bluuebunny/crossref_metadata_2025 huggingface dataset:
Enzymatic conversion of human blood group A kidneys to universal blood group O
Authors: MacMillan Serena , Hosgood Sarah A. , Walker-Panse Léonie , Rahfeld Peter , Macdonald Spence S. , Kizhakkedathu Jayachandran N. , Withers Stephen G. , Nicholson Michael L.
Published: March 2024

ABO blood group compatibility restrictions present the first barrier to donor-recipient matching in kidney transplantation. Here, we present the use of two enzymes, FpGalNAc deacetylase and FpGalactosaminidase, from the bacterium Flavonifractor plautii to enzymatically convert blood group A antigens from the renal vasculature of human kidneys to ‘universal’ O-type. Using normothermic machine perfusion (NMP) and hypothermic machine perfusion (HMP) strategies, we demonstrate blood group A antigen loss of approximately 80% in as little as 2 h NMP and HMP. Furthermore, we show that treated kidneys do not bind circulating anti-A antibodies in an ex vivo model of ABO-incompatible transplantation and do not activate the classical complement pathway. This strategy presents a solution to the donor organ shortage crisis with the potential for direct clinical translation to reduce waiting times for patients with end stage renal disease.
Chiral BINOL-phosphate assembled single hexagonal nanotube in aqueous solution for confined rearrangement acceleration
Authors: Li Kang , Qin Wei-Min , Su Wen-Xia , Hu Jia-Min , Cai Yue-Peng
Published: March 2024

Creating microenvironments that mimic an enzyme’s active site is a critical aspect of supramolecular confined catalysis. In this study, we employ the commonly used chiral 1,1’-bi-2-naphthol (BINOL) phosphates as subcomponents to construct supramolecular hollow nanotube in an aqueous medium through non-covalent intermolecular recognition and arrangement. The hexagonal nanotubular structure is characterized by various techniques, including X-ray, NMR, ESI-MS, AFM, and TEM, and is confirmed to exist in a homogeneous aqueous solution stably. The nanotube’s length in solution depends on the concentration of chiral BINOL-phosphate as a monomer. Additionally, the assembled nanotube can accelerate the rate of the 3-aza-Cope rearrangement reaction by up to 85-fold due to the interior confinement effect. Based on the detailed kinetic and thermodynamic analyses, we propose that the chain-like substrates are constrained and pre-organized into a reactive chair-like conformation, which stabilizes the transition state of the reaction in the confined nanospace of the nanotube. Notably, due to the restricted conformer with less degrees of freedom, the entropic barrier is significantly reduced compared to the enthalpic barrier, resulting in a more pronounced acceleration effect.
A conserved NR5A1-responsive enhancer regulates SRY in testis-determination
Authors: Houzelstein Denis , Eozenou Caroline , Lagos Carlos F. , Elzaiat Maëva , Bignon-Topalovic Joelle , Gonzalez Inma , Laville Vincent , Schlick Laurène , Wankanit Somboon , Madon Prochi , Kirtane Jyotsna , Athalye Arundhati , Buonocore Federica , Bigou Stéphanie , Conway Gerard S. , Bohl Delphine , Achermann John C. , Bashamboo Anu , McElreavey Ken
Published: March 2024

The Y-linked SRY gene initiates mammalian testis-determination. However, how the expression of SRY is regulated remains elusive. Here, we demonstrate that a conserved steroidogenic factor-1 (SF-1)/NR5A1 binding enhancer is required for appropriate SRY expression to initiate testis-determination in humans. Comparative sequence analysis of SRY 5’ regions in mammals identified an evolutionary conserved SF-1/NR5A1-binding motif within a 250 bp region of open chromatin located 5 kilobases upstream of the SRY transcription start site. Genomic analysis of 46,XY individuals with disrupted testis-determination, including a large multigenerational family, identified unique single-base substitutions of highly conserved residues within the SF-1/NR5A1-binding element. In silico modelling and in vitro assays demonstrate the enhancer properties of the NR5A1 motif. Deletion of this hemizygous element by genome-editing, in a novel in vitro cellular model recapitulating human Sertoli cell formation, resulted in a significant reduction in expression of SRY. Therefore, human NR5A1 acts as a regulatory switch between testis and ovary development by upregulating SRY expression, a role that may predate the eutherian radiation. We show that disruption of an enhancer can phenocopy variants in the coding regions of SRY that cause human testis dysgenesis. Since disease causing variants in enhancers are currently rare, the regulation of gene expression in testis-determination offers a paradigm to define enhancer activity in a key developmental process.
Electroreduction of unactivated alkenes using water as hydrogen source
Authors: Wang Yanwei , Wang Qian , Wu Lei , Jia Kangping , Wang Minyan , Qiu Youai
Published: March 2024

