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1.
ACS ES T Water ; 4(7): 2968-2980, 2024 Jul 12.
Article in English | MEDLINE | ID: mdl-39021580

ABSTRACT

Per- and polyfluoroalkyl substances (PFAS) make up a diverse group of industrially derived organic chemicals that are of significant concern due to their detrimental effects on human health and ecosystems. Although other technologies are available for removing PFAS, adsorption remains a viable and effective method. Accordingly, the current study reported a novel type of graphene oxide (GO)-based adsorbent and tested their removal performance toward removing PFAS from water. Among the eight adsorbents tested, GO modified by a cationic surfactant, cetyltrimethylammonium chloride (CTAC), GO-CTAC was found to be the best, showing an almost 100% removal for all 11 PFAS tested. The adsorption kinetics were best described by the pseudo-second-order model, indicating rapid adsorption. The isotherm data were well supported by the Toth model, suggesting that PFAS adsorption onto GO-CTAC involved complex interactions. Detailed characterization using scanning electron microscopy-energy dispersive X-ray spectroscopy, Fourier transform infrared, thermogravimetric analysis, X-ray diffraction, and X-ray photoelectron spectroscopy confirmed the proposed adsorption mechanisms, including electrostatic and hydrophobic interactions. Interestingly, the performance of GO-CTAC was not influenced by the solution pH, ionic strength, or natural organic matter. Furthermore, the removal efficiency of PFAS at almost 100% in river water demonstrated that GO-CTAC could be a suitable adsorbent for capturing PFAS in real surface water.

2.
Rev Assoc Med Bras (1992) ; 70(7): e20240275, 2024.
Article in English | MEDLINE | ID: mdl-39045942

ABSTRACT

OBJECTIVE: It has been determined that adropin has a role in tissue healing. This study aimed to determine the effects of head trauma on the tissues and blood levels of patients admitted to the emergency department. METHODS: The study group was divided into two to compare the adropin level in healthy individuals and patients with head trauma. Blood tests from patients and healthy volunteers were compared using the adropin kit. Adropin levels, Glasgow Coma Scale, and revised scores of trauma patients were recorded and analyzed. RESULTS: All patients in the trauma group had significantly higher adropin levels than the control group. Among these patients, the adropin level of the discharged patients was higher than the others. In addition, patients with high Glasgow Coma Scale and normal blood pressure were found to have higher adropin levels than the others. CONCLUSION: Although adropin cannot make a sharp distinction in determining the prognosis, the increase in its level in trauma patients shows that it triggers a protective mechanism.


Subject(s)
Biomarkers , Blood Proteins , Brain Injuries, Traumatic , Glasgow Coma Scale , Intercellular Signaling Peptides and Proteins , Peptides , Humans , Case-Control Studies , Intercellular Signaling Peptides and Proteins/blood , Brain Injuries, Traumatic/blood , Male , Female , Blood Proteins/analysis , Adult , Middle Aged , Peptides/blood , Biomarkers/blood , Prognosis , Young Adult
3.
J Craniofac Surg ; 2024 May 17.
Article in English | MEDLINE | ID: mdl-38758547

ABSTRACT

Regio temporalis is a site where botulinum neurotoxin is applied for various medical reasons, such as migraine, bruxism, and myofascial pain syndrome. The region is also one of the target regions in flap surgery. This study aimed to define the region topographically. In addition, it was aimed to reveal the intramuscular nerve distribution of the temporalis.11 fixed cephalus (cadaver head) and 2 fresh cephalus were used. The lateral canthus of the eye was marked as point A, and the middle of the ear tragus as point B. The transverse and vertical distances of the branching point of the superficial temporal artery to the A and B points were measured. Transverse distances of the superficial temporal artery and superficial temporal vein to A and B points were measured. The muscle was examined in 5 equal parts (L0-L1-L2-L3-L4), and each part's vertical muscle and tendon lengths were examined. Intramuscular nerve density was demonstrated by applying the modified Sihler staining to fresh temporalis'. Superficial temporal artery had an average transverse distance of 8.56±1.9 mm in women and 12.56±1.94 mm in men from the middle of the ear tragus. The artery was 64.21±5.59 mm posterior in females and 63.48±6.53 mm in males from the lateral canthus of the eye. Our study determined that the branching point of the superficial temporal artery was below the upper level of the arcus zygomaticus in 10% of cases and above it in 90% of cases. In our study, the L2 point had the highest vertical muscle length at 45.67 mm, while the L3 point had the highest vertical tendon length at 41.25 mm. The point where the muscle length had the highest ratio with 1.49 compared to the tendon length, was the L2 point. The temporalis' for which the modified Sihler staining was applied was examined in 5 quadrants. It was determined that the nerve densities were in the second and third quadrants from anterior to posterior. The distance of superficial landmarks to neurovascular structures is extremely important in interventions to the regio temporalis. Considering the average distances given in our study is important in avoiding damage in surgical procedures and not injecting into vascular structures. The point where the muscle length had the highest ratio of 1.49 compared to the tendon length was the L2 point. The area in line with this point is the most suitable area for injection. The L2 point is also the most suitable area for injection as it has the highest muscle length. Since the nerve densities were observed in the modified Sihler staining applied temporalis' 2 and 3 quadrants from anterior to posterior, botulinum neurotoxin injections to these areas will give more effective results.

