Validation of causal inference data using DirectLiNGAM in an environmental small-scale model and calculation settings

The development of data science has been needed in environmental fields such as marine, weather, and soil data. In general, the datasets are large in some cases, but they are often small because they contain observation data that the analyses themselves are limited. In such a case, the data are statistically evaluated by increasing or decreasing the levels of factors using differential analysis, resulting in the essential factors are estimated. However, there is no consistent approach to the means of assessing strong associations as a group between factors. Causal inference method has the possibility to output effective results for small data, and the results are expected to provide important information for understanding the potential highly association between factors, not necessarily the inference with big data. Here, we describe essential checkpoints and settings for the calculation by a direct method for learning a linear non-Gaussian structural equation model (DirectLiNGAM) and validation methods for the calculation results by using DirectLiNGAM with small-scale model data as an additional discussion of DirectLiNGAM portion of the related research article. Thus, this study provides the statistical validation methods for the association networks, treatments, and interventions for structural inference as a group of essential factors.•Causal inference with DirectLiNGAM•Validation of correlation coefficient and feature importance•Validation using causal effect object and propensity scores.

Alteration of shoaling behavior and dysbiosis in the gut of medaka (Oryzias latipes) exposed to 2-μm polystyrene microplastics

There is global concern that microplastics may harm aquatic life. Here, we examined the effects of fine polystyrene microplastics (PS-MPs, 2-μm diameter, 0.1 mg/L, 2.5 × 107 particles/L) on the behavior and the microbiome (linked to brain-gut interaction) of a fish model using medaka, Oryzias latipes. We found that shoaling behavior was reduced in PS-MP-exposed medaka compared with control fish during the exposure period, but it recovered during a depuration period. There was no difference in swimming speed between the PS-MP-exposed and control groups during the exposure period. Analysis of the dominant bacterial population (those comprising ≥1% of the total bacterial population) in the gut of fish showed that exposure to PS-MPs tended to increase the relative abundance of the phylum Fusobacteria and the genus Vibrio. Furthermore, structural-equation modeling of gut bacteria on the basis of machine-learning data estimated strong relationship involved in the reduction of the functional bacterial species of minority (<1% of the total bacterial population) such as the genera Muribaculum (an undefined role), Aquaspirillum (a candidate for nitrate metabolism and magnetotactics), and Clostridium and Phascolarctobacterium (potential producers of short-chain fatty acids, influencing behavior by affecting levels of neurotransmitters) as a group of gut bacteria in association with PS-MP exposure. Our results suggest that fish exposure to fine microplastics may cause dysbiosis and ultimately cause social behavior disorders linked to brain-gut interactions. This effect could be connected to reduction of fish fitness in the ecosystem and reduced fish survival.

A Thermophile-Fermented Compost Modulates Intestinal Cations and the Expression of a Juvenile Hormone-Binding Protein Gene in the Female Larvae of Hercules Beetle Dynastes hercules (Coleoptera: Scarabaeidae)

The Hercules beetle larvae grow by feeding on humus, and adding a thermophile-fermented compost to the humus can upregulate the growth of female larvae. In this study, the effects of compost on the intestinal environment, including pH, cation concentrations, and organic acid concentrations of intestinal fluids, were investigated, and the RNA profile of the fat body was determined. Although the total intestinal potassium ions were similar between the larvae grown without compost (control larvae) and those with compost (compost larvae), the proportion of potassium ions in the midgut of the compost larvae drastically increased. In the midgut, an unidentified organic acid was the most abundant, and its concentration increased in the compost larvae. Transcriptome analysis showed that a gene encoding hemolymph juvenile-binding protein (JHBP) was expressed in the compost female larvae and not in the control female larvae. Expression of many genes involved in the defensive system was decreased in the compost female larvae. These results suggest that the female-specific enhancement of larval growth by compost was associated with the increased JHBP expression under conditions in which the availability of nutrition from the humus was improved by an increase in potassium ions in the midgut.

Dilution rates and their transition modes influence organic acid productivity and bacterial community structure on continuous meta-fermentation using complex microorganisms

We investigated the effect of dilution rates (D) (0.05, 0.15, and 0.4 h-1) and its transition mode strategies (constant, up, and down modes) on organic acid productivity and bacterial community structure on continuous meta-fermentation using complex microorganisms. The number of bacterial species decreased with increasing D in the constant mode while up and down modes maintained high and low values, respectively, regardless of the changing D values. Caldibacillus hisashii was the predominant species in all modes at all D values, while other bacterial species, including Anaerosalibacter bizertensis and Clostridium cochlearium were predominant in only certain modes and D values. The highest total organic acid productivity of 3.16 g L-1 h-1 was obtained with 82.2% lactic acid selectivity at D = 0.4 h⁻1 in constant mode. Heterofermentation occurred in the up mode, while the down mode exhibited the maximum butyric acid productivity of 0.348 g L-1 h-1 with 43.8% selectivity at D = 0.05 h-1. The constant, up, and down modes showed the distinct main products of lactic, acetic and formic, and butyric acids, respectively. In this study, we proposed a new parameter of species-specific productivity (SSP) to estimate which species and how much a bacterium quantitatively contributes to the targeted organic acid productivity in continuous meta-fermentation. SSP was determined based on the abundance of functional genes encoding key enzymes from the results of 16S amplicon analysis. In conclusion, D values and their transition modes affect productivity by changing the bacterial community structure, and are a significant factor in establishing a highly productive process in continuous meta-fermentation.

