Novel machine learning method allerStat identifies statistically significant allergen-specific patterns in protein sequences.

Cutting-edge technologies such as genome editing and synthetic biology allow us to produce novel foods and functional proteins. However, their toxicity and allergenicity must be accurately evaluated. It is known that specific amino acid sequences in proteins make some proteins allergic, but many of these sequences remain uncharacterized. In this study, we introduce a data-driven approach and a machine-learning method to find undiscovered allergen-specific patterns (ASPs) among amino acid sequences. The proposed method enables an exhaustive search for amino acid subsequences whose frequencies are statistically significantly higher in allergenic proteins. As a proof-of-concept, we created a database containing 21,154 proteins of which the presence or absence of allergic reactions are already known and applied the proposed method to the database. The detected ASPs in this proof-of-concept study were consistent with known biological findings, and the allergenicity prediction performance using the detected ASPs was higher than extant approaches, indicating this method may be useful in evaluating the utility of synthetic foods and proteins.

Impact of Atomic Defects on Ceria Surfaces on Chemical Mechanical Polishing of Silica Glass Surfaces.

This study investigates the impact of atomic defects, such as oxygen vacancies and Ce3+ ions, on cerium oxide (ceria) surfaces during chemical mechanical polishing (CMP) for silica glass finishing. Using density functional theory (DFT) and reactive molecular dynamics simulations, the interaction of orthosilicic molecules and silica glass with dry and wet ceria surfaces is explored. Defects alter the surface reactivity, leading to the dissociation of orthosilicic acid on oxygen vacancies, forming a strong Si-O-Ce bond. Hydroxylated surfaces exhibit easier oxygen vacancy formation and thermodynamically favored substitution of hydroxyl groups with orthosilicic acid. A new ReaxFF library for silica/ceria interfaces with defects is validated using DFT outcomes. Reactive MD simulations demonstrate that ceria surfaces with 30% Ce3+ ions on (111) planes exhibit higher polishing efficiency, attributed to increased Si-O-Ce bond formation. The simultaneous presence of oxygen vacancies and various acidic and basic sites on ceria surfaces enhances the polishing efficiency, involving acid-base reactions with silica. Defective surfaces show superior efficiency by removing silicate chains, contrasting with nondefective surfaces removing isolated orthosilicate units. This study provides insights into optimizing CMP processes for high-precision glass industry surface finishing.

A major flood caused by a typhoon did not affect the population genetic structure of a river mayfly metapopulation.

Floods affect the population structure of organisms that inhabit streams. In recent decades, the scale of floods has become larger due to climate change. Under these circumstances, on 12 October 2019, the largest typhoon in the history of observation in Japan struck the Japanese Archipelago. This typhoon caused heavy rainfall in various places, and the Chikuma-Shinano River System (Japan's largest) suffered great damage. Eight years before the large-scale disturbance in the river system, the population structure of the mayfly Isonychia japonica was studied in detail using quantitative sampling (population numbers and biomass) and by sequencing the mtDNA cytochrome c oxidase subunit I. To understand the impact of the flood on the population and genetic structures, we repeated the same research approximately 1 year after the flood. Direct comparison of sites before and after the flood revealed no significant changes between pre- and post-flood population genetic structure. This indicates high in situ resistance and/or resilience recovery of the populations to the disturbance. We hypothesize that this high resistance/resilience to flood disturbance is a result of strong selection for such traits in the rivers of the Japanese Archipelago, which are short, steep, flow rapidly and violently, and are strongly affected by floods.

Effects of the preservation medium and storage duration of domestic cat ovaries on the maturational and developmental competence of oocytes in vitro.

We examined the effectiveness of saline, Euro-Collins solution (EC), and ET-Kyoto solution (ET-K) as preservation media for the cold storage of feline ovaries. Ovaries were maintained in these media at 4°C for 24, 48, or 72 h until oocyte retrieval. The ET-K group exhibited a higher oocyte maturation rate than the saline group after 72 h of storage. Moreover, ET-K could sustain the competence of the feline oocytes to cleave after 48 h, and the morula formation rate of the ET-K group was higher than that of the other groups after 24 and 48 h. Furthermore, the ET-K group exhibited a higher blastocyst formation rate than the other groups after storage for 24 h, and only ET-K retained the developmental competence in blastocysts after 48 h of storage. In addition, regarding the cell numbers of the blastocysts, there was no significant difference among the tested groups. In conclusion, our results indicate that ET-K is a suitable preservation medium for feline ovaries.

Canine induced pluripotent stem cell maintenance under feeder-free and chemically-defined conditions.

