unprecedented pace. To this end, cryopreservation plays a critical role, serving as an enabling process, providing on-demand access to biological material, facilitating large scale production, storage, and distribution of living materials. Despite serving a critical role and substantial improvements over the last several decades, cryopreservation often remains a bottleneck impacting numerous areas including cell therapy, tissue engineering, and tissue banking. Studies have illustrated the impact and benefit of controlling cryopreservation-induced delayed-onset cell death (CIDOCD) through various “front end” strategies, such as specialized media, new cryoprotective agents, and molecular control during cryopreservation. While proving highly successful, a substantial level of cell death and loss of cell function remains associated with cryopreservation. Recently, we focused on developing technologies (RevitalICE™) designed to reduce the impact of CIDOCD through buffering the cell stress response during the post-thaw recovery phase in an effort to improve the recovery of previously cryopreserved samples. In this study, we investigated the impact of modulating apoptotic caspase activation, oxidative stress, unfolded protein response, and free radical damage in the initial 24 h post-thaw on overall cell survival. Human hematopoietic progenitor cells in vitro cryopreserved in both traditional extracellular-type and intracellular-type cryopreservation freeze media were utilized as a model cell system to assess impact on survival. Our findings demonstrated that through the modulation of several of these pathways, improvements in cell recovery were obtained, regardless of the freeze media and dimethyl sulfoxide concentration utilized. Specifically, through the use of oxidative stress inhibitors, an average increase of 20% in overall viability was observed. Furthermore, the results demonstrated that by using the post-thaw recovery reagent on samples cryopreserved in intracellular-type media (Unisol™), improvements in overall cell survival approaching 80% of non-frozen controls were attained. While improvements in overall survival were obtained, an assessment on the impact of specific cell subpopulations and functionality remains to be completed. While work remains, these results represent an important step forward in the development of improved cryopreservation processes for use in discovery science, and commercial and clinical settings.
Freeze-Dried Curdlan/Whey Protein Isolate-Based Biomaterial as Promising Scaffold for Matrix-Associated Autologous Chondrocyte Transplantation—A Pilot In-Vitro Study
Authors: Klimek Katarzyna , Tarczynska Marta , Truszkiewicz Wieslaw , Gaweda Krzysztof , Douglas Timothy E. L. , Ginalska Grazyna
Published: January 2022

The purpose of this pilot study was to establish whether a novel freeze-dried curdlan/whey protein isolate-based biomaterial may be taken into consideration as a potential scaffold for matrix-associated autologous chondrocyte transplantation. For this reason, this biomaterial was initially characterized by the visualization of its micro- and macrostructures as well as evaluation of its mechanical stability, and its ability to undergo enzymatic degradation in vitro. Subsequently, the cytocompatibility of the biomaterial towards human chondrocytes (isolated from an orthopaedic patient) was assessed. It was demonstrated that the novel freeze-dried curdlan/whey protein isolate-based biomaterial possessed a porous structure and a Young’s modulus close to those of the superficial and middle zones of cartilage. It also exhibited controllable degradability in collagenase II solution over nine weeks. Most importantly, this biomaterial supported the viability and proliferation of human chondrocytes, which maintained their characteristic phenotype. Moreover, quantitative reverse transcription PCR analysis and confocal microscope observations revealed that the biomaterial may protect chondrocytes from dedifferentiation towards fibroblast-like cells during 12-day culture. Thus, in conclusion, this pilot study demonstrated that novel freeze-dried curdlan/whey protein isolate-based biomaterial may be considered as a potential scaffold for matrix-associated autologous chondrocyte transplantation.
Structure and Function of the ABCD1 Variant Database: 20 Years, 940 Pathogenic Variants, and 3400 Cases of Adrenoleukodystrophy
Authors: Mallack Eric J. , Gao Kerry , Engelen Marc , Kemp Stephan
Published: January 2022

