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Modern Applied Statistics With S

The clinical features and immune responses of asymptomatic individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have not been well described We studied 37 asymptomatic individuals in the Wanzhou District who were diagnosed with RT-PCR-confirmed SARS-CoV-2 infections but without any relevant clinical symptoms in the preceding 14 d and during hospitalization Asymptomatic individuals were admitted to the government-designated Wanzhou People's Hospital for centralized isolation in accordance with policy1 The median duration of viral shedding in the asymptomatic group was 19 d (interquartile range (IQR), 15-26 d) The asymptomatic group had a significantly longer duration of viral shedding than the symptomatic group (log-rank P = 0028) The virus-specific IgG levels in the asymptomatic group (median S/CO, 34; IQR, 16-107) were significantly lower (P = 0005) relative to the symptomatic group (median S/CO, 205; IQR, 58-382) in the acute phase Of asymptomatic individuals, 933% (28/30) and 811% (30/37) had reduction in IgG and neutralizing antibody levels, respectively, during the early convalescent phase, as compared to 968% (30/31) and 622% (23/37) of symptomatic patients Forty percent of asymptomatic individuals became seronegative and 129% of the symptomatic group became negative for IgG in the early convalescent phase In addition, asymptomatic individuals exhibited lower levels of 18 pro- and anti-inflammatory cytokines These data suggest that asymptomatic individuals had a weaker immune response to SARS-CoV-2 infection The reduction in IgG and neutralizing antibody levels in the early convalescent phase might have implications for immunity strategy and serological surveys

/pdf/clinical-and-immunological-assessment-of-asymptomatic-sars-2k5scibe7c.pdf

Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections.

The newly emergent human virus SARS-CoV-2 (severe acute respiratory syndrome-coronavirus 2) is resulting in high fatality rates and incapacitated health systems. Preventing further transmission is a priority. We analyzed key parameters of epidemic spread to estimate the contribution of different transmission routes and determine requirements for case isolation and contact tracing needed to stop the epidemic. Although SARS-CoV-2 is spreading too fast to be contained by manual contact tracing, it could be controlled if this process were faster, more efficient, and happened at scale. A contact-tracing app that builds a memory of proximity contacts and immediately notifies contacts of positive cases can achieve epidemic control if used by enough people. By targeting recommendations to only those at risk, epidemics could be contained without resorting to mass quarantines ("lockdowns") that are harmful to society. We discuss the ethical requirements for an intervention of this kind.

Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing.