Canine induced pluripotent stem cells (ciPSCs) provide a platform for regenerative veterinary medicine, disease modeling, and drug discovery. However, in the conventional method, ciPSCs are maintained using chemically-undefined media containing unknown animal components under on-murine embryonic fibroblast feeder conditions, which were reported to modify cell surface of iPSCs and increases the risk of immune rejection when the cells are transplanted into patients. Moreover, in the conventional method, ciPSCs are mechanically passaged, which requires much time and effort. Therefore, the large-scale expansion of ciPSCs is difficult, which should be resolved for using ciPSCs in clinical application and research. Here, it was shown that StemFit® AK02N and iMatrix-511 could maintain the pluripotency of ciPSCs using conventional culture method. Furthermore, it was demonstrated that the feeder-free and chemically-defined ciPSC culture systems using StemFit® AK02N and iMatrix-511 could stably maintain and allow the easy expansion of ciPSCs generated using N2B27 and StemFit® AK02N, without causing karyotype abnormalities. ciPSCs expressed several pluripotency markers and formed teratomas, including cells derived from three germ layers.

Status Estimation and In-Process Connection of Kanbans Using BLE Beacons and LPWA Network to Implement Intra-Traceability for the Kanban System.

IoT-based measurement systems for manufacturing have been widely implemented. As components that can be implemented at low cost, BLE beacons have been used in several systems developed in previous research. In this work, we focus on the Kanban system, which is a measure used in manufacturing strategy. The Kanban system emphasizes inventory management and is used to produce only required amounts. In the Kanban system, the Kanban cards are rotated through the factory along with the products, and when the products change to a different process route, the Kanban card is removed from the products and the products are assigned to another Kanban. For this reason, a single Kanban cannot trace products from plan to completion. In this work, we propose a system that uses a Bluetooth low energy (BLE) beacon to connect Kanbans in different routes but assigned to the same products. The proposed method estimates the beacon status of whether the Kanban is inside or outside a postbox, which can then be computed by a micro controller at low computational cost. In addition, the system connects the Kanbans using the beacons as paired connection targets. In an experiment, we confirmed that the system connected 70% of the beacons accurately. We also confirmed that the system could connect the Kanbans at a small implementation cost.

Facile and Versatile Synthesis of End-Functionalized Poly(phenylacetylene)s: A Multicomponent Catalytic System for Well-Controlled Living Polymerization of Phenylacetylenes.

A rhodium-based multicomponent catalytic system for well-controlled living polymerization of phenylacetylenes has been developed. The catalytic system is composed of readily available and bench-stable [Rh(nbd)Cl]2 , aryl boronic acid derivatives, diphenylacetylene, 50 % aqueous KOH, and PPh3 . This system offers a method for the facile and versatile synthesis of various end-functionalized cis-stereoregular poly(phenylacetylene)s because components from aryl boronic acids and diphenylacetylene were introduced to the initiating end of the polymers. The polymerization reaction shows a typical living nature with a high initiation efficiency, and the molecular weight of the resulting poly(phenylacetylene)s can be readily controlled with very narrow molecular-weight distributions (Mw /Mn =1.02-1.09). The experimental results suggest that the present catalytic system has a higher polymerization activity than the polymerization activities of other rhodium-based catalytic systems previously reported.

Canine induced pluripotent stem cells can be successfully maintained in weekend-free culture systems.

Canine induced pluripotent stem cells (ciPSCs) can provide useful insights into novel therapies in both veterinary and medical fields. However, limited accessibility to the present culture medium and requirement of considerable time, effort, and cost for routine ciPSC maintenance restrict advancement in ciPSC research. In addition, it is unknown whether ciPSC culture conditions influence differentiation propensity. We investigated the availability of the common human pluripotent stem cells (hPSCs) culture systems for ciPSC maintenance and the differentiation propensities of the ciPSCs maintained in these culture systems. StemFlex and mTeSR Plus supported PSC-like colony formation and pluripotency markers expression in ciPSCs even after five passages. Additionally, ciPSCs were maintained under weekend-free culture conditions with a stable growth rate, pluripotency marker expression, and differentiation abilities using vitronectin (VTN-N) and Geltrex. Following maintenance of spontaneously differentiated ciPSCs under various conditions by embryoid body formation, there were few differences in the differentiation propensities of ciPSCs among the tested culture conditions. Thus, ciPSCs were successfully cultured under weekend-free conditions for ciPSC maintenance using StemFlex or mTeSR Plus with VTN-N or Geltrex. The present study offers simpler and more effort-, time-, and cost-saving options for ciPSC culture systems, which may lead to further development in research using ciPSCs.

