bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying Intratumoral Heterogeneity and Immunoarchitecture Generated In-Silico by a Spatial Quantitative Systems Pharmacology Model
Authors: Nikfar Mehdi , Mi Haoyang , Gong Chang , Kimko Holly , Popel Aleksander S.
Published: May 2023

Spatial heterogeneity is a hallmark of cancer. Tumor heterogeneity can vary with time and location. The tumor microenvironment (TME) encompasses various cell types and their interactions that impart response to therapies. Therefore, a quantitative evaluation of tumor heterogeneity is crucial for the development of effective treatments. Different approaches, such as multiregional sequencing, spatial transcriptomics, analysis of autopsy samples, and longitudinal analysis of biopsy samples, can be used to analyze the intratumoral heterogeneity (ITH) and temporal evolution and to reveal the mechanisms of therapeutic response. However, because of the limitations of these data and the uncertainty associated with the time points of sample collection, having a complete understanding of intratumoral heterogeneity role is challenging. Here, we used a hybrid model that integrates a whole-patient compartmental quantitative-systems-pharmacology (QSP) model with a spatial agent-based model (ABM) describing the TME; we applied four spatial metrics to quantify model-simulated intratumoral heterogeneity and classified the TME immunoarchitecture for representative cases of effective and ineffective anti-PD-1 therapy. The four metrics, adopted from computational digital pathology, included mixing score, average neighbor frequency, Shannon’s entropy and area under the curve (AUC) of the G-cross function. A fifth non-spatial metric was used to supplement the analysis, which was the ratio of the number of cancer cells to immune cells. These metrics were utilized to classify the TME as “cold”, “compartmentalized” and “mixed”, which were related to treatment efficacy. The trends in these metrics for effective and ineffective treatments are in qualitative agreement with the clinical literature, indicating that compartmentalized immunoarchitecture is likely to result in more efficacious treatment outcomes.
Exploratory Genome-Wide Association Analysis to Identify Pharmacogenetic Determinants of Response to R-CHOP in Diffuse Large B-Cell Lymphoma
Authors: Perrone Gabriele , Rigacci Luigi , Urru Sara , Kovalchuk Sofya , Brugia Marco , Fabbri Alberto , Iovino Lorenzo , Puccini Benedetta , Cencini Emanuele , Orciuolo Enrico , Birtolo Silvia , Melosi Alessandro , Santini Simone , Landini Ida , Roviello Giandomenico , Santi Raffaella , Macciotta Alessandra , Ricceri Fulvio , Bosi Alberto , Bocchia Monica , Petrini Mario , Mini Enrico , Nobili Stefania
Published: May 2023

R-CHOP standard chemotherapy is successful in about 60% of diffuse large B-cell lymphoma (DLBCL) patients. Unresponsive patients have a poor prognosis, and predictive biomarkers of response to R-CHOP are lacking. We conducted the first prospective GWAS study aimed at exploring constitutional biomarkers predictive of R-CHOP efficacy and toxicity. Overall, 216 any-stage chemonaïve DLBCL patients candidate to R-CHOP were enrolled. The median age of the 185 eligible patients was 59.2 years, 49.7% were women and 45.4% were stage I–II patients. According to the Revised International Prognostic Index (R-IPI), 14.1%, 56.8% and 29.2% were in the very good, good and poor prognosis groups, respectively. Of the patients, 85.9% produced a complete response. Highly significant associations (i.e., p < 5 × 10−8) were found between progression-free survival (PFS) and six SNPs (i.e., rs116665727, rs1607795, rs75614943, rs77241831, rs117500207, rs78466241). Additionally, five SNPs (i.e., rs74832512, rs117500207, rs35789195, rs11721010, rs12356569) were highly associated with overall survival (OS). Wild-type patients showed a prolonged PFS or OS compared with patients carrying deleterious alleles (p < 0.001). No association with the adequate significant threshold was observed between SNPs and the objective response or toxicity. In the future, these SNPs, alone or in combination, after a proper validation in an independent cohort, could contribute to improving the prediction of R-CHOP response.
The p38/MK2 Pathway Functions as Chk1-Backup Downstream of ATM/ATR in G2-Checkpoint Activation in Cells Exposed to Ionizing Radiation
Authors: Luo Daxian , Mladenov Emil , Soni Aashish , Stuschke Martin , Iliakis George
Published: May 2023

We have recently reported that in G2-phase cells (but not S-phase cells) sustaining low loads of DNA double-strand break (DSBs), ATM and ATR regulate the G2-checkpoint epistatically, with ATR at the output-node, interfacing with the cell cycle through Chk1. However, although inhibition of ATR nearly completely abrogated the checkpoint, inhibition of Chk1 using UCN-01 generated only partial responses. This suggested that additional kinases downstream of ATR were involved in the transmission of the signal to the cell cycle engine. Additionally, the broad spectrum of kinases inhibited by UCN-01 pointed to uncertainties in the interpretation that warranted further investigations. Here, we show that more specific Chk1 inhibitors exert an even weaker effect on G2-checkpoint, as compared to ATR inhibitors and UCN-01, and identify the MAPK p38α and its downstream target MK2 as checkpoint effectors operating as backup to Chk1. These observations further expand the spectrum of p38/MK2 signaling to G2-checkpoint activation, extend similar studies in cells exposed to other DNA damaging agents and consolidate a role of p38/MK2 as a backup kinase module, adding to similar backup functions exerted in p53 deficient cells. The results extend the spectrum of actionable strategies and targets in current efforts to enhance the radiosensitivity in tumor cells.
Structural Transition of the Nucleosome during Transcription Elongation
Authors: Kujirai Tomoya , Ehara Haruhiko , Sekine Shun-ichi , Kurumizaka Hitoshi
Published: May 2023

