Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements.

Standardization and quality assurance of microbiome community analysis by high-throughput DNA sequencing require widely accessible and well-characterized reference materials. Here, we report on newly developed DNA and whole-cell mock communities to serve as control reagents for human gut microbiota measurements by shotgun metagenomics and 16S rRNA gene amplicon sequencing. The mock communities were formulated as near-even blends of up to 20 bacterial species prevalent in the human gut, span a wide range of genomic guanine-cytosine (GC) contents, and include multiple strains with Gram-positive type cell walls. Through a collaborative study, we carefully characterized the mock communities by shotgun metagenomics, using previously developed standardized protocols for DNA extraction and sequencing library construction. Further, we validated fitness of the mock communities for revealing technically meaningful differences among protocols for DNA extraction and metagenome/16S rRNA gene amplicon library construction. Finally, we used the mock communities to reveal varying performance of metagenome-based taxonomic profilers and the impact of trimming and filtering of sequencing reads on observed species profiles. The latter showed that aggressive preprocessing of reads may result in substantial GC-dependent bias and should thus be carefully evaluated to minimize unintended effects on species abundances. Taken together, the mock communities are expected to support a myriad of applications that rely on well-characterized control reagents, ranging from evaluation and optimization of methods to assessment of reproducibility in interlaboratory studies and routine quality control. IMPORTANCE Application of high-throughput DNA sequencing has greatly accelerated human microbiome research and its translation into new therapeutic and diagnostic capabilities. Microbiome community analyses results can, however, vary considerably across studies or laboratories, and establishment of measurement standards to improve accuracy and reproducibility has become a priority. The here-developed mock communities, which are available from the NITE Biological Resource Center (NBRC) at the National Institute of Technology and Evaluation (NITE, Japan), provide well-characterized control reagents that allow users to judge the accuracy of their measurement results. Widespread and consistent adoption of the mock communities will improve reproducibility and comparability of microbiome community analyses, thereby supporting and accelerating human microbiome research and development.

Influence of prior oral ethinylestradiol use on the efficacy of enzalutamide for the treatment of castration-resistant prostate cancer in men.

OBJECTIVE: To elucidate the effect of prior use of ethinylestradiol on enzalutamide treatment for men with castration-resistant prostate cancer. METHODS: We retrospectively analyzed data from 99 consecutive patients (median age 72 years, range 50-88 years) treated with enzalutamide for castration-resistant prostate cancer between May 2014 and November 2015 after receiving several lines of hormonal therapy. RESULTS: A total of 45 patients were given ethinylestradiol before enzalutamide. The prostate-specific antigen response rate (decline in prostate-specific antigen >50% from baseline) of patients receiving ethinylestradiol and enzalutamide were 51.1% and 41.4%, respectively. Cross-resistance between ethinylestradiol and enzalutamide was clearly observed in the setting of pre-docetaxel. In multivariate analysis, the T stage and number of therapies before enzalutamide were the only significant predictors of prostate-specific antigen response to enzalutamide. However, in patients treated pre-docetaxel use, prior use of ethinylestradiol was a significant predictor of prostate-specific antigen response to enzalutamide, whereas ethinylestradiol did not affect the overall survival of these patients. CONCLUSIONS: Cross-resistance between ethinylestradiol and enzalutamide in the setting of pre-docetaxel therapy seems to be evident. Therefore, ethinylestradiol should be used prudently before enzalutamide in this setting.

Butanol production from alkali-pretreated rice straw by co-culture of Clostridium thermocellum and Clostridium saccharoperbutylacetonicum.

The co-culture of cellulolytic Clostridium thermocellum NBRC 103400 and butanol-producing Clostridium saccharoperbutylacetonicum strain N1-4 produced 5.5 g/L of butanol from 40 g/L of delignified rice straw pretreated with 1% (wt/vol) NaOH. The addition of cellulase (100 U/g biomass) in a co-culture system significantly increased butanol production to 6.9 g/L using 40 g/L of delignified rice straw. Compared to the control, this increase in butanol production was attributed to the enhancement of exoglucanase activity on lignocellulose degradation in experimental samples. The results showed that the co-culture system in conjunction with enhanced exoglucanase activity resulted in cost-effective butanol production from delignified rice straw.

Oncological outcomes of hormonal therapy with a gonadotropin-releasing hormone agonist combined with a steroidal or non-steroidal antiandrogen in patients with prostate cancer.