Herein, we report an electroreduction of unactivated alkyl alkenes enabled by [Fe]-H, which is provided through the combination of anodic iron salts and the silane generated in situ via cathodic reduction, using H2O as an H-source. The catalytic amounts of Si-additive work as an H-carrier from H2O to generate a highly active silane species in situ under continuous electrochemical conditions. This approach shows a broad substrate scope and good functional group compatibility. In addition to hydrogenation, the use of D2O instead of H2O provides the desired deuterated products in good yields with excellent D-incorporation (up to >99%). Further late-stage hydrogenation of complex molecules and drug derivatives demonstrate potential application in the pharmaceutical industry. Mechanistic studies are performed and provide support for the proposed mechanistic pathway.
Autonomous closed-loop mechanistic investigation of molecular electrochemistry via automation
Authors: Sheng Hongyuan , Sun Jingwen , Rodríguez Oliver , Hoar Benjamin B. , Zhang Weitong , Xiang Danlei , Tang Tianhua , Hazra Avijit , Min Daniel S. , Doyle Abigail G. , Sigman Matthew S. , Costentin Cyrille , Gu Quanquan , Rodríguez-López Joaquín , Liu Chong
Published: March 2024

Electrochemical research often requires stringent combinations of experimental parameters that are demanding to manually locate. Recent advances in automated instrumentation and machine-learning algorithms unlock the possibility for accelerated studies of electrochemical fundamentals via high-throughput, online decision-making. Here we report an autonomous electrochemical platform that implements an adaptive, closed-loop workflow for mechanistic investigation of molecular electrochemistry. As a proof-of-concept, this platform autonomously identifies and investigates an EC mechanism, an interfacial electron transfer (E step) followed by a solution reaction (C step), for cobalt tetraphenylporphyrin exposed to a library of organohalide electrophiles. The generally applicable workflow accurately discerns the EC mechanism’s presence amid negative controls and outliers, adaptively designs desired experimental conditions, and quantitatively extracts kinetic information of the C step spanning over 7 orders of magnitude, from which mechanistic insights into oxidative addition pathways are gained. This work opens opportunities for autonomous mechanistic discoveries in self-driving electrochemistry laboratories without manual intervention.
The CHK1 inhibitor prexasertib in BRCA wild-type platinum-resistant recurrent high-grade serous ovarian carcinoma: a phase 2 trial
Authors: Giudice Elena , Huang Tzu-Ting , Nair Jayakumar R. , Zurcher Grant , McCoy Ann , Nousome Darryl , Radke Marc R. , Swisher Elizabeth M. , Lipkowitz Stanley , Ibanez Kristen , Donohue Duncan , Malys Tyler , Lee Min-Jung , Redd Bernadette , Levy Elliot , Rastogi Shraddha , Sato Nahoko , Trepel Jane B. , Lee Jung-Min
Published: March 2024

The multi-cohort phase 2 trial NCT02203513 was designed to evaluate the clinical activity of the CHK1 inhibitor (CHK1i) prexasertib in patients with breast or ovarian cancer. Here we report the activity of CHK1i in platinum-resistant high-grade serous ovarian carcinoma (HGSOC) with measurable and biopsiable disease (cohort 5), or without biopsiable disease (cohort 6). The primary endpoint was objective response rate (ORR). Secondary outcomes were safety and progression-free survival (PFS). 49 heavily pretreated patients were enrolled (24 in cohort 5, 25 in cohort 6). Among the 39 RECISTv1.1-evaluable patients, ORR was 33.3% in cohort 5 and 28.6% in cohort 6. Primary endpoint was not evaluable due to early stop of the trial. The median PFS was 4 months in cohort 5 and 6 months in cohort 6. Toxicity was manageable. Translational research was an exploratory endpoint. Potential biomarkers were investigated using pre-treatment fresh biopsies and serial blood samples. Transcriptomic analysis revealed high levels of DNA replication-related genes (POLA1, POLE, GINS3) associated with lack of clinical benefit [defined post-hoc as PFS < 6 months]. Subsequent preclinical experiments demonstrated significant cytotoxicity of POLA1 silencing in combination with CHK1i in platinum-resistant HGSOC cell line models. Therefore, POLA1 expression may be predictive for CHK1i resistance, and the concurrent POLA1 inhibition may improve the efficacy of CHK1i monotherapy in this hard-to-treat population, deserving further investigation.
Coconut rhinoceros beetle digestive symbiosis with potential plant cell wall degrading microbes
Authors: Han Chiao-Jung , Cheng Chih-Hsin , Yeh Ting-Feng , Pauchet Yannick , Shelomi Matan
Published: March 2024

Coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is an invasive palm pest whose larvae eat wood, yet lack the necessary digestive enzymes. This study confirmed endogenous CRB cellulase is inactive, suggesting microbial fermentation. The inner lining of the CRB hindgut has tree-like structures covered with a conspicuous biofilm. To identify possible symbionts, 16 S rRNA amplicon sequencing was used on individuals from across Taiwan. Several taxa of Clostridia, an anaerobic class including many cellulolytic bacteria, were highly abundant in most individuals from all locations. Whole metagenome sequencing further confirmed many lignocellulose degrading enzymes are derived from these taxa. Analyses of eggs, larvae, adults, and soil found these cellulolytic microbes are not transmitted vertically or transstadially. The core microbiomes of the larval CRB are likely acquired and enriched from the environment with each molt, and enable efficient digestion of wood.
Effect of solution ions on the charge and performance of nanofiltration membranes
Authors: Roth Rebecca S. , Birnhack Liat , Avidar Mor , Hjelvik Elizabeth A. , Straub Anthony P. , Epsztein Razi
Published: March 2024

