bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial Genome Variation in Polish Elite Athletes
Authors: Piotrowska-Nowak Agnieszka , Safranow Krzysztof , Adamczyk Jakub G. , Sołtyszewski Ireneusz , Cięszczyk Paweł , Tońska Katarzyna , Żekanowski Cezary , Borzemska Beata
Published: August 2023

Energy efficiency is one of the fundamental athletic performance-affecting features of the cell and the organism as a whole. Mitochondrial DNA (mtDNA) variants and haplogroups have been linked to the successful practice of various sports, but despite numerous studies, understanding of the correlation is far from being comprehensive. In this study, the mtDNA sequence and copy number were determined for 99 outstanding Polish male athletes performing in power (n = 52) or endurance sports (n = 47) and 100 controls. The distribution of haplogroups, single nucleotide variant association, heteroplasmy, and mtDNA copy number were analyzed in the blood and saliva. We found no correlation between any haplogroup, single nucleotide variant, especially rare or non-synonymous ones, and athletic performance. Interestingly, heteroplasmy was less frequent in the study group, especially in endurance athletes. We observed a lower mtDNA copy number in both power and endurance athletes compared to controls. This could result from an inactivity of compensatory mechanisms activated by disadvantageous variants present in the general population and indicates a favorable genetic makeup of the athletes. The results emphasize a need for a more comprehensive analysis of the involvement of the mitochondrial genome in physical performance, combining nucleotide and copy number analysis in the context of nuclear gene variants.
CD74 Promotes a Pro-Inflammatory Tumor Microenvironment by Inducing S100A8 and S100A9 Secretion in Pancreatic Cancer
Authors: Hong Woosol Chris , Lee Da Eun , Kang Hyeon Woong , Kim Myeong Jin , Kim Minsoo , Kim Ju Hyun , Fang Sungsoon , Kim Hyo Jung , Park Joon Seong
Published: August 2023

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive form of pancreatic cancer with a poor prognosis and low survival rates. The prognostic and predictive biomarkers of PDAC are still largely unknown. The receptor CD74 was recently identified as a regulator of oncogenic properties in various cancers. However, the precise molecular mechanism of CD74 action in PDAC remains little understood. We investigated the role of CD74 by silencing CD74 in the pancreatic cancer cell line Capan-1. CD74 knockdown led to reductions in cell proliferation, migration, and invasion and increased apoptosis. Moreover, silencing CD74 resulted in the decreased expression and secretion of S100A8 and S100A9. An indirect co-culture of fibroblasts and tumor cells revealed that fibroblasts exposed to conditioned media from CD74 knockdown cells exhibited a reduced expression of inflammatory cytokines, suggesting a role of CD74 in influencing cytokine secretion in the tumor microenvironment. Overall, our study provides valuable insights into the critical role of CD74 in regulating the oncogenic properties of pancreatic cancer cells and its influence on the expression and secretion of S100A8 and S100A9. Taken together, these findings indicate CD74 as a potential diagnostic biomarker and therapeutic target for pancreatic cancer.
Lessons from Animal Models in Sjögren’s Syndrome
Authors: Mieliauskaitė Diana , Kontenis Vilius , Šiaurys Almantas
Published: August 2023

Primary Sjögren’s syndrome (pSS) is a connective tissue disease characterized by a wide spectrum of clinical features, extending from a benign glandular disease to an aggressive systemic disorder and/or lymphoma. The pathogenesis of Sjögren’s syndrome (SS) is not completely understood, but it is assumed that pathogenesis of SS is multifactorial. The studies based on the animal models of SS provided significant insight in SS disease pathogenesis and management. The aim of this review is to summarize current studies on animal models with primary SS-like symptoms and discuss the impact of these studies on better understanding pathogenesis and management of Sjögren’s syndrome. Databases PubMed, Web of Science, Scopus and Cochrane library were searched for summarizing studies on animal models in SS. Available data demonstrate that animal models are highly important for our understanding of SS disease.
Drug Repositioning for Refractory Benign Tumors of the Central Nervous System
Authors: Tamura Ryota
Published: August 2023

Drug repositioning (DR) is the process of identifying novel therapeutic potentials for already-approved drugs and discovering new therapies for untreated diseases. DR can play an important role in optimizing the pre-clinical process of developing novel drugs by saving time and cost compared with the process of de novo drug discovery. Although the number of publications related to DR has rapidly increased, most therapeutic approaches were reported for malignant tumors. Surgical resection represents the definitive treatment for benign tumors of the central nervous system (BTCNS). However, treatment options remain limited for surgery-, chemotherapy- and radiation-refractory BTCNS, as well as malignant tumors. Meningioma, pituitary neuroendocrine tumor (PitNET), and schwannoma are the most common BTCNS. The treatment strategy using DR may be applied for refractory BTCNS, such as Grade 2 meningiomas, neurofibromatosis type 2-related schwannomatosis, and PitNETs with cavernous sinus invasion. In the setting of BTCNS, stable disease can provide significant benefit to the patient. DR may provide a longer duration of survival without disease progression for patients with refractory BTCNS. This article reviews the utility of DR for refractory BTCNS.
Sialic-Acid-Related Enzymes of B Cells and Monocytes as Novel Markers to Discriminate Improvement Categories and to Fulfill Two Remission Definitions in Rheumatoid Arthritis
Authors: Liou Lieh-Bang , Tsai Ping-Han , Fang Yao-Fan , Chen Yen-Fu , Chen Chih-Chieh , Lai Jenn-Haung
Published: August 2023

