bluuebunny/crossref_metadata_2025 huggingface dataset:
Observing one-divalent-metal-ion dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo
Authors: Chang Caleb , Zhou Grace , Gao Yang
Published: May 2024

Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysisin crystallowith His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.
Protocol for assessing the impact of the 6thNational Audit Project recommendations on practice
Authors: Clark Sigrún Eyrúnardóttir , Moppett Iain , Moonesinghe S. Ramani , Vindrola-Padros Cecilia
Published: May 2024

1.

Patient safety has been a growing area of concern, especially within perioperative care where risks of major complications during surgery exist. Anaphylaxis in the operating theatre is a life-threatening drug reaction that happens suddenly, without warning and can affect anyone. The 6th National Audit Project (NAP6) of the Royal College of Anaesthetists (RCoA): Perioperative Anaphylaxis was the largest ever prospective study of anaphylaxis related to anaesthesia and surgery. The findings from the audit were collated into a report and included recommendations for improved patient care. The purpose of this study is to understand the perceptions of the NAP6 recommendations and their impact on practice. This study will use ethnographic qualitative methods in the form of observations, interviews and a documentary analysis. The sessions targeted for observations will include departmental or hospital meetings, and educational or training sessions, related to perioperative anaphylaxis. The target sample size of 78 healthcare professionals across six hospitals within England, will include individuals with roles specific to anaesthesia, surgery, immunology, allergy and governance. Additionally, six stakeholders will be interviewed who can provide insights into the NAP6 recommendations at the national level. Across the six sites, local collaborators will share any relevant documents related to perioperative anaphylaxis or the NAP-6 recommendations. The study has received regulatory approvals from the Health Research Authority and has been funded by the National Institute for Health and Care Research.
Predicting attention deficits and functional recovery after glioma resection through functional executive networks: insights from dynamic properties
Authors: Saviola Francesca , Zigiotto Luca , Jovicich Jorge , Sarubbo Silvio
Published: May 2024

Background

Postoperative short-term attentional and executive dysfunctions are common after brain tumor resection, significantly impacting patients’ quality of life and functional recovery. The current study investigated whether presurgical functional dynamics of key brain networks supporting executive functioning could predict postoperative neuropsychological outcomes.

Methods

Twenty-two patients with gliomas underwent longitudinal resting-state fMRI scans (before and three-months after surgery), along with neuropsychological assessments (before, one-week and three-months after surgery). Co-activation patterns analysis (CAPs) characterized the functional dynamic properties of executive networks, including the Fronto-parietal (FPN) and Dorsal Attention networks (DAN). Temporal network properties were examined for stability, integration, and centrality over timepoints. Partial least squares analyses and linear models explored associations between network dynamics and cognitive functioning.

Results

Immediate post-surgical attentional deficits were linked to pre-surgical FPN properties revealing associated dynamic patterns of network activation. Pre-surgical FPN temporal properties predicted not only immediate appearance or persistence of post-resection deficits, but also the longitudinal progression of attentional performance otherwise neglected. However, regardless of the severity of attentional deficit, at three months post-surgery, temporal properties and neuropsychological profiles did not significantly differ from the pre-surgical ones, indicating recovery to baseline beyond treatment strategies.

Conclusions

Our study demonstrates that presurgical dynamic properties of intrinsic executive networks alone can predict short-term postoperative neuropsychological outcomes, highlighting the clinical utility of temporal functional connectivity. These findings emphasize the potential for using intrinsic brain activity dynamics as predictive markers for postoperative recovery and planning tailored rehabilitation interventions for cognitive deficits.

Key messages

What is already known on this topic:

Attentive deficits are common in short-term post-glioma neurosurgery, yet their anticipation remains a challenge.

What this study adds:

Integrating presurgical intrinsic fMRI dynamic connectivity properties within executive networks with pre-surgical attention scores enables the prediction of the severity of attentive deficits post-surgery.

How this study might affect research, practice or policy:

The proposed prognostic framework has the potential to significantly impact patient outcome in neuro oncological treatments by informing the planning of tailored interventions, both at the level of pre-treatment and for post-treatment rehabilitation planning.
Possum faeces, the "canary in the coalmine" heralding the emergence of Buruli ulcer in an Australian urban centre.
Authors: McNamara Bridgette J , Cornish Jack , Blasdell Kim Rebecca , Athan Eugene , Clarke Naomi E , Pe Tiffany , Hussain Mohammad Akthar , Muleme Michael , Tay EE Laine , Dunn Michael , Boyd Vicky , Karawita Anjana , O'Brien Daniel P
Published: May 2024

Buruli ulcer (BU) endemicity is changing in Victoria, Australia. This study describes the emergence of BU cases in urban Geelong and examines timing and proximity of human cases to environmentalMycobacterium ulceransDNA detection in possum faeces. From 2011-2022, 80 BU cases were reported, with clusters emerging in new endemic areas from 2019 onwards. Temporal analysis revealed cases occurred nearM. ulceranspositive possum faeces, that preceded human cases by up to 39 months. Median diagnosis delay in these emerging areas was 7 weeks, longer than in established BU endemic areas. The findings emphasise the geographic and temporal association between BU emergence and possum faecalM. ulceranspresence, suggesting monitoring possum faeces as a viable early warning sign of increased BU risk in such areas. This proactive approach can enable early action to improve clinician and community BU awareness, or development of innovative control strategies, to reduce disease burden.
Diffusion Tensor Phenomapping of the Healthy and Pressure-Overloaded Human Heart
Authors: Rock Christopher A. , Chen Y. Iris , Wang Ruopeng , Philip Anne L. , Keil Boris , Weiner Rory B. , Elmariah Sammy , Mekkaoui Choukri , Nguyen Christopher T. , Sosnovik David E.
Published: May 2024

