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Soil and root samples were collected from two plots (5.5 x 6 m) cultivated with bamboo Phyllostachys reticulata (syn. P. bambusoides) at the USDA Southeastern Fruit and Tree Nut Research Station in Byron, Georgia, USA, in November 2021, December 2022, and December 2023. Each soil sample consisted of five randomly collected subsamples, which were analyzed for the presence of plant-parasitic nematodes as part of regular monitoring. No aboveground symptoms were seen in the field plots, but roots showed discoloration and stunted growth (Fig. 1A). An average population density of 160, 36, and 188 second-stage juveniles (J2) of cyst nematodes (Heterodera spp.) per 100 cm3 of soil was detected in 2021, 2022, and 2023, respectively. To confirm the cyst nematode parasitism, three healthy P. reticulata plants were transplanted into 10 cm diameter pots filled with nematode-infested soil and grown in a greenhouse at 25-28°C. After three months, young cysts containing eggs protruding from the bamboo roots were seen, confirming nematode parasitism (Fig. 1B and C). Morphological and molecular analyses were conducted to identify the nematode species. The J2 body shape was cylindrical with three incisures in lateral field and well-developed rounded stylet knobs. Measurements of J2 (n = 10) included the length (range = 406.0-518.1 μm, mean = 458.2 ± 16.1 μm) and width (16.0-17.2 μm, 16.6 ± 0.5 μm) of body, labial region height (3.0-3.6 μm, 3.2 ± 0.2 μm), stylet (17.2-18.9 μm, 18.02 ± 0.6 μm), tail (61.1-65.9 μm, 63.1 ± 5.8 μm), body width at anus (9.7-12.4 μm, 10.8 ± 0.3 μm), and hyaline tail terminus (35.4-53.0 μm, 44.0 ± 3.8 μm). The cysts (n = 5) were relatively lemon-shaped, light to dark brown in color with projected neck and vulval cone that lacked fenestration, bullae, and underbridge. Morphometrics were body length including neck (420.5-745.0 μm, 550.4 ± 72 μm), body width (345.0-544.1 μm, 430.1 ± 59 μm), and L/W ratio (1.0-1.4 μm, 1.1 ± 0.1 μm). The morphometric of vulval cone included fenestral length (48 to 69 µm, 60.2 ± 4.0 µm), fenestral width (43 to 51 µm, 48.9 ± 4.0 µm) and vulval slit (47 to 58 µm, 49.1 ± 2.6 µm). Morphology and morphometric measurements of the cysts and J2 (Fig. 2A-C) were comparable to previous reports of Korean cyst nematode, H. koreana from other Asian countries (Mundo-Ocampo et al., 2008; Wang et al., 2012; Tanha Maafi and Taheri, 2015; Sekimoto et al., 2017). For molecular diagnosis, DNA was extracted from single cysts (n= 3) using DNeasy Blood and Tissue Kit, and 28S rRNA and partial cytochrome oxidase I (COI) gene fragments were amplified using D2A/D3B and Het-coxiF/Het-coxiR primer sets, respectively according to Subbotin et al. (2015) and Hajihassani et al. (2018). PCR products were then purified by a DNA Clean & Concentrator kit (Zymo Research, CA, USA) and sequenced at Genewiz (South Plainfield, NJ, USA). The resulting sequences were deposited into the GenBank database and subjected to BLASTn searches. Sequence analysis of the 28S rRNA gene (GenBank accession number OL812726) showed that the H. koreana isolate from Georgia was 100% identical (692/692 bp) with H. koreana populations from Japan and South Korea. Analysis of the H. koreana isolate from Georgia based on the COI sequence (OL813218 and OL813219) revealed 100% similarity (421/422 bp) with a population of H. koreana from Japan and 98% similarity (409/409 bp) with a population from South Korea. To our knowledge, this is the first report of H. koreana parasitizing P. reticulata in Georgia as the second state in the USA. This nematode was first reported in Florida infecting fish pole bamboo (P. aurea) propagated from plant material from the Far East (Inserra et al. 1999). This report expands the information on the geographical distribution of H. koreana. Given the significant potential for damage to bamboo, precautions should be taken to prevent the nematode's spread to unaffected regions.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a promising technique for the rapid identification microorganisms. The aim of this study was to create a new database for the accurate identification of Candidozyma auris (formerly known as Candida auris ) and 11 species of the Candidozyma haemuli species complex, including C. chanthaburiensis , C. duobushaemuli , C. haemuli , C. heveicola , C. khanbhai , C. konsanensis , C. metrosideri , C. ohialehuae , C. pseudohaemuli , C. ruelliae , and C. vulturna . Seventy-one Candidozyma isolates from different national institutions were studied. Thirty-seven strains were used to create a MALDI-TOF (microTyper MS) database using the formic acid extraction method. The validation of this database was performed with 34 other strains of the genus Candidozyma , and the result was compared with the identification results when using DBRs v1.0.0.4 (Tianrui, China). Our library allowed a 100% identification of the evaluated strains with all strains showing log scores of >2.0. Repeatability and reproducibility tests result showed a coefficient of variation of the log score values of less than 5%. The MALDI-TOF MS system can identify C. auris and related species quickly and accurately. This method will play a crucial role in accurately diagnosing infectious agents of the genus Candidozyma in clinical practice., Importance: Importance Candidozyma auris , also known as Candida auris , has quickly spread across the world, and prompt identification of C. auris from infected individuals is critical. However, a standard identification method is lacking for the identification of C. auris in clinical and public health laboratories. To make matters worse, its biochemical assimilation profile was found to be similar to that of closely related and even no-related species, leading to frequent misidentification. To improve diagnostics of this and closely related species, we created a database of reference mass spectra resulting in the efficient and correct identification of all Candidozyma species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Moreover, potential pathogenic species of Candidozyma can be effectively identified by MALDI-TOF MS, and differentiated from non-clinically relevant phylogenetic relatives. Thus, MALDI-TOF MS may help expedite laboratory diagnosis and treatment of C. auris and related species of clinical importance and help the clinician to decide on early treatment.

Chemical investigation of the Liuweizhiji Gegen-Sangshen oral liquid afforded one new diphenyl ether derivative (1), together with one known compound (2). Their structures were established by 1D and 2D NMR, and HR-ESI-MS spectroscopic analysis and the absolute configuration of 1 was confirmed by ECD calculation. Compounds 1 and 2 were evaluated for the cytotoxic activities, and compounds 1 and 2 showed weak cytotoxic activities towards HepG2 human liver cancer cells, with IC 50 values of 97.3 and 79.6 μM, respectively., (© 2024 John Wiley & Sons Ltd.)

Background: Medicinal plants are crucial for traditional healers in preparing remedies and also hold significant importance for the modern pharmaceutical industry, facilitating drug discovery processes. Accurate and effective identification and classification of Ethiopian indigenous medicinal plants are vital for their conservation and preservation. However, the existing identification and classification process is time-consuming, and tedious, and demands the expertise of specialists. Botanists traditionally rely on traditional and experience-based methods for identifying various medicinal plant species., Objective: This research aims to develop an efficient deep learning model through transfer learning for the identification and classification of Ethiopian indigenous medicinal plant species., Materials and Methods: A custom dataset of 1853 leaf images from 35 species was prepared and labeled by botanist experts. Experiments have been done with the use of pretrained deep learning models, specifically VGG16, VGG19, Inception-V3, and Xception., Results: The results demonstrate that fine-tuning the models significantly improves training and test accuracy, indicating the potential of deep learning in this domain. VGG19 outperforms other models with a test accuracy of 94%, followed by VGG16, Inception-V3, and Xception with test accuracies of 92%, 91%, and 87%, respectively. The study successfully addresses the challenges in the identification and classification of Ethiopian indigenous medicinal plant species., Conclusion: With an inspiring accuracy performance of 95%, it can be concluded that fine-tuning emerged as a highly effective strategy for boosting the performance of deep learning models., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Italian ryegrass ( Lolium multiflorum L.) is widely cultivated as an important forage grass worldwide because of its high nutritional value and good palatability. Anthracnose caused by Colletotrichum species was a common and new emerging disease of Italian ryegrass. In this study, 88 Colletotrichum isolates were collected from diseased leaves of Italian ryegrass planting regions in Sichuan, Chongqing, and Guizhou provinces of southwestern China between 2019 and 2022. By the pure culture technique, 15 representative single-spore isolates were obtained for further study. Multilocus phylogenetic analysis coupled with morphological features showed that these isolates were finally identified as six new record species: C. cereale of the C. graminicola species complex, C. fioriniae and C. nymphaeae of the C. acutatum species complex, C. boninense and C. citricola of the C. boninense species complex, and C. nageiae . Pathogenicity tests indicated that all species could induce anthracnose symptoms; of these, C. cereale was more invasive than other species, followed by C. fioriniae , C. nageiae , C. citricola , and C. boninense ; C. nymphaeae was the weakest pathogenic species to Italian ryegrass plants ( P ≤ 0.05). Fungicide sensitivity assays showed that iprodione, propineb, and oxime·tebuconazole had strong inhibitory effects on the mycelial growth of six Colletotrichum species; in addition, azoxystrobin and fludioxonil also significantly inhibited the mycelial growth of C. nymphaeae and C. fioriniae , respectively. These results provide the basis for the diagnosis and detection in the field, pathogen identification, and management of anthracnose on Italian ryegrass., Competing Interests: The author(s) declare no conflict of interest.