The enzymes α-2,6-sialyltransferase 1 (ST6Gal1), neuraminidase 1 (Neu1), α-2,3-sialyltransferase 1 (ST3Gal1), and neuraminidase 3 (Neu3) are known to affect immune cell function. However, it is not known whether the levels of these enzymes relate to remission definitions or differentiate American College of Rheumatology (ACR), European League Against Rheumatism (EULAR), and Simplified Disease Activity Index (SDAI) responses in patients with rheumatoid arthritis (RA). We measured the ST6Gal1, Neu1, ST3Gal1, and Neu3 levels of B cells and monocytes in RA patients and correlated the cells’ enzyme levels/ratios with the improvement in the ACR, EULAR and SDAI responses and with the two remission definitions. The difference in the B-cell Neu1 levels differed between the ACR 70% improvement and non-improvement groups (p = 0.043), between the EULAR good major response (improvement) and non-good response groups (p = 0.014), and also between the SDAI 50% or 70% improvement and non-improvement groups (p = 0.001 and 0.018, respectively). The same held true when the RA patients were classified by positive rheumatoid factor or the use of biologics. The B-cell Neu1 levels significantly indicated 2005 modified American Rheumatism Association and 2011 ACR/EULAR remission definitions (area under the curve (AUC) = 0.674 with p = 0.001, and AUC = 0.682 with p < 0.001, respectively) in contrast to the CRP and ESR (all AUCs < 0.420). We suggest that B-cell Neu1 is superior for discriminating ACR, EULAR, and SDAI improvement and is good for predicting two kinds of remission definitions.
Phosphate Additives for Aging Inhibition of Impregnated Activated Carbon against Hazardous Gases
Authors: Nir Ido , Shepelev Vladislav , Pevzner Alexander , Marciano Daniele , Rosh Lilach , Amitay-Rosen Tal , Rotter Hadar
Published: August 2023

Impregnated activated carbons (IACs) used in air filtration gradually lose their efficacy for the chemisorption of noxious gases when exposed to humidity due to impregnated metal deactivation. In order to stabilize IACs against aging, and to prolong the filters’ shelf life, inorganic phosphate compounds (phosphoric acid and its three salts, NaHPO4, Na2HPO4, and Na3PO4) were used as anti-aging additives for two different chromium-free IACs impregnated with copper, zinc, molybdenum, and triethylenediamine (TEDA). Phosphoric acid, monosodium, and disodium phosphate were found to be very efficient in inhibiting the aging of IACs over long periods against cyanogen chloride (the test agent) chemisorption, with the latter being the most efficient. However, the efficiency of phosphate as an anti-aging additive was not well correlated with its ability to inhibit the migration of metal impregnants, especially copper, from the interior to the external surface of carbon granules. Unlike organic additives, the inorganic phosphate additives did not decrease the surface area of the IAC or its physical adsorption capacity for toluene. Using a phosphate additive in IAC used in collective protection and personal filters can improve the safety of the user and the environment and dramatically reduce the need to replace these filters after exposure to humid environments. This has safety, economic, logistical, and environmental advantages.
Recent Advances in Miscanthus Macromolecule Conversion: A Brief Overview
Authors: Mironova Galina F. , Budaeva Vera V. , Skiba Ekaterina A. , Gismatulina Yulia A. , Kashcheyeva Ekaterina I. , Sakovich Gennady V.
Published: August 2023

Miscanthus is a valuable renewable feedstock and has a significant potential for the manufacture of diverse biotechnology products based on macromolecules such as cellulose, hemicelluloses and lignin. Herein, we overviewed the state-of-the art of research on the conversion of miscanthus polymers into biotechnology products comprising low-molecular compounds and macromolecules: bioethanol, biogas, bacterial cellulose, enzymes (cellulases, laccases), lactic acid, lipids, fumaric acid and polyhydroxyalkanoates. The present review aims to assess the potential of converting miscanthus polymers in order to develop sustainable technologies.
Targeting SARS-CoV-2 Non-Structural Proteins
Authors: Tam Donald , Lorenzo-Leal Ana C. , Hernández Luis Ricardo , Bach Horacio
Published: August 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped respiratory β coronavirus that causes coronavirus disease (COVID-19), leading to a deadly pandemic that has claimed millions of lives worldwide. Like other coronaviruses, the SARS-CoV-2 genome also codes for non-structural proteins (NSPs). These NSPs are found within open reading frame 1a (ORF1a) and open reading frame 1ab (ORF1ab) of the SARS-CoV-2 genome and encode NSP1 to NSP11 and NSP12 to NSP16, respectively. This study aimed to collect the available literature regarding NSP inhibitors. In addition, we searched the natural product database looking for similar structures. The results showed that similar structures could be tested as potential inhibitors of the NSPs.
Tryptophan Modulation in Cancer-Associated Cachexia Mouse Models
Authors: Agulló-Ortuño M. Teresa , Mancebo Esther , Grau Montserrat , Núñez Sobrino Juan Antonio , Paz-Ares Luis , López-Martín José A. , Flández Marta
Published: August 2023