In eukaryotes, genomic DNA is tightly wrapped in chromatin. The nucleosome is a basic unit of chromatin, but acts as a barrier to transcription. To overcome this impediment, the RNA polymerase II elongation complex disassembles the nucleosome during transcription elongation. After the RNA polymerase II passage, the nucleosome is rebuilt by transcription-coupled nucleosome reassembly. Nucleosome disassembly–reassembly processes play a central role in preserving epigenetic information, thus ensuring transcriptional fidelity. The histone chaperone FACT performs key functions in nucleosome disassembly, maintenance, and reassembly during transcription in chromatin. Recent structural studies of transcribing RNA polymerase II complexed with nucleosomes have provided structural insights into transcription elongation on chromatin. Here, we review the structural transitions of the nucleosome during transcription.
Oxidative Stress and Inflammation Biomarkers in Postoperative Pain Modulation in Surgically Treated Patients with Laryngeal Cancer—Pilot Study
Authors: Savic Vujovic Katarina , Zivkovic Andjela , Dozic Ivan , Cirkovic Andja , Medic Branislava , Srebro Dragana , Vuckovic Sonja , Milovanovic Jovica , Jotic Ana
Published: May 2023

(1) Background: Surgical treatment of laryngeal carcinoma includes different types of laryngectomies with neck dissection. Surgical tissue damage triggers an inflammatory response, leading to the release of pro-inflammatory molecules. This increases reactive oxygen species production and decreases antioxidant defense mechanisms, leading to postoperative oxidative stress. The aim of this study was to assess the correlation between oxidative stress (malondialdehyde, MDA; glutathione peroxidase, GPX; superoxide dismutase, SOD) and inflammation (interleukin 1, IL-1; interleukin-6, IL-6; C–reactive protein, CRP) parameters and postoperative pain management in patients surgically treated with laryngeal cancer. (2) Methods: This prospective study included 28 patients with surgically treated laryngeal cancer. Blood samples were taken for the analysis of oxidative stress and inflammation parameters before the operative treatment and after the operative treatment (1st postoperative day and 7th postoperative day). The concentrations of MDA, SOD, GPX, IL-1, IL-6, and CRP in the serum were determined by coated enzyme-linked immunosorbent assay (ELISA). The visual analog scale (VAS) was used for pain assessment. (3) Results and conclusion: There was a correlation between oxidative stress and inflammation biomarkers and postoperative pain modulation in surgically treated patients with laryngeal cancer. Age, more extensive surgery, CRP values, and use of tramadol were predictors for oxidative stress parameters.
Crystallization of Poly(ethylene oxide)-Based Triblock Copolymers in Films Swollen-Rich in Solvent Vapors
Authors: Babutan Iulia , Todor-Boer Otto , Atanase Leonard Ionut , Vulpoi Adriana , Botiz Ioan
Published: May 2023

In this study, we employed a polymer processing method based on solvent vapor annealing in a confined environment to swell-rich thin films of polybutadiene-b-poly(2-vinylpyridine)-b-poly(ethylene oxide) triblock copolymers and to promote their crystallization. As revealed by optical and atomic force microscopy, thin films of triblock copolymers containing a rather short crystalline poly(ethylene oxide) block that was massively obstructed by the other two blocks were unable to crystallize following the spin-casting process, and their further swelling in solvent vapors was necessary in order to produce polymeric crystals displaying a dendritic morphology. In comparison, thin films of triblock copolymers containing a much longer poly(ethylene oxide) block that was less obstructed by the other two blocks were shown to crystallize into dendritic structures right after the spin-casting procedure, as well as upon rich swelling in solvent vapors.
Multi-Objective Optimization of Dimensional Accuracy in Electric Hot Incremental Sheet Forming
Authors: Li Zhengfang , He Songlin , An Zhiguo , Gao Zhengyuan , Lu Shihong
Published: May 2023

The forming defects of parts mainly include fracture, springback, thermal expansion, and rough surface during electric hot incremental forming, in which the springback and thermal expansion directly affects the dimensional accuracy of parts. In this paper, the combined optimization of process parameters and unsupported distances was proposed to control the dimensional accuracy of forming parts in the electric hot incremental sheet forming process. The predictive model of major errors was established through the response surface methodology, and then the multi-objective optimal model was obtained using Non-dominated Sorting Genetic Algorithms-II (NSGA-II). Meanwhile, a multi-objective optimal result was determined according to the error compensation feature of the forming process. On this basis, the effect of unsupported distances on dimensional errors was analyzed in detail, and a valid unsupported distance was proposed to further improve the forming accuracy of the whole forming region. Finally, the experimental result demonstrated that the combined optimal method proposed was accurate and feasible.
The Influence of Different Types of SiO2 Precursors and Ag Addition on the Structure of Selected Titania-Silica Gels
Authors: Adamczyk Anna
Published: May 2023