Purposes: Rapid and accurate identification of non-tuberculous mycobacteria (NTM) is crucial yet challenging, promoting the development of novel molecular techniques such as amplification-based targeted high-throughput sequencing and metagenomic unbiased high-throughput sequencing. We aimed to evaluate the diagnostic value of these molecular techniques for NTM infection., Methods: A total of 115 clinical specimens from patients with confirmed NTM infection were subjected to multiplex polymerase chain reaction detection techniques (multi-PCR), metagenomic Next-Generation Sequencing (mNGS), targeted Next-Generation Sequencing (tNGS), and targeted Nanopore sequencing (tNanopore). Positivity rates and species identification were compared among these techniques., Results: The sensitivity of mNGS, tNGS, and multi-PCR in NTM-infection diagnosis was 44.3%, 42.6%, and 36.5%, respectively, while the sensitivity of the three methods in combination increased to 54.8%. The pathogen identification results of mNGS, tNGS and multi-PCR were matched in 80.6% (25/31) samples at the species level, among which 14 samples (45.2%) was completely matched at the subspecies level. The results of tNanopore, tNGS and mNGS at the species level were completely matched in 73.3% (22/30) samples., Conclusions: These molecular assays demonstrated comparable performance in precisely identifying NTM species in clinical specimens, showing their promising potential as efficient and alternative tools for the rapid diagnosis of NTM disease., Competing Interests: Declarations Ethical approval This study was approved by the ethics committees of Zhongshan Hospital Fudan University, under the tracking numbers of B2020-411R. All patients provided written informed consent. Consent to publish Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

This study presents an analytical approach coupling novel ambient ionization sources with trapped ion mobility spectrometry (TIMS) and tandem mass spectrometry (MS/MS) for the rapid characterization of fentanyl analogs. Two ambient ionization sources were illustrated for minimal sample preparation and rapid analysis: electrospray ionization (nESI) and direct analysis in real time (DART). Fentanyl analogs can be separated using nESI-TIMS-MS/MS based on differences in their mobility and/or fragmentation pattern; reference mobility spectra are reported for 234 single standards. In contrast, DART-TIMS-MS/MS allowed for the characterization of 201 compounds due to differences in the protonation pattern and efficiency when compared to nESI. The TIMS high resolving power (R > 80) allowed baseline separation for most isomers and mobility trends were established for methylated and fluorinated isomers, with the more compact ortho-substituted analogs showing distinct separation from para- and meta-substituted species. This multi-dimensional strategy offers a comprehensive characterization of fentanyl analogs and other synthetic opioids with minimal sample preparation. This analysis shows significant potential for high-throughput screening (<5 min) and high sensitivity detection (

Background: Microsporidia is an obligate intracellular eukaryote, which is capable of parasitizing vertebrates and invertebrates. Nosema ceranae, which can infect both Apis mellifera and Apis cerana, poses a serious threat and causes heavy losses to the worldwide apiculture. During infection, polar tube, a highly specialized invasion structure, ejected from the spore to deliver the sporoplasm into host cells to cause infection. Although seven different polar tube proteins (PTP1 ~ 7) have been reported from various microsporidia and showed key functions associated with spore invasion and proliferation, no systematic analysis on identification and characterization of polar tube proteins from N. ceranae was found., Methods and Results: The polar tube proteins 2 (NcPTP2) was identified from the total polar tube proteins of N. ceranae by LC&#95;MS/MS and the transcriptional profile was performed by RT-PCR. Sequence characterization analysis revealed that NcPTP2 was rich in lysine and had a signal peptide at the N-terminal. It had 3 potential O-glycosylation sites and 6 potential N-glycosylation sites. 25 phosphorylation sites were found on serine, tyrosine and threonine sites. Sequence alignment analysis revealed that NcPTP2 was homologous and had conserved cysteine residues with PTP2 proteins from other microsporidia. Indirect immunofuorescence analysis (IFA) and Immunoelectron Microscopy analysis (IEM) confirmed that NcPTP2 was localized on the polar tube of the germinated spores. The interaction between NcPTP2 and spore wall protein in N. ceranae indicated its potential function in anchoring and coiling of polar tube in spore., Conclusion: NcPTP2 was the first subcellular localized polar tube protein in N. ceranae and this work could provide an important basis for further analyzing the biological functions of polar tube proteins and uncovering the infection mechanism of N. ceranae to the host cells., Competing Interests: Declarations Conflict of interest No conflicts of interest, financial or otherwise, are declared by the authors. Ethical approval It is not applicable., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Background: Uricase is a bio-drug used to reduce urate accumulation in gout disease. Thus, there is a continuous demand for screening soil samples derived from a variety of different sources in order to isolate a strain that possesses a high potential for producing uricase., Methods: Streptomyces sp. strain NEAE-5 demonstrated a significant capacity for uricase production was identified based on the physiological, morphological and biochemical characteristics, as well as 16S rDNA sequencing analysis. Using a Plackett-Burman statistical design, the impact of eighteen process factors on uricase production by Streptomyces griseorubens strain NEAE-5 was investigated. Using central composite design, the most important variables that had a favourable positive impact on uricase production by Streptomyces griseorubens strain NEAE-5 were further optimized., Results: It is clear that the morphological and chemotaxonomic features of Streptomyces sp. strain NEAE-5 are typical for the Streptomyces genus. Phylogenetic analysis indicated that Streptomyces sp. strain NEAE-5 belongs to the genus Streptomyces and closely related to Streptomyces griseorubens which it has a 95-96% identity in 16S rDNA gene sequencing. Accordingly, the strain is proposed to be identified as Streptomyces griseorubens strain NEAE-5. The three factors that had the significant positive impacts on uricase production were uric acid, hypoxanthine, and yeast extract. As a result, the best conditions for achieving the highest experimental uricase production by Streptomyces griseorubens strain NEAE-5 after central composite design were (g/L): uric acid 6.96, glycerol 5, hypoxanthine 5.51, MgSO 4 .7H 2 O 0.1, KNO 3 2, CaCl 2 0.5, K 2 HPO 4 0.5, NaCl 0.5, yeast extract 1.08. In addition, the period of incubation is seven days, pH 7.5 and 37 °C with an inoculum size of 2 mL (10 5  cfu/mL) /100 mL medium., Conclusions: After optimization, the obtained uricase activity was 120.35 U/mL, indicating that the Streptomyces griseorubens strain NEAE-5 is a potent uricase producer and that the statistical approach used for optimization was appropriate., Competing Interests: Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Background: Sexual dimorphism plays a vital role in individual identification, and body dimensions can contribute to establishing a biological profile for identification purposes. Aims and Objectives: To determine the reliability of the Heel-Ball Index (HBI) in estimating sex from foot dimensions and footprint dimensions and also to investigate the potential of dimensions and indices, using a standardized value, in estimating sex, from foot dimensions and footprint dimensions. Materials and Methods: In this study, a group of 112 young Indian adults aged 18 to 22, consisting of 56 males and 56 females, was examined. The foot breadth at ball (BBAL) and foot breadth at heel (BHEL) of both feet were measured using sliding digital calipers from foot and footprint dimensions. Results: Significant sexual dimorphism was observed in BBAL, BHEL, and HBI (HBI = BHEL/BBAL × 100) measurements in both feet of both sexes. Conclusion: HBI yielded better accuracy for foot dimensions than footprint dimensions. It was also found that utilizing absolute foot dimensions (BBAL and BHEL) yielded more accurate results in estimating sex compared to the HBI, which is calculated as a ratio of absolute measurements., Competing Interests: The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2024.)