Granular flow experiment using artificial gravity generator at International Space Station

Studying the gravity-dependent characteristics of regolith, fine-grained granular media covering extra-terrestrial bodies is essential for the reliable design and analysis of landers and rovers for space exploration. In this study, we propose an experimental approach to examine a granular flow under stable artificial gravity conditions for a long duration generated by a centrifuge at the International Space Station. We also perform a discrete element simulation of the granular flow in both artificial and natural gravity environments. The simulation results verify that the granular flows in artificial and natural gravity are consistent. Further, regression analysis of the experimental results reveals that the mass flow rate of granular flow quantitatively follows a well-known physics-based law with some deviations under low-gravity conditions, implying that the bulk density of the granular media decreases with gravity. This insight also indicates that the bulk density considered in simulation studies of space probes under low-gravity conditions needs to be tuned for their reliable design and analysis.

Estimation of silent phenotypes of calf antibiotic dysbiosis

Reducing antibiotic usage among livestock animals to prevent antimicrobial resistance has become an urgent issue worldwide. This study evaluated the effects of administering chlortetracycline (CTC), a versatile antibacterial agent, on the performance, blood components, fecal microbiota, and organic acid concentrations of calves. Japanese Black calves were fed with milk replacers containing CTC at 10 g/kg (CON group) or 0 g/kg (EXP group). Growth performance was not affected by CTC administration. However, CTC administration altered the correlation between fecal organic acids and bacterial genera. Machine learning (ML) methods such as association analysis, linear discriminant analysis, and energy landscape analysis revealed that CTC administration affected populations of various types of fecal bacteria. Interestingly, the abundance of several methane-producing bacteria at 60 days of age was high in the CON group, and the abundance of Lachnospiraceae, a butyrate-producing bacterium, was high in the EXP group. Furthermore, statistical causal inference based on ML data estimated that CTC treatment affected the entire intestinal environment, potentially suppressing butyrate production, which may be attributed to methanogens in feces. Thus, these observations highlight the multiple harmful impacts of antibiotics on the intestinal health of calves and the potential production of greenhouse gases by calves.

An agroecological structure model of compost-soil-plant interactions for sustainable organic farming

Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that amino acids, antioxidant activity, flavonoids and/or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus and nitrogen compounds were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by the compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen.

Dataset of night-time emissions of the Earth in the near UV range (290-430 nm), with 6.3 km resolution in the latitude range -51.6<L<+51.6 degrees, acquired on board the International Space Station with the Mini-EUSO detector

The data presented in this article are related to the research paper entitled "Observation of night-time emissions of the Earth in the near UV range from the International Space Station with the Mini-EUSO detector" (Remote Sensing of Environment, Volume 284, January 2023, 113336, https://doi.org/10.1016/j.rse.2022.113336). The data have been acquired with the Mini-EUSO detector, an UV telescope operating in the range 290-430 nm and located inside the International Space Station. The detector was launched in August 2019, and it has started operations from the nadir-facing UV-transparent window in the Russian Zvezda module in October 2019. The data presented here refer to 32 sessions acquired between 2019-11-19 and 2021-05-06. The instrument consists of a Fresnel-lens optical system and a focal surface composed of 36 multi-anode photomultiplier tubes, each with 64 channels, for a total of 2304 channels with single photon counting sensitivity. The telescope, with a square field-of-view of 44°, has a spatial resolution on the Earth surface of 6.3 km and saves triggered transient phenomena with a temporal resolution of 2.5 µs and 320 µs. The telescope also operates in continuous acquisition at a 40.96 ms scale. In this article, large-area night-time UV maps obtained processing the 40.96 ms data, taking averages over regions of some specific geographical areas (e.g., Europe, North America) and over the entire globe, are presented. Data are binned into 0.1° × 0.1° or 0.05° × 0.05° cells (depending on the scale of the map) over the Earth's surface. Raw data are made available in the form of tables (latitude, longitude, counts) and .kmz files (containing the .png images). These are - to the best of our knowledge - the highest sensitivity data in this wavelength range and can be of use to various disciplines.

Computational estimation of sediment symbiotic bacterial structures of seagrasses overgrowing downstream of onshore aquaculture

Coastal seagrass meadows are essential in blue carbon and aquatic ecosystem services. However, this ecosystem has suffered severe eutrophication and destruction due to the expansion of aquaculture. Therefore, methods for the flourishing of seagrass are still being explored. Here, data from 49 public coastal surveys on the distribution of seagrass and seaweed around the onshore aquaculture facilities are revalidated, and an exceptional area where the seagrass Zostera marina thrives was found near the shore downstream of the onshore aquaculture facility. To evaluate the characteristics of the sediment for growing seagrass, physicochemical properties and bacterial ecological evaluations of the sediment were conducted. Evaluation of chemical properties in seagrass sediments confirmed a significant increase in total carbon and a decrease in zinc content. Association analysis and linear discriminant analysis refined bacterial candidates specified in seagrass overgrown- and nonovergrown-sediment. Energy landscape analysis indicated that the symbiotic bacterial groups of seagrass sediment were strongly affected by the distance close to the seagrass-growing aquaculture facility despite their bacterial population appearing to fluctuate seasonally. The bacterial population there showed an apparent decrease in the pathogen candidates belonging to the order Flavobacteriales. Moreover, structure equation modeling and a linear non-Gaussian acyclic model based on the machine learning data estimated an optimal sediment symbiotic bacterial group candidate for seagrass growth as follows: the Lachnospiraceae and Ruminococcaceae families as gut-inhabitant bacteria, Rhodobacteraceae as photosynthetic bacteria, and Desulfobulbaceae as cable bacteria modulating oxygen or nitrate reduction and oxidation of sulfide. These observations confer a novel perspective on the sediment symbiotic bacterial structures critical for blue carbon and low-pathogenic marine ecosystems in aquaculture.

