bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-Assembly of a Novel Pentapeptide into Hydrogelated Dendritic Architecture: Synthesis, Properties, Molecular Docking and Prospective Applications
Authors: Jitaru Stefania-Claudia , Enache Andra-Cristina , Cojocaru Corneliu , Drochioiu Gabi , Petre Brindusa-Alina , Gradinaru Vasile-Robert
Published: January 2024

Currently, ultrashort oligopeptides consisting of fewer than eight amino acids represent a cutting-edge frontier in materials science, particularly in the realm of hydrogel formation. By employing solid-phase synthesis with the Fmoc/tBu approach, a novel pentapeptide, FEYNF-NH2, was designed, inspired by a previously studied sequence chosen from hen egg-white lysozyme (FESNF-NH2). Qualitative peptide analysis was based on reverse-phase high performance liquid chromatography (RP-HPLC), while further purification was accomplished using solid-phase extraction (SPE). Exact molecular ion confirmation was achieved by matrix-assisted laser desorption–ionization mass spectrometry (MALDI-ToF MS) using two different matrices (HCCA and DHB). Additionally, the molecular ion of interest was subjected to tandem mass spectrometry (MS/MS) employing collision-induced dissociation (CID) to confirm the synthesized peptide structure. A combination of research techniques, including Fourier-transform infrared spectroscopy (FTIR), fluorescence analysis, transmission electron microscopy, polarized light microscopy, and Congo red staining assay, were carefully employed to glean valuable insights into the self-assembly phenomena and gelation process of the modified FEYNF-NH2 peptide. Furthermore, molecular docking simulations were conducted to deepen our understanding of the mechanisms underlying the pentapeptide’s supramolecular assembly formation and intermolecular interactions. Our study provides potential insights into amyloid research and proposes a novel peptide for advancements in materials science. In this regard, in silico studies were performed to explore the FEYNF peptide’s ability to form polyplexes.
Agency, Protection, and Punishment: Separating Women’s Experiences of Deposit in Early to Mid-Colonial New Spain, 1530–1680
Authors: Holler Jacqueline
Published: January 2024

In the diverse multiethnic setting of colonial New Spain, women faced challenges in separating themselves from marriages they considered unendurable. The Catholic Church, which exercised hegemony over definitions of marriage in the colony, controlled access to permanent, formal separation or “ecclesiastical divorce”, while secular courts offered shorter-term separations generally aimed at reunifying couples. Outside of these options, flight, concealment, and bigamy, or “self-divorce,” offered the only recourse for women seeking to leave an untenable relationship. While it is well known that few women sought (and even fewer were granted) ecclesiastical divorce, it is clear that many women sought separation through formal and informal means. Using ecclesiastical petitions for divorce, this paper investigates the experience of deposit (depósito) for New Spain’s separated women. Deposit was likely a primary goal of women’s divorce petitions. Moreover, the hegemony of marriage was less complete in reality than in ideology; the number of single women in the colony is now known to be vast, and their networks substantial. Building on Bird’s and Megged’s insights on separation and singleness, this paper argues that studying deposit reveals a custom that offered women of all classes a substantial degree of respite and agency in separation, particularly in the early colony, when institutional options were less formalized. Sometimes, depósito permitted lengthy separations that blurred into permanency, while at other times it served as a crucial safety valve. Nonetheless, the practice was a contested terrain on which husbands also sought to exercise power and control. Deposit, therefore, was a highly ambivalent form of “separation” in Latin America. This was undoubtedly true both in the early-colonial period and thereafter, but as colonial society matured and institutional deposit became more possible and common, men’s power was enhanced. Studying the practice before the late seventeenth century therefore reveals some of the ways that early colonial societal flux authorized female agency.
Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut
Authors: Joshi Pushpesh , Soni Pooja , Sharma Vinay , Manohar Surendra S. , Kumar Sampath , Sharma Shailendra , Pasupuleti Janila , Vadez Vincent , Varshney Rajeev K. , Pandey Manish K. , Puppala Naveen
Published: January 2024

Peanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality.
Genetic Basis of Pigment Dispersion Syndrome and Pigmentary Glaucoma: An Update and Functional Insights
Authors: Rong Shisong , Yu Xinting , Wiggs Janey L.
Published: January 2024

Pigment Dispersion Syndrome (PDS) and Pigmentary Glaucoma (PG) comprise a spectrum of ocular disorders characterized by iris pigment dispersion and trabecular meshwork changes, resulting in increased intraocular pressure and potential glaucomatous optic neuropathy. This review summarizes recent progress in PDS/PG genetics including rare pathogenic protein coding alterations (PMEL) and susceptibility loci identified from genome-wide association studies (GSAP and GRM5/TYR). Areas for future research are also identified, especially the development of efficient model systems. While substantial strides have been made in understanding the genetics of PDS/PG, our review identifies key gaps and outlines the future directions necessary for further advancing this important field of ocular genetics.
Large Deletions, Cleavage of the Telomeric Repeat Sequence, and Reverse Transcriptase-Mediated DNA Damage Response Associated with Long Interspersed Element-1 ORF2p Enzymatic Activities
Authors: Kines Kristine J. , Sokolowski Mark , DeFreece Cecily , Shareef Afzaal , deHaro Dawn L. , Belancio Victoria P.
Published: January 2024