Precise identification of species is fundamental in microbial genomics and is crucial for understanding the microbial communities. While the 16S rRNA gene, particularly its V3-V4 regions, has been extensively employed for microbial identification, however has limitations in achieving species-level resolution. Advancements in long-read sequencing technologies have highlighted the rRNA operon as a more accurate marker for microbial classification and analysis than the 16S rRNA gene. This study aims to compare the accuracy of species classification and microbial community analysis using the rRNA operon versus the 16S rRNA gene. We evaluated the species classification accuracy of the rRNA operon,16S rRNA gene, and 16S rRNA V3-V4 regions using a BLAST-based method and a k-mer matching-based method with public data available from NCBI. We further performed simulations to model microbial community analysis. We accessed the performance using each marker in community composition estimation and differential abundance analysis. Our findings demonstrate that the rRNA operon offers an advantage over the 16S rRNA gene and its V3-V4 regions for species-level classification within the genus. When applied to microbial community analysis, the rRNA operon enables a more accurate determination of composition. Using the rRNA operon yielded more reliable results in differential abundance analysis as well., Importance: We quantitatively demonstrated that the rRNA operon outperformed the 16S rRNA and its V3-V4 regions in accuracy for both individual species identification and species-level microbial community analysis. Our findings can provide guidelines for selecting appropriate markers in the field of microbial research., Competing Interests: The authors declare no conflict of interest.

The TCP gene family encodes plant transcription factors crucial for regulating growth and development. While TCP genes have been identified in various species, they have not been studied in Phoebe bournei (Hemsl.). This study identified 29 TCP genes in the P. bournei genome, categorizing them into Class I (PCF) and Class II (CYC/TB1 and CIN). We conducted analyses on the PbTCP gene at both the protein level (physicochemical properties) and the gene sequence level (subcellular localization, chromosomal distribution, phylogenetic relationships, conserved motifs, and gene structure). Most P. bournei TCP genes are localized in the nucleus, except PbTCP9 in the mitochondria and PbTCP8 in both the chloroplast and nucleus. Chromosomal mapping showed 29 TCP genes unevenly distributed across 10 chromosomes, except chromosome 8 and 9. We also analyzed the promoter cis-regulatory elements, which are mainly involved in plant growth and development and hormone responses. Notably, most PbTCP transcription factors respond highly to light. Further analysis revealed three subfamily genes expressed in five P. bournei tissues: leaves, root bark, root xylem, stem xylem, and stem bark, with predominant PCF genes. Using qRT-PCR, we examined six representative genes- PbTCP16 , PbTCP23 , PbTCP7 , PbTCP29 , PbTCP14 , and PbTCP15 -under stress conditions such as high temperature, drought, light exposure, and dark. PbTCP14 and PbTCP15 showed significantly higher expression under heat, drought, light and dark stress. We hypothesize that TCP transcription factors play a key role in growth under varying light conditions, possibly mediated by auxin hormones. This work provides insights into the TCP gene family's functional characteristics and stress resistance regulation in P. bournei .

Background: Young carers are children or adolescents who provide significant care to another family member who has an illness or disability. This situation impacts their physical and mental health, and their social and school life. Nonetheless, this vulnerable population is often covert, which makes YCs' identification a major challenge. One of the methods in the literature to identify them consists of obtaining the adolescent's report of a relative's illness or disability, coupled with the standardized psychometric evaluation of their level of care. To date, no research had compared adolescents' and parents' perspectives using this method, while this would enable to gain insights on YCs' identification. The objective of this study was to compare parents' and adolescents' reports on the identification of an ill or disabled relative within the household, and adolescents' levels of caring activities., Methods: Survey data were collected from 776 adolescents (mean age = 12.76 years; 55.50% of females) and one of their parents (mean age = 44.31 years; 83.76% of females). They completed questionnaires evaluating their sociodemographic characteristics, illnesses or disabilities within their household, and adolescents' levels of caring activities (MACA-YC 18). Cohen's κ for interrater agreement, Student's t-tests and chi-square tests of independence were performed for child-parent responses comparisons., Results: Fewer adolescents reported that there was an ill or disabled relative within the household compared with their parents. Only 27.56% of the dyads agreed both on the person who was ill or disabled and the illness or disability. The dyads were more often in agreement when the ill or disabled relative had a serious somatic illness and was the mother. On the other hand, adolescents reported engaging in higher levels of caregiving activities than indicated by their parents' assessments., Conclusion: This study highlights the difference of perception between parents and adolescents both on illness and disability reports, and on adolescents' levels of caring activities. These two points of view seem complementary, suggesting that combining adolescents' and parents' perspectives can aid in better identifying young carers., (© 2024 The Author(s). Child: Care, Health and Development published by John Wiley & Sons Ltd.)

Accurate bacterial identification is essential for determining the causative agent of an infection, thus facilitating appropriate treatment and management strategies in both human and animal health contexts. Some species in the Vibrio genus are recognized pathogens, associated with a variety of infections. However, identification of these bacteria is oftentimes controversial. Therefore, we aimed to evaluate different identification approaches in terms of their reliability in distinguishing Vibrio species. To achieve this, we selected a set of 40 Vibrio isolates previously recovered from water and floating plastic samples in a large bay environment and identified them employing MALDI-TOF mass spectrometry, and rrs and pyrH gene sequencing. A subset of isolates was also submitted to whole genome sequencing. Overall, MALDI-TOF was found to be a fast-screening methodology for identification, notably at genus-level. However, for better species discrimination, pyrH gene sequencing stood out as a more reliable tool in contrast to rrs gene sequencing and MALDI-TOF, as corroborated by whole genome sequencing analysis., (© 2024. The Author(s).)

Migrant deaths have persistently intensified in the last 30 years, followed by inconsistent engagement of official policies to tackle the lack of identifications. Forensic anthropologists have been increasingly involved in the recovery, analysis and identification of human remains associated with migrants, and are therefore the most well-versed practitioners in raising awareness of policy makers about this plight. This review describes the current state-of-the-art of the forensic anthropological practice and research on unidentified migrants. The focus of the review is twofold: one section explores the current legal, logistical, and administrative issues related to management and identification activities, primarily in Europe and North America. The second section addresses the scientific contributions and new challenges that forensic anthropologists face when analyzing skeletal remains from underrepresented and unreferenced population groups. According to this literature review, forensic anthropologists are the professionals most actively involved in addressing the issue of unidentified migrants. Despite significant efforts, several challenges still hinder identifications in this context, including the inability to create comprehensive databases for collecting postmortem and antemortem data. Recently, scientific research in forensic anthropology has begun to address the limitations in developing reliable biological profiles for deceased migrants, as these groups are often inadequately represented in existing skeletal reference populations. Finally, this review highlights the global efforts of the scientific community to integrate these victims into a well-established identification system, aiming to foster public responsibility and promote the adoption of unified and innovative strategies to comprehensively address and resolve this social, scientific, and humanitarian crisis., Competing Interests: Declaration of Competing Interest The authors declare that they have no competing interest., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

The intensive labour and time required for conventional methods to identify bacterial fish pathogens have revealed the need to develop alternative methods. Raman spectroscopy has been used in the rapid optical identification of bacterial pathogens in recent years as an alternative method in microbiology. Strains of bacterial fish pathogens (Vibrio anguillarum, Lactococcus garvieae and Yersinia ruckeri) that often cause infectious diseases in fish were here identified and analyzed in terms of their biochemical structures in different media and at different incubation times, and the data were specified by using Raman spectroscopy. The results demonstrated that Raman spectroscopy presents species-specific Raman spectra of each disease-causing bacteria and that it would be more appropriate to choose general microbiological media over selective media for routine studies. Additionally, it was found that species-specific band regions did not differ in 24- and 48-hour cultures, but there could be a difference in peak intensity which may lead to difficult characterization of spectrum. The current study, conducted for the first time with bacterial fish pathogens under different incubation conditions, is believed to provide a basis for the routine use of Raman spectroscopy for quick pathogen identification and the precise determination of the methodology for further research.

Metagenomics has been greatly accelerated by the development of next-generation sequencing (NGS) technologies, which allow scientists to discover and describe novel microorganisms without the need for conventional culture techniques. Examining integrative bioinformatics methods used in viral interaction research, this study highlights metagenomic data from various contexts. Accurate viral identification depends on high-purity genetic material extraction, appropriate NGS platform selection, and sophisticated bioinformatics tools like VirPipe and VirFinder. The efficiency and precision of metagenomic analysis are further improved with the advent of AI-based techniques. The diversity and dynamics of viral communities are demonstrated by case studies from a variety of environments, emphasizing the seasonal and geographical variations that influence viral populations. In addition to speeding up the discovery of new viruses, metagenomics offers thorough understanding of virus-host interactions and their ecological effects. This review provides a promising framework for comprehending the complexity of viral communities and their interactions with hosts, highlighting the transformational potential of metagenomics and bioinformatics in viral research., Competing Interests: Declaration of competing interest The authors declare that there is not any competing of interest., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Background: Ticks are ecto-parasites of domestic animals, rodents, and wildlife living for periods at a time on one or more vertebrate hosts. They are important vectors of viral, bacterial, or parasitic diseases in livestock and humans. Crimean-Congo haemorrhagic fever virus and the spotted fever rickettsiae are some of the tick-borne diseases of public health importance reported in Kenya. Their distribution and public health risks among communities, especially pastoralists, remain poorly characterized due to limited surveillance, affected partly by inadequate capacity for tick identification arising from a limited number of skilled taxonomists. Materials and Methods: The aim of this survey was to identify tick species currently circulating in different livestock hosts in northern Kenya. Ticks were sampled from cattle, sheep, goats, and camels in Turkana, Isiolo, Baringo, and West Pokot counties, and differential identification was carried out using morphological identification keys followed by molecular characterization based on the cytochrome c oxidase I gene (cox1). Haplotypes were determined using the DnaSP v6 software and phylogenetic relationships inferred using the maximum likelihood algorithm. Results: A total of 12,206 ticks were collected, from Turkana (45.4%), Isiolo (23.1%), Baringo (22.7%), and West Pokot (8.8%) counties in Kenya. Ten species were confirmed by molecular analysis; H. rufipes, H. impeltatum, H. dromedarii, R. pravus, R. camicasi, R. pulchellus, R. evertsi evertsi, A. variegatum, A. gemma, and A. lepidum. There was no disparity in the morphological and molecular identification of Amblyomma species. However, molecular analysis provided insight into the complexity of morphological identification especially among Hyalomma and Rhipicephalus species. High haplotype diversities (0.857-1.000) and low nucleotide diversities (0.00719-0.06319) were observed in all the tick samples tested. Conclusion: The findings highlight the diversity of tick species in dry pastoral ecologies in Kenya and the importance of confirming morphological identification by molecular analysis thus contributing to accurate mapping of tick-borne disease distribution and risk.