Cancer cachexia is a multifactorial syndrome that interferes with treatment and reduces the quality of life and survival of patients. Currently, there is no effective treatment or biomarkers, and pathophysiology is not clear. Our group reported alterations on tryptophan metabolites in cachectic patients, so we aim to investigate the role of tryptophan using two cancer-associated cachexia syngeneic murine models, melanoma B16F10, and pancreatic adenocarcinoma that is KPC-based. Injected mice showed signs of cancer-associated cachexia as reduction in body weight and raised spleen weight, MCP1, and carbonilated proteins in plasma. CRP and Myostatin also increased in B16F10 mice. Skeletal muscle showed a decrease in quadriceps weight and cross-sectional area (especially in B16F10). Higher expression of atrophy genes, mainly Atrogin1, was also observed. Plasmatic tryptophan levels in B16F10 tumor-bearing mice decreased even at early steps of tumorigenesis. In KPC-injected mice, tryptophan fluctuated but were also reduced and in cachectic patients were significantly lower. Treatment with 1-methyl-tryptophan, an inhibitor of tryptophan degradation, in the murine models resulted in the restoration of plasmatic tryptophan levels and an improvement on splenomegaly and carbonilated proteins levels, while changes in plasmatic inflammatory markers were mild. After the treatment, CCR2 expression in monocytes diminished and lymphocytes, Tregs, and CD8+, were activated (seen by increased in CD127 and CD25 expression, respectively). These immune cell changes pointed to an improvement in systemic inflammation. While treatment with 1-MT did not show benefits in terms of muscle wasting and atrophy in our experimental setting, muscle functionality was not affected and central nuclei fibers appeared, being a feature of regeneration. Therefore, tryptophan metabolism pathway is a promising target for inflammation modulation in cancer-associated cachexia.
Establishment of RNA Interference Genetic Transformation System and Functional Analysis of FlbA Gene in Leptographium qinlingensis
Authors: Gan Tian , An Huanli , Tang Ming , Chen Hui
Published: August 2023

Leptographium qinlingensis is a pathogenic fungus of Pinus armandii that is epidemic in the Qinling Mountains. However, an effective gene interference strategy is needed to characterize the pathogenic genes in this fungus on a functional level. Using the RNA silencing vector pSilent-1 as a template, we established an RNA interference genetic transformation system mediated by Agrobacterium tumefaciens GV3101, which is suitable for the gene study for Leptographium qinlingensis by homologous recombination and strain interference system screening. The LqFlbA gene was silenced using the RNA interference approach described above, and the resulting transformants displayed various levels of silencing with a gene silencing effectiveness ranging from 41.8% to 91.4%. The LqFlbA-RNAi mutant displayed altered colony morphology, sluggish mycelium growth, and diminished pathogenicity toward the host P. armandii in comparison to the wild type. The results indicate that this method provides a useful reverse genetic system for studying the gene function of L. qinlingensis, and that LqFlbA plays a crucial role in the growth, development, and pathogenicity of L. qinlingensis.
Depressive-like Behaviors Induced by mGluR5 Reduction in 6xTg in Mouse Model of Alzheimer’s Disease
Authors: Kim Youngkyo , Kim Jinho , Kang Shinwoo , Chang Keun-A
Published: August 2023

Alzheimer’s disease (AD) is one representative dementia characterized by the accumulation of amyloid beta (Aβ) plaques and neurofibrillary tangles (NFTs) in the brain, resulting in cognitive decline and memory loss. AD is associated with neuropsychiatric symptoms, including major depressive disorder (MDD). Recent studies showed a reduction in mGluR5 expression in the brains of stress-induced mice models and individuals with MDD compared to controls. In our study, we identified depressive-like behavior and memory impairment in a mouse model of AD, specifically in the 6xTg model with tau and Aβ pathologies. In addition, we investigated the expression of mGluR5 in the brains of 6xTg mice using micro-positron emission tomography (micro-PET) imaging, histological analysis, and Western blot analysis, and we observed a decrease in mGluR5 levels in the brains of 6xTg mice compared to wild-type (WT) mice. Additionally, we identified alterations in the ERK/AKT/GSK-3β signaling pathway in the brains of 6xTg mice. Notably, we identified a significant negative correlation between depressive-like behavior and the protein level of mGluR5 in 6xTg mice. Additionally, we also found a significant positive correlation between depressive-like behavior and AD pathologies, including phosphorylated tau and Aβ. These findings suggested that abnormal mGluR5 expression and AD-related pathologies were involved in depressive-like behavior in the 6xTg mouse model. Further research is warranted to elucidate the underlying mechanisms and explore potential therapeutic targets in the intersection of AD and depressive-like symptoms.
Determination of Kinetic Parameters and Identification of the Rate-Determining Steps in the Oxygen Exchange Process for LaNi0.6Fe0.4O3−δ
Authors: Porotnikova Natalia , Zakharov Dmitriy , Khodimchuk Anna , Kurumchin Edhem , Osinkin Denis
Published: August 2023

The mixed ionic and electronic oxide LaNi0.6Fe0.4O3−δ (LNF) is a promising ceramic cathode material for solid oxide fuel cells. Since the reaction rate of oxygen interaction with the cathode material is extremely important, the present work considers the oxygen exchange mechanism between O2 and LNF oxide. The kinetic dependence of the oxygen/oxide interaction has been determined by two isotopic methods using 18O-labelled oxygen. The application of the isotope exchange with the gas phase equilibrium (IE-GPE) and the pulsed isotope exchange (PIE) has provided information over a wide range of temperatures (350–800 °C) and oxygen pressures (10–200 mbar), as each method has different applicability limits. Applying mathematical models to treat the kinetic relationships, the oxygen exchange rate (rH, atom × cm−2 × s−1) and the diffusion coefficient (D, cm2/s) were calculated. The values of rH and D depend on both temperature and oxygen pressure. The activation energy of the surface exchange rate is 0.73 ± 0.05 eV for the PIE method at 200 mbar, and 0.48 ± 0.02 eV for the IE-GPE method at 10–20 mbar; for the diffusion coefficient, the activation energy equals 0.62 ± 0.01 eV at 10–20 mbar for the IE-GPE method. Differences in the mechanism of oxygen exchange and diffusion on dense and powder samples are observed due to the different microstructure and surface morphology of the samples. The influence of oxygen pressure on the ratio of contributions of different exchange types to the total oxygen exchange rate is demonstrated. For the first time, the rate-determining step in the oxygen exchange process for LNF material has been identified. This paper discusses the reasons for the difference in the mechanisms of oxygen exchange and diffusion.
Giant Arachnoid Granulations: A Systematic Literature Review
Authors: Mehta Rupal I. , Mehta Rashi I.
Published: August 2023

