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Parasites & Vectors Jun 2024Mosquitoes are important vectors of pathogens. They are usually collected with CO-baited traps and subsequently identified by morphology. This procedure is very...
BACKGROUND
Mosquitoes are important vectors of pathogens. They are usually collected with CO-baited traps and subsequently identified by morphology. This procedure is very time-consuming. Automatic counting traps could facilitate timely evaluation of the local risk for mosquito-borne pathogen transmission or decision-making on vector control measures, but the counting accuracy of such devices has rarely been validated in the field.
METHODS
The Biogents (BG)-Counter 2 automatically counts mosquitoes by discriminating the size of captured objects directly in the field and transmits the data to a cloud server. To assess the accuracy of this counting device, 27 traps were placed at 19 sampling sites across Germany and used in daily, weekly or bimonthly intervals from April until October 2021. The BG-Counter 2 was attached to a CO-trap (BG-Pro trap = CO-Pro) and the same trap was converted to also attract gravid mosquitoes (upside-down BG-Pro trap with a water container beneath = CO-Pro-gravid). All captured mosquitoes were identified by morphology. The number of females (unfed and gravid), mosquito diversity and the number of identified specimens in relation to the counting data of the BG-Counter were compared between the two trapping devices to evaluate sampling success and counting accuracy.
RESULTS
In total 26,714 mosquitoes were collected during 854 trap days. The CO-Pro-gravid trap captured significantly more mosquitoes per trap day for all specimens, gravid females and non-gravid females, while there was no difference in the mosquito diversity. The linear model with the captured mosquitoes as a response and the counted specimens as a predictor explained only a small degree of the variation within the data (R = 0.16), but per individual trap the value could reach up to 0.62 (mean R = 0.23). The counting accuracy for the daily samples had a significant positive correlation with sample size, resulting in higher accuracy for the CO-Pro-gravid trap and higher accuracy for sites and sampling months with high mosquito abundance.
CONCLUSIONS
While the accuracy of the BG-Counter 2 is quite low, the device is able to depict mosquito phenology and provide information about local population dynamics.
Topics: Animals; Mosquito Control; Mosquito Vectors; Female; Culicidae; Germany
PubMed: 38937756
DOI: 10.1186/s13071-024-06338-x -
Pediatric Radiology Jun 2024Cervical lymphadenopathy is common in children and has diverse causes varying from benign to malignant, their similar manifestations making differential diagnosis...
BACKGROUND
Cervical lymphadenopathy is common in children and has diverse causes varying from benign to malignant, their similar manifestations making differential diagnosis difficult.
OBJECTIVE
This study aimed to investigate whether radiomic models using conventional magnetic resonance imaging (MRI) could classify pediatric cervical lymphadenopathy.
METHODS
A total of 419 cervical lymph nodes from 146 patients, and encompassing four common etiologies (Kikuchi disease, reactive hyperplasia, suppurative lymphadenitis and malignancy), were randomly divided into training and testing sets in a ratio of 7:3. For each lymph node, 1,218 features were extracted from T2-weighted images. Then, the least absolute shrinkage and selection operator (LASSO) models were used to select the most relevant ones. Two models were built using a support vector machine classifier, one was to classify benign and malignant lymph nodes and the other further distinguished four different diseases. The performance was assessed by receiver operating characteristic curves and decision curve analysis.
RESULTS
By LASSO, 20 features were selected to construct a model to distinguish benign and malignant lymph nodes, which achieved an area under the curve (AUC) of 0.89 and 0.80 in the training and testing sets, respectively. Sixteen features were selected to construct a model to distinguish four different cervical lymphadenopathies. For each etiology, Kikuchi disease, reactive hyperplasia, suppurative lymphadenitis, and malignancy, an AUC of 0.97, 0.91, 0.88, and 0.87 was achieved in the training set, and an AUC of 0.96, 0.80, 0.82, and 0.82 was achieved in the testing set, respectively.
CONCLUSION
MRI-derived radiomic analysis provides a promising non-invasive approach for distinguishing causes of cervical lymphadenopathy in children.
PubMed: 38937304
DOI: 10.1007/s00247-024-05954-0 -
Molecules and Cells Jun 2024Genome editing has developed rapidly in various research fields for targeted genome modifications in many organisms, including cells, plants, viruses, and animals. The...
