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Abstract Background Hypophosphatemia due to excessive carbohydrate administration is considered the primary pathogenesis of refeeding syndrome. However, its association with liver injury and hypoglycemia, often seen in severe malnutrition before re-nutrition, remains unclear. Autophagy reportedly occurs in the liver of patients with severe malnutrition. This study aimed to clarify the pathophysiology of liver injury and hypoglycemia by focusing on liver volume. Methods Forty-eight patients with anorexia nervosa with a body mass index (BMI) of

RNA-seq is a tool for measuring gene expression and is commonly used to identify differentially expressed genes (DEGs). Gene clustering has been widely used to classify DEGs with similar expression patterns, but rarely used to identify DEGs themselves. We recently reported that the clustering-based method (called MBCdeg1 and 2) for identifying DEGs has great potential. However, these methods left room for improvement. This study reports on the improvement (named MBCdeg3). We compared a total of six competing methods: three conventional R packages (edgeR, DESeq2, and TCC) and three versions of MBCdeg (i.e., MBCdeg1, 2, and 3) corresponding to three different normalization algorithms. As MBCdeg3 performs well in many simulation scenarios of RNA-seq count data, MBCdeg3 replaces MBCdeg1 and 2 in our previous report. • MBCdeg3 is a method for both identification and classification of DEGs from RNA-seq count data. • MBCdeg3 is available as a function of R, which is common in the field of expression analysis. • MBCdeg3 performs well in a variety of simulation scenarios for RNA-seq count data.

Abstract Background Acute mountain sickness (AMS) affects around 30% of people climbing Mt. Fuji, but its pathogenesis is incompletely understood. The influence of a rapid ascent to high altitude by climbing and summiting Mt. Fuji on cardiac function in the general population is unknown, and its association with altitude sickness has not been clarified. Methods Subjects climbing Mt. Fuji were included. Heart rate, oxygen saturation, systolic blood pressure, cardiac index (CI) and stroke volume index were measured multiple times at 120 m as baseline values and at Mt. Fuji Research Station (MFRS) at 3,775 m. Each value and its difference from the baseline value (Δ) of subjects with AMS (defined as Lake Louise Score [LLS] ≥ 3 with headache after sleeping at 3,775 m) were compared with those of non-AMS subjects. Results Eleven volunteers who climbed from 2,380 m to MFRS within 8 h and stayed overnight at MFRS were included. Four suffered AMS. Compared with the non-AMS subjects, CI in the AMS subjects was significantly higher than that before sleeping (median [interquartile range]: 4.9 [4.5, 5.0] vs. 3.8 [3.4, 3.9] mL/min/m2; p = 0.04), and their ΔCI was significantly higher before sleeping (1.6 [1.4, 2.1] vs. 0.2 [0.0, 0.7] mL/min/m2; p

Plants employ self-incompatibility (SI) to promote cross-fertilization. In Brassicaceae, this process is regulated by the formation of a complex between the pistil determinant S receptor kinase (SRK) and the pollen determinant S-locus protein 11 (SP11, also known as S-locus cysteine-rich protein, SCR). In our previous study, we used the crystal structures of two eSRK–SP11 complexes in Brassica rapa S8 and S9 haplotypes and nine computationally predicted complex models to demonstrate that only the SRK ectodomain (eSRK) and SP11 pairs derived from the same S haplotype exhibit high binding free energy. However, predicting the eSRK–SP11 complex structures for the other 100 + S haplotypes and genera remains difficult because of SP11 polymorphism in sequence and structure. Although protein structure prediction using AlphaFold2 exhibits considerably high accuracy for most protein monomers and complexes, 46% of the predicted SP11 structures that we tested showed

Abstract Age-related changes in the posterior extensor muscles of the cervical and lumbar spine have been reported in some studies; however, longitudinal changes in the thoracic spine of healthy subjects are rarely reported. Therefore, this study aimed to evaluate changes in the cross-sectional areas (CSAs) of posterior extensor muscles in the thoracic spine over 10 years and identify related factors. The subjects of this study were 85 volunteers (mean age: 44.7 ± 11.5) and the average follow-up period was about 10 years. The CSAs of the transversospinalis muscles, erector spinae muscles, and total CSAs of the extensor muscles from T1/2 to T11/12 were measured on magnetic resonance imaging. The extent of muscle fat infiltration was assessed by the signal intensity (luminance) of the extensor muscles’ total cross-section compared to a section of pure muscle. We applied a Poisson regression model, which is included in the generalized linear model, and first examined the univariate (crude) association between each relevant factor (age, sex, body mass index, lifestyle, back pain, neck pain, neck stiffness, and intervertebral disc degeneration) and CSA changes. Then, we constructed a multivariate model, which included age, sex, and related factors in the univariate analysis. The mean CSAs of the transversospinalis muscles, erector spinae muscles, and total CSAs of the extensor muscles significantly increased over 10 years. Exercise habit was associated with increased CSAs of the erector spinae muscles and the total area of the extensor muscles. The cross-section mean luminance significantly increased from baseline, indicating a significant increase of fat infiltration in the posterior extensor muscles. Progression of disc degeneration was inversely associated with increased fat infiltration in the total extensor muscles.