Amendment of a thermophile-fermented compost to humus improves the growth of female larvae of the Hercules beetle Dynastes hercules (Coleoptera: scarabaeidae)

AIMS

Hercules beetle is a popular pet and large adult individuals are considered valuable. Incorporating compost prepared from marine animals and fermented by thermophilic bacteria into the humus benefits the gut microflora of several livestock. Here, we evaluated whether this compost improves the growth of the Hercules beetle (Dynastes hercules hercules) larvae.

METHODS AND RESULTS

We mixed the compost grains with the humus at a final concentration of 1% (w/w) and transferred ∼90 days old Hercules beetle larvae to fresh humus with or without the compost. After 72 days rearing period, only the female larvae reared in the humus with compost exhibited superior growth, compared with those grown in compost-free humus. The gut bacterial composition was determined at 0 and 46 day after transferring the larvae to humus with or without compost. Improved growth of the female larvae was associated with increased abundance of Mollicutes and decreased abundance of Gammaproteobacteria.

CONCLUSION

The thermophile-fermented compost has a probiotic effect on the female Hercules beetle larvae that is mediated by altered gut microflora.

An evaluation of homeostatic plasticity for ecosystems using an analytical data science approach

The natural world is constantly changing, and planetary boundaries are issuing severe warnings about biodiversity and cycles of carbon, nitrogen, and phosphorus. In other views, social problems such as global warming and food shortages are spreading to various fields. These seemingly unrelated issues are closely related, but it can be said that understanding them in an integrated manner is still a step away. However, progress in analytical technologies has been recognized in various fields and, from a microscopic perspective, with the development of instruments including next-generation sequencers (NGS), nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC/MS), and liquid chromatography-mass spectrometry (LC/MS), various forms of molecular information such as genome data, microflora structure, metabolome, proteome, and lipidome can be obtained. The development of new technology has made it possible to obtain molecular information in a variety of forms. From a macroscopic perspective, the development of environmental analytical instruments and environmental measurement facilities such as satellites, drones, observation ships, and semiconductor censors has increased the data availability for various environmental factors. Based on these background, the role of computational science is to provide a mechanism for integrating and understanding these seemingly disparate data sets. This review describes machine learning and the need for structural equations and statistical causal inference of these data to solve these problems. In addition to introducing actual examples of how these technologies can be utilized, we will discuss how to use these technologies to implement environmentally friendly technologies in society.

A potential network structure of symbiotic bacteria involved in carbon and nitrogen metabolism of wood-utilizing insect larvae

Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive microbial structures are expected to reveal a novel rule underlying wood biomass processing. Here, structural inferences for inhabitant bacteria involved in carbon and nitrogen metabolism for beetle larvae, an insect model, were performed to explore the potential rules. Bacterial analysis of larval feces showed enrichment of the phyla Chroloflexi, Gemmatimonadetes, and Planctomycetes, and the genera Bradyrhizobium, Chonella, Corallococcus, Gemmata, Hyphomicrobium, Lutibacterium, Paenibacillus, and Rhodoplanes, as bacteria potential involved in plant growth promotion, nitrogen cycle modulation, and/or environmental protection. The fecal abundances of these bacteria were not necessarily positively correlated with their abundances in the habitat, indicating that they were selectively enriched in the feces of the larvae. Correlation and association analyses predicted that common fecal bacteria might affect carbon and nitrogen metabolism. Based on these hypotheses, structural equation modeling (SEM) statistically estimated that inhabitant bacterial groups involved in carbon and nitrogen metabolism were composed of the phylum Gemmatimonadetes and Planctomycetes, and the genera Bradyrhizobium, Corallococcus, Gemmata, and Paenibacillus, which were among the fecal-enriched bacteria. Nevertheless, the selected common bacteria, i.e., the phyla Acidobacteria, Armatimonadetes, and Bacteroidetes and the genera Candidatus Solibacter, Devosia, Fimbriimonas, Gemmatimonas Opitutus, Sphingobium, and Methanobacterium, were necessary to obtain good fit indices in the SEM. In addition, the composition of the bacterial groups differed depending upon metabolic targets, carbon and nitrogen, and their stable isotopes, δ¹³C and δ¹⁵N, respectively. Thus, the statistically derived causal structural models highlighted that the larval fecal-enriched bacteria and common symbiotic bacteria might selectively play a role in wood biomass carbon and nitrogen metabolism. This information could confer a new perspective that helps us use wood biomass more efficiently and might stimulate innovation in environmental industries in the future.

Noninvasive fecal metabolic profiling for the evaluation of characteristics of thermostable lactic acid bacteria, Weizmannia coagulans SANK70258, for broiler chickens

Weizmannia coagulans SANK70258 is a spore-forming thermostable lactic acid bacterium and an effective probiotic for the growth of livestock animals, but its growth-promoting mechanism remains unclear. Here, the composition of fecal metabolites in broilers continuously administered with W. coagulans SANK70258 was assessed under a regular program with antibiotics, which was transiently given for 6 days after birth. Oral administration of W. coagulans to broiler chicks tended to increase the average daily gain of body weights thereafter. The composition of fecal metabolites in the early chick stage (Day 10 after birth) was dramatically altered by the continuous exposure. The levels of short-chain fatty acids (SCFAs) propionate and butyrate markedly increased, while those of acetate, one of the SCFAs, and lactate were reduced. Simultaneously, arabitol, fructose, mannitol, and erythritol, which are carbohydrates as substrates for gut microbes to produce SCFAs, also increased along with altered correlation. Correlation network analyses classified the modularity clusters (|r| > 0.7) among carbohydrates, SCFAs, lactate, amino acids, and the other metabolites under the two conditions. The characteristic diversities by the exposure were visualized beyond the perspective associated with differences in metabolite concentrations. Further, enrichment pathway analyses showed that metabolic composition related to biosynthesis and/or metabolism for SCFAs, amino acids, and energy were activated. Thus, these observations suggest that W. coagulans SANK70258 dramatically modulates the gut metabolism of the broiler chicks, and the metabolomics profiles during the early chick stages may be associated with growth promotion.