4.
Adv Healthc Mater ; : e2400508, 2024 Apr 29.
Article in English | MEDLINE | ID: mdl-38683016

ABSTRACT

Salmonella, the most prevalent food-borne pathogen, poses significant medical and economic threats. Swift and accurate on-site identification and serotyping of Salmonella is crucial to curb its spread and contamination. Here, a synthetic biology cascade reaction is presented on a paper substrate using CRISPR-Cas12a and recombinase polymerase amplification (RPA), enabling the programming of a standard toehold RNA switch for a genome of choice. This approach employs just one toehold RNA switch design to differentiate between two different Salmonella serotypes, i.e., S. Typhimurium and S. Enteritidis, without the need for reengineering the toehold RNA switch. The sensor exhibits high sensitivity, capable of visually detecting as few as 100 copies of the whole genome from a model Salmonella pathogen on a paper substrate. Furthermore, this robust assay is successfully applied to detect whole genomes in contaminated milk and lettuce samples, demonstrating its potential in real sample analysis. Due to its versatility and practical features, genomes from different organisms can be detected by merely changing a single RNA element in this universal cell-free cascade reaction.

5.
J Hazard Mater ; 471: 134390, 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38678712

ABSTRACT

The extensive use of per- and polyfluoroalkyl substances (PFAS) in many industrial and consumer contexts, along with their persistent nature and possible health hazards, has led to their recognition as a prevalent environmental issue. While various PFAS removal methods exist, adsorption remains a promising, cost-effective approach. This study evaluated the PFAS adsorption performance of a surfactant-modified clay by comparing it with commercial clay-based adsorbents. Furthermore, the impact of environmental factors, including pH, ionic strength, and natural organic matter, on PFAS adsorption by the modified clay (MC) was evaluated. After proving that the MC was regenerable and reusable, magnetic modified clay (MMC) was synthesized, characterized, and tested for removing a wide range of PFAS in pure water and snowmelt. The MMC was found to have similar adsorption performance as the MC and was able to remove > 90% of the PFAS spiked to the snowmelt. The superior and much better performance of the MMC than powdered activated carbon points to its potential use in removing PFAS from real water matrices at an industrial scale.

6.
Surg Radiol Anat ; 46(1): 33-40, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38092974

ABSTRACT

PURPOSE: The aim of this study is to reveal the location of the zygomaticofacial foramina, the variations of their numbers, and their connections between the zygomatico-orbital and zygomaticotemporal foramina. METHODS: Ethics committee approval of our study was received by the Istanbul Medical Faculty Clinical Research Ethics Committee (date:30.07.2021, number:358356). 171 zygomatic bones of unknown gender from the Department of Anatomy, Istanbul University, were included in this study. The number of zygomaticofacial foramina and their connections with the zygomatico-orbital foramen and the zygomaticotemporal foramina were examined. Also, the morphometric distances between the zygomaticofacial foramen were calculated. Evaluation of the data was done with SPPS v.21. RESULTS: The number of zygomaticofacial foramina was found as 299. It was found single, double, three, four, five and six foramina, in 52 (30.4%), 52 (30.4%), 24 (14.03%), 10 (5.85%), 5 (2.93%), 1 (0.58%) zygomatic bone, respectively. Zygomaticofacial foramen was absent in 27 (15.8%) bones. Of these 299 foramina, 129 were found to be connected with zygomatico-orbital foramen and 23 with zygomaticotemporal foramen. It was noted that 147 zygomaticofacial foramina had no connection with any foramina. The distances between the zygomaticofacial foramen and the frontozygomatic suture, temporal process, maxillary process, the lowest point of the zygomatic bone, and orbital rim were found as 25.30 ± 2.81mm, 18.74 ± 3.56mm, 21.56 ± 4.16mm, 18.72 ± 2.57mm, 6.67 ± 3.27mm, respectively. CONCLUSION: Consequently, the location and variations of ZFF are of great importance for maxillofacial surgery and regional block anesthesia. Knowing its location and variations will help prevent complications during any surgical intervention in this region.


Subject(s)
Orbit , Skull , Humans , Orbit/anatomy & histology , Zygoma/anatomy & histology , Face , Cranial Sutures
7.
Exp Clin Transplant ; 21(2): 139-142, 2023 02.
Article in English | MEDLINE | ID: mdl-36919722

ABSTRACT

OBJECTIVES: The most frequent postoperative morbidity following living donor liver transplant is biliary complications, which can happen for both anatomical and procedural reasons. MATERIALS AND METHODS: We conducted a retrospective analysis of 104 patients who were living liver donors undergoing hepatectomy from January 2011 to April 2022. We evaluated all perioperative finding such as age, sex, remnant liver volume, biliary anatomy, theduration of operation time and hospitalization, and blood loss. RESULTS: Clavien-Dindo classification grade III complications were observed in 24% of all donors, with rate of biliary complications of 7.6% (n = 8). All biliary complications were typified as biliary leakage, and an endoscopic retrograde cholangiopancreatography procedure was performed for 5 patients. We analyzed the clinical and surgical features and discovered that the duration of hospitalization was longer in the biliary leakage group than the group without leakage (15.7 ± 5.8 days vs. 30.8 ± 9.3 days, respectively; P < .08). There was no significant statistical relationship between age, the duration of operation time, intraoperative blood loss, and remnant liver volume versus biliary leakage (P = .074, P = .217, P = .219, and P = .363, respectively). CONCLUSIONS: Early detection and treatment of complications are ensured during the perioperative process by carefuldonor selection andaccurate identification of the patient atrisk for biliary complications.


Subject(s)
Biliary Tract Diseases , Liver Transplantation , Humans , Liver Transplantation/adverse effects , Liver Transplantation/methods , Hepatectomy/adverse effects , Living Donors , Retrospective Studies , Liver/surgery , Biliary Tract Diseases/etiology , Postoperative Complications/etiology , Postoperative Complications/surgery
8.
Oncology ; 101(5): 321-327, 2023.
Article in English | MEDLINE | ID: mdl-36809752

ABSTRACT

INTRODUCTION: This study examined the difference in overall survival (OS) between peritoneal metastatic gastric cancer (PMGC) patients who underwent neoadjuvant chemotherapy followed by cytoreductive surgery ± hyperthermic intraperitoneal chemotherapy (CRS ± HIPEC) and those who did not have surgery but instead received palliative chemotherapy. METHODS: This retrospective study included 80 patients who were followed up with the diagnosis of PMGC, those undergoing neoadjuvant chemotherapy followed by CRS ± HIPEC (CRS ± HIPEC group) and those receiving chemotherapy only (non-surgical group), in the medical oncology clinic between April 2011 and December 2021. Clinicopathological features, treatments, and OS of the patients were compared. RESULTS: There were 32 patients in the SRC CRS ± HIPEC group and 48 in the non-surgical group. In the CRS ± HIPEC group, CRS + HIPEC was performed on 20 patients, and only CRS was performed on 12 patients. All of the patients who underwent CRS + HIPEC, and 5 of the patients who underwent only CRS received neoadjuvant chemotherapy. While the median OS was 19.7 (15.5-23.8) months in the CRS ± HIPEC group, the median OS was 6.8 (3.5-10.2) months in the non-surgical group (p < 0.001). CONCLUSION: As a result, CRS + HIPEC significantly improves survival in PMGC patients. With experienced surgical centres and appropriate patient selection, the life expectancy of patients with PM can be extended.