Generation of canine induced pluripotent stem cells under feeder-free conditions using Sendai virus vector encoding six canine reprogramming factors.

Although it is in its early stages, canine induced pluripotent stem cells (ciPSCs) hold great potential for innovative translational research in regenerative medicine, developmental biology, drug screening, and disease modeling. However, almost all ciPSCs were generated from fibroblasts, and available canine cell sources for reprogramming are still limited. Furthermore, no report is available to generate ciPSCs under feeder-free conditions because of their low reprogramming efficiency. Here, we reanalyzed canine pluripotency-associated genes and designed canine LIN28A, NANOG, OCT3/4, SOX2, KLF4, and C-MYC encoding Sendai virus vector, called 159cf. and 162cf. We demonstrated that not only canine fibroblasts but also canine urine-derived cells, which can be isolated using a noninvasive and straightforward method, were successfully reprogrammed with or without feeder cells. ciPSCs existed in undifferentiated states, differentiating into the three germ layers in vitro and in vivo. We successfully generated ciPSCs under feeder-free conditions, which can promote studies in veterinary and consequently human regenerative medicines.

Efficient model selection for predictive pattern mining model by safe pattern pruning.

Predictive pattern mining is an approach used to construct prediction models when the input is represented by structured data, such as sets, graphs, and sequences. The main idea behind predictive pattern mining is to build a prediction model by considering unified inconsistent notation sub-structures, such as subsets, subgraphs, and subsequences (referred to as patterns), present in the structured data as features of the model. The primary challenge in predictive pattern mining lies in the exponential growth of the number of patterns with the complexity of the structured data. In this study, we propose the safe pattern pruning method to address the explosion of pattern numbers in predictive pattern mining. We also discuss how it can be effectively employed throughout the entire model building process in practical data analysis. To demonstrate the effectiveness of the proposed method, we conduct numerical experiments on regression and classification problems involving sets, graphs, and sequences.

First Total Synthesis of Tanzawaic Acid B.

The first total synthesis of (+)-tanzawaic acid B, a natural polyketide bearing a pentadienoic ester and octalin moiety, has been accomplished. The synthetic improvement from previous synthetic conditions facilitated our gram-scale synthesis of the chiral octalin that possesses seven stereogenic centers and that is the core skeleton of almost all of the tanzawaic acid family.

Correction to "First Total Synthesis of Tanzawaic Acid B".

[This corrects the article DOI: 10.1021/acsomega.3c03634.].

Iron-catalyzed chemo- and stereoselective hydromagnesiation of diarylalkynes and diynes.

Diarylalkynes are chemo- and stereoselectively hydromagnesiated in high yields at room temperature with an iron species generated in situ from FeCl(2)and EtMgBr. Functional groups such as bromide, iodide, amine, phenoxide, and alkene are well tolerated. Under similar conditions, diynes are chemo-, regio-, and stereoselectively hydromagnesiated. The resulting alkenylmagnesium compounds are a platform for further functionalization as a one-pot reaction.

Reduced Klotho expression level in kidney aggravates renal interstitial fibrosis.

Renal expression of the klotho gene is markedly suppressed in chronic kidney disease (CKD). Since renal fibrosis is the final common pathology of CKD, we tested whether decreased Klotho expression is a cause and/or a result of renal fibrosis in mice and cultured renal cell lines. We induced renal fibrosis by unilateral ureteral obstruction (UUO) in mice with reduced Klotho expression (kl/+ mice) and compared them with wild-type mice. The UUO kidneys from kl/+ mice expressed significantly higher levels of fibrosis markers such as α-smooth muscle actin (α-SMA), fibronectin, and transforming growth factor-ß(1) (TGF-ß(1)) than those from wild-type mice. In addition, in cultured renal fibroblast cells (NRK49F), the levels of α-SMA and PAI1 expression were significantly suppressed by addition of recombinant Klotho protein to the medium. The similar effects were observed by a TGF-ß(1) receptor inhibitor (ALK5 inhibitor). These observations suggest that low renal Klotho expression enhances TGF-ß(1) activity and is a cause of renal fibrosis. On the other hand, TGF-ß(1) reduced Klotho expression in renal cultured epithelial cells (inner medullary collecting duct and human renal proximal tubular epithelium), suggesting that low renal Klotho expression is a result of renal fibrosis. Taken together, renal fibrosis can trigger a deterioration spiral of Klotho expression, which may be involved in the pathophysiology of CKD progression.

Canine induced pluripotent stem cells efficiently differentiate into definitive endoderm in 3D cell culture conditions using high-dose activin A.