The continuous evolution of deep learning has garnered significant attention in spectroscopy. This study focuses on identifying wheat flour, presenting a more efficient and accurate method by combining two-dimensional correlation spectroscopy (2D-COS) and deep learning techniques. A data set of 316 near-infrared (NIR) spectral samples of four types of wheat flour was collected. By applying three disparate 2D-COS techniques, i.e., synchronous, asynchronous, and integrated, we crafted 948 2D-COS images. These images, obtained by transforming the original one-dimensional spectra into 2D representations, offer richer information for deep learning analysis. The study introduced an 18-layer residual network incorporating a convolutional attention mechanism, specifically tailored for the 2D-COS analysis of wheat flour, aimed at enhancing the model's discriminative capabilities by refining the residual neural network's structure. Achieving an unprecedented recognition accuracy of 100% through methodical optimization and rigorous training on the synchronous 2D-COS data set of wheat flour, the proposed model is a testament to the efficacy of deep learning in spectroscopic analysis. To further exhibit the confluence of 2D-COS with deep learning, t-distributed stochastic neighbor embedding was employed to visualize the distinctive 2D-COS features within the deep learning architecture. Additionally, the model's performance was juxtaposed with prevailing NIR spectral recognition methods, including random forest, gradient boosting decision tree, and artificial neural network. This comparison cemented the proposed approach's superiority in wheat flour categorization. The findings of this study not only introduce a novel and efficient solution for wheat flour quality analysis but also underscore the significant potential of deep learning techniques in spectroscopy applications., Competing Interests: Declaration of Conflicting InterestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Waste from the olive industry is a noticeable source of antioxidant compounds that can be extracted and reused to produce raw materials related to the chemical, cosmetic, food and pharmaceutical sectors. This work studies the phenolic composition of olive leaf samples using liquid chromatography with ultraviolet detection coupled to mass spectrometry (LC-UV-MS). Olive leaf waste samples have been crushed, homogenized, and subjected to a solid-liquid extraction treatment with mechanical shaking at 80 °C for 2 h using Natural Deep Eutectic Solvents (NaDES). The phenolic compound identification in the resulting extracts has been carried out by high-resolution mass spectrometry (HRMS) using data-dependent acquisition mode using an Orbitrap HRMS instrument. >60 different phenolic compounds have been annotated tentatively, of which about 20 have been confirmed from the corresponding standards. Some of the most noticeable compounds are oleuropein and its aglycone and glucoside form, luteolin-7-O-glucoside, 3-hydroxytyrosol, and verbascoside., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influencethe work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

Background: Tobacco use has been the leading cause of disease and death in South Korea. Early detection of tobacco use and evidence-based interventions play pivotal roles in facilitating tobacco cessation., Methods: In accordance with the earlier iterations of the Lifetime Health Maintenance Program (2009) and recent recommendations from the United States Preventive Services Task Force (USPSTF; 2021), two themes were chosen for investigation: the identification of and intervention for tobacco use. The USPSTF recommendations were formulated by conducting an overview of reviews. In this study, literature searches and quality assessments of reviews were conducted., Results: The findings highlighted the efficacy of physician-led identification and advising in promoting tobacco cessation, with robust evidence supporting the implementation of behavioral and pharmacological interventions. These interventions significantly increased the likelihood of successful cessation compared with usual care. Digital interventions, such as internet- or mobile-based interventions, showed additive effects for quitting., Conclusion: Identification and targeted interventions are essential for tobacco cessation. By leveraging evidencebased strategies and enhancing access to resources, healthcare providers can empower individuals to achieve successful tobacco cessation and improve overall health outcomes.

The uncontrolled release of aqueous film-forming foam (AFFF) ingredients during a major fire incident in Reilingen, Germany, in 2008 led to significant soil and groundwater contamination. As the identity of fluorochemical surfactants in AFFF are often veiled due to company secrets, it is important to characterize AFFF contaminations and their impact on the environment comprehensively. In this study, we adapted a systematic approach combining a suitable extraction method with liquid chromatography high-resolution quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) for an extensive non-targeted analysis. Our analysis identified 124 per- and polyfluoroalkyl substances (PFAS) from 42 subclasses in the contaminated soil (confidence levels of identification between 1 and 3). Typical for AFFF-impacted field sites, these included anionic, cationic, and zwitterionic substances with perfluoroalkyl chains spanning from 3 to 14 carbon atoms. Furthermore, we identified 1 previously unreported substance, and detected 9 PFAS subclasses for the first time in soil. AFFFs have long been employed to extinguish large hydrocarbon fires, yet their environmental consequences remain a concern. This study sheds light on the complex composition of AFFFs at this particularly contaminated area, emphasizing the necessity for extensive contaminant characterization as sound basis for informed management strategies to mitigate their adverse effects. AFFF PFAS are often named differently in the literature, leading to inconsistency in terminology. To address this issue, we introduced partially new terminology for AFFF-related PFAS to establish consistent terminology, to facilitate communication of identified compounds, and to ensure that the chemical structure can be directly derived from acronyms., (© 2024. The Author(s).)

Purpose: To develop and validate a radiomic model for differentiating pulmonary invasive adenocarcinomas from benign lesions based on follow-up longitudinal CT images., Methods: This is a retrospective study including 336 patients (161 with invasive adenocarcinomas and 175 with benign lesions) who underwent baseline (T0) and follow-up (T1) CT scans from January 2016 to June 2022. The patients were randomized in a 7:3 ratio into training and test sets. Radiomic features were extracted from lesion volumes of interest on longitudinal CT images at T0 and T1. Differences in radiomic features between T1 and T0 were defined as delta-radiomic features. Logistic regression was used to build models based on clinicoradiological (CR), T0, T1, and delta radiomic features and compute signatures. Finally, a nomogram based on the CR, T0, T1 and delta signatures was constructed. Model performance was evaluated for calibration, discrimination, and clinical utility., Results: The T1 radiomic model was superior to the other independent models. In the training set, it had an area under the curve (AUC) of 0.858), superior to the CR model (AUC 0.694), the T0 radiomic model (AUC 0.825), and the delta radiomic model (AUC 0.734). In the test set, it had an AUC of 0.817, again outperforming the CR model (AUC 0.578), the T0 radiomic model (AUC 0.789), and the delta radiomic model (AUC 0.647). The nomogram incorporating the CR, T0, T1 and delta signatures showed the best predictive performance in both the training (AUC: 0.906) and test sets (AUC: 0.856), and it exhibited excellent fit with calibration curves. Decision curve analysis provided additional validation of the clinical utility of the nomogram., Conclusion: A nomogram utilizing radiomic features extracted from longitudinal CT images can enhance the discriminative capability between pulmonary invasive adenocarcinomas and benign lesions., (© 2024. The Author(s).)

As a naturally widely-occurring dietary, cosmetic, and therapeutic flavonoid, kaempferol has gained much consideration for its nutritional and pharmaceutical properties in recent years. Although there have been performed a high number of studies associated with different aspects of kaempferol's analytical investigations, the lack of a comprehensive summary of the various methods and other plant sources that have been reported for this compound is being felt, especially for many biological applications. This study, aimed to provide a detailed compilation consisting of sources (plant species) and analytical information that was precisely related to the natural flavonoid (kaempferol). There is a trend in analytical research that supports the application of modern eco-friendly instruments and methods. In conclusion, ultrasound-assisted extraction (UAE) is the most general advanced method used widely today for the extraction of kaempferol. During recent years, there is an increasing tendency towards the identification of kaempferol by different methods., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Characterizing seeds of tropical weeds is crucial for future research to understand their ability to disperse in space and time through their seeds, and building up seed banks. Seeds of 55 weed species occurring on Reunion Island were collected and characterized. Seeds were described by their shape, size, color, texture, hairiness, or particular markings. Seed traits were recorded in a database in French and English. It has been published on the CIRAD AMATROP dataverse, which centralizes datasets on tropical weeds. It will be updated as new weed seeds from tropical regions are characterized. In a long-term perspective, these data allow for creating a multicriteria identification key to identify seeds to study seed stocks in agricultural fields., (© 2024 The Author(s).)