Considering growing efforts to understand and improve the solute-specific selectivity of nanofiltration (NF) membranes, we explored the ion-specific effects that govern the charge and performance of a loose polyamide NF membrane that is commonly used for solute-solute separations. Specifically, we systematically evaluated the zeta potential of the membrane under different conditions of pH, salinity, and ionic composition, and correlated the obtained data with membrane performance tested under similar conditions. Our results identify the pKa of both carboxylic and amine groups bonded to the membrane surface and suggest that the highly polarizable chloride anions in the solution adsorb to the polyamide, increasing its negative charge. We also show that monovalent cations of different “stickiness” can neutralize the negative membrane charge to different extents due to their varying tendency to sorb to the polymer matrix or screen the fixed carboxyl groups on the membrane surface. Notably, our correlation between zeta potential measurements and permeability experiments indicates the substantial contribution of solution ions to Donnan exclusion in NF membranes.
Cell-in-cell phenomena across the tree of life
Authors: Kapsetaki Stefania E. , Cisneros Luis H. , Maley Carlo C.
Published: March 2024

Cells in obligately multicellular organisms by definition have aligned fitness interests, minimum conflict, and cannot reproduce independently. However, some cells eat other cells within the same body, sometimes called cell cannibalism. Such cell-in-cell events have not been thoroughly discussed in the framework of major transitions to multicellularity. We performed a systematic screening of 508 articles, from which we chose 115 relevant articles in a search for cell-in-cell events across the tree of life, the age of cell-in-cell-related genes, and whether cell-in-cell events are associated with normal multicellular development or cancer. Cell-in-cell events are found across the tree of life, from some unicellular to many multicellular organisms, including non-neoplastic and neoplastic tissue. Additionally, out of the 38 cell-in-cell-related genes found in the literature, 14 genes were over 2.2 billion years old, i.e., older than the common ancestor of some facultatively multicellular taxa. All of this suggests that cell-in-cell events may have originated before the origins of obligate multicellularity. Thus, our results show that cell-in-cell events exist in obligate multicellular organisms, but are not a defining feature of them. The idea of eradicating cell-in-cell events from obligate multicellular organisms as a way of treating cancer, without considering that cell-in-cell events are also part of normal development, should be abandoned.
Identification and validation of a metabolism-related gene signature for predicting the prognosis of paediatric medulloblastoma
Authors: Su Jun , Xie Qin , Xie Longlong
Published: March 2024

Medulloblastoma (MB) is a malignant brain tumour that is highly common in children and has a tendency to spread to the brain and spinal cord. MB is thought to be a metabolically driven brain tumour. Understanding tumour cell metabolic patterns and characteristics can provide a promising foundation for understanding MB pathogenesis and developing treatments. Here, by analysing RNA-seq data of MB samples from the Gene Expression Omnibus (GEO) database, 12 differentially expressed metabolic-related genes (DE-MRGs) were chosen for the construction of a predictive risk score model for MB. This model demonstrated outstanding accuracy in predicting the outcomes of MB patients and served as a standalone predictor. An evaluation of functional enrichment revealed that the risk score showed enrichment in pathways related to cancer promotion and the immune response. In addition, a high risk score was an independent poor prognostic factor for MB in patients with different ages, sexes, metastasis stages and subgroups (SHH and Group 4). Consistently, the metabolic enzyme ornithine decarboxylase (ODC1) was upregulated in MB patients with poor survival time. Inhibition of ODC1 in primary and metastatic MB cell lines decreased cell proliferation, migration and invasion but increased immune infiltration. This study could aid in identifying metabolic targets for MB as well as optimizing risk stratification systems and individual treatment plans for MB patients via the use of a metabolism-related gene prognostic risk score signature.
Exploring the surge current degradation of natural ester oil-based nanofluids
Authors: Tsovilis Thomas , Peppas George , Staikos Evangelos , Hadjicostas Alexandros , Datsios Zacharias
Published: March 2024

The surge endurance of natural ester oil-based nanofluids against surge events is investigated experimentally. The focus of this work is the examination, through dielectric spectroscopy measurements, of the alteration of the real and imaginary parts of the complex relative permittivity of iron oxide nanofluids as a result of an accelerated degradation test employing a sequence of repetitive current impulses produced via a 12 kV/6 kA combination wave generator. The target is the exploration of a possible implementation of nanofluids as multipurpose liquids that act, in addition to insulation and coolants, as surge absorption media. Promising experimental results are discussed and compared with those of mineral oil that is widely used as a conventional insulating liquid in power transformers.
Process design for acidic and alcohol based deep eutectic solvent pretreatment and high pressure homogenization of palm bunches for nanocellulose production
Authors: Sonyeam Janejira , Chaipanya Ratanaporn , Suksomboon Sudarat , Khan Mohd Jahir , Amatariyakul Krongkarn , Wibowo Agung , Posoknistakul Pattaraporn , Charnnok Boonya , Liu Chen Guang , Laosiripojana Navadol , Sakdaronnarong Chularat
Published: March 2024