In this paper, samples of titania-silica system were obtained by the sol-gel method as bulk materials, using titanium propoxide Ti(C3H7O)4 to introduce titania and two precursors of SiO2: TEOS tetraethoxysilane Si(OC2H5)4 and DDS dimethyldiethoxysilane (CH3)2(C2H5O)2Si. To enhance antibacterial properties, Ag was added to gels of selected compositions. The main aim of the performed studies was to find the correlations between the structural changes and the applied precursor of silica. Simultaneously, the influence of different compositions of gels and the addition of Ag on the specimens’ structure was investigated. To study the structure, two complementary methods, FTIR (Fourier Transform InfraRed) spectroscopy and X-ray diffraction, were applied. The analysis of the FTIR spectra and the XRD patterns made it possible to confirm the amorphous state of all dried gels and establish the presence of TiO2 polymorphs: anatase and rutile in all annealed samples. The addition of Ag atoms into the gels caused the crystallization of cristobalite phase in addition to titania polymorphs. The presence of crystalline Ag phase in the annealed gels allowed the calculation dimensions of Ag crystallites based on the Scherrer equation. The use of DDS as a silica precursor led to easier and faster crystallization of different TiO2 phases in the annealed samples and parallel increases in the depolymerization of silica lattice.
Production of LM28 Tubes by Mechanical Alloying and Using Friction Stir Extrusion
Authors: Asadi Parviz , Akbari Mostafa , Talebi Mahyar , Peyghami Maryam , Sadowski Tomasz , Aliha Mohammad Reza Mohammad
Published: May 2023

Friction Stir Extrusion (FSE), the focus of this research, is a process that has tremendous potential for shaping and improving the mechanical properties of the final product as well as the mechanical alloying. In this study, a cylindrical sample of LM13 aluminum, to which silicon powder is added, is extruded by the penetration of a tool and takes the shape of a tube. The microstructure of the aluminum tube produced is studied using a light microscope. Various tests, including compression and wear tests, are performed to evaluate the wear and mechanical properties of the tubes produced. Additionally, the process is simulated using the finite element method (FEM), and the strain and temperature distributions in the tubes are examined to understand the impact of tool advancing speed better. The strain and temperature are highest on the inner surface, where the tubes meet the tool. Moreover, as the advancing speed increases from 25 to 40 mm/min, the maximum temperature in the tubes increases from 350 to 400 °C. The surface quality of the samples is directly related to the advancing speed, so the surface quality improves as the advancing speed increases. The results obtained from the compression and wear tests show that the compression strength has increased by about 17%, and the wear resistance has improved by about 20%.
Surgical Management of Brain Tumors with Focused Ultrasound
Authors: Mehkri Yusuf , Pierre Kevin , Woodford Samuel Joel , Davidson Caroline Grace , Urhie Ogaga , Sriram Sai , Hernandez Jairo , Hanna Chadwin , Lucke-Wold Brandon
Published: May 2023

Focused ultrasound is a novel technique for the treatment of aggressive brain tumors that uses both mechanical and thermal mechanisms. This non-invasive technique can allow for both the thermal ablation of inoperable tumors and the delivery of chemotherapy and immunotherapy while minimizing the risk of infection and shortening the time to recovery. With recent advances, focused ultrasound has been increasingly effective for larger tumors without the need for a craniotomy and can be used with minimal surrounding soft tissue damage. Treatment efficacy is dependent on multiple variables, including blood–brain barrier permeability, patient anatomical features, and tumor-specific features. Currently, many clinical trials are currently underway for the treatment of non-neoplastic cranial pathologies and other non-cranial malignancies. In this article, we review the current state of surgical management of brain tumors using focused ultrasound.
The Impact of Interprofessional Education on Health Profession Students’ Professional Identity
Authors: Ciani Gioia J. , Grimaldi Gary , Macalintal Maribel , Orner David
Published: May 2023

Establishing interprofessional identity is critical in preparing health care teams to work in collaborative environments and enhance efficacy of patient care. Accreditation standards for health profession programs have been implemented to include interprofessional education (IPE), yet there remains obfuscation regarding occupational therapy’s (OT) professional identity. The purpose of this prospective pre-post test study was to assess an experiential IPE event for health profession students (n = 170 from ten health profession programs) to: (1) determine the effectiveness of role playing and team-based case discussions on students’ knowledge and perceptions toward each other’s professions, and (2) specifically assess the impact of the IPE event on students’ perceptions toward OT roles and responsibilities. Health profession students were asked to complete a survey prior to and at the conclusion of the IPE event, which included the validated Interdisciplinary Education Perception Scale (IEPS) and non-standardized closed and open-ended questions. Quantitative analysis of responses showed a significant improvement in interdisciplinary perceptions after the experience as evidenced by higher IEPS scores. Post-test open-ended responses confirmed this finding. Health profession programs were stratified, revealing positive significant differences regarding OT. These findings suggest role-playing and team-based case discussions for IPE can have a positive impact on students’ interprofessional perceptions and understanding of OT.
CCUS Strategies as Most Viable Option for Global Warming Mitigation
Authors: Gambelli Alberto Maria
Published: May 2023

The decarbonization of energy-consuming industrial sectors is nowadays becoming one of the most relevant challenges to counteract global warming and the consequences related to it [...]
Nitrogen Deposition May Benefit to Larix olgensis Root Soils
Authors: Qu Tongbao , Li Meixuan , Zhao Xiaoting , Luo Heyi , Zhao Lei
Published: May 2023