Current techniques to image the microstructure of the heart with diffusion tensor MRI (DTI) are highly under-resolved. We present a technique to improve the spatial resolution of cardiac DTI by almost 10-fold and leverage this to measure local gradients in cardiomyocyte alignment or helix angle (HA). We further introduce a phenomapping approach based on voxel-wise hierarchical clustering of these gradients to identify distinct microstructural microenvironments in the heart. Initial development was performed in healthy volunteers (n=8). Thereader, subjects with severe but well-compensated aortic stenosis (AS, n=10) were compared to age-matched controls (CTL, n=10). Radial HA gradient was significantly reduced in AS (8.0±0.8°/mm vs. 10.2±1.8°/mm, p=0.001) but the other HA gradients did not change significantly. Four distinct microstructural clusters could be idenJfied in both the CTL and AS subjects and did not differ significantly in their properties or distribution. Despite marked hypertrophy, our data suggest that the myocardium in well-compensated AS can maintain its microstructural coherence. The described phenomapping approach can be used to characterize microstructural plasticity and perturbation in any organ system and disease.
Genome Sequencing is Critical for Forecasting Outcomes Following Congenital Cardiac Surgery
Authors: Watkins W. Scott , Hernandez E. Javier , Miller Thomas , Blue Nathan , Zimmerman Raquel , Griffiths Eric , Frise Erwin , Bernstein Daniel , Boskovski Marko , Brueckner Martina , Chung Wendy , Gaynor J. William , Gelb Bruce , Goldmuntz Elizabeth , Gruber Peter , Newburger Jane , Roberts Amy , Morton Sarah , Mayer John , Seidman Christine , Seidman Jonathan , Shen Yufeng , Wagner Michael , Yost H. Joseph , Yandell Mark , Tristani-Firouzi Martin
Published: May 2024

While exome and whole genome sequencing have transformed medicine by elucidating the genetic underpinnings of both rare and common complex disorders, its utility to predict clinical outcomes remains understudied. Here, we used artificial intelligence (AI) technologies to explore the predictive value of genome sequencing in forecasting clinical outcomes following surgery for congenital heart defects (CHD). We report results for a cohort of 2,253 CHD patients from the Pediatric Cardiac Genomics Consortium with a broad range of complex heart defects, pre- and post-operative clinical variables and exome sequencing. Damaging genotypes in chromatin-modifying and cilia-related genes were associated with an elevated risk of adverse post-operative outcomes, including mortality, cardiac arrest and prolonged mechanical ventilation. The impact of damaging genotypes was further amplified in the context of specific CHD phenotypes, surgical complexity and extra-cardiac anomalies. The absence of a damaging genotype in chromatin-modifying and cilia-related genes was also informative, reducing the risk for adverse postoperative outcomes. Thus, genome sequencing enriches the ability to forecast outcomes following congenital cardiac surgery.
Associations between perinatal biomarkers of maternal dairy fat intake and child cognitive development: results from the EDEN mother-child cohort
Authors: Yuan Wen Lun , Armand Martine , Peyre Hugo , Sarté Catherine , Charles Marie Aline , Heude Barbara , Bernard Jonathan Y.
Published: May 2024

Background/Objective

Offspring’s optimal neurodevelopment depends on maternal dietary lipids supply during the perinatal period. Dairy products are an important source of fat in Western diets. This study aimed at examining the associations between maternal dairy fat intake during pregnancy, evaluated through biomarkers in perinatal biofluids (C15:0 and C17:0) and child’s cognitive outcomes.

Subjects/Methods

Participants (N up to 1200) were French mother-child pairs from the EDEN cohort study. Biomarkers were assessed in the following biofluids: maternal red blood cells (RBC) membrane at 24 weeks’ gestation, cord RBC membrane and colostrum. Cognitive outcomes were language abilities scores at ages 2 and 3 years and overall cognitive development scores at ages 3 and 5-6 years. Associations were assessed using multiple linear regression models adjusted for factors related to family socioeconomic context, maternal lifestyle and healthy diet score. Interaction of any breastfeeding duration on the associations with dairy fat biomarkers in colostrum was studied.

Results

Positive associations were observed between levels of C17:0 in cord RBC and C15:0 in maternal RBC with language abilities. In children breastfed for at least 6 months, C15:0 level in colostrum was positively associated with language abilities at age 3 years and overall cognitive development at ages 3 and 5-6 years whereas C17:0 level was only associated with overall cognitive development at age 3 years.

