c-trie++: A Dynamic Trie Tailored for Fast Prefix Searches

Given a dynamic set $K$ of $k$ strings of total length $n$ whose characters are drawn from an alphabet of size $\sigma$, a keyword dictionary is a data structure built on $K$ that provides locate, prefix search, and update operations on $K$. Under the assumption that $\alpha = w / \lg \sigma$ characters fit into a single machine word $w$, we propose a keyword dictionary that represents $K$ in $n \lg \sigma + \Theta(k \lg n)$ bits of space, supporting all operations in $O(m / \alpha + \lg \alpha)$ expected time on an input string of length $m$ in the word RAM model. This data structure is underlined with an exhaustive practical evaluation, highlighting the practical usefulness of the proposed data structure, especially for prefix searches - one of the most elementary keyword dictionary operations

Lipids from Vitellaria paradoxa Gaertn Seeds by Supercritical CO2: Extraction and Optimization of Parameters by Response Surface Methodology

Supercritical carbon dioxide (CO2) was employed to extract lipids from Vitellaria paradoxa Gaertn seeds in semi–batch process at various operating conditions to optimize extraction process. The extraction processes were carried out at 40 – 60 oC and 20 – 40 MPa with 2 – 4 ml min–1 CO2 flow rates. Analysis of variance (ANOVA) with 33 factorial design combined with statistical was used to optimize variables in the process of Vitellaria paradoxa Gaertn seeds lipids extraction with supercritical CO2. The FT–IR spectra indicated that the Vitellaria paradoxa Gaertn seeds components were extracted by supercritical CO2. The SEM images also indicated that the physical changes in the surface of the Vitellaria paradoxa Gaertn seeds occurred after supercritical CO2 extraction treatment. The maximum of extracted lipids was 0.47 g/g–sample when the extraction was conducted at a temperature of 80 oC and pressure of 40 MPa with CO2 flow rate of 3 ml min–1. The GC–MS analysis showed that the extracted lipids mainly composed of palmitic acid (C16:0), stearic acid (C18:0), oleic acid (C18:1), and linoleic acid (C18:2). The analysis of experimental design demonstrated that pressure and temperature were the influential variables on the lipids extraction

Economical Wet Extraction of Lipid from labyrinthula Aurantiochytrium limacinum by Using Liquefied Dimethyl Ether

Recently, a simple method for the extraction of lipids from wet biomass using liquefied dimethyl ether (DME) without drying, cell disruption, or heating was proposed. Here, the versatility of this method was evaluated for labyrinthula Aurantiochytrium limacinum (A. limacinum). The liquefied DME was passed through the extractor that filled by A. limacinum at different time intervals. The extraction of lipids from A. limacinum of moisture-rich microorganism was successfully achieved, the yield of lipid was 46.1 wt% of the dry weight of the sample. In comparison, the yields of lipid were 21.3 wt%, 43.6 wt% and 50.7 wt% when supercritical carbon dioxide (SCCO2), hexane-Soxhlet and Bligh-Dyer (BD) extraction methods were applied as extractants, respectively. However, the drying and cell-disruption process were required in SCCO2, hexane-Soxhlet, and BD extraction methods

Effect of Hochu-ekki-to (TJ-41), a Japanese Herbal Medicine, on Daily Activity in a Murine Model of Chronic Fatigue Syndrome

We aimed to evaluate the effect of a Japanese herbal medicine, Hochu-ekki-to (TJ-41), on daily activity in a murine model of chronic fatigue syndrome (CFS). CFS was induced by repeated injection of Brucella abortus (BA) antigen every 2 weeks. TJ-41 was orally administered to mice in a dose of 500 mg/kg/day for 1 week before injecting BA and for 4 weeks thereafter. We evaluated daily running activity in mice receiving TJ-41 as compared with that in untreated mice. Survival of both mouse groups was also monitored during the observation period. Body weight (BW), spleen weight (SW), SW/ BW ratio and expression levels of interleukin-10 (IL-10) mRNA in spleen were determined in both groups at the time of sacrifice. The daily activity was significantly higher in the treated group than in the control. Two mice in the untreated group died 2 days after the second injection of BA, whereas no mice in the group treated with TJ-41 died. The SW and SW/BW ratio were significantly lower in the treated mice than in the control. Suppressed IL-10 mRNA levels were observed in the spleens of the mice treated with TJ-41. Our data suggest that Hochu-ekki-to might possess an inhibitory effect on the marked decrease in running activity following BA injection