Abstract Shiga toxin (Stx), a major virulence factor of enterohemorrhagic Escherichia coli (EHEC), can cause fatal systemic complications. Recently, we identified a potent inhibitory peptide that binds to the catalytic A-subunit of Stx. Here, using biochemical structural analysis and X-ray crystallography, we determined a minimal essential peptide motif that occupies the catalytic cavity and is required for binding to the A-subunit of Stx2a, a highly virulent Stx subtype. Molecular dynamics simulations also identified the same motif and allowed determination of a unique pharmacophore for A-subunit binding. Notably, a series of synthetic peptides containing the motif efficiently inhibit Stx2a. In addition, pharmacophore screening and subsequent docking simulations ultimately identified nine Stx2a-interacting molecules out of a chemical compound database consisting of over 7,400,000 molecules. Critically, one of these molecules markedly inhibits Stx2a both in vitro and in vivo, clearly demonstrating the significance of the pharmacophore for identifying therapeutic agents against EHEC infection.

Abstract Background RNA-seq is a tool for measuring gene expression and is commonly used to identify differentially expressed genes (DEGs). Gene clustering is used to classify DEGs with similar expression patterns for the subsequent analyses of data from experiments such as time-courses or multi-group comparisons. However, gene clustering has rarely been used for analyzing simple two-group data or differential expression (DE). In this study, we report that a model-based clustering algorithm implemented in an R package, MBCluster.Seq, can also be used for DE analysis. Results The input data originally used by MBCluster.Seq is DEGs, and the proposed method (called MBCdeg) uses all genes for the analysis. The method uses posterior probabilities of genes assigned to a cluster displaying non-DEG pattern for overall gene ranking. We compared the performance of MBCdeg with conventional R packages such as edgeR, DESeq2, and TCC that are specialized for DE analysis using simulated and real data. Our results showed that MBCdeg outperformed other methods when the proportion of DEG (P DEG ) was less than 50%. However, the DEG identification using MBCdeg was less consistent than with conventional methods. We compared the effects of different normalization algorithms using MBCdeg, and performed an analysis using MBCdeg in combination with a robust normalization algorithm (called DEGES) that was not implemented in MBCluster.Seq. The new analysis method showed greater stability than using the original MBCdeg with the default normalization algorithm. Conclusions MBCdeg with DEGES normalization can be used in the identification of DEGs when the P DEG is relatively low. As the method is based on gene clustering, the DE result includes information on which expression pattern the gene belongs to. The new method may be useful for the analysis of time-course and multi-group data, where the classification of expression patterns is often required.

Objectives: The spleen is a key organ of the immune system. Asplenia has been reported to increase the risk of sepsis from overwhelming post-splenectomy infection. However, there are few reports on the association between splenic volume and mortality in patients with no history of splenectomy. This study focused on splenic volume of patients with sepsis and evaluated the association between splenic volume and mortality. Methods: We retrospectively investigated 232 patients with sepsis. The splenic volume was calculated by using computed tomography scans obtained on admission. The patients were categorized into tertiles based on their splenic volume, and the relationship between splenic volume and mortality was evaluated. Odds ratio curves based on splenic volume were created to assess the continuous associations between splenic volume and outcome with a logistic regression model. Results: The patients with sepsis were divided into three groups according to the first (73.6 cm3) and second (128.7 cm3) tertile values of splenic volume. Kaplan–Meier estimation of the probability of the patients’ survival followed up to 28 days showed significant differences between the groups (p= 0.03). The hazard ratio for 28-day mortality in the first tertile group was 3.46 (95% CI 1.3–10.2; p = 0.01) as compared with patients in the third tertile group. Patients with smaller spleens had increased odds ratios for mortality in the logistic regression model. Conclusions: Splenic volume appeared to be an independent predictor of poor prognosis.

Abstract We comment on the study by Batra et al. on the efficacy of probiotics in the prevention of ventilator-associated pneumonia in critically ill ICU patients. They also reported that probiotics administration was not associated with a statistically significant reduction in the incidence of diarrhea (OR 0.59; CI 0.34, 1.03; P = 0.06; I 2 = 38%). However, their meta-analysis missed one RCT, and when we repeated the analysis including this RCT, we found that probiotics administration significantly reduced the incidence of diarrhea (OR 0.51; CI 0.28, 0.92; P = 0.02; I 2 = 45.6%). We thus believe that probiotics administration is effective in reducing the incidence of diarrhea in ventilated critically ill ICU patients.

A compound from Thai black ginger, KPMF-8, was previously found to dramatically promote activation of SIRT1 towards a peptide substrate. Zhang et al. now show that KPMF-8 can be taken up by cells through culture media, directly interacts with SIRT1, and promotes its deacetylation activity toward native substrate more effectively than resveratrol.

