Search results for: molecular diagnosis

Authors: S. Guruprasad, M. Z. Kurian, H. N. Suma

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Medical imaging modalities are becoming life saving components. These modalities are very much essential to doctors for proper diagnosis, treatment planning and follow up. Some modalities provide anatomical information such as Computed Tomography (CT), Magnetic Resonance Imaging (MRI), X-rays and some provides only functional information such as Positron Emission Tomography (PET). Therefore, single modality image does not give complete information. This paper presents the fusion of structural information in CT and functional information present in PET image. This fused image is very much essential in detecting the stages and location of abnormalities and in particular very much needed in oncology for improved diagnosis and treatment. We have implemented and compared image fusion techniques like pyramid, wavelet, and principal components fusion methods along with hybrid method of DWT and PCA. The performances of the algorithms are evaluated quantitatively and qualitatively. The system is implemented and tested by using MATLAB software. Based on the MSE, PSNR and ENTROPY analysis, PCA and DWT-PCA methods showed best results over all experiments.

Keywords: image fusion, pyramid, wavelets, principal component analysis

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Authors: Miceska Simona, Škof Erik, Frković Grazio Snježana, Jeričević Anja, Smrkolj Špela, Cvjetićanin Branko, Novaković Srdjan, Grčar Kuzmanov Biljana, Kloboves-Prevodnik Veronika

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Objectives: High-grade serous ovarian cancer (HGSOC) is characterized by the dissemination of the tumor cells (TC) in the peritoneal cavity forming malignant ascites at the time of diagnosis or recurrence. Still, cytology itself has been underutilized as a modality for the diagnosis of HGSOC from ascites, and histological examination from the tumor tissue is yet the only validated method used. The objective of this study was to evaluate the reliability of cytology in the diagnosis of HGSOC in relation to the histopathological examination. Methods: The study included 42 patients with histologically confirmed HGSOC, accompanied by malignant ascites. To confirm the malignancy of the TC in the ascites and to define their immunophenotype, immunohistochemical reaction (IHC) of the following antigens: Calretinin, MOC, WT1, PAX8, p53, p16 & Ki-67 was evaluated on ascites cytospins and tissue blocks. For complete cytological determination of HGSOC, BRCA 1/2 gene mutation was determined from ascites, tissue block, and blood. BRCA1/2 mutation from blood was performed to define the type of mutation, somatic vs germline. Results: Among 42 patients, the immunophenotype of HGSOC from ascites was confirmed in 36 cases (86%). For more profound analysis, the patients were divided in 3 groups regarding the number of TC present in the ascites: patients with less than 10% TC, 10% TC, and more than 10% TC. From all included patients, in the group with less than 10% TC, there were 10 cases, and only 5 of them(50%) showed HGSOC phenotype; 12 cases had equally 10% of TC, and 11 cases (92%) showed HGSOC phenotype; 20 cases had more than 10% TC and all of them (100%) confirmed the HGSOC immunophenotype from ascites. Only 33 patients were eligible for further BRCA1/2 analysis. Eleven BRCA1/2 mutations were detected from thetissue block: 6 germline and 5 somatic. In 2 cases with less than 10% TC, BRCA1/2 mutation was not detected; 4 cases had 10% TC, and 2 of them (50%) confirmed the mutation; 4 cases had more than 10% TC, and all showed 100% reliability with the tumor tissue. Conclusions: Cytology is a highly reliable method for determining the immunophenotype of HGSOC and BRCA1/2 mutation if more than 10% of tumor cells are present in the ascites. This may present an additional non-invasive clinical approach for fast and effective diagnose in the future, especially in inoperable conditions or relapses.

Keywords: cytology, ascites, high-grade serous ovarian cancer, immunophenotype, BRCA1/2

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Authors: Mohamed Hamada Abdelkader Fayed

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Background: To evaluate the diagnostic accuracy of (ADD-RS) with D-dimer as a screening test to exclude AAS. Methods: We conducted research for the studies examining the diagnostic accuracy of (ADD- RS)+ D-dimer to exclude the diagnosis of AAS, We searched MEDLINE, Embase, and Cochrane of Trials up to 31 December 2020. Results: We identified 3 studies using (ADD-RS) with D-dimer as a diagnostic tool for AAS, involving 3261 patients were AAS was diagnosed in 559(17.14%) patients. Overall results showed that the pooled sensitivities were 97.6 (95% CI 0.95.6, 99.6) at (ADD-RS)≤1(low risk group) with D-dimer and 97.4(95% CI 0.95.4,, 99.4) at (ADD-RS)>1(High risk group) with D-dimer., the failure rate was 0.48% at low risk group and 4.3% at high risk group respectively. Conclusions: (ADD-RS) with D-dimer was a useful screening test with high sensitivity to exclude Acute Aortic Syndrome.