Cyanobacterial pigments have attracted considerable attention in industry due to their bioactive potential and natural origin. In the present study, the growth dynamics and pigment composition, in terms of chlorophyll a , total carotenoids and phycobiliprotein content, of four cyanobacterial strains isolated from thermal springs, namely Oscillatoria subbrevis CZS 2201, Phormidium ambiguum CZS 2205, Nostoc calcicola TSZ 2203, and Synechococcus sp. CZS 2204, were investigated. The analysis revealed that the maximum quantity of chlorophyll a and total carotenoids was observed in Oscillatoria subbrevis CZS 2201 (26.49 and 3.44 µg mL -1 ), followed by Phormidium ambiguum CZS 2205 (18.64 and 2.32 µg mL -1 ), whereas a minimum amount was detected in Synechococcus sp. CZS 2204 (12.13 and 1.24 µg mL -1 ), respectively. In addition, Oscillatoria subbrevis CZS 2201 showed higher quantity of phycobiliproteins, especially C-phycocyanin (45.81 mg g -1 ), C-phycoerythrin (64.17 mg g -1 ) and C-allophycocyanin (27.45 mg g -1 ). Moreover, carotenoid derivatives of Oscillatoria subbrevis CZS 2201 were also identified, among which β-carotene was the dominant form (1.94 µg mL -1 ), while the accumulation of zeaxanthin and myxoxanthophyll was relatively high (0.53 and 0.41 µg mL -1 , respectively) compared with echinenone and cryptoxanthin (0.34 and 0.23 µg mL -1 , respectively). The study revealed that Oscillatoria subbrevis CZS 2201 was a potent producer of secondary carotenoids, including myxoxanthophyll.

This multi-year study (2014-2019) compared identification of rare and unusual Gram-negative organisms (GNOs) by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (VITEK MS, bioMérieux, Laval Que.) to 16S rRNA gene sequencing (16S) according to our laboratories routine workflow; 16S is done if initial MALDI-TOF MS gave discordant, wrong, or no results. GNB isolates were first analyzed by standard phenotypic methods and MALDI-TOF MS using direct deposit-full formic acid extraction; proteomics was repeated if no result occurred. Medically approved 16S analyses were done using fast protocols. Isolate sequences were analyzed using the Integrated Database Network System (IDNS3) bacterial database (SmartGene, Lausanne, Switzerland). Three hundred thirty-one GNOs including 251 (76%) aerobic Gram-negative bacilli (GNB), 63 (19%) fastidious Gram-negative coccobacilli (fGNCBs), and 17 (5%) Campylobacterales (CAMPB) isolates were recovered from 304 specimens; >1 isolate was recovered from 19 (6%). GNOs were mainly recovered from blood cultures (31.6%) and lower respiratory specimens (43%) (one-half were isolated from cystic fibrosis patients). Accurate genus vs species identities were obtained for 67.7% and 32.5% aerobic GNBs, 73% and 60% fGNCBs, and 23.5% CAMPB (with no discrepant species), respectively. Wrong or no results were obtained for 81 (32.3%) aerobic GNBs, 17 (27%) fGNCBs, and 13 (72.2%) CAMPB. No results or misidentifications occurred for 33% of aerobic GNBs, 26% of fGNCBs, and 76.5% of CAMPB due to absence of species in the instrument's database. VITEK MS performance remained stable for aerobic GNBs and fGNCBs but improved for CAMPB with addition of Campylobacter rectus and Campylobacter curvus to the database. 16S remains important for identification of GNOs when proteomics fails.IMPORTANCEMatrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has transformed the identification of commonly encountered Gram-negative organisms (GNOs) in the clinical laboratory, but rare and unusual organisms continue to challenge the technology. This study verified performance of VITEK MS for identification of a broad range of rare and unusual clinical GNO isolates by our large reference laboratory workflow over a multi-year period. Although most GNOs were accurately identified by MALDI-TOF MS, a small number of clinical isolates (~1%-6%) required 16S sequencing for identification depending on the GNO category. Approximately one-third of aerobic Gram-negative bacilli (GNBs) and two-thirds of Campylobacterales could not be accurately identified by proteomics due to lack of an organism in the instrument's database. MALDI-TOF MS databases should be continuously updated and validated, and laboratories should have a workflow for identification of unusual or rarely encountered aerobic, fastidious, and Campylobacterales GNOs that includes 16S rRNA gene sequencing whenever proteomics cannot give a definitive identification.

Klebsiella pneumoniae species complex (KpSC) members, including the most important species K. pneumoniae (phylogroup Kp1 of the KpSC), are important opportunistic pathogens that display increasing rates of antimicrobial resistance worldwide. As they are widespread in food and the environment, there is a need for fast, sensitive, and reliable methods to detect KpSC members in complex matrices. Previously, the ZKIR real-time PCR assay was developed to detect all KpSC members without distinction. Given that Kp1 is the clinically most significant phylogroup of the KpSC, here, we aimed to simultaneously identify Kp1 while detecting all KpSC members. Three TaqMan probes were developed and used: the Kp1 probe to specifically identify this phylogroup; the zkir P1 probe to detect phylogroups Kp1-Kp5 and Kp7; and the zkir P2 probe to detect phylogroup Kp6. The new triplex assay was tested on a total of 95 KpSC and 19 non-KpSC strains from various sources, representing the different phylogroups as defined by whole genome sequencing. The results showed almost complete specificity, as the expected PCR results were obtained for 112 (98%) strains. The new triplex real-time PCR assay, called ZKIR-T, enables the detection of all KpSC taxa while discriminating Kp1, which will be useful for rapid screening and to focus downstream analyses on chosen phylogroups of the KpSC., Importance: The pathogens of the Klebsiella pneumoniae species complex are widespread in food and animals and are among the main pathogens responsible for multidrug resistant infections in humans. In this study, we developed a highly sensitive detection assay that enables detection of this group of bacteria, with the simultaneous identification of the most common and clinically important species. This triplex one-reaction assay was shown to be highly sensitive and precise, enabling fast screening of varied samples for the presence of KpSC and K. pneumoniae sensu stricto.

Advanced oxidation processes (AOPs) are rapidly evolving but still lack well-established protocols for reliably identifying oxidative reactive species (ORSs). This Perspective presents both the radical and nonradical ORSs that have been identified or proposed, along with the extensive controversies surrounding oxidative mechanisms. Conventional identification tools, such as quenchers, probes, and spin trappers, might be inadequate for the analytical demands of systems in which multiple ORSs coexist, often yielding misleading results. Therefore, the challenges of identifying these complex, short-lived, and transient ORSs must be fully acknowledged. Refining analytical methods for ORSs is necessary, supported by rigorous experiments and innovative paradigms, particularly through kinetic analysis based on in situ spectroscopic techniques and multiple-probe strategies. To demystify these complex ORSs, future efforts should be made to develop advanced tools and strategies to enhance the mechanism understanding. In addition, integrating real-world conditions into experimental designs will establish a reliable framework in fundamental studies, providing more accurate insights and effectively guiding the design of AOPs.

Antioxidant cyclic peptides were successfully identified from a corn protein hydrolysate. Hydrolysate by Alcalase + Flavourzyme showed the highest cyclic peptide purity (48.36 ± 1.81 %) and higher antioxidant activities compared with other hydrolysate. The success of peptide cyclization in hydrolysate was demonstrated by thermogravimetric analysis and thin-layer chromatography (TLC) analysis. Thermogravimetric analysis showed that the thermal stability of hydrolysate after cyclization was significantly increased, which was related to the formation of cyclic peptides. Peptides with molecular weight less than 1000 Da accounted for more than 80 % in hydrolysate after cyclization. After separation using gel silica chromatography and semi-preparative reverse phase high performance liquid chromatography (RP-HPLC), 22 novel antioxidant cyclic peptides were identified by ultra performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC-Q-TOF-MS) and orbitrap-tandem mass spectrometry (Orbitrap-MS/MS). Synthetic cyclic peptides with the same sequence were synthesized and characterized for their antioxidant activity. Molecular docking suggested that the free radical molecules could bind with the cyclic backbone and side chain of cyclic peptides through hydrogen bonding, hydrophobic interaction as well as electrostatic interaction. This study has important implications for the high-value utilization of corn protein and new cyclic peptides drugs or functional food development., Competing Interests: Declaration of competing interest The authors declare that they have no personal relationships or known competing financial interests that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

A new species of the genus Boulenophrys is described from the coastal hills of eastern Fujian Province, China. The new taxon can be distinguished from all recognized congeners by a combination of discrete morphological character state differences and genetic divergences in the combined mitochondrial 16S + CO1 genes. We also provide a map showing the distribution pattern of Boulenophrys species in Fujian and a provincial-specific key, which will aid their conservation by helping the local authorities accurately identify species during field identifications and data collection efforts., Competing Interests: The authors have declared that no competing interests exist., (Shi-Shi Lin, Hong-Hui Chen, Yuan-Hang Li, Zhao-Ning Peng, Zhao-Chi Zeng, Jian Wang.)

