Topological data analysis for revealing dynamic brain reconfiguration in MEG data.

In recent years, the focus of the functional connectivity community has shifted from stationary approaches to the ones that include temporal dynamics. Especially, non-invasive electrophysiological data (magnetoencephalography/electroencephalography (MEG/EEG)) with high temporal resolution and good spatial coverage have made it possible to measure the fast alterations in the neural activity in the brain during ongoing cognition. In this article, we analyze dynamic brain reconfiguration using MEG images collected from subjects during the rest and the cognitive tasks. Our proposed topological data analysis method, called Mapper, produces biomarkers that differentiate cognitive tasks without prior spatial and temporal collapse of the data. The suggested method provides an interactive visualization of the rapid fluctuations in electrophysiological data during motor and cognitive tasks; hence, it has the potential to extract clinically relevant information at an individual level without temporal and spatial collapse.

Biliary stents are forgotten more frequently in elderly patients

Background/aim: Plastic biliary stents that remain in situ for more than 12 months, called forgotten biliary stents (FBSs), can cause complications such as cholangitis, stent migration, stent occlusion, and perforation. Materials and methods: The medical records of patients who underwent ERCP procedures from December 2016 to December 2020 were analysed retrospectively. Data on patient characteristics, indications for ERCP and stenting, stent types, stenting duration, complications, and causes of FBSs were obtained from the hospital's database. Results: A total of 48 cases with FBSs were analysed. The mean age (SD) of the patients was 71.23 years (±12.165), the male-to-female ratio was 23/25 (0.92), and the mean stenting duration was 27.12 months (range: 12­84 months). The most common indication for biliary stenting was irretrievable choledochal stones (40/48). Stone formation (79%) and proximal stent migration (26.4%) were the most frequent complications. The patients in the FBS group were significantly older than those from whom stents were removed in a timely manner (71.23 vs. 62.43 years, p < 0.001). Endoscopic treatment was possible in all cases; surgery was not required in any case. The most common cause of FBSs cited by patients was not having been informed about the need for long-term management of their stents (n = 14, 29.2%) Conclusion: FBSs are potentially problematic particularly in elderly patients. Communication with the patient to remind them of the need for stent management is important for preventing FBSs.

The Relationship between Ocular Vascular Changes and the Levels of Malondialdehyde and Vascular Endothelial Growth Factor in Patients with Inflammatory Bowel Disease.

Background: We evaluated ocular hemodynamic changes, malondialdehyde(MDA) and vascular endothelial growth factor (VEGF) levels in patients with IBD.Methods: We used ocular color Doppler ultrasonography to analyze 56 eyes with Crohn's disease (CD), 62 eyes with ulcerative colitis (UC), 68 eyes of healthy volunteers. We measured peak systolic velocity (PSV),end-diastolic velocity (EDV),and the resistivity index (RI) of ophthalmic artery (OA) and central retinal artery (CRA). MDA and VEGF levels were measured in the plasma samples.Results: MDA levels were significantly higher in both UC and CD patients, whereas VEGF levels were only higher in the CD group (p = .003,p < .001,p = .01).The PSV and EDV of the OA were significantly lower in CD patients (p = .017,p = .001). The EDV of the CRA was significantly lower in CD patients than UC patients and controls (p = .014,p < .001).Conclusions: CD patients exhibited decreased blood flow in both the OA and CRA. Ocular vascular flow was only affected in CD patients. We found that ocular ischemia may occur in CD patients even in the absence of any clinical finding.

Grain analysis of atomic force microscopy images via persistent homology.

Atomic force microscopy (AFM) is an established technique in nanoscale grain analysis due to its accuracy in producing 3-dimensional images. Even though height threshold and watershed algorithms are commonly used to determine the grain size and number of grains, they mostly require image processing that result in the change of topographical features of the surface that generates misleading conclusions. In this study, we use persistent homology, a method of representing topological features, to obtain more accurate information about the granular surfaces from unprocessed AFM images than the conventional methods. The method is also useful as a robust alternative to common parameters describing the topography of the AFM images. Most of these parameters such as arithmetic roughness and root-mean-squared roughness are represented by a single number which results in uncertainty in characterization of different surfaces. Persistent homology provides more precise summary about surface properties than a single parameter.

Use of SpyGlass for peroral cholangioscopy in the diagnosis and treatment of hepatobiliary diseases in over five years follow-up: A single centre experience.