Conclusion

Our results suggest that maternal higher intake of dairy fat during perinatal period could be potentially associated with offspring’s better cognitive development. These pioneering results call for external validation to challenge their causality.
Interactive Segmentation of Lung Tissue and Lung Excursion in Thoracic Dynamic MRI Based on Shape-guided Convolutional Neural Networks
Authors: Xie Lipeng , Udupa Jayaram K. , Tong Yubing , McDonough Joseph M. , Cahill Patrick J. , Anari Jason B. , Torigian Drew A.
Published: May 2024

Purpose

Lung tissue and lung excursion segmentation in thoracic dynamic magnetic resonance imaging (dMRI) is a critical step for quantitative analysis of thoracic structure and function in patients with respiratory disorders such as Thoracic Insufficiency Syndrome (TIS). However, the complex variability of intensity and shape of anatomical structures and the low contrast between the lung and surrounding tissue in MR images seriously hamper the accuracy and robustness of automatic segmentation methods. In this paper, we develop an interactive deep-learning based segmentation system to solve this problem.

Material & Methods

Considering the significant difference in lung morphological characteristics between normal subjects and TIS subjects, we utilized two independent data sets of normal subjects and TIS subjects to train and test our model. 202 dMRI scans from 101 normal pediatric subjects and 92 dMRI scans from 46 TIS pediatric subjects were acquired for this study and were randomly divided into training, validation, and test sets by an approximate ratio of 5:1:4. First, we designed an interactive region of interest (ROI) strategy to detect the lung ROI in dMRI for accelerating the training speed and reducing the negative influence of tissue located far away from the lung on lung segmentation. Second, we utilized a modified 2D U-Net to segment the lung tissue in lung ROIs, in which the adjacent slices are utilized as the input data to take advantage of the spatial information of the lungs. Third, we extracted the lung shell from the lung segmentation results as the shape feature and inputted the lung ROIs with shape feature into another modified 2D U-Net to segment the lung excursion in dMRI. To evaluate the performance of our approach, we computed the Dice coefficient (DC) and max-mean Hausdorff distance (MM-HD) between manual and automatic segmentations. In addition, we utilized Coefficient of Variation (CV) to assess the variability of our method on repeated dMRI scans and the differences of lung tidal volumes computed from the manual and automatic segmentation results.

Results

The proposed system yielded mean Dice coefficients of 0.96±0.02 and 0.89±0.05 for lung segmentation in dMRI of normal subjects and TIS subjects, respectively, demonstrating excellent agreement with manual delineation results. The Coefficient of Variation and p-values show that the estimated lung tidal volumes of our approach are statistically indistinguishable from those derived by manual segmentations.

Conclusions

The proposed approach can be applied to lung tissue and lung excursion segmentation from dynamic MR images with high accuracy and efficiency. The proposed approach has the potential to be utilized in the assessment of patients with TIS via dMRI routinely.
Multi-strain modeling of influenza vaccine effectiveness in older adults and its dependence on antigenic distance
Authors: Urdy Severine , Hanke Matthias , Toledo Ana I. , Ratto Nicolas , Jacob Evgueni , Peyronnet Emmanuel , Gourlet Jean-Baptiste , Chaves Sandra S. , Thommes Edward , Coudeville Laurent , Boissel Jean-Pierre , Courcelles Eulalie , Brueziere Lara
Published: May 2024

Influenza vaccine effectiveness (VE) varies seasonally due to host, virus and vaccine characteristics. To investigate how antigenic matching and dosage impact VE, we developed a mechanistic knowledge-based mathematical model. Immunization with a split vaccine is modeled for exposure to A/H1N1 or A/H3N2 virus strains. The model accounts for cross-reactivity of immune cells elicited during previous immunizations with new antigens. We simulated vaccine effectiveness (sVE) of high dose (HD) versus standard dose (SD) vaccines in the older population, from 2011 to 2022. We find that sVE is highly dependent on antigenic matching and that higher dosage improves immunogenicity, activation and memory formation of immune cells. Across all simulations, the HD vaccine performs better than the SD vaccine, supporting the use of the HD vaccine in the older population. This model could be adapted to predict the impact of alternative virus strain selection on clinical outcomes in future influenza seasons.
Interpretable machine learning model for data driven classification of Oral Health Related Quality of Life in Patients with Type 2 Diabetes Mellitus
Authors: Srivastava Roomani , Murali R , Jain Meena , Jadhav Kshitij
Published: May 2024