Development of a novel feeding method for Japanese black calves with thermophile probiotics at postweaning

AIMS

Probiotic effects of compost containing thermophiles on productivity have been reported in domestic animals, although not cattle. We evaluated the effects of administering Caldibacillus hisashii, a thermophile contained in compost, on growth, blood components, faecal organic acid concentrations and microbiota population in Japanese black calves.

METHODS AND RESULTS

Calves were administered C. hisashii from 3 to 5 mo of age. Administering C. hisashii decreased feed intake without affecting body weight, indicating that feed efficiency is improved by administration. Administering C. hisashii decreased plasma insulin concentration without affecting glucose and nonesterified fatty acid concentrations. Chao1 was decreased by exposure at 5 mo of age. Similarly, weighted- and unweighted UniFrac distances were affected by treatment at 5 mo of age. Faecal abundance of the phylum Bacteroidetes tended to be increased by exposure. Faecal propionic acid concentration was correlated positively with faecal abundance of phylum Bacteroidetes but negatively with that of Firmicutes. Interestingly, the population of the genus Methanobrevibacter, representing the majority of methanogens, was lowered by exposure and was negatively correlated with faecal propionic acid concentration.

CONCLUSION

Administration of C. hisashii has the potential to improve growth performance of Japanese black calves and to contribute to reducing environmental load, which may be associated with altered endocrine kinetics and gut microbial populations.

SIGNIFICANCE AND IMPACTS OF THE STUDY

This study revealed that isolated thermophiles included in compost may exert probiotic effects on calves.

A Review of the EUSO-Balloon Pathfinder for the JEM-EUSO Program

EUSO-Balloon is a pathfinder for JEM-EUSO, the mission concept of a spaceborne observatory which is designed to observe Ultra-High Energy Cosmic Ray (UHECR)-induced Extensive Air Showers (EAS) by detecting their UltraViolet (UV) light tracks "from above." On August 25, 2014, EUSO-Balloon was launched from Timmins Stratospheric Balloon Base (Ontario, Canada) by the balloon division of the French Space Agency CNES. After reaching a floating altitude of 38 km, EUSO-Balloon imaged the UV light in the wavelength range ∼290-500 nm for more than 5 hours using the key technologies of JEM-EUSO. The flight allowed a good understanding of the performance of the detector to be developed, giving insights into possible improvements to be applied to future missions. A detailed measurement of the photoelectron counts in different atmospheric and ground conditions was achieved. By means of the simulation of the instrument response and by assuming atmospheric models, the absolute intensity of diffuse light was estimated. The instrument detected hundreds of laser tracks with similar characteristics to EASs shot by a helicopter flying underneath. These are the first recorded laser tracks measured from a fluorescence detector looking down on the atmosphere. The reconstruction of the direction of the laser tracks was performed. In this work, a review of the main results obtained by EUSO-Balloon is presented as well as implications for future space-based observations of UHECRs.

Chemical-Mediated Microbial Interactions Can Reduce the Effectiveness of Time-Series-Based Inference of Ecological Interaction Networks

Network-based assessments are important for disentangling complex microbial and microbial–host interactions and can provide the basis for microbial engineering. There is a growing recognition that chemical-mediated interactions are important for the coexistence of microbial species. However, so far, the methods used to infer microbial interactions have been validated with models assuming direct species-species interactions, such as generalized Lotka–Volterra models. Therefore, it is unclear how effective existing approaches are in detecting chemical-mediated interactions. In this paper, we used time series of simulated microbial dynamics to benchmark five major/state-of-the-art methods. We found that only two methods (CCM and LIMITS) were capable of detecting interactions. While LIMITS performed better than CCM, it was less robust to the presence of chemical-mediated interactions, and the presence of trophic competition was essential for the interactions to be detectable. We show that the existence of chemical-mediated interactions among microbial species poses a new challenge to overcome for the development of a network-based understanding of microbiomes and their interactions with hosts and the environment.

Meta-fermentation system with a mixed culture for the production of optically pure l-lactic acid can be reconstructed using the minimum isolates with a simplified pH control strategy

Meta-l-lactic acid fermentation from non-treated kitchen refuse was reconstructed using a combination of isolated bacterial strains under several pH control strategies. The meta-fermentation system was successfully reconstructed using a combination of Weizmannia coagulans MN-07, Caldibacillus thermoamylovorans OM55-6, and Caldibacillus hisashii N-11 strains. Additionally, a simplified constant pH control strategy was employed, which decreased fermentation time and increased production. The optimum pH (6.5) for the reconstructed meta-fermentation was favorable for the respective pure cultures of the three selected strains. The l-lactic acid production performance of the reconstructed meta-fermentation system was as follows: concentration, 24.5 g L^-1 ; optical purity, 100%; productivity, 0.341 g L^-1 h^-1 ; yield, 1.06 g g^-1 . These results indicated that constant pH control was effective in the reconstructed meta-fermentation with the best performance of l-lactic acid production at pH optimal for the selected bacterial growth, while the switching from swing pH control would suppress the activities of unfavorable bacterial species in un-isolated meta-fermentation.