BACKGROUND/AIMS: The use of cholangioscopy for the diagnosis and treatment of hepatobiliary diseases is gradually becoming more common. We aimed to review our peroral cholangioscopy interventions, using the first-generation SpyGlass Direct Visualization System (SDVS) and summarize our experience in terms of procedures and results. MATERIALS AND METHODS: Forty-one patients who underwent this procedure at our Gastroenterology Clinic between February 2010 and October 2014 were included in this study. Patients were monitored for a median (IQR) of 44 (range 38-72) months. Demographic characteristics of these patients, results of the radiological and biochemical evaluation performed prior to the procedure, cholangioscopy findings together with the data relating to the procedure, histopathological diagnosis, clinical findings and results, and their effects on patient prognosis were assessed. RESULTS: In total, 41 patients underwent 46 cholangioscopy procedures. Of them, 21 (51.2%) were male. The most frequent clinical indications for cholangioscopy was the need to further investigate indeterminate stricture (n=16; 39%) and indeterminate filling defect (n=7; 17.1%). The procedure was considered successful in 39 patients with 41 (95.1%) receiving diagnostic and 33 (80.5%) receiving therapeutic benefits. The sensitivity and specificity for SVDS-guided biopsies and brush cytology were 80% and 87.5%; 26.6% and 75%, respectively. Complications related to the procedure occurred in a total of three patients (7.3%), two with cholangitis and one with perforation of gall bladder. CONCLUSION: Our experience shows that cholangioscopy procedures, performed with SDVS, are clinically applicable and safe in the diagnosis and treatment of hepatobiliary diseases.

Synthesis of new water-soluble ionic liquids and their antibacterial profile against gram-positive and gram-negative bacteria.

A series of imidazolium bromide salts (NIM-Br 1a, 1b and 1c) bearing different lengths of alkyl chains were synthesized and theirin vitro antibacterial activities were determined by measuring the minimum inhibitory concentration (MIC) values for Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Enterococcus faecalis. In addition, these imidazolium derivatives were also evaluated against biofilm produced by these bacterial strains. All compounds were found to be effective against Gram-positive and Gram-negative bacteria, and also more effective on the S. aureus biofilm production than the others.

Does MDR1 Analysis Predict Medical Therapy Modifications in Patients with Atrial Fibrillation?

OBJECTIVE: To evaluate the effects of multi-drug resistance gene (MDR1) gene factor which is significant in medicinereceptor relationship, on readmission to the emergency department (ED) and medical therapy modifications in patients with atrial fibrillation (AF) readmitting to the emergency department. STUDY DESIGN: Descriptive, analytical study. PLACE AND DURATION OF STUDY: Department of Emergency Medicine, Adnan Menderes University, Aydin, Turkey, from January 2016 to January 2017. METHODOLOGY: Fifty patients who did not have AF with rapid ventricular response, and 32 controls have been included in the study. Electronic recording system of the hospital was checked regularly to detect any readmission of these patients due to palpitation; and they were asked whether they had any ED readmission and any changes in medical therapy by calling them during the one-year period. Then, MDR1 1236TC, 2677TG and 3435TC gene analyses and medical treatment regimens of the patients after 1 year were compared. RESULTS: No significant differences were found neither between the study and the control group nor between the genders in the study group regarding the results of MDR1 gene analyses. Besides, there were no differences in medical treatment regimens compared to MDR1 gene analyses in the group with AF. There were no statistically significant differences in the results of MDR1 gene analysis in patients whose medical treatment regimen had been changed during the one-year period. CONCLUSION: MDR1 gene analyses did not have any significant effect on the development of AF, readmission to the ED and modification of the treatment regimenin the Turkish population.

Uncovering Dynamic Brain Reconfiguration in MEG Working Memory n-Back Task Using Topological Data Analysis.

The increasing availability of high temporal resolution neuroimaging data has increased the efforts to understand the dynamics of neural functions. Until recently, there are few studies on generative models supporting classification and prediction of neural systems compared to the description of the architecture. However, the requirement of collapsing data spatially and temporally in the state-of-the art methods to analyze functional magnetic resonance imaging (fMRI), electroencephalogram (EEG) and magnetoencephalography (MEG) data cause loss of important information. In this study, we addressed this issue using a topological data analysis (TDA) method, called Mapper, which visualizes evolving patterns of brain activity as a mathematical graph. Accordingly, we analyzed preprocessed MEG data of 83 subjects from Human Connectome Project (HCP) collected during working memory n-back task. We examined variation in the dynamics of the brain states with the Mapper graphs, and to determine how this variation relates to measures such as response time and performance. The application of the Mapper method to MEG data detected a novel neuroimaging marker that explained the performance of the participants along with the ground truth of response time. In addition, TDA enabled us to distinguish two task-positive brain activations during 0-back and 2-back tasks, which is hard to detect with the other pipelines that require collapsing the data in the spatial and temporal domain. Further, the Mapper graphs of the individuals also revealed one large group in the middle of the stimulus detecting the high engagement in the brain with fine temporal resolution, which could contribute to increase spatiotemporal resolution by merging different imaging modalities. Hence, our work provides another evidence to the effectiveness of the TDA methods for extracting subtle dynamic properties of high temporal resolution MEG data without the temporal and spatial collapse.

