Investigation of the presence of Capnophilic bacteria in routine urine cultures

Capnophilic Escherichia coli (CEC) strains are rarely isolated from urinary tract infections (UTIs). The purpose of this research was to look into the incidence and traits of the CEC strains that cause UTIs. Nine (0.11%) epidemiologically unrelated CEC isolates with varying antibiotic susceptibility patterns were identified from patients with various co-morbidities after the evaluation of 8500 urine samples. Three of these strains belonged to the O25b-ST131 clone, and none of them possessed the yadF gene. Due to adverse incubation conditions, CEC isolation is difficult. Although rare, capnophilic incubation of urine cultures may be considered particularly for patients with underlying predisposing conditions.

Management of Biliary Complications in Liver Transplant Recipients with Duct-To-Duct Anastomosis: A Single-Center Experience

BACKGROUND

The aims of this study were to investigate biliary complications in liver transplant recipients with choledochocholedocho stomy anastomosis, to identify the risk factors for the development of such complications, and to evaluate the success of endoscopic approaches in liver transplant recipients.

METHODS

Between January 2013 and May 2021, a total of 238 patients with liver diseases underwent liver transplantation: 174 recipients undergoing choledochocholedochostomy anastomosis were included in the analysis.

RESULTS

Their median age was 54.0 years. The median posttransplant follow-up period was 29 months. Hepatitis B virus infection (33%) was the most common indication for liver transplantation. Most patients (87%) received living donor liver transplantation. The overall prevalence of posttransplant biliary complications was 31%. Anastomotic biliary strictures were the most common biliary complications (72%), followed by biliary leakage (13%). The median time between endoscopic retrograde cholangiography and liver transplantation was 4 months, with a mean of 3 ± 1.6 sessions. Endoscopic retrograde cholangiography-guided drainage and balloon dilation with or without stent placement was the most common treatment modalities for recipients with biliary strictures. The overall success rate of endoscopic treatment modalities was 83.3%, with 65% of the recipients exhibiting complete biochemical and endoscopic responses. The response did not differ significantly between living donor liver transplantation and cadaveric donor liver transplant recipients (P > .05). Three recipients required revision surgery for biliary complication repair. Six patients died due to biliary sepsis.

CONCLUSION

Biliary stricture and leakages were the most common biliary complications after liver transplantation. Endoscopic treatment was successful in most recipients.

Non-invasive fibrosis markers for assessment of liver fibrosis in chronic hepatitis delta

Assessment of liver fibrosis by non-invasive means is clinically important. Studies in chronic hepatitis delta (CHD) are scarce. We evaluated the performance of eight serum fibrosis markers [fibrosis-4 score (FIB-4), aspartate aminotransferase (AST) to alanine aminotransferase (ALT) ratio (AAR), age-platelet index (API), AST-to platelet-ratio-index (APRI), Goteborg University Cirrhosis Index (GUCI), Lok index, cirrhosis discriminant score (CDS) and Hui score] in CHD and chronic hepatitis B (CHB). Liver stiffness was assessed by transient elastography (TE) in CHD. The ability of fibrosis markers to detect significant fibrosis and cirrhosis were evaluated in 202 CHB and 108 CHD patients using published and new cut-offs through receiver operating characteristics (ROC) analysis. The latter was also applied to obtain cut-offs for TE. APRI, Fib-4, API and Hui score were assessed for significant fibrosis, and APRI, GUCI, Lok index, CDS and AAR for cirrhosis determination. Fibrosis markers displayed weak performance in CHB for significant fibrosis with area under ROC (AUROC) curves between 0.62 and 0.71. They did slightly better for CHD. TE displayed an AUROC of 0.92 and performed better than serum fibrosis markers (p < 0.05 for fibrosis markers). For cirrhosis determination, CDS and Lok Index displayed an AUROC of 088 and 0.89 in CHB and GUCI, Lok index and APRI displayed AUROCs around 0.90 in CHD. TE displayed the best AUROC (0.95). Hence TE is superior to serum fibrosis markers for diagnosing significant liver fibrosis and cirrhosis. GUCI, Lok index and APRI displayed a reasonable performance in CHD, which needs further confirmation.

Optimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissues

Formalin-fixed paraffin-embedded (FFPE) tissue is a widely available clinical specimen for retrospective studies. The possibility of long-term clinical follow-up of FFPE samples makes them a valuable source to evaluate links between molecular and clinical information. Working with FFPE samples in the molecular research area, especially using high-throughput molecular techniques such as microarray gene expression profiling, has come into prominence. Because of the harmful effects of formalin fixation process such as degradation of nucleic acids, cross-linking with proteins, and chemical modifications on DNA and RNA, there are some limitations in gene expression profiling studies using FFPE samples. To date many studies have been conducted to evaluate gene expression profiling using microarrays (Thomas et al., Thomas et al. (2013) [1]; Scicchitano et al., Scicchitano et al. (2006) [2]; Frank et al., Frank et al. (2007) [3]; Fedorowicz et al., Fedorowicz et al. (2009) [4]). However, there is still no generally accepted, efficient and standardized procedure for microarray analysis of FFPE samples. This paper describes the microarray data presented in our recently accepted to be published article showing a standard protocol from deparaffinization of FFPE tissue sections and RNA extraction to microarray gene expression analysis. Here we represent our data in detail, deposited in the gene expression omnibus (GEO) database with the accession number GSE73883. Four combinations of two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) were evaluated to determine which combination gives the best percentage of present call. The study presents a dataset for comparative analysis which has a potential in terms of providing a robust protocol for gene expression profiling with FFPE tissue samples.

Evaluating Left-Censored Data Through Substitution, Parametric, Semi-parametric, and Nonparametric Methods: A Simulation Study

In this study, an attempt was made to determine the degrees of bias in particular sampling sizes and methods. The aim of the study was to determine deviations from the median, the mean, and the standard deviation (SD) in different sample sizes and at different censoring rates for log-normal, exponential, and Weibull distributions in the case of full and censored data sampling. Thus, the concept of "censoring" and censoring types was handled in the first place. Then substitution, parametric (MLE), nonparametric (KM), and semi-parametric (ROS) methods were introduced for the evaluation of left-censored observations. Within the scope of the present study, the data were produced uncensored based on the different parameters of each distribution. Then the datasets were left-censored at the ratios of 5, 25, 45, and 65 %. The censored data were estimated through substitution (LOD and LOD/[Formula: see text]), parametric (MLE), semi-parametric (ROS), and nonparametric (KM) methods. In addition, evaluation was made by increasing the sample size from 20 to 300 by tens. Performance comparison was made between the uncensored dataset and the censored dataset on the basis of deviations from the median, the mean, and the SD. The results of simulation studies show that LOD/[Formula: see text] and ROS methods give better results than other methods in deviation from the mean in different sample sizes and at different censoring rates, while ROS gives better results than other methods in deviation from the median in almost all sample sizes and at almost all censoring rates.

Repeatability and reproducibility of a new optical biometer in normal and keratoconic eyes

PURPOSE

To evaluate the repeatability and reproducibility of measurements obtained by a new optical biometer (Nidek AL-Scan) in normal eyes and keratoconic eyes.

SETTING

Department of Ophthalmology, Turgut Özal University, Medical School, Ankara, Turkey.

DESIGN

Evaluation of diagnostic technology.

METHODS

To assess the repeatability and reproducibility of the optical biometer, 2 independent examiners performed 3 consecutive measurements. The following parameters were evaluated: central corneal thickness (CCT), anterior chamber depth, axial length (AL), corneal dioptric power in the flattest meridian (flat keratometry [K]) and in the steepest meridian (steep K), and white-to-white (WTW) distance. Repeatability was assessed using the within-subject standard deviation (S(w)), repeatability, and precision. Reproducibility was evaluated using the 95% limits of agreement proposed by Bland and Altman.

RESULTS

Thirty healthy subjects and 27 patients with keratoconus were evaluated. Both examiners achieved high repeatability for all parameters in each group except for the steep K measurement in keratoconic eyes performed by examiner 2 (S(w) = 3.341). The WTW in normal eyes and the CCT and steep K in keratoconic eyes showed less repeatability. In both groups, the smallest range of agreement was in AL measurements whereas the largest was in CCT measurements. In keratoconic eyes, the range of agreement for steep K was also greater (3.766).

CONCLUSIONS

The precision of the measurements obtained by the new optical biometer was high.

FINANCIAL DISCLOSURE

No author has a financial or proprietary interest in any material or method mentioned.

Integrating patient reported outcome measures and computerized adaptive test estimates on the same common metrics: an example from the assessment of activities in rheumatoid arthritis

AIM

This study aimed to explore the potential of an inclusive and fully integrated measurement system for the Activities component of the International Classification of Functioning, Disability and Health (ICF), incorporating four classical scales, including the Health Assessment Questionnaire (HAQ), and a Computerized Adaptive Testing (CAT).

METHODS

Three hundred patients with rheumatoid arthritis (RA) answered relevant questions from four questionnaires. Rasch analysis was performed to create an item bank using this item pool. A further 100 RA patients were recruited for a CAT application. Both real and simulated CATs were applied and the agreement between these CAT-based scores and 'paper-pencil' scores was evaluated with intraclass correlation coefficient (ICC). Anchoring strategies were used to obtain a direct translation from the item bank common metric to the HAQ score.