The Mangshan pit viper, Protobothrops mangshanensis , is a rare, highly endangered snake native to the mountainous regions of Hunan Province in China. Snakes possess abdominal scent glands, which have been chemically studied in several species. These glands can contain various lipids and peptides, but very often also complex mixtures of carboxylic acids. We report here the occurrence of novel methyl-branched unsaturated acids found in the secretions of six captive individuals living in a zoo. The structures of these compounds, 4.6-dimethylalk-5-enoates in a homologous series from C 11 -C 16 , were characterized by GC-MS and GC-IR analysis and various microderivatization reactions including hydrogenation and esterification leading to methyl and pyridylmethyl esters. In addition, dimethyloxazoline formation helped to localize the double bond. The synthesis of methyl 4,6-dimethyldodec-5-enoate allowed the correct assignment of structures and showed the ( E )-configuration of the double bond for the major naturally occurring diastereomers. These acids occur in small amounts compared to the major glandular components, cholesterol, and 1- O -hexadecylglycerol, as well as other common long-chain alcohols and amides. Although a general defensive function has been proposed for snake abdominal scent glands, the specific chemistry and moderate amounts of acids reported here may suggest a function in chemical signaling for the Mangshan pit viper. In addition, proline-containing diketopiperazines were identified for the first time in snake scent glands, although an artificial formation from amino acids likely present in the secretion cannot be excluded., (Copyright © 2024, Holste et al.)

In the food industry, sulfides are commonly used as preservatives and flavor regulators. However, long-term excessive intake of sulfides can lead to serious health problems. Therefore, developing efficient sulfide detection methods is particularly important. Here, we have effectively synthesized a novel bifunctional copper hydroxide nitrate (Cu 2 (OH) 3 NO 3 ) nanozyme with outstanding peroxidase-like and laccase-like behaviors in basic deep eutectic solvents (DES). Because the various types of sulfides have diverse regulatory effects on the two catalytic behaviors of Cu 2 (OH) 3 NO 3 , a two channel nanozyme sensor array based on the peroxidase-like and laccase-like behaviors of Cu 2 (OH) 3 NO 3 was constructed and successfully used for the identification of six kinds of sulfides (Na 2 S, Na 2 S 2 O 3 , Na 2 SO 3 , Na 2 SO 4 , NaHSO 3 , and Na 2 S 2 O 8 ). Remarkably, the sensor array has achieved successful discrimination among six sulfides present in wine, egg, and milk samples. Finally, the sensor array has successfully distinguished and differentiated three actual samples (wine, egg, and milk). This study is of great significance in promoting the efficient construction of array units and improving the effective identification of sulfides in complex food samples., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The current trend is the promotion of antioxidants that are beneficial for both health and the environment. Candida utilis have garnered considerable attention due to their commendable attributes such as non-toxicity and the ability to thrive in waste. Therefore, Candida utilis was used as raw material to isolate and identify new antioxidant peptides by employing methods such as ultrafiltration, DEAE Sepharose Fast Flow, and liquid chromatography-tandem mass spectrometry. The antioxidant mechanism of peptides was investigated by molecular docking. The properties of antioxidant peptides were evaluated using a variety of computational tools. This study resulted in the identification of two novel antioxidant peptides. According to the molecular docking results, the antioxidant mechanism of Candida utilis peptides operates by obstructing the entry to the myeloperoxidase activity cavity. The (-) CDOCKER energy of antioxidant peptides was 6.2 and 6.1 kcal/mol, respectively. Additionally, computer predictions indicated that antioxidant peptides exhibited non-toxicity and poor solubility., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Growing evidence supports the transcription of enhancer RNAs (eRNAs) and their important roles in gene regulation. However, their interactions with other biomolecules and their corresponding functionality remain poorly understood. In an attempt to facilitate mechanistic research, this study presents eRNA-IDO, the first integrative computational platform for the identification, interactome discovery, and functional annotation of human eRNAs. eRNA-IDO comprises two modules: eRNA-ID and eRNA-Anno. Functionally, eRNA-ID can identify eRNAs from de novo assembled transcriptomes. eRNA-ID includes eight kinds of enhancer makers, enabling users to customize enhancer regions flexibly and conveniently. In addition, eRNA-Anno provides cell-/tissue-specific functional annotation for both new and known eRNAs by analyzing the eRNA interactome from prebuilt or user-defined networks between eRNAs and protein-coding genes. The prebuilt networks include the Genotype-Tissue Expression (GTEx)-based co-expression networks in normal tissues, The Cancer Genome Atlas (TCGA)-based co-expression networks in cancer tissues, and omics-based eRNA-centric regulatory networks. eRNA-IDO can facilitate research on the biogenesis and functions of eRNAs. The eRNA-IDO server is freely available at http://bioinfo.szbl.ac.cn/eRNA&#95;IDO/., (© The Author(s) 2024. Published by Oxford University Press and Science Press on behalf of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.)

Plastics and, in particular, microplastics (MPs) (< 5 mm) are emerging environmental pollutants responsible for interconnected risks to environmental, human, and animal health. The livestock sector is highly affected by these contaminants, with 50-60 % of the foreign bodies found in slaughtered domestic cattle being recognized as plastic-based materials. Additionally, microplastics were recently detected inside ruminant bodies and in their feces. MPs presence in ruminants could be explained by the intensive usage of plastic materials on farms, in particular to store feeds (i.e. to cover horizontal silos and to wrap hay bales). Although feed could be one of the main sources of plastics, especially of microplastics, a specific protocol to detect them in ruminant feeds is not actually present. Hence, the aim of this study was to optimize a specific protocol for the extraction, quantification, and identification of five microplastic polymers (high-density polyethylene, low-density polyethylene, polyamide fibers/particles, polyethylene terephthalate and polystyrene) from feeds typically used in ruminant diets (corn silage, hay, high protein feedstuff and total mixed ration). Several combinations of Fenton reactions and KOH digestion were tested. The final extraction protocol involved a KOH digestion (60 °C for 24 h), followed by two/three cycles of Fenton reactions. The extraction recoveries were of 100 % for high-density, low-density polyethylene, polyamide particles, and polystyrene and higher than 85 % for polyethylene terephthalate and polyamide fibers. Finally, the optimized protocol was successfully applied in the extraction of microplastics from real feed samples. All the feeds contained microplastics, particularly polyethylene, thus confirming the exposure of ruminants to MPs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Kidney stones are the most common urinary system diseases, and early identification is of great significance. The purpose of this study was to use routine urine and blood detection indices to build a deep learning (DL) model to identify the presence of kidney stones in the early stage. A retrospective analysis was conducted on patients with kidney stones who were treated at West China Hospital of Sichuan University from January 2020 to June 2023. A total of 1130 individuals presenting with kidney stones and 1230 healthy subjects were enrolled. The first blood and urine laboratory data of participants at our hospital were collected, and the data were divided into a training dataset (80%) and a verification dataset (20%). Additionally, a long short-term memory (LSTM)-based adaptive feature weighting model was trained for the early identification of kidney stones, and the results were compared with those of other models. The performance of the model was evaluated by the area under the subject working characteristic curve (AUC). The important predictive factors are determined by ranking the characteristic importance of the predictive factors. A total of 17 variables were screened; among the top 4 characteristics according to the weight coefficient in this model, urine WBC, urine occult blood, qualitative urinary protein, and microcyte percentage had high predictive value for kidney stones in patients. The accuracy of the kidney stone (KS-LSTM) learning model was 89.5%, and the AUC was 0.95. Compared with other models, it has better performance. The results show that the KS-LSTM model based on routine urine and blood tests can accurately identify the presence of kidney stones. And provide valuable assistance for clinicians to identify kidney stones in the early stage., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: Plastids originated from an ancient endosymbiotic event and evolved into the photosynthetic organelles in plant cells. They absorb light energy and carbon dioxide, converting them into chemical energy and oxygen, which are crucial for plant development and adaptation. However, little is known about the plastid genome to light adaptation. Petrocosmea, a member of the Gesneriaceae family, comprises approximately 70 species with diverse light environment, serve as an ideal subject for studying plastomes adapt to light., Results: In this study, we selected ten representative species of Petrocosmea from diverse light environments, assembled their plastid genomes, and conducted a comparative genomic analysis. We found that the plastid genome of Petrocosmea is highly conserved in both structure and gene content. The phylogenetic relationships reconstructed based on the plastid genes were divided into five clades, which is consistent with the results of previous studies. The vast majority of plastid protein-coding genes were under purifying selection, with only the rps8 and rps16 genes identified under positive selection in different light environments. Notably, significant differences of evolutionary rate were observed in NADH dehydrogenase, ATPase ribosome, and RNA polymerase between Clade A and the other clades. Additionally, we identified ycf1 and several intergenic regions (trnH-psbA, trnK-rps16, rpoB-trnC, petA-psbJ, ccsA-trnL, rps16-trnQ, and trnS-trnG) as candidate barcodes for this emerging ornamental horticulture., Conclusion: We newly assembled ten plastid genomes of Petrocosmea and identified several hypervariable regions, providing genetic resources and candidate markers for this promising emerging ornamental horticulture. Furthermore, our study suggested that rps8 and rps16 were under positive selection and that the evolutionary patterns of NADH dehydrogenase, ATPase ribosome, and RNA polymerase were related to the diversity light environment in Petrocosmea. This revealed an evolutionary scenario for light adaptation of the plastid genome in plants., (© 2024. The Author(s).)