Effects of feeding high volumes of milk replacer on reproductive performance and on concentrations of metabolites and hormones in blood of Japanese black heifer calves

We evaluated the effects of feeding high volumes of milk replacer on growth and reproductive performances in Japanese black heifers. Fifty-one heifers were fed milk replacer at 9 L/day for 60 days (9 L × 60 days; n = 18) or 41 days (9 L × 41 days; n = 15), or at 7 L/day for 40 days (7 L × 40 days; n = 18). Artificial insemination (AI) was performed on heifers with ≥270 kg body weight and ≥116 cm body height at 300 days of age. The age at the first AI was 0.35 month later for 7 L × 40 days than the other groups (p < .01). However, age at calving did not differ among treatments (22.1 months). The interval from the first AI to pregnancy tended to be ~2 months longer for the 9 L × 60 days than the other groups (p = .07). Our results showed that feeding high volumes of milk replacer may reduce the age at calving via an improved rate of growth. In addition, we propose that feeding a maximum of 7 L milk replacer for 40 days may be the most appropriate rearing regime because the success of pregnancy per AI may be reduced in calves fed a maximum of 9 L for 41 and 60 days.

Androgen deprivation-induced elevated nuclear SIRT1 promotes prostate tumor cell survival by reactivation of AR signaling

The NAD⁺-dependent deacetylase, Sirtuin 1 (SIRT1) is involved in prostate cancer pathogenesis. However, the actual contribution is unclear as some reports propose a protective role while others suggest it is harmful. We provide evidence for a contextual role for SIRT1 in prostate cancer. Our data show that (i) mice orthotopically implanted with SIRT1-silenced LNCaP cells produced smaller tumors; (ii) SIRT1 suppression mimicked AR inhibitory effects in hormone responsive LNCaP cells; and (iii) caused significant reduction in gene signatures associated with E2F and MYC targets in AR-null PC-3 and E2F and mTORC1 signaling in castrate-resistant ARv7 positive 22Rv1 cells. Our findings further show increased nuclear SIRT1 (nSIRT1) protein under androgen-depleted relative to androgen-replete conditions in prostate cancer cell lines. Silencing SIRT1 resulted in decreased recruitment of AR to PSA enhancer selectively under androgen-deprivation conditions. Prostate cancer outcome data show that patients with higher levels of nSIRT1 progress to advanced disease relative to patients with low nSIRT1 levels. Collectively, we demonstrate that lowering SIRT1 levels potentially provides new avenues to effectively prevent prostate cancer recurrence.

Discontinuous Involvement of Spermatic Cord Soft Tissue in Testicular Germ Cell Tumors: A Multi-Institution Experience

Introduction/Objective

In the 8th Edition AJCC Cancer Staging Manual, discontinuous involvement of spermatic cord soft tissue (DISC) by testicular germ cell tumors (GCT) is regarded as metastatic deposit (pM1), placing the patient in clinical prognostic stage group (CPSG) III. We conducted a multi-institution study to corroborate or refute the current recommendations. Methods: Thirty-eight cases of GCT with spermatic cord involvement were collected from 13 institutions in Europe, Phillipines and America. Clinical and pathologic data was obtained.

Results

Tumors included 28 (73%) non-seminomatous and 10 (26%) seminomatous GCTs. Mean testicular tumor size was 6.6 cm (range 1.3-18). After review by an uropathologist, cases were classified as cord LVI [T2] (n=3), continuous cord involvement (CCI) [T3] (n=13), and DISC (n=22). Mean cord tumor size for DISC was 0.9 cm (range 0.1-4.5).

CPSG was available for 33 and follow-up (FU) for22 patients with a mean length of FU of 38 months (range 2-144). Seven (39%) DISC patients were CPSG II (regional LN metastases), and 11 (61%) CPSG III (distant metastases). On FU, 5 (45%) DISC patients had no evidence of disease (NED); 6 (55%) were alive with disease (AWD). Three (25%)

CCI patients were CPSG I (local disease), 6 (50%) CPSG II, and 3 (25%) CPSG III. On FU, 6 (60%) CCI patients were NED, 4 (40%) AWD. Cord LVI patients were one in each CPSG. One cord LVI patient was NED, the others were lost at FU. All DISC (100%) patients with available CPSG had advanced disease (CPSG II or III), compared to 75% of CCI, and 67% of cord LVI patients.

Conclusion

Although it did not reach statistical significance (p=0.054; Fisher’s exact test), DISC patients were more likely to have CPSG II and III compared to CCI patients. Our findings suggest a worse behavior in patients with DISC, supporting a higher pathologic stage than CCI.

Collisional formation of top-shaped asteroids and implications for the origins of Ryugu and Bennu

Asteroid shapes and hydration levels can serve as tracers of their history and origin. For instance, the asteroids (162173) Ryugu and (101955) Bennu have an oblate spheroidal shape with a pronounced equator, but contain different surface hydration levels. Here we show, through numerical simulations of large asteroid disruptions, that oblate spheroids, some of which have a pronounced equator defining a spinning top shape, can form directly through gravitational reaccumulation. We further show that rubble piles formed in a single disruption can have similar porosities but variable degrees of hydration. The direct formation of top shapes from single disruption alone can explain the relatively old crater-retention ages of the equatorial features of Ryugu and Bennu. Two separate parent-body disruptions are not necessarily required to explain their different hydration levels.

Hayabusa2 arrives at the carbonaceous asteroid 162173 Ryugu-A spinning top-shaped rubble pile

The Hayabusa2 spacecraft arrived at the near-Earth carbonaceous asteroid 162173 Ryugu in 2018. We present Hayabusa2 observations of Ryugu's shape, mass, and geomorphology. Ryugu has an oblate "spinning top" shape, with a prominent circular equatorial ridge. Its bulk density, 1.19 ± 0.02 grams per cubic centimeter, indicates a high-porosity (>50%) interior. Large surface boulders suggest a rubble-pile structure. Surface slope analysis shows Ryugu's shape may have been produced from having once spun at twice the current rate. Coupled with the observed global material homogeneity, this suggests that Ryugu was reshaped by centrifugally induced deformation during a period of rapid rotation. From these remote-sensing investigations, we identified a suitable sample collection site on the equatorial ridge.

