Deep learning as a new tool in the diagnosis of mycosis fungoides.

Mycosis Fungoides (MF) makes up the most of the cutaneous lymphomas. As a malignant disease, the greatest diagnostical challenge is to timely differentiate MF from inflammatory diseases. Contemporary computational methods successfully identify cell nuclei in histological specimens. Deep learning methods are especially favored for such tasks. A deep learning model was used to detect nuclei Hematoxylin-Eosin(H-E) stained micrographs. Nuclear properties are extracted after detection. A multi-layer perceptron classifier is used to detect lymphocytes specifically among the detected nuclei. The comparisons for each property between MF and non-MF were carried out using statistical tests the results are compared with the findings in the literature to provide a descriptive analysis as well. Random forest classifier method is used to build a model to classify MF and non-MF lymphocytes. 10 nuclear properties were statistically significantly different between MF and non-MF specimens. MF nuclei were smaller, darker and more heterogenous. Lymphocyte detection algorithm had an average 90.5% prediction power and MF detection algorithm had an average 94.2% prediction power. This project aims to fill the gap between computational advancement and medical practice. The models could make MF diagnoses easier, more accurate and earlier. The results also challenge the manually examined and defined nuclear properties of MF with the help of data abundance and computer objectivity.

Hypochlorous Acid: A Novel Agent Against Echinococcus granulosus Protoscoleces.

Objective: We aimed to determine the scolicidal effect of hypochlorous acid and its efficiency at different concentrations. Materials and Methods: We tested the effectiveness of hypochlorous acid in-vitro on sterile gauze at different concentrations in test tubes. In addition, we compared its effectiveness with the scolicidal activity of other agents, povidone-iodine 10% and chlorhexidine-gluconate 0.04%. Results: Hypochlorous acid was 100% effective in 5 minutes at 1/1 (200 ppm/mL), 1/10 (20 ppm/ml), and 1/100 (2 ppm/mL) concentrations and in 10 minutes at 1/1000 (0.2 ppm/mL) concentration. Povidone-iodine 10%, and chlorhexidine-gluconate 0.04% were studied undiluted and were effective at all study times. Hypochlorous acid maintained the same scolicidal activity on gauze at all study times at the described dilutions. Conclusion: Hypochlorous acid is an effective scolicidal agent in 5 minutes at even 1/100 concentrations. In addition, it maintains the same scolicidal activity on gauze used in surgery to wall the surgical site.

Morphological features of the chiasma tendinum and its relation with surface landmarks and pulleys: a cadaveric study.

AIM: Chiasma tendinum (Camper's chiasm) is of great importance in the delicate movements and stability of the fingers and takes place poorly in the literature. This study aims to reveal the morphometric details of the chiasma tendinum in relation with pulleys and other relevant structures. MATERIALS AND METHODS: Palm and 2nd to 5th fingers of 10 (6 male, 4 female) formalin fixed cadavers were used bilaterally. After determining the superficial reference points on the fingers, the skin and the tendon sheath were incised, and then measurements of chiasma tendinum and related tendons were performed. The measurements were analyzed with respect to fingers, genders, and sides. Finally, the types of chiasma tendinum were identified and then grouped as symmetrical, asymmetrical, and pseudo chiasm. RESULTS: Pulley and chiasma tendinum positions were correlated with finger length (p < 0.01). Pulley lengths were significantly less in females. Asymmetrical chiasma tendinum types were found in 45% of the fingers. In most comparisons, values for fifth finger were significantly different than that of other fingers and chiasma tendinum types differed according to fingers and gender. The case of no fiber exchange was observed only in the 5th finger in 15%. CONCLUSION: Findings related to the prediction of location of the pulleys and chiasma tendinum according to the superficial signs, awareness of cases where one of the two arms of the flexor digitorum superficialis is extremely thin and no fiber exchanges that may be risk factors for spontaneous tendon rupture may help provide more accurate approaches in relevant clinical applications.

Morphometric Features of the Latissimus Dorsi Muscle in Fetal Cadavers With Meningomyelocele for Prenatal Surgery.

PURPOSE: Latissimus dorsi (LD) flaps are frequently used in the prenatal meningomyelocele (MMC) repairs; on that basis, this study aims to reveal the morphometric features of LD, thoracodorsal artery (TDA) and nerve (TDN) in fetal cadavers with MMC defects, with an anatomical perspective. METHODS: The study was conducted on 7 formalin-fixed human fetal cadavers (4 males and 3 females) with MMC defects, aged from 18 to 27 weeks of gestation. The size of LD, TDA, and TDN including their area, length, and width were measured by a digital caliper and digital image analysis software. Our direct measurements were compared with the corresponding estimations of a previous study in the literature which provides regression formulae based on gestational age. RESULTS: The fetal cadavers with MMC had bilateral LD. No significant differences were found in the numerical data of anatomical structures between the sides or the sexes. LD size (ie, area, length and width) was approximately 3% to 10% smaller in the fetuses with MMC defects than that of the normal fetuses. Unilateral LD flap in a 22-week-old fetus with a large MMC was evaluated as insufficient to close the defects. CONCLUSION: Ten percent shrinkage in the area of LD might be too critical to be disregarded by surgeons during the closure of MMC defects. The dimensional findings about LD (area, length, and width) may be helpful in planning of LD flap harvesting for the repairs of MMC.