Efficiently mining and identification of new compounds from the extensive MS/MS datasets of plant extracts poses a significant challenge due to the structural diversity and compositional complexity inherent in natural products (NPs). Various data post-processing techniques have been developed to simplify the interpretation of MS/MS data; however, they often suffer from limited specificity and precision. Meanwhile, structure annotation following data post-processing is particularly time-consuming. In this study, we introduced an innovative strategy named MS-SMART, which integrates three intelligent algorithms: automatic mining of diagnostic ions, rapid filtration of alkaloids from untargeted MS/MS data, and structural recommendations for filtered components. The feasibility of this approach for rapidly discovering novel compounds was demonstrated using berberine-type alkaloids as an example. Firstly, diagnostic ions were automatically extracted and validated using available reference data. Subsequently, berberine-type compounds were filtered from raw MS/MS data. Finally, the structures of the target components were recommended using building blocks derived from berberines reported in various plants. A total of 103, 198, 60, 80 and 51 berberines were efficiently identified in diverse families and genera, including Stephaniae Epigaeae Radix, Coptidis Rhizoma, Phellodendri Chinensis Cortex, Phellodendri Amurensis Cortex and Corydalis Decumbentis Rhizoma, with 99, 169, 50, 64 and 40 new compounds identified, respectively. Among these, 8, 14, 8, 7 and 12 berberines were confirmed by reference compounds. This strategy provides a new research paradigm for the rapid discovery and identification of different types of new compounds in complex samples., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

To determine the etiological agents responsible for acute pneumonia in puppies in China, this study utilized bronchoalveolar lavage (BAL) fluid extraction to enable the isolation, culture, biochemical identification, and 16S rRNA PCR amplification of the pathogens. Following preliminary identification, the pathogens underwent analysis for antibiotic resistance phenotypes and resistance genes. Additionally, the study examined the presence of virulence genes, conducted multilocus sequence typing (MLST), and performed whole-genome sequencing (WGS). The findings revealed that all four isolated pathogens were characterized as extraintestinal pathogenic Escherichia coli (ExPEC). The examined ExPEC strains demonstrated resistance to cephalosporins, tetracyclines, and penicillins, while remaining susceptible to aminoglycosides, beta-lactamase inhibitors, carbapenems, chloramphenicols, and sulfonamides. An analysis of virulence genes identified the presence of eight genes, namely CNF-I , fyuA , fimC , papC , ompA , fimH , irp2 , and iroN , which are implicated in their invasiveness and potential to inflict tissue damage. The MLST analysis revealed that all ExPEC strains were classified under either sequence type ST131 (Achtman database) or ST43 (Pasteur database). The study further determined that these strains were absent in the kennel's drinking water source, thereby ruling out water contamination as a potential factor in the emergence of ST131-type ExPEC. This study offers a theoretical framework and empirical evidence for elucidating the potential pathogenic mechanisms and clinical therapeutic strategies of ExPEC in the etiology of acute pneumonia in puppies.

Three new species of Rhogadopsis Brèthes, 1913 ( R.clausulata sp. nov. , R.obliqoides sp. nov. and R.setosipunctata sp. nov. An identification key to the species of Rhogadopsisunicarinata (Fischer, 1959) is a new combination and a new synonym of R.mediocarinata (Fischer, 1963), syn. nov. An identification key to the species of Rhogadopsis known from South Korea is provided., Competing Interests: The authors have declared that no competing interests exist., (Yunjong Han, Cornelis van Achterberg, Hyojoong Kim.)

A lack of soft tissue leads to difficulties in facial reconstruction and further identification in the absence of DNA (deoxyribonucleic acid), finger print and dental data. If these data are not available, then identification based on facial soft tissue thickness (FSTT) is the next reliable method. There is no data in the literature about facial soft tissue thickness in Montenegrin population. Once the measurement is performed, a software algorithm based on the multidetector computerized tomography (MDCT) imaged bone structures and use of FSTT would be able to provide a useful picture of the face for identification purposes. This prospective research was performed by MDCT head examinations of 83 adults aged 18-85, living in Montenegro. The FSTT was measured at eight central points (glabella (GL), nasion (NA), rhinion (RHI), mid-philtrum (MID), upper lip (UL), lower lip (LL), mental eminence (ME), and the point beneath the chin (BC)), and five bilateral points (frontal tubers (FT), supraorbital (SO), external orbital marginal point (EX), zygomatic arch (ZY), and middle masseter (MST)). It was observed that the points RHI, MID, UL, LL, ME, FT, SO and MST are thicker in men compared to women. With an increase in BMI, FSTT in the central points also increases, as well as bilaterally at the ZY, FT, SO and MST points. With aging, there is an increase of the thickness of the FSTT at the RHI and bilaterally at the EX and ZY, while at the MID, LL and MST, the thickness decreases with aging, in both sexes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The development of effective recycling technologies is essential for the recovery and reuse of the raw materials required for lithium-ion batteries (LIBs). Future recycling processes depend on accessible information, necessitating the implementation of a digital battery passport. The European battery regulation mandates the use of a machine-readable identifier physically attached to the batteries for accessing digital information. Since externally applied optical labels are vulnerable to mechanical damage, technologies for identification without these restrictions could be beneficial. This study demonstrates that magnetic supraparticles (SPs) can be used for contactless identification of lithium nickel manganese cobalt oxide (NMC) battery pouch cells via magnetic particle spectroscopy (MPS) and that multiple pouch cells can be discriminated based on their specific magnetic code. A comparison of three independent model scenarios revealed that the detection of SPs and the impact on cell performance are dependent on the integration location. The results validate the concept of magnetic identification in metallic environments with MPS as an alternative to optical labeling methods. This study provides a foundation for the development of a new selective labeling and identification technology for batteries, with the potential to facilitate recycling and contribute to a more sustainable future., (© 2024 The Authors. ChemSusChem published by Wiley-VCH GmbH.)

In cases of unidentified deceased persons, sex determination is a routine task in forensic medicine. However, the binary biological sex categories 'female' and 'male' may be challenged if it is not clear whether the information in the missing persons databases refers to the biological sex or the (felt and lived) gender. An umbrella term for people who do not identify with their birth sex (which usually is the biological, chromosomal sex) is 'transgender'. In recent decades, the legal and social situation of transgender people has changed in many countries making it easier to live their felt gender more openly. This development highlights the issue of potential challenges in the postmortem identification of transgender individuals. Serious problems in corresponding cases may be rare-but they must be considered and addressed in forensic practice to minimize the risk of delayed or failed identification. The impact of (trans)gender on the identification of human remains was examined by a narrative literature review under special consideration of the prevalences of transgender identities in general populations and in the group of unidentified deceased; possible actions to avoid problems in the postmortem identification of transgender persons in forensic practice are being proposed. One can assume that 1 of 200 people in the United States, the European Union and comparable societies is transgender with an opposite-sex identification, and 2 to 3 of 100 people live outside the typical female/male binary, with numbers increasing. If legally possible, an increasing number of transgender individuals will change their name and gender in civil registration. Transgender individuals are likely to be overrepresented in suicides and in victims of homicides. Although there are no precise data on the prevalence of transgender individuals in the group of unidentified deceased, the remarkably high reported prevalence in the general population and the over-representation of transgender individuals in suicides and homicides suggest that the topic is relevant to forensic practice. An autopsy does not always provide evidence of transgender identity, for example in skeletal remains. Particularly in unsolved cases, the possibility that an unidentified person may have been transgender should be considered. Knowledge and awareness of forensic practitioners on this topic should be strengthened by research and training. Databases and data reporting should be optimized. Recording in antemortem databases should clearly distinguish between 'biological sex' and 'apparent sex /lived gender identity'. When collecting postmortem data, a clear distinction should be made between "chromosomal sex" and "sex based on morphological findings". CLINICAL TRIAL NUMBER: Not applicable (review article)., (© 2024. The Author(s).)