Atmospheric nitrogen deposition affects the health of forest ecosystems by altering soil microbial activity. However, the effects of nitrogen addition levels, morphology and ecosystem type on whether nitrogen addition is beneficial or detrimental to soil health is controver-sial, and most studies have focused on the negative effects on microbial structure. Based on this, this study conducted a four-year experiment of nitrogen (NaNO3) addition at two levels (10 and 20 kg N hm−2·yr−1) in the understory soil of Larix olgensis in northeastern China to study soil microbial properties, soil enzyme activities, and to analyze soil physi-cochemical properties and the correlation between them. The results showed that nitrogen addition reduced soil pH and increased soil NH4+-N and NO3−-N contents, thus promoting the activities of Urease (Ure), Acid phosphatase (ACP) and N-Acetamidoglucosidase (NAG) and inhibiting the activity of Leucine aminopeptidase (LAP) in soil, further improving the diversity and richness of soil microorganisms and increasing the dominant taxa of beneficial microorganisms. This may be due to soil acidification caused by the addition of nitrogen, which increases the effectiveness of nitrogen in the soil, improving soil properties, moving soil health in a beneficial direction, promoting beneficial microbial activity, and making the soil more suitable for the growth of the acid-loving tree species L. olgensis. In general, N addition favored the development of soil bacterial communities and the maintenance of soil nutrient status, and had a positive effect on the soil nutrient status of L. olgensis. The results of this study may provide an important scientific basis for adaptive management of forest ecosystems in the context of global nitrogen deposition.
Production of Nattokinase from Hemp Seed Meal by Solid-State Fermentation and Improvement of Its Nutritional Quality
Authors: Zhang Min , Li Tao , Guo Gege , Liu Zhaoxing , Hao Ning
Published: May 2023

Fermented foods have gained immense popularity in recent years due to their distinct flavor profile. Given the increasing demand, there is a growing focus on optimizing their nutritional quality while also reducing their costs. In this study, using a novel approach, hemp seed meal was utilized as a solid fermentation substrate to produce nattokinase (NK). Using a combination of one-factor-at-a-time experiments, Plackett–Burman design, and Box–Behnken design, the optimal fermentation conditions of Bacillus subtilis 13932 (NK-producing strain) were determined. The initial ratio of HSM (hemp seed meal) to water was 1:2.0 (v:w), the thickness of the substrate was 2.9 cm, the bacterial inoculum volume was 10% (v:w), the relative humidity was 75.2%, the temperature was set at 35 °C, and the fermentation time was 20 h. The NK activity under these conditions was measured to be 7067.12 IU/g. During fermentation, 15.15% of soluble peptides were produced, which exhibited hydroxyl radical removal ability and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical removal ability of 14.85%, down from 32.96%. Furthermore, trypsin inhibitor and urease in HSM decreased by 42.6% and 73.6%, respectively, improving the nutritional quality of HSM. Sensory evaluations indicated that HSM is expected to be a popular food, highlighting the potential of using HSM as a solid fermentation substrate for NK production.
G-Quadruplexes in Nuclear Biomolecular Condensates
Authors: Pavlova Iuliia , Iudin Mikhail , Surdina Anastasiya , Severov Vjacheslav , Varizhuk Anna
Published: May 2023

G-quadruplexes (G4s) have long been implicated in the regulation of chromatin packaging and gene expression. These processes require or are accelerated by the separation of related proteins into liquid condensates on DNA/RNA matrices. While cytoplasmic G4s are acknowledged scaffolds of potentially pathogenic condensates, the possible contribution of G4s to phase transitions in the nucleus has only recently come to light. In this review, we summarize the growing evidence for the G4-dependent assembly of biomolecular condensates at telomeres and transcription initiation sites, as well as nucleoli, speckles, and paraspeckles. The limitations of the underlying assays and the remaining open questions are outlined. We also discuss the molecular basis for the apparent permissive role of G4s in the in vitro condensate assembly based on the interactome data. To highlight the prospects and risks of G4-targeting therapies with respect to the phase transitions, we also touch upon the reported effects of G4-stabilizing small molecules on nuclear biomolecular condensates.
An Improved Machine Learning-Based Approach to Assess the Microbial Diversity in Major North Indian River Ecosystems
Authors: Choudhury Nalinikanta , Sahu Tanmaya Kumar , Rao Atmakuri Ramakrishna , Rout Ajaya Kumar , Behera Bijay Kumar
Published: May 2023

The rapidly evolving high-throughput sequencing (HTS) technologies generate voluminous genomic and metagenomic sequences, which can help classify the microbial communities with high accuracy in many ecosystems. Conventionally, the rule-based binning techniques are used to classify the contigs or scaffolds based on either sequence composition or sequence similarity. However, the accurate classification of the microbial communities remains a major challenge due to massive data volumes at hand as well as a requirement of efficient binning methods and classification algorithms. Therefore, we attempted here to implement iterative K-Means clustering for the initial binning of metagenomics sequences and applied various machine learning algorithms (MLAs) to classify the newly identified unknown microbes. The cluster annotation was achieved through the BLAST program of NCBI, which resulted in the grouping of assembled scaffolds into five classes, i.e., bacteria, archaea, eukaryota, viruses and others. The annotated cluster sequences were used to train machine learning algorithms (MLAs) to develop prediction models to classify unknown metagenomic sequences. In this study, we used metagenomic datasets of samples collected from the Ganga (Kanpur and Farakka) and the Yamuna (Delhi) rivers in India for clustering and training the MLA models. Further, the performance of MLAs was evaluated by 10-fold cross validation. The results revealed that the developed model based on the Random Forest had a superior performance compared to the other considered learning algorithms. The proposed method can be used for annotating the metagenomic scaffolds/contigs being complementary to existing methods of metagenomic data analysis. An offline predictor source code with the best prediction model is available at (https://github.com/Nalinikanta7/metagenomics).
Comparison of Growth Patterns and Metabolite Composition of Different Ginseng Cultivars (Yunpoong and K-1) Grown in a Vertical Farm
Authors: Lee Ga Oun , Jang Seong-Nam , Kim Min Ju , Cho Du Yong , Cho Kye Man , Lee Ji Hyun , Son Ki-Ho
Published: May 2023