L1 elements can cause DNA damage and genomic variation via retrotransposition and the generation of endonuclease-dependent DNA breaks. These processes require L1 ORF2p protein that contains an endonuclease domain, which cuts genomic DNA, and a reverse transcriptase domain, which synthesizes cDNA. The complete impact of L1 enzymatic activities on genome stability and cellular function remains understudied, and the spectrum of L1-induced mutations, other than L1 insertions, is mostly unknown. Using an inducible system, we demonstrate that an ORF2p containing functional reverse transcriptase is sufficient to elicit DNA damage response even in the absence of the functional endonuclease. Using a TK/Neo reporter system that captures misrepaired DNA breaks, we demonstrate that L1 expression results in large genomic deletions that lack any signatures of L1 involvement. Using an in vitro cleavage assay, we demonstrate that L1 endonuclease efficiently cuts telomeric repeat sequences. These findings support that L1 could be an unrecognized source of disease-promoting genomic deletions, telomere dysfunction, and an underappreciated source of chronic RT-mediated DNA damage response in mammalian cells. Our findings expand the spectrum of biological processes that can be triggered by functional and nonfunctional L1s, which have impactful evolutionary- and health-relevant consequences.
Dysregulation of the Skin–Liver Axis in Prurigo Nodularis: An Integrated Genomic, Transcriptomic, and Population-Based Analysis
Authors: Marani Melika , Madan Vrinda , Le Thomas K. , Deng Junwen , Lee Kevin K. , Ma Emily Z. , Kwatra Shawn G.
Published: January 2024

Pruritus has long been linked to hepatic dysfunction; however, there are limited data characterizing the association between liver disease and prurigo nodularis (PN), a chronic inflammatory skin disease featuring severe pruritis. We thus conducted a cross-sectional analysis of hepatic comorbidities in PN patients using TriNetX, a large global health research network. This analysis revealed that PN patients had a higher risk (p < 0.001) of developing liver cirrhosis, acute and subacute hepatic failure, inflammatory liver disease, chronic hepatitis, nonalcoholic steatohepatitis, portal hypertension, fatty liver, chronic passive congestion of the liver, and hepatocellular carcinoma compared with healthy controls. The cumulative incidence of liver disease was about three times higher in PN patients compared with healthy controls. These findings provided the basis for translational studies to investigate a genetic mechanism for this association. Cutaneous transcriptomic analysis performed on PN patients revealed the dysregulation of genes related to hepatic failure in lesional PN compared with both nonlesional PN and control skin. Similarly, gene set variation analysis (GSVA) revealed a significantly increased (p < 0.05) activation of liver metabolism, chronic hepatic failure, acute hepatic failure, cholestatic liver disease, polycystic liver disease, and hepatocellular carcinoma pathways in lesional PN compared with control skin. A subsequent genome-wide association study (GWAS) identified shared single-nucleotide polymorphisms (SNPs) in the genes AR, EDIL3, MACROD2, PCSK5, RUNX1T1, TENM4, and ZEB2 between PN and liver disease from the FinnGen cohort. Significant dysregulation of the skin–liver axis in PN patients may explain the increased incidence and severity of hepatic comorbidities and help identify future therapeutic targets for PN.
The Gut Microbiome Correlated to Chemotherapy Efficacy in Diffuse Large B-Cell Lymphoma Patients
Authors: Xu Zhuo-Fan , Yuan Li , Zhang Yan , Zhang Wei , Wei Chong , Wang Wei , Zhao Danqing , Zhou Daobin , Li Jingnan
Published: January 2024

The gut microbiome (GMB) has been extensively reported to be associated with the development and prognosis of human diseases. This study aims to investigate the relationship between GMB composition and chemotherapy efficacy in diffuse large B-cell lymphoma (DLBCL). We demonstrated that DLBCL patients at diagnosis have altered GMB compositions. Significant enrichment of the Proteobacteria phylum in DLBCL patients was observed. Gene analysis showed a high abundance of virulence factors genes. We found baseline GMB to be associated with clinical outcomes. The emergence of Lactobacillus fermentum was correlated with better treatment outcome. Our pilot results suggested a correlation between GMB composition and DLBCL development and prognosis. Clues from our study, together with previous research, provided a rational foundation for further investigation on the pathogenesis, prognosis value, and targeted therapy of GMB in DLBCL.
Exploring Engineering Students’ Perceptions of Diversity and Inclusion in a Southern Public University: A Case Study
Authors: Wu Shenghua , Burleson Andrew , Islam Samantha , Gossen Drew , Oyelere Abeeb
Published: January 2024