Keywords: aortic dissection detection risk score, D-dimer, acute aortic syndrome, diagnostic accuracy

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Authors: John Rothrock

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Background: The role of transthoracic echocardiography (TTE) in the diagnosis and management of patients with acute ischemic stroke remains controversial. While many stroke subspecialist reserve TTE for selected patients, others consider the procedure obligatory for most or all acute stroke patients. This study was undertaken to assess the cost vs. benefit of 'routine' TTE. Methods: We examined a consecutive series of patients who were admitted to a single institution in 2019 for acute ischemic stroke and underwent TTE. We sought to determine the frequency with which the results of TTE led to a new diagnosis of cardioembolism, redirected therapeutic cerebrovascular management, and at least potentially influenced the short or long-term clinical outcome. We recorded the direct cost associated with TTE. Results: There were 1076 patients in the study group, all of whom underwent TTE. TTE identified an unsuspected source of possible/probable cardioembolism in 62 patients (6%), confirmed an initially suspected source (primarily endocarditis) in an additional 13 (1%) and produced findings that stimulated subsequent testing diagnostic of possible/probable cardioembolism in 7 patients ( < 1%). TTE results potentially influenced the clinical outcome in a total of 48 patients (4%). With a total direct cost of $1.51 million, the mean cost per case wherein TTE results potentially influenced the clinical outcome in a positive manner was $31,375. Diagnostically and therapeutically, TTE was most beneficial in 67 patients under the age of 55 who presented with 'cryptogenic' stroke, identifying patent foramen ovale in 21 (31%); closure was performed in 19. Conclusions: The utility of TTE in the setting of acute ischemic stroke is modest, with its yield greatest in younger patients with cryptogenic stroke. Given the greater sensitivity of transesophageal echocardiography in detecting PFO and evaluating the aortic arch, TTE’s role in stroke diagnosis would appear to be limited.

Keywords: cardioembolic, cost-benefit, stroke, TTE

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Authors: Saimir Heta, Kastriot Haxhirexha, Virtut Velmishi, Nevila Alliu, Ilma Robo

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Background: Testicular rotation can occur at any age. The possibility to save the testicle is the fastest possible surgical intervention which is indicated by the presence of acute pain even at rest. The time element is more important to diagnose and proceed further with surgical intervention. Testicular damage is a consequence which mainly depends on the moment of onset of symptoms, at the time when the symptoms are diagnosed, the earliest action to be performed is surgical intervention. Sometimes medical tests are needed to confirm a diagnosis, or to help identify another cause for symptoms; for example, the urine test, that is used to check for infection, associated with the scrotal ultrasound test. Control of blood flow to the longitudinal supply vessels of the testicles is indicated. The sign that indicates testicular rotation is a reduction in blood flow. This is the element which is distinguished from ultrasound examination. Surgery may be needed to determine if the patient’s symptoms are caused by the rotation of the testis or any other condition. Discussion: As a surgical intervention of the emergency, the torsion of the test depends very much on the duration of the torsion, as the success in the life of the testicle depends on the fastest surgical intervention. From the previous clinic, it is noted that in any case presented to the pediatric patient diagnosed with testicular rotation, there is always a link with personal history that the patient refers to the presence of a previous episode of testicular trauma. Literature supports this fact very logically. Conclusions: Salvation without testicular atrophy depends closely on establishing the diagnosis of testicular rotation as soon as possible. Following the logic above, it can be said that the diagnosis for rotation should be performed as soon as possible, to avoid consequences that will not be favorable for the patient.

Keywords: acute scrotum, test torsion, newborns, clinical presentation

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Authors: Chih Jou Hsiao, Chung Ming Lo, Li Chun Hsieh

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Brain tumor is not the cancer having high incidence rate, but its high mortality rate and poor prognosis still make it as a big concern. On clinical examination, the grading of brain tumors depends on pathological features. However, there are some weak points of histopathological analysis which can cause misgrading. For example, the interpretations can be various without a well-known definition. Furthermore, the heterogeneity of malignant tumors is a challenge to extract meaningful tissues under surgical biopsy. With the development of magnetic resonance imaging (MRI), tumor grading can be accomplished by a noninvasive procedure. To improve the diagnostic accuracy further, this study proposed a computer-aided diagnosis (CAD) system based on MRI features to provide suggestions of tumor grading. Gliomas are the most common type of malignant brain tumors (about 70%). This study collected 34 glioblastomas (GBMs) and 73 lower-grade gliomas (LGGs) from The Cancer Imaging Archive. After defining the region-of-interests in MRI images, multiple quantitative morphological features such as region perimeter, region area, compactness, the mean and standard deviation of the normalized radial length, and moment features were extracted from the tumors for classification. As results, two of five morphological features and three of four image moment features achieved p values of <0.001, and the remaining moment feature had p value <0.05. Performance of the CAD system using the combination of all features achieved the accuracy of 83.18% in classifying the gliomas into LGG and GBM. The sensitivity is 70.59% and the specificity is 89.04%. The proposed system can become a second viewer on clinical examinations for radiologists.

Keywords: brain tumor, computer-aided diagnosis, gliomas, magnetic resonance imaging

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Authors: Abu Salim Mustafa

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Brucellosis is a zoonotic disease endemic in Kuwait. Human brucellosis can be caused by several Brucella species with Brucella melitensis causing the most severe and Brucella abortus the least severe disease. Furthermore, relapses are common after successful chemotherapy of patients. The classical biochemical methods of culture and serology for identification of Brucellae provide information about the species and serotypes only. However, to differentiate between relapse and reinfection/epidemiological investigations, the identification of genotypes using molecular methods is essential. In this study, four molecular methods [16S rRNA gene sequencing, real-time PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus variable-number tandem-repeat analysis (MLVA)-16] were evaluated for the identification and typing of 75 strains of Brucella isolated in Kuwait. The 16S rRNA gene sequencing suggested that all the strains were B. melitensis and real-time PCR confirmed their species identity as B. melitensis. The ERIC-PCR band profiles produced a dendrogram of 75 branches suggesting each strain to be of a unique type. The cluster classification, based on ~ 80% similarity, divided all the ERIC genotypes into two clusters, A and B. Cluster A consisted of 9 ERIC genotypes (A1-A9) corresponding to 9 individual strains. Cluster B comprised of 13 ERIC genotypes (B1-B13) with B5 forming the largest cluster of 51 strains. MLVA-16 identified all isolates as B. melitensis and divided them into 71 MLVA-types. The cluster analysis of MLVA-16-types suggested that most of the strains in Kuwait originated from the East Mediterranean Region, a few from the African group and one new genotype closely matched with the West Mediterranean region. In conclusion, this work demonstrates that B. melitensis, the most pathogenic species of Brucella, is prevalent in Kuwait. Furthermore, MLVA-16 is the best molecular method, which can identify the Brucella species and genotypes as well as determine their origin in the global context. Supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: Brucella, ERIC-PCR, MLVA-16, RT-PCR, 16S rRNA gene sequencing

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Authors: Sakiru Badmos, David R. Cole, Alberto Striolo

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It is known that confinement in nm-size pores affects many structural and transport properties of water and co-existing volatile species. Of particular interest for fluids in sub-surface systems, in catalysis, and in separations are reports that confinement can enhance the solubility of gases in water. Equilibrium molecular dynamics simulations were performed for aqueous H₂S confined in slit-shaped silica pores at 313K. The effect of pore width on the H₂S solubility in water was investigated. Other properties of interest include the molecular distribution of the various fluid molecules within the pores, the hydration structure for solvated H₂S molecules, and the dynamical properties of the confined fluids. The simulation results demonstrate that confinement reduces the H₂S solubility in water and that the solubility increases with pore size. Analysis of spatial distribution functions suggests that these results are due to perturbations on the coordination of water molecules around H₂S due to confinement. Confinement is found to dampen the dynamical properties of aqueous H₂S as well. Comparing the results obtained for aqueous H₂S to those reported elsewhere for aqueous CH₄, it can be concluded that H₂S permeates hydrated slit-shaped silica nano-pores faster than CH₄. In addition to contributing to better understanding the behavior of fluids in subsurface formations, these observations could also have important implications for developing new natural gas sweetening technologies.