The geomorphology, color, and thermal properties of Ryugu: Implications for parent-body processes

The near-Earth carbonaceous asteroid 162173 Ryugu is thought to have been produced from a parent body that contained water ice and organic molecules. The Hayabusa2 spacecraft has obtained global multicolor images of Ryugu. Geomorphological features present include a circum-equatorial ridge, east-west dichotomy, high boulder abundances across the entire surface, and impact craters. Age estimates from the craters indicate a resurfacing age of [Formula: see text] years for the top 1-meter layer. Ryugu is among the darkest known bodies in the Solar System. The high abundance and spectral properties of boulders are consistent with moderately dehydrated materials, analogous to thermally metamorphosed meteorites found on Earth. The general uniformity in color across Ryugu's surface supports partial dehydration due to internal heating of the asteroid's parent body.

Abstract P4-08-16: Validation of the AJCC eighth edition prognostic stage compared with the anatomic stage for breast cancer with a Japanese single-institutional cohort

Background: The American Joint Committee for Cancer (AJCC) 8th edition cancer staging system for breast cancer incorporated biologic factors in addition to the 7th edition anatomic stage. We analyzed how the new AJCC 8th edition prognostic stage refined its stratification compared with the anatomic stage.

Methods: We reviewed the data of 4,134 patients with stage I to III breast cancer who underwent surgery at Tokyo Metropolitan Komagome Hospital between 2000 and 2016. The anatomic stage and prognostic stage were re-staged according to the AJCC 8th edition staging manual. Patients who received neoadjuvant chemotherapy or had bilateral breast cancer and those with unknown clinicopathologic factors were excluded. The 21-gene Oncotype DX breast recurrence score was not used for staging in this study.

Results: A total of 2,469 patients with a median follow-up of 4.7 years (range 0.1-15.5 years) were identified. According to the anatomic stage, there were 1,259 patients of stage IA, 132 of IB, 591 of IIA, 206 of IIB, 130 of IIIA, 14 of IIIB and 73 of IIIC. According to the prognostic stage, there were 1,610 patients of stage IA, 331 of IB, 236 of IIA, 73 of IIB, 85 of IIIA, 43 of IIIB and 27 of IIIC. Sixty-four patients (2.6%) could not be assigned using the new staging system for the presence of micrometastases in lymph nodes with tumors larger than 2 cm. The 5-year disease-free survival (DFS) rates according to the anatomic stage were 97.4% for stage IA, 97.1% for IB, 95.8% for IIA, 86.5% for IIB, 77.9% for IIIA, 49.2% for IIIB and 54.9% for IIIC. According to the prognostic stage, the 5-year DFS rates were 97.9% for stage IA, 92.9% for IB, 91.2% for IIA, 79.8% for IIB, 67.4% for IIIA, 53.3% for IIIB and 38.7% for IIIC. Compared with the AJCC anatomic stage, the prognostic stage was increased in 148 patients (6.2%) and decreased in 808 patients (32.8%). For those in whom the stage changed, the change was by one stage up or down in 463 (19.3%), by 2 stages up or down in 401 (16.7%) and by 3 stages up or down in 92 (3.8%). Of the 1,842 patients with hormone receptor (HR)-positive and human epidermal growth factor 2 (HER2)-negative (HR+/HER2-) disease, 40.5% (745/1842) of cases were downstaged, and 0.7% (1/1842) were upstaged.

Discussion: The AJCC 8th edition prognostic staging system provided more refined stratification than the anatomic stage. In the Japanese cohort, the proportion of the downstaging rate was higher than the upstaging rate, and the prognostic evaluation of HR+ patients in particular was improved.

Citation Format: Miyamoto H, Saita C, Onishi M, Goto R, Iwamoto N, Honda Y, Aruga T. Validation of the AJCC eighth edition prognostic stage compared with the anatomic stage for breast cancer with a Japanese single-institutional cohort [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-08-16.

Medication-related osteonecrosis of the jaw after tooth extraction in cancer patients: a multicenter retrospective study

Root amputation, immunosuppressive therapy, mandibular tooth extraction, pre-existing inflammation, and longer duration of treatment with bone-modifying agents were significantly associated with an increased risk of medication-related osteonecrosis of the jaw. Hopeless teeth should be extracted without drug holiday before the development of inflammation in cancer patients receiving high-dose bone-modifying agents.

INTRODUCTION

No studies have comprehensively analyzed the influence of pre-existing inflammation, surgical procedure-related factors such as primary wound closure, demographic factors, and drug holiday on the incidence of medication-related osteonecrosis of the jaw (MRONJ). The purpose of this study was to retrospectively investigate the relationships between these various factors and the development of MRONJ after tooth extraction in cancer patients receiving high-dose bone-modifying agents (BMAs) such as bisphosphonates or denosumab.

METHODS

Risk factors for MRONJ after tooth extraction were evaluated with univariate and multivariate analyses. The following parameters were investigated in all patients: demographics, type and duration of BMA use, whether BMA use was discontinued before tooth extraction (drug holiday), the duration of such discontinuation, the presence of pre-existing inflammation, and whether additional surgical procedures (e.g., incision, removal of bone edges, root amputation) were performed.

RESULTS

We found that root amputation (OR = 22.62), immunosuppressive therapy (OR = 16.61), extraction of mandibular teeth (OR = 12.14), extraction of teeth with pre-existing inflammation, and longer duration (≥ 8 months) of high-dose BMA (OR = 7.85) were all significantly associated with MRONJ.

