Modeling and predicting individual variation in COVID-19 vaccine-elicited antibody response in the general population

As we learned during the COVID-19 pandemic, vaccines are one of the most important tools in infectious disease control. To date, an unprecedentedly large volume of high-quality data on COVID-19 vaccinations have been accumulated. For preparedness in future pandemics beyond COVID-19, these valuable datasets should be analyzed to best shape an effective vaccination strategy. We are collecting longitudinal data from a community-based cohort in Fukushima, Japan, that consists of 2,407 individuals who underwent serum sampling two or three times after a two-dose vaccination with either BNT162b2 or mRNA-1273. Using the individually reconstructed time courses of the vaccine-elicited antibody response based on mathematical modeling, we first identified basic demographic and health information that contributed to the main features of the antibody dynamics, i.e., the peak, the duration, and the area under the curve. We showed that these three features of antibody dynamics were partially explained by underlying medical conditions, adverse reactions to vaccinations, and medications, consistent with the findings of previous studies. We then applied to these factors a recently proposed computational method to optimally fit an "antibody score", which resulted in an integer-based score that can be used as a basis for identifying individuals with higher or lower antibody titers from basic demographic and health information. The score can be easily calculated by individuals themselves or by medical practitioners. Although the sensitivity of this score is currently not very high, in the future, as more data become available, it has the potential to identify vulnerable populations and encourage them to get booster vaccinations. Our mathematical model can be extended to any kind of vaccination and therefore can form a basis for policy decisions regarding the distribution of booster vaccines to strengthen immunity in future pandemics.

Aorta and main pulmonary artery segmentation using stacked U-Net and localization on non-contrast-enhanced computed tomography images

BACKGROUND

The contact between the aorta, main pulmonary artery (MPA), main pulmonary vein, vena cava (VC), and esophagus affects segmentation of the aorta and MPA in non-contrast-enhanced computed tomography (NCE-CT) images.

PURPOSE

A two-stage stacked U-Net and localization of the aorta and MPA were developed for the segmentation of the aorta and MPA in NCE-CT images.

METHODS

Normal-dose NCE-CT images of 24 subjects with chronic thromboembolic pulmonary hypertension (CTEPH) and low-dose NCE-CT images of 100 subjects without CTEPH were used in this study. The aorta is in contact with the ascending aorta (AA) and MPA, the AA with the VC, the aortic arch (AR) with the VC and esophagus, and the descending aorta (DA) with the esophagus. These contact surfaces were manually annotated. The contact surfaces were quantified using the contact surface ratio (CSR). Segmentation of the aorta and MPA in NCE-CT images was performed by localization of the aorta and MPA and a two-stage stacked U-Net. Localization was performed by extracting and processing the trachea and main bronchus. The first stage of the stacked U-Net consisted of a 2D U-Net, 2D U-Net with a pre-trained VGG-16 encoder, and 2D attention U-Net. The second stage consisted of a 3D U-Net with four input channels: the CT volume and three segmentation results of the first stage. The model was trained and tested using 10-fold cross-validation. Segmentation of the entire volume was evaluated using the Dice similarity coefficient (DSC). Segmentation of the contact area was also assessed using the mean surface distance (MSD). The statistical analysis of the evaluation underwent a multi-comparison correction. CTEPH and non-CTEPH cases were classified based on the vessel diameters measured from the segmented MPA.

RESULTS

For the noncontact surfaces of AA, the MSD of stacked U-Net was 0.31 ± 0.10 mm (p < 0.05) and 0.32 ± 0.13 mm (p < 0.05) for non-CTEPH and CTEPH cases, respectively. For contact surfaces with a CSR of 0.4 or greater in AA, the MSD was 0.52 ± 0.23 mm (p < 0.05), and 0.68 ± 0.29 mm (p > 0.05) for non-CTEPH and CTEPH cases, respectively. MSDs were lower than those of 2D and 3D U-Nets for contact and noncontact surfaces; moreover, MSDs increased slightly with larger CSRs. However, the stacked U-Net achieved MSDs of approximately 1 pixel for a wide contact surface. The area under the receiver operating characteristic curve for CTEPH and non-CTEPH classification using the right main pulmonary artery (RMPA) diameter was 0.97 (95% confidence interval [CI]: 0.94-1.00).

CONCLUSIONS

Segmentation of the aorta and MPA on NCE-CT images were affected by vascular and esophageal contact. The application of stacked U-Net and localization techniques for non-CTEPH and CTEPH cases mitigated the impact of contact, suggesting its potential for diagnosing CTEPH.