Quantitative and Neurovascular Anatomy of the Growing Gracilis Muscle in the Human Fetuses.

This study is intended to obtain the algebraic growth dynamics of the gracilis in fetuses and determine the variations of neurovascular pedicle(s) of the gracilis, to aid infant surgeries. Forty fetuses (19 males and 21 females) were included in the study. Gestational mean age of the fetuses was 22.40 ±â€Š2.67 (range, 18-28) weeks. Numerical values were obtained using a digital caliper and a digital image analysis software. Linear functions for the surface area, width, anterior, and posterior margin lengths of the gracilis were calculated, respectively, as: y = -289.307 + 20.501 × age (weeks), y = -7.113 + 0.622 × age (weeks), y = -24.421 + 3.434 × age (weeks), and y = -24.397 + 3.314 × age (weeks). In addition, length and width of the gracilis tendon were calculated as y = -6.676 + 0.934 × age (weeks) and y = -0.732 + 0.074 × age (weeks), respectively. Parameters of the gracilis had no statistically significant difference regarding side and sex (P > 0.05). In all the specimens, the gracilis was innervated by the anterior branch of the obturator nerve. Blood supply of the gracilis was identified to be derived from 1 single artery in 38 sides of total 80 (47.5%), from 2 arteries in 36 (45%) and from 3 arteries in 6 (7.5%). In 74 sides (92.5%), the nerve was superficial to the main artery, whereas in 6 sides (7.5%), it was deeper. The data of the present study could be beneficial for surgeons in infant surgeries to treat conditions such as obstetrical brachial plexus paralysis, facial palsy, or anal incontinence. Linear functions can be utilized to better evaluate the growth course of the gracilis in fetuses and to predict the dimensions thereof. Additionally, comprehending the structure and recognizing the variations of the gracilis nerves and arteries can help to protect the neurovascular pedicle(s) of the gracilis during the operations.

Morphometric properties of the levator scapulae, rhomboid major, and rhomboid minor in human fetuses.

PURPOSE: The main objective of this study is to showcase the growth dynamics of levator scapulae, rhomboid major, and rhomboid minor algebraically, to help plan surgeries on newborns and young infants. METHODS: Twenty-five formalin-fixed fetuses (11 male-14 female) with a mean gestational age of 21.80 ± 2.61 (range 18-27) weeks present in the inventory of Mersin University Faculty of Medicine Anatomy Department were dissected. Surface area of levator scapulae, rhomboid major, and rhomboid minor was calculated using digital image analysis software; width and length parameters were measured using digital calipers. RESULTS: Neither sex nor side significant differences were observed in relation with the numerical data of levator scapulae, rhomboid major, and rhomboid minor (p > 0.05). Algebraic parameters such as surface area, width and length were detected to exhibit a linear growth from 18th to 27th week. Linear functions for levator scapulae, rhomboid major and rhomboid minor surface areas were obtained as y = - 136.871 + 10.598 × age (weeks), y = - 480.567 + 33.147 × age (weeks) and y = - 128.090 + 8.843 × age (weeks), respectively. CONCLUSION: The results and data of this study can potentially be beneficial in planning of surgeries for many infancy diseases such as trapezius paralysis, obstetrical brachial plexus palsy, Sprengel's disease, or winged scapula. Linear functions calculated in this study are expected to provide a better understanding of the growth dynamics of levator scapulae, rhomboid major, and rhomboid minor in fetal term and more precise estimation of muscle sizes.

[A sepsis case caused by a rare opportunistic pathogen: Bacillus pumilus]. / Nadir görülen firsatçi patojen Bacillus pumilus'un neden oldugu bir sepsis olgusu.