Differential diagnosis of Crohn's disease using antibodies to glycoprotein 2 and Saccharomyces cerevisiae.

BACKGROUND/AIMS: Glycoprotein 2 (GP2), the major autoantigen of Crohn's disease (CD)-specific pancreatic autoantibodies, is reportedly correlated with several characteristics of CD. We investigated this serological marker in Turkish patients with CD and assessed its utility in combination with anti-Saccharomyces cerevisiae antibodies (ASCAs) for differential diagnosis of CD. MATERIALS AND METHODS: A total of 60 patients with CD, 62 patients with ulcerative colitis (UC), and 46 healthy controls with a definite diagnosis who were similar in age and sex were enrolled in the study conducted from November 2011 to October 2012. ASCA and anti-GP2 levels were measured using commercially available kits. RESULTS: Anti-GP2 IgA and IgG levels were higher in patients with CD (25%) than in those with UC (5%) and controls (2%). The seroprevalence of anti-GP2 IgA was markedly higher than that of IgG in patients with CD in contrast to previous studies. The specificity and positive predictive value of seropositivity for both ASCA and anti-GP2 were 100%. ASCA IgA seropositivity was correlated with a complicated disease course and a history of surgery. There was no correlation between anti-GP2 seropositivity and disease location, disease behavior, or a history of surgery. CONCLUSION: The combination of ASCA and anti-GP2 may enable differentiation of CD from UC. As ASCA seropositivity is associated with a more complicated disease course, patients seropositive for ASCA at the initial diagnosis should undergo more intense therapy.

Predicting critical duration and reversibility of damage in acute mesenteric ischemia: An experimental study.

BACKGROUND: The objective of the current study was to investigate the value of the ischemic biomarkers endothelial cell-specific molecule-1 (endocan) and signal peptide-CUB-EGF domain-containing protein-1 (SCUBE-1) in the diagnosis and assessment of earlystage and irreversible damage in acute mesenteric ischemia. METHODS: An experimental mesenteric ischemia reperfusion model was designed using 54 rats. Nine groups were created: Three sham groups [Groups I (30th minute), IV (2nd hour), and VII (6th hour)], in which only blood and tissue specimens were sampled; 3 ischemia groups [Groups II (30th minute), V (2nd hour), and VIII (6th hour)], in which blood and tissue specimens were sampled after ligation of the superior mesenteric artery (SMA); and 3 reperfusion groups [Groups III (30th minute), VI (2nd hour), and IX (6th hour)], in which blood and tissue specimens were sampled after declamping the SMA and reperfusion for 1 hour. SCUBE-1 and endocan samples obtained from blood and tissue were examined histopathologically. RESULTS: The SCUBE-1 level was higher in the ischemia groups when compared with the sham groups (p<0.05), and the endocan level was markedly different in the late ischemia (6th hour) group. When these 2 markers were used together to assess irreversible mesenteric damage in the histopathological examination, the sensitivity in distinguishing between reversible or irreversible damage was 94.1% with a specificity of 73.7%. CONCLUSION: The elevation of SCUBE-1 alone seems to be significant for predicting early mesenteric ischemia in laboratory rats. The combination of SCUBE-1 and endocan may be useful to detect irreversible intestinal damage.

Gene Coexpression Network Comparison via Persistent Homology.

Persistent homology, a topological data analysis (TDA) method, is applied to microarray data sets. Although there are a few papers referring to TDA methods in microarray analysis, the usage of persistent homology in the comparison of several weighted gene coexpression networks (WGCN) was not employed before to the very best of our knowledge. We calculate the persistent homology of weighted networks constructed from 38 Arabidopsis microarray data sets to test the relevance and the success of this approach in distinguishing the stress factors. We quantify multiscale topological features of each network using persistent homology and apply a hierarchical clustering algorithm to the distance matrix whose entries are pairwise bottleneck distance between the networks. The immunoresponses to different stress factors are distinguishable by our method. The networks of similar immunoresponses are found to be close with respect to bottleneck distance indicating the similar topological features of WGCNs. This computationally efficient technique analyzing networks provides a quick test for advanced studies.