Abstract Quite a few changes and challenges have arisen in society in general as technology has advanced and the aging population has increased. These can lead to the recognition of the shortcomings of a society’s traditional systems and the various changes that are needed, especially in providing emergency medical care. A super-aged society has been developing in Japan, and the emergency care system needs to change according to these new demographics and society’s needs. The focus has been shifting from critical care and trauma to medical and surgical conditions involving the elderly. Challenges in triage, ambulance diversion, and staffing are discussed in this review. Possible solutions currently underway, such as a public helpline, smartphone app system, coordination by designated hospitals, and universal coverage/government support, are discussed as future directions. Emergency medicine in Japan needs to develop in a more flexible way to meet the upcoming robust challenges of the changing demographics.

For Pseudomonas aeruginosa (PA), infection control and appropriate antimicrobial treatment have become important issues. Diagnosis is critical in managing PA infection, but conventional methods are not highly accurate or rapid. We developed a new PA quantification system based on 23S rRNA-targeted reverse transcription quantitative PCR (RT-qPCR). We confirmed that RT-qPCR can quantify PA directly from clinical samples quickly (within 6 h) and with high sensitivity (blood, 1 cell/mL; stool, 100 cells/g) and without cross-reaction. Also, under antibiotic treatment, PA viable counts detected by this system correlated well with the inflammatory response of infected Caco-2 cells compared to other methods such as culturing and qPCR. Next, we utilized this system on fecal samples collected from 65 septic ICU patients and 44 healthy volunteers to identify ICU infection status. We confirmed that the PA detection ratio in ICU patients was significantly higher than that in healthy volunteers (49.2% vs. 13.6%, P

Self-incompatibility responses in Brassica are induced by haplotype-specific interactions between the pistil-expressed SRK receptor and pollen-expressed SP11 ligand. Here, via crystal structures and molecular dynamic simulations, the authors provide a model to explain why binding of cognate partners is favoured and how haplotypes can be distinguished.

Aim Hyperglycemia is a common response to acute illness, but it is not often seen in critical conditions. The frequency and cause of hypoglycemia in septic patients have not been well elucidated. In this study, we focused on sepsis‐associated hypoglycemia in the early phase and evaluated the impact of hypoglycemia on mortality. Methods We performed a retrospective review of 265 patients with sepsis admitted to a tertiary medical center. Blood glucose levels on admission were evaluated and analyzed by a Cox proportional hazard model. Results We categorized patients with sepsis into five groups according to blood glucose levels. Seven patients (2.6%) were admitted with severe hypoglycemia (≤40 mg/dL), 19 (7.2%) with mild hypoglycemia (41–70 mg/dL), 103 (38.9%) with euglycemia (71–140 mg/dL), 58 (21.9%) with mild hyperglycemia (141–180 mg/dL), and 78 (29.4%) with hyperglycemia (>180 mg/dL). There was a significant difference in 28‐day mortality between those with severe hypoglycemia and euglycemia (71.4% versus 8.7%; P

Aim Sepsis causes a systemic inflammatory reaction by destroying intestinal flora, which leads to a poor prognosis. In this study, we sought to clarify the characteristics of fecal flora and metabolites in a mouse model of sepsis by comprehensive metagenomic and metabolomic analysis. Methods We performed a cecal ligation and puncture model procedure to create a mild sepsis model. We collected fecal samples on day 0 (healthy condition) and days 1 and 7 after the cecal ligation and puncture to determine the microbiome and metabolites. We analyzed fecal flora using 16S rRNA gene sequencing and metabolites using capillary electrophoresis mass spectrometry with time‐of‐flight analysis. Results The abundance of bacteria belonging to the family Enterobacteriaceae significantly increased, but that of order Clostridiales such as the families Lachnospiraceae and Ruminococcaceae decreased on day 1 after the cecal ligation and puncture compared with those before the cecal ligation and puncture. The family Enterobacteriaceae significantly decreased, but that of order Clostridiales such as the families Lachnospiraceae and Ruminococcaceae increased on day 7 compared with those on day 1 after the cecal ligation and puncture. In the fecal metabolome, 313 metabolites were identified. Particularly, essential amino acids such as valine and non‐essential amino acids such as glycine increased remarkably following injury. Betaine and trimethylamine also increased. In contrast, short‐chain fatty acids such as isovaleric acid, butyric acid, and propionic acid decreased. Conclusion The fecal microbiota following injury showed that Enterobacteriaceae increased in acute phase, and Lachnospiraceae and Ruminococcaceae increased in subacute phase. The metabolites revealed an increase in essential amino acids and choline metabolites and a decrease in short‐chain fatty acids.