This study analyzed growth patterns, biological compounds, antioxidant properties, ginsenoside contents, metabolites, and the annual net production of ‘Yunpoong’ and ‘K-1’ to find the optimal harvesting time of ginseng sprouts. One-year-old ginseng seedlings were cultivated in a container-type vertical farm under a temperature of 20 °C, a humidity of 60%, and average light intensity of 46.4 µmol m−2 s−1 (16 h photoperiod). Growth patterns at 2, 3, 4, and 5 weeks after transplanting (WAT) differed between cultivars. Regarding biological compounds and antioxidant properties, ‘Yunpoong’ took 5 WAT (43.59%; 2,2-diphenyl-1-picryl-hydrazine-hydrate radical scavenging activity, 1.47 OD593nm; ferric reducing antioxidant power assay, 78.01%; 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) radical scavenging activity), and ‘K-1’ took 4 WAT (0.98 Re mg g−1; total flavonoid contents, 35.93%; DPPH) to show a high content. Two cultivars showed the highest total ginsenoside contents at 5 WAT. Most of the analyzed metabolites had a higher content in ‘Yunpoong’ than in ‘K-1’. In both cultivars, it was confirmed that the longer the growth period (3 − > 5 WAT), the lower the yield and the annual ginsenoside net production. Therefore, ‘Yunpoong’ and ‘K-1’ cultivars should be grown as ginseng sprouts in the vertical farms for approximately 3 WAT and 4 WAT, respectively.
Differential Functional Contribution of BK Channel Subunits to Aldosterone-Induced Channel Activation in Vascular Smooth Muscle and Eventual Cerebral Artery Dilation
Authors: Mysiewicz Steven C. , Hawks Sydney M. , Bukiya Anna N. , Dopico Alex M.
Published: May 2023

Calcium/voltage-activated potassium channels (BK) control smooth muscle (SM) tone and cerebral artery diameter. They include channel-forming α and regulatory β1 subunits, the latter being highly expressed in SM. Both subunits participate in steroid-induced modification of BK activity: β1 provides recognition for estradiol and cholanes, resulting in BK potentiation, whereas α suffices for BK inhibition by cholesterol or pregnenolone. Aldosterone can modify cerebral artery function independently of its effects outside the brain, yet BK involvement in aldosterone’s cerebrovascular action and identification of channel subunits, possibly involved in steroid action, remains uninvestigated. Using microscale thermophoresis, we demonstrated that each subunit type presents two recognition sites for aldosterone: at 0.3 and ≥10 µM for α and at 0.3–1 µM and ≥100 µM for β1. Next, we probed aldosterone on SM BK activity and diameter of middle cerebral artery (MCA) isolated from β1−/− vs. wt mice. Data showed that β1 leftward-shifted aldosterone-induced BK activation, rendering EC50~3 μM and ECMAX ≥ 10 μM, at which BK activity increased by 20%. At similar concentrations, aldosterone mildly yet significantly dilated MCA independently of circulating and endothelial factors. Lastly, aldosterone-induced MCA dilation was lost in β1−/− mice. Therefore, β1 enables BK activation and MCA dilation by low µM aldosterone.
Electron-Induced Decomposition of 5-Bromo-4-thiouracil and 5-Bromo-4-thio-2′-deoxyuridine: The Effect of the Deoxyribose Moiety on Dissociative Electron Attachment
Authors: Izadi Farhad , Szczyrba Adrian , Datta Magdalena , Ciupak Olga , Demkowicz Sebastian , Rak Janusz , Denifl Stephan
Published: May 2023

When modified uridine derivatives are incorporated into DNA, radical species may form that cause DNA damage. This category of molecules has been proposed as radiosensitizers and is currently being researched. Here, we study electron attachment to 5-bromo-4-thiouracil (BrSU), a uracil derivative, and 5-bromo-4-thio-2′-deoxyuridine (BrSdU), with an attached deoxyribose moiety via the N-glycosidic (N1-C) bond. Quadrupole mass spectrometry was used to detect the anionic products of dissociative electron attachment (DEA), and the experimental results were supported by quantum chemical calculations performed at the M062X/aug-cc-pVTZ level of theory. Experimentally, we found that BrSU predominantly captures low-energy electrons with kinetic energies near 0 eV, though the abundance of bromine anions was rather low compared to a similar experiment with bromouracil. We suggest that, for this reaction channel, proton-transfer reactions in the transient negative ions limit the release of bromine anions.
Detection of Elevated Level of Tetrahydrobiopterin in Serum Samples of ME/CFS Patients with Orthostatic Intolerance: A Pilot Study
Authors: Gottschalk Carl Gunnar , Whelan Ryan , Peterson Daniel , Roy Avik
Published: May 2023

Myalgic encephalomyelitis or chronic fatigue syndrome (ME/CFS) is a multisystem chronic illness characterized by severe muscle fatigue, pain, dizziness, and brain fog. Many patients with ME/CFS experience orthostatic intolerance (OI), which is characterized by frequent dizziness, light-headedness, and feeling faint while maintaining an upright posture. Despite intense investigation, the molecular mechanism of this debilitating condition is still unknown. OI is often manifested by cardiovascular alterations, such as reduced cerebral blood flow, reduced blood pressure, and diminished heart rate. The bioavailability of tetrahydrobiopterin (BH4), an essential cofactor of endothelial nitric oxide synthase (eNOS) enzyme, is tightly coupled with cardiovascular health and circulation. To explore the role of BH4 in ME/CFS, serum samples of CFS patients (n = 32), CFS patients with OI only (n = 10; CFS + OI), and CFS patients with both OI and small fiber polyneuropathy (n = 12; CFS + OI + SFN) were subjected to BH4 ELISA. Interestingly, our results revealed that the BH4 expression is significantly high in CFS, CFS + OI, and CFS + OI + SFN patients compared to age-/gender-matched controls. Finally, a ROS production assay in cultured microglial cells followed by Pearson correlation statistics indicated that the elevated BH4 in serum samples of CFS + OI patients might be associated with the oxidative stress response. These findings suggest that the regulation of BH4 metabolism could be a promising target for understanding the molecular mechanism of CFS and CFS with OI.
Sambucus ebulus (Elderberry) Fruits Modulate Inflammation and Complement System Activity in Humans
Authors: Kiselova-Kaneva Yoana , Nashar Milka , Roussev Bogdan , Salim Ayshe , Hristova Minka , Olczyk Pawel , Komosinska-Vassev Katarzyna , Dincheva Ivayla , Badjakov Ilian , Galunska Bistra , Ivanova Diana
Published: May 2023

