Search Results (160)

As one of the most commonly used and important data carriers, tables have the advantages of high structuring, strong readability and strong flexibility. However, in reality, tables usually present various forms, such as Excel, images, etc. Among them, the information in the table image cannot be read directly, let alone further applied. Therefore, the research related to image-based table recognition is crucial. It contains the table structure recognition and the table content recognition. Among them, table structure recognition is the most important and difficult task because the table structure is abstract and changeable. In order to address this problem, we propose an innovative table structure recognition method, named TSRDet (Table Structure Recognition based on object Detection). It includes a row-column detection method, named SACNet (StripAttention-CenterNet) and the corresponding post-processing. SACNet is an improved version of the original CenterNet. The specific improvements include the following: firstly, we introduce the Swin Transformer as the encoder to obtain the global feature map of the image. Then, we propose a plug-and-play row-column attention module, including a channel attention module and a row-column spatial attention module. It improves the detection accuracy of rows and columns by capturing long-range row-column feature maps in the image. After completing the row-column detection, this paper also designs a simple and fast post-processing to generate the table structure based on the row-column detection results. Experimental results show that for row-column detection, SACNet has high detection accuracy, even at a high IoU threshold. Specifically, when the threshold is 0.75, its mAP of row detection and column detection still exceeds 90%, which is 91.40% and 92.73% respectively. In addition, in the comparative experiment with the existing object detection methods, SACNet’s performance was significantly better than that of all others. For table structure recognition, the TEDS-Struct score of TSRDet is 95.7%, which shows competitive performance in table structure recognition, and verifies the rationality and superiority of the proposed method. Full article

Underground mines are considered one of the riskiest facilities for human activities due to numerous accidents and geotechnical failures recorded worldwide over the last century, which have resulted in unsafe labor conditions, poor health outcomes, injuries, and fatalities. One significant cause of these accidents is the inadequate or nonexistent capacity for the real-time monitoring of safety conditions in underground mines. In this context, new emerging technologies linked to the Industry 4.0 paradigm, such as sensors, the Internet of Things (IoT), and LoRaWAN (Long Range Wide Area Network) wireless connectivity, are being implemented for planning the efficient, safe, and sustainable performance of underground mine labor environments. This paper studies the implementation of an ecosystem composed of IoT sensors and LoRa wireless connectivity in a data-acquisition system, which eliminates the need for expensive cabling and manual monitoring in mining operations. Laying cables in an underground mine necessitates cable support and protection against issues, such as machinery operations, vehicle movements, mine operator activities, and groundwater intrusion. As the underground mine expands, additional sensors typically require costly cable installations unless wireless connectivity is employed. The results of this review indicate that an IoT LoRaWAN-based wireless sensor network (WSN) provides real-time data under complex conditions, effectively transmitting data through physical barriers. This network presents an attractive low-cost solution with reliable, simple, scalable, secure, and competitive characteristics compared to cable installations and manually collected readings, which are more sporadic and prone to human error. Reliable data on the behavior of the underground mine enhances productivity by improving key performance indicators (KPIs), minimizing accident risks, and promoting sustainable environmental conditions for mine operators. Finally, the adoption of IoT sensors and LoRaWAN wireless connectivity technologies provides information of the underground mine in real-time, which supports better decisions by the mining industry managers, by ensuring compliance with safety regulations, improving the productive performance, and fostering a roadmap towards more environmentally friendly labor conditions. Full article

A novel vibriophage vB_VpaM_XM1 (XM1) was described in the present study. Morphological analysis revealed that phage XM1 had Myovirus morphology, with an oblate icosahedral head and a long contractile tail. The genome size of XM1 is 46,056 bp, with a G + C content of 42.51%, encoding 69 open reading frames (ORFs). Moreover, XM1 showed a narrow host range, only lysing Vibrio xuii LMG 21346 (T) JL2919, Vibrio parahaemolyticus 1.1997, and V. parahaemolyticus MCCC 1H00029 among the tested bacteria. One-step growth curves showed that XM1 has a 20-min latent period and a burst size of 398 plaque-forming units (PFU)/cell. In addition, XM1 exhibited broad pH, thermal, and salinity stability, as well as strong lytic activity, even at a multiplicity of infection (MOI) of 0.001. Multiple genome comparisons and phylogenetic analyses showed that phage XM1 is grouped in a clade with three other phages, including Vibrio phages Rostov 7, X29, and phi 2, and is distinct from all known viral families that have ratified by the standard genomic analysis of the International Committee on Taxonomy of Viruses (ICTV). Therefore, the above four phages might represent a new viral family, tentatively named Weiviridae. The broad physiological adaptability of phage XM1 and its high lytic activity and host specificity indicated that this novel phage is a good candidate for being used as a therapeutic bioagent against infections caused by certain V. parahaemolyticus strains. Full article