Understanding the present landscape of students’ perceptions and the representation of diversity and inclusion within engineering textbooks is paramount for the effective development and execution of diversity and inclusion initiatives. This case study, conducted in the College of Engineering at the University of South Alabama, aims to assess the current perceptions of diversity among its engineering students. The study encompasses three fundamental elements: textbook evaluations, comprehensive student surveys comprising 30 questions that explore various facets of the engineering curriculum, student organizations, and the workforce, along with in-person interviews. The summarized findings provide invaluable insights for faculty, instructors, and administrators, facilitating informed decision making and program enhancement in the realm of diversity and inclusion.
Macrophage Inflammatory Proteins (MIPs) Contribute to Malignant Potential of Colorectal Polyps and Modulate Likelihood of Cancerization Associated with Standard Risk Factors
Authors: Wierzbicki Jarosław , Bednarz-Misa Iwona , Lewandowski Łukasz , Lipiński Artur , Kłopot Anna , Neubauer Katarzyna , Krzystek-Korpacka Małgorzata
Published: January 2024

Better understanding of molecular changes leading to neoplastic transformation is prerequisite to optimize risk assessment and chemopreventive and surveillance strategies. Data on macrophage inflammatory proteins (MIPs) in colorectal carcinogenesis are scanty and their clinical relevance remains unknown. Therefore, transcript and protein expression of CCL3, CCL4, CXCL2, and CCL19 were determined in 173 and 62 patients, respectively, using RT-qPCR and immunohistochemistry with reference to polyps’ characteristics. The likelihood of malignancy was modeled using probit regression. With the increasing malignancy potential of hyperplastic–tubular–tubulo-villous–villous polyps, the expression of CCL3, CCL4, and CCL19 in lesions decreased. CCL19 expression decreased also in normal mucosa while that of CXCL2 increased. Likewise, lesion CCL3 and lesion and normal mucosa CCL19 decreased and normal CXCL2 increased along the hyperplasia–low–high dysplasia grade. The bigger the lesion, the lower CCL3 and higher CXCL2 in normal mucosa. Singular polyps had higher CCL3, CCL4, and CCL19 levels in normal mucosa. CCL3, CCL4 and CXCL2 modulated the likelihood of malignancy associated with traditional risk factors. There was no correlation between the protein and mRNA expression of CCL3 and CCL19. In summary, the polyp-adjacent mucosa contributes to gaining potential for malignancy by polyps. MIPs may help in specifying cancerization probability estimated based on standard risk factors.
Complement Cascade Proteins Correlate with Fibrosis and Inflammation in Early-Stage Type 1 Diabetic Kidney Disease in the Ins2Akita Mouse Model
Authors: Tserga Aggeliki , Saulnier-Blache Jean Sébastien , Palamaris Kostantinos , Pouloudi Despoina , Gakiopoulou Harikleia , Zoidakis Jerome , Schanstra Joost Peter , Vlahou Antonia , Makridakis Manousos
Published: January 2024

Diabetic kidney disease (DKD) is characterized by histological changes including fibrosis and inflammation. Evidence supports that DKD is mediated by the innate immune system and more specifically by the complement system. Using Ins2Akita T1D diabetic mice, we studied the connection between the complement cascade, inflammation, and fibrosis in early DKD. Data were extracted from a previously published quantitative-mass-spectrometry-based proteomics analysis of kidney glomeruli of 2 (early DKD) and 4 months (moderately advanced DKD)-old Ins2Akita mice and their controls A Spearman rho correlation analysis of complement- versus inflammation- and fibrosis-related protein expression was performed. A cross-omics validation of the correlation analyses’ results was performed using public-domain transcriptomics datasets (Nephroseq). Tissue sections from 43 patients with DKD were analyzed using immunofluorescence. Among the differentially expressed proteins, the complement cascade proteins C3, C4B, and IGHM were significantly increased in both early and later stages of DKD. Inflammation-related proteins were mainly upregulated in early DKD, and fibrotic proteins were induced in moderately advanced stages of DKD. The abundance of complement proteins with fibrosis- and inflammation-related proteins was mostly positively correlated in early stages of DKD. This was confirmed in seven additional human and mouse transcriptomics DKD datasets. Moreover, C3 and IGHM mRNA levels were found to be negatively correlated with the estimated glomerular filtration rate (range for C3 rs = −0.58 to −0.842 and range for IGHM rs = −0.6 to −0.74) in these datasets. Immunohistology of human kidney biopsies revealed that C3, C1q, and IGM proteins were induced in patients with DKD and were correlated with fibrosis and inflammation. Our study shows for the first time the potential activation of the complement cascade associated with inflammation-mediated kidney fibrosis in the Ins2Akita T1D mouse model. Our findings could provide new perspectives for the treatment of early DKD as well as support the use of Ins2Akita T1D in pre-clinical studies.
Propagation of Saffron (Crocus sativus L.) Using Cross-Cuttings under a Controlled Environment
Authors: El Merzougui Soumaya , Boudadi Imane , Lachguer Khadija , Beleski David G. , Lagram Khalid , Lachheb Mohamed , Ben El Caid Mohamed , Pereira Vania M. , Nongdam Potshangbam , Serghini Mohammed Amine , Vendrame Wagner A.
Published: January 2024