Giant arachnoid granulations (GAGs) are minimally investigated. Here, we systematically review the available data in published reports to better understand their etiologies, nomenclature, and clinical significance. In the literature, 195 GAGs have been documented in 169 persons of varied ages (range, 0.33 to 91 years; mean, 43 ± 20 years; 54% female). Prior reports depict intrasinus (i.e., dural venous sinus, DVS) (84%), extrasinus (i.e., diploic or calvarial) (15%), and mixed (1%) GAG types that exhibit pedunculated, sessile, or vermiform morphologies. GAG size ranged from 0.4 to 6 cm in maximum dimension (mean, 1.9 ± 1.1 cm) and encompassed symptomatic or non-symptomatic enlarged arachnoid granulations (≥1 cm) as well as symptomatic subcentimeter arachnoid granulations. A significant difference was identified in mean GAG size between sex (females, 1.78 cm; males, 3.39 cm; p < 0.05). The signs and symptoms associated with GAGs varied and include headache (19%), sensory change(s) (11%), and intracranial hypertension (2%), among diverse and potentially serious sequelae. Notably, brain herniation was present within 38 GAGs (22%). Among treated individuals, subsets were managed medically (19 persons, 11%), surgically (15 persons, 9%), and/or by endovascular DVS stenting (7 persons, 4%). Histologic workup of 53 (27%) GAG cases depicted internal inflammation (3%), cystic change consistent with fluid accumulation (2%), venous thrombosis (1%), hemorrhage (1%), meningothelial hyperplasia (1%), lymphatic vascular proliferation (1%), and lymphatic vessel obliteration (1%). This review emphasizes heterogeneity in GAG subtypes, morphology, composite, location, symptomatology, and imaging presentations. Additional systematic investigations are needed to better elucidate the pathobiology, clinical effects, and optimal diagnostic and management strategies for enlarged and symptomatic arachnoid granulation subtypes, as different strategies and size thresholds are likely applicable for medical, interventional, and/or surgical treatment of these structures in distinct brain locations.
Why Does the Antioxidant Complex Twendee X® Prevent Dementia?
Authors: You Fukka , Harakawa Yoshiaki , Yoshikawa Toshikazu , Inufusa Haruhiko
Published: August 2023

Alzheimer’s disease (AD) is a complex neurodegenerative disease characterized by cognitive and short-term memory impairments. The disease involves multiple pathological factors such as amyloid plaque formation, mitochondrial dysfunction, and telomere shortening; however, oxidative stress and diabetes mellitus are significant risk factors. The onset of AD begins approximately 20 years before clinical symptoms manifest; therefore, treating AD after symptoms become evident is possibly too late to have a significant effect. As such, preventing AD or using an effective treatment at an early stage is important. Twendee X® (TwX) is an antioxidant formulation consisting of eight ingredients. TwX has been proven to prevent the progression to dementia in patients with mild cognitive impairment (MCI) in a multicenter, randomized, double-blind, placebo-controlled, prospective intervention trial. As well, positive data has already been obtained in several studies using AD model mice. Since both diabetes and aging are risk factors for AD, we examined the mechanisms behind the effects of TwX on AD using the spontaneous hyperglycemia model and the senescence model of aged C57BL/6 mice in this study. TwX was administered daily, and its effects on diabetes, autophagy in the brain, neurogenesis, and telomere length were examined. We observed that TwX protected the mitochondria from oxidative stress better than a single antioxidant. TwX not only lowered blood glucose levels but also suppressed brain neurogenesis and autophagy. Telomeres in TWX-treated mice were significantly longer than those in non-treated mice. There are many factors that can be implicated in the development and progression of dementia; however, multiple studies on TwX suggest that it may offer protection against dementia, not only through the effects of its antioxidants but also by targeting multiple mechanisms involved in its development and progression, such as diabetes, brain neurogenesis, telomere deficiency, and energy production.
Organically Templated Uranyl Sulfates and Selenates: Structural Complexity and Crystal Chemical Restrictions for Isotypic Compounds Formation
Authors: Durova Elizaveta V. , Kuporev Ivan V. , Gurzhiy Vladislav V.
Published: August 2023

This paper reviews the state of the art in the structural chemistry of organically templated uranyl sulfates and selenates, which are considered as the most representative groups of U-bearing synthetic compounds. In total, there are 194 compounds known for both groups, the crystal structures of which include 84 various organic molecules. Structural studies and topological analysis clearly indicate complex crystal chemical limitations in terms of the isomorphic substitution implementation, since the existence of isotypic phases has to date been confirmed only for 24 compounds out of 194, which is slightly above 12%. The structural architecture of the entire compound depends on the combination of the organic and oxyanion parts, changes in which are sometimes realized even while maintaining the topology of the U-bearing complex. An increase in the size of the hydrocarbon part and number of charge functional groups of the organic cation leads to the formation of rare and more complex topologies. In addition, the crystal structures of two novel uranyl sulfates and one uranyl selenate, templated by isopropylammonium cations, are reported.
From Pathogenesis to Therapeutics: A Review of 150 Years of Huntington’s Disease Research
Authors: Jiang Andrew , Handley Renee R. , Lehnert Klaus , Snell Russell G.
Published: August 2023