This research aimed to study on nanocellulose production from palm bunch using process design and cost analysis. Choline chloride based deep eutectic solvent pretreatment was selected for high-purity cellulose separation at mild condition, followed by nano-fibrillation using mechanical treatment. Three types of choline chloride-based deep eutectic solvents employing different hydrogen-bond donors (HBDs) namely lactic acid, 1,3-butanediol and oxalic acid were studied. The optimal cellulose extraction condition was choline chloride/lactic acid (ChLa80C) pretreatment of palm empty bunch at 80 °C followed by bleaching yielding 94.96%w/w cellulose content in product. Size reduction using ultrasonication and high-pressure homogenization produced nanocellulose at 67.12%w/w based on cellulose in raw material. Different morphologies of nanocellulose were tunable in the forms of nanocrystals, nano-rods and nanofibers by using dissimilar deep eutectic solvents. This work offered a sustainable and environmentally friendly process as well as provided analysis of DES pretreatment and overview operating cost for nanocellulose production. Application of nanocellulose for the fabrication of highly functional and biodegradable material for nanomedicine, electronic, optical, and micromechanical devices is achievable in the near future.
Identification of molecular subtypes and a prognostic signature based on m6A/m5C/m1A-related genes in lung adenocarcinoma
Authors: Zhang Yu , Jia Qiuye , Li Fangfang , Luo Xuan , Wang Zhiyuan , Wang Xiaofang , Wang Yanghao , Zhang Yinglin , Li Muye , Bian Li
Published: March 2024

Lung cancer, specifically the histological subtype lung adenocarcinoma (LUAD), has the highest global occurrence and fatality rate. Extensive research has indicated that RNA alterations encompassing m6A, m5C, and m1A contribute actively to tumorigenesis, drug resistance, and immunotherapy responses in LUAD. Nevertheless, the absence of a dependable predictive model based on m6A/m5C/m1A-associated genes hinders accurately predicting the prognosis of patients diagnosed with LUAD. In this study, we collected patient data from The Cancer Genome Atlas (TCGA) and identified genes related to m6A/m5C/m1A modifications using the GeneCards database. The “ConsensusClusterPlus” R package was used to produce molecular subtypes by utilizing genes relevant to m6A/m5C/m1A identified through differential expression and univariate Cox analyses. An independent prognostic factor was identified by constructing a prognostic signature comprising six genes (SNHG12, PABPC1, IGF2BP1, FOXM1, CBFA2T3, and CASC8). Poor overall survival and elevated expression of human leukocyte antigens and immune checkpoints were correlated with higher risk scores. We examined the associations between the sets of genes regulated by m6A/m5C/m1A and the risk model, as well as the immune cell infiltration, using algorithms such as ESTIMATE, CIBERSORT, TIMER, ssGSEA, and exclusion (TIDE). Moreover, we compared tumor stemness indices (TSIs) by considering the molecular subtypes related to m6A/m5C/m1A and risk signatures. Analyses were performed based on the risk signature, including stratification, somatic mutation analysis, nomogram construction, chemotherapeutic response prediction, and small-molecule drug prediction. In summary, we developed a prognostic signature consisting of six genes that have the potential for prognostication in patients with LUAD and the design of personalized treatments that could provide new versions of personalized management for these patients.
Clinical and mutational characteristics of oculocutaneous albinism type 7
Authors: Kruijt C. C. , de Wit G. C. , van Minderhout H. M. , Schalij-Delfos N. E. , van Genderen M. M.
Published: March 2024

The purpose of this paper is to expand on the phenotype of oculocutaneous albinism type 7 (OCA7). We described three patients with OCA7: two from a consanguineous family of Kurdish origin and one patient of Dutch origin. We compared them with all patients described to date in the literature. All newly described patients had severely reduced visual acuity (VA), nystagmus, hypopigmentation of the fundus, severe foveal hypoplasia, and chiasmal misrouting. None had iris translucency. All patients had normal pigmentation of skin and hair. We found one novel mutation in the Dutch patient: c.565G > A; p.(Gly189Ser). We compared our patients to the 15 described in the literature to date. All 18 patients had substantially pigmented skin and hair, very poor VA (0.4–1.3 logMAR), nystagmus, (mild) ocular hypopigmentation, foveal hypoplasia, and misrouting. Although pigmentation levels were mildly affected in OCA7, patients had a severe ocular phenotype with VA at the poorer end of the albinism spectrum, severe foveal hypoplasia, and chiasmal misrouting. OCA7 patients had a phenotype restricted to the eyes, and similar to that of X-linked ocular albinism. We therefore propose to rename the disorder in ocular albinism type 2. Unfolding the role of LRMDA in OCA7, may bring us a step closer in identifying the responsible factors for the co-occurrence of foveal hypoplasia and misrouting.
Effect of gamma rays on the essential oil and biochemical characteristics of the Satureja mutica Fisch & C. A. Mey
Authors: Mahdi Navehsi Fatemeh , Abdossi Vahid , Abbaszadeh Bohloul , Azimi Razieh , Dianat Marjan
Published: March 2024