Saffron (Crocus sativus L.) is a valuable geophyte plant and one of the most expensive spices in the world. Recently, the demand for saffron spice has increased in worldwide markets owing to its enormous application and value. However, the production of saffron is limited by the vegetative propagation technique and the limited number of high-quality corms planted. Furthermore, climatic changes, notably increasing temperatures, negatively influence saffron multiplication and growth. Thus, it is important to develop alternative cultivation and propagation techniques for saffron under a controlled environment, which could ensure an increase in saffron yield and avoid the negative impact of climatic changes. The present study aimed to develop an alternative method for vegetative propagation of Crocus sativus under controlled conditions. The effect of different cross-cuttings, including basal cuttings (BCs) and top-to-bottom cuttings (CTBs), was evaluated on shoot, leaf, flower, and daughter corm production. All the growth parameters examined were influenced by the cutting treatment applied. The results showed that the highest number of shoots formed was obtained by BCs and CTBs, with an average of 6.68 and 5.47 shoots per corm, respectively, compared to the control with an average of 2.70 shoots per corm. The cutting treatment positively affected the formation of daughter corms in which, the high mean number of corms recorded was obtained by the BC treatment. Meanwhile, the lower size of the daughter corms was obtained after the cross-cutting treatment. This is the first report that provides an alternative propagation for saffron using a controlled environment, which could help to improve the production of saffron.
An Overview of Orthoptera Mass Occurrences in Croatia from 1900 to 2023
Authors: Kasalo Niko , Tvrtković Nikola , Bogić Domagoj , Kokan Bože , Vuković Marijana , Kučinić Mladen , Skejo Josip
Published: January 2024

During the last century, well-known locust species, such as Calliptamus italicus and Dociostaurus maroccanus, have produced outbreaks of varying degrees in the Balkans. The literature data on outbreaks in the region are scarce, and Croatia is not an exception. This study summarized the data on 23 Orthoptera mass occurrences in Croatia from 1900 to 2023 from 28 localities, representing 12 species. This is a low level of outbreak activity compared with other locust and pest grasshopper species in other parts of the world. The species with the most reporting is C. italicus with altogether six mass occurrences, while second is Barbitistes ocskayi and Miramella irena with three records, and in the third, place D. maroccanus and Gryllotalpa sp., each with two mass occurrences having been reported. One of the most notable swarms is that of Anacridium aegyptium which occurred around Šibenik in 1998, and this paper provides the first account of it, 25 years after it took place. The most recent outbreaks took place in 2022, and the most notable one was that of D. maroccanus swarm in Štikovo. The 2022 and 2023 reports were brief and muted, despite the affected agriculturists claiming significant damages.
An Advanced Deep Learning Framework for Multi-Class Diagnosis from Chest X-ray Images
Authors: Sanida Maria Vasiliki , Sanida Theodora , Sideris Argyrios , Dasygenis Minas
Published: January 2024

Chest X-ray imaging plays a vital and indispensable role in the diagnosis of lungs, enabling healthcare professionals to swiftly and accurately identify lung abnormalities. Deep learning (DL) approaches have attained popularity in recent years and have shown promising results in automated medical image analysis, particularly in the field of chest radiology. This paper presents a novel DL framework specifically designed for the multi-class diagnosis of lung diseases, including fibrosis, opacity, tuberculosis, normal, viral pneumonia, and COVID-19 pneumonia, using chest X-ray images, aiming to address the need for efficient and accessible diagnostic tools. The framework employs a convolutional neural network (CNN) architecture with custom blocks to enhance the feature maps designed to learn discriminative features from chest X-ray images. The proposed DL framework is evaluated on a large-scale dataset, demonstrating superior performance in the multi-class diagnosis of the lung. In order to evaluate the effectiveness of the presented approach, thorough experiments are conducted against pre-existing state-of-the-art methods, revealing significant accuracy, sensitivity, and specificity improvements. The findings of the study showcased remarkable accuracy, achieving 98.88%. The performance metrics for precision, recall, F1-score, and Area Under the Curve (AUC) averaged 0.9870, 0.9904, 0.9887, and 0.9939 across the six-class categorization system. This research contributes to the field of medical imaging and provides a foundation for future advancements in DL-based diagnostic systems for lung diseases.
Personalized Multimodal Lifestyle Intervention as the Best-Evidenced Treatment for Chronic Pain: State-of-the-Art Clinical Perspective
Authors: Nijs Jo , Malfliet Anneleen , Roose Eva , Lahousse Astrid , Van Bogaert Wouter , Johansson Elin , Runge Nils , Goossens Zosia , Labie Céline , Bilterys Thomas , Van Campenhout Jente , Polli Andrea , Wyns Arne , Hendrix Jolien , Xiong Huan-Yu , Ahmed Ishtiaq , De Baets Liesbet , Huysmans Eva
Published: January 2024