Type 2 Diabetes Mellitus(T2DM) is a debilitating condition with a number of complications including those of the oral cavity which can further deteriorate patient’s general and oral health related quality of life (OHRQoL). Machine Learning (ML) can help assign an individual’s propensity to develop poor OHRQoL, given a set of variables, and at the same time identify the most important features contributing to this outcome. Previously inferential statistical methods have attempted to explain this, albeit with limited success. The aim of this cross sectional study is to determine the impact on OHRQoL in T2DM patients, and identify features most likely to be associated with this outcome and to compare ML and DL analytical methods with inferential statistics. Twelve-hundred T2DM patients were subjected to OHRQoL and demographic data questionnaires and WHO Oral Health Assessment form. K-means Clustering was performed to label individuals as having or not having an impact on OHRQoL. Class imbalance was addressed by undersampling of the majority class using informed subset selection. Further, using the collected data as input features we developed ML algorithms (Naive Bayes(NB), Random Forest(RF), Logistic Regression(LR), Kernel Support Vector Machine(SVM) and Artificial Neural Network(ANN)), to accurately classify individuals with or with-out poor oral health related quality of life (OHRQoL) and utilized SHapley Additive exPlanations (SHAP) analysis for feature importance. The best performing model was SVM (AUC=0.983; Sensitivity=1) for classifying the patients into into poor OHRQoL. SHAP values were highest for Age, Prosthetic Need, Tobacco use and years since onset of diabetes. Features closely related to diabetes, that is, periodontal pockets and loss of attachment were not identified as relevant by inferential statistics, but were deemed as important features associated with poor OHRQoL by SHAP analysis.
Hardware-Powered Ultra Low Latency (HarPULL) Brain State Dependent TMS Technology
Authors: Makarova Milana , Fedosov Nikita , Nekrasova Julia , Ossadtchi Alexey
Published: May 2024

Objective Upcoming neuroscientific research will require bidirectional and context dependent interaction with nervous tissue. To facilitate the future neuroscientific discoveries we have created HarPULL, a genuinely real-time system for tracking oscillatory brain state. Approach. The HarPULL technology ensures reliable, accurate and affordable real-time phase and amplitude tracking based on the state-space estimation framework operationalized by Kalman filtering. To avoid data transfer delays and to obtain a truly real-time system the algorithm is implemented on the computational core of an EEG amplifier controlled by a real-time operating system. Systems performance is tested with simulated and real data both online and offline and within a real-time state dependent TMS using a phantom and human subjects. Main results. We show that taking into account the 1/f nature of the brain noise and the use of the steady state colored Kalman filter further improves phase tracking performance in both simulated and real data. We use HarPULL to trigger the TMS device contingent upon the target phase and amplitude combination and demonstrate minimal delay (2 ms) between the occurrence of the predetermined rhythm phase in the cortex and the corresponding magnetic stimulus. Using this setup in the real-time setting we observe a significant modulation of the motor evoked potentials (MEP) by the sensorimotor rhythm state. Finally, we use HarPULL and for the first time obtain phase-dependent muscle cortical representation (MCR) maps in real-time. We show better delineation between the representations of several muscles when the stimulation is performed in the excitation state. Significance. HarPULL is the first truly real-time technology for the instantaneous tracking of the brain rhythmic activity. Our technological solution establishes a nearly instantaneous non-invasive contact with a living brain which has a broad range of clinical, diagnostic and scientific applications.
The Genetic Landscape of Pediatric Postural Orthostatic Tachycardia Syndrome
Authors: Qu Huiqi , Qu Jingchun , Chang Xiao , Williams Nolan , Mentch Frank , Snyder James , Lemma Maria , Nguyen Kenny , Behr Meckenzie , March Michael , Connolly John J , Glessner Joseph T , Boris Jeffrey R , Hakonarson Hakon
Published: May 2024

Background: Postural orthostatic tachycardia syndrome (POTS) is a complex disorder with serious health consequences, while its etiology remains largely elusive. Objective: To investigate the genetic landscape of POTS using genomic approaches in a unique pediatric cohort. Methods: We conducted a combined genome wide genotyping and whole exome sequencing (WES) study to systemically examine the molecular mechanisms of POTS pathogenesis. The patients for were genotyped as two independent cohorts, a family cohort of 100 complete families and a case control cohort of 207 unrelated European cases and 4,063 ethnicity-matched controls. The WES component consisted of a subset of the genotyped subjects, including 87 unrelated European cases and 2,719 unrelated European controls. Results: Due to the heterogeneous phenotype of POTS, unlike traditional phenotypes for association study, it is unlikely that any loci will reach genome-wide significance. Instead, we conducted an over-representation analysis (ORA) by considering all genes that showed nominal significance. The ORA identified gene sets linked to Cell-Cell Junction, Early Estrogen Response, and Substance-Related Disorders, with statistical significance. Moreover, WES revealed 55 genes with genome-wide significance through rare variant burden analysis, harboring 92 variants classified as pathogenic or likely pathogenic by ClinVar. Conclusions and Relevance: This study showcases the complex interplay between common and rare genetic variants in POTS development, marking an pioneering step forward in deciphering its complex etiologies. The insights gained from this research enriches our understanding of POTS, offering new avenues for precise treatment strategies and highlighting the need for continued research in this area.
A qualitative and quantitative analysis of changes in prostate MRI T2WI signals with different abstinence durations
Authors: Ma Wenjun , Ren Baoming , Gao Yanjun , Bai Weixian
Published: May 2024

PURPOSE

To investigate the effect of abstinence duration on image quality of prostate with high-field magnetic resonance imaging(MRI);

MATERIALS AND METHODS

This study included males who underwent prostate MRI in Xi’an No.3 Hospital from November 2021 to November 2022.And these males were divided into two groups according to whether they had ejaculation before MRI examination within 3 days. Two radiologists blinded evaluated the boundary sharpness of the peripheral zone (PZ) and central gland (CG) of prostate using a three-point Likert-scale. The region of interests (ROIs) of the PZ and CG at both sides on the sagittal T2W image were drawn and the signal intensity (SI) of ROIs was measured, then the SI ratio (SIR) was calculated. The Wilcoxon’s test and the independent-samples T test was utilized to compare the differences of the two groups;