Biologic markers in prostatic intraepithelial neoplasia: immunohistochemical and cytogenetic analyses

Objective:We evaluated the biological properties of High-grade prostatic intraepithelial neoplasia (PIN) by immunohistochemistry and fluorescence in situ hybridization (FISH) analysis in relation to normal tissue and carcinoma lesions. Materials and Methods:Immunohistochemical staining and FISH were performed on23formalin-fixed radical prostatectomy specimens taken from patients with PIN. Assays were performed using MIB-1, chromogranin A (CGA) and an anti-androgen receptor antibody (AR). A centromere probe for chromosome8was used to test for aneuploidy. Results:The MIB-1index of cancerous specimens (16.2±10.5%) was significantly higher than that of benign (1.9±1.6%, p<0.0001) or PIN (4.0±4.5%, p<0.0001) specimens. The percentage of CGA positive cells was significantly lower in normal tissue (1.2±1.8%) than in PIN (3.5±2.9%, p=0.012) or carcinoma (5.4±4.9%, p=0.005) lesions. Positive staining for AR was consistently observed in the nuclei of both benign and malignant epithelial cells, but positive cytoplasmic staining was also seen in PIN epithelial cells. No significant difference in FISH detected anomalies were found between PIN and carcinoma specimens. Conclusions:Our studies concerning proliferative activity, NE differentiation and chromosomal anomalies of prostatic specimens support the hypothesis that PIN is a biologically intermediate stage in the pathogenesis of prostatic carcinoma. The cellular distribution of AR was altered in PIN cells, but the role of AR in PIN is not yet clear

Poor Outcome due to the Plasmacytoid Variant of Urothelial Carcinoma

A 72-year-old man visited our hospital due to pollakiuria and lower abdominal pain. Urinary cytology was positive, and cystoscopy revealed diffuse edematous nonpapillary tumor. We performed transurethral biopsy, and clinical stage T3 plasmacytoid variant of urothelial carcinoma (PUC) was diagnosed. Although we planned for radical cystectomy, peritoneal dissemination and lung and pelvic lymph node metastases appeared 3 weeks after the initial visit. We also planned for chemotherapy; however, the metastases rapidly progressed, and he died 7 weeks after the biopsy. PUC is rare and shows an aggressive clinical course and poor prognosis

Micropapillary Variant of UC in an HD Patient

The micropapillary variant of urothelial carcinoma (MPUC) is an aggressive form of urothelial carcinoma with high metastatic potential and a poor prognosis. Although various therapies have been reported, there is still no established treatment strategy for MPUC due to its rarity. The incidence of urinary tract malignancies is higher in patients undergoing hemodialysis (HD) than in healthy individuals. Here, we report the case of an 82-year-old man on HD with end-stage kidney disease who visited our hospital for macrohematuria. Cystoscopy followed by computed tomography and urine cytology revealed a sessile papillary tumor around the left bladder wall. We performed transurethral resection of the bladder tumor. Based on histopathological and imaging findings indicative of clinical-stage T3N0M0 MPUC, we performed radical cystectomy. Histopathology revealed a pathological stage T4aN0M0 MPUC. Two months after the cystectomy, the patient complained of constipation and painful defecation due to local recurrence and rectal invasion. While colostomy was performed to improve defecation 3 months after cystectomy, he did not receive any chemotherapy due to his progressively worsening general condition. Six months after cystectomy, he died following rapid metastases. Our findings, in this case, confirm that bladder cancer in HD patients tends to be pathologically more advanced. Therefore, regular screening is recommended for its early detection in HD patients

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection