Predicting DNA toehold-mediated strand displacement rate constants using a DNA-BERT transformer deep learning model.

Dynamic DNA nanotechnology is driving exciting developments in molecular computing, cargo delivery, sensing and detection. Combining this innovative area of research with the progress made in machine learning will aid in the design of sophisticated DNA machinery. Herein, we present a novel framework based on a transformer architecture and a deep learning model which can predict the rate constant of toehold-mediated strand displacement, the underlying process in dynamic DNA nanotechnology. Initially, a dataset of 4450 DNA sequences and corresponding rate constants were generated in-silico using KinDA. Subsequently, a 1D convolution neural network was trained using specific local features and DNA-BERT sequence embedding to produce predicted rate constants. As a result, the newly trained deep learning model predicted toehold-mediated strand displacement rate constants with a root mean square error of 0.76, during testing. These findings demonstrate that DNA-BERT can improve prediction accuracy, negating the need for extensive computational simulations or experimentation. Finally, the impact of various local features during model training is discussed, and a detailed comparison between the One-hot encoder and DNA-BERT sequences representation methods is presented.

Minimally Invasive Detection of IDH1 Mutation With Cell-Free Circulating Tumor DNA and D-2-Hydroxyglutarate, D/L-2-Hydroxyglutarate Ratio in Gliomas.

Isocitrate dehydrogenase-1 (IDH1) mutation is accepted as one of the earliest events in tumorigenesis in gliomas. This mutation causes preferential accumulation of D- relative to L-enantiomer of 2-hydroxyglutarate (2-HG). Minimally invasive techniques to detect IDH1 mutation may prove useful for clinical practice. We adopted 2 different diagnostic approaches to detect IDH1 mutation status in glioma patients: Evaluation of D- and L-2-HG levels in cerebrospinal fluid (CSF), urine, and plasma, and identification of IDH1 mutation using cell-free circulating tumor DNA (ctDNA) in CSF and plasma. Forty-nine glioma patients in different stages were included. Levels of D- and L-2-HG were determined using liquid chromatography-tandem mass spectrometry; IDH1 R132H mutation was determined by digital-PCR. D-2-HG levels and D/L-2-HG ratio (rDL) in CSF and rDL in plasma were significantly higher in the mutant group than in the wild-type group (p = 0.029, 0.032, 0.001, respectively). The IDH1 mutation detection rates in CSF- and plasma-ctDNA were 63.2% and 25.0%, respectively. These data indicate that D-2-HG values in CSF and rDL in plasma and CSF can be considered as significant contributors to the identification of IDH1 mutation status. In addition, detection of IDH1 mutation in CSF-ctDNA from glioma patients provides a basis for future use of ctDNA for minimally invasive clinical assessment of gliomas.

Treatment of Intractable Midbrain Tremor with a Pedinculopontine Nucleus Radiofrequency Lesion.

In this report, we present the case of a 21-year-old female with midbrain tremor involving atypical features, treated using a pedinculopontine nucleus lesion. Different targets for the treatment of midbrain tremor using radiofrequency lesion have been reported. In this case, stimulation of the thalamic ventralis intermedius nucleus and subthalamic nucleus produced no satisfactory improvement in tremor frequency and amplitude. A third goal was to obtain a significant response in terms of these outcomes with pedinculopontine nucleus stimulation. According to the literature, this is the first case of midbrain tremor treated with a pedinculopontine nucleus radiofrequency thermocoagulation lesion.

The prostatic adenocarcinoma with mucinous features: A review of the literature with three case reports.

Mucinous adenocarcinoma of the prostate is one of the rare variants of the prostatic carcinoma, and its incidence among all prostatic carcinomas is reported to be 0.3% in the literature. If the tumor variant containing extracellular mucin in <25% of the resected tumor mass, the histology is defined as adenocarcinoma with mucinous features. The mucinous adenocarcinoma of the prostate displays similar prognostic features with the classic adenocarcinoma. In this study, the treatment and surveillance processes of our three patients with prostatic adenocarcinoma with mucinous features were presented along with a literature review.

The relationship between serum irisin levels and erectile dysfunction in diabetic men (irisin and erectile dysfunction in diabetic patients).