There are 16 species in the genus Satureja L. (Lamiaceae), of which 10 are native. This research aimed to investigate the effect of gamma rays and storage conditions and duration on the percentage and components of the essential oil and some biochemical characteristics of Satureja mutica Fisch & C.A. Mey at the Research Institute of Forests and Rangelands. Plants were collected at the full flowering stage and exposed to different doses of gamma rays (0, 2.5, 5, 7.5, and 10 kGy) at the Atomic Energy Organization, Iran. The samples were kept in a refrigerator (4 °C) and in the shade (25 ± 2 °C) for 0, 120, and 240 h. This experiment was performed in a completely randomized design. Essential oil extraction was done by water distillation for 2 h. The composition of their essential oil components was identified using GC and GC/MS. Some biochemical traits, including phenol content, antioxidant capacity, and carbohydrate content, were measured. The results indicated that irradiation on the percentage of essential oil showed a statistically significant difference. In addition, the interaction effect of irradiation × storage conditions, irradiation × duration of storage, on the percentage of essential oil was significant. According to a comparison of the means, 2.5 kGy irradiation produced the highest percentage of essential oil (0.4%); in contrast, a significant decrease was detected in components with 7.5 and 10 kGy irradiation. It was observed that the percentage of some essential oil compounds decreased with the gamma-ray intensity increase. 2.5 kGy of gamma rays and shade storage conditions for 240 h led to the highest content of p-cymene and carvacrol. Nevertheless, the highest thymol content was obtained under refrigeration conditions without irradiation. The maximum phenol content and antioxidant capacity were obtained when the plants were irradiated with 2.5 and 7.5 kGy gamma rays. However, the maximum carbohydrate rate was observed in non-irradiated plants. It was concluded that low-intensity gamma rays could improve the percentage of essential oil and main components like p-cymene and carvacrol in S. mutica Fisch & C.A. Mey.
From wires to waves, a novel sensor system for in vivo pressure monitoring
Authors: Wright Daniel Nilsen , Züchner Mark , Annavini Eis , Escalona Manuel J. , Hammerlund Teige Lena , Whist Tvedt Lars Geir , Lervik Andreas , Haga Henning A. , Guiho Thomas , Clausen Ingelin , Glott Thomas , Boulland Jean-Luc
Published: March 2024

Pressure monitoring in various organs of the body is essential for appropriate diagnostic and therapeutic purposes. In almost all situations, monitoring is performed in a hospital setting. Technological advances not only promise to improve clinical pressure monitoring systems, but also engage toward the development of fully implantable systems in ambulatory patients. Such systems would not only provide longitudinal time monitoring to healthcare personnel, but also to the patient who could adjust their way-of-life in response to the measurements. In the past years, we have developed a new type of piezoresistive pressure sensor system. Different bench tests have demonstrated that it delivers precise and reliable pressure measurements in real-time. The potential of this system was confirmed by a continuous recording in a patient that lasted for almost a day. In the present study, we further characterized the functionality of this sensor system by conducting in vivo implantation experiments in nine female farm pigs. To get a step closer to a fully implantable system, we also adapted two different wireless communication solutions to the sensor system. The communication protocols are based on MICS (Medical Implant Communication System) and BLE (Bluetooth Low Energy) communication. As a proof-of-concept, implantation experiments in nine female pigs demonstrated the functionality of both systems, with a notable technical superiority of the BLE.
Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences
Authors: Raj Neenu , Sukumaran Sandhya , Jose Anjaly , Nisha K. , Roul Subal Kumar , Rahangdale Shikha , Kizhakudan Shoba Joe , Gopalakrishnan A.
Published: March 2024

Nemipterus randalli, commonly known as Randall’s threadfin bream, is a commercially important marine finfish. Understanding its genetic structure is critical to effective management and conservation efforts. Previous investigations on population structure in this species were limited by geographic coverage. In this study, we utilized the mitochondrial Cytochrome b gene and nuclear Ribosomal protein gene intron Rp S7 sequences to investigate the population genetic structure, demography and genetic diversity of N. randalli along Indian waters. Our results revealed high haplotype diversity but low nucleotide diversity. AMOVA revealed that the variation among the population was highly significant. Hierarchical AMOVA provided further evidence of significant genetic differentiation between the west and east coasts, which was corroborated by the Bayesian tree and the median-joining network diagram. The mtDNA sequences revealed significant genetic structure between populations based on fixation index analysis following the isolation-by-distance model. Furthermore, the neutrality test and mismatch analysis suggest that N. randalli populations may have experienced a population expansion. However, nuclear marker RpS7, showed a high level of polymorphism, which obscured the population structuring observed with the mitochondrial marker. Consequently, concordant results were not obtained when comparing the mitochondrial and nuclear DNA sequences. The strong genetic differentiation between the east and west coast observed using mitochondrial marker could be attributed to a combination of geographic and environmental factors. These findings lay the groundwork for developing effective conservation and management strategies for N. randalli, considering its genetic structure.
The updated genome of the Hungarian population of Aedes koreicus
Authors: Nagy Nikoletta Andrea , Tóth Gábor Endre , Kurucz Kornélia , Kemenesi Gábor , Laczkó Levente
Published: March 2024