Keywords: confinement, interfacial properties, molecular dynamic simulation, sub-surface formations

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Authors: Gökçe Erdemir, İlhan Yaylım, Serap Erdem-Kuruca, Musa Mutlu Can

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It has been determined that the main reason for the death of cancer disease is caused by metastases rather than the primary tumor. The cells that leave the primary tumor and enter the circulation and cause metastasis in the secondary organs are called "circulating tumor cells" (CTCs). The presence and number of circulating tumor cells has been associated with poor prognosis in many major types of cancer, including breast, prostate, and colorectal cancer. It is thought that knowledge of circulating tumor cells, which are seen as the main cause of cancer-related deaths due to metastasis, plays a key role in the diagnosis and treatment of cancer. The fact that tissue biopsies used in cancer diagnosis and follow-up are an invasive method and are insufficient in understanding the risk of metastasis and the progression of the disease have led to new searches. Liquid biopsy tests performed with a small amount of blood sample taken from the patient for the detection of CTCs are easy and reliable, as well as allowing more than one sample to be taken over time to follow the prognosis. However, since these cells are found in very small amounts in the blood, it is very difficult to capture them and specially designed analytical techniques and devices are required. Methods based on the biological and physical properties of the cells are used to capture these cells in the blood. Early diagnosis is very important in following the prognosis of tumors of epithelial origin such as breast, lung, colon and prostate. Molecules such as EpCAM, vimentin, and cytokeratins are expressed on the surface of cells that pass into the circulation from very few primary tumors and reach secondary organs from the circulation, and are used in the diagnosis of cancer in the early stage. For example, increased EpCAM expression in breast and prostate cancer has been associated with prognosis. These molecules can be determined in some blood or body fluids to be taken from patients. However, more sensitive methods are required to be able to determine when they are at a low level according to the course of the disease. The aim is to detect these molecules found in very few cancer cells with the help of sensitive, fast-sensing biosensors, first in breast cancer cells reproduced in vitro and then in blood samples taken from breast cancer patients. In this way, cancer cells can be diagnosed early and easily and effectively treated.

Keywords: electrochemical biosensors, breast cancer, circulating tumor cells, EpCAM, Vimentin, Cytokeratins

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Authors: Meltem Koray, Arda Ozgon, Duygu Ofluoglu, Mehmet Yaltirik

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Oral ulcerations can be seen as a side effect of different drugs. These ulcers usually appear within a few weeks following drug treatment. In most of cases, these ulcers resist to conventional treatments, such as anesthetics, antiseptics, anti-inflammatory agents, cauterization, topical tetracycline and corticosteroid treatment. The diagnosis is usually difficult, especially in patients receiving multiple drug therapies. Hyaluronan or hyaluronic acid (HA) is a biomaterial that has been introduced as an alternative approach to enhance wound healing and also used for oral ulcer treatment. The aim of this report is to present the treatment of drug-induced oral ulceration on maxillary mucosa with HA gel. 60-year-old male patient was referred to Department of Oral and Maxillofacial Surgery complaining of oral ulcerations during few weeks. He had received chemotherapy and radiotherapy in 2014 with the diagnosis of nasopharyngeal carcinoma, and he has accompanying systemic diseases such as; cardiological, neurological diseases and gout. He is medicated with Escitalopram (Cipralex® 20mg), Quetiapine (Seroquel® 100mg), Mirtazapine (Zestat® 15mg), Acetylsalicylic acid (Coraspin® 100mg), Ramipril-hydrochlorothiazide (Delix® 2.5mg), Theophylline anhydrous (Teokap Sr® 200mg), Colchicine (Colchicum Dispert® 0.5mg), Spironolactone (Aldactone® 100mg), Levothyroxine sodium (Levotiron® 50mg). He had painful oral ulceration on the right side of maxillary mucosa. The diagnosis was 'drug-induced oral ulceration' and HA oral gel (Aftamed® Oral gel) was prescribed 3 times a day for 2 weeks. Complete healing was achieved within 3 weeks without any side effect and discomfort. We suggest that HA oral gel is a potentially useful local drug which can be an alternative for management of drug-induced oral ulcerations.

Keywords: drug-induced, hyaluronic acid, oral ulceration, maxillary mucosa

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Authors: Elizabeth O. Odewale, Sachithra T. Wanasinghe, Aaron S. Rury