Subject(s)
Hyperthermia, Induced , Peritoneal Neoplasms , Stomach Neoplasms , Humans , Neoadjuvant Therapy , Stomach Neoplasms/pathology , Hyperthermic Intraperitoneal Chemotherapy , Combined Modality Therapy , Retrospective Studies , Cytoreduction Surgical Procedures , Chemotherapy, Cancer, Regional Perfusion , Peritoneal Neoplasms/drug therapy , Survival Rate , Antineoplastic Combined Chemotherapy Protocols/therapeutic use
9.
Nanoscale ; 14(37): 13500-13504, 2022 Sep 29.
Article in English | MEDLINE | ID: mdl-36102688

ABSTRACT

We have developed a 'recombinase amplified CRISPR enhanced chain reaction' (RACECAR) assay that can detect as little as 40 copies of hepatitis B virus (HBV) genome using a benchtop spectrofluorometer. The limit of detection was determined to be 3 copies of HBV genome. The specificity of RACECAR was confirmed against hepatitis A virus (HAV). This assay can detect the genomic targets directly in serum samples without an extraction step. The 4 h-long fluorometric assay was developed by combining three tiers of isothermal amplification processes and can be repurposed for any target of choice. This highly modular reaction setup is an untapped resource that can be incorporated into the front-runners of molecular diagnostics.


Subject(s)
Clustered Regularly Interspaced Short Palindromic Repeats , Recombinases , DNA, Viral/genetics , Genome, Viral , Hepatitis B virus/genetics , Nucleic Acid Amplification Techniques , Recombinases/genetics , Sensitivity and Specificity
10.
Sisli Etfal Hastan Tip Bul ; 56(2): 238-243, 2022.
Article in English | MEDLINE | ID: mdl-35990297

ABSTRACT

Objectives: Pancreaticoduodenectomy (PD) is one of the most challenging operations in gastrointestinal system due to the difficulty of dissection areas and the need for complex reconstruction. The aim of this study is to compare the morbidity, post-operative pancreatic fistula (POPF), and mortality rates of the cases we have from the learning period for minimally invasive PD and our previous open PD cases with similar fistula risk scores (FRSs). Methods: Patients with similar age, ASA score, pre-operative drainage, and FRS were included in the study. A total of 71 patients, 48 of whom were operated with open surgery and 23 with minimally invasive methods, were included in the study. Results: When the statistical analysis performed, no statistically significant difference was found between open surgery and minimally invasive surgery groups in terms of age, gender, ASA score, pre-operative drainage, pancreatic texture, and treatment of pancreatic leakage (p=0.27, p=0.09, p=0.4, p=0.39, p=0.76, and p=0.36, respectively). There was a statistically significant difference between two groups in terms of clinically relevant pancreatic anastomotic leakage (Grade-B and Grade-C fistula) (p=0.11). The rate of Grade-BL and B leakage was higher in the minimally invasive surgery group, while Grade-C fistula was not observed in any patient (p=0.002). However, there was no statistically significant difference between the two groups in terms of the management of pancreatic leakage and related morbidity (p=0.36). There was no significant difference between the two groups in terms of tumor size, number of lymph nodes removed, FRS, amount of intraoperative bleeding, and diameter of Wirsung and common bile duct (p=0.15, p=0.20, p=0.145, p=0.80, and p=0.073, respectively). Considering the operation time, it was found that the operation time was longer in patients who received minimally invasive surgical treatment and this was statistically significant (p<0.0001). Conclusion: As a result, we believe that minimally invasive PD operation can be performed with similar morbidity and acceptable CR-POPF rates when compared with the open PD with similar FRS at the learning stage.