Huntington’s disease (HD) is a debilitating neurodegenerative genetic disorder caused by an expanded polyglutamine-coding (CAG) trinucleotide repeat in the huntingtin (HTT) gene. HD behaves as a highly penetrant dominant disorder likely acting through a toxic gain of function by the mutant huntingtin protein. Widespread cellular degeneration of the medium spiny neurons of the caudate nucleus and putamen are responsible for the onset of symptomology that encompasses motor, cognitive, and behavioural abnormalities. Over the past 150 years of HD research since George Huntington published his description, a plethora of pathogenic mechanisms have been proposed with key themes including excitotoxicity, dopaminergic imbalance, mitochondrial dysfunction, metabolic defects, disruption of proteostasis, transcriptional dysregulation, and neuroinflammation. Despite the identification and characterisation of the causative gene and mutation and significant advances in our understanding of the cellular pathology in recent years, a disease-modifying intervention has not yet been clinically approved. This review includes an overview of Huntington’s disease, from its genetic aetiology to clinical presentation and its pathogenic manifestation. An updated view of molecular mechanisms and the latest therapeutic developments will also be discussed.
Job Vacancy Ranking with Sentence Embeddings, Keywords, and Named Entities
Authors: Vanetik Natalia , Kogan Genady
Published: August 2023

Resume matching is the process of comparing a candidate’s curriculum vitae (CV) or resume with a job description or a set of employment requirements. The objective of this procedure is to assess the degree to which a candidate’s skills, qualifications, experience, and other relevant attributes align with the demands of the position. Some employment courses guide applicants in identifying the key requirements within a job description and tailoring their experience to highlight these aspects. Conversely, human resources (HR) specialists are trained to extract critical information from numerous submitted resumes to identify the most suitable candidate for their organization. An automated system is typically employed to compare the text of resumes with job vacancies, providing a score or ranking to indicate the level of similarity between the two. However, this process can become time-consuming when dealing with a large number of applicants and lengthy vacancy descriptions. In this paper, we present a dataset consisting of resumes of software developers extracted from a public Telegram channel dedicated to Israeli hi-tech job applications. Additionally, we propose a natural language processing (NLP)-based approach that leverages neural sentence representations, keywords, and named entities to achieve state-of-the-art performance in resume matching. We evaluate our approach using both human and automatic annotations and demonstrate its superiority over the leading resume–vacancy matching algorithm.
Exploring Evaluation Methods for Interpretable Machine Learning: A Survey
Authors: Alangari Nourah , El Bachir Menai Mohamed , Mathkour Hassan , Almosallam Ibrahim
Published: August 2023

In recent times, the progress of machine learning has facilitated the development of decision support systems that exhibit predictive accuracy, surpassing human capabilities in certain scenarios. However, this improvement has come at the cost of increased model complexity, rendering them black-box models that obscure their internal logic from users. These black boxes are primarily designed to optimize predictive accuracy, limiting their applicability in critical domains such as medicine, law, and finance, where both accuracy and interpretability are crucial factors for model acceptance. Despite the growing body of research on interpretability, there remains a significant dearth of evaluation methods for the proposed approaches. This survey aims to shed light on various evaluation methods employed in interpreting models. Two primary procedures are prevalent in the literature: qualitative and quantitative evaluations. Qualitative evaluations rely on human assessments, while quantitative evaluations utilize computational metrics. Human evaluation commonly manifests as either researcher intuition or well-designed experiments. However, this approach is susceptible to human biases and fatigue and cannot adequately compare two models. Consequently, there has been a recent decline in the use of human evaluation, with computational metrics gaining prominence as a more rigorous method for comparing and assessing different approaches. These metrics are designed to serve specific goals, such as fidelity, comprehensibility, or stability. The existing metrics often face challenges when scaling or being applied to different types of model outputs and alternative approaches. Another important factor that needs to be addressed is that while evaluating interpretability methods, their results may not always be entirely accurate. For instance, relying on the drop in probability to assess fidelity can be problematic, particularly when facing the challenge of out-of-distribution data. Furthermore, a fundamental challenge in the interpretability domain is the lack of consensus regarding its definition and requirements. This issue is compounded in the evaluation process and becomes particularly apparent when assessing comprehensibility.
In Situ Preparation of 2D Co-B Nanosheets@1D TiO2 Nanofibers as a Catalyst for Hydrogen Production from Sodium Borohydride
Authors: Maafa Ibrahim M. , Zouli Nasser , Abutaleb Ahmed , Yousef Ayman , Qudsieh Isam Y. , Matar Saleh M. , Adam Abdel Samed M. , El-Halwany M. M.
Published: August 2023