The progressive neurometabolic disorder X-linked adrenoleukodystrophy (ALD) is caused by pathogenic variants in the ABCD1 gene, which encodes the peroxisomal ATP-binding transporter for very-long-chain fatty acids. The clinical spectrum of ALD includes adrenal insufficiency, myelopathy, and/or leukodystrophy. A complicating factor in disease management is the absence of a genotype–phenotype correlation in ALD. Since 1999, most ABCD1 (likely) pathogenic and benign variants have been reported in the ABCD1 Variant Database. In 2017, following the expansion of ALD newborn screening, the database was rebuilt. To add an additional level of confidence with respect to pathogenicity, for each variant, it now also reports the number of cases identified and, where available, experimental data supporting the pathogenicity of the variant. The website also provides information on a number of ALD-related topics in several languages. Here, we provide an updated analysis of the known variants in ABCD1. The order of pathogenic variant frequency, overall clustering of disease-causing variants in exons 1–2 (transmembrane domain spanning region) and 6–9 (ATP-binding domain), and the most commonly reported pathogenic variant p.Gln472Argfs*83 in exon 5 are consistent with the initial reports of the mutation database. Novel insights include nonrandom clustering of high-density missense variant hotspots within exons 1, 2, 6, 8, and 9. Perhaps more importantly, we illustrate the importance of collaboration and utility of the database as a scientific, clinical, and ALD-community-wide resource.
Microfluidic Platforms Designed for Morphological and Photosynthetic Investigations of Chlamydomonas reinhardtii on a Single-Cell Level
Authors: Széles Eszter , Nagy Krisztina , Ábrahám Ágnes , Kovács Sándor , Podmaniczki Anna , Nagy Valéria , Kovács László , Galajda Péter , Tóth Szilvia Z.
Published: January 2022

Chlamydomonas reinhardtii is a model organism of increasing biotechnological importance, yet, the evaluation of its life cycle processes and photosynthesis on a single-cell level is largely unresolved. To facilitate the study of the relationship between morphology and photochemistry, we established microfluidics in combination with chlorophyll a fluorescence induction measurements. We developed two types of microfluidic platforms for single-cell investigations: (i) The traps of the “Tulip” device are suitable for capturing and immobilizing single cells, enabling the assessment of their photosynthesis for several hours without binding to a solid support surface. Using this “Tulip” platform, we performed high-quality non-photochemical quenching measurements and confirmed our earlier results on bulk cultures that non-photochemical quenching is higher in ascorbate-deficient mutants (Crvtc2-1) than in the wild-type. (ii) The traps of the “Pot” device were designed for capturing single cells and allowing the growth of the daughter cells within the traps. Using our most performant “Pot” device, we could demonstrate that the FV/FM parameter, an indicator of photosynthetic efficiency, varies considerably during the cell cycle. Our microfluidic devices, therefore, represent versatile platforms for the simultaneous morphological and photosynthetic investigations of C. reinhardtii on a single-cell level.
An Approach for Material Model Identification of a Composite Coating Using Micro-Indentation and Multi-Scale Simulations
Authors: Shojaei Pouya , Scazzosi Riccardo , Trabia Mohamed , O’Toole Brendan , Giglio Marco , Zhang Xing , Liao Yiliang , Manes Andrea
Published: January 2022