11.
Transplant Proc ; 54(1): 153-157, 2022.
Article in English | MEDLINE | ID: mdl-34996597

ABSTRACT

According to GLOBOCAN 2020 data, the incidence of ovarian cancer is 1.6%. Ovarian cancer ranks 19th in incidence and 15th in mortality with a rate of 2.1%. High-grade serous ovarian cancer is the most common subtype of malignant ovarian tumors, and around 70% to 80% of all ovarian malignancies are included in this group. The incidence of gynecologic malignancies in liver transplant recipients is between 0% and 1.5%, and the duration of diagnosis for gynecologic cancer after transplantation is between 1 and 59 months. A 52-year-old patient was admitted to our hospital complaining of a periumbilical nodule. Her medical history revealed she had a cadaver liver transplantation in 2003 because of cirrhosis due to hepatitis B. On her physical examination, an erythematous nodular lesion was observed in the umbilical region. Ultrasonography demonstrated diffuse ascites and approximately 30 mm of a soft tissue density with lobulated contours located on the periumbilical skin. Both cytology and biopsy results were reported consistent with high-grade serous ovarian cancer. She underwent an operation, she had no problems during the postoperative follow-ups, and she was discharged on the eighth postoperative day. According to the 2018 International Federation of Gynecology and Obstetrics staging criteria for ovarian cancer, the patient's cancer was stage IVB. The patient received 6 cycles of adjuvant chemotherapy that included carboplatin (AUC = 6) and paclitaxel (175 mg/m2). The patient was evaluated as having a complete response according to Response Evaluation Criteria in Solid Tumors. The patient has been disease-free for 11 months after diagnosis.


Subject(s)
Liver Transplantation , Ovarian Neoplasms , Carboplatin , Child, Preschool , Disease-Free Survival , Female , Humans , Liver Transplantation/adverse effects , Neoplasm Staging , Ovarian Neoplasms/diagnosis , Ovarian Neoplasms/pathology , Paclitaxel
12.
Anal Chem ; 94(2): 1195-1202, 2022 01 18.
Article in English | MEDLINE | ID: mdl-34964601

ABSTRACT

Here, we report a biomarker-free detection of various biological targets through a programmed machine learning algorithm and an automated computational selection process termed algorithmically guided optical nanosensor selector (AGONS). The optical data processed/used by algorithms are obtained through a nanosensor array selected from a library of nanosensors through AGONS. The nanosensors are assembled using two-dimensional nanoparticles (2D-nps) and fluorescently labeled single-stranded DNAs (F-ssDNAs) with random sequences. Both 2D-np and F-ssDNA components are cost-efficient and easy to synthesize, allowing for scaled-up data collection essential for machine learning modeling. The nanosensor library was subjected to various target groups, including proteins, breast cancer cells, and lethal-7 (let-7) miRNA mimics. We have demonstrated that AGONS could select the most essential nanosensors while achieving 100% predictive accuracy in all cases. With this approach, we demonstrate that machine learning can guide the design of nanosensor arrays with greater predictive accuracy while minimizing manpower, material cost, computational resources, instrumentation usage, and time. The biomarker-free detection attribute makes this approach readily available for biological targets without any detectable biomarker. We believe that AGONS can guide optical nanosensor array setups, opening broader opportunities through a biomarker-free detection approach for most challenging biological targets.


Subject(s)
Biosensing Techniques , MicroRNAs , Nanoparticles , Biosensing Techniques/methods , DNA, Single-Stranded
13.
Am Surg ; 88(2): 273-279, 2022 Feb.
Article in English | MEDLINE | ID: mdl-33517709

ABSTRACT

BACKGROUND: Delayed gastric emptying (DGE) is one of the most common complications after Whipple surgery. This situation delays postoperative oral food intake and prolongs hospitalization. Postoperative DGE often develops due to complications such as intra-abdominal abscess, collections, and anastomosis leaks, and these are called secondary DGE. The pathogenesis of primary DGE is still unknown, and there are insufficient data in the literature about the treatment. In this study, patients undergoing Whipple operation were examined separately as primary and secondary DGE. We discussed the causes and treatments of these patients, and also we aimed to present the therapeutic effect of endoscopy for primary DGE after the Whipple procedure. METHODS: From March 2014 to March 2018, data of 262 patients who underwent the Whipple procedure were collected prospectively. We observed that postoperative DGE developed in 53 (21.7%) patients. We retrospectively divided the patients by etiology into 2 groups as primary and secondary and graded DGE according to the International Study Group of Pancreatic Surgery. We defined patients who did not have secondary causes such as intra-abdominal abscess as primary DGE. Appropriate interventional procedures were performed for patients with secondary causes. We performed endoscopic intervention with therapeutic intent for patients who had primary DGE. RESULTS: The overall rate of DGE was 21.7% (n = 53) among 262 patients undergoing the Whipple procedure. It was observed that in 31 (58.5%) of these 53 patients, DGE was developed due to secondary causes. Interventional procedures were performed to these patients when necessary. A total of 22 (41.5%) patients developed primary DGE. Of these, 9 patients were grade A, 7 were grade B, and 6 were grade C. The mean duration of hospitalization for secondary DGE and primary DGE was 20.36 and 28.7 days, respectively. After endoscopic intervention with therapeutic intent to primary DGE patients, we observed that patients tolerated solid meal after 12 hours in grade B and after 26 hours in grade C patients. CONCLUSION: Delayed gastric emptying, which is a common complication after Whipple operation and which deteriorates the quality of life and prolongs the duration of hospital stay, should be treated according to the cause. In secondary DGE, treatment modalities must be focused on intra-abdominal causes such as hematoma, collection, and abcess. We suggest that the primary DGE which is unresponsive to medical treatments could be treated endoscopically. After endoscopic intervention, patients with primary DGE can be started oral intake on the same day and discharged more quickly.