High-Throughput 3D Imaging Flow Cytometry of Suspended Adherent 3D Cell Cultures

3D cell cultures are indispensable in recapitulating in vivo environments. Among the many 3D culture methods, culturing adherent cells on hydrogel beads to form spheroid-like structures is a powerful strategy for maintaining high cell viability and functions in the adherent states. However, high-throughput, scalable technologies for 3D imaging of individual cells cultured on the hydrogel scaffolds are lacking. This study reports the development of a high throughput, scalable 3D imaging flow cytometry platform for analyzing spheroid models. This platform is realized by integrating a single objective fluorescence light-sheet microscopy with a microfluidic device that combines hydrodynamic and acoustofluidic focusing techniques. This integration enabled unprecedentedly high-throughput and scalable optofluidic 3D imaging, processing 1310 spheroids consisting of 28 117 cells min-1 . The large dataset obtained enables precise quantification and comparison of the nuclear morphology of adhering and suspended cells, revealing that the adhering cells have smaller nuclei with less rounded surfaces. This platform's high throughput, robustness, and precision for analyzing the morphology of subcellular structures in 3D culture models hold promising potential for various biomedical analyses, including image-based phenotypic screening of drugs with spheroids or organoids.

Sparse-firing regularization methods for spiking neural networks with time-to-first-spike coding

The training of multilayer spiking neural networks (SNNs) using the error backpropagation algorithm has made significant progress in recent years. Among the various training schemes, the error backpropagation method that directly uses the firing time of neurons has attracted considerable attention because it can realize ideal temporal coding. This method uses time-to-first-spike (TTFS) coding, in which each neuron fires at most once, and this restriction on the number of firings enables information to be processed at a very low firing frequency. This low firing frequency increases the energy efficiency of information processing in SNNs. However, only an upper limit has been provided for TTFS-coded SNNs, and the information-processing capability of SNNs at lower firing frequencies has not been fully investigated. In this paper, we propose two spike-timing-based sparse-firing (SSR) regularization methods to further reduce the firing frequency of TTFS-coded SNNs. Both methods are characterized by the fact that they only require information about the firing timing and associated weights. The effects of these regularization methods were investigated on the MNIST, Fashion-MNIST, and CIFAR-10 datasets using multilayer perceptron networks and convolutional neural network structures.

Computation harvesting from nature dynamics for predicting wind speed and direction

Natural phenomena generate complex dynamics because of nonlinear interactions among their components. The dynamics can be exploited as a kind of computational resource. For example, in the framework of natural computation, various natural phenomena such as quantum mechanics and cellular dynamics are used to realize general purpose calculations or logical operations. In recent years, simple collection of such nature dynamics has become possible in a sensor-rich society. For example, images of plant movement that have been captured indirectly by a surveillance camera can be regarded as sensor outputs reflecting the state of the wind striking the plant. Herein, based on ideas of physical reservoir computing, we present a methodology for wind speed and direction estimation from naturally occurring sensors in movies. Then we demonstrate its effectiveness through experimentation. Specifically using the proposed methodology, we investigate the computational capability of the nature dynamics, revealing its high robustness and generalization performance for computation.

Identification of In-Droplet Multicellular Communities by Light-Induced Combinatorial DNA Barcoding

A microdroplet co-culture system is useful for the parallel assessment of numerous possible cell-cell interactions by generating isolated subcommunities from a pool of heterogeneous cells. However, the integration of single-cell sequencing into such analysis has been limited due to the lack of effective molecular identifiers for each in-droplet subcommunity. Herein, we present a strategy for generating in-droplet subcommunity identifiers using DNA-functionalized microparticles encapsulated within microdroplets. These microparticles serve as initial information carriers, where their combinations act as distinct identifiers for in-droplet subcommunity. Upon optical trigger, DNA barcoding molecules encoding the microparticle information are once released in the microdroplets and then tag cell membranes. The tagged DNA molecules then serve as a second information carrier readable by single-cell sequencing to reconstitute the community in silico in the single-cell RNA sequencing data space.

TP53 mutations in Romanian patients with colorectal cancer

BACKGROUND

Colorectal cancer (CRC) has been ranked as the second most deadly cancer and the third most diagnosed cancer cases for the year 2020. Specifically for Romania, the number of CRC-related deaths in 2019 was estimated at 6307 people, with a standardized mortality rate of 33.8 per 100,000 inhabitants. Although the tumor protein 53 (TP53) gene is intensively studied, there are few data on TP53 mutations in Romanian CRC. Furthermore, since genetic alterations may show geographical differences, our study aimed to analyze the clinical status and TP53 somatic variation in Romanian CRC patients.