RESULTS

Mean age of 300 patients was 52.3 ± 11.7 years; disease duration was 11.3 ± 8.0 years; 74.7% were women. After testing for the assumptions of Rasch analysis, a 28-item Activities item bank was created. The agreement between CAT-based scores and paper-pencil scores were high (ICC = 0.993). Using those HAQ items in the item bank as anchoring items, another Rasch analysis was performed with HAQ-8 scores as separate items together with anchoring items. Finally a conversion table of the item bank common metric to the HAQ scores was created.

CONCLUSION

A fully integrated and inclusive health assessment system, illustrating the Activities component of the ICF, was built to assess RA patients. Raw score to metric conversions and vice versa were available, giving access to the metric by a simple look-up table.

Transarterial chemoembolization for treatment of hepatocellular carcinoma: A single center experience

BACKGROUND/AIMS

We aimed to determine the effect of transarterial chemoembolization treatment on survival in patients with hepatocellular carcinoma and to investigate the efficacy and tolerability of two different transarterial chemoembolization procedures, conventional transarterial chemoembolization and drug-eluting beads, in these patients.

MATERIALS AND METHODS

A total of 40 patients with hepatocellular carcinoma treated with transarterial chemoembolization between January 2007 and March 2011 were included. Thirty-seven patients had Child-Pugh class A and the remaining 3 had class B. Intra-arterial administration of doxorubicin with lipiodol-based conventional transarterial chemoembolization or drug-eluting beads-transarterial chemoembolization was performed. Eighty sessions were performed with a median of 2 sessions. Sixteen patients were treated with conventional transarterial chemoembolization and 11 with drug-eluting beads-based transarterial chemoembolization, and 13 were treated with both treatment procedures in separate sessions. Primary outcome was defined as patient survival after treatment.

RESULTS

The median follow-up was 19 months. The median overall survival of patients was 23.2 months. The survival of patients with Child-Pugh class A was significantly better than that of patients with class B (24 vs 6 months, p=0.004). No statistically significant difference in survival was observed between conventional transarterial chemoembolization and drug-eluting beads-based transarterial chemoembolization treatments (p>0.05). Baseline low serum albumin level (p=0.003) and the presence of portal vein thrombosis (p=0.011) negatively affected patient survival. Side effects of conventional transarterial chemoembolization and drug-eluting beads-based transarterial chemoembolization were similar.

CONCLUSIONS

Based on the results of this study and in comparison with the findings in the literature, transarterial chemoembolization treatment was seen to improve overall survival and provide better outcome in selected patients with hepatocellular carcinoma. No differences in survival or side effects were observed between the two transarterial chemoembolization treatment modalities.

Prognostic Value of Metabolic Tumor Volume Measured by 18F-FDG PET/CT in Esophageal Cancer Patients

Objective: In this study, we aimed to explore prognostic importance of definition of preoperative metabolic tumor volume in esophageal cancer patients.

Methods: 22 patients who have histologically proven stage IIA-III esophageal cancer and underwent ¹⁸F-FDG PET/CT for preoperative staging of disease were included to the study. After ¹⁸F-FDG PET/CT, all the patients underwent surgery within 4 weeks period. Patients have been followed up until death or Sept 15^th, 2012. Dates of death were recorded for survival analysis. During evaluation of ¹⁸F-FDG PET/CT images, metabolic tumor volumes were calculated by drawing the isocontour region of interests from all visually positive FGD uptake lesions.

Results: 22 patients (15M, 7F; mean age: 65.1±8.4, min-max:48-80) underwent ¹⁸F-FDG PET/CT for preoperative staging of esophageal cancer. Preoperative diagnosis was squamous cell and adeno cancer in 17 (%77) and 5 (%23) patients, respectively. Location of primary tumor is distal, proximal and mid-esophagus in 13 (%59), 6 (%27) and 3 (%13) patients, respectively. Primary tumor of all the patients were FDG avid (mean SUV_max: 18.85±7.0; range: 5.5-35.1). Additionally, ¹⁸F-FDG uptake was seen in mediastinal lymph nodes in 13 patients (5.45±8.15; range: 2.6-29.9). Mean metabolic tumor volumes of primary esophageal lesions were calculated as 8.77±8.46cm³ (range: 2.3-34.2). Mean MTV of lymph nodes was 2.44±1.01cm³ (range: 0.4-3.6). Mean total metabolic tumor volume was calculated as 9.99±8.58cm³ (range: 2.3-27.3). 10 patients died during 447±121 days follow-up period. Mean survival time was 11.9±1.5 months (95%CI: 8.99-14.74) for entire patient group. Total metabolic tumor volume had a significant effect on survival (p=0.045) according to Cox proportional hazards regression analysis. One unit increase in MTV caused 1.1 (95%CI:1.003-1.196) fold increase in hazard, at any time.

Conclusion: Definition of preoperative metabolic tumor volume has a prognostic value in the prediction of postoperative survival times. Patients who have higher preoperative metabolic tumor volumes could be good candidates for more aggressive chemo-radiation therapy regiments.

Conflict of interest:None declared.