Vector-borne diseases pose a potential risk to human and animal welfare, and understanding their spread requires genomic resources. The mosquito Aedes koreicus is an emerging vector that has been introduced into Europe more than 15 years ago but only a low quality, fragmented genome was available. In this study, we carried out additional sequencing and assembled and characterized the genome of the species to provide a background for understanding its evolution and biology. The updated genome was 1.1 Gbp long and consisted of 6099 contigs with an N50 value of 329,610 bp and a BUSCO score of 84%. We identified 22,580 genes that could be functionally annotated and paid particular attention to the identification of potential insecticide resistance genes. The assessment of the orthology of the genes indicates a high turnover at the terminal branches of the species tree of mosquitoes with complete genomes, which could contribute to the adaptation and evolutionary success of the species. These results could form the basis for numerous downstream analyzes to develop targets for the control of mosquito populations.
Neutrophil to lymphocytes ratio in deep infiltrating endometriosis as a new toll for clinical management
Authors: Dominoni Mattia , Pasquali Marianna Francesca , Musacchi Valentina , De Silvestri Annalisa , Mauri Matteo , Ferretti Virginia Valeria , Gardella Barbara
Published: March 2024

Several mechanisms, including altered local and systemic immune system, apoptosis, and new angiogenesis, are responsible for the development and progression of endometriosis. Over the years many markers have been studied, like CA 125 and, recently, neutrophil-to-lymphocyte ratio (NLR). This tool is cost-effectiveness and non-invasiveness as a marker of systemic inflammatory diseases. The aim of this study is to assess the role of NLR in the real-life management of patients with endometriosis in order to evaluate the possible association between this value and symptoms. We performed a retrospective analysis of 199 premenopausal women affected by endometriosis, from January 2013 to December 2020, evaluating the characteristics of disease, the symptoms and the NLR. Analyzing the neutrophiles, the mean ± SD value was 6.1 ± 4.5 × 103/ul, while for lymphocytes mean ± SD value was 1.8 ± 0.7.NLR was categorized according to its median value (> 2.62 vs ≤ 2.62). The comparison between NLR values and CA 125, endometriosis stage, dysmenorrhea and presence of chronic pelvic pain, adjusting for previous therapy did not find a significant association. An interesting result, although not significant, was the association between NLR and chronic pelvic pain (OR = 1.9). In the sub-group of patients without previous therapy this association is even stronger (OR = 4.8, 95% CI 0.5–50.2, p = 0.190). The link between NLR and chronic pelvic pain can provide a further hint to the clinician even when taking symptoms into account to develop a particular therapeutic treatment related to the various expressions of NLR. Finally, NLR may enable the creation of customized follow-up protocols that divide patients into high- and low-risk categories for endometriosis recurrence.
Risk assessment and source analysis of heavy metals in soil around an asbestos mine in an arid plateau region, China
Authors: Li Xuwei , Ding Da , Xie Wenyi , Zhang Ya , Kong Lingya , Li Ming , Li Mei , Deng Shaopo
Published: March 2024

Asbestos is widely used in construction, manufacturing, and other common industrial fields. Human activities such as mining, processing, and transportation can release heavy metals from asbestos into the surrounding soil environment, posing a health hazard to the mining area's environment and its surrounding residents. The purpose of the present study was to determine the extent of ecological and human health damage caused by asbestos pollution, as well as the primary contributors to the contamination, by examining a large asbestos mine and the surrounding soil in China. The level of heavy metal pollution in soil and sources were analyzed using methods such as the geo-accumulation index (Igeo), potential ecological risk index (RI), and positive matrix factorization (PMF) model. A Monte Carlo simulation-based health risk model was employed to assess the health risks of heavy metals in the study area’s soil to human beings. The results showed that the concentrations of As, Pb, Cr, Cu, and Ni in the soil were 1.74, 0.13, 13.31, 0.33, and 33.37 times higher than the local soil background values, respectively. The Igeo assessment indicated significant accumulation effects for Ni, Cr, and As. The RI evaluation revealed extremely high comprehensive ecological risks (RI ≥ 444) in the vicinity of the waste residue heap and beneficiation area, with Ni exhibiting strong individual potential ecological risk (Eir ≥ 320). The soil health risk assessment demonstrated that As and Cr posed carcinogenic risks to adults, with mean carcinogenic indices (CR) of 1.56E − 05 and 4.14E − 06, respectively. As, Cr, and Cd posed carcinogenic risks to children, with mean CRs of 1.08E − 04, 1.61E − 05, and 2.68E − 06, respectively. Cr also posed certain non-carcinogenic risks to both adults and children. The PMF model identified asbestos contamination as the primary source of heavy metals in the soil surrounding the asbestos mining area, contributing to 79.0%. According to this study, it is recommended that management exercise oversight and regulation over the concentrations of Ni, Cr, Cd, and As in the soil adjacent to asbestos mines, establish a designated control zone to restrict population activities, and locate residential zones at a safe distance from the asbestos mine production zone.
Diagnostic value of IgG antibody and stool antigen tests for chronic Helicobacter pylori infections in Ibb Governorate, Yemen
Authors: Al Ofairi Bashir A. , Saeed Marwan K. , Al-Qubaty Mohammed , Abdulkareem Ahmed. M. , Al-Jahrani Majed A.
Published: March 2024