Background The new coronavirus disease (COVID‐19) causes gastrointestinal symptoms as well as respiratory symptoms. Case Presentation A 60‐year‐old man was transferred with respiratory difficulty. He was diagnosed as having COVID‐19 and was intubated and placed on mechanical ventilation. He suffered from diarrhea from day 12 and produced a maximum of approximately 6,384 mL/day of watery diarrhea on day 21. He required massive transfusion. Adsorbents and pectin‐containing oligomeric formulas were administered, which decreased the amount of diarrhea. Fecal metagenomic analysis showed the proportions of the genera Enterococcus and Staphylococcus were the most dominate at the genus level. The proportion of Bacteroidetes was

Antifreeze proteins (AFPs) are proteins that protect cellular fluids and body fluids from freezing by inhibiting the nucleation and growth of ice crystals and preventing ice recrystallization, thereby contributing to the maintenance of life in living organisms. They exist in fish, insects, microorganisms, and fungi. However, the number of known AFPs is currently limited, and it is essential to construct a reliable dataset of AFPs and develop a bioinformatics tool to predict AFPs. In this work, we first collected AFPs sequences from UniProtKB considering the reliability of annotations and, based on these datasets, developed a prediction system using random forest. We achieved accuracies of 0.961 and 0.947 for non-redundant sequences with less than 90% and 30% identities and achieved the accuracy of 0.953 for representative sequences for each species. Using the ability of random forest, we identified the sequence features that contributed to the prediction. Some sequence features were common to AFPs from different species. These features include the Cys content, Ala-Ala content, Trp-Gly content, and the amino acids’ distribution related to the disorder propensity. The computer program and the dataset developed in this work are available from the GitHub site: https://github.com/ryomiya/Prediction-and-analysis-of-antifreeze-proteins.

Abstract Objective Differential expression (DE) is a fundamental step in the analysis of RNA-Seq count data. We had previously developed an R/Bioconductor package (called TCC) for this purpose. While this package has the unique feature of an in-built robust normalization method, its use has so far been limited to R users only. There is thus, a need for an alternative to DE analysis by TCC for non-R users. Results Here, we present a graphical user interface for TCC (called TCC-GUI). Non-R users only need a web browser as the minimum requirement for its use (https://infinityloop.shinyapps.io/TCC-GUI/). TCC-GUI is implemented in R and encapsulated in Shiny application. It contains all the major functionalities of TCC, including DE pipelines with robust normalization and simulation data generation under various conditions. It also contains (i) tools for exploratory analysis, including a useful score termed average silhouette that measures the degree of separation of compared groups, (ii) visualization tools such as volcano plot and heatmap with hierarchical clustering, and (iii) a reporting tool using R Markdown. By virtue of the Shiny-based GUI framework, users can obtain results simply by mouse navigation. The source code for TCC-GUI is available at https://github.com/swsoyee/TCC-GUI under MIT license.

Abstract Recent technical improvements in single-cell RNA sequencing (scRNA-seq) have enabled massively parallel profiling of transcriptomes, thereby promoting large-scale studies encompassing a wide range of cell types of multicellular organisms. With this background, we propose CellFishing.jl, a new method for searching atlas-scale datasets for similar cells and detecting noteworthy genes of query cells with high accuracy and throughput. Using multiple scRNA-seq datasets, we validate that our method demonstrates comparable accuracy to and is markedly faster than the state-of-the-art software. Moreover, CellFishing.jl is scalable to more than one million cells, and the throughput of the search is approximately 1600 cells per second.

Objectives:. To evaluate the relationship between the procalcitonin value in blood on hospital admission and its subsequent change and prognosis among sepsis patients. Design:. A single-center, retrospective, observational study. Setting:. Critical care center in Japan. Patients:. Sepsis patients 18 years old or older admitted from January 1, 2015, to March 31, 2018. Interventions:. None. Measurement and Main Results:. Among 173 sepsis patients enrolled, the median age was 74 years old (interquartile range, 64–79 yr old), and there were 102 men. The median value of procalcitonin in blood on hospital admission was 14.8 ng/mL (interquartile range, 3.5–78.4 ng/mL), and the median change in serum procalcitonin value between hospital admission and the next day was 0 ng/mL (interquartile range, –4.5 to 5.2 ng/mL). Mortality at 28 days after hospital admission was 5.8% (10/173). In univariate logistic regression analysis, elderly (crude odds ratio, 5.314; 95% CI, 1.094–25.806; p = 0.044), procalcitonin value of less than 33.2 ng/mL on hospital admission (p = 0.007), and change in serum procalcitonin of less than 0.0 ng/mL (crude odds ratio, 5.056; 95% CI, 1.041–24.545; p = 0.046) were associated with mortality at 28 days after hospital admission. The mortality of patients with a procalcitonin value of less than 33.2 ng/mL on hospital admission and change in serum procalcitonin of less than 0.0 ng/mL was 18.6% (8/43) and was significantly higher than that of other patients (p < 0.001). Conclusions:. Our study showed the sepsis patients with a procalcitonin value in blood of less than 33.2 ng/mL on hospital admission and change in serum procalcitonin of less than 0.0 ng/mL had high mortality at 28 days after hospital admission.