Irisin is an exercise-induced myokine that alleviates endothelial dysfunction and reduces insulin resistance in type 2 diabetes mellitus. We conducted this cross-sectional prospective study to determine the association of serum irisin levels and erectile dysfunction in type 2 diabetic patients. We compared 34 diabetic patients with erectile dysfunction with 30 diabetic patients without erectile dysfunction. In our study, serum irisin levels were found to be statistically significantly higher in diabetic patients without erectile dysfunction compared to those with erectile dysfunction (p = .016) and according to correlation analysis, irisin levels had a significantly negative correlation with the serum HbA1C value (r = -.294, p = .018). Based on the results of our study, we think that this molecule can be used in the diagnosis or treatment of erectile dysfunction in diabetic patients, if these findings are supported by larger studies.

Computed tomography vs. magnetic resonance imaging in unstable cervical spine injuries.

BACKGROUND: This study aimed to investigate the role of computed tomography (CT) in identifying missed unstable blunt cervical injuries. METHODS: Patients admitted to the emergency department between June 2014 and June 2018 with a diagnosis of blunt cervical trauma were included in this study. All participants underwent cervical magnetic resonance imaging (MRI) after an initial cervical CT investigation. All imaging results were reviewed, and decisions were taken by the consensus of a team consisting of an emergency medicine specialist, a neuroradiologist, and a neurosurgeon. Other variables included age, sex, the Glasgow Coma Scale, medical comorbidities, multi-trauma, neurological deficits, accompanying intracranial hemorrhage, extremity fractures, and the mechanism of the injury. RESULTS: Data for 195 patients were analyzed. The mean (±standard deviation) age of the participants was 47.34±21.90 years, and 140 (71.8%) were males. Eighteen patients (9.2%) were below age <18. The most frequent mechanism of injury was fall from height (n=100; 51.3%). Using MRI as the gold standard, the sensitivity of CT in diagnosing unstable cervical injury was 77.7% (95% CI [67.1-86.1]), while its specificity was 100.0% (95% CI [59.0-100.0]). CONCLUSION: Although computed tomography is relatively good in diagnosing unstable cervical injuries, its sensitivity in detecting positive cases is not as successful. Thus, the use of MRI in patients with an unstable injury seems to be warranted.

MRI-guided frame-based stereotactic brainstem biopsy procedure: A single-center experience / Procedimiento de biopsia de tronco de cerebro estereotáctico guiado por marco de imágenes por resonancia magnética (IRM): Una experiencia en un solo centro

Introduction and objectives: This study aims at presenting our experience of the MRI-guided frame-based stereotactic brainstem biopsy method, and evaluating the outcomes of the procedure. Patients and methods: The current study involved 18 cases that underwent MRI-guided frame-based stereotactic biopsy for brainstem lesions between 2011 and 2018 in our clinic. The relevant data regarding the technique of the biopsy procedure, morbidity, histopathological diagnosis it yields and diagnostic accuracy was retrospectively analyzed. Results: Stereotactic biopsy procedure was performed on 18 patients, including 16 adults and two children. MRI was used as guidance for the biopsy procedure in all patients. The adult patients had the biopsy under local anesthesia; as for the pediatric patients local anesthesia plus sedation was used. All patients received diagnosis based on the histopathological examination of their biopsy samples. No equivocal or negative results, and no major morbidity or mortality was seen in the patients after the procedure. Conclusions: MRI-guided frame-based stereotactic biopsy can be considered as a safe and efficient diagnostic method for brainstem lesions when its diagnostic yield and its morbidity and/or mortality rates are evaluated. Choosing the best trajectory for each lesion, using MRI as guidance for targeting, taking a limited number of biopsy samples are valuable criteria for the decreased morbidity rates in stereotactic brainstem biopsy procedures