The citrus yellow vein clearing virus (CYVCV) is an emerging threat to the U.S. citrus industry. Reports from China shows it cause significant reductions in fruit yield and growth, particularly in lemon trees. In 2022, CYVCV was detected in a wide range of citrus cultivars in localized urban properties in Tulare, California. In 2024, a CYVCV-infected lemon tree was detected in Hacienda Heights in Los Angeles County, California, geographically separated from the Tulare foci. Through long-read sequencing technology, the whole-genome sequence of a CYVCV isolate from Hacienda Heights (designated as CYVCV-CA-HH1, Accession number PP840891.1) was obtained. Sequence alignments and neighbornet analysis strongly suggested that the CYVCV-CA-HH1 isolate has a different origin than the Tulare CYVCV (CYVCV CA-TL) isolates. The CYVCV CA-TL isolates were grouped with those from South Asia (India and Pakistan) and the Middle East (Türkiye), while the CYVCV-CA-HH1 isolate was grouped with isolates from East Asia (China and South Korea). Maximum likelihood phylogenetic analysis further supports this finding, showing that the CYVCV-CA-HH1 isolate shares the most recent common ancestor with a South Korean lineage, which derives from Chinese isolates. Together, our data suggest a diverse geological origin of CYVCV isolates in California. Full article

Salmonella Mbandaka is one of the most globally widespread serovars, occurring in many sources and included among twenty serovars that contribute to human salmonellosis in Europe. In Poland, it has been noted in non-human sources since 1996, being found firstly in feeds and later in waterfowl and chicken. Over the years, it gained epidemiological importance, being isolated from a wide range of animal species, including livestock. Generally, it is characterized by sensitivity to most antimicrobials and the ability to form biofilms. The occurrence of cephalosporin-resistant Salmonella in non-human sources is an extremely rare phenomenon in Poland. In this report, we characterized the full genome of the ESBL-producing S. Mbandaka strain isolated from a broiler farm environment (boot swab sample) in Poland in 2022. The isolate was serotyped as S. Mbandaka according to the White–Kaufmann–Le Minor scheme. Antimicrobial susceptibility testing performed with the microbroth dilution method showed its resistance to ampicillin, cefotaxime, ceftazidime, ciprofloxacin, and nalidixic acid. The whole-genome sequence was reconstructed using short and long reads and assembled into the complete chromosome and three plasmids: IncI1 pST113 (89,439 bp), Col(pHAD28) (2699 bp), and Col440 (2495 bp). The strain belonged to sequence type ST413. Plasmid analysis showed bla_CTX-M-8 mobilization on IncI1(alpha) surrounded with insertion sequences. The analyzed genome content draws attention to the possibility of the horizontal spread of the resistance genes. To the best of our knowledge, this is the first report of bla_CTX-M-8-positive Salmonella in Poland. Full article

Dinoflagellates are one of the largest groups of marine microalgae and exhibit diverse trophic strategies. Some dinoflagellates can produce secondary metabolites that are known to be toxic, which can lead to ecologically harmful blooms. Amphidinium carterae is one species of dinoflagellate that produces toxic compounds and is used as a model for dinoflagellate studies. The impact of the microbiome on A. carterae growth and metabolite synthesis is not yet fully understood, nor is the impact of bacterial data on sequencing and assembly. An antibiotic cocktail was previously shown to eliminate 16S amplification from the dinoflagellate culture. Even with drastically reduced bacterial numbers during antibiotic treatment, bacterial sequences were still present. In this experiment, we used novel Nanopore long-read sequencing techniques on A. carterae cultures to assemble 15 full bacterial genomes ranging from 2.9 to 6.0 Mb and found that the use of antibiotics decreased the percentage of reads mapping back to bacteria. We also identified shifts in the microbiome composition and identified a potentially deleterious bacterial species arising in the absence of the antibiotic treatment. Multiple antibiotic resistance genes were identified, as well as evidence that the bacterial population does not contribute to toxic secondary metabolite synthesis. Full article