Genome editing has developed rapidly in various research fields for targeted genome modifications in many organisms, including cells, plants, viruses, and animals. The CRISPR/Cas9 system stands as a potent tool in gene editing for generating cells and animal models with high precision. The clinical potential of CRISPR/Cas9 has been extensively reported, with applications in genetic disease correction, inhibition of viral replication, and personalized or targeted therapeutics for various cancers. In this study, we provide a guide on single guide RNA (sgRNA) design, cloning sgRNA into plasmid vectors, single-cell isolation via transfection, and identification of knockout clones using next-generation sequencing. In addition, by providing the results of insertion into mammalian cell lines through next generation sequencing (NGS), we offer useful information to those conducting research on human and animal cell lines.
PubMed: 38936509
DOI: 10.1016/j.mocell.2024.100087 -
Medical Image Analysis Jun 2024In real-world clinical settings, traditional deep learning-based classification methods struggle with diagnosing newly introduced disease types because they require...
In real-world clinical settings, traditional deep learning-based classification methods struggle with diagnosing newly introduced disease types because they require samples from all disease classes for offline training. Class incremental learning offers a promising solution by adapting a deep network trained on specific disease classes to handle new diseases. However, catastrophic forgetting occurs, decreasing the performance of earlier classes when adapting the model to new data. Prior proposed methodologies to overcome this require perpetual storage of previous samples, posing potential practical concerns regarding privacy and storage regulations in healthcare. To this end, we propose a novel data-free class incremental learning framework that utilizes data synthesis on learned classes instead of data storage from previous classes. Our key contributions include acquiring synthetic data known as Continual Class-Specific Impression (CCSI) for previously inaccessible trained classes and presenting a methodology to effectively utilize this data for updating networks when introducing new classes. We obtain CCSI by employing data inversion over gradients of the trained classification model on previous classes starting from the mean image of each class inspired by common landmarks shared among medical images and utilizing continual normalization layers statistics as a regularizer in this pixel-wise optimization process. Subsequently, we update the network by combining the synthesized data with new class data and incorporate several losses, including an intra-domain contrastive loss to generalize the deep network trained on the synthesized data to real data, a margin loss to increase separation among previous classes and new ones, and a cosine-normalized cross-entropy loss to alleviate the adverse effects of imbalanced distributions in training data. Extensive experiments show that the proposed framework achieves state-of-the-art performance on four of the public MedMNIST datasets and in-house echocardiography cine series, with an improvement in classification accuracy of up to 51% compared to baseline data-free methods. Our code is available at https://github.com/ubc-tea/Continual-Impression-CCSI.
PubMed: 38936223
DOI: 10.1016/j.media.2024.103239 -
Ticks and Tick-borne Diseases Jun 2024Radicular pain is the most predominant symptom among adults with Lyme neuroborreliosis (LNB) but the duration preceding and following diagnosis remains unknown. We aimed...
BACKGROUND
Radicular pain is the most predominant symptom among adults with Lyme neuroborreliosis (LNB) but the duration preceding and following diagnosis remains unknown. We aimed to investigate whether patients with LNB have increased obtainment of analgesics before and after diagnosis and for how long.
METHODS
We performed a nationwide, population-based, matched cohort study (2009-2021). all Danish residents with LNB (positive Borrelia burgdorferi intrathecal antibody index test and cerebrospinal fluid pleocytosis) were included. To form a comparison cohort, individuals from the general population were randomly extracted and matched 10:1 to patients with LNB on age and sex. Outcomes were obtainment of simple analgesics, antiepileptics, tricyclic antidepressants, serotonin and noradrenaline reuptake inhibitors, tramadol, and other opioids. We calculated monthly and six-monthly proportions of individuals with obtainment of analgesics and absolute risk differences.
RESULTS
1,056 patients with LNB and 10,560 comparison cohort members were included. An increased proportion of patients with LNB obtained analgesics from 3 months before study inclusion, especially simple analgesics, tramadol, and other opioids. Within the 0-1-month period after study inclusion, patients with LNB most frequently obtained simple analgesics (15 %), antiepileptics (11 %), and tramadol (10 %). Thereafter, obtainment of analgesics declined within a few months. A slightly larger proportion of patients with LNB obtained antiepileptics up to 2.5 years after diagnosis.
CONCLUSIONS
Up to 3 months preceding diagnosis, LNB was preceded by increased obtainment of analgesics, which suggests diagnostic delay. Importantly, most patients with LNB did not obtain analgesics after the immediate disease course, although obtainment remained more frequent up to 2.5 years after.
PubMed: 38936014
DOI: 10.1016/j.ttbdis.2024.102371 -
PLoS Neglected Tropical Diseases Jun 2024Usutu virus (USUV) is a zoonotic arbovirus infecting mainly wild birds. It is transmitted by ornithophilic mosquitoes, mainly of the genus Culex from birds to birds and...