RESULTS

A total of fifty young males were included in the study. There were twenty males abstinence more than 3-days, and thirty males were abstinence within 3-days. The qualitative analysis showed that the different structure of prostate in abstinence group was easier to identify than in ejaculation group(P≤0.05). The quantitative analysis showed that the SIR of PZ and CG in the ejaculation group were lower than in the abstinence group (allP≤0.05), and the peripheral zone was significantly lower;

CONCLUSION

In order to make the results more accurate, we suggested that the abstinence should more than 3 days prior to the examination.
The use of artificial intelligence in the diagnosis of carious lesions: Systematic review and meta-analysis
Authors: Arias Pecorari Vanessa Gallego , Almeida Cezário Laís Renata , de Barros Arato Caio Vieira , de Lima Costa Tainá , Cortellazzi Karine Laura , Pecorari Roberto Fiório , Silva José Erasmo
Published: May 2024

Background

The use of Artificial Intelligence (AI) has many applications in the healthcare field. Dental caries is a disease with a prevalence rate of over 50% in Brazil. The diagnosis of caries is usually based on a clinical examination and supplementary tests such as X-rays. The accuracy of a diagnostic test is evaluated by its sensitivity, specificity, and accuracy. Various algorithms and neural network configurations are being used for caries diagnosis.

Objective

This systematic review evaluated the sensitivity, specificity, and accuracy of using deep machine learning through a convolutional neural network in diagnosing dental caries.

Methods

This systematic review was conducted in accordance with the Preferred Reporting Items for Systematic review and Meta-Analyses (PRISMA) 2020 guidelines and registered with Prospero (ID CRD42024411477). We used the PubMed, MEDLINE, and LILACS databases and MeSH and DECs descriptors in the search.

Results

After analyzing the eligibility of the articles, we selected 33 for full-text reading and included 13 in the meta-analysis. We used the sensitivity, specificity, accuracy data, and the number of positive and negative tests to generate a 2x2 table with TP, FP, FN, TN rates, and accuracy. We evaluated the heterogeneity of the SROC curve using the Zhou & Dendurkuri I 2 approach. The results showed that the sensitivity and specificity of the machine learning for detecting dental caries were 0.79 and 0.87, respectively, and the AUC of the SROC curve was 0.885.

Conclusion

The literature presented a variety of convolutional neural networks [CNN] architecture, image acquisition methods, and training volumes, which could lead to heterogeneity. However, the accuracy of using artificial intelligence for caries diagnosis was high, making it an essential tool for dentistry.
Characteristics and needs of Vietnamese technical intern trainees (care workers) in Japan: A qualitative study
Authors: Hara Koji , Yamamura Tomokazu , Ningyi Li , Huong Pham Thu
Published: May 2024

Background

Foreign caregivers are assuming increasing importance in Japan due to a significant shortage of caregivers. To secure and train stable human resources, it is important to understand the needs and challenges of foreign caregivers.

Objective

To identify the needs and challenges of Vietnamese technical interns, the largest group of foreign caregivers in Japan, to facilitate system reforms for foreign caregivers and a more efficient recruitment process.

Methods

A semi-structured interview survey was conducted with 27 Vietnamese technical interns (caregivers). Interview items included reasons for choosing technical internship in Japan, desired length of stay, and expectations in Japan, as well as career advancement after returning home. Descriptive statistics and k-means clustering were used to analyze the data.

Results

Survey results showed that all respondents had made their own decision to come to Japan and wanted to pursue caregiver certification; 44% had also considered other countries apart from Japan; most wanted to stay in Japan for as long as possible; 37% wanted to live in Japan permanently. The k-means method revealed three clusters: Japanophile cluster or those who preferred Japan for its landscape, culture, and national character; Word-of-mouth cluster or those influenced by personal referrals; and Intellectual cluster or those influenced by Japan’s economic development and care levels.

Conclusions

Vietnamese technical interns hoped to study advanced Japanese, become certified care workers, and work in the nursing field after returning to their home country. They also tended to want to stay in Japan for a longer period than that assumed for technical internship programs. Our findings indicate that support for obtaining qualifications, Japanese language skills, and caregiving skills are important to secure stable foreign caregivers. Since each cluster had different backgrounds and reasons, motives, and assumptions for coming to Japan, it is necessary to tailor recruitment, training, and support for each cluster.
An Anthropomorphic Diagnosis System of Pulmonary Nodules using Weak Annotation-Based Deep Learning
Authors: Xie Lipeng , Xu Yongrui , Zheng Mingfeng , Chen Yundi , Sun Min , Archer Michael A. , Wan Yuan , Mao Wenjun , Tong Yubing
Published: May 2024

Purpose

To develop an anthropomorphic diagnosis system of pulmonary nodules (PN) based on Deep learning (DL) that is trained by weak annotation data and has comparable performance to full-annotation based diagnosis systems.