Contemporary speciation provides a unique opportunity to directly observe the traits and environmental responses of a new species. Cardamine insueta is an allotriploid species that appeared within the past 150 years in a Swiss village, Urnerboden. In contrast to its two progenitor species, Cardamine amara and Cardamine rivularis that live in wet and open habitats, respectively, C. insueta is found in-between their habitats with temporal water level fluctuation. This triploid species propagates clonally and serves as a triploid bridge to form higher ploidy species. Although niche separation is observed in field studies, the mechanisms underlying the environmental robustness of C. insueta are not clear. To characterize responses to a fluctuating environment, we performed a time-course analysis of homeolog gene expression in C. insueta in response to submergence treatment. For this purpose, the two parental (C. amara and C. rivularis) genome sequences were assembled with a reference-guided approach, and homeolog-specific gene expression was quantified using HomeoRoq software. We found that C. insueta and C. rivularis initiated vegetative propagation by forming ectopic meristems on leaves, while C. amara did not. We examined homeolog-specific gene expression of three species at nine time points during the treatment. The genome-wide expression ratio of homeolog pairs was 2:1 over the time-course, consistent with the ploidy number. By searching the genes with high coefficient of variation of expression over time-course transcriptome data, we found many known key transcriptional factors related to meristem development and formation upregulated in both C. rivularis and rivularis-homeolog of C. insueta, but not in C. amara. Moreover, some amara-homeologs of these genes were also upregulated in the triploid, suggesting trans-regulation. In turn, Gene Ontology analysis suggested that the expression pattern of submergence tolerant genes in the triploid was inherited from C. amara. These results suggest that the triploid C. insueta combined advantageous patterns of parental transcriptomes to contribute to its establishment in a new niche along a water-usage gradient.

Summary: Alzheimer’s disease (AD) is a progressive neurodegenerative disease caused by accumulations of Aβ peptides. Production and fibrillation of Aβ are downregulated by BRI2 and BRI3, which are physiological inhibitors of amyloid precursor protein (APP) processing and Aβ oligomerization. Here, we identify nuclear receptor binding protein 1 (NRBP1) as a substrate receptor of a Cullin-RING ubiquitin ligase (CRL) that targets BRI2 and BRI3 for degradation. Moreover, we demonstrate that (1) dimerized NRBP1 assembles into a functional Cul2- and Cul4A-containing heterodimeric CRL through its BC-box and an overlapping cryptic H-box, (2) both Cul2 and Cul4A contribute to NRBP1 CRL function, and (3) formation of the NRBP1 heterodimeric CRL is strongly enhanced by chaperone-like function of TSC22D3 and TSC22D4. NRBP1 knockdown in neuronal cells results in an increase in the abundance of BRI2 and BRI3 and significantly reduces Aβ production. Thus, disrupting interactions between NRBP1 and its substrates BRI2 and BRI3 may provide a useful therapeutic strategy for AD. : Yasukawa et al. demonstrate that BRI2 and BRI3, physiological inhibitors of Aβ production and aggregation, are substrates of NRBP1-ubiquitin ligase. In the presence of TSC22D3 and TSC22D4, a dimer of the substrate receptor NRBP1 assembles into a functional Cul2- and Cul4A-containing heterodimeric CRL through overlapping BC-box and cryptic H-box motifs on NRBP1. Keywords: E3 ubiquitin ligase, CRL, Cullin, ubiquitination, NRBP1, Alzheimer’s disease, amyloid β, amyloid-β precursor protein/APP, BRI2/ITM2B, BRI3/ITM2C

Abstract Background This study was performed to gain insights into novel therapeutic approaches for acute systemic inflammation in heatstroke. Bone marrow-derived mononuclear cells (BMMNCs) secrete anti-inflammatory proteins and have protective effects against acute inflammation. Recent evidence suggested that transplantation of BMMNCs can reduce the acute tissue injury caused by regional myocardial reperfusion and the lung dysfunction induced by lipopolysaccharides. We evaluated whether BMMNCs attenuate systemic inflammatory response induced by severe heatstroke. Material and methods Anesthetized 12-week-old male Wistar rats were subjected to heat stress (41.8 °C for 30 min) with/without transplantation of BMMNCs. Bone marrow cells were harvested from the femur and tibia of other Wistar rats. BMMNCs were separated by density centrifugation, dissolved in phosphate-buffered saline (PBS), and injected intravenously immediately after heat stress (HS-BMMNCs group). The control group was administered an equal volume of PBS, and the sham group underwent the same procedure without heat stress. Results Seven-day survival improved significantly in the HS-BMMNCs group versus control group (83.3% vs 41.7%). Transplantation of BMMNCs significantly suppressed serum levels of pro-inflammatory mediators, such as tumor necrosis factor-alpha, interleukin-6 and histone H3 at 3, 6, and 12 h after heat stress. Besides, the elevation of serum syndecan-1, a main component of the vascular endothelial glycocalyx layer, in the BMMNCs group was significantly suppressed compared to that in the control group at 6 and 12 h after heat stress. Histological analysis revealed that edema of the alveolar septum and vascular endothelial injury in the lung were evident in the control group 6 h after heat stress, whereas the morphological alteration was ameliorated in the HS-BMMNCs group. Also, histological analysis using BMMNCs derived from green fluorescent protein transgenic rats showed that the transplanted BMMNCs migrated into lung, kidney, and spleen at 24 h after heat stress but did not engraft to host tissues. Conclusion Transplantation of BMMNCs attenuated acute systemic inflammation and vascular endothelial injury, reduced organ dysfunction, and improved survival in a rat heatstroke model. These findings provide a possible therapeutic strategy against critical heatstroke.