Usutu virus (USUV) is a zoonotic arbovirus infecting mainly wild birds. It is transmitted by ornithophilic mosquitoes, mainly of the genus Culex from birds to birds and to several vertebrate dead-end hosts. Several USUV lineages, differing in their virulence have emerged in the last decade and now co-circulate in Europe, impacting human populations. However, their relative transmission and effects on their mosquito vectors is still not known. We thus compared the vector competence and survival of Culex pipiens mosquitoes experimentally infected with two distinct USUV lineages, EU2 and EU3, that are known to differ in their virulence and replication in vertebrate hosts. Infection rate was variable among blood feeding assays but variations between EU2 and EU3 lineages were consistent suggesting that Culex pipiens was equally susceptible to infection by both lineages. However, EU3 viral load increased with viral titer in the blood meal while EU2 viral load was high at all titers which suggest a greater replication of EU2 than EU3 in mosquito. While their relative transmission efficiencies are similar, at least at low blood meal titer, positive correlation between transmission and blood meal titer was observed for EU3 only. Contrary to published results in vertebrates, EU3 induced a higher mortality to mosquitoes (i.e. virulence) than EU2 whatever the blood meal titer. Therefore, we found evidence of lineage-specific differences in vectorial capacity and virulence to both the vector and vertebrate host which lead to balanced propagation of both viral lineages. These results highlight the need to decipher the interactions between vectors, vertebrate hosts, and the diversity of arbovirus lineages to fully understand transmission dynamics.
PubMed: 38935783
DOI: 10.1371/journal.pntd.0012295 -
Journal of Magnetic Resonance Imaging :... Jun 2024MR elastography (MRE) at 60 Hz is widely used for staging liver fibrosis. MRE with lower frequencies may provide inflammation biomarkers.
BACKGROUND
MR elastography (MRE) at 60 Hz is widely used for staging liver fibrosis. MRE with lower frequencies may provide inflammation biomarkers.
PURPOSE
To establish a practical simultaneous dual-frequency liver MRE protocol at both 30 Hz and 60 Hz during a single examination and validate the occurrence of second harmonic waves at 30 Hz.
STUDY TYPE
Retrospective.
SUBJECTS
One hundred six patients (48 females, age: 50.0 ± 13.4 years) were divided as follows: Cohort One (15 patients with chronic liver disease [CLD] and 25 healthy volunteers) with simultaneous dual-frequency MRE. Cohort Two (66 patients with CLD) with second harmonic MRE.
FIELD STRENGTH/SEQUENCE
3-T, single- or dual-frequency MRE at 30 Hz and 60 Hz.
ASSESSMENT
Liver stiffness (LS) in both cohorts was evaluated with manually placed volumetric ROIs by two independent analyzers. Image quality was assessed by three independent readers on a 4-point scale (0-3: none/failed, fair, moderate, excellent) based on the depth of wave propagation with 1/3 incremental penetration. The success rate was derived from the percentage of nonzero quality scores.
STATISTICAL TESTS
Measurement agreement, bias, and repeatability of LS were assessed using intraclass correlation coefficients (ICCs), Bland-Altman plots, and repeatability coefficient (RC). Mann-Whitney U tests were used to evaluate the differences in image quality between different methods. A P-value <0.05 was considered statistically significant.
RESULTS
Success rate was 97.5% in Cohort One and 91% success rate for the second harmonic MRE in Cohort Two. The second harmonic and conventional MRE showed excellent agreement in LS (all ICCs >0.90). The quality scores for the second harmonic wave images were lower than those from the conventional MRE (Z = -4.523).
DATA CONCLUSION
Compared with conventional and second harmonic methods, simultaneous dual-frequency had better image quality, high success rate and the advantage of intrinsic co-registration, while the second harmonic method can be an alternative if custom waveform is not available.
EVIDENCE LEVEL
3 TECHNICAL EFFICACY: Stage 1.
PubMed: 38935749
DOI: 10.1002/jmri.29493 -
Systematic Biology Jun 2024Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of...
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art methods rely on carefully designed heuristics for tree search, using different data structures for easy manipulation (e.g., classes in object-oriented programming languages) and readable representation of trees (e.g., Newick-format strings). Here, we present Phylo2Vec, a parsimonious encoding for phylogenetic trees that serves as a unified approach for both manipulating and representing phylogenetic trees. Phylo2Vec maps any binary tree with n leaves to a unique integer vector of length n - 1. The advantages of Phylo2Vec are fourfold: i) fast tree sampling, (ii) compressed tree representation compared to a Newick string, iii) quick and unambiguous verification if two binary trees are identical topologically, and iv) systematic ability to traverse tree space in very large or small jumps. As a proof of concept, we use Phylo2Vec for maximum likelihood inference on five real-world datasets and show that a simple hill-climbing-based optimisation scheme can efficiently traverse the vastness of tree space from a random to an optimal tree.