The stool antigen test (SAT) and the serumHelicobacter pylori(H. pylori) IgG antibody assays exhibit significant utility in the clinical diagnosis ofH. pyloriinfection and in distinguishing between acute and chronic infections. The main objective of the current study was to identify the diagnostic value of serumH. pyloriIgG antibody and SAT in the detection ofH. pyloriinfections among chronicH. pylori-infected patients residing in Ibb Governorate, Yemen. 200 patients withH. pyloriinfection, confirmed through positive results in the serum immunochromatographic antibody test, were selected forH. pyloriinfection confirmation using serumH. pyloriIgG antibodies and SAT across diverse hospitals, gastroenterology, and Hepatology clinics in Ibb Governorate. After the selection of patients, blood and stool specimens were obtained from all participants and underwent analysis via the Statistical Package for the Social Sciences (SPSS). The prevalence ofH. pyloriinfection demonstrated variability based on the confirmatory tests, with rates of 54% for SAT and 78.5% for serumH. pyloriIgG antibody, contrasting with a 100% prevalence observed in the screening serum immunochromatographic antibody test. Clinically, the study categorizedH. pyloriinfections into four stages, whereby a significant proportion of patients (40.5%) exhibited positivity for both serumH. pyloriIgG antibody and SAT, indicative of active chronic infections. The majority of positive cases only manifested serumH. pyloriIgG antibody presence (chronic infections) at 38%, whereas 13.5% exclusively tested positive for SAT, corresponding to acute infections. Moreover, 88% of patients did not have either serumH. pyloriIgG antibody or SAT (absence of infections) during confirmatory tests. Noteworthy is the study's approach employing multiple tests forH. pyloriinfection detection, focusing predominantly on chronic infections-prevailing types caused byH. pylori. The results revealed a significant association between serum levels ofH. pyloriIgG antibody and SAT results with the presence of diverse gastrointestinal symptoms among patients, which increased with longH. pyloriinfection durations.
Predicting current and future habitat of Indian pangolin (Manis crassicaudata) under climate change
Authors: Qasim Siddiqa , Mahmood Tariq , Rakha Bushra Allah , Nadeem Muhammad Sajid , Akrim Faraz , Aslam Asad , Belant Jerrold L.
Published: March 2024

Climate change is among the greatest drivers of biodiversity loss, threatening up to 15–30% of described species by the end of the twenty-first century. We estimated the current suitable habitat and forecasted future distribution ranges of Indian pangolin (Manis crassicaudata) under climate change scenarios. We collected occurrence records of Indian pangolin using burrow counts, remote camera records and previously published literature in Pakistan during 2021–2023. We downloaded bioclimatic data for current (1970–2000) and future (2041–2060, 2061–2080, 2081–2100) climate scenarios from the WorldClim database using the Hadley Global Environment Model (HadGEM3-GC31-LL). We used MaxEnt software to predict current and future distributions of Indian pangolin, then computed the amount of habitat lost, gained, and unchanged across periods. We obtained 560 Indian pangolin occurrences overall, 175 during the study, and 385 from our literature search. Model accuracy was very good (AUC = 0.885, TSS = 0.695), and jackknife tests of variable importance showed that the contribution of annual mean temperature (bio1) was greatest (33.4%), followed by the mean temperature of the coldest quarter (bio-12, 29.3%), temperature seasonality (bio 4, 25.9%), and precipitation seasonality (bio 15, 11.5%). The maxent model predicted that during the current time period (1970–2000) highly suitable habitat for Indian pangolin was (7270 km2, 2.2%), followed by moderately suitable (12,418 km2, 3.7%), less suitable (49,846 km2, 14.8%), and unsuitable habitat (268,355 km2, 79.4%). Highly suitable habitat decreased in the western part of the study area under most SSPs and in the central parts it declined under all SSPs and in future time periods. The predicted loss in the suitable habitat of the Indian pangolin was greatest (26.97%) under SSP 585 followed by SSP 126 (23.67%) during the time 2061–2080. The gain in suitable habitat of Indian pangolin was less than that of losses on average which ranged between 1.91 and 13.11% under all SSPs during all time periods. While the stable habitat of the Indian pangolin ranged between 64.60 and 83.85% under all SSPs during all time periods. Our study provides the current and future habitat ranges of Indian pangolin in the face of a changing climate. The findings of our study could be helpful for policymakers to set up conservation strategies for Indian pangolin in Pakistan.
Electrophysiological signatures of spelling sensitivity development from primary school age to adulthood
Authors: Larionova Ekaterina , Rebreikina Anna , Martynova Olga
Published: March 2024

Recognizing spelling errors is important for correct writing and reading, and develops over an extended period. The neural bases of the development of orthographic sensitivity remain poorly understood. We investigated event-related potentials (ERPs) associated with spelling error recognition when performing the orthographic decision task with correctly spelled and misspelled words in children aged 8–10 years old, early adolescents aged 11–14 years old, and adults. Spelling processing in adults included an early stage associated with the initial recognition of conflict between orthography and phonology (reflected in the N400 time window) and a later stage (reflected in the P600 time window) related to re-checking the spelling. In children 8–10 years old, there were no differences in ERPs to correct and misspelled words; in addition, their behavioral scores were worse than those of early adolescents, implying that the ability to quickly recognize the correct spelling is just beginning to develop at this age. In early adolescents, spelling recognition was reflected only at the later stage, corresponding to the P600 component. At the behavioral level, they were worse than adults at recognizing misspelled words. Our data suggest that orthographic sensitivity can develop beyond 14 years.
Mathematical topology and geometry-based classification of tauopathies
Authors: Sugiyama Masumi , Kosik Kenneth S. , Panagiotou Eleni
Published: March 2024