Introducción y objetivos: Este estudio tiene como objetivo presentar nuestra experiencia del método estereotáctico de biopsia del tronco encefálico guiado por IRM, y evaluar los resultados del procedimiento. Pacientes y métodos: El estudio actual incluyó 18 casos que se sometieron a biopsia estereotáctica basada en un marco guiada por IRM para lesiones del tronco encefálico entre 2011 y 2018 en nuestra clínica. Los datos relevantes con respecto a la técnica del procedimiento de biopsia, la morbilidad, el diagnóstico histopatológico que produce y la precisión diagnóstica se analizaron retrospectivamente. Resultados: Se realizó un procedimiento de biopsia estereotáctica en 18 pacientes, incluidos 16 adultos y 2 niños. La RM se utilizó como guía para el procedimiento de biopsia en todos los pacientes. Los pacientes adultos se hicieron la biopsia bajo anestesia local; en cuanto a los pacientes pediátricos se utilizó anestesia local más sedación. Todos los pacientes recibieron un diagnóstico basado en el examen histopatológico de sus muestras de biopsia. No hubo resultados equívocos ni negativos, y no se observó una mayor morbilidad o mortalidad en los pacientes después del procedimiento. Conclusiones: La biopsia estereotáctica basada en un marco guiada por IRM se puede considerar como un método de diagnóstico seguro y eficiente para las lesiones del tronco cerebral cuando se evalúa su rendimiento diagnóstico y sus tasas de morbilidad y/o mortalidad. La elección de la mejor trayectoria para cada lesión, utilizando la RM como guía para la selección, tomando un número limitado de muestras de biopsia, son criterios valiosos para la disminución de las tasas de morbilidad en los procedimientos de biopsia estereotáctica del tronco cerebral

Magnetic Resonance Imaging-guided Stereotactic Biopsy: A Review of 83 Cases with Outcomes.

BACKGROUND: The purpose of this study was to determine the relationship between the radiological and histopathological distribution of the cerebral lesions diagnosed with stereotactic biopsy (STB) procedure and its outcomes. MATERIALS AND METHODS: In the current study, a retrospective analysis of 83 patients that underwent the STB in our clinic from January 2011 to December 2015 was made. T1-weighted contrast-enhanced cranial magnetic resonance imaging examinations were performed on patients on whom Leksell stereotactic frame system was installed. The histopathological and the radiological data derived from the STB procedure were classified. RESULTS: In terms of localization, glial tumor (56.6%) was the most common lesion in all regions, except for the multifocal lesions. Contrary to the common knowledge, lymphoma (14.4%) was found to be the most common lesion among multifocal lesions. The success of obtaining positive STB samples in the current series was 95.2% and the complication rate was 3.6%. CONCLUSION: Had a routine computed tomography scan been performed on each patient in this series, the number of clinically insignificant small intracerebral hematomas would have probably been higher. Nevertheless, the rate of the STB sampling accuracy and the complication rate were similar to those reported in the relevant literature.

MRI-guided frame-based stereotactic brainstem biopsy procedure: A single-center experience.

INTRODUCTION AND OBJECTIVES: This study aims at presenting our experience of the MRI-guided frame-based stereotactic brainstem biopsy method, and evaluating the outcomes of the procedure. PATIENTS AND METHODS: The current study involved 18 cases that underwent MRI-guided frame-based stereotactic biopsy for brainstem lesions between 2011 and 2018 in our clinic. The relevant data regarding the technique of the biopsy procedure, morbidity, histopathological diagnosis it yields and diagnostic accuracy was retrospectively analyzed. RESULTS: Stereotactic biopsy procedure was performed on 18 patients, including 16 adults and two children. MRI was used as guidance for the biopsy procedure in all patients. The adult patients had the biopsy under local anesthesia; as for the pediatric patients local anesthesia plus sedation was used. All patients received diagnosis based on the histopathological examination of their biopsy samples. No equivocal or negative results, and no major morbidity or mortality was seen in the patients after the procedure. CONCLUSIONS: MRI-guided frame-based stereotactic biopsy can be considered as a safe and efficient diagnostic method for brainstem lesions when its diagnostic yield and its morbidity and/or mortality rates are evaluated. Choosing the best trajectory for each lesion, using MRI as guidance for targeting, taking a limited number of biopsy samples are valuable criteria for the decreased morbidity rates in stereotactic brainstem biopsy procedures.

DTI-Based Neuronavigation Guided Eloquent Area Glioma Resection with Awake Craniotomy: Supra-Functional Resection of Eloquent Area Gliomas.