Pre-treatment genotyping of four well-characterized toxicity risk-variants in the dihydropyrimidine dehydrogenase gene (DPYD) has been widely implemented in Europe to prevent serious adverse effects in cancer patients treated with fluoropyrimidines. Current genotyping practices are largely limited to selected commonly studied variants and are unable to determine phasing when more than one variant allele is detected. Recent evidence indicates that common DPYD variants modulate the functional impact of deleterious variants in a phase-dependent manner, where a cis- or a trans-configuration translates into different toxicity risks and dosing recommendations. DPYD is a large gene with 23 exons spanning nearly a mega-base of DNA, making it a challenging candidate for full-gene sequencing in the diagnostic setting. Herein, we present a time- and cost-efficient long-read sequencing approach for capturing the complete coding region of DPYD. We demonstrate that this method can reliably produce phased genotypes, overcoming a major limitation with current methods. This method was validated using 21 subjects, including two cancer patients, each of whom carried multiple DPYD variants. Genotype assignments showed complete concordance with conventional approaches. Furthermore, we demonstrate that the method is robust to technical challenges inherent in long-range sequencing of PCR products, including reference alignment bias and PCR chimerism. Full article

The long-term use of steel strip in various industries makes it an important semi-finished product, which makes it necessary to improve its chemical composition and mechanical properties, reduce its thickness and weight, expand the range of new types of steel strip and increase its production. This entails a large number of technological operations dependent on precise temperature measurement and control. In some industrial plants, the steel strip is in continuous motion, which makes the use of contact measuring devices impossible. When using non-contact measuring devices such as pyrometers or thermal imaging cameras, the emissivity of the materials being measured is a problematic parameter, as setting an incorrect emissivity value to the measuring device results in inaccurate temperature readings. The essence of this research was to establish a measurement method and to perform experimental measurements of the emissivity of a polished steel strip used in a continuous annealing line, the subsequent processing of the data from these measurements and their evaluation. The emissivity measurements were carried out for 5 types of steel strip of different parameters, while the measurement itself was carried out in the long wavelength range of 7.5–14 µm and at strip temperatures of 100–300 °C. Depending on the type of steel strip, the mean emissivity values ranged from 0.0835– to 0.1143. The emissivity of the steel strip increased with increasing strip temperature, and it was not a linear dependence. The emissivity values determined in this research could be applied to measuring equipment in actual production, which could improve the accuracy of temperature measurement in the heat treatment of polished steel strip. Thermal camera measurements in the long wavelength range, taking thermal images and their processing and determining the emissivity value of polished steel strips are the parts of this research that make it different from other already published research. Full article

Background: Gastric electrical stimulation (GES) therapy is indicated for the treatment of drug-refractory gastroparesis (GP). However, the long-term effects of GES therapy on GP symptom control and identification of the optimal parameters to activate this long-term efficacy have not been investigated. Methods: We conducted a retrospective cohort analysis of 57 GP patients who received GES and pyloroplasty (PP). The interrogation of the GES system and assessment of GP symptoms were conducted at the initiation of GES therapy and during follow-up visits. We determined the changes in GES parameters including voltage (V), impedance (I), and current (C). The outcome was total symptom score (TSS), which was measured by self-reported GP symptoms. Results: The mean age of patients was 44 (±14) years, and 72% were females. The etiology for GP was diabetes mellitus in 72% and idiopathic in 28%. The median duration of GES follow-up was 47 months (range 5–73) A significant decrease was found in individual symptom scores and the TSS (−10.8; 95%CI: −12.6, −9.08) compared to baseline scores (p < 0.0001). During follow-up, readings for I (515 vs. 598 Ω), V (3.3 vs. 4.8 V), and C (6.5 vs. 8.4 mA) significantly increased (p ≤ 0.0001 for all parameters). Higher GES settings were associated with lower TSS in the adjusted analysis (RC, −1.97; 95%CI: −3.81, −0.12, p = 0.037). Conclusions: these findings suggest that adjusting GES parameters over time based on optimizing symptom improvement should be incorporated into the long-term care of patients receiving gastric neurostimulation therapy. Full article