SUBJECTS AND METHODS

DNA from 40 randomly selected cases of CRC was extracted from formalin-fixed paraffin-embedded tissues and sequenced using direct Sanger sequencing techniques, and variants were annotated according to the recommendations of the Human Genome Variation Society. Novel variants were analyzed using MutationTaster2021 to predict their effects.

RESULTS

The mean age was 63.6 years (range 33-85 years) with a male to female ratio of 2.3. More than 45% (18/40) had an advanced cancer stage (≥ stage III). Mutations were found in 21/40 cases (52.5%), with one case having two mutations, giving a total of twenty-two mutations in the TP53 coding DNA. These mutations include 3 (13.6%) insertion-deletion mutations, two of which are novel frameshift mutations: c.165delT (in exon 4) and c.928_935dup (in exon 9), both of which are predicted to lead to nonsense-mediated mRNA decay and are classified as deleterious. The remaining 19 (86.36%) were substitution mutations: 1 nonsense and 18 (81.8%) missense mutations, with G > A (n = 7/19; 36.8%) and C > T (n = 6/19; 31.5%) transitions being the most common. The G > T transversion was found in 21.05% (4/19) of the substitution mutations.

CONCLUSION

We have described two novel frameshift mutations in TP53. The discovery of novel mutations following the efforts of The Cancer Genome Atlas and other large-scale cancer genome sequencing projects may be further evidence of the heterogeneous nature of mutations in cancer and may indicate that the identification of carcinogenic mutations is not yet saturated. Further sequencing is therefore needed, especially in less studied populations. Importantly, consideration of their geographical environment will shed light on population-specific carcinogenesis.

Conditional Knockout of Bmal1 in Corticotropin-Releasing Factor Neurons Does Not Alter Sleep–Wake Rhythm in Mice

Sleep and wakefulness are regulated by both the homeostatic mechanism and circadian clock. In mammals, the central circadian clock, the suprachiasmatic nucleus, in the hypothalamus plays a crucial role in the timing of physiology and behavior. Recently, we found that the circadian regulation of wakefulness was transmitted via corticotropin-releasing factor (CRF) neurons in the paraventricular nucleus of the hypothalamus to orexin neurons in the lateral hypothalamus. However, it is still unclear how the molecular clock in the CRF neurons contributes to the regulation of sleep and wakefulness. In the present study, we established CRF neuron-specific Bmal1-deficient mice and measured locomotor activity or electroencephalography and electromyography. We found that these mice showed normal circadian locomotor activity rhythms in both light–dark cycle and constant darkness. Furthermore, they showed normal daily patterns of sleep and wakefulness. These results suggest that Bmal1 in CRF neurons has no effect on either circadian locomotor activity or sleep and wakefulness.

Mammalian antiviral systems directed by small RNA

There are strong incentives for human populations to develop antiviral systems. Similarly, genomes that encode antiviral systems have had strong selective advantages. Protein-guided immune systems, which have been well studied in mammals, are necessary for survival in our virus-laden environments. Small RNA–directed antiviral immune systems suppress invasion of cells by non-self genetic material via complementary base pairing with target sequences. These RNA silencing-dependent systems operate in diverse organisms. In mammals, there is strong evidence that microRNAs (miRNAs) regulate endogenous genes important for antiviral immunity, and emerging evidence that virus-derived nucleic acids can be directly targeted by small interfering RNAs (siRNAs), PIWI-interacting RNAs (piRNAs), and transfer RNAs (tRNAs) for protection in some contexts. In this review, we summarize current knowledge of the antiviral functions of each of these small RNA types and consider their conceptual and mechanistic overlap with innate and adaptive protein-guided immunity, including mammalian antiviral cytokines, as well as the prokaryotic RNA-guided immune system, CRISPR. In light of recent successes in delivery of RNA for antiviral purposes, most notably for vaccination, we discuss the potential for development of small noncoding RNA–directed antiviral therapeutics and prophylactics.

Viruses are all around us and are likely inside some of the reader’s cells at this moment. Organisms are accommodated to this reality and encode various immune systems to limit virus replication. In mammals, the best studied immune systems are directed by proteins that specifically recognize viruses. These include diverse antibodies and T cell receptors, which recognize viral proteins, and pattern recognition receptors, some of which can recognize viral nucleic acids. In other organisms, including bacteria, immune systems directed by small RNAs are also well known; spacer-derived guide RNAs in CRISPR/Cas immune systems are one prominent example. The small RNAs directing these systems derive their specificity via complementary base pairing with their targets, which include both host and viral nucleic acids. Rather than having “traded in” these systems for more advanced protein-directed systems, increasing evidence supports the perspective that small RNA–directed immune systems remain active in mammalian antiviral immunity in some contexts. Here, we review what is known so far about the emerging roles of mammalian siRNAs, miRNAs, piRNAs, and tRNAs in directing immunity to viruses.