AIM: To determine the treatment outcome of combined androgen blockade (CAB) therapy using the non-steroidal antiandrogen bicalutamide or the steroidal antiandrogen chlormadinone in patients with prostate cancer. PATIENTS AND METHODS: In total, 124 patients with prostate cancer enrolled in the present study were randomized to receive CAB therapy using a gonadotropin-releasing hormone (GnRH) agonist, combined with bicalutamide or chlormadinone. The survival of patients was analyzed. RESULTS: The 5-year cancer-specific survival for the bicalutamide- and chlormadinone-treated groups were 91.7% and 86.6%, respectively, with no significant difference (p=0.39). Five-year overall survival was significantly (p=0.029) better in the bicalutamide-treated group. Moreover, M1 patients in the chlormadinone group had significantly lower cancer-specific and overall survival compared to those in the bicalutamide-treated group. However, in the case of M0 patients, no significant difference in cancer-specific nor in overall survival was observed. CONCLUSION: CAB therapy using chlormadinone led to a significantly poorer survival outcome versus the use of bicalutamide. However, because this survival trend was not observed in M0 cases, chlormadinone may still be an option for CAB therapy, depending on clinical stage and the severity of adverse effects, such as hot flashes.

Spontaneous bladder rupture diagnosis based on urinary appearance of mesothelial cells: a case report.

INTRODUCTION: Spontaneous bladder rupture is an extremely rare clinical event that is associated with urinary ascites and apparent acute renal failure. This event is difficult to diagnose clinically, even with advanced techniques such as computed tomography; however, the timely diagnosis of this condition is critical. Here, we report a case of a patient who experienced a spontaneous intraperitoneal bladder rupture 10 years after postoperative pelvic irradiation for the treatment of uterine cancer. In this report of a rare case, we describe the contribution of the appearance of mesothelial cells in the urine to the diagnosis of this condition. CASE PRESENTATION: Our patient was a 71-year-old Asian woman who experienced lower abdominal pain and vomiting of two days duration. On admission, abdominal computed tomography showed intraperitoneal fluid collection and her blood tests revealed acute renal failure and hyperkalemia. She underwent hemodialysis and a transurethral catheter was inserted. The transurethral catheter was removed three days after her admission. Four days after the catheter removal, her symptoms recurred and her serum creatinine and blood urea nitrogen levels were elevated. We noted the presence of mesothelial cells in her urine, which led to a diagnosis of intraperitoneal bladder rupture. She underwent surgical repair of her bladder and hyperbaric oxygen therapy, and was discharged after her renal function returned to normal. CONCLUSION: Urine analysis is a simple and non-invasive test and we believe that a thorough urine analysis may contribute to the early diagnosis of an intraperitoneal bladder rupture. We think that the findings presented in this case report will significantly enhance our understanding of the etiology of bladder rupture. Moreover, these case findings may help nephrologists and urologists to rapidly diagnose this condition.

Simultaneous determination of 5 psychotropic drugs of various types in an autopsy case of acute multiple drug poisoning.

We attempted the simultaneous determination of 5 drugs, mirtazapine, sertraline, chlorpromazine, amoxapine and zolpidem, detected in a gas chromatography-mass spectrometry screening test in an autopsy case. The solid-phase extraction of the analytes from biological samples was achieved using Oasis(®)HLB cartridges (Waters, Milford, MA, USA). Gas chromatography was performed on a HP-5MS fused silica capillary column (30 m × 0.25 mm i.d., 0.25 µm film thickness, Agilent Technologies). The mass spectrometer was operated with an electron energy of 70 eV in electron impact mode. The qualitative and quantitative analyses were performed in full-scan mode and the selected ion monitoring mode, respectively. The total ion chromatogram showed good separation of these drugs. Linear graphs were obtained with good correlation coefficients for these drugs from 0.001 to 2.0 µg/mL (r(2)=0.9909-0.9986) using imipramine-d6 as an internal standard. The recoveries of these drugs were found to be 62.8-88.0% in spiked whole blood. Mirtazapine, sertraline, chlorpromazine, amoxapine and zolpidem were found in post-mortem samples of the deceased at concentrations of 2.67, 0.07, 0.25, 0.32 and 0.68 µg/mL, respectively. The concentration of mirtazapine was within the lethal level and those of amoxapine and zolpidem were within the toxic level. We diagnosed that the cause of death was acute multiple drug poisoning. The simple and practical procedure used in this study is useful for the simultaneous determination of psychotropic drugs of various types in post-mortem biological samples.

ABO genotyping by TaqMan assay and allele frequencies in a Japanese population.