Methods

The proposed system uses deep learning (DL) models to classify PNs (benign vs. malignant) with weak annotations, which eliminates the need for time-consuming and labor-intensive manual annotations of PNs. Moreover, the PN classification networks, augmented with handcrafted shape features acquired through the ball-scale transform technique, demonstrate capability to differentiate PNs with diverse labels, including pure ground-glass opacities, part-solid nodules, and solid nodules.

Results

The experiments were conducted on two lung CT datasets: (1) public LIDC-IDRI dataset with 1,018 subjects, (2) In-house dataset with 2740 subjects. Through 5-fold cross-validation on two datasets, the system achieved the following results: (1) an Area Under Curve (AUC) of 0.938 for PN localization and an AUC of 0.912 for PN differential diagnosis on the LIDC-IDRI dataset of 814 testing cases, (2) an AUC of 0.943 for PN localization and an AUC of 0.815 for PN differential diagnosis on the in-house dataset of 822 testing cases. These results demonstrate comparable performance to full annotation-based diagnosis systems.

Conclusions

Our system can efficiently localize and differentially diagnose PNs even in resource-limited environments with good robustness across different grade and morphology sub-groups in the presence of deviations due to the size, shape, and texture of the nodule, indicating its potential for future clinical translation.

An anthropomorphic diagnosis system of pulmonary nodules (PN) based on deep learning and weak annotation was found to achieve comparable performance to full-annotation dataset-based diagnosis systems, significantly reducing the time and the cost associated with the annotation.

Key Points

A fully automatic system for the diagnosis of PN in CT scans using a suitable deep learning model and weak annotations was developed to achieve comparable performance (AUC = 0.938 for PN localization, AUC = 0.912 for PN differential diagnosis) with the full-annotation based deep learning models, reducing around 30%∼80% of annotation time for the experts.

The integration of the hand-crafted feature acquired from human experts (natural intelligence) into the deep learning networks and the fusion of the classification results of multi-scale networks can efficiently improve the PN classification performance across different diameters and sub-groups of the nodule.
A β-Galactosidase acting on unique galactosides: the structure and function of a β-1,2-galactosidase fromBacteroides xylanisolvens, an intestinal bacterium
Authors: Nakazawa Yutaka , Kageyama Masumi , Matsuzawa Tomohiko , Liang Ziqin , Kobayashi Kaito , Shimizu Hisaka , Masuhiro Miho , Motouchi Sei , Kumano Saika , Tanaka Nobukiyo , Kuramochi Kouji , Nakai Hiroyuki , Taguchi Hayao , Nakajima Masahiro
Published: May 2024

Galactosides are major carbohydrates that are found in plant cell walls and various prebiotic oligosaccharides. Studying the detailed biochemical functions of β-galactosidases in degrading these carbohydrates is important. In particular, identifying β-galactosidases with new substrate specificities could help in the production of potentially beneficial oligosaccharides. In this study, we identified a β-galactosidase with novel substrate specificity fromBacteroides xylanisolvens, an intestinal bacterium. The enzyme did not show hydrolytic activity toward natural β-galactosides during the first screening. However, when α-D-galactosyl fluoride (α-GalF) as a donor substrate and galactose or D-fucose as an acceptor substrate were incubated with a nucleophile mutant, reaction products were detected. The galactobiose produced from the α-GalF and galactose was identified as β-1,2-galactobiose using NMR. Kinetic analysis revealed that this enzyme effectively hydrolyzed β-1,2-galactobiose and β-1,2-galactotriose. In the complex structure with methyl β-galactopyranose as a ligand, the ligand is only located at subsite +1. The 2-hydroxy group and the anomeric methyl group of methyl β-galactopyranose faces in the direction of subsite −1 and the solvent, respectively. This observation is consistent with the substrate specificity of the enzyme regarding linkage position and chain length. Overall, we concluded that the enzyme is a β-galactosidase acting on β-1,2-galactooligosaccharides.

Synopsis

The structural and functional analysis of β-galactosidase from an intestinal bacterium led to the discovery of a new β-galactosidase hydrolyzing unique β-1,2-galactooligosaccharides.
Full factorial construction of synthetic microbial communities
Authors: Diaz-Colunga Juan , Catalan Pablo , San Roman Magdalena , Arrabal Andrea , Sanchez Alvaro
Published: May 2024

Constructing combinatorially complete species assemblages is often necessary to dissect the complexity of microbial interactions and to find optimal microbial consortia. At the moment, this is accomplished through either painstaking, labor intensive liquid handling procedures, or through the use of state-of-the-art microfluidic devices. Here we present a simple, rapid, low-cost, and highly accessible liquid handling methodology for assembling all possible combinations of a library of microbial strains, which can be implemented with basic laboratory equipment. To demonstrate the usefulness of this methodology, we construct a combinatorially complete set of consortia from a library of eightPseudomonas aeruginosastrains, and empirically measure the community-function landscape of biomass productivity, identify the highest yield community, and dissect the interactions that lead to its optimal function. This easy to implement, inexpensive methodology will make the assembly of combinatorially complete microbial consortia easily accessible for all laboratories.
Large donor CRISPR for whole-CDS replacement of cell adhesion molecule LRRTM2
Authors: Pollitt Stephanie L , Levy Aaron D , Anderson Michael C , Blanpied Thomas A
Published: May 2024

The cell adhesion molecule LRRTM2 is crucial for synapse development and function. However, our understanding of its endogenous trafficking has been limited due to difficulties in manipulating its coding sequence (CDS) using standard genome editing techniques. We instead replaced the whole LRRTM2 CDS by adapting the recent CRISPR method Targeted Knock-in using Two Guides (TKIT), enabling complete control of LRRTM2. In primary rat hippocampal cultures, N-terminally tagged, endogenous LRRTM2 was found in 80% of synapses, and synaptic LRRTM2 content correlated with PSD-95 and AMPAR levels. LRRTM2 was also enriched with AMPARs outside synapses, demonstrating the sensitivity of this method to detect relevant new biology. Finally, we leveraged total genomic control to increase the synaptic levels of LRRTM2 via simultaneous mutation of its C-terminal domain, which did not correspondingly increase AMPAR enrichment. The coding region of thousands of genes span lengths suitable for whole-CDS replacement, suggesting this simple approach will enable straightforward structure-function analysis in diverse cellular systems.
Induced systemic resistance by the root colonization ofTrichoderma atrovirideis independent from the chitin-mediated signaling pathway in Arabidopsis
Authors: Sakai Ayae , Yamagata Hisako , Naito Keigo , Tominaga Takaya , Ifuku Shinsuke , Kaminaka Hironori
Published: May 2024

Beneficial root endophytic fungi induce systemic responses, growth promotion, and induced systemic resistance (ISR) in the colonized host plants. Soil application of chitin, a main component of fungal cell walls, also systemically induces disease resistance. Thus, chitin recognition and its downstream signaling pathway are supposed to mediate ISR triggered by beneficial fungi colonizing the root. This study compared systemic disease resistance and transcriptional responses induced byTrichoderma, a representative beneficial root endophytic fungus, and chitin in Arabidopsis. A significant plant growth promotion was observed under root colonization by the three tested beneficial fungi,Trichoderma atroviride,Serendipita indica, andS. vermifera. Still, onlyT. atrovirideandS. indicatriggered ISR against the necrotrophic fungal pathogenAlternaria brassicicola. Induced systemic resistance triggered byT. atroviridewas compromised in the chitin-receptor mutant, while systemic resistance caused by soil application of chitin was not. Transcriptome analysis demonstrated that the chitin-regulated genes are mostly shared with those regulated byT. atroviride, but many of the latter were specific. However, the commonly enriched gene ontologies for those regulated genes indicated thatT. atrovirideinoculation and chitin application systemically control similar transcriptional responses, mainly associated with cell wall functions. Taken together,Trichodermacould trigger ISR primarily independently from the chitin-mediated signaling pathway; however, chitin andTrichodermawould systemically induce similar cellular functions in ISR aboveground.
Label-free Assessment of Complement-Dependent Cytotoxicity of Therapeutic Antibodies via a Whole-Cell MALDI Mass Spectrometry Bioassay
Authors: Schmidt Stefan , Geisel Alexander , Enzlein Thomas , Fröhlich Björn C. , Pritchett Louise , Verneret Melanie , Graf Christian , Hopf Carsten
Published: May 2024

Potency assessment of monoclonal antibodies or corresponding biosimilars in cell-based assays is an essential prerequisite in biopharmaceutical research and development. However, cellular bioassays are still subject to limitations in sample throughput, speed, and often need costly reagents or labels as they are based on an indirect readout by luminescence or fluorescence. In contrast, whole-cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry (MS) has emerged as a direct, fast and label-free technology for functional drug screening being able to unravel the molecular complexity of cellular response to pharmaceutical reagents. However, this approach has not yet been used for cellular testing of biologicals. In this study, we have conceived, developed and bench-marked a label-free MALDI-MS based cell bioassay workflow for the functional assessment of complement-dependent cytotoxicity (CDC) of Rituximab antibody. By computational evaluation of response profiles followed by subsequentm/zfeature annotation via fragmentation analysis and trapped ion mobility MS, we identified adenosine triphosphate and glutathione as readily MS-assessable metabolite markers for CDC and demonstrate that robust concentration-response characteristics can be obtained by MALDI-TOF MS. Statistical assay performance indicators suggest that whole-cell MALDI-TOF MS could complement the toolbox for functional cellular testing of biopharmaceuticals.
Paralogue-selective degradation of the lysine acetyltransferase EP300
Authors: Chen Xuemin , Crawford McKenna C. , Xiong Ying , Shaik Anver Basha , Suazo Kiall F. , Penkalapati Manini S. , Williams Joycelyn H. , Andressen Thorkell , Swenson Rolf E. , Meier Jordan L.
Published: May 2024