Sambucus ebulus (SE) fruits are used for immune stimulation and amelioration of gastrointestinal inflammatory conditions. Currently, there is no scientific evidence of their effects on various aspects of the immune response mechanisms in humans. The purpose of this study was to evaluate the immunomodulatory potential of SE fruit infusion intake in healthy humans. Anthocyanin content was determined with UPLC-ESI-MS/MS. Fifty-three volunteers enrolled in a 4-week SE infusion intake intervention. Blood count, serum total protein, Interleukin 1 beta (IL-1β), Interleukin 6 (IL-6), Tumor Necrosis Factor Alpha (TNFα), High-sensitivity C-reactive protein (hs-CRP), C3, and C4 levels were measured on automatic analyzers, and Interleukin 8 (IL-8) was measured manually with an ELISA kit. Cyanidin-3-O-galactoside (48.15 mg/g DW), followed by cyaniding-3-sambubioside (43.41 ± 1.07 mg/g DW), were the most abundant anthocyanins in SE samples. A significant decrease in total protein (2.82%), IL-6 (20.15%), TNFα (5.38%), IL-8 (5.50%), C3 (4.16%), and C4 (14.29%) was established in the whole group. Total protein, IL-8, TNFα, and C4 decreased in women (3.11%, 4.76%, 5.09%, and 11.11%), and IL-6 decreased (40.61%) in men. Hb (1.20%) and hematocrit (1.55%) levels decreased in the whole group and in the women group (1.61% and 2.20%). SE fruits exert immune-modulatory activity as revealed by decreased pro-inflammatory status and complement activity markers in healthy volunteers after a 4-week intervention.
Butyrophilins: Dynamic Regulators of Protective T Cell Immunity in Cancer
Authors: Kumari Rinkee , Hosseini Elaheh Sadat , Warrington Kristen E. , Milonas Tyler , Payne Kyle K.
Published: May 2023

The efficacy of current immunotherapies remains limited in many solid epithelial malignancies. Recent investigations into the biology of butyrophilin (BTN) and butyrophilin-like (BTNL) molecules, however, suggest these molecules are potent immunosuppressors of antigen-specific protective T cell activity in tumor beds. BTN and BTNL molecules also associate with each other dynamically on cellular surfaces in specific contexts, which modulates their biology. At least in the case of BTN3A1, this dynamism drives the immunosuppression of αβ T cells or the activation of Vγ9Vδ2 T cells. Clearly, there is much to learn regarding the biology of BTN and BTNL molecules in the context of cancer, where they may represent intriguing immunotherapeutic targets that could potentially synergize with the current class of immune modulators in cancer. Here, we discuss our current understanding of BTN and BTNL biology, with a particular focus on BTN3A1, and potential therapeutic implications for cancer.
NatB Catalytic Subunit Depletion Disrupts DNA Replication Initiation Leading to Senescence in MEFs
Authors: Elurbide Jasmin , Carte Beatriz , Guedes Joana , Aldabe Rafael
Published: May 2023

Alpha-aminoterminal acetyltransferase B (NatB) is a critical enzyme responsible for acetylating the aminoterminal end of proteins, thereby modifying approximately 21% of the proteome. This post-translational modification impacts protein folding, structure, stability, and interactions between proteins which, in turn, play a crucial role in modulating several biological functions. NatB has been widely studied for its role in cytoskeleton function and cell cycle regulation in different organisms, from yeast to human tumor cells. In this study, we aimed to understand the biological importance of this modification by inactivating the catalytic subunit of the NatB enzymatic complex, Naa20, in non-transformed mammal cells. Our findings demonstrate that depletion of NAA20 results in decreased cell cycle progression and DNA replication initiation, ultimately leading to the senescence program. Furthermore, we have identified NatB substrates that play a role in cell cycle progression, and their stability is compromised when NatB is inactivated. These results underscore the significance of N-terminal acetylation by NatB in regulating cell cycle progression and DNA replication.
Three Major Causes of Metabolic Retinal Degenerations and Three Ways to Avoid Them
Authors: Kovács-Valasek Andrea , Rák Tibor , Pöstyéni Etelka , Csutak Adrienne , Gábriel Robert
Published: May 2023