Abstract Background Commensal microbiota deteriorate in critically ill patients. The preventive effects of probiotic/synbiotic therapy on microbiota and septic complications have not been thoroughly clarified in patients with sepsis. The objective of this study was to evaluate whether synbiotics have effects on gut microbiota and reduce complications in mechanically ventilated patients with sepsis. Methods Sepsis patients who were mechanically ventilated in the intensive care unit (ICU) were included in this randomized controlled study. Patients receiving daily synbiotics (Bifidobacterium breve strain Yakult, Lactobacillus casei strain Shirota, and galactooligosaccharides) initiated within 3 days after admission (the Synbiotics group) were compared with patients who did not receive synbiotics (the No-Synbiotics group). The primary outcome was infectious complications including enteritis, ventilator-associated pneumonia (VAP), and bacteremia within 4 weeks from admission. The secondary outcomes included mortality within 4 weeks, fecal bacterial counts, and organic acid concentration. Enteritis was defined as the acute onset of continuous liquid stools for more than 12 h. Results Seventy-two patients completed this trial; 35 patients received synbiotics and 37 patients did not receive synbiotics. The incidence of enteritis was significantly lower in the Synbiotics than the No-Synbiotics group (6.3% vs. 27.0%; p

Abstract Background and purpose The Japanese Clinical Practice Guidelines for Management of Sepsis and Septic Shock 2016 (J-SSCG 2016), a Japanese-specific set of clinical practice guidelines for sepsis and septic shock created jointly by the Japanese Society of Intensive Care Medicine and the Japanese Association for Acute Medicine, was first released in February 2017 and published in the Journal of JSICM, [2017; Volume 24 (supplement 2)] https://doi.org/10.3918/jsicm.24S0001 and Journal of Japanese Association for Acute Medicine [2017; Volume 28, (supplement 1)] http://onlinelibrary.wiley.com/doi/10.1002/jja2.2017.28.issue-S1/issuetoc. This abridged English edition of the J-SSCG 2016 was produced with permission from the Japanese Association of Acute Medicine and the Japanese Society for Intensive Care Medicine. Methods Members of the Japanese Society of Intensive Care Medicine and the Japanese Association for Acute Medicine were selected and organized into 19 committee members and 52 working group members. The guidelines were prepared in accordance with the Medical Information Network Distribution Service (Minds) creation procedures. The Academic Guidelines Promotion Team was organized to oversee and provide academic support to the respective activities allocated to each Guideline Creation Team. To improve quality assurance and workflow transparency, a mutual peer review system was established, and discussions within each team were open to the public. Public comments were collected once after the initial formulation of a clinical question (CQ) and twice during the review of the final draft. Recommendations were determined to have been adopted after obtaining support from a two-thirds (> 66.6%) majority vote of each of the 19 committee members. Results A total of 87 CQs were selected among 19 clinical areas, including pediatric topics and several other important areas not covered in the first edition of the Japanese guidelines (J-SSCG 2012). The approval rate obtained through committee voting, in addition to ratings of the strengths of the recommendation, and its supporting evidence were also added to each recommendation statement. We conducted meta-analyses for 29 CQs. Thirty-seven CQs contained recommendations in the form of an expert consensus due to insufficient evidence. No recommendations were provided for five CQs. Conclusions Based on the evidence gathered, we were able to formulate Japanese-specific clinical practice guidelines that are tailored to the Japanese context in a highly transparent manner. These guidelines can easily be used not only by specialists, but also by non-specialists, general clinicians, nurses, pharmacists, clinical engineers, and other healthcare professionals.

Patients suffering from critical illness have host inflammatory responses against injuries, such as infection and trauma, that can lead to tissue damage, organ failure, and death. Modulation of host immune response as well as infection and damage control are detrimental factors in the management of systemic inflammation. The gut is the motor of multiple organ failure following injury, and it is recognized that gut dysfunction is one of the causative factors of disease progression. The gut microbiota has a role in maintaining host immunity, and disruption of the gut microbiota might induce an immunosuppressive condition in critically ill patients. Treatment with probiotics and synbiotics has been reported to attenuate systemic inflammation by maintaining gut microbiota and to reduce postoperative infectious complications and ventilator-associated pneumonia. The administration of prophylactic probiotics/synbiotics could be an important treatment option for preventing infectious complications and modulating immunity. Further basic and clinical research is needed to promote intestinal therapies for critically ill patients.