Introduction: Endoderm-derived organs support indispensable functions in the body. Pluripotent stem cells can generate endoderm-derived cells or tissues and have excellent therapeutic potential to replace the functions of endodermal tissues. However, there is no viable method to induce endodermal precursor cells, definitive endoderm (DE), from canine induced pluripotent stem cells (ciPSCs). Methods: A ciPSC line was used in this study. In order to induce DE, ciPSCs were cultured with high dose activin A and fetal bovine serum. We considered the optimal differentiation period and starting cell density. Next, to reduce the remaining undifferentiated cells and improve the DE induction efficiency, DE was induced from 3D cell aggregates with knockout serum replacement instead of fetal bovine serum. Finally, hepatic and pancreatic induction were performed to investigate whether DE could differentiate into downstream lineages. Results: After differentiation, some cells expressed the DE markers FOXA2 and SOX17. DE induction period and starting cell density were found to be important for efficient DE induction. However, some cells remained undifferentiated even after optimization of cell density and culture period. Cell differentiation under 3D culture conditions reduced undifferentiated cells and the replacement of fetal bovine serum with knockout serum replacement improved the DE induction efficiency. After hepatic and pancreatic induction, cells expressed some early hepatic and pancreatic markers. Conclusions: A ciPSC line was successfully differentiated to DE efficiently using a high dose of activin A with knockout serum replacement under 3D cell culture conditions. We believe that this study will be fundamental to achieving the generation of canine endodermal tissues from ciPSCs.

Polyvinyl alcohol coating prevents platelet adsorption and improves mechanical property of polycaprolactone-based small-caliber vascular graft.

The low patency of synthetic vascular grafts hinders their practical applicability. Polyvinyl alcohol (PVA) is a non-toxic, highly hydrophilic polymer; thus, we created a PVA-coated polycaprolactone (PCL) nanofiber vascular graft (PVA-PCL graft). In this study, we examine whether PVA could improve the hydrophilicity of PCL grafts and evaluate its in vivo performance using a rat aorta implantation model. A PCL graft with an inner diameter of 1 mm is created using electrospinning (control). The PCL nanofibers are coated with PVA, resulting in a PVA-PCL graft. Mechanical property tests demonstrate that the PVA coating significantly increases the stiffness and resilience of the PCL graft. The PVA-PCL surface exhibits a much smaller sessile drop contact angle when compared with that of the control, indicating that the PVA coating has hydrophilic properties. Additionally, the PVA-PCL graft shows significantly less platelet adsorption than the control. The proposed PVA-PCL graft is implanted into the rat's abdominal aorta, and its in vivo performance is tested at 8 weeks. The patency rate is 83.3% (10/12). The histological analysis demonstrates autologous cell engraftment on and inside the scaffold, as well as CD31/α-smooth muscle positive neointima regeneration on the graft lumen. Thus, the PVA-PCL grafts exhibit biocompatibility in the rat model, which suggests that the PVA coating is a promising approach for functionalizing PCL.

Insulin therapy maintains the performance of PVA-coated PCL grafts in a diabetic rat model.

Vascular tissue engineering has shown promising results in "healthy" animal models. However, studies on the efficacy of artificial grafts under "pathological conditions" are limited. Therefore, in this study, we aimed to characterize the performance of polyvinyl alcohol (PVA)-coated poly-ε-caprolactone (PCL) grafts (PVA-PCL grafts) under diabetic conditions. To this end, PCL grafts were produced via electrospinning and coated with the hydrophilic PVA polymer, while a diabetic rat model (DM) was established via streptozotocin injection. Thereafter, the performance of the graft in the infrarenal abdominal aorta of the rats was evaluated in vivo. Thus, we observed that the healthy group showed CD31 positive/αSM positive cells in the graft lumen. Further, the patency rate of the PVA-PCL graft was 100% at 2 weeks (n = 7), while all the DM rats (n = 8) showed occluded grafts. However, the treatment of DM rats with neutral protamine Hagedorn insulin (tDM) significantly improved the patency rate (100%; n = 5). Furthermore, the intimal coverage rate corresponding to the tDM group was comparable to that of the healthy group at 2 weeks (tDM vs. healthy: 16.1% vs. 14.7%, p = 0.931). Therefore, the present study demonstrated that the performance of the PVA-PCL grafts was impaired in DM rats; however, insulin treatment reversed this impairment. These findings highlighted the importance of using a model that more closely resembles the cases that are encountered in clinical practice to achieve a clinically applicable vascular graft with a small diameter.