The predictive value of the inflammatory markers P-selectin and MCP1 in determining the length of stay and 30-day survival in the differentiation of sepsis patients.

OBJECTIVE: Sepsis is the leading disease that is diagnosed late and still has a mortal course in emergency departments. The primary factors that will reduce both morbidity and mortality are early diagnosis and an early treatment approach. Therefore, in this study, P-selectin and MCP1 levels, which are known to be markers of inflammation, were examined in patients being followed up in intensive care. METHODS: Patients evaluated with a preliminary diagnosis of sepsis in the emergency intensive care unit between September 2015 and August 2016 were classified as having sepsis or infection according to the Q- SOFA criteria, and the P- selectin values were compared. RESULTS: In the sepsis group, GCS was determined as 13 (12-13), SBP 90 (80-110), tachypnea 24 (22-26), lactate 3.8 (0.6-16.0), MAP 70 (60-77), and LOS 16 days (9.5-20.3). In the ROC analysis, the sensitivity of P-selectin and MCP1 in the differentiation of patients with and without sepsis was 95.7%, and 73.8%, and the specificity was 97.8% and 73.8%, respectively. According to the cutoff values, the sensitivity and specificity in the prediction of patient mortality were 71.4% and 65.6% in P- selectin and 78.6% and 65.6% in MCP1. CONCLUSIONS: The P-selectin and MCP1 values in the emergency department can differentiate sepsis patients according to the Q-SOFA criteria and showed 30-day mortality at a significant level. Therefore, in patients with suspected sepsis in an emergency department, MCP1 can be of benefit to physicians in their decisions regarding LOS and transfer to intensive care.

TAFRO Syndrome: A Case Report from Turkey and Review of the Literature.

TAFRO syndrome is a rare subtype of the Castleman's disease which has been described over the last years. The name of TAFRO syndrome comes from thrombocytopenia, anasarca, myelofibrosis, renal dysfunction, and organomegaly. We report a young Turkish male patient presented with fever, night sweats, fatigue, nausea, bilateral pretibial pitting edema, abdominal pain and watery diarrhea. PET/CT revealed multiple lymphadenopathies in cervical, axillary, mediastinal, paraaortic, mesenteric and inguinal lymph nodes. Excisional lymph node biopsy showed atretic germinal centers and expanded interfollicular areas, containing sheets of plasma cells. The R-CHOP regimen was started, and his signs and symptoms improved after the treatment. The current case confirms the unique presentation of this syndrome, helping to understand its clinical course and treatment strategy.

Treatment methods following suicidal self-administration of IV organophosphate: What can additional lipid administration change?

Organic phosphor compounds are highly toxic and life-threatening compounds that are widely used in agriculture, households and gardens worldwide. While oral intakes are observed frequently, toxic effects can also be seen through contract or inhalation. However, toxic cases through the parenteral route have rarely been reported. We had three main aims: first, to present a male patient who self-administered 2ml of monocrotophos intravenously to commit suicide. Our second goal was to present the current multiple treatment methods, such as fast general support, antidote treatment, lipid emulsion treatment, and plasmapheresis along with the literature. Third, we aimed to emphasize that with these treatments, patients' intensive care needs, intermediate symptoms, and hospitalization periods can be decreased and thus mortality and morbidity increase can be prevented.

Role of H-FABP values in determining the etiologic factors of the cardiac injuries.

INTRODUCTION: Cardiac injury resulting from blunt thoracic trauma is a frequent clinical occurrence which is difficult to diagnose. Our purpose in this study was to research whether H-FABP, which is a new marker for the diagnosis of cardiac injury, can be used in this patient group. METHODS: 50 patients with blunt thoracic injury who were admitted to our emergency service within a period of 8 months and 50 cases as controls were included in our study. RESULTS: Of the 50 patients with blunt thoracic injury in our study, 88% were male while 12% were female. The average age of the patients was 43 ± 15.15. While 27 (54%) of the 50 patients with blunt thoracic injury had cardiac injury, 23 (46%) did not have cardiac injury. The results of the statistical analyses showed a significant association between thorax trauma and cTnI, CPK, CPKMB and H-FABP (p<0.05). While there was a significant association between cardiac injury resulting from thoracic trauma and cTnI, ECG and TTE (p<0.05), there was no significant association between CPK, CPKMB and H-FABP (p>0.05). CONCLUSION: In thoracic traumas, cardiac injury diagnosis can be made as a result of the assessment with Troponin-I, ECG and ECHO. For cardiac injury diagnosis, wide scale prospective studies are needed for H-FABP use.