PubMed: 38935520
DOI: 10.1093/sysbio/syae030 -
ELife Jun 2024The Zanzibar archipelago of Tanzania has become a low-transmission area for . Despite being considered an area of pre-elimination for years, achieving elimination has...
BACKGROUND
The Zanzibar archipelago of Tanzania has become a low-transmission area for . Despite being considered an area of pre-elimination for years, achieving elimination has been difficult, likely due to a combination of imported infections from mainland Tanzania and continued local transmission.
METHODS
To shed light on these sources of transmission, we applied highly multiplexed genotyping utilizing molecular inversion probes to characterize the genetic relatedness of 282 isolates collected across Zanzibar and in Bagamoyo district on the coastal mainland from 2016 to 2018.
RESULTS
Overall, parasite populations on the coastal mainland and Zanzibar archipelago remain highly related. However, parasite isolates from Zanzibar exhibit population microstructure due to the rapid decay of parasite relatedness over very short distances. This, along with highly related pairs within , suggests ongoing low-level local transmission. We also identified highly related parasites across that reflect human mobility on the main island of Unguja and identified a cluster of highly related parasites, suggestive of an outbreak, in the Micheweni district on Pemba island. Parasites in asymptomatic infections demonstrated higher complexity of infection than those in symptomatic infections, but have similar core genomes.
CONCLUSIONS
Our data support importation as a main source of genetic diversity and contribution to the parasite population in Zanzibar, but they also show local outbreak clusters where targeted interventions are essential to block local transmission. These results highlight the need for preventive measures against imported malaria and enhanced control measures in areas that remain receptive to malaria reemergence due to susceptible hosts and competent vectors.
FUNDING
This research was funded by the National Institutes of Health, grants R01AI121558, R01AI137395, R01AI155730, F30AI143172, and K24AI134990. Funding was also contributed from the Swedish Research Council, Erling-Persson Family Foundation, and the Yang Fund. RV acknowledges funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/R015600/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 program supported by the European Union. RV also acknowledges funding by Community Jameel.
Topics: Tanzania; Plasmodium falciparum; Malaria, Falciparum; Humans; Genotype
PubMed: 38935423
DOI: 10.7554/eLife.90173 -
Indian Journal of Public Health Oct 2023Japanese encephalitis (JE) is an emerging zoonotic disease caused by JE virus (JEV) and transmitted to humans from pigs or aquatic birds by vector mosquitoes in...
BACKGROUND
Japanese encephalitis (JE) is an emerging zoonotic disease caused by JE virus (JEV) and transmitted to humans from pigs or aquatic birds by vector mosquitoes in southeast Asian countries. In this study, JEV infection rate among vector mosquitoes and domestic pigs was determined by detecting viral RNA and anti-JEV antibody (immunoglobulin G), respectively.
MATERIALS AND METHODS
A total of 146 pool mosquitoes of Culexvishnui subgroup and 278 pig blood samples were analyzed by reverse transcriptase polymerase chain reaction and enzyme-linked immunosorbent assay methods, respectively. E and premembrane (PrM) gene of JEV detected among vectors were sequenced and a phylogenetic tree was constructed.
RESULTS
Five (5.81%) pools of Culextritaeniorhynchus were positive for JEV with pooled infection rate 1.70/1000 mosquitoes. A total of 108 (38.84%) blood samples were positive for anti-JEV antibody. Phylogenetic analysis revealed that our own E and PrM gene sequence of JEV belonging to Genotype III and showed 96.95% sequence similarities with the vaccine strain SA14-14-2.
CONCLUSION
It was observed that domestic pigs of northern West Bengal were highly infected with JEV. Hence, the transmission should be blocked by pig vaccination. A pilot study may be undertaken for mass vaccination of the prevailing pig population to observe any reduced rate of JEV transmission from both pig to pig and pig to human.
Topics: Animals; India; Encephalitis, Japanese; Swine; Encephalitis Virus, Japanese; Mosquito Vectors; Culex; Phylogeny; Enzyme-Linked Immunosorbent Assay; Antibodies, Viral; Swine Diseases; Reverse Transcriptase Polymerase Chain Reaction; RNA, Viral
PubMed: 38934834
DOI: 10.4103/ijph.ijph_1734_22