Short chain fatty acids-producing and mucin-degrading intestinal bacteria predict the progression of early Parkinson's disease.

To elucidate the relevance of gut dysbiosis in Parkinson's disease (PD) in disease progression, we made random forest models to predict the progression of PD in two years by gut microbiota in 165 PD patients. The area under the receiver operating characteristic curves (AUROCs) of gut microbiota-based models for Hoehn & Yahr (HY) stages 1 and 2 were 0.799 and 0.705, respectively. Similarly, gut microbiota predicted the progression of Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) III scores in an early stage of PD with AUROC = 0.728. Decreases of short-chain fatty acid-producing genera, Fusicatenibacter, Faecalibacterium, and Blautia, as well as an increase of mucin-degrading genus Akkermansia, predicted accelerated disease progression. The four genera remained unchanged in two years in PD, indicating that the taxonomic changes were not the consequences of disease progression. PD patients with marked gut dysbiosis may thus be destined to progress faster than those without gut dysbiosis.

Arabidopsis HsfA1 transcription factors function as the main positive regulators in heat shock-responsive gene expression.

Arabidopsis DREB2A is a key transcription factor of heat- and drought-responsive gene expression, and DREB2A expression is induced by these stresses. We analyzed the DREB2A promoter and found a heat shock element that functions as a cis-acting element in the heat shock (HS)-responsive expression of DREB2A. Among the 21 Arabidopsis heat shock factors, we chose 4 HsfA1-type proteins as candidate transcriptional activators (HsfA1a, HsfA1b, HsfA1d, and HsfA1e) based on transactivation activity and expression patterns. We generated multiple mutants and found that the HS-responsive expression of DREB2A disappeared in hsfa1a/b/d triple and hsfa1a/b/d/e quadruple mutants. Moreover, HS-responsive gene expression, including that of molecular chaperones and transcription factors, was globally and drastically impaired in the hsfa1a/b/d triple mutant, which exhibited greatly reduced tolerance to HS stress. HsfA1 protein accumulation in the nucleus was negatively regulated by their interactions with HSP90, and other factors potentially strongly activate the HsfA1 proteins under HS stress. The hsfa1a/b/d/e quadruple mutant showed severe growth retardation, and many genes were downregulated in this mutant even under non-stress conditions. Our study indicates that HsfA1a, HsfA1b, and HsfA1d function as main positive regulators in HS-responsive gene expression and four HsfA1-type proteins are important in gene expression for normal plant growth.

Clinical outcomes in patients with chronic kidney disease: a 5-year retrospective cohort study at a University Hospital in Japan.

BACKGROUND: Latent chronic kidney disease (CKD) population appears to be a serious health problem in Japan. The purposes of the present study were to determine risk factors for CKD progression and to evaluate the rate of decline in estimated glomerular filtration rate (eGFR). METHODS: A retrospective cohort study of adult patients with CKD was conducted at a University Hospital in Japan. The primary outcome was rate of change in eGFR over time. Age-based eGFR was calculated by the Modification of Diet in Renal Disease study equation for Japan. Blood and urine specimens were collected at study entry along with information regarding blood pressure (BP), body mass index and medications. Patients were monitored for up to 5 years. RESULTS: A total of 1115 patients were enrolled with mean (SD) age of 63.1 (16.5) years; 43.1% were women, and 16.4% had diabetes. At study entry, body mass index was 23.3 (3.9) kg/m(2), and mean BP was 125.4 (16.0) mmHg. Systolic BP, creatinine, uric acid and urinary protein levels differed significantly among patients grouped by CKD stages, and the values tended to increase in the higher disease stages. Time-to-event analysis showed that 3.45% of patients experienced a 50% eGFR decline. The slope of the eGFR decline was -1.01 (mL/min per 1.73 m(2)) per year, as assessed by repeated-measures analysis (-1.18 in men and -0.78 in women). In addition, the slope of the decline tended to be smaller in the higher CKD stages (stage 5, -0.31%; stage 4, -1.32%; stage 3, -0.75%; stage 2, -1.10%; stage 1, -2.33%). Serum creatinine and diabetes were identified as predictors of CKD progression by time-to-event analysis, but not by repeated-measures analysis. Conversely, urinary occult blood, blood glucose, and treatment with angiotensin-converting enzyme inhibitors, and anti-platelet agents were identified by repeated-measures analysis but not by time-to-event analysis. CONCLUSIONS: The slope of the eGFR decline was influenced by CKD stages, underlying diseases and medications taken by patients. Long-term follow-up of patients will provide critical insights into factors affecting progression of CKD.