The transcriptional coactivators EP300 and CREBBP are critical regulators of gene expression that share high sequence identity but exhibit non-redundant functions in basal and pathological contexts. Here, we report the development of a bifunctional small molecule, MC-1, capable of selectively degrading EP300 over CREBBP. Using a potent aminopyridine-based inhibitor of the EP300/CREBBP catalytic domain in combination with a VHL ligand, we demonstrate that MC-1 preferentially degrades EP300 in a proteasome-dependent manner. Mechanistic studies reveal that selective degradation cannot be predicted solely by target engagement or ternary complex formation, suggesting additional factors govern paralogue-specific degradation. MC-1 inhibits cell proliferation in a subset of cancer cell lines and provides a new tool to investigate the non-catalytic functions of EP300 and CREBBP. Our findings expand the repertoire of EP300/CREBBP-targeting chemical probes and offer insights into the determinants of selective degradation of highly homologous proteins.
A heterogeneous population code at the first synapse of vision
Authors: Herzog Tessa , Yoshimatsu Takeshi , Moya-Diaz Jose , James Ben , Lagnado Leon , Baden Tom
Published: May 2024

Vision begins when photoreceptors convert light fluctuations into temporal patterns of glutamate release that drive the retinal network. The input-output relation at this first stage has not been systematically measuredin vivoso it is not known how it operates across a photoreceptor population. Using kHz-rate glutamate imaging in zebrafish, we find that individual red cones encode visual stimuli with high reliability and time-precision, but routinely vary in sensitivity to luminance, contrast, and frequency across the population. Variations in input-output relations are generated by feedback from the horizontal cell network that effectively decorrelate feature representation. A model capturing how zebrafish sample their visual environment indicates that this heterogeneity expands the dynamic range of the retina to improve the coding of natural scenes. Moreover, we find that different kinetic release components are used to encode distinct stimulus features in parallel: sustained release linearly encodes low amplitude light and dark contrasts, but transient release encodes large amplitude dark contrasts. Together, this study reveals an unprecedented degree of functional heterogeneity within same-type photoreceptors and illustrates how separation of different visual features begins in the first synapse in vision.
A temperature-sensitive and interferon-silent Sendai virus vector for CRISPR-Cas9 delivery and gene editing in primary human cells
Authors: Stevens Christian S , Carmichael Jillian , Watkinson Ruth , Kowdle Shreyas , Reis Rebecca A , Hamane Kory , Jang Jason , Park Arnold , Pernet Olivier , Khamaikawin Wannisa , Hong Patrick , Thibault Patricia , Gowlikar Aditya , An Dong Sung , Lee Benhur
Published: May 2024

The transformative potential of gene editing technologies hinges on the development of safe and effective delivery methods. In this study, we developed a temperature-sensitive and interferon-silent Sendai virus (ts SeV) as a novel delivery vector for CRISPR-Cas9 and for efficient gene editing in sensitive human cell types without inducing IFN responses. ts SeV demonstrates unprecedented transduction efficiency in human CD34+ hematopoietic stem and progenitor cells (HSPCs) including transduction of the CD34+/CD38-/CD45RA-/CD90+(Thy1+)/CD49fhighstem cell enriched subpopulation. The frequency ofCCR5editing exceeded 90% and bi-allelicCCR5editing exceeded 70% resulting in significant inhibition of HIV-1 infection in primary human CD14+ monocytes. These results demonstrate the potential of the ts SeV platform as a safe, efficient, and flexible addition to the current gene-editing tool delivery methods, which may help to further expand the possibilities in personalized medicine and the treatment of genetic disorders.
The Ccm3-GckIII signaling axis regulates Rab11-dependent recycling to the apical compartment
Authors: Burguete Alondra S. , Song Yanjun , Ghabrial Amin S.
Published: May 2024

Kinase cascades underlie many signaling pathways and are key regulators of development and morphogenesis. We have characterized a Hippo-like kinase cascade consisting of Thousand and One kinase (Tao), Germinal Center Kinase III (GckIII/Wheezy), and Tricornered (Trc) that plays an essential role in morphogenesis of tracheal terminal cell tubes inDrosophila. In this cascade, GckIII is the central kinase and is thought to act together with its binding partner, Cerebral Cavernous Malformations 3 (Ccm3). As suggested by its name,Drosophila Ccm3is the ortholog of a human vascular disease gene. As such, defining the Ccm3 pathway is critical to understanding both normal development and disease. Here we generate and characterize a null allele ofCcm3inDrosophila. We uncover a maternal contribution ofCcm3to embryonic development, show that maternal/zygotic null embryos have defective multicellular tracheal tubes, and that tracheal terminal cells derived from zygotic clones that also lack maternalCcm3, show fully penetrant tube dilation defects identical to those we previously described for other pathway genes. We show that wildtype Ccm3 colocalizes with p-GckIII during early embryogenesis, and that in larval terminal cells, is found in the nucleus as well as associated with the apical membrane. We further demonstrate thatMouse protein 25 (Mo25),known to encode a protein that binds and stabilizes GckIII proteins in the active conformation, is required to preventCcm3-like tube dilations, showing that Mo25 and Ccm3, together with Tao, are required to fully activate GckIII, which directly phosphorylates and activates Tricornered (Trc). We show that this Ccm3 signaling cassette operates in other epithelial tissues such as the wing, and in non-epithelial tissues such as motor neurons. Lastly, we define a role of Ccm3-GckIII signaling in the distribution of active Rab11, leading us to propose that persistent local Rab11 activity results in elevated recycling of membrane and apical determinants to the apical domain, and consequent dilation of tubes. We validate this model by showing that loss of Rab11 activity ameliorates the tube dilation defects of pathway mutants.