AIM: To present an overview of our awake craniotomy practices performed with complementary use of diffusion tensor imaging (DTI)-based neuronavigation (DTI-bN) and cortical-subcortical electrical stimulation for glioma resection located in eloquent areas, and the clinical outcomes of these practices regarding neurological morbidity and residual tumour volume. MATERIAL AND METHODS: This study was conducted between October 2016 and December 2017 involving 18 cases. The DTIbN method, in addition to cortical-subcortical stimulation, was done with awake craniotomy. Changes in the neurological status of the patients and results of the method regarding residual tumour volume were recorded. This retrospective study use data obtained from patients' records and radiological examinations. RESULTS: Of the 18 patients, a gross total resection was performed on nine patients (50%), a near total resection was performed on seven patients (38.8%) and a subtotal resection was performed on two patients (11.1%). Intraoperative neurological deterioration was observed in 14 of 18 patients during their surgical procedures, and neurological examinations in the sixth post-operative month revealed permanent deficits in two patients. CONCLUSION: This study is one of the rare series to have presented the results of the use DTI-bN method as well as corticalsubcortical stimulation during awake craniotomy, according to literature review. In 88% of cases, tumour resection rates are over 90%.

A Case of Vago-Glossopharyngeal Neuralgia Caused by Choroid Plexus.

Vascular compression has been reported to be the most common reason for vago-glossopharyngeal neuralgia (VGN). The treatment may include medications, ganglion blockade with a radiofrequency ablation, and microvascular decompression (MVD). A review of the literature reveals that VGN may develop due to choroid plexus compression, and the number of reported cases is very limited. The current case is the fifth in the relevant literature. In this paper, choroid plexus compression has been shown intraoperatively during the treatment of rare idiopathic VGN using MVD. Complaints of the patient have been resolved following the choroid plexus excision.

Iatrogenic Vascular Injuries Due to Spinal Surgeries: Endovascular Perspective.

AIM: Iatrogenic vascular injuries due to spinal surgeries are rare but serious complications. Surgical management of these injuries is challenging with high morbidity rates. In this study we aim to present the results of endovascular management of iatrogenic vascular injuries due to spinal surgeries. MATERIAL AND METHODS: We retrospectively reviewed 11 patients (5 male, 6 female) who had vascular injuries due to cervical and lumbar spinal surgeries. Clinical findings were bleeding (n=5), leg edema (n=6) and right heart failure with severe dyspnea (n=1). The age range of the patients were between 42-67 (mean: 57.1). Six patients were reviewed with imaging before the procedures and the rest of the patients (n=5) were directly referred to the angiography unit for diagnosis and possible endovascular treatment. RESULTS: The types of surgeries were; cervical surgery (n=5) and lumbar disc operation (n=6). The type of vascular injuries were; vertebral artery stenosis (n=1), vertebral artery pseudoaneurysm (n=3), vertebral artery occlusion (n=1) and iliac arteriovenous fistula (n=6). The type of endovascular treatments were; parent artery occlusion (PAO) (n=2), covered stent graft implantation (n=6) and intrasaccular coil embolization of pseudoaneurysm (n=1). The remaining 2 patients were managed conservatively. No major complications or mortality occured during endovascular interventions. No bleeding or ischemia occured in the follow-up period. CONCLUSION: Iatrogenic vascular injuries due to spinal surgeries are rare but serious complications. Endovascular interventions are safe and effective in the diagnosis and treatment of such vascular injuries.

Awake Craniotomy Procedure: Its Effects on Neurological Morbidity and Recommendations.

AIM: To present our experience with the awake craniotomy (AC) method starting from the preoperative period, to report the morbidity and the functional outcomes along with the complications in patients who underwent AC, and to make recommendations for possible problems. MATERIAL AND METHODS: This study involved 46 cases- 2 of which were pediatric cases with lesions localized in the functional area - who were operated with the AC method between September 2011 and January 2016 at our clinic. The age range was 12 to 81 years. The average age was 48 years. Both preoperative and postoperative (1, 3, 6 and 12 months) neurological examinations were recorded. RESULTS: Of the 46 patients who had AC surgery in this series, 17 were observed to have neurological deterioration in the intraoperative period. At the month 1 follow-up, 13 of these 17 patients were observed to have full neurological recovery. Moreover, 4 patients that developed hemiplegia were able to mobilize with support at the month 6 follow-up. All patients were observed to have a return of language skills to baseline preoperative function on month 1 follow-up. CONCLUSION: When the results of the AC method were examined, it was observed that persistent postoperative neurological deficit rates were very low in the follow-up period. Based on our practice presented here, it could be concluded that the precise synchrony between the surgeon, the anesthesia team and the patient is required for successful AC and the preservation of language and motor functions.