ABO genotyping have become common tools for forensic casework. We developed a new rapid ABO genotyping method using a fast real-time PCR system with the TaqMan® Sample-to-SNP™ Kit. Eight single nucleotide polymorphism (SNP) sites in the ABO gene (nt 261, 297, 467, 657, 703, 829, 930 and 1061) were selected to determine the ABO genotypes. ABO genotypes were easily determined by examining allelic discrimination patterns. This method enabled analyses to be completed in about 1h per plate with no postmortem change influences. The detection limit in each SNP site was examined as 100pg per reaction. ABO genotyping from 1000 Japanese individuals was also examined to determine the distribution of ABO genotypes and allele frequencies. Thus, 31 genotypes were clearly identified, and these were controlled by four common and seven rare alleles. The power of discrimination, heterozygosity and polymorphism information contents were 0.913, 0.775 and 0.812, respectively. Therefore, selecting these eight SNP sites could be useful for high specific ABO genotyping. This rapid, sensitive and accurate genotyping method is useful for forensic casework.

[Efficacy of naftopidil in patients with overactive bladder associated with benign prostatic hyperplasia: prospective randomized controlled study to compare differences in efficacy between morning and evening medication].

A total of 100 patients with benign prostatic hyperplasia (BPH) and overactive bladder (OAB) symptoms (BPH/OAB), enrolled between June 2006 to March 2008, were randomly divided into 2 groups of morning medication (M) and evening medication (E) groups, then 50 mg of naftopidil was given once a day after breakfast or supper for 8 weeks. Data were available for efficacy analysis on 80 patients (M group ; 43, E group ; 37). Naftopidil significantly improved the overall international prostatic symptom score ; from 19.2±7.9 to 11.7±5.8 in the M group and from 19.4±6.4 to 12.3±6.8 in the E group (p<0.0001), QOL score from 4.9±0.8 to 3.2±1.4 in the M group and from 5.0±0.8 to 3.6±1.3 in the E group (p<0.0001), and OAB symptom score from 7.8±2.6 to 5.0±2.5 in the M group (p<0.0001) and from 8.6±2.9 to 5.8± 3.3 in the E group (p<0.0001). There was no significant difference in the incidence of adverse effects between the M group (6.1%) and E group (2.2%). These results suggest that naftopidil improves storage symptoms as well as voiding symptoms regardless of timing of administration.

Analysis of the sarcomere protein gene mutation on cardiomyopathy - Mutations in the cardiac troponin I gene.

Developments in the molecular genetic studies of cardiomyopathy (CM) have led to discovery of a large number of mutations in the genes encoding the sarcomeric proteins. In this study, comprehensive screening of TNNI3 was performed in 36 consented autopsy cases diagnosed as CM, in order to evaluate the prevalence of gene mutations in sudden death caused by CM. In DCM cases, a new missense mutation Pro16Thr was detected. A single nucleotide polymorphism at -8 position of intron 3 (IVS 3 -8 T>A) was identified, which had a significant difference in allele frequency between DCM and control cases. From these results, it was indicated that this study contribute to genetic based diagnosis, risk stratification and prevention of sudden death caused by CM.

Interstitial pneumonia probably associated with sorafenib treatment: An alert of an adverse event.

There has been no literature which reports a case of interstitial lung disease associated with sorafenib. However, a recent post-marketing survey in Japan revealed that interstitial pneumonia occurred in 4 among approximately 2 000 Japanese patients treated with sorafenib. In this article, we describe a Japanese patient with severe interstitial pneumonia probably caused by sorafenib treatment for metastatic renal cell carcinoma. Oncologists supervising future clinical trials for lung cancer should be alert to the fact that sorafenib can potentially induce serious interstitial lung disease, although this might depend on racial differences.

A case of V-A shunt catheters migration into the pulmonary artery.

A man in his sixties, who developed CPA at home, was transferred to the emergency center. Since CT images revealed a tube-shaped foreign body in the pulmonary artery, pulmonary embolism was initially suspected; however, this did not lead to a definite diagnosis. Autopsy revealed that the foreign body in the cadaver was a fragment of a V-A shunt catheter implanted about 30 years previously for the treatment of hydrocephalus. Although fibrous adhesion of a part of the catheter to the pulmonary artery wall was seen, suggesting that a fracture of the catheter had occurred a long time before, it was not known when the fracture had occurred. Since no pulmonary arterial obstruction secondary to the catheter or new thrombi, which had been initially suspected, were observed, the cause of death was determined to be ischemic cardiac failure. A fracture of a shunt catheter may be typically associated with some clinical manifestations, which are often found and treated. In this case, however, no symptoms appeared and the fracture of the shunt catheter remained untreated for a long time. This case was therefore considered to be extremely rare, and is an example of how a serious iatrogenic disease could occur.

Case report: Etizolam and its major metabolites in two unnatural death cases.