Subject(s)
Endoscopy, Gastrointestinal , Gastroparesis/surgery , Pancreaticoduodenectomy/adverse effects , Postoperative Complications/surgery , Abdominal Abscess/complications , Eating , Gastroparesis/epidemiology , Gastroparesis/etiology , Gastroparesis/mortality , Humans , Intubation, Gastrointestinal/methods , Length of Stay , Pancreatic Fistula/complications , Pancreaticoduodenectomy/methods , Postoperative Complications/epidemiology , Postoperative Complications/etiology , Postoperative Complications/mortality , Prospective Studies , Time Factors
14.
Arch Iran Med ; 24(10): 771-778, 2021 10 01.
Article in English | MEDLINE | ID: mdl-34816700

ABSTRACT

BACKGROUND: The aim of this study was to evaluate the potential effects of biliary drainage before pancreaticoduodenectomy on postoperative outcomes. METHODS: This study was conducted retrospectively on data from 820 cases of pancreaticoduodenectomy performed in the Gastrointestinal Surgery Department of Ankara City Hospital between April 1999 and August 2019. Twenty years of collected patient data were re-examined and 805 patients were divided into two groups as those who underwent preoperative biliary drainage (PBD) and those who did not (non-PBD). Demographic data of patients, and preoperative, operative and postoperative details, including morbidity, were collected and compared between the two groups. RESULTS: There were 574 (71.3%) patients in the PBD group and 231 (28.6%) patients in the non-PBD group. Total complications according to Clavien-Dindo classification were significantly higher in the PBD group (P<0.001). Intraabdominal hemorrhage, delayed gastric emptying and wound infection were found to be higher in the PBD group but the rate of pancreatic fistula was similar in both groups. There was no difference between the two groups in terms of complications according to preoperative bilirubin levels. In drained patients with normal bilirubin levels, wound infections were significantly higher in a group with diameter of common bile duct>8 mm (P=0.020). CONCLUSION: PBD is not associated with anastomotic leakage after pancreaticoduodenectomy. Wound infection, delayed gastric emptying and intraabdominal hemorrhage were significantly associated with PBD. Preoperative bilirubin level had no effect on these results. In subgroup analysis, in patients undergoing drainage, if bilirubin falls below 5 mg/dL, the risk of wound infection was still high in patients with bile duct diameter>8 mm.


Subject(s)
Pancreaticoduodenectomy , Preoperative Care , Drainage , Humans , Pancreatectomy , Pancreaticoduodenectomy/adverse effects , Postoperative Complications/epidemiology , Retrospective Studies , Treatment Outcome
15.
ACS Synth Biol ; 10(7): 1785-1791, 2021 07 16.
Article in English | MEDLINE | ID: mdl-34142793

ABSTRACT

CRISPR-Cas12a is a powerful platform for DNA-based diagnostics. The detection scheme relies on unselective shredding of a fluorescent ssDNA reporter upon target DNA recognition. To extend the reporter library beyond ssDNAs, we discovered a fluorescent reporter type using a dsDNA template. In this design, the fluorescence of the dsDNA reporter is quenched via contact-quenching mechanism. Upon detection, the quenched fluorescence recovers with the activation Cas12a complex. Here, we compared the probing performance of two dsDNA reporters with two ssDNA reporters. The rate of the Cas12a trans-cleavage reaction was studied using one of the dsDNA reporters under different settings. The detection of different sizes of dsDNA or ssDNA targets was studied systematically under three different temperatures. Lower thresholds for ssDNA and dsDNA target size were identified. The mismatch tolerance and target specificity were examined for both ssDNA and dsDNA targets, separately. The probing performance of the dsDNA reporter was evaluated in a random DNA pool with and without target strands. We report that dsDNA can serve as a tunable fluorescence reporter template expanding the toolbox for Cas12a-based diagnostics.


Subject(s)
CRISPR-Cas Systems , DNA/genetics , Genes, Reporter , DNA, Single-Stranded/genetics
16.
Arch Iran Med ; 24(1): 43-47, 2021 01 01.
Article in English | MEDLINE | ID: mdl-33588567

ABSTRACT

BACKGROUND: Choledochal cysts are seen commonly in Asian populations, but rarely in Western populations. The pathogenesis of these premalignant lesions is not fully understood yet and the risk of malignant transformation increases with age. The overall malignancy risk is 10%-15% in East Asian countries. In this study, we aimed to present our surgical experience as a hepatobiliary center to the literature. METHODS: We retrospectively analyzed the data from the medical records of 70 patients operated for choledochal cyst between 2008-2019. RESULTS: Sixty-two of the 70 (89%) patients were female and 8 (11%) were male, the mean age was 45.89 ± 15.32 years. Overall, 44 (63%) patients had type I (a+b+c), 20 (28%) type V (Caroli), 2 (3%) type II, 2 (3%) type III and 2 (3%) type IVb cysts. The most common operation was cyst excision combined with hepaticojejunostomy (n: 26, 37%). The median diameter of the resected cysts was 3 cm (min- max: 1-11 cm). Malignancy was observed only in three (4%) patients with type III, type Ib, and type V cyts, who were 19, 38, and 72 years old, respectively. Mortality was not observed, morbidity was determined totally in 30 (43%) cases during early and late postoperative periods. CONCLUSION: Type of surgery in choledochal cysts differs according to the type of the cyst. Malignancy was observed at a rate of 4% in all age groups. Although the frequency of malignancy varies, the main treatment of choice should be surgery because malignancy can be seen at a young age.


Subject(s)
Choledochal Cyst/surgery , Adult , Choledochal Cyst/classification , Female , Humans , Male , Middle Aged , Precancerous Conditions/surgery , Retrospective Studies , Turkey
17.
Anal Chem ; 93(4): 1934-1938, 2021 02 02.
Article in English | MEDLINE | ID: mdl-33404234

ABSTRACT

Hybridization chain reaction (HCR) is a DNA-based target-induced cascade reaction. Due to its unique enzyme-free amplification feature, HCR is often employed for sensing applications. Much like DNA nanostructures that have been designed to respond to a specific stimulus, HCR employs nucleic acids that reconfigure and assemble in the presence of a specific trigger. Despite its standalone capabilities, HCR is highly modular; therefore, it can be advanced and repurposed when coupled with latest discoveries. To this effect, we have developed a gel electrophoresis-based detection approach which combines the signal amplification feature of HCR with the programmability and sensitivity of the CRISPR-Cas12a system. By incorporating CRISPR-Cas12a, we have achieved greater sensitivity and reversed the signal output from TURN OFF to TURN ON. CRISPR-Cas12a also enabled us to rapidly reprogram the assay for the detection of both ssDNA and dsDNA target sequences by replacing a single reaction component in the detection kit. Detection of conserved, both ssDNA and dsDNA, regions of tobacco curly shoot virus (TCSV) and hepatitis B virus (HepBV) genomes is demonstrated with this methodology. This low-cost gel electrophoresis assay can detect as little as 1.5 fmol of the target without any additional target amplification steps and is about 100-fold more sensitive than HCR-alone approach.