While deposited thin film coatings can help enhance surface characteristics such as hardness and friction, their effective incorporation in product design is restricted by the limited understanding of their mechanical behavior. To address this, an approach combining micro-indentation and meso/micro-scale simulations was proposed. In this approach, micro-indentation testing was conducted on both the coating and the substrate. A meso-scale uniaxial compression finite element model was developed to obtain a material model of the coating. This material model was incorporated within an axisymmetric micro-scale model of the coating to simulate the indentation. The proposed approach was applied to a Ti/SiC metal matrix nanocomposite (MMNC) coating, with a 5% weight of SiC nanoparticles deposited over a Ti-6Al-4V substrate using selective laser melting (SLM). Micro-indentation testing was conducted on both the Ti/SiC MMNC coating and the Ti-6Al-4V substrate. The results of the meso-scale finite element indicated that the MMNC coating can be represented using a bi-linear elastic-plastic material model, which was incorporated within an axisymmetric micro-scale model. Comparison of the experimental and micro-scale model results indicated that the proposed approach was effective in capturing the post-indentation behavior of the Ti/SiC MMNC coating. This methodology can also be used for studying the response of composite coatings with different percentages of reinforcements.
Plasma-Assisted MOCVD Growth of Non-Polar GaN and AlGaN on Si(111) Substrates Utilizing GaN-AlN Buffer Layer
Authors: Arifin Pepen , Sutanto Heri , Sugianto  , Subagio Agus
Published: January 2022

We report the growth of non-polar GaN and AlGaN films on Si(111) substrates by plasma-assisted metal-organic chemical vapor deposition (PA-MOCVD). Low-temperature growth of GaN or AlN was used as a buffer layer to overcome the lattice mismatch and thermal expansion coefficient between GaN and Si(111) and GaN’s poor wetting on Si(111). As grown, the buffer layer is amorphous, and it crystalizes during annealing to the growth temperature and then serves as a template for the growth of GaN or AlGaN. We used scanning electron microscopy (SEM), atomic force microscopy (AFM), and X-ray diffraction (XRD) characterization to investigate the influence of the buffer layer on crystal structure, orientation, and the morphology of GaN. We found that the GaN buffer layer is superior to the AlN buffer layer. The thickness of the GaN buffer layer played a critical role in the crystal quality and plane orientation and in reducing the cracks during the growth of GaN/Si(111) layers. The optimum GaN buffer layer thickness is around 50 nm, and by using the optimized GaN buffer layer, we investigated the growth of AlGaN with varying Al compositions. The morphology of the AlGaN films is flat and homogenous, with less than 1 nm surface roughness, and has preferred orientation in a-axis.
Influence of Dolomite Rock Powder and Iron Tailings Powder on the Electrical Resistivity, Strength and Microstructure of Cement Pastes and Concrete
Authors: Liu Yang , Hao Wenru , He Wei , Meng Xia , Shen Yinlan , Du Tao , Wang Hui
Published: January 2022

Dolomite rock powder (the waste stone residue in the production of machine-made sand and stone processing) and iron tailings powder formed by mineral processing industry are solid wastes, which occupy land resources, pollute the environment and release toxic substances without reasonable processing. The dolomite rock powder and iron tailings powder composing a large number of active substances could be advantageous to the cement-based materials. In this study, the electrical resistivity of cement paste and concrete was measured. Meanwhile, the influence of dolomite rock powder and iron tailings powder on the compressive strength of concrete was investigated. The electric flux of concrete was determined to estimate the chloride ion permeability. The scanning electron microscope (SEM) and X-ray diffraction were obtained to investigate the hydration of cement paste. Results showed the electrical resistivity of all specimens presented in this order: specimens with iron tailings < specimens with dolomite rock powder < blank specimens < specimens with ground granulated blast-furnace slag (GGBS) < specimens with fly ash. The correlation between electrical resistivity and curing age of cement paste or concrete has been deduced as a quadratic function. The addition of GGBS could improve the compressive strength of concrete. Meanwhile, when the other three types of mineral admixtures were added, 5% by mass ratio of the total binder materials was the optimum for the compressive strength. The curing ages, the fly ash, the GGBS and 5% dolomite rock powder or 5% iron tailings powder demonstrated a positive effect on the chloride ion impermeability. However, when higher dosages of dolomite rock powder or iron tailings powder were added, the effect was the opposite. Finally, the compactness of the microstructure and the Ca(OH)2 of cement paste could be improved by a small dosage of dolomites or iron tailings (less than 5%).