Chronic pain is the most prevalent disease worldwide, leading to substantial disability and socioeconomic burden. Therefore, it can be regarded as a public health disease and major challenge to scientists, clinicians and affected individuals. Behavioral lifestyle factors, such as, physical (in)activity, stress, poor sleep and an unhealthy diet are increasingly recognized as perpetuating factors for chronic pain. Yet, current management options for patients with chronic pain often do not address lifestyle factors in a personalized multimodal fashion. This state-of-the-art clinical perspective aims to address this gap by discussing how clinicians can simultaneously incorporate various lifestyle factors into a personalized multimodal lifestyle intervention for individuals with chronic pain. To do so the available evidence on (multimodal) lifestyle interventions targeting physical (in)activity, stress, sleep and nutritional factors, specifically, was reviewed and synthetized from a clinical point of view. First, advise is provided on how to design a personalized multimodal lifestyle approach for a specific patient. Subsequently, best-evidence recommendations on how to integrate physical (in)activity, stress, sleep and nutritional factors as treatment targets into a personalized multimodal lifestyle approach are outlined. Evidence supporting such a personalized multimodal lifestyle approach is growing, but further studies are needed.
Using Upper Arm Vein as Temporary Pacemaker Access Site: A Next Step in Minimizing the Invasiveness of Transcatheter Aortic Valve Replacement
Authors: Rooijakkers Maxim J. P. , Versteeg Geert A. A. , van Wely Marleen H. , Rodwell Laura , van Nunen Lokien X. , van Geuns Robert Jan , van Garsse Leen A. F. M. , Geuzebroek Guillaume S. C. , Verkroost Michel W. A. , Heijmen Robin H. , van Royen Niels
Published: January 2024

Background The femoral vein is commonly used as a pacemaker access site during transcatheter aortic valve replacement (TAVR). Using an upper arm vein as an alternative access site potentially causes fewer bleeding complications and shorter time to mobilization. We aimed to assess the safety and efficacy of an upper arm vein as a temporary pacemaker access site during TAVR. Methods We evaluated all patients undergoing TAVR in our center between January 2020 and January 2023. Upper arm, femoral, and jugular vein pacemaker access was used in 255 (45.8%), 191 (34.3%), and 111 (19.9%) patients, respectively. Clinical outcomes were analyzed according to pacemaker access in the overall population and in a propensity-matched population involving 165 upper arm and 165 femoral vein patients. Primary endpoint was Bleeding Academic Research Consortium (BARC) type 2, 3, or 5 pacemaker access site-related bleeding. Results In the overall population, primary endpoint was lowest for upper arm, followed by femoral and jugular vein access (2.4% vs. 5.8% vs. 10.8%, p = 0.003). Time to mobilization was significantly longer (p < 0.001) in the jugular cohort compared with the other cohorts. In the propensity-matched cohort, primary endpoint showed a trend toward lower occurrence in the upper arm compared with the femoral cohort (2.4% vs. 6.1%, p = 0.10). Time to mobilization was significantly shorter (480 vs. 1140 min, p < 0.001) in the upper arm cohort, with a comparable skin-to-skin time (83 vs. 85 min, p = 0.75). Cross-over from upper arm pacemaker access was required in 17 patients (6.3% of attempted cases via an upper arm vein). Conclusions Using an upper arm vein as a temporary pacemaker access site is safe and feasible. Its use might be associated with fewer bleeding complications and shorter time to mobilization compared with the femoral vein.
Distribution and Clinicopathological Features of Mott Cells (Plasma Cells Containing Russell Bodies) in Gastric Cancer: Presence of Mott Cells Is Associated with Favorable Prognosis
Authors: Kobayashi Go , Imai Takeharu , Sentani Kazuhiro
Published: January 2024

Gastric cancer (GC) is still one of the leading causes of cancer-related mortality. We previously reported the relationship between histological heterogeneity of tumor cells and molecular features in GC. The tumor microenvironment also has a crucial role in GC progression and therapeutic resistance. In this study, we focused on the tumor microenvironment, especially inflammatory cells in GC. Using GC tissue slides, we investigated the distribution and clinicopathological significance of inflammatory cell counts including eosinophils, neutrophils, lymphocytes, and plasma cells. Additionally, we investigated the relationship between Mott cells (plasma cells containing Russell bodies) and clinicopathological features. In neoplastic gastric mucosa, a high number of plasma cells was associated with low T-grade, early stage, and good prognosis. We then focused on Mott cells and found that their presence in neoplastic gastric mucosa was associated with lower T and N grades, early stage, and Helicobacter pylori infection and was inversely associated with CD44 and EGFR expression. Additionally, the presence of Mott cells was associated with good prognosis in advanced GC and was an independent favorable prognostic predictor. The presence of Mott cells in GC might be one useful prognostic predictor, and Mott cells might have an important role in the carcinogenesis of H. pylori infection.
Antigenic Relatedness between Mannans from Coccidioides immitis and Coccidioides posadasii Spherules and Mycelia
Authors: Burnham-Marusich Amanda R. , Zayac Kathleen R. , Galgiani John N. , Lewis Lourdes , Kozel Thomas R.
Published: January 2024