According to the World Health Organization (WHO), viral diseases continue to emerge and represent a serious issue to public health In the last twenty years, several viral epidemics such as the severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 to 2003, and H1N1 influenza in 2009, have been recorded Most recently, the Middle East respiratory syndrome coronavirus (MERS-CoV) was first identified in Saudi Arabia in 2012 In a timeline that reaches the present day, an epidemic of cases with unexplained low respiratory infections detected in Wuhan, the largest metropolitan area in China's Hubei province, was first reported to the WHO Country Office in China, on December 31, 2019 Published literature can trace the beginning of symptomatic individuals back to the beginning of December 2019 As they were unable to identify the causative agent, these first cases were classified as "pneumonia of unknown etiology " The Chinese Center for Disease Control and Prevention (CDC) and local CDCs organized an intensive outbreak investigation program The etiology of this illness is now attributed to a novel virus belonging to the coronavirus (CoV) family, COVID-19 On February 11, 2020, the WHO Director-General, Dr Tedros Adhanom Ghebreyesus, announced that the disease caused by this new CoV was a "COVID-19," which is the acronym of "coronavirus disease 2019" In the past twenty years, two additional coronavirus epidemics have occurred  SARS-CoV provoked a large-scale epidemic beginning in China and involving two dozen countries with approximately 8000 cases and 800 deaths, and the MERS-CoV that began in Saudi Arabia and has approximately 2,500 cases and 800 deaths and still causes as sporadic cases This new virus seems to be very contagious and has quickly spread globally In a meeting on January 30, 2020, per the International Health Regulations (IHR, 2005), the outbreak was declared by the WHO a Public Health Emergency of International Concern (PHEIC) as it had spread to 18 countries with four countries reporting human-to-human transmission An additional landmark occurred on February 26, 2020, as the first case of the disease, not imported from China, was recorded in the United States Initially, the new virus was called 2019-nCoV Subsequently, the task of experts of the International Committee on Taxonomy of Viruses (ICTV) termed it the SARS-CoV-2 virus as it is very similar to the one that caused the SARS outbreak (SARS-CoVs) The CoVs have become the major pathogens of emerging respiratory disease outbreaks They are a large family of single-stranded RNA viruses (+ssRNA) that can be isolated in different animal species  For reasons yet to be explained, these viruses can cross species barriers and can cause, in humans, illness ranging from the common cold to more severe diseases such as MERS and SARS  Interestingly, these latter viruses have probably originated from bats and then moving into other mammalian hosts — the Himalayan palm civet for SARS-CoV, and the dromedary camel for MERS-CoV — before jumping to humans The dynamics of SARS-Cov-2 are currently unknown, but there is speculation that it also has an animal origin The potential for these viruses to grow to become a pandemic worldwide seems to be a serious public health risk Concerning COVID-19, the WHO raised the threat to the CoV epidemic to the "very high" level, on February 28, 2020 Probably, the effects of the epidemic caused by the new CoV has yet to emerge as the situation is quickly evolving World governments are at work to establish countermeasures to stem possible devastating effects Health organizations coordinate information flows and issues directives and guidelines to best mitigate the impact of the threat At the same time, scientists around the world work tirelessly, and information about the transmission mechanisms, the clinical spectrum of disease, new diagnostics, and prevention and therapeutic strategies are rapidly developing Many uncertainties remain with regard to both the virus-host interac ion and the evolution of the epidemic, with specific reference to the times when the epidemic will reach its peak At the moment, the therapeutic strategies to deal with the infection are only supportive, and prevention aimed at reducing transmission in the community is our best weapon Aggressive isolation measures in China have led to a progressive reduction of cases in the last few days In Italy, in geographic regions of the north of the peninsula, political and health authorities are making incredible efforts to contain a shock wave that is severely testing the health system In the midst of the crisis, the authors have chosen to use the "Statpearls" platform because, within the PubMed scenario, it represents a unique tool that may allow them to make updates in real-time  The aim, therefore, is to collect information and scientific evidence and to provide an overview of the topic that will be continuously updated

/pdf/features-evaluation-and-treatment-coronavirus-covid-19-20k4uevtsr.pdf

Features, Evaluation and Treatment Coronavirus (COVID-19)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly throughout the world since the first cases of coronavirus disease 2019 (COVID-19) were observed in December 2019 in Wuhan, China. It has been suspected that infected persons who remain asymptomatic play a significant role in the ongoing pandemic, but their relative number and effect have been uncertain. The authors sought to review and synthesize the available evidence on asymptomatic SARS-CoV-2 infection. Asymptomatic persons seem to account for approximately 40% to 45% of SARS-CoV-2 infections, and they can transmit the virus to others for an extended period, perhaps longer than 14 days. Asymptomatic infection may be associated with subclinical lung abnormalities, as detected by computed tomography. Because of the high risk for silent spread by asymptomatic persons, it is imperative that testing programs include those without symptoms. To supplement conventional diagnostic testing, which is constrained by capacity, cost, and its one-off nature, innovative tactics for public health surveillance, such as crowdsourcing digital wearable data and monitoring sewage sludge, might be helpful.

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Prevalence of Asymptomatic SARS-CoV-2 Infection : A Narrative Review.

Preliminary report on the shell fighting behaviour of Pagurus filholi in two different climate regions in Japan

Chromosome fusion is deleterious among oncogenic chromosome rearrangements, and has been proposed to cause multiple tumor-driving abnormalities. Conventional methodologies, however, lack the strictness of the experimental controls on the fusion such as the exact timing, the number and the types of fusion in a given cell. Here, we developed a human cell-based sister chromatid fusion visualization system (FuVis), in which a single defined sister chromatid fusion is induced by CRISPR/Cas9 concomitantly with mCitrine expression. Fused chromosome developed numerical and structural abnormalities, including chromosome fragmentation, an indicative of eventual chromothripsis. Live cell imaging and hierarchical Bayesian modeling indicated that micronucleus (MN) is generated in the first few cell cycle, and that cells with MN tend to possess cell cycle abnormalities. These results demonstrate that, although most cells can tolerate a single fusion, even a single sister chromatid fusion destabilizes cell cycle through MN formation.

https://www.biorxiv.org/content/biorxiv/early/2019/04/12/607341.full.pdf

A Single Defined Sister Chromatid Fusion Destabilizes Cell Cycle through Micronuclei Formation

To get camouflage successful, an animal and camouflage as a body-part need to be integrated into the environment. When an individual grows, the camouflage is usually modified to maintain integrity. How does the animal maintain the whole body-camouflage system as an individual? We studied the cap making behavior of the sponge crab, Lauridromia dehaani that can carry an artificial sponge as a cap. We obtained the behavioral data including repeated samples from the same individual. The multilevel or hierarchical models are often used to deal with the clustered data. However, the evaluation of the appropriateness of the hierarchical model is a challenge in statistical modeling. This is because the hierarchical model is a statistically non-regular model. Here, we apply marginal-level WAIC (Widely Applicable Information Criterion) to assess the appropriateness of the assumption of the hierarchical structure. We found that the hierarchical models remarkably outperformed non-hierarchical ones in decision making of material size and cap making by the crab, although the performance improvements of the models were small for cap hole making. Our analyses revealed that not only large individuals tend to choose and shape large caps, but also the individual-specific bias emerges in the behavior.

https://www.biorxiv.org/content/biorxiv/early/2019/08/12/330787.full.pdf

Individuality emerging in cap making by sponge crab

Rapid movements of limbs and appendages, faster than those produced by simple muscle contraction alone, are generated through mechanical networks consisting of springs and latches. The latch plays a central role in these spring-loaded mechanisms, but the structural details of the latch are not always known. The mandibles of the trapjaw ant Odontomachus kuroiwae closes the mandible extremely quickly to capture prey or to perform mandible-powered defensive jumps to avoid potential threats. The jump is mediated by a mechanical spring and latch system embodied in the mandible. An ant can strike the tip of the mandible onto the surface of an obstacle (prey, predator, or ground) in order to bounce its body away from potential threats. The angular velocity of the closing mandible was 2.3×104 rad/s. Latching of the joint is a key mechanism to aid the storage of energy required to power the ballistic movements of the mandibles. We have identified the fine structure of two latch systems on the mandible forming a ‘balljoint’ using an X-ray micro-computational tomography system (X-ray micro-CT) and X-ray live imaging with a synchrotron. Here we describe the surface of the inner section of the socket and a projection on the lip of the ball. The X-ray live imaging and movements of the 3D model show that the ball with a detent ridge slipped into a socket and over the socket ridge before snapping back at the groove edge. Our results give insight into the complex spring-latch systems that underpin ultra-fast movements in biological systems.

https://www.biorxiv.org/content/biorxiv/early/2022/12/06/2022.12.05.519247.full.pdf

Embodied Latch Mechanism of the Mandible to Power at an Ultrahigh Speed in the Trap-jaw Ants Odontomachus kuroiwae

Getting camouflaged with environmental material can improve survivability of animals. How animals select and customize the material to fit it to their body design remains unclear. To address the question, we examined the cap making behavior of the sponge crab, Lauridromia dehaani that carries sponge as a cap. We tested their preference to size of original material, the whole area size of cap that the crabs cut off, and its hole size of the caps that the crabs customize to make it suitable for their body. Three different sizes of artificial sponge were given to the crabs experimentally so that they could choose one sponge among them. We video recorded the process of cap making behavior, and measured the size of caps. Although a certain fixed behavioral pattern was observed in the cap making behavior, choice and size of cap hole considerably varied even in a single individual. To fully consider the individuality, we incorporated it into hierarchical statistical models. Estimating the parameters in the models by a Bayesian approach revealed that large individuals tended to choose large sponges with the variability specific to each individual. Furthermore, the individual-specific tendency was also observed in the relationship of the carapace width and the cap hole size. These results imply that the crabs update the cap making behavior by recalibration, given that they have to molt to become large. These findings might give a new insight into body extending capability of crustaceans.

https://www.biorxiv.org/content/biorxiv/early/2019/02/07/330787.full.pdf

Katsushi Kagaya

Papers

Preliminary report on the shell fighting behaviour of Pagurus filholi in two different climate regions in Japan

A Single Defined Sister Chromatid Fusion Destabilizes Cell Cycle through Micronuclei Formation

Individuality emerging in cap making by sponge crab

Embodied Latch Mechanism of the Mandible to Power at an Ultrahigh Speed in the Trap-jaw Ants Odontomachus kuroiwae

Customizing material into embodied cap by sponge crab