The high prevalence of Bacillus species in nature and the detection of these bacteria as contaminant in cultures may lead diagnostic dilemma, however they should still be considered as a pathogen particularly in case of repeated positive cultures from patients with risk factors. Bacillus pumilus is a bacteria, though rarely, been reported as the causative agent of various infections such as sepsis, endocarditis, skin infections and food poisoning in human. In this report, a sepsis case in an immunocompetent patient caused by B.pumilus was presented. A 38-year-old female patient was admitted to emergency service of our hospital with the complaints of headache, dizziness and diarrhea. She had not any risk factors except a history of heart valve replacement operation two years ago. In physical examination, she had abdominal retention, high fever and hypotension, together with the high levels of sedimentation rate (ESR) and C-reactive protein (CRP). The patient was hospitalized with the preliminary diagnosis of sepsis. Three sets of blood samples at two different periods were taken for the culture. All blood culture vials had a positive signal at the second day of incubation in BD BACTEC™ 9050 system, therefore subcultures were performed in sheep blood agar, chocolate agar and MacConkey agar, and incubated in aerobic and anaerobic conditions. Beta-haemolytic, gray-colored large colonies were isolated from anaerobic culture at the end of 18-24 hours incubation, and Gram staining from colonies showed gram-positive rods. The isolate was identified as B.pumilus with 99% accuracy rate by using BD Phoenix™ 100 identification system. This result was also confirmed by MALDI-TOF based VITEK® MS system and 16S rRNA sequencing by Illumina MiSeq® platform. Antibiotic susceptibility test performed by BD Phoenix™ 100 system and the isolate was found to be resistant against penicillin, while it was susceptible to vancomycin, erythromycin, clindamycin, levofloxacin, and trimethoprim-sulfamethoxazole. Initial treatment of patient was started with intravenous ceftriaxone and metronidazole empirically. Hypotension and fever returned to normal levels at the second and third days of the treatment, respectively. Metronidazole treatment was stopped at seventh day, and treatment was completed to 14 day with ceftriaxone alone. At the end of the treatment course, general condition of the patient was completely good, ESR and CRP were also decreased to normal levels. In conclusion, although most of the reported bloodstream infections that are caused by B.pumilus are intravascular catheter-related, artificial heart valves should also be considered as a risk factor even though vegetation was not detected in our patient.

[Molecular epidemiology, antimicrobial resistance and characterization of extended-spectrum beta-lactamases of Salmonella enterica serotype Paratyphi B clinical isolates]. / Salmonella enterica serotip Paratyphi B klinik izolatlarinin moleküler epidemiyolojisi, antimikrobiyal direnci ve genislemis spektrumlu beta-laktamazlarinin karakterizasyonu.

Although Salmonella enterica serotype Paratyphi B is the less frequently isolated serotype worldwide and in Turkey, it is the most common serotype in our hospital, with a marked increase in 2007. The purpose of this study was to investigate the antibiotic susceptibility and the extended spectrum beta-lactamase (ESBL) profile, and molecular epidemiology of S. Paratyphi B isolates detected in our hospital microbiology laboratory. Seventy isolates identified as S. Paratyphi B from 109 Salmonella isolates obtained from clinical specimens from different patients between October 2005 and December 2012, were included in the study. In addition to conventional methods, isolates were identified using the Phoenix automated microbiology system (Becton Dickinson, USA). Serotyping of the isolates was performed on the basis of slide agglutination and the Kauffmann-White scheme. The antibiotic susceptibility of the isolates was determined using the BD Phoenix' automated system and disk diffusion test. ESBL enzymes were investigated using the combined disk test, isoelectric focusing, polymerase chain reaction (PCR) and sequence analysis. The molecular epidemiology of the 51 isolates obtained between October 2005 and August 2008 was examined with pulsed-field gel electrophoresis (PFGE) using the XbaI enzyme. S. Paratyphi B isolates were obtained from 70 specimens (46 blood, 16 fecal, 4 bone marrow, 2 urine and 2 wound) each from different patients. Resistance to nalidixic acid was determined in 18.6%, resistance to ampicillin, cefotaxime and cefepime in 2.9% and to ceftazidime and co-trimoxazole in 1.4% of the isolates. ESBL production was detected only in two isolates; in one TEM-1 was accompanied by CTX-M-15 and in the other isolate CTX-M-3 was found. Forty-six of the 51 isolates (90%) were found to be genetically related by PFGE and were placed in cluster A. The distribution of the isolates in cluster A revealed six subtypes as A1 (n= 7), A2 (n= 11), A3 (n= 7), A4 (n= 18), A5 (n= 2) and A6 (n= 1). Three different patterns not related to the cluster A were determined in the remaining five isolates (two were B, one of each was C, D and E). In conclusion, although the rate of antibiotic resistance was low in the S. Paratyphi B isolates in our hospital, rare types of ESBLs such as CTX-M-3 and CTX-M-15 were detected in Salmonellae. As far as the current literature is considered, this is the first report in Turkey of blaCTX-M-15 in Salmonella spp. and blaCTX-M-3 genes in S. Paratyphi B. The results may indicate a possible future threat to the treatment of Salmonella infections. Since most of the isolates were genetically related, this might suggest an epidemic in our region.

Investigation of an outbreak of Serratia marcescens in a neonatal intensive care unit.