Honeybees are an indispensable pollinator in nature with pivotal ecological, economic, and scientific value. However, a full-length transcriptome for Apis mellifera, assembled with the advanced third-generation nanopore sequencing technology, has yet to be reported. Here, nanopore sequencing of the midgut tissues of uninoculated and Nosema ceranae-inoculated A. mellifera workers was conducted, and the full-length transcriptome was then constructed and annotated based on high-quality long reads. Next followed improvement of sequences and annotations of the current reference genome of A. mellifera. A total of 5,942,745 and 6,664,923 raw reads were produced from midguts of workers at 7 days post-inoculation (dpi) with N. ceranae and 10 dpi, while 7,100,161 and 6,506,665 raw reads were generated from the midguts of corresponding uninoculated workers. After strict quality control, 6,928,170, 6,353,066, 5,745,048, and 6,416,987 clean reads were obtained, with a length distribution ranging from 1 kb to 10 kb. Additionally, 16,824, 17,708, 15,744, and 18,246 full-length transcripts were respectively detected, including 28,019 nonredundant ones. Among these, 43,666, 30,945, 41,771, 26,442, and 24,532 full-length transcripts could be annotated to the Nr, KOG, eggNOG, GO, and KEGG databases, respectively. Additionally, 501 novel genes (20,326 novel transcripts) were identified for the first time, among which 401 (20,255), 193 (13,365), 414 (19,186), 228 (12,093), and 202 (11,703) were respectively annotated to each of the aforementioned five databases. The expression and sequences of three randomly selected novel transcripts were confirmed by RT-PCR and Sanger sequencing. The 5′ UTR of 2082 genes, the 3′ UTR of 2029 genes, and both the 5′ and 3′ UTRs of 730 genes were extended. Moreover, 17,345 SSRs, 14,789 complete ORFs, 1224 long non-coding RNAs (lncRNAs), and 650 transcription factors (TFs) from 37 families were detected. Findings from this work not only refine the annotation of the A. mellifera reference genome, but also provide a valuable resource and basis for relevant molecular and -omics studies. Full article

The use of sensor networks in monitoring applications has increased; they are useful in security, environmental, and health applications, among others. These networks usually transmit data through short-range stations, which makes them attractive for incorporation into applications and devices for use in places without access to satellite or mobile signals, for example, forests, seas, and jungles. To this end, unmanned aerial vehicles (UAVs) have attractive characteristics for data collection and transmission in remote areas without infrastructure. Integrating systems based on wireless sensors and UAVs seems to be an economical and easy-to-use solution. However, the main difficulty is the amount of data sent, which affects the communication time and even the flight status of the UAV. Additionally, factors such as the UAV model and the hardware used for these tasks must be considered. Based on those difficulties mentioned, this paper proposes a system based on long-range (LoRa) technology. We present a low-cost wireless sensor network that is flexible, easy to deploy, and capable of collecting/sending data via LoRa transceivers. The readings obtained are packaged and sent to a UAV. The UAV performs predefined flights at a constant height of 30 m and with a direct line-of-sight (LoS) to the stations, during which it collects information from two data stations, concluding that it is possible to carry out a correct data transmission with a flight speed of 10 m/s and a transmission radius of 690 m for a group of three packages confirmed by 20 messages each. Thus, it is possible to collect data from routes of up to 8 km for each battery charge, considering the return of the UAV. Full article

The emerging heteropathotype shigatoxigenic (STEC) and extra-intestinal pathogenic Escherichia coli (ExPEC) O80:H2 has been the second leading cause of pediatric HUS in France since the mid-2010s. In contrast with other highly pathogenic STEC serotypes, for which ruminants have clearly been identified as the main human infection source, this heteropathotype’s reservoir remains unknown. In this context, we describe for the first time the isolation of seven STEC O80:H2 strains from healthy cattle on a single cattle farm in France. This study aimed at (i) characterizing the genome and (ii) investigating the phylogenetic positions of these O80:H2 STEC strains. The virulomes, resistomes, and phylogenetic positions of the seven bovine isolates were investigated using in silico typing tools, antimicrobial susceptibility testing and cgMLST analysis after short-read whole genome sequencing (WGS). One representative isolate (A13P112V1) was also subjected to long-read sequencing. The seven isolates possessed ExPEC-related virulence genes on a pR444_A-like mosaic plasmid, previously described in strain RDEx444 and known to confer multi-drug resistance. All isolates were clonally related and clustered with human clinical strains from France and Switzerland with a range of locus differences of only one to five. In conclusion, our findings suggest that healthy cattle in France could potentially act as a reservoir of the STEC-ExPEC O80:H2 pathotype. Full article