An imbalance of homeostasis in the retina leads to neuron loss and this eventually results in a deterioration of vision. If the stress threshold is exceeded, different protective/survival mechanisms are activated. Numerous key molecular actors contribute to prevalent metabolically induced retinal diseases—the three major challenges are age-related alterations, diabetic retinopathy and glaucoma. These diseases have complex dysregulation of glucose-, lipid-, amino acid or purine metabolism. In this review, we summarize current knowledge on possible ways of preventing or circumventing retinal degeneration by available methods. We intend to provide a unified background, common prevention and treatment rationale for these disorders and identify the mechanisms through which these actions protect the retina. We suggest a role for herbal medicines, internal neuroprotective substances and synthetic drugs targeting four processes: parainflammation and/or glial cell activation, ischemia and related reactive oxygen species and vascular endothelial growth factor accumulation, apoptosis and/or autophagy of nerve cells and an elevation of ocular perfusion pressure and/or intraocular pressure. We conclude that in order to achieve substantial preventive or therapeutic effects, at least two of the mentioned pathways should be targeted synergistically. A repositioning of some drugs is considered to use them for the cure of the other related conditions.
WGS Revealed Novel BBS5 Pathogenic Variants, Missed by WES, Causing Ciliary Structure and Function Defects
Authors: Karam Adella , Delvallée Clarisse , Estrada-Cuzcano Alejandro , Geoffroy Véronique , Lamouche Jean-Baptiste , Leuvrey Anne-Sophie , Nourisson Elsa , Tarabeux Julien , Stoetzel Corinne , Scheidecker Sophie , Porter Louise Frances , Génin Emmanuelle , Redon Richard , Sandron Florian , Boland Anne , Deleuze Jean-François , Le May Nicolas , Dollfus Hélène , Muller Jean
Published: May 2023

Bardet–Biedl syndrome (BBS) is an autosomal recessive ciliopathy that affects multiple organs, leading to retinitis pigmentosa, polydactyly, obesity, renal anomalies, cognitive impairment, and hypogonadism. Until now, biallelic pathogenic variants have been identified in at least 24 genes delineating the genetic heterogeneity of BBS. Among those, BBS5 is a minor contributor to the mutation load and is one of the eight subunits forming the BBSome, a protein complex implied in protein trafficking within the cilia. This study reports on a European BBS5 patient with a severe BBS phenotype. Genetic analysis was performed using multiple next-generation sequencing (NGS) tests (targeted exome, TES and whole exome, WES), and biallelic pathogenic variants could only be identified using whole-genome sequencing (WGS), including a previously missed large deletion of the first exons. Despite the absence of family samples, the biallelic status of the variants was confirmed. The BBS5 protein’s impact was confirmed on the patient’s cells (presence/absence and size of the cilium) and ciliary function (Sonic Hedgehog pathway). This study highlights the importance of WGS and the challenge of reliable structural variant detection in patients’ genetic explorations as well as functional tests to assess a variant’s pathogenicity.
Self-Organization of Enzyme-Catalyzed Reactions Studied by the Maximum Entropy Production Principle
Authors: Dobovišek Andrej , Vitas Marko , Blaževič Tina , Markovič Rene , Marhl Marko , Fajmut Aleš
Published: May 2023

The self-organization of open reaction systems is closely related to specific mechanisms that allow the export of internally generated entropy from systems to their environment. According to the second law of thermodynamics, systems with effective entropy export to the environment are better internally organized. Therefore, they are in thermodynamic states with low entropy. In this context, we study how self-organization in enzymatic reactions depends on their kinetic reaction mechanisms. Enzymatic reactions in an open system are considered to operate in a non-equilibrium steady state, which is achieved by satisfying the principle of maximum entropy production (MEPP). The latter is a general theoretical framework for our theoretical analysis. Detailed theoretical studies and comparisons of the linear irreversible kinetic schemes of an enzyme reaction in two and three states are performed. In both cases, in the optimal and statistically most probable thermodynamic steady state, a diffusion-limited flux is predicted by MEPP. Several thermodynamic quantities and enzymatic kinetic parameters, such as the entropy production rate, the Shannon information entropy, reaction stability, sensitivity, and specificity constants, are predicted. Our results show that the optimal enzyme performance may strongly depend on the number of reaction steps when linear reaction mechanisms are considered. Simple reaction mechanisms with a smaller number of intermediate reaction steps could be better organized internally and could allow fast and stable catalysis. These could be features of the evolutionary mechanisms of highly specialized enzymes.
AEC and AFMSC Transplantation Preserves Fertility of Experimentally Induced Rat Varicocele by Expressing Differential Regenerative Mechanisms
Authors: Peserico Alessia , Barboni Barbara , Russo Valentina , Nardinocchi Delia , Turriani Maura , Cimini Costanza , Bernabò Nicola , Parolini Ornella , Silini Antonietta Rosa , Antonucci Ivana , Stuppia Liborio , Berardinelli Paolo , Falanga Ilaria , Perruzza Davide , Valbonetti Luca , Mauro Annunziata
Published: May 2023

Amniotic membrane and amniotic fluid derived cells are regarded as a promising stem cell source for developing regenerative medicine techniques, although they have never been tested on male infertility diseases such as varicocele (VAR). The current study aimed to examine the effects of two distinct cell sources, human Amniotic Fluid Mesenchymal Stromal Cells (hAFMSCs) and amniotic epithelial cells (hAECs), on male fertility outcomes in a rat induced VAR model. To explain cell-dependent enhancement of reproductive outcomes in rats transplanted with hAECs and hAFMSCs, insights on testis morphology, endocannabinoid system (ECS) expression and inflammatory tissue response have been carried out alongside cell homing assessment. Both cell types survived 120 days post-transplantation by modulating the ECS main components, promoting proregenerative M2 macrophages (Mφ) recruitment and a favorable anti-inflammatory IL10 expression pattern. Of note, hAECs resulted to be more effective in restoring rat fertility rate by enhancing both structural and immunoresponse mechanisms. Moreover, immunofluorescence analysis revealed that hAECs contributed to CYP11A1 expression after transplantation, whereas hAFMSCs moved towards the expression of Sertoli cell marker, SOX9, confirming a different contribution into the mechanisms leading to testis homeostasis. These findings highlight, for the first time, a distinct role of amniotic membrane and amniotic fluid derived cells in male reproduction, thus proposing innovative targeted stem-based regenerative medicine protocols for remedying high-prevalence male infertility conditions such as VAR.
Lipid Emulsion Inhibits Amlodipine-Induced Nitric Oxide-Mediated Vasodilation in Isolated Rat Aorta
Authors: Park Kyeong-Eon , Lee Soo Hee , Bae Sung Il , Hwang Yeran , Ok Seong-Ho , Ahn Seung Hyun , Sim Gyujin , Chung Soonghee , Sohn Ju-Tae
Published: May 2023