Neurodegenerative diseases, like Alzheimer’s, are associated with the presence of neurofibrillary lesions formed by tau protein filaments in the cerebral cortex. While it is known that different morphologies of tau filaments characterize different neurodegenerative diseases, there are few metrics of global and local structure complexity that enable to quantify their structural diversity rigorously. In this manuscript, we employ for the first time mathematical topology and geometry to classify neurodegenerative diseases by using cryo-electron microscopy structures of tau filaments that are available in the Protein Data Bank. By employing mathematical topology metrics (Gauss linking integral, writhe and second Vassiliev measure) we achieve a consistent, but more refined classification of tauopathies, than what was previously observed through visual inspection. Our results reveal a hierarchy of classification from global to local topology and geometry characteristics. In particular, we find that tauopathies can be classified with respect to the handedness of their global conformations and the handedness of the relative orientations of their repeats. Progressive supranuclear palsy is identified as an outlier, with a more complex structure than the rest, reflected by a small, but observable knotoid structure (a diagrammatic structure representing non-trivial topology). This topological characteristic can be attributed to a pattern in the beginning of the R3 repeat that is present in all tauopathies but at different extent. Moreover, by comparing single filament to paired filament structures within tauopathies we find a consistent change in the side-chain orientations with respect to the alpha carbon atoms at the area of interaction.
Effect of pre-season and in-season training on anthropometric variables, somatotype, body composition and body proportion in elite basketball players
Authors: Díaz-Martínez A. S. , Vaquero-Cristóbal R. , Albaladejo-Saura M. , Esparza-Ros F.
Published: March 2024

The aims of the study were: 1) to evaluate the changes in anthropometric variables, body composition, somatotype and body proportions of elite basketball players throughout the pre-season period; 2) to evaluate the changes in anthropometric variables, body composition, somatotype and body proportions of elite basketball players throughout the in-season period; and 3) to observe if the age and position influenced the variables analyzed. A total of 17 players belonging to the men’s ACB league team competing in the Euroleague (age = 23.42 ± 5.28 years-old) participated in the study. The players underwent an anthropometric measurement before and after the pre-season, as well as four evaluations throughout the in-season. Anthropometric indices, somatotype components according to Heath and Carter, and adiposity were calculated. The results show that during the pre-season, body mass, BMI, sum of 6 and 8 skinfolds, waist/hip ratio, adipose tissue (kg), adipose tissue percentage, and endomorphy decreased, while ectomorphy increased. However, no significant changes were found in the variables analyzed throughout the season; except for endomorphy, which increased along the in-season. Playing position and age did not have a significant influence on the changes in the anthropometric variables throughout the pre-season and the in-season. In conclusion, while changes in the anthropometric variables in the pre-season were observed, these remained the same during the in-season.
Complete electromagnetic consideration of plasmon mode excitation in graphene rectangles by incident terahertz wave
Authors: Mashinsky K. V. , Popov V. V. , Fateev D. V.
Published: March 2024

The excitation of terahertz plasmon modes in a graphene rectangle by normally incident linearly polarized electromagnetic wave has been theoretically studied. The complete electromagnetic approach based on formulation of the integral equations for sought-for electromagnetic quantities has been developed. The influence of edge-field effects on excitation of plasmon modes for different polarization of the incident wave and different shapes of graphene rectangle has been studied. The absorption cross-section spectra and the charge density distributions in graphene rectangle for different plasmon modes have been studied. It has been found that the edge-field effect, which results in spreading the plasmon field beyond the geometric boundaries of graphene rectangle, leads to considerable red shifts of the plasmon mode frequencies and modifies the plasmon mode dispersion.
Caldomycin, a new guanidopolyamine produced by a novel agmatine homocoupling enzyme involved in homospermidine biosynthesis
Authors: Kobayashi Teruyuki , Sakamoto Akihiko , Hisano Tamao , Kashiwagi Keiko , Igarashi Kazuei , Takao Koichi , Uemura Takeshi , Furuchi Takemitsu , Sugita Yoshiaki , Moriya Toshiyuki , Oshima Tairo , Terui Yusuke
Published: March 2024

An extreme thermophilic bacterium, Thermus thermophilus produces more than 20 unusual polyamines, but their biosynthetic pathways, including homospermidine, are not yet fully understood. Two types of homospermidine synthases have been identified in plants and bacteria, which use spermidine and putrescine or two molecules of putrescine as substrates. However, homospermidine synthases with such substrate specificity have not been identified in T. thermophilus. Here we identified a novel agmatine homocoupling enzyme that is involved in homospermidine biosynthesis in T. thermophilus. The reaction mechanism is different from that of a previously described homospermidine synthase, and involves conjugation of two molecules of agmatine, which produces a diamidino derivative of homospermidine (caldomycin) as an immediate precursor of homospermidine. We conclude that there is a homospermidine biosynthetic pathway from agmatine via caldomycin synthase followed by ureohydrolase in T. thermophilus. Furthermore, it is shown that caldomycin is a novel compound existing in nature.