Impact of sleep on the microbiome of oral biofilms

Dysbiosis of the oral microbiome is associated with diseases such as periodontitis and dental caries. Because the bacterial counts in saliva increase markedly during sleep, it is broadly accepted that the mouth should be cleaned before sleep to help prevent these diseases. However, this practice does not consider oral biofilms, including the dental biofilm. This study aimed to investigate sleep-related changes in the microbiome of oral biofilms by using 16S rRNA gene sequence analysis. Two experimental schedules—post-sleep and pre-sleep biofilm collection—were applied to 10 healthy subjects. Subjects had their teeth and oral mucosa professionally cleaned 7 days and 24 h before sample collection. Samples were collected from several locations in the oral cavity: the buccal mucosa, hard palate, tongue dorsum, gingival mucosa, tooth surface, and saliva. Prevotella and Corynebacterium had higher relative abundance on awakening than before sleep in all locations of the oral cavity, whereas fluctuations in Rothia levels differed depending on location. The microbiome in different locations in the oral cavity is affected by sleep, and changes in the microbiome composition depend on characteristics of the surfaces on which oral biofilms form.

Effect of advanced periodontal self-care in patients with early-stage periodontal diseases on endothelial function: An open-label, randomized controlled trial

Although a significant association between periodontal disease and atherosclerotic cardiovascular disease has been reported, their cause-to-effect relationship remains controversial. This randomized controlled clinical trial aimed to investigate the effect of advanced self-care on atherosclerotic cardiovascular disease-related vascular function markers flow-mediated brachial artery dilatation (FMD) and serum asymmetric dimethylarginine (ADMA) level in patients with early-stage periodontal disease. The study was designed as a parallel group, 3-month follow-up, open-label, randomized controlled trial. The control group received standard care for periodontal diseases, whereas the test group additionally applied disinfectant using a custom-fabricated prescription tray for advanced self-care twice a day. Overall, 110 patients provided data for FMD and serum ADMA level. No significant improvements in FMD were observed in the control (mean increase, −0.1%; 95% confidence interval [CI], −1.0–0.8; P = 0.805) or test (mean increase, −0.3%; 95% CI, −1.1–0.4; P = 0.398) group. No significant changes in serum ADMA levels were observed (mean reduction, 0.01 μmol/L; 95% CI, −0.00–0.02; P = 0.366 and mean reduction, 0.00 μmol/L; 95% CI, −0.01–0.01; P = 0.349, respectively). No significant between-group differences were found in FMD (mean difference, −0.2%; 95% CI, −1.4–0.9; p = 0.708) or serum ADMA levels (mean difference, 0.01 nmol/L; 95% CI, −0.00–0.03; p = 0.122). Significant improvements in the average probing pocket depth were observed in the control and test groups. The bleeding on probing score in the test group was significantly reduced, while that in the control group was reduced, although not significantly. Periodontal care for a 3-month duration did not provide better endothelial function although improvements of periodontal status in patients with early-stage periodontal diseases. This trial is registered in UMIN Clinical Trials Registry (www.umin.ac.jp/ctr/; ID: UMIN000023395).

Revisiting the guidelines for ending isolation for COVID-19 patients

Since the start of the COVID-19 pandemic, two mainstream guidelines for defining when to end the isolation of SARS-CoV-2-infected individuals have been in use: the one-size-fits-all approach (i.e. patients are isolated for a fixed number of days) and the personalized approach (i.e. based on repeated testing of isolated patients). We use a mathematical framework to model within-host viral dynamics and test different criteria for ending isolation. By considering a fixed time of 10 days since symptom onset as the criterion for ending isolation, we estimated that the risk of releasing an individual who is still infectious is low (0-6.6%). However, this policy entails lengthy unnecessary isolations (4.8-8.3 days). In contrast, by using a personalized strategy, similar low risks can be reached with shorter prolonged isolations. The obtained findings provide a scientific rationale for policies on ending the isolation of SARS-CoV-2-infected individuals.

A wearable light-touch contact device for human balance support

There is an urgent need for the development of ways to address the major issue of falls among today's globally aging population. The authors here outline a new approach referred to as virtual light-touch contact to mitigate postural sway during ambulatory and stationary periods, and propose a wearable light-touch (WLT) system featuring a virtual partition around the user that allows determination of virtual forces resulting from related contact. The data produced are used to create vibrotactile fingertip feedback, which supports comprehensive perception of the partition. Non-impaired subjects were recruited to support evaluation of the prototype system (incorporating tactile stimulation and motion-capture technology), with outcomes showing successful mitigation of postural sway in a heel-to-toe tandem stance. Research performed with 150 able-bodied volunteers to validate the performance of the new set-up (incorporating an acceleration sensor and a voice coil motor to render the light-touch effect) suggested that the proposed WLT approach supports human balance on a level comparable to that of the light-touch effect.