Subject(s)
CRISPR-Cas Systems , Electrophoresis, Gel, Two-Dimensional/methods , Biosensing Techniques/methods , DNA/chemistry , Nucleic Acid Amplification Techniques/methods , Nucleic Acid Hybridization/methods
18.
Turk J Surg ; 37(2): 156-161, 2021 Jun.
Article in English | MEDLINE | ID: mdl-37275188

ABSTRACT

Objectives: During the COVID-19 pandemic, most of the elective surgeries had to be postponed. However, it is not possible to delay the surgical treat- ment of cancer patients for a long time. The aim of this study was to present how gastrointestinal system surgery operations are managed without delay and how employee safety is ensured , together with the results of the last five months. For this purpose, a preclinical and clinical screening system was created. Material and Methods: Data of the patients who presented to our outpatient clinic between April 1st 2020 and August 31st 2020 were retrospectively reviewed. Results: During the last five months of the pandemic, a total of 387 patients were hospitalized and 309 of these patients underwent surgical procedures. 165 of the patients who underwent surgery were newly diagnosed malignancy patients. All patients who were hospitalized were subjected to a screening for COVID-19 during the preclinical, clinical and surgical period. In the preclinical period, five patients were found positive and were directed to COVID-19 treatment without hospitalization. In the clinical period, six patients were isolated by showing symptoms during the hospitalization period. Only one of these patients received surgical treatment. The remaining five patients underwent endoscopic and interventional procedures. In this process, COVID-19 positivity was detected in a total of five healthcare workers. Conclusion: With this preclinical and clinical screening method, it is shown that a COVID-19 sterile environment can be provided by early detection of positive cases in both patients and healthcare workers. In this way, the possibility of surgical continuity was demonstrated.

19.
Chembiochem ; 22(4): 662-665, 2021 02 15.
Article in English | MEDLINE | ID: mdl-33022809

ABSTRACT

Two dimensional nanoparticles (2D-NPs) along with other nanoscale materials have been deemed to be the next generation of artificial enzymes (nanozymes). The low-cost bulk-scale production, ease of storage and modification of such nanomaterials have given nanozymes an advantage over traditional enzymes. Many studies have been aimed at developing methods to increase the performance of these nanozymes, and also identify interfering agents. To investigate the interference of a number of metal cations, we studied the effect of Ti2+ , Fe2+ , Ag+ , Hg2+ , Co2+ , Cu2+ , Ni2+ , Pb2+ , Ca2+ , Zn2+ and Mn2+ in a nanozyme assays of 2D-NPs using ABTS radical formation. Ti2+ , Co2+ , Cu2+ , Ni2+ , Ca2+ , Zn2+ and Mn2+ ions did not display any notable effect on the peroxidase-like activity of nGO, MoS2 and WS2 2D-NPs. However, Fe2+ , Ag+ , Hg2+ and Pb2+ ions' effects on the overall ABTS reaction were significant enough to be visualised by partial least square discriminant analysis (PLSDA). We report that, similar to that of many natural enzymes, the nanozyme activity of 2D-NPs is regulated by a number of metal cations allowing their identification and discrimination by using a statistical analysis tool.


Subject(s)
Cations/chemistry , Metal Nanoparticles/chemistry , Metals/chemistry , Molybdenum/chemistry , Peroxidase/metabolism , Sulfides/chemistry , Tungsten Compounds/chemistry , Catalysis , Oxidation-Reduction , Peroxidase/chemistry
20.
Chem Commun (Camb) ; 56(53): 7313-7316, 2020 Jul 02.
Article in English | MEDLINE | ID: mdl-32478344

ABSTRACT

Hydrogels are networks of polymers that can be used for packaging different payload types. They are proven to be versatile materials for various biomedical applications. Implanted hydrogels with encapsulated drugs have been shown to release the therapeutic payloads at disease sites. Hydrogels are usually made through chemical polymerization reactions. Whereas, DNA is a naturally occurring biopolymer which can assemble into highly ordered structures through noncovalent interactions. Here, we have employed a small molecule, cyanuric acid (CA), to assemble polyA-tailed DNA motif into a hydrogel. Encapsulation of a small molecule chemotherapeutic drug, a fluorescent molecule, two proteins and several nanoparticle formulations has been studied. Release of doxorubicin, small fluorescent molecule and fluorescently-labeled antibodies has been demonstrated.


Subject(s)
Cross-Linking Reagents/chemistry , DNA/chemistry , Drug Carriers/chemistry , Hydrogels/chemistry , Poly A/chemistry , Triazines/chemistry , Antibodies/chemistry , Doxorubicin/chemistry , Drug Compounding , Drug Liberation , Fluorescent Dyes/chemistry , Molecular Conformation , Nanoparticles/chemistry , Polymerization
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