In this study, 2D Co-B nanosheet-decorated 1D TiO2 nanofibers (2D Co-B NS-decorated 1D TiO2 NFs) are synthesized via electrospinning and an in situ chemical reduction technique. The as-prepared catalyst showed excellent catalytic performance in H2 generation from sodium borohydride (SBH). When compared to naked Co-B nanoparticles, the catalytic activity of the 2D Co-B NS-decorated 1D TiO2 NFs catalyst for the hydrolysis of SBH is significantly enhanced, as demonstrated by the high hydrogen generation rate (HGR) of 6020 mL min−1 g−1 at 25 °C. The activation energy of hydrolysis was measured to be 30.87 kJ mol−1, which agreed with the reported values. The catalyst also showed good stability. Moreover, the effects of SBH, catalyst concentration, and temperature on the catalytic performance of 2D Co-B NS-decorated 1D TiO2 NFs were studied to gain a comprehensive understanding of the dehydrogenation mechanism of SBH. Based on these findings, we conclude that 2D Co-B NS-decorated 1D TiO2 NFs are effective catalytic materials for the dehydrogenation of SBH.
Breeding Polyommatus icarus Serves as a Large-Scale and Environmentally Friendly Source of Precisely Tuned Photonic Nanoarchitectures
Authors: Piszter Gábor , Bálint Zsolt , Kertész Krisztián , Szatmári Lajos , Sramkó Gábor , Biró László Péter
Published: August 2023

The colour of the butterfly wing serves as an important sexual and species-specific signal. Some species produce structural colouration by developing wing scales with photonic nanoarchitectures. These nanostructures are highly conservative, allowing only a ±10 nm peak wavelength deviation in the reflectance spectra of the blue structural colour in natural Common Blue (Polyommatus icarus) populations. They are promising templates of future artificial photonic materials and can be used in potential applications, too. In this work, we present methodology and infrastructure for breeding laboratory populations of Common Blue as a cost-effective and environmentally friendly source of nanostructures. Our technology enables the production of approximately 7500 wing samples, equivalent to 0.5–1 m2 of photonic nanoarchitecture surface within a year in a single custom-made insectarium. To ascertain the reliability of this method, we compared reflectance properties between different populations from distant geographic locations. We also provide genetic background of these populations using microsatellite genotyping. The laboratory population showed genetic erosion, but even after four generations of inbreeding, only minimal shifts in the structural colouration were observed, indicating that wild Common Blue populations may be a reliable source of raw material for photonic surfaces.
The Adenylate Cyclase-Encoding Gene crac Is Involved in Clonostachys rosea Mycoparasitism
Authors: Yu Shu-Fan , Sun Zhan-Bin , Li Shi-Dong , Hu Ya-Feng , Ren Qing , Xu Jia-Liang , Song Han-Jian , Sun Man-Hong
Published: August 2023

Clonostachys rosea is an excellent biocontrol fungus against numerous fungal plant pathogens. The cAMP signaling pathway is a crucial signal transduction pathway in fungi. To date, the role of the cAMP signaling pathway in C. rosea mycoparasitism remains unknown. An adenylate cyclase-encoding gene, crac (an important component of the cAMP signaling pathway), was previously screened from C. rosea 67-1, and its expression level was dramatically upregulated during the C. rosea mycoparasitization of the sclerotia of Sclerotinia sclerotiorum. In this study, the function of crac in C. rosea mycoparasitism was explored through gene knockout and complementation. The obtained results show that the deletion of crac influenced the growth rate and colony morphology of C. rosea, as well as the tolerance to NaCl and H2O2 stress. The mycoparasitic effects on the sclerotia of S. sclerotiorum and the biocontrol capacity on soybean Sclerotinia stem rot in ∆crac-6 and ∆crac-13 were both attenuated compared with that of the wild-type strain and complementation transformants. To understand the regulatory mechanism of crac during C. rosea mycoparasitism, transcriptomic analysis was conducted between the wild-type strain and knockout mutant. A number of biocontrol-related genes, including genes encoding cell wall-degrading enzymes and transporters, were significantly differentially expressed during C. rosea mycoparasitism, suggesting that crac may be involved in C. rosea mycoparasitism by regulating the expression of these DEGs. These findings provide insight for further exploring the molecular mechanism of C. rosea mycoparasitism.
A New Insight into 6-Pentyl-2H-pyran-2-one against Peronophythora litchii via TOR Pathway
Authors: Wu Yinggu , Li Xinyu , Dong Li , Liu Tong , Tang Zhengbin , Lin Runmao , Norvienyeku Justice , Xing Mengyu
Published: August 2023

The litchi downy blight disease of litchi caused by Peronophythora litchii accounts for severe losses in the field and during storage. While ample quantitative studies have shown that 6-pentyl-2H-pyran-2-one (6PP) possesses antifungal activities against multiple plant pathogenic fungi, the regulatory mechanisms of 6PP-mediated inhibition of fungal pathogenesis and growth are still unknown. Here, we investigated the potential molecular targets of 6PP in the phytopathogenic oomycetes P. litchii through integrated deployment of RNA-sequencing, functional genetics, and biochemical techniques to investigate the regulatory effects of 6PP against P. litchii. Previously we demonstrated that 6PP exerted significant oomyticidal activities. Also, comparative transcriptomic evaluation of P. litchii strains treated with 6PP Revealed significant up-regulations in the expression profile of TOR pathway-related genes, including PlCytochrome C and the transcription factors PlYY1. We also noticed that 6PP treatment down-regulated putative negative regulatory genes of the TOR pathway, including PlSpm1 and PlrhoH12 in P. litchii. Protein-ligand binding analyses revealed stable affinities between PlYY1, PlCytochrome C, PlSpm1, PlrhoH12 proteins, and the 6PP ligand. Phenotypic characterization of PlYY1 targeted gene deletion strains generated in this study using CRISPR/Cas9 and homologous recombination strategies significantly reduced the vegetative growth, sporangium, encystment, zoospore release, and pathogenicity of P. litchii. These findings suggest that 6PP-mediated activation of PlYY1 expression positively regulates TOR-related responses and significantly influences vegetative growth and the virulence of P. litchii. The current investigations revealed novel targets for 6PP and underscored the potential of deploying 6PP in developing management strategies for controlling the litchi downy blight pathogen.
Antimicrobial and Antioxidant Activities of Endophytic Fungi Associated with Arrabidaea chica (Bignoniaceae)
Authors: Gurgel Raiana Silveira , de Melo Pereira Dorothy Ívila , Garcia Ana Vyktória França , Fernandes de Souza Anne Terezinha , Mendes da Silva Thaysa , de Andrade Cleudiane Pereira , Lima da Silva Weison , Nunez Cecilia Veronica , Fantin Cleiton , de Lima Procópio Rudi Emerson , Albuquerque Patrícia Melchionna
Published: August 2023