Immunoassays for cell wall mannans that are excreted into serum and urine have been used as an aid in the diagnosis of many disseminated fungal infections, including coccidioidomycosis. Antigen-detection immunoassays are critically dependent on the detection of an analyte, such as mannan, by antibodies that are specific to the analyte. The goal of this study was to evaluate the extent of cross-reactivity of polyclonal antibodies raised against Coccidioides spp. Analysis of antigenic relatedness between mannans from C. posadasii and C. immitis spherules and mycelia showed complete relatedness when evaluated by the method of Archetti and Horsfall, which was originally used to study the antigenic relationships between Influenzae virus isolates. In a further effort to validate the suitability of the antigenic relatedness calculation methodology for polysaccharide antigens, we also applied the method of Archetti and Horsfall to published results that had previously identified the major capsular serotypes of Cryptococcus species. The results of this analysis showed that Archetti and Horsfall’s antigenic relatedness calculation correctly identified the major cryptococcal serotypes. Together, these results suggest that the method is applicable to polysaccharide antigens, and that immunoassays that detect Coccidioides mannans are likely to have good reactivity across Coccidioides species (inclusivity) due to the species’ high level of antigenic relatedness.
Specifically Targeting Metacaspases of Candida: A New Therapeutic Opportunity
Authors: Bienvenu Anne-Lise , Ballut Lionel , Picot Stephane
Published: January 2024

The World Health Organization (WHO) recently published a list of fungal priority pathogens, including Candida albicans and C. auris. The increased level of resistance of Candida is raising concern, considering the availability of only four classes of medicine. The WHO is seeking novel agent classes with different targets and mechanisms of action. Targeting Candida metacaspases to control intrinsic cell death could provide new therapeutic opportunities for invasive candidiasis. In this review, we provide the available evidence for Candida cell death, describe Candida metacaspases, and discuss the potential of Candida metacaspases to offer a new specific target. Targeting Candida cell death has good scientific rationale given that the fungicidal activity of many marketed antifungals is mediated, among others, by cell death triggering. But none of the available antifungals are specifically activating Candida metacaspases, making this target a new therapeutic opportunity for non-susceptible isolates. It is expected that antifungals based on the activation of fungi metacaspases will have a broad spectrum of action, as metacaspases have been described in many fungi, including filamentous fungi. Considering this original mechanism of action, it could be of great interest to combine these new antifungal candidates with existing antifungals. This approach would help to avoid the development of antifungal resistance, which is especially increasing in Candida.
The Autophagy-Related Musa acuminata Protein MaATG8F Interacts with MaATG4B, Regulating Banana Disease Resistance to Fusarium oxysporum f. sp. cubense Tropical Race 4
Authors: Huang Huoqing , Tian Yuzhen , Huo Yile , Liu Yushan , Yang Wenlong , Li Yuqing , Zhuo Mengxia , Xiang Dandan , Li Chunyu , Yi Ganjun , Liu Siwen
Published: January 2024

Banana is one of the most important fruits in the world due to its status as a major food source for more than 400 million people. Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes substantial losses of banana crops every year, and molecular host resistance mechanisms are currently unknown. We here performed a genomewide analysis of the autophagy-related protein 8 (ATG8) family in a wild banana species. The banana genome was found to contain 10 MaATG8 genes. Four MaATG8s formed a gene cluster in the distal part of chromosome 4. Phylogenetic analysis of ATG8 families in banana, Arabidopsis thaliana, citrus, rice, and ginger revealed five major phylogenetic clades shared by all of these plant species, demonstrating evolutionary conservation of the MaATG8 families. The transcriptomic analysis of plants infected with Foc TR4 showed that nine of the MaATG8 genes were more highly induced in resistant cultivars than in susceptible cultivars. Finally, MaATG8F was found to interact with MaATG4B in vitro (with yeast two-hybrid assays), and MaATG8F and MaATG4B all positively regulated banana resistance to Foc TR4. Our study provides novel insights into the structure, distribution, evolution, and expression of the MaATG8 family in bananas. Furthermore, the discovery of interactions between MaATG8F and MaATG4B could facilitate future research of disease resistance genes for the genetic improvement of bananas.
Investigating Efficient Risk-Stratified Pathways for the Early Detection of Clinically Significant Prostate Cancer
Authors: Morote Juan , Borque-Fernando Ángel , Esteban Luis M. , Celma Ana , Campistol Miriam , Miró Berta , Méndez Olga , Trilla Enrique
Published: January 2024

Risk-stratified pathways (RSPs) are recommended by the European Association of Uro-logy (EAU) to improve the early detection of clinically significant prostate cancer (csPCa). RSPs can reduce magnetic resonance imaging (MRI) demand, prostate biopsies, and the over-detection of insignificant PCa (iPCa). Our goal is to analyze the efficacy and cost-effectiveness of several RSPs by using sequential stratifications from the serum prostate-specific antigen level and digital rectal examination, the Barcelona risk calculators (BCN-RCs), MRI, and Proclarix™. In a cohort of 567 men with a serum PSA level above 3.0 ng/mL who underwent multiparametric MRI (mpMRI) and targeted and/or systematic biopsies, the risk of csPCa was retrospectively assessed using Proclarix™ and BCN-RCs 1 and 2. Six RSPs were compared with those recommended by the EAU that, stratifying men from MRI, avoided 16.7% of prostate biopsies with a prostate imaging–reporting and data system score of <3, with 2.6% of csPCa cases remaining undetected. The most effective RSP avoided mpMRI exams in men with a serum PSA level of >10 ng/mL and suspicious DRE, following stratifications from BCN-RC 1, mpMRI, and Proclarix™. The demand for mpMRI decreased by 19.9%, prostate biopsies by 19.8%, and over-detection of iPCa by 22.7%, while 2.6% of csPCa remained undetected as in the recommended RSP. Cost-effectiveness remained when the Proclarix™ price was assumed to be below EUR 200.
Prevention in Hepatology
Authors: Muñoz-Restrepo Ana-Maria , Navas Maria-Cristina , Daza Jimmy , Girala Marcos , Ridruejo Ezequiel , Gerken Guido , Teufel Andreas
Published: January 2024