Pediatric Awake Craniotomy for Brain Lesions.

Awake craniotomy is a special method to prevent motor deficits during the resection of lesions that are located in, or close to, functional areas. Although it is more commonly performed in adult patients, reports of pediatric cases undergoing awake craniotomy are limited in the literature. In our clinic, where we frequently use awake craniotomy in adult patients, we performed this method in 2 selected pediatric cases for lesion surgery. At an early age, these 2 cases diagnosed with epilepsy presented cerebral lesions, but since the lesions enclosed functional areas, surgical resection was not regarded as a treatment option at this time. In these 2 pediatric cases, we successfully completed lesion surgery with awake craniotomy. The method and the techniques employed during surgery are presented concomitant with other reports in the literature.

Primary glioblastoma of the medulla spinalis: a report of three cases and review of the literature.

Primary spinal glioblastoma multiforme (spinal GBM) is not a very common entity. This paper presents an outline of this rare neoplasm, its clinical presentation, course, management and outcome and reports a 3-case series of spinal GBM. In this 3-case series with spinal GBM, one of the patients was operated for hydrocephalous 10 months later following the tumor surgery and another patient had cerebral metastasis after the surgery. In the postoperative period, two of the cases received radiotherapy and one received combined radiotherapy and chemotherapy with steroid therapy together following the tumor surgery. The review of the pertinent literature has revealed that due to the scarcity of the reported cases of primary spinal GBMs, this issue requires a closer look. GBM behaves more aggressive in medulla spinalis than it behaves when it originates from cerebrum. It may disseminate to the cerebrum during its course and it may cause hydrocephalus due to this dissemination (metastasis).

Case report: cranioplasty infection due to Roseomonas gilardii at a university hospital in Turkey.

Roseomonas is a pink-pigmented, nonfermentative, oxidative, Gram-negative coccobacilli that has clinical importance as opportunistic pathogen which can lead to infections especially in immunosuppressed individuals. It is relatively less reported in many centers. These microorganisms are detected after several days growth in culture environment, and typical pink, mucoid colonies are detected. We are reported a case of cranioplasty infection that took place in a patient with with cranial abscess formation due to Roseomonas gilardii at Izmir University School of Medicine Medicalpark Hospital.

Semi-rigid ureterorenoscopy in children without ureteral dilatation.

OBJECTIVES: We aimed to retrospectively review the efficiency of ureterorenoscopy (URS) applied without ureteral dilatation for evaluating pediatric ureteral pathologies. METHODS: The files of pediatric patients hospitalized in our clinic between January 2000 and June 2006 due to ureteral stone disease were reviewed and evaluated retrospectively. The ages, medical histories, physical examination results, preoperative routine blood and urinary tests, and culture results were recorded. Ureteral orifice dilatation was not needed in any of the patients. Due to the risk of mucosal trauma and edema development in the ureteral orifice and intramural ureter, 3F and 4F catheters were applied in all patients following the ureterorenoscopy. These catheters were removed 24 h after the procedure. RESULTS: The files of 54 pediatric patients with a mean age of 8.5 years (range 1-16 years) were evaluated retrospectively. While diagnostic URS was applied in 12 (22.2%) of the patients, ureteral calculi were determined in 42 (77.8%) patients and the stones were fragmented by pneumatic lithotripter. Twenty-five of the stones were localized in the lower ureter, 16 in the mid-ureter, and 3 in upper ureter. The mean stone size was found to be 7.1 mm (range 4-12). None of the stones migrated to the proximal region. In 2 patients open ureterolithotomy was applied; stones were localized in the upper ureter in both of these patients. CONCLUSIONS: Ureterorenoscopy can be successfully and safely applied without the need for ureteral dilatation in ureteral pathologies of children.