The mammalian circadian pacemaker regulates wakefulness via CRF neurons in the paraventricular nucleus of the hypothalamus

In mammals, the daily rhythms of physiological functions are timed by the central circadian clock located in the suprachiasmatic nucleus (SCN) of the hypothalamus. Although the importance of the SCN for the regulation of sleep/wakefulness has been suggested, little is known about the neuronal projections from the SCN, which regulate sleep/wakefulness. Here, we show that corticotropin-releasing factor (CRF) neurons in the hypothalamic paraventricular nucleus mediate circadian rhythms in the SCN and regulate wakefulness. Optogenetic activation of CRF neurons promoted wakefulness through orexin/hypocretin neurons in the lateral hypothalamus. In vivo Ca²⁺ recording showed that CRF neurons were active at the initiation of wakefulness. Furthermore, chemogenetic suppression and ablation of CRF neurons decreased locomotor activity and time in wakefulness. Last, a combination of optical manipulation and Ca²⁺ imaging revealed that neuronal activity of CRF neurons was negatively regulated by GABAergic neurons in the SCN. Our findings provide notable insights into circadian regulation of sleep/wakefulness in mammals.

Water demand management: Visualising a public good

Recent studies on water demand management show that providing visual information on water usage along with social comparisons with neighbouring households resulted in more efficient water usage. However, social comparisons can be discomforting for participants, especially in the case of downward or negative evaluations. To avoid this, some studies promote the use of social identity, a social norm approach that avoids comparisons. Past studies using social comparison used infographics, whereas other study types have used only textual (non-graphic) information. Therefore, in this study, we created a visualisation of water usage to highlight the importance of water as a shared resource, that is, as a public good, and feedback over six months according to the participants’ water usage. A difference-in-difference analysis indicated that the feedback was marginally significant in decreasing water consumption immediately and continuously, especially for the middle and low use households, during the summer months, which is a period of perceived water shortage. From the questionnaire survey, we found that households felt that they determined their water usage based on their preference and were satisfied with the outcome.

RANKL biology: bone metabolism, the immune system, and beyond

Receptor activator of NF-κB (RANK) ligand (RANKL) induces the differentiation of monocyte/macrophage-lineage cells into the bone-resorbing cells called osteoclasts. Because abnormalities in RANKL, its signaling receptor RANK, or decoy receptor osteoprotegerin (OPG) lead to bone diseases such as osteopetrosis, the RANKL/RANK/OPG system is essential for bone resorption. RANKL was first discovered as a T cell-derived activator of dendritic cells (DCs) and has many functions in the immune system, including organogenesis, cellular development. The essentiality of RANKL in the bone and the immune systems lies at the root of the field of "osteoimmunology." Furthermore, this cytokine functions beyond the domains of bone metabolism and the immune system, e.g., mammary gland and hair follicle formation, body temperature regulation, muscle metabolism, and tumor development. In this review, we will summarize the current understanding of the functions of the RANKL/RANK/OPG system in biological processes.

Synthetic "smart gel" provides glucose-responsive insulin delivery in diabetic mice

Although previous studies have attempted to create "electronics-free" insulin delivery systems using glucose oxidase and sugar-binding lectins as a glucose-sensing mechanism, no successful clinical translation has hitherto been made. These protein-based materials are intolerant of long-term use and storage because of their denaturing and/or cytotoxic properties. We provide a solution by designing a protein-free and totally synthetic material-based approach. Capitalizing on the sugar-responsive properties of boronic acid, we have established a synthetic polymer gel-based insulin delivery device confined within a single catheter, which exhibits an artificial pancreas-like function in vivo. Subcutaneous implantation of the device in healthy and diabetic mice establishes a closed-loop system composed of "continuous glucose sensing" and "skin layer"-regulated insulin release. As a result, glucose metabolism was controlled in response to interstitial glucose fluctuation under both insulin-deficient and insulin-resistant conditions with at least 3-week durability. Our "smart gel" technology could offer a user-friendly and remarkably economic (disposable) alternative to the current state of the art, thereby facilitating availability of effective insulin treatment not only to diabetic patients in developing countries but also to those patients who otherwise may not be strongly motivated, such as the elderly, infants, and patients in need of nursing care.