BACKGROUND: Serratia marcescens is a well-known but relatively uncommon cause of nosocomial infections, particularly in neonatal intensive care unit (NICU) patients. We investigated an outbreak of S marcescens in the NICU at the Farabi Hospital of Karadeniz Technical University in Trabzon, Turkey. METHODS: Between March 21 and May 27, 2006, nine of the neonates were identified with cultures of S marcescens, and there were three deaths because of septicemia. For the purpose of identifying the source of infection, 85 environmental samples, two breast milk samples from two babies' mothers, and 38 hand-washing samples from the health care workers (HCWs) were collected for the detection of S marcescens. All the S marcescens isolates were genotyped by pulsed-field gel electrophoresis with endonuclease SpeI restriction enzyme. RESULTS: Serratia marcescens was identified from one hand-washing sample and two breast milk samples. None of the environmental samples yielded S marcescens. Of the 13 isolates analyzed, four belonged to one major genotype, whereas eight (6 from neonates and 2 from breast milk) were indistinguishable; two isolates (2 from neonates) were closely related; and three isolates (2 other neonates and 1 from HCW's hand) were different. Our intensive efforts failed to determine the source of the outbreak despite the finding that S marcescens strain was isolated from a HCW's hand. CONCLUSION: Present investigation suggested that an outbreak of S marcescens infection was caused by a major clone in our NICU, possibly transmitted through the hands of HCWs, emphasizing that strict hand washing before and after contact with patients must be the rule of the thumb.

[Resistance rates of Mycobacterium tuberculosis complex strains isolated from clinical specimens]. / Klinik Örneklerden Izole Edilen Mycobacterium tuberculosis Kompleks Suslarinin Antibiyotiklere Direnç Oranlari

The aim of this study was to investigate isoniazid, rifampicin, streptomycin and ethambutol resistance rates of Mycobacterium tuberculosis complex strains isolated from clinical specimens in the Mycobacteriology Laboratories of Karadeniz Technical University Hospital between January 2005-March 2010. A total of 212 M.tuberculosis complex strains, 152 (71.7%) of which were isolated from respiratory specimens and 60 (28.3%) from non-respiratory system specimens, were included to the study. M.tuberculosis complex strains were determined by polymerase chain reaction using primers specific for the IS6110 gene region. Single isolate of each patient were enrolled in the study. Antituberculosis drug susceptibility testing was performed by BACTEC MGIT 960 (Becton Dickinson, USA). Of the 212 isolates, 157 (74.05%) were susceptible to all of the four antimycobacterial agents while 55 (25.9%) were found resistant to one or more of the drugs. The monodrug resistance rates were found as 6.1% for isoniazid, 0.5% for rifampicin, 5.2% for streptomycin, and 2.4% for ethambutol. The number of multidrug resistant isolates characterized with resistance to isoniazid and rifampicin were 10 (4.8%). Our findings indicated that the rates of mono and multidrug resistant M.tuberculosis complex strains were significantly lower than the rates previously reported from our region and similar to the average country-base resistance rates reported by the Ministry of Health. Continuous monitoring of M.tuberculosis antimicrobial resistance at regional level would greatly aid to the success of the tuberculosis surveillance program in Turkey.

Evaluation of a new rapid lateral flow chromatography test for the diagnosis of Helicobacter pylori.

OBJECTIVE: The rapid, simple and non-invasive diagnosis of Helicobacter pylori (H. pylori) infection is important in implementing chemotherapy in appropriate manner, and in assessing persistent H. pylori infection after eradication therapy. The ImmunoCard STAT! HpSA kit (Meridian Bioscience, Europe) is a lateral flow chromatography test which utilizes a monoclonal anti-H. pylori antibody. In this study, we investigated the usefulness of the ImmunoCard STAT! HpSA test before and after eradication therapy on patients referred to undergo upper gastrointestinal endoscopy. METHODS: Sixty-five consecutive patients who were referred to undergo upper gastrointestinal endoscopy at the Department of Gastroenterology, Karadeniz Technical University Medical School, Turkey between February and August 2005 were included in this study. The ImmunoCard STAT! HpSA was compared with 4 invasive tests (histology, gram staining, rapid urease test, and culture). The reference method was defined as positive when 2 of the 4 invasive tests were positive. A negative H. pylori status was considered when all 4 tests present concordant negative results. RESULTS: Overall, the ImmunoCard STAT! HpSA test had 77.8% sensitivity, 79.3% specificity, 82.4% positive predictive value (PPV) and 74.2% negative predictive value (NPV) in all patients. With regard to pre-treatment values, the sensitivity was 70.6%, specificity 70.6%, PPV 100% and NPV 100% while on post-treatment group the sensitivity was 84.2%, specificity 64.7%, PPV 72.7% and NPV 78.6%. CONCLUSION: Our results indicate that the ImmunoCard STAT! HpSA test is a rapid, simple, and helpful procedure not only to determine H. pylori infection but also to assess the success of eradication therapy.