Aims: This study aimed to analyse and determine the risk factors of disease aggravation faced by older patients with non-communicable diseases (NCDs) and their interwoven correlations., Design: We employed a descriptive and cross-sectional study, which followed the STROBE guidelines for reporting., Methods: We conducted a semi-structured in-depth interview with 26 older patients with NCDs from a hospital in Qingdao, China between July and August 2022 on the basis of the literature review. Then, we analysed data using the directed content analysis and determined risk factors through a focus group discussion and the Delphi consultation. Afterward, we combined interpretive structural modelling and hierarchical holographic modelling to construct a hierarchical structure model and drew relationship framework diagrams to exhibit diversified risk factors and complex interwoven correlations., Results: We identified 30 risk factors from individual, interpersonal, organisational, community and policy levels. The hierarchical structure model constructed by interpretive structural modelling demonstrated a four-layer structure, and the individual and interpersonal levels were at the highest layer. The relationship framework diagrams demonstrated the identification process of risk factors and interwoven correlations at individual and organisational levels., Conclusions: Risk factors causing disease aggravation amongst older patients with NCDs are diverse. To delay the progression of NCDs, we should comprehensively explore risk factors, interpret the root causes and effects of risks from multiple perspectives and consider the interaction amongst multi-level risk factors to develop precise measures related to risk control., Impact: Controlling risk factors is an effective measure to postpone disease aggravation. Through this study, we provide a scientific and comprehensive basis for clinical risk screening so that healthcare providers can sense potential risk factors for disease aggravation in older patients' surroundings and formulate targeted nursing measures according to the risk factors faced by different patients., Patient or Public Contribution: Patients participated in interviews to supplement risk factors included in our study. Experts provided opinions on the inclusion, exclusion and modification of risk factors., (© 2024 John Wiley & Sons Ltd.)

Culicoides, among the tiniest and most abundant hematophagous insects globally, serve as vectors for a variety of pathogens such as viruses, bacteria, parasites, protozoa, and nematodes. This study aimed to identify Culicoides species and assess their spatial distribution and seasonal occurrence in selected districts of the Central, South, and West Gondar zones, Northwest Ethiopia. A cross-sectional study was conducted between January to July 2023. A total of 44 UV light- onderstepoort traps were deployed in the study districts near specific areas. The traps were operational from dusk (6:00 PM) until dawn (6:00 AM) and were suspended at a height of 1.5 to 2 m above the ground. Poisson regression was used to assess associations, the Shannon diversity index to measure diversity, and QGIS 3.22.6 to create maps. In this study, 8,857 Culicoides were captured across the 44 trapping sites. Of the total flies captured flies, 8,838 were identified as belonging to 12 distinct species, while the classification of the remaining 19 flies remained unclear. Notably, C. kingi (54.01%) was the most prevalent species, followed by C. imicola (44.55%). The abundance of Culicoides observed from January to late April (3505) was significantly lower compared to the wet season (5355), with a marked increase in the capture of C. kingi (2499) from May to late July. A statistically significant association (p < 0.05) was observed between the occurrence of Culicoides and factors such as district, sampling point, and season. Spatial analysis revealed that C. kingi had a broader range of suitability than other Culicoides species, with high suitability observed in East Dembia. The diversity index analysis indicated that Culicoides species diversity was higher in samples from animal pens (H = 0.73) and during the wet season (H = 0.75). Additionally, this study documented the presence of eight Culicoides species namely C. corsicus, C. kibunensis, C. reioxi, C. kiouxi, C. saharienines, C. desertorum, C. reithi, and C. festivipennis, which have not been previously documented in Ethiopia. In conclusion, the study highlighted that the occurrence of Culicoides species was higher in East Dembia, with moderate presence in Wegera and West Armacho. Further research is needed to assess the impact of various Culicoides species on animal and human health, as well as their economic implications, and to develop corresponding control strategies based on these findings., (© 2024. The Author(s).)

The industrial preparation of kudzu starch (KS) significantly reduces the remaining of flavonoids like puerarin (PU) in the product, weakening its biological activity and making pre-treatments on kudzu crucial. Ultrasonic technique, widely used for modifying biomolecules, can enhance nutrient interactions like those between starch and polyphenols in foods. Thus, a puerarin-kudzu starch (PKS) complex was prepared with the introduction of ultrasonic pretreatment. The results indicated that sonication increased the binding of PU to KS from 0.399 ± 0.01 to 0.609 ± 0.05 mg/g. Particle size analysis and SEM revealed that the particles of the ultrasonic puerarin-kudzu starch complex (UPKS) were larger than those of the untreated complexes. XRD, UV-vis, and FT-IR spectroscopic analyses indicated that hydrogen bonding primarily governs the interaction between PU and KS. Additionally, incorporating PU decreased the starch structure's orderliness, while ultrasonic treatment altered the helical configuration of straight-chain starch, leading to the formation of a new, ordered structure through the creation of new hydrogen bonds. Additionally, gels formed from UPKS exhibited higher viscosity, elasticity, and shear stress, suggesting that ultrasound significantly altered the intermolecular interactions between PKS. In conclusion, the use of ultrasound under optimal conditions has demonstrated its effectiveness in preparing PKS complexes, highlighting its significant potential to produce high value-added kudzu-based products., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

In order to explore the endophytic resources of Alhagi sparsifolia Shap. and identified novel antibacterial substances. Thirty endophytic fungal strains were isolated from the stems and roots of A. sparsifolia Shap. Morphological and molecular biology methods were used to identify ten strains of fungi, including four strains of Aspergillus niger , three strains of Alternaria alternata , two strains of Aspergillus flavus , and one strain of Fusarium incarnatum . All these strains were isolated from A. sparsifolia Shap. for the first time, and of these Aspergillus was the dominant genus. Antibacterial activity of the ten strains against Escherichia coli , Staphylococcus aureus , Candida albicans , and Pseudomonas aeruginosa were evaluated using the disc diffusion method. The results demonstrated that the metabolites from all the strains had inhibitory effects on at least one indicator bacterium. Notably, the endophytic fungi AFJ3 and AFG6 demonstrated strong broad-spectrum antibacterial activity, particularly against E. coli , with inhibition zones measuring 32.0 ± 0.3 and 31.3 ± 0.3 mm, respectively. The three endophytic fungi (AFG1, AFG2, and AFG3) isolated from the roots demonstrated significant antibacterial activity against P. aeruginosa forming an inhibition zone of diameter 31.3 ± 0.1, 25.6 ± 0.2, and 25.6 ± 0.2 mm, respectively. However, the strains of endophytic fungi demonstrated no significant inhibitory effects on C. albicans . Ultra-high performance liquid chromatography with quadrupole time-of-flight mass spectrometry/mass spectrometry (UPLC-QTOF-MS/MS) analysis depicted that the ethyl acetate phase of AFJ3 and AFG6 fermentation broth predominantly contained organic acids, phenolic acids, flavonoids, and fatty acids. These secondary metabolites often exhibited good antibacterial activity. This study broadens our understanding of endophytic fungi in A. sparsifolia Shap. The antibacterial activity of some strains of endophytic fungi was significant, making it worthy of further research on their active material., Competing Interests: The authors declare that there are no financial or other relationships that might lead to a conflict of interest of the present article., (© 2024 The Authors.)

The failure of bonded composite materials is accompanied by specific failure modes. These are specifically Mode I, Mode II, Mode III, and their combination (so-called mixed mode). These modes depend on the direction and type of loading. The mechanical properties describing the damage initiation and the damage evolution are unique according to the type of adhesive and present mode of failure. However, a few research studies have focused on an adhesive thicknesses greater than 0.2 mm. The main objective of this research is to investigate the mechanical properties of a bonded joint with large adhesive thickness loaded according to Modes I and II. The observed failure parameters, the cohesive and damage parameters, are identified by minimizing the difference between the force-displacement diagram obtained from the experimental data for both Mode I and Mode II. The finite element model is confronted with these parameters and is evaluated based on their agreement. Compared to other studies with a small adhesive layer thickness, the values of failure parameters are lower. The results show that the adhesive thickness has an influence on the values of cohesive and damage parameters and that these parameter values decrease significantly compared to a small adhesive thickness. The obtained parameters can be further used to predict the fracture toughness of other bonded joints loaded in any direction.