CONCLUSIONS

Tooth extraction should not necessarily be postponed in cancer patients receiving high-dose BMA. The effectiveness of a short-term drug holiday was not confirmed, as drug holidays had no significant impact on MRONJ incidence. Tooth extraction may be acceptable during high-dose BMA therapy until 8 months after initiation.

Immunohistochemical Analysis of Human Lung Cancers with Anti-ras p21 Monoclonal Antibodies

The expression of ras oncogene product p21 in human malignant pleurisy and primary lung cancer was studied immunocyto-histochemically with monoclonal antibodies (MoAbs) rp-28 and rp-35 against ras p21. In pleural effusion cells, cancer cells revealed more intensively positive reaction with MoAb rp-35 than with MoAb rp-28, especially in the plasma membrane, and no positive reaction was obtained in any kind of inflammation cells with the exception of faintly positive reaction in the cytoplasm of macrophages.

In primary lung cancers, well or moderately differentiated adenocarcinoma tissues showed higher reactivity with MoAb rp-28 than those of poorly differentiated adenocarcinoma or any other histological subtype of lung cancer. With MoAb rp-35, intensively positive reaction was obtained in most of cases with all different histological subtypes of lung cancer. The staining in cancer cells was usually localized intensively to the plasma membrane and weakly to the cytoplasm with both MoAbs. Normal bronchial epithelial and glandular tissues showed only cytoplasmic staining. These two MoAbs, especially MoAb rp-35, may be useful in clinicopathological applications for the diagnosis of malignant pleurisy and primary lung cancer.

Abstract P3-01-09: Re-evaluating the “10% rule” for sentinel lymph node biopsy with radioactive method in breast cancer; a single institutional retrospective study

Background:

When multiple radioactive sentinel lymph nodes (SLNs) are present during sentinel lymph node biopsy (SLNB), excision of those SLNs with &gt;10% radioactive count per minute (high-CPM) of the most radioactive node (“10% rule”) has been proposed. Although this “10% rule” may avoid excessive removal of SLNs,the risk of false negative and remnant positive SLNs in the patients who have SLNs with &lt;10% CPM (low-CPM) remain unclear. The purpose of this analysis is to determine the clinical validity of this “10% rule” for early breast cancer patients.

Method:

We reviewed the records of successful SLNBs using the radioisotope (RI) method performed between January 2001 and December 2016 in our institution. The radioactive count from each excised SLN was measured. Non-radioactive lymph nodes were excluded from this analysis. All SLNs were pathologically assessed by 2mm serial section with hematoxylin and eosin staining.

Results:

In the 3,043 patients with successful SLNB,the median number of radioactive SLNs removed was 2 (mean, 1.8; range, 1-10) and 599 patients (19.7%) had SLNs with low-CPM. The total number of radioactive SLNs was 5,472, and 875 (16.0%) out of 5,472 SLNs were low-CPM. Sixty-one (7.0%) out of these 875 SLNs with low CPM in 56 patients (1.8%) had metastatic disease by pathological assessment. The number of metastatic SLN with low-CPM was one in 51 patients and two in 5 patients. Nineteen patients (0.6%) had no metastatic lesion in SLNs with high-CPM.

Discussion and Conclusions:

If SLNB was performed by RI method alone with “10% rule”, false negative rate increased by 0.6% and underestimation increased up to 1.8%. Furthermore, 19.7% of the patients have the benefit of avoiding excessive removal of SLNs.Considering the risk and benefit, “10% rule” is a high validitymethod to capture metastatic SLNs even in the setting that ALND will not be performed.

Citation Format: Miyamoto H, Aruga T, Onishi M, Goto R, Iwamoto N, Idera N, Horiguchi K, Honda Y. Re-evaluating the “10% rule” for sentinel lymph node biopsy with radioactive method in breast cancer; a single institutional retrospective study [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-01-09.

Novel pH control strategy for efficient production of optically active l-lactic acid from kitchen refuse using a mixed culture system

Uninvestigated control factors of meta-fermentation, the fermentative production of pure chemicals and fuels in a mixed culture system, were examined for production of optically pure l-lactic acid (LA) from food waste. In meta-fermentations by pH swing control, l-LA production with 100% optical purity (OPl-LA) was achieved even using unsterilized model kitchen refuse medium with preferential proliferation of l-LA-producing Bacillus coagulans, a minor member in the seed, whereas agitation decreased OPl-LA drastically. pH constant control shortened the fermentation time but decreased OPl-LA and LA selectivity (SLA) by stimulating growth of heterofermentative Bacillus thermoamylovorans. Deliberately switching from pH swing control to constant control exhibited the best performance for l-LA production: maximum accumulation, 39.2gL(-1); OPl-LA, 100%; SLA, 96.6%; productivity, 1.09gL(-1)h(-1). These results present a novel pH control strategy for efficient l-LA production in meta-fermentation based on a concept different from that of pure culture systems.