The endophytic fungal community of the Amazonian medicinal plant Arrabidaea chica (Bignoniaceae) was evaluated based on the hypothesis that microbial communities associated with plant species in the Amazon region may produce metabolites with interesting bioactive properties. Therefore, the antimicrobial and antioxidant activities of the fungal extracts were investigated. A total of 107 endophytic fungi were grown in liquid medium and the metabolites were extracted with ethyl acetate. In the screening of fungal extracts for antimicrobial activity, the fungus identified as Botryosphaeria mamane CF2-13 was the most promising, with activity against E. coli, S. epidermidis, P. mirabilis, B. subtilis, S. marcescens, K. pneumoniae, S. enterica, A. brasiliensis, C. albicans, C. tropicalis and, especially, against S. aureus and C. parapsilosis (MIC = 0.312 mg/mL). Screening for antioxidant potential using the DPPH elimination assay showed that the Colletotrichum sp. CG1-7 endophyte extract exhibited potential activity with an EC50 of 11 µg/mL, which is equivalent to quercetin (8 µg/mL). The FRAP method confirmed the antioxidant potential of the fungal extracts. The presence of phenolic compounds and flavonoids in the active extracts was confirmed using TLC. These results indicate that two of the fungi isolated from A. chica exhibit significant antimicrobial and antioxidant potential.
Characteristics of Kidney Transplant Recipients with Prolonged Pre-Transplant Dialysis Duration as Identified by Machine Learning Consensus Clustering: Pathway to Personalized Care
Authors: Thongprayoon Charat , Tangpanithandee Supawit , Jadlowiec Caroline C. , Mao Shennen A. , Mao Michael A. , Vaitla Pradeep , Acharya Prakrati C. , Leeaphorn Napat , Kaewput Wisit , Pattharanitima Pattharawin , Suppadungsuk Supawadee , Krisanapan Pajaree , Nissaisorakarn Pitchaphon , Cooper Matthew , Craici Iasmina M. , Cheungpasitporn Wisit
Published: August 2023

Longer pre-transplant dialysis duration is known to be associated with worse post-transplant outcomes. Our study aimed to cluster kidney transplant recipients with prolonged dialysis duration before transplant using an unsupervised machine learning approach to better assess heterogeneity within this cohort. We performed consensus cluster analysis based on recipient-, donor-, and transplant-related characteristics in 5092 kidney transplant recipients who had been on dialysis ≥ 10 years prior to transplant in the OPTN/UNOS database from 2010 to 2019. We characterized each assigned cluster and compared the posttransplant outcomes. Overall, the majority of patients with ≥10 years of dialysis duration were black (52%) or Hispanic (25%), with only a small number (17.6%) being moderately sensitized. Within this cohort, three clinically distinct clusters were identified. Cluster 1 patients were younger, non-diabetic and non-sensitized, had a lower body mass index (BMI) and received a kidney transplant from younger donors. Cluster 2 recipients were older, unsensitized and had a higher BMI; they received kidney transplant from older donors. Cluster 3 recipients were more likely to be female with a higher PRA. Compared to cluster 1, cluster 2 had lower 5-year death-censored graft (HR 1.40; 95% CI 1.16–1.71) and patient survival (HR 2.98; 95% CI 2.43–3.68). Clusters 1 and 3 had comparable death-censored graft and patient survival. Unsupervised machine learning was used to characterize kidney transplant recipients with prolonged pre-transplant dialysis into three clinically distinct clusters with variable but good post-transplant outcomes. Despite a dialysis duration ≥ 10 years, excellent outcomes were observed in most recipients, including those with moderate sensitization. A disproportionate number of minority recipients were observed within this cohort, suggesting multifactorial delays in accessing kidney transplantation.
Attenuated Total Reflection Fourier-Transform Infrared Spectral Discrimination in Human Tissue of Oesophageal Transformation to Adenocarcinoma
Authors: Maitra Ishaan , Morais Camilo L. M. , Lima Kássio M. G. , Ashton Katherine M. , Bury Danielle , Date Ravindra S. , Martin Francis L.
Published: August 2023