Infectious bronchitis virus (IBV) causes a highly contagious respiratory disease in chickens, leading to significant economic losses in the poultry industry worldwide. IBV exhibits a high mutation rate, resulting in the continuous emergence of new variants and strains. A complete genome analysis of IBV is crucial for understanding its characteristics. However, it is challenging to obtain whole-genome sequences from IBV-infected clinical samples due to the low abundance of IBV relative to the host genome. Here, we present a novel approach employing next-generation sequencing (NGS) to directly sequence the complete genome of IBV. Through in silico analysis, six primer pairs were designed to match various genotypes, including the GI-19 lineage of IBV. The primer sets successfully amplified six overlapping fragments by long-range PCR and the size of the amplicons ranged from 3.7 to 6.4 kb, resulting in full coverage of the IBV genome. Furthermore, utilizing Illumina sequencing, we obtained the complete genome sequences of two strains belonging to the GI-19 lineage (QX genotype) from clinical samples, with 100% coverage rates, over 1000 × mean depth coverage, and a high percentage of mapped reads to the reference genomes (96.63% and 97.66%). The reported method significantly improves the whole-genome sequencing of IBVs from clinical samples; thus, it can improve understanding of the epidemiology and evolution of IBVs. Full article

Background and Objectives: Enterococcus faecalis (E. faecalis) is a primary pathogen responsible for dental abscesses, which cause inflammation and pain when trapped between the crown and soft tissues of an erupted tooth. Therefore, this study aims to use specific phages as an alternative method instead of classical treatments based on antibiotics to destroy multidrug-resistant E. faecalis bacteria for treating dental issues. Materials and Methods: In the current study, twenty-five bacterial isolates were obtained from infected dental specimens; only five had the ability to grow on bile esculin agar, and among these five, only two were described to be extensive multidrug-resistant isolates. Results: Two bacterial isolates, Enterococcus faecalis A.R.A.01 [ON797462.1] and Enterococcus faecalis A.R.A.02, were identified biochemically and through 16S rDNA, which were used as hosts for isolating specific phages. Two isolated phages were characterized through TEM imaging, which indicated that E. faecalis_phage-01 had a long and flexible tail, belonging to the family Siphoviridae, while E. faecalis_phage-02 had a contractile tail, belonging to the family Myoviridae. Genetically, two phages were identified through the PCR amplification and sequencing of the RNA ligase of Enterococcus phage vB_EfaS_HEf13, through which our phages shared 97.2% similarity with Enterococcus phage vB-EfaS-HEf13 based on BLAST analysis. Furthermore, through in silico analysis and annotations of the two phages’ genomes, it was determined that a total of 69 open reading frames (ORFs) were found to be involved in various functions related to integration excision, replication recombination, repair, stability, and defense. In phage optimization, the two isolated phages exhibited a high specific host range with Enterococcus faecalis among six different bacterial hosts, where E. faecalis_phage-01 had a latent period of 30 min with 115.76 PFU/mL, while E. faecalis_phage-02 had a latent period of 25 min with 80.6 PFU/mL. They were also characterized with stability at wide ranges of pH (4–11) and temperature (10–60 °C), with a low cytotoxic effect on the oral epithelial cell line at different concentrations (1000–31.25 PFU/mL). Conclusions: The findings highlight the promise of phage therapy in dental medicine, offering a novel approach to combating antibiotic resistance and enhancing patient outcomes. Further research and clinical trials will be essential to fully understand the therapeutic potential and safety profile of these bacteriophages in human populations. Full article

Human cytomegalovirus (HCMV) is a pathogen with high prevalence in the general population that is responsible for high morbidity and mortality in immunocompromised individuals and newborns, while remaining mainly asymptomatic in healthy individuals. The HCMV genome is 236,000 nucleotides long and encodes approximately 200 genes in more than 170 open reading frames, with the highest rate of genetic polymorphisms occurring in the envelope glycoproteins. HCMV infection is treated with antiviral drugs such as ganciclovir, valganciclovir, cidofovir, foscarnet, letermovir and maribavir targeting viral enzymes, DNA polymerase, kinase and the terminase complex. One of the obstacles to successful therapy is the emergence of drug resistance, which can be tested phenotypically or by genotyping using Sanger sequencing, which is a widely available but less sensitive method, or next-generation sequencing performed in samples with a lower viral load to detect minority variants, those representing approximately 1% of the population. The prevalence of drug resistance depends on the population tested, as well as the drug, and ranges from no mutations detected to up to almost 50%. A high prevalence of resistance emphasizes the importance of testing the patient whenever resistance is suspected, which requires the development of more sensitive and rapid tests while also highlighting the need for alternative therapeutic targets, strategies and the development of an effective vaccine. Full article