Treatment of pregnant women with a diagnosis of inflammatory bowel disease.

The frequency of diagnosis of inflammatory bowel disease (IBD) has increased in younger populations. For this reason, pregnancy in patients with IBD is a topic of interest, warranting additional focus on disease management during this period. The main objective of this article is to summarize the latest findings and guidelines on the management of potential problems from pregnancy to the breastfeeding stage. Fertility is decreased in patients with active IBD. Disease remission prior to conception will likely decrease the rate of pregnancy-related complications. Most of the drugs used for IBD treatment are safe during both pregnancy and breastfeeding. Two exceptions are methotrexate and thalidomide, which are contraindicated in pregnancy. Anti-tumor necrosis factor agents are not advised during the third trimester as they exhibit increased transplacental transmission and potentially cause immunosuppression in the fetus. Radiological and endoscopic examinations and surgical interventions should be performed only when absolutely necessary. Surgery increases the fetal mortality rate. The delivery method should be determined with consideration of the disease site and presence of progression or flare up. Treatment planning should be a collaborative effort among the gastroenterologist, obstetrician, colorectal surgeon and patient.

The diagnostic significance of signal peptide-complement C1r/C1s, Uegf, and Bmp1-epidermal growth factor domain-containing protein-1 levels in pulmonary embolism.

BACKGROUND: Pulmonary embolism (PE) is a common and potentially life-threatening disorder. Patients with PE often have nonspecific symptoms, and the diagnosis is often delayed. AIM: The aim of our study was to investigate the role of signal peptide-complement C1r/C1s, Uegf, and Bmp1-epidermal growth factor domain-containing protein 1 (SCUBE1) used in the diagnosis of PE. METHODS: The study was designed prospectively. A total of 57 patients who were admitted to emergency service with clinically suspected PE were included in the study. The patients diagnosed with PE were defined as PE group (n = 32), and the patients with undetectable embolism on computerized tomographic pulmonary angiography were defined as non-PE group (n = 25). Twenty-five age- and sex-matched healthy cases were chosen for the study. Routine biochemical analysis, complete blood count, D-dimer, SCUBE1, and arterial blood gas analysis were performed early after admission. RESULTS: Mean SCUBE1 levels were higher in the PE group (0.90 ng/mL) than in the non-PE (0.38 ng/mL) and control groups (0.47 ng/mL) (P < 0.01). A cutoff point of 0.49 ng/mL for SCUBE1 indicated 100% sensitivity and 64% specificity in patients with PE. Mean D-dimer levels were not different between PE and non-PE groups (P = 0.591). A multivariable logistic regression analysis (with dichotomous PE groups as the response variable; age, gender, chest pain, syncope, diabetes mellitus, chronic obstructive pulmonary disease, hypertension, D-dimer, neutrophil-lymphocytes ratio, and SCUBE1 variables as predictors) showed that the significant and independent predictors of PE diagnosis were SCUBE1 and chest pain. CONCLUSION: This study suggests that serum SCUBE1 measurement might be used as a diagnostic biomarker in PE.

Prognostic value of neglected biomarker in sepsis patients with the old and new criteria: predictive role of lactate dehydrogenase.

OBJECTIVES: This study examined the pH, lactate dehydrogenase (LDH), and heart rate values on the first day of hospitalization in patients with a prediagnosis of sepsis and biomarkers that may predict mortality. METHODS: Patients hospitalized in an emergency intensive care unit with a diagnosis of systemic inflammatory response syndrome were classified as having sepsis (n = 28), septic shock (n = 8), or severe sepsis (n = 8) according to International Sepsis Guidelines (old criteria). Forty-four patients were classified as having sepsis (n = 4), septic shock (n = 30), or infection (n = 10) according to The Third International Consensus Definitions for Sepsis and Septic Shock (new criteria). The effects of these patients' laboratory values on survival between groups were compared. Significant values were evaluated by χ2 automatic interaction detection analysis. RESULTS: When the patients were categorized according to the new classification criteria, there was an increase in the number of septic shock patients and a decrease in the number of sepsis patients. In addition, 10 patients were removed from the sepsis category. There was a significant difference between ex and discharged patients in terms of heart rate, pH, sodium bicarbonate, lactate, and LDH (P= .007, P= .002, P= .034, P= .009, and P= .002, respectively). Based on a χ2 automatic interaction detection analysis of the significant values, pH, LDH, and heart rate were prominent predictors of prognosis. CONCLUSIONS: Systemic pH, LDH, and heart rate values may be used to determine the best time to discharge patients from intensive care to other, more affordable hospital units.