Body mass index, body fat percentage, and the effect of body fat mass on SWL success.

OBJECTIVES: In the present study, we investigated the effects of the Body Mass Index (BMI), the Body Fat Percentage (BFP), and the Body Fat Mass (BFM) on success of SWL, prospectively. PATIENTS AND METHODS: The BMI, BFP, BFM values of patients, who were treated by SWL due to upper urinary system stone disease (pelvis renalis, upper ureter, kidney lower and upper calices) between January and December 2005 in our hospital's urolithiasis center, were measured. Patients with stones smaller than 5 mm or larger than 20 mm and patients who had a stone localized somewhere other than in the upper urinary system, were not included in the study. Patients evaluated to be clinically successful according to the SWL were put in group 1, and the other patients who were not successful were included in group 2. RESULTS: About 158 (97 male, 61 female) patients aged between 16 and 92 (mean 36.69 (+/-13.22) years), put on SWL therapy due to presence of upper urinary system stone disease, were included in the study. While the mean BMI was 23.97 +/- 0.4 in group 1 and 25.98 +/- 0.5 (P = 0.02) in group 2, BFP was 23.85 +/- 0.8 in group 1 and 29.19 +/- 1.1 (P = 0.001) in group 2, and BFM was determined to be 16.74 +/- 0.7 and 21.19 +/- 1.01 (P = 0.001) in group 2. Regarding all the parameters (BMI, BFP, BFM), the statistical analyses carried out between the groups showed significant differences. CONCLUSION: BFP and BFM parameters are also important factors along with the BMI in providing a successful SWL treatment. All the parameters should be considered regarding the success of the treatment and the patients should be informed.

Risk factors for lower urinary tract infection and bacterial stent colonization in patients with a double J ureteral stent.

OBJECTIVE: We investigated the potential risk factors for lower urinary tract infection and bacterial stent colonization in patients with double-J stents. PATIENTS AND METHODS: A total of 195 double-J stents from 190 patients (95 men and 95 women, mean age 40.22 years) were examined. In all patients, prophylactic antimicrobial therapy was administered at the time of stenting. The stents and urine samples were removed aseptically and the proximal and distal tip segments of the stents were obtained. Three culture specimens were obtained from each stent segment and urine sample. Chi-square tests, odds ratio, and relative risk were used for the statistical analysis. RESULTS: Bacterial colonies were found in 24% (47 of 190) of the urine samples, 31% (61 of 195) of the proximal stent segments, and 34% (67 of 195) of the distal stent segments. Of the pathogens identified, Escherichia coli (34 of 47) was the most common. Diabetes mellitus (P < 0.01), chronic renal failure (P < 0.001), and pregnancy (P < 0.01) were found to be risk factors for lower urinary tract infection in patients with stents. An increased stent colonization rate was associated with implantation time, age, and female sex, but these were not statistically significant for lower urinary tract infection CONCLUSION: Diabetes mellitus, chronic renal failure, and pregnancy are associated with a higher risk of lower urinary tract infection. Therefore, patients in these categories should be monitored carefully for infectious complications.

Prevention of pain and infective complications after transrectal prostate biopsy: a prospective study.

AIM: To investigate the effects of lidocaine gel and parenteral antibiotics and povidine lavage in the treatment of pain occurring during prostate biopsy in terms of infective complications. PATIENTS AND METHODS: Eighty patients with indications for prostate biopsy were randomized into two groups. One group underwent lavage with povidine iodine solution and lidocaine gel, and the other received cephtriaxon and lavage. Pain experienced by the patients was measured by visual analog scale (VAS). Blood samples were taken 15 and 60 min after the procedure, and urine culture antibiograms were taken 60 min after the procedure. RESULTS: The average pain score was 3.70 in Group 1 and 4.25 in Group 2; the difference between the groups was not statistically significant (P > 0.05). Likewise, no statistically significant difference between groups was found by the chi square test in either urine or blood cultures (P > 0.05). CONCLUSIONS: Lavage with betadine prior to transrectal prostate biopsy is adequate in the prevention of infective complications; however, because lidocaine gel is not effective against pain, alternative methods for pain management need to be developed.