This study presents ATR-FTIR (attenuated total reflectance Fourier-transform infrared) spectral analysis of ex vivo oesophageal tissue including all classifications to oesophageal adenocarcinoma (OAC). The article adds further validation to previous human tissue studies identifying the potential for ATR-FTIR spectroscopy in differentiating among all classes of oesophageal transformation to OAC. Tissue spectral analysis used principal component analysis quadratic discriminant analysis (PCA-QDA), successive projection algorithm quadratic discriminant analysis (SPA-QDA), and genetic algorithm quadratic discriminant analysis (GA-QDA) algorithms for variable selection and classification. The variables selected by SPA-QDA and GA-QDA discriminated tissue samples from Barrett’s oesophagus (BO) to OAC with 100% accuracy on the basis of unique spectral “fingerprints” of their biochemical composition. Accuracy test results including sensitivity and specificity were determined. The best results were obtained with PCA-QDA, where tissues ranging from normal to OAC were correctly classified with 90.9% overall accuracy (71.4–100% sensitivity and 89.5–100% specificity), including the discrimination between normal and inflammatory tissue, which failed in SPA-QDA and GA-QDA. All the models revealed excellent results for distinguishing among BO, low-grade dysplasia (LGD), high-grade dysplasia (HGD), and OAC tissues (100% sensitivities and specificities). This study highlights the need for further work identifying potential biochemical markers using ATR-FTIR in tissue that could be utilised as an adjunct to histopathological diagnosis for early detection of neoplastic changes in susceptible epithelium.
Progress in Research on Stem Cells in Neonatal Refractory Diseases
Authors: Huang Fangjun , He Yang , Zhang Meng , Luo Keren , Li Jiawen , Li Jiali , Zhang Xinyu , Dong Xiaoyan , Tang Jun
Published: August 2023

With the development and progress of medical technology, the survival rate of premature and low-birth-weight infants has increased, as has the incidence of a variety of neonatal diseases, such as hypoxic–ischemic encephalopathy, intraventricular hemorrhage, bronchopulmonary dysplasia, necrotizing enterocolitis, and retinopathy of prematurity. These diseases cause severe health conditions with poor prognoses, and existing control methods are ineffective for such diseases. Stem cells are a special type of cells with self-renewal and differentiation potential, and their mechanisms mainly include anti-inflammatory and anti-apoptotic properties, reducing oxidative stress, and boosting regeneration. Their paracrine effects can affect the microenvironment in which they survive, thereby affecting the biological characteristics of other cells. Due to their unique abilities, stem cells have been used in treating various diseases. Therefore, stem cell therapy may open up the possibility of treating such neonatal diseases. This review summarizes the research progress on stem cells and exosomes derived from stem cells in neonatal refractory diseases to provide new insights for most researchers and clinicians regarding future treatments. In addition, the current challenges and perspectives in stem cell therapy are discussed.
Trace Elements and Their Management in Dialysis Patients—Pathophysiology and Clinical Manifestations
Authors: Wakino Shu
Published: August 2023

Recently, as the number of elderly dialysis patients has been increasing, complications associated with low nutritional status such as infectious disease have had a strong influence on the prognosis of dialysis patients. Nutritional disorders are caused by the inadequate intake of the three major nutrients—proteins, fats, and carbohydrates—as well as vitamin and mineral deficiencies. Minerals are composed of various elements, including small-amount elements and trace elements, which are present in the human body in very small quantities lower than that of iron. In dialysis and predialysis patients, zinc, manganese, and selenium are the three major elements that are significantly depleted as compared to normal subjects; these deficiencies are sometimes symptomatic. Zinc deficiency is manifest as anemia, taste abnormality, and delayed wound healing, while selenium deficiency is associated with impaired cardiac function and immunocompromised condition. Zinc has multiple functions, since various enzymes, including DNA polymerase and RNA polymerase, need zinc as a cofactor, while selenium is a component of selenoproteins, including glutathione peroxidase and thioredoxin reductases, which are major antioxidative stress enzymes. These elements can only be supplemented exogenously and contribute to the sustainable QOL of dialysis patients. On the other hand, as regards other trace elements, including copper, chromium, manganese, lead, arsenic, etc., the association of their deficiency or intoxication with various involvements of dialysis patients were investigated, although all investigations were performed in cross-sectional studies or observational studies. Therefore, the supplementation of these elements is inconclusive, given the scarcity of other intervention studies. More conclusive studies are endorsed for the establishment of proper supplementation strategies.
Beyond Colonial Boundaries: Reimagining the Rozvi through Landscapes, Identities and Indigenous Epistemologies
Authors: Machiridza Lesley Hatipone , Kapumha Russell
Published: August 2023

The land, ‘things’/objects, and memory in the form of narratives and metaphors are intricately bound together. They all constitute the iconography of a shared set of ideas, beliefs, feelings, values, practices, and performances that objectify collective identities. Respectively, these complex entangled tangible and spiritual/invisible indices of identities situated in places deserve special archaeological devotion. However, since African archaeology and history remains trapped in Eurocentric colonial metanarratives, indigenous epistemologies and ontologies have somehow remained on the margins of knowledge production processes. This deliberate erasure and silencing continues to impede archaeology’s capacity to explore hidden meanings and values that people imbue to places and landscapes through time. Owing to this setback, multiple precolonial group identities in parts of Zimbabwe, South Africa, Botswana, and Mozambique such as Torwa, Twamamba, Rozvi, Singo, and Venda, among others, remain vague and subjectively tied to the archaeology of Butua/Torwa (AD 1400–1644) and Rozvi (AD 1685–1830) state systems. The failure to read the landscape as both a repository of memory and an agent for collective identities continues to compound our archaeological challenges. Against this background, Rozvi oral narratives and the Insiza cluster Khami-phase sites in southwestern Zimbabwe are subjected to renewed scrutiny. Following a critical review of colonial archives and Rozvi traditions, it turned out that instead of contradicting ‘science’, oral traditions actually amplify our reading of the archaeological record, only if handled properly.