A simultaneous analytical method for etizolam and its main metabolites (alpha-hydroxyetizolam and 8-hydroxyetizolam) in whole blood was developed using solid-phase extraction, TMS derivatization and ion trap gas chromatography tandem mass spectrometry (GC-MS/MS). Separation of etizolam, TMS derivatives of alpha-hydroxyetizolam and 8-hydroxyetizolam and fludiazepam as internal standard was performed within about 17 min. The inter-day precision evaluated at the concentration of 50 ng/mL etizolam, alpha-hydroxyetizolam and 8-hydroxyetizolam was evaluated 8.6, 6.4 and 8.0% respectively. Linearity occurred over the range in 5-50 ng/mL. This method is satisfactory for clinical and forensic purposes. This method was applied to two unnatural death cases suspected to involve etizolam. Etizolam and its two metabolites were detected in these cases.

[A case of renal pelvic squamous cell carcinoma accompanied with humoral hypercalcemia of malignancy (HHM)].

A 78-year-old male was urgently admitted to our hospital because of consciousness disturbance. Laboratory data showed marked hypercalcemia (17.0 mg/dl), hypophosphatemia, low intact PTH level, high PTH relating peptide (PTHrP) level, normal osteocalcin and normal 1-25(OH)2D level. Computed tomography revealed a right renal tumor with extracapsular extension. Bone scintigram appeared normal. We performed right nephrectomy under the diagnosis of right renal tumor. Pathological diagnosis was poorly differentiated squamous cell carcinoma (SCC) of the right pelvis. Immunohistochemical study of the resected specimen for PTHrP was positive. Therefore, we diagnosed it as renal pelvic SCC with humoral hypercalcemia of malignancy (HHM). After nephrectomy, serum calcium returned to normal, but 5 months after nephrectomy, local recurrence appeared and serum calcium was re-elevated. She died 7 months after nephrectomy.

Predictive value of serum macrophage colony-stimulating factor for development of aortic calcification in haemodialysis patients: a 6 year longitudinal study.

BACKGROUND: Accelerated atherosclerosis is a major complication in patients on haemodialysis (HD). Macrophage colony-stimulating factor (MCSF) is a representative regulator of activation of monocytes and macrophages, and plays important roles in the development of atherosclerosis in HD patients. However, the long-term predictive value of the serum MCSF level for the development of aortic calcification under HD conditions has not been reported. METHODS: Serum MCSF level was measured in 40 HD patients. The aortic calcification index (ACI) was also calculated on computed tomography once each year for 6 years. Predictive value was examined by logistic regression analysis. RESULTS: At baseline, there was a significant correlation between serum MCSF and ACI (r = 0.43, P<0.01). A significant increase in ACI was first noted at 4 years post-baseline and the increase was maintained thereafter in the high MCSF group. No such changes were noted in the low MCSF group. Univariate analysis identified high levels of calcium x phosphorus product, triglyceride, C-reactive protein (CRP), MCSF and presence of diabetes mellitus as significant predictors for increased ACI at 6 years. However, among these five factors, high levels of CRP and MCSF were the only independent and significant predictors (odds ratio = 24.0, P = 0.03 and odds ratio = 22.8, P = 0.02, respectively). CONCLUSIONS: Our results demonstrated that MCSF is associated with the process of atherosclerosis in HD patients. Furthermore, the serum MCSF level is an independent long-term predictor of increased ACI. These results provide useful information for preventive strategies against atherosclerotic disease under HD conditions.

Three cases of sudden death due to butane or propane gas inhalation: analysis of tissues for gas components.

We report three cases of sudden death due to inhalation of portable cooking stove fuel (case 1), cigarette lighter fuel (case 2), and liquefied petroleum gas (LPG) (case 3). Specimens of blood, urine, stomach contents, brain, heart, lung, liver, kidney, and fat were collected and analyzed for propylene, propane, isobutane, and n-butane by headspace gas chromatography. n-Butane was the major substance among the volatiles found in the tissues of cases 1 and 2, and propane was the major substance in case 3. A combination of the autopsy findings and the gas analysis results revealed that the cause of death was ventricular fibrillation induced by hard muscle exercise after gas inhalation in cases 1 and 2, and that the cause of death in case 3 might be hypoxia. It is possible that the victim in case 3 was under anesthetic toxicity of accumulated isobutane which is a minor component of liquefied petroleum gas.

[A case of prostate cancer with invasion to the middle ureter].

A 69-year-old male was diagnosed as having prostate cancer with ureter invasion. His serum prostate specific antigen level was not so high (19.6 ng/ml) before treatment, but clinical stage was D2, poorly differentiated adenocarcinoma of prostate. He was treated with chemoendocrine therapy. Prostate cancer with continuous invasion to the middle ureter is rare. To the best of our knowledge, this is the 6th case report of such an unusual invasion of prostate cancer.