Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads.

The human gut bacteriophage community (phageome) plays an important role in the host's health and disease; however, the entire structure is poorly understood, partly owing to the generation of many incomplete genomes in conventional short-read metagenomics. Here, we show long-read metagenomics of amplified DNA of low-biomass phageomes with multiple displacement amplification (MDA), involving the development of a novel bioinformatics tool, split amplified chimeric read algorithm (SACRA), that efficiently pre-processed numerous chimeric reads generated through MDA. Using five samples, SACRA markedly reduced the average chimera ratio from 72% to 1.

ASC-deficiency impairs host defense against Aeromonas hydrophila infection in Japanese medaka, Oryzias latipes.

Apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC) is a component of inflammasome, which plays crucial roles in the inflammatory response. In mammals, ASC regulates caspase-1 activation, thereby inducing pyroptosis and producing activated inflammatory cytokines. In addition, ASC also interacts with receptor-interacting protein kinase 2 (RIPK2) and induces nuclear factor-κB (NF-κB) activation.

Interleukin-17A/F1 from Japanese pufferfish (Takifugu rubripes) stimulates the immune response in head kidney and intestinal cells.

In mammals, interleukin (IL)-17A and IL-17F, mainly produced by Th17 cells, are hallmark inflammatory cytokines that play important roles in the intestinal mucosal immune response. In contrast, three mammalian IL-17A and IL-17F counterparts (IL-17A/F1-3) have been identified in teleosts, and most of their functions have been described in the lymphoid organs. However, their function in the intestinal mucosal immune response is poorly understood.

Interleukin-17A/F1 Deficiency Reduces Antimicrobial Gene Expression and Contributes to Microbiome Alterations in Intestines of Japanese medaka ().

In mammals, interleukin (IL)-17A and F are hallmark inflammatory cytokines that play key roles in protection against infection and intestinal mucosal immunity. In the gastrointestinal tract (GI), the induction of antimicrobial peptide (AMP) production via Paneth cells is a fundamental role of IL-17A and F in maintaining homeostasis of the GI microbiome and health. Although mammalian IL-17A and F homologs (referred to as IL-17A/F1-3) have been identified in several fish species, their function in the intestine is poorly understood.

Required Chlorination Doses to Fulfill the Credit Value for Disinfection of Enteric Viruses in Water: A Critical Review.

A credit value of virus inactivation has been assigned to the disinfection step in international and domestic guidelines for wastewater reclamation and reuse. To fulfill the credit value for water disinfection, water engineers need to apply an appropriate disinfection strength, expressed as a CT value (mg × min/L), which is a product of disinfectant concentration and contact time, against enteric viruses in wastewater. In the present study, we extracted published experimental data on enteric virus inactivation using free chlorine and monochloramine and applied the Tobit analysis and simple linear regression analysis to calculate the range of CT values (mg × min/L) needed for 4-log inactivation.

Sign-constrained linear regression for prediction of microbe concentration based on water quality datasets.

This study presents a novel methodology for estimating the concentration of environmental pollutants in water, such as pathogens, based on environmental parameters. The scientific uniqueness of this study is the prevention of excess conformity in the model fitting by applying domain knowledge, which is the accumulated scientific knowledge regarding the correlations between response and explanatory variables. Sign constraints were used to express domain knowledge, and the effect of the sign constraints on the prediction performance using censored datasets was investigated.

Requirements for Transparency and Communicability of Regulatory Science.

This article presents the results of a study attempting to provide examples that implement transparency and communicability elements of Ethical Rules Principle of Best Available Regulatory Science (BARS) and Metrics for Evaluation of Regulatory Science Claims (MERSC). It starts with an overview of regulatory science and briefly summarizes principles of BARS and key pillars of MERSC. Subsequently, the BARS/MERSC system is used to evaluate the linear nonthreshold (LNT) process used in cancer assessments and the similar process used for evaluating in particulate matter (PM) exposure.

Palmitoyl lactic acid induces adipogenesis and a brown fat-like phenotype in 3T3-L1 preadipocytes.

Brown adipose tissue is specialized to generate heat by dissipating chemical energy and may provide novel strategies for obesity treatment in humans. Recently, advances in understanding the pharmacological and dietary agents that contribute to the browning of white adipose tissue have been made to alleviate obesity by promoting energy expenditure. Krill oil is widely used as a health supplement in humans.

Regulating Ionizing Radiation Based on Metrics for Evaluation of Regulatory Science Claims.

This article attempts to reconcile differences within the relevant scientific community on the effect of exposure to low levels of ionizing radiation notably the applicability of linear nonthreshold (LNT) process at exposures below a certain limit. This article applies an updated version of Metrics for Evaluation of Regulatory Science Claims (MERSC) derived form Best Available Regulatory Science (BARS) to the arguments provided by the proponents and opponents of LNT. Based on BARS/MERSC, 3 categories of effects of exposure to ionizing radiation are identified.

Virus Particle Detection by Convolutional Neural Network in Transmission Electron Microscopy Images.

A new computational method for the detection of virus particles in transmission electron microscopy (TEM) images is presented. Our approach is to use a convolutional neural network that transforms a TEM image to a probabilistic map that indicates where virus particles exist in the image. Our proposed approach automatically and simultaneously learns both discriminative features and classifier for virus particle detection by machine learning, in contrast to existing methods that are based on handcrafted features that yield many false positives and require several postprocessing steps.

Regulatory science requirements of labeling of genetically modified food.

This paper provides an overview of the evolution of food labeling in the USA. It briefly describes the three phases of agricultural development consisting of naturally occurring, cross-bred, and genetically engineered, edited or modified crops, otherwise known as Genetically Modified Organisms (GMO). It uses the Best Available Regulatory Science (BARS) and Metrics for Evaluation of Regulatory Science Claims (MERSC) to evaluate the scientific validity of claims applicable to GMO and the Best Available Public Information (BAPI) to evaluate the pronouncements by public media and others.

Whole-Genome Sequence of subsp. Strain 91-197, Isolated from Hybrid Striped Bass ( sp.) in the United States.

subsp. is a causative bacterium of fish pasteurellosis, which has caused serious economic damage to aquaculture farms worldwide. Here, the whole-genome sequence of subsp.

Complete Genome Sequence of subsp. Strain OT-51443 Isolated from Yellowtail () in Japan.

Pseudotuberculosis caused by infection of subsp. has caused serious economic damages to aquaculture farms worldwide. Here, the whole-genome sequence of subsp.

On-site Direct Detection of Astaxanthin from Salmon Fillet Using Raman Spectroscopy.

A new technology employing Raman spectroscopy is attracting attention as a powerful biochemical technique for the detection of beneficial and functional food nutrients, such as carotenoids and unsaturated fatty acids. This technique allows for the dynamic characterization of food nutrient substances for the rapid determination of food quality. In this study, we attempt to detect and measure astaxanthin from salmon fillets using this technology.

Draft Genome Sequence of the Fish Pathogen Mycobacterium pseudoshottsii Strain JCM15466, a Species Closely Related to M. marinum.

Mycobacterium pseudoshottsii is a slowly growing photochromogenic mycobacterium and fish pathogen isolated from wild marine fishes. M. pseudoshottsii closely resembles M.

Golden rice: scientific, regulatory and public information processes of a genetically modified organism.

Historically, agricultural development evolved in three phases. During the first phase the plants were selected on the basis of the availability of a plant with desirable properties at a specific location. The second phase provided the agricultural community with crossbreeding plants to achieve improvement in agricultural production.

Scientific foundation of regulating ionizing radiation: application of metrics for evaluation of regulatory science information.

This paper starts by describing the historical evolution of assessment of biologic effects of ionizing radiation leading to the linear non-threshold (LNT) system currently used to regulate exposure to ionizing radiation. The paper describes briefly the concept of Best Available Science (BAS) and Metrics for Evaluation of Scientific Claims (MESC) derived for BAS. It identifies three phases of regulatory science consisting of the initial phase, when the regulators had to develop regulations without having the needed scientific information; the exploratory phase, when relevant tools were developed; and the standard operating phase, when the tools were applied to regulations.

Development of archetypes for non-ranking classification and comparison of European National Health Technology Assessment systems.

Introduction: European countries are increasingly utilising health technology assessment (HTA) to inform reimbursement decision-making. However, the current European HTA environment is very diverse, and projects are already underway to initiate a more efficient and aligned HTA practice within Europe. This study aims to identify a non-ranking method for classifying the diversity of European HTA agencies process and the organisational architecture of the national regulatory review to reimbursement systems.

Linear non-threshold: separating facts from fiction.

The Linear Non-Threshold (LNT) process is used by virtually all governmental agencies to compute incidence of cancer as a consequence of exposure to a carcinogen. This comment applies the concept of Best Available Science (BAS) Metrics for Evaluation of Scientific Claims (MESC) derived from BAS to issues related to reliability of LNT hypothesis. This paper identifies the level of maturity of the LNT hypothesis and the associated uncertainties.

Refining the benefit-risk framework for the assessment of medicines: valuing and weighting benefit and risk parameters.

A common framework is necessary for the transparent articulation of the benefits and risks of a therapeutic product across disparate stakeholders. The assignment of value and weighting to each component parameter presents challenges deriving from different stakeholder objectives, methods, and perspectives. Building on prior experiences with a validated framework approach, this forum focused on identifying challenges and approaches to the assignment of values and weightings using a case study applied to a hypothetical medicinal product.

Expediting patients' access to medicines by improving the predictability of drug development and the regulatory approval process.

Ideally, well-designed global pharmaceutical development programs that include simultaneous submissions to multiple regulatory agencies can result in predictable regulatory approvals and expedited access to medicines for all patients. The workshops described herein investigated current trends in development and submission strategies along with regulatory review performance data in order to consider whether barriers to predictable expedited approval outcomes can be overcome through innovative clinical development approaches and a better understanding of review processes and procedures, particularly as these relate to the assessment of a product's risk-benefit profile.

Measuring benefit and balancing risk: strategies for the benefit-risk assessment of new medicines in a risk-averse environment.

Measuring the benefits and risks of medicines is the underlying theme whenever the development, review, and regulation of new medicines are discussed. Workshop participants were asked to take the first steps toward defining a framework for benefit-risk (BR) assessment. The framework identifies the essential elements that both regulators and companies should consider throughout the development, review, and postmarketing experience of new medicines in order to apply a consistent approach toward the assessment of BR balance.

Perceived long-term prognosis of teeth with orthodontically resorbed roots.

Objectives: To investigate the perceived significance of root resorption in the dental community. STUDY DESIGN AND SAMPLE: Mail out survey questionnaire accompanied by morphed images of 10-50% root resorption. General practitioners, periodontists, prosthodontists and orthodontists were the participants.