This study aimed to examine the effect of lipid emulsion on the vasodilation induced by a toxic dose of amlodipine in isolated rat aorta and elucidate its mechanism, with a particular focus on nitric oxide. The effects of endothelial denudation, NW-nitro-L-arginvine methyl ester (L-NAME), methylene blue, lipid emulsion, and linolenic acid on the amlodipine-induced vasodilation and amlodipine-induced cyclic guanosine monophosphate (cGMP) production were examined. Furthermore, the effects of lipid emulsion, amlodipine, and PP2, either alone or combined, on endothelial nitric oxide synthase (eNOS), caveolin-1, and Src-kinase phosphorylation were examined. Amlodipine-induced vasodilation was higher in endothelium-intact aorta than in endothelium-denuded aorta. L-NAME, methylene blue, lipid emulsion, and linolenic acid inhibited amlodipine-induced vasodilation and amlodipine-induced cGMP production in the endothelium-intact aorta. Lipid emulsion reversed the increased stimulatory eNOS (Ser1177) phosphorylation and decreased inhibitory eNOS (Thr495) phosphorylation induced via amlodipine. PP2 inhibited stimulatory eNOS, caveolin-1, and Src-kinase phosphorylation induced via amlodipine. Lipid emulsion inhibited amlodipine-induced endothelial intracellular calcium increase. These results suggest that lipid emulsion attenuated the vasodilation induced via amlodipine through inhibiting nitric oxide release in isolated rat aorta, which seems to be mediated via reversal of stimulatory eNOS (Ser1177) phosphorylation and inhibitory eNOS (Thr495) dephosphorylation, which are also induced via amlodipine.
DT-PICS: An Efficient and Cost-Effective SNP Selection Method for the Germplasm Identification of Arabidopsis
Authors: Xiong Liwen , Li Zirong , Li Weihua , Li Lanzhi
Published: May 2023

Germplasm identification is essential for plant breeding and conservation. In this study, we developed a new method, DT-PICS, for efficient and cost-effective SNP selection in germplasm identification. The method, based on the decision tree concept, could efficiently select the most informative SNPs for germplasm identification by recursively partitioning the dataset based on their overall high PIC values, instead of considering individual SNP features. This method reduces redundancy in SNP selection and enhances the efficiency and automation of the selection process. DT-PICS demonstrated significant advantages in both the training and testing datasets and exhibited good performance on independent prediction, which validates its effectiveness. Thirteen simplified SNP sets were extracted from 749,636 SNPs in 1135 Arabidopsis varieties resequencing datasets, including a total of 769 DT-PICS SNPs, with an average of 59 SNPs per set. Each simplified SNP set could distinguish between the 1135 Arabidopsis varieties. Simulations demonstrated that using a combination of two simplified SNP sets for identification can effectively increase the fault tolerance in independent validation. In the testing dataset, two potentially mislabeled varieties (ICE169 and Star-8) were identified. For 68 same-named varieties, the identification process achieved 94.97% accuracy and only 30 shared markers on average; for 12 different-named varieties, the germplasm to be tested could be effectively distinguished from 1,134 other varieties while grouping extremely similar varieties (Col-0) together, reflecting their actual genetic relatedness. The results suggest that the DT-PICS provides an efficient and accurate approach to SNP selection in germplasm identification and management, offering strong support for future plant breeding and conservation efforts.
Natural Killer Cells and Immunotherapy
Authors: Noh Ji-Yoon , Jung Haiyoung
Published: May 2023

Natural killer (NK) cells are innate immune cells that demonstrate cytolytic activity against tumor cells, virus-infected cells and other physiologically stressed cells, such as senescent cells [...]
Simulated Autonomous Driving Using Reinforcement Learning: A Comparative Study on Unity’s ML-Agents Framework
Authors: Savid Yusef , Mahmoudi Reza , Maskeliūnas Rytis , Damaševičius Robertas
Published: May 2023

Advancements in artificial intelligence are leading researchers to find use cases that were not as straightforward to solve in the past. The use case of simulated autonomous driving has been known as a notoriously difficult task to automate, but advancements in the field of reinforcement learning have made it possible to reach satisfactory results. In this paper, we explore the use of the Unity ML-Agents toolkit to train intelligent agents to navigate a racing track in a simulated environment using RL algorithms. The paper compares the performance of several different RL algorithms and configurations on the task of training kart agents to successfully traverse a racing track and identifies the most effective approach for training kart agents to navigate a racing track and avoid obstacles in that track. The best results, value loss of 0.0013 and a cumulative reward of 0.761, were yielded using the Proximal Policy Optimization algorithm. After successfully choosing a model and algorithm that can traverse the track with ease, different objects were added to the track and another model (which used behavioral cloning as a pre-training option) was trained to avoid such obstacles. The aforementioned model resulted in a value loss of 0.001 and a cumulative reward of 0.068, proving that behavioral cloning can help achieve satisfactory results where the in game agents are able to avoid obstacles more efficiently and complete the track with human-like performance, allowing for a deployment of intelligent agents in racing simulators.