Empirical Bayes is a choice framework for differential expression (DE) analysis for multi-group RNA-seq count data. Its characteristic ability to compute posterior probabilities for predefined expression patterns allows users to assign the pattern with the highest value to the gene under consideration. However, current Bayesian methods such as baySeq and EBSeq can be improved, especially with respect to normalization. Two R packages (baySeq and EBSeq) with their default normalization settings and with other normalization methods (MRN and TCC) were compared using three-group simulation data and real count data. Our findings were as follows: (1) the Bayesian methods coupled with TCC normalization performed comparably or better than those with the default normalization settings under various simulation scenarios, (2) default DE pipelines provided in TCC that implements a generalized linear model framework was still superior to the Bayesian methods with TCC normalization when overall degree of DE was evaluated, and (3) baySeq with TCC was robust against different choices of possible expression patterns. In practice, we recommend using the default DE pipeline provided in TCC for obtaining overall gene ranking and then using the baySeq with TCC normalization for assigning the most plausible expression patterns to individual genes.

Purpose: To validate the effectiveness of percutaneous pedicle screw (PPS) fixation for spinal fractures associated with diffuse idiopathic skeletal hyperostosis (DISH) by comparing surgical outcomes for PPS fixation and conventional open posterior fixation. Patients with DISH are vulnerable to unstable spinal fractures caused by trivial trauma, and these fractures have high rates of delayed paralysis, postoperative complications, and mortality. Methods: This retrospective study assessed surgical outcomes for 16 patients with DISH (12 men; mean age 76.1 ± 9.4 years) who underwent PPS fixation for spinal fractures (pedicle screw (PS) group), and for a control group of 25 patients with DISH (18 men; mean age 77.9 ± 9.9 years) who underwent conventional open fixation (O group) at our affiliated hospitals from 2007 to 2017. We evaluated the preoperative physical condition (American Society of Anesthesiologists (ASA) classification), neurological status (Frankel grade), and improvement after surgery, fusion length, operating time, estimated blood loss, and perioperative complications. Results: Preoperatively, the PS group consisted of one ASA-1 patient, eight ASA-2 patients, six ASA-3 patients, and one ASA-4 patient; by Frankel grade, there were 2 grade B patients, 13 grade C, 4 grade D, and 6 grade E patients. The O group had 2 ASA-1 patients, 13 ASA-2, 9 ASA-3, and 1 ASA-4 patients. Frankel grades in the O group reflected severe neurological deficits, with 3 grade C patients, 2 grade D, and 11 grade E ( p = 0.032) patients. The two groups had similar rates of neurological improvement (33.3% of PS and 40.0% of O patients; p = 0.410) and mean fusion length (PS 5.1 ± 0.8 segments; O 4.9 ± 1.2). The mean operating time and estimated blood loss were 168.1 ± 46.7 min and 133.9 ± 116.5 g, respectively, in the PS group, and 224.6 ± 49.8 min and 499.9 ± 368.5 g in the O group. Three O-group patients died of hypovolemic shock, respiratory failure, and pneumonia, respectively, within a year of surgery. Conclusion: Conventional open posterior fixation and PPS fixation for DISH-related spinal fractures were similar in fusion length and neurological improvement. However, PPS fixation was less invasive and had lower complication rates.

The incidence of heatstroke has been increasing. Heatstroke has been shown to affect physiological barrier functions. However, there are few studies of the effect of heat stress on the blood-brain barrier (BBB) function. In this study, we investigated the influence of heat stress on brain microvascular endothelial cells in vivo and in vitro. Heatstroke model mice administered Texas Red-dextran showed leakage outside the brain vessel walls. In addition, trans-endothelial electrical resistance (TEER) value was significantly reduced in induced pluripotent stem (iPS) cell-derived brain microvascular endothelial cells under heat stress by reducing claudin-5 expression. In addition, our results showed that the expression level of P-glycoprotein (P-gp) was increased in iPS cell-derived brain microvascular endothelial cells under heat stress. Furthermore, serum from heatstroke model mice could impair the BBB integrity of iPS cell-derived brain microvascular endothelial cells. These results suggest that BBB integrity was affected by heat stress in vivo and in vitro and provide important insights into the development of new therapeutic strategies for heatstroke patients.

B-cell antigen receptor (BCR) or antibody diversity arises from somatic recombination of immunoglobulin (Ig) gene segments and is concentrated within the Ig heavy (H) chain complementarity-determining region 3 (CDR-H3). We performed high-throughput sequencing of the expressed antibody heavy-chain repertoire from adult torafugu. We found that torafugu use between 70 and 82% of all possible V (variable), D (diversity), and J (joining) gene segment combinations and that they share a similar frequency distribution of these VDJ combinations. The CDR-H3 sequence repertoire observed in individuals is biased with the preferential use of a small number of VDJ, dominated by sequences containing inserted nucleotides. We uncovered the common CDR-H3 amino-acid (aa) sequences shared by individuals. Common CDR-H3 sequences feature highly convergent nucleic-acid recombination compared with private ones. Finally, we observed differences in repertoires between IgM and IgT, including the unequal usage frequencies of V gene segment and the biased number of nucleotide insertion/deletion at VDJ junction regions that leads to distinct distributions of CDR-H3 lengths.