The prevention of liver disease has improved significantly in the last few decades, to the point that it can now be considered a true success story. The wide variety of interventions, including comprehensive vaccination strategies, novel medications, lifestyle changes, and even preventive surgeries, have reduced the morbidity and mortality of chronic liver diseases. However, the prevalence of chronic liver diseases is increasing worldwide. Currently, fatty liver disease alone is estimated to be present in as much as 30% of the adult population. Furthermore, there is a trend towards increasing incidences of chronic hepatitis B, and a global lack of success in efforts to eliminate chronic hepatitis C. Thus, improving and efficiently rolling out existing and successful prevention strategies for chronic liver diseases will play an essential role in healthcare throughout the upcoming decades. In this review, we summarize the current options and concepts for preventing chronic liver diseases, highlight their limitations, and provide an outlook on probable future developments to improve awareness, integrated care, and the analysis of big data.
The Role of Extracellular Vesicles in SARS-CoV-2-Induced Acute Kidney Injury: An Overview
Authors: Bernal Carter , How-Volkman Christiane , Spencer Madison , El-Shamy Ahmed , Mohieldin Ashraf M.
Published: January 2024

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions worldwide since its outbreak in the winter of 2019. While extensive research has primarily focused on the deleterious respiratory effects of SARS-CoV-2 in recent years, its pan-tropism has become evident. Among the vital organs susceptible to SARS-CoV-2 infection is the kidney. Post SARS-CoV-2 infection, patients have developed coronavirus disease 19 (COVID-19), with reported incidences of COVID-19 patients developing acute kidney injury (AKI). Given COVID-19’s multisystemic manifestation, our review focuses on the impact of SARS-CoV-2 infection within the renal system with an emphasis on the current hypotheses regarding the role of extracellular vesicles (EVs) in SARS-CoV-2 pathogenesis. Emerging studies have shown that SARS-CoV-2 can directly infect the kidney, whereas EVs are involved in the spreading of SARS-CoV-2 particles to other neighboring cells. Once the viral particles are within the kidney system, many proinflammatory signaling pathways are shown to be activated, resulting in AKI. Hence, clinical investigation of urinary proinflammatory components and total urinary extracellular vesicles (uEVs) with viral particles have been used to assess the severity of AKI in patients with COVID-19. Remarkedly, new emerging studies have shown the potential of mesenchymal stem cell-derived EVs (MSC-EVs) and ACE2-containing EVs as a hopeful therapeutic tool to inhibit SARS-CoV-2 RNA replication and block viral entry, respectively. Overall, understanding EVs’ physiological role is crucial and hopefully will rejuvenate our therapeutic approach towards COVID-19 patients with AKI.
Evaluation of Thermodynamic and Kinetic Contributions to Over-Extraction of Extractables by Nonpolar Organic Solvents in Comparison to Lipids in Exhaustive and Exaggerated Extractions of Medical Devices Based on Abraham Solvation Model and Solvent–Material Interactions Using Low-Density Polyethylene as a Representative Material
Authors: Li Jianwei
Published: January 2024

The thermodynamic and kinetic contributions to the over-extraction of extractables by nonpolar organic solvents relative to biological lipids in exhaustive and exaggerated extractions of medical devices are studied based on the Abraham solvation model and solvent–material interactions, using low-density polyethylene (LDPE) as an exemplary material. The thermodynamic effect is evaluated by the partition constant of extractables between LDPE and extraction solvents, hexane and lipids, defined as the concentration in the polymer phase divided by the concentration in the solvent phase. The Abraham solvation model is used to correlate the measured LDPE-lipid partition constant (log10Pldpe/lipid) to construct the predictive model. Similar models are also derived from the thermodynamic cycle conversion, using the system constants of LDPE-water and Lipid-water partition systems. These constructed models, together with the predictive LDPE-hexane (log10Pldpe/hexane) model established from a previous study, are used to predict and compare the ranges and values of Pldpe/s (s = lipids and hexane) for the observed LDPE extractables over a wide hydrophobicity range in log10Po/w from zero to 30. The solvent-LDPE interactions are examined by the degree of swelling of LDPE by hexane (or other nonpolar solvents) and lipids, including the solvent diffusion rates into the material. These parameters allow the evaluation of kinetic effect on the over-extraction. The extent of over-extraction is compiled directly by experimental “overall” or “specific” migration data or indirectly calculated by the diffusion coefficient of extractables when extracted by hexane or lipids. It is concluded from this study that the extractables distribution between LDPE and lipids highly favors the lipid phase thermodynamically (Pldpe/lipid<1), and the values of Pldpe/lipid are always lower than those of Pldpe/hexane, thereby indicating that the thermodynamic effect is not the cause of over-extraction. It is the kinetic effect that dominantly contributes to the over-extraction, as supported by the material swelling and solvent diffusion rates. Finally, the extent of over-extraction has been established from a few folds to over a hundred-fold, and the median value is 7. Furthermore, the methods adopted and developed in this study can be invaluable tools in other disciplines such as the reliable prediction of extractables from other device materials and environmental sampling.
Projective Geometry as a Model for Hegel’s Logic
Authors: Redding Paul
Published: January 2024