Development of a systematic feedback isolation approach for targeted strains from mixed culture systems

Elucidation of functions of bacteria in a mixed culture system (MCS) such as composting, activated sludge system is difficult, since the system is complicating with many unisolated bacteria. Here, we developed a systematic feedback isolation strategy for the isolation and rapid screening of multiple targeted strains from MCS. Six major strains (Corynebacterium sphenisci, Bacillus thermocloacae, Bacillus thermoamylovorans, Bacillus smithii, Bacillus humi, and Bacillus coagulans), which are detected by denaturing gradient gel electrophoresis (DGGE) analysis in our previous study on MCS for l-lactic acid production, were targeted for isolation. Based on information of suitable cultivation conditions (e.g., media, pH, temperature) from the literature, feedback isolation was performed to form 136 colonies. The following direct colony matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was optimised as the second screening to narrow down 20 candidate colonies from similar spectra patterns with six closest type strains. This step could distinguish bacteria at the species level with distance similarity scores ≥0.55 corresponding to 16S rRNA gene sequence similarity ≥98.2%, suggesting that this is an effective technique to minimize isolates close to targeted type strains. Analysis of 16S rRNA gene sequences indicated that two targeted strains and one strain related to the target had successfully been isolated, showing high similarities (99.5-100%) with the sequences from the DGGE bands, and that the other candidates were affiliated with three strains that were closely related to the target species. This study proposes a new method for systematic feedback isolation that may be useful for isolating targeted strains from MCS for further investigation.

Thermophile-fermented compost extract as a possible feed additive to enhance fecundity in the laying hen and pig: Modulation of gut metabolism

Recently, we reported that the oral administration of an extract of compost fermented with marine animal resources and thermophilic Bacillus species should confer health benefits in fish, pigs and rodents. Herein, the relations between fecundity and gut metabolites in laying hens and pigs on farms after oral exposure to compost were investigated. On the hen farms, the egg production of hens continuously administered the extract was maintained at significantly higher levels compared with the hens not administered the extract. On the swine farms, after the compost treatment, the shipping dates of fattening pigs were shortened, with an improvement in the death rate of the pigs. When the levels of fecal organic acids, such as short-chain fatty acids, lactate, and ammonium, as indicators of gut metabolism and energy sources for peripheral tissues, were examined, the levels of the acetate, propionate, and butyrate in the feces of the hens and pigs in the compost-treated group were not always different from those in the untreated control group. However, the levels of lactate were consistently low in the feces of both animals after the compost treatment. The fecal ammonium concentrations in old hens (age 597-672 days) and 2-month-old piglets from the compost-fed mother sows were low when compared with the untreated groups. The concentrations of free organic acids and their related compounds in the animal products (eggs and pig loins) were nearly equal to those in the untreated control products. Thus, the oral administration of the thermophile-fermented compost should improve the fecundity of hens and pigs by modifying their gut metabolism.

Sonoelastographic Findings of Carpal Tunnel Injection

PURPOSE

The objectives of this study were to compare sonoelastographic color findings of the perineural area between carpal tunnel syndrome patients and healthy volunteers, and to analyze elastographic findings in that area before and immediately after intracarpal tunnel injection in carpal tunnel syndrome patients.

MATERIALS AND METHODS

We studied both hands of 15 healthy volunteers (7 men, 8 women; mean age: 60.1 years, range: 41 - 88 years) and 72 hands from 70 patients with symptomatic carpal tunnel syndrome (24 men, 46 women; mean age: 54.2 years, range: 24 - 83 years). Sonoelastographic color distribution was assessed in the perineural area between the median nerve and adjacent flexor tendons. The color elastograms were graded using the following system: Grade 1 as red (softest), grade 2 as yellow (soft), grade 3 as green (hard), grade 4 as blue (hardest). The patients were treated with corticosteroid injection and were reassessed with sonoelastography immediately after the injection.

RESULTS

The median color grading in the perineural area of carpal tunnel syndrome patients was grade 3 (3.1 ± 0.3, mean ± 95 % Cl), which was stiffer than that of healthy volunteers (grade 1, 1.9 ± 0.4) (p < 0.0001). Immediately after injection, the diffusion of the injected fluid was observed as having a softer appearance (grade 1, 1.4 ± 0.2) (p < 0.0001).

CONCLUSION

The perineural area surrounding the median nerve in carpal tunnel syndrome patients was stiffer than that in healthy volunteers. Diffusion of the injected fluid in the carpal tunnel was seen as a softer finding after injection in real time using sonoelastography.

Bacillus hisashii sp. nov., isolated from the caeca of gnotobiotic mice fed with thermophile-fermented compost

A taxonomic study was performed on 15 bacterial isolates from the caeca of gnotobiotic mice that had been fed with thermophile-fermented compost. The 15 isolates were thermophilic, Gram-stain-positive, facultatively anaerobic, endospore-forming bacteria, and were most closely related to Bacillus thermoamylovorans CNCM I-1378T. The 16S rRNA gene sequence of strain N-11T, selected as representative of this new group, showed a similarity of 99.4 % with Bacillus thermoamylovorans CNCM I-1378T, 94.7 % with Bacillus thermolactis R-6488T, and 94.4 % with Bacillus kokeshiiformis MO-04T. The isolates were then classified into two distinct groups based on a (GTG)5-fingerprint analysis. Two isolates, N-11T and N-21, were the representatives of these two groups, respectively.` The N-11T and N-21 isolates showed 66–71 % DNA–DNA relatedness with one other, but had less than 37 % DNA–DNA relatedness with B. thermoamylovorans LMG 18084T. The other 13 isolates showed DNA–DNA relatedness values above 74 % with the N-11T isolate. All 15 isolates grew at 25–60 °C (optimum 50 °C), pH 6–8 (optimum pH 7) and were capable of growing on a medium containing 6 % (w/v) NaCl (optimum 0.5 %). The 15 isolates could be distinguished from B. thermoamylovorans LMG 18084T because they showed Tween 80 hydrolysis activity and did not produce acid from melibiose. The major fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and several unidentified phospholipids. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The menaquinone was MK-7. The DNA G+C content was 37.9 mol%. Based on the phenotypic properties, the 15 strains represent a novel species of the genus Bacillus, for which the name Bacillus hisashii sp. nov. is proposed. The type strain is N-11T ( = NRBC 110226T = LMG 28201T).