Dioxygenase (dOx) utilizes stereospecific oxidation on aromatic molecules; consequently, dOx has potential applications in bioremediation and stereospecific oxidation synthesis. The reactive components of dOx comprise a Rieske structure Cys2[2Fe-2S]His2 and a non-heme reactive oxygen center (ROC). Between the Rieske structure and the ROC, a universally conserved Asp residue appears to bridge the two structures forming a Rieske-Asp-ROC triad, where the Asp is known to be essential for electron transfer processes. The Rieske and ROC share hydrogen bonds with Asp through their His ligands; suggesting an ideal network for electron transfer via the carboxyl side chain of Asp. Associated with the dOx is an itinerant charge carrying protein Ferredoxin (Fdx). Depending on the specific cognate, Fdx may also possess either the Rieske structure or a related structure known as 4-Cys-[2Fe-2S] (4-Cys). In this study, we extensively explore, at different levels of theory, the behavior of the individual components (Rieske and ROC) and their interaction together via the Asp using a variety of density function methods, basis sets, and a method known as Generalized Ionic Fragment Approach (GIFA) that permits setting up spin configurations manually. We also report results on the 4-Cys structure for comparison. The individual optimized structures are compared with observed spectroscopic data from the Rieske, 4-Cys and ROC structures (where information is available). The separate pieces are then combined together into a large Rieske-Asp-ROC (donor/bridge/acceptor) complex to estimate the overall coupling between individual components, based on changes to the partial charges. The results suggest that the partial charges are significantly altered when Asp bridges the Rieske and the ROC; hence, long range coupling through hydrogen bonding effects via the intercalated Asp bridge can drastically affect the partial charge distributions compared to the individual isolated structures. The results are consistent with a proton coupled electron transfer mechanism.

In vertebrates, most iron is present as heme or is chelated by proteins. Thus, Gram-positive pathogens such as Staphylococcus aureus have evolved an iron-regulated surface determinant (Isd) system that transports heme across thick cell walls into the cytoplasm. Recent studies have demonstrated that heme is rapidly transferred between the NEAr Transporter (NEAT) domains of the Isd system, despite its high affinity toward each domain, suggesting the presence of an intermediate NEAT•heme•NEAT complex. In the present study, we performed short restrained molecular dynamics (MD) simulations to dock the acceptor NEAT domain to the donor NEAT•heme complex and obtained models where the two NEAT domains were arranged with two-fold pseudo symmetry around the heme molecule. After turning off the restraints, complex structures were stably maintained during subsequent unrestrained MD simulations, except for the hydrogen bond between the propionate group of the heme molecule and the donor NEAT domain, potentially facilitating the transition of heme from the donor to the acceptor. Subsequent structural optimization using the quantum mechanics/molecular mechanics (QM/MM) method showed that two tyrosine residues, one from each NEAT domain, were simultaneously coordinated to the ferric heme iron in the intermediate complex only if they were deprotonated. Based on these results, we propose a reaction scheme for heme transfer between NEAT domains.

In November 2023, NTT announced tsuzumi, a large language model (LLM) based on NTT laboratories' over-40 years of accumulated research in natural language processing. The tsuzumi LLM excels in Japanese-language processing ability, and its key features include being lightweight and providing multimodal support, which enables handling of non-text media. Its lightweight model reduces power consumption and makes on-premises use possible. Its multimodal feature enables comprehension of photos and diagrams, distinguishing tsuzumi from other publicly available LLMs. In this article, we give an overview of tsuzumi on the basis of these key features. [ABSTRACT FROM AUTHOR]

Strigolactones (SLs) are plant apocarotenoids with diverse roles and structures. Canonical SLs, widespread and characterized by structural variations in their tricyclic lactone (ABC-ring), are classified into two types based on C-ring configurations. The steric C-ring configuration emerges during the BC-ring closure, downstream of the biosyn-thetic intermediate, carlactonoic acid (CLA). Most plants produce either type of canonical SLs stereoselectively, e.g., tomato (Solanum lycopersicum) yields orobanchol with an α-oriented C-ring. The mechanisms driving SL structural diversification are partially understood, with limited insight into functional implications. Furthermore, the exact molecular mechanism for the stereoselective BC-ring closure reaction is yet to be known. We identified an enzyme, the stereoselective BC-ring-forming factor (SRF), from the dirigent protein (DIR) family, specifically the DIR-f subfamily, whose biochemical function had not been characterized, making it a key enzyme in stereoselective canonical SL biosynthesis with the α-oriented C-ring. We first confirm the precise catalytic function of the tomato cytochrome P450 SlCYP722C, previously shown to be involved in orobanchol biosynthesis [T. Wakabayashi et al., Sci. Adv. 5, eaax9067 (2019)], to convert CLA to 18-oxocarlactonoic acid. We then show that SRF catalyzes the stereoselective BC-ring closure reaction of 18-oxocarlactonoic acid, forming orobanchol. Our methodology combines experimental and computational techniques, including SRF structure prediction and conducting molecular dynamics simulations, suggesting a catalytic mechanism based on the conrotatory 4π-electrocyclic reaction for the stereoselective BC-ring formation in orobanchol. This study sheds light on the molecular basis of how plants produce SLs with specific stereochemistry in a controlled manner. [ABSTRACT FROM AUTHOR]