Recently, historians have discussed the relevance of the nineteenth-century mathematical discipline of projective geometry for early modern classical logic in relation to possible solutions to semantic problems facing it. In this paper, I consider Hegel’s Science of Logic as an attempt to provide a projective geometrical alternative to the implicit Euclidean underpinnings of Aristotle’s syllogistic logic. While this proceeds via Hegel’s acceptance of the role of the three means of Pythagorean music theory in Plato’s cosmology, the relevance of this can be separated from any fanciful “music of the spheres” approach by the fact that common mathematical structures underpin both music theory and projective geometry, as suggested in the name of projective geometry’s principal invariant, the “harmonic cross-ratio”. Here, I demonstrate this common structure in terms of the phenomenon of “inverse foreshortening”. As with recent suggestions concerning the relevance of projective geometry for logic, Hegel’s modifications of Aristotle respond to semantic problems of his logic.
Effects of Oil and Solid Body Temperatures on Elastohydrodynamic Lubrication Film Formation
Authors: Gao Junbin , Yang Ping , Li Xinming , Jin Xuyang , Tian Ye , Cheng Ziyang , Yan Xu
Published: January 2024

The present study focuses on investigating the influence of oil and solid body temperatures on elastohydrodynamic lubrication (EHL) film formation. Experimental and numerical simulation methods are employed to examine three heating methods: oil and ball heating, disc heating, and entire system heating. A preliminary comparison between the measured results and numerical simulations confirms the impact of heating methods on film formation while validating the availability of the numerical models. Further numerical analysis reveals that in the case of oil and ball heating, the temperature gradient induced by differences in solid body temperatures plays a more significant role in film formation compared to the conventional thermal-viscosity wedge effect caused by EHL film shear. This effect is further amplified at large sliding–rolling ratios and in steel–steel contacts. The overall film formation is primarily governed by the oil inlet temperature, whereas local film formation characterized by a dimple shape is influenced by both thermal gradient effects and thermal-viscosity wedge effects. This study provides valuable insights for selecting appropriate heating methods in experiments as well as understanding how temperature differences affect film formation in practical engineering.
Algorithmic Information Theory for the Precise Engineering of Flexible Material Mechanics
Authors: Luo Liang , Stylios George K.
Published: January 2024

The structure of fibrous assemblies is highly complex, being both random and regular at the same time, which leads to the complexity of its mechanical behaviour. Using algorithms such as machine learning to process complex mechanical property data requires consideration and understanding of its information principles. There are many different methods and instruments for measuring flexible material mechanics, and many different mechanics models exist. There is a need for an evaluation method to determine how close the results they obtain are to the real material mechanical behaviours. This paper considers and investigates measurements, data, models and simulations of fabric’s low-stress mechanics from an information perspective. The simplification of measurements and models will lead to a loss of information and, ultimately, a loss of authenticity in the results. Kolmogorov complexity is used as a tool to analyse and evaluate the algorithmic information content of multivariate nonlinear relationships of fabric stress and strain. The loss of algorithmic information content resulting from simplified approaches to various material measurements, models and simulations is also evaluated. For example, ignoring the friction hysteresis component in the material mechanical data can cause the model and simulation to lose more than 50% of the algorithm information, whilst the average loss of information using uniaxial measurement data can be as high as 75%. The results of this evaluation can be used to determine the authenticity of measurements and models and to identify the direction for new measurement instrument development and material mechanics modelling. It has been shown that a vast number of models, which use unary relationships to describe fabric behaviour and ignore the presence of frictional hysteresis, are inaccurate because they hold less than 12% of real fabric mechanics data. The paper also explores the possibility of compressing the measurement data of fabric mechanical properties.
Extraction of Palladium from Spent Nuclear Fuel Reprocessing Solutions
Authors: Safiulina Alfiya M. , Borisova Nataliya E. , Karpyuk Ekaterina A. , Ivanov Alexey V. , Lopatin Dmitry A.
Published: January 2024

New solvent systems for selective separation of palladium from nuclear wastes represent a prospective way to reduce the total waste volume and induce this metal’s extraction. For this purpose, the potential of modern green solvent room-temperature ionic liquid was assessed with diamide-type extractants based on N-heterocycles and S-donating thiodiglicolic acid. The N-donating heterocyclic extractants demonstrate structure-dependent high selectivity toward palladium in the presence of various impurity metals (such as Zr, Cs, Sr, Mo, Ce, Fe, and Cr) from spent nuclear fuel. Palladium is extracted into the organic phase quite selectively with a separation factor greater than a thousand for all extractants. Ionic liquid media are capable of selective palladium separation from platinum group metals and synergetically increase the selectivity of the extractants.