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Cavity polaritons form when molecular excitons strongly couple to photons in carefully constructed optical cavities. These polaritons, which are hybrid light-matter states possessing a unique combination of photonic and excitonic properties, present the opportunity to manipulate the properties of various semiconductor materials. The systematic manipulation of materials through polariton formation could potentially improve the functionalities of many optoelectronic devices such as lasers, light-emitting diodes, photon-based quantum computers, and solar cells. However, the prospects of leveraging polariton formation for novel devices and device operation depend on more complete connections between the properties of molecular chromophores, and the hybrid light-matter states they form, which remains an outstanding scientific goal. Specifically, for most optoelectronic applications, it is paramount to understand how polariton formation affects the spectra of light absorbed by molecules coupled strongly to cavity photons. An essential feature of a polariton state is its dispersive energy, which occurs due to the enhanced spatial delocalization of the polaritons relative to bare molecules. To leverage the spatial delocalization of cavity polaritons, angle-resolved photoluminescence excitation spectroscopy was employed in characterizing light emission from the polaritonic states. Using lasers of appropriate energies, the polariton branches were resonantly excited to understand how molecular light absorption changes under different strong light-matter coupling conditions. Since an excited state has a finite lifetime, the photon absorbed by the polariton decays non-radiatively into lower-lying molecular states, from which radiative relaxation to the ground state occurs. The resulting fluorescence is collected across several angles of excitation incidence. By modeling the behavior of the light emission observed from the lower-lying molecular state and combining this result with the output of angle-resolved transmission measurements, inferences are drawn about how the behavior of molecules changes when they form polaritons. These results show how the intrinsic properties of molecules, such as the excitonic lifetime, affect the rate at which the polaritonic states relax. While it is true that the lifetime of the photon mediates the rate of relaxation in a cavity, the results from this study provide evidence that the lifetime of the molecular exciton also limits the rate of polariton relaxation.

Keywords: flourescece, molecules in cavityies, optical cavity, photoluminescence excitation, spectroscopy, strong coupling

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Authors: A. Maciejak, M. Kiliszek, G. Opolski, D. Tulacz, A. Segiet, K. Matlak, S. Dobrzycki, G. Sygitowicz, B. Burzynska, M. Gora

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Introduction and aims: Acute myocardial infarction (AMI) is one of the most severe cardiovascular diseases affecting millions of patients each year worldwide. An early and accurate diagnosis of AMI is essential for optimal treatment. Therefore, new approaches that can complement and improve current strategies for AMI diagnosis are urgently needed. Recent studies have revealed the presence of stable circulating myocardial-derived microRNAs (miRNAs) in human peripheral blood, suggesting that such miRNAs could serve as potential biomarkers of infarction. The present study aimed to identify differentially expressed circulating miRNAs in ST-segment elevation myocardial infarction (STEMI) patients. Materials and methods: miRNA expression profile analysis was performed using Exiqon Serum/Plasma Focus microRNA PCR panel in plasma samples of n=16 patients on the first day of AMI (admission) and in samples from the same patients collected six months after AMI. Selected miRNAs were validated by RT-qPCR using serum samples from an independent set of n=14 AMI patients. Results: The profiling study identified 46 species of plasma miRNAs that were differentially expressed (p < 0.05) on admission compared to six months after AMI. The validation in the independent group of patients confirmed that miR-133b and miR-22-5p were significantly up-regulated upon AMI. Conclusions: Our results suggest that miRNA expression profiling provides better understanding of the changes that occur in the acute phase of MI in the myocardium and could be useful in determination of the potential role of extracellular miRNAs as paracrine signaling molecules. miR-22-5p represents a novel promising biomarker for the diagnosis of acute myocardial infarction.

Keywords: acute myocardial infarction, circulating microRNAs, microRNA expression profiling, miR-22-5p

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Authors: Yosep Chong, Yejin Kim, Jingyun Choi, Hwanjo Yu, Eun Jung Lee, Chang Suk Kang

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For the past decades, immunohistochemistry (IHC) has been playing an important role in the diagnosis of human neoplasms, by helping pathologists to make a clearer decision on differential diagnosis, subtyping, personalized treatment plan, and finally prognosis prediction. However, the IHC performed in various tumors of daily practice often shows conflicting and very challenging results to interpret. Even comprehensive diagnosis synthesizing clinical, histologic and immunohistochemical findings can be helpless in some twisted cases. Another important issue is that the IHC data is increasing exponentially and more and more information have to be taken into account. For this reason, we reached an idea to develop an expert supporting system to help pathologists to make a better decision in diagnosing human neoplasms with IHC results. We gave probabilistic decision tree algorithm and tested the algorithm with real case data of lymphoid neoplasms, in which the IHC profile is more important to make a proper diagnosis than other human neoplasms. We designed probabilistic decision tree based on Bayesian theorem, program computational process using MATLAB (The MathWorks, Inc., USA) and prepared IHC profile database (about 104 disease category and 88 IHC antibodies) based on WHO classification by reviewing the literature. The initial probability of each neoplasm was set with the epidemiologic data of lymphoid neoplasm in Korea. With the IHC results of 131 patients sequentially selected, top three presumptive diagnoses for each case were made and compared with the original diagnoses. After the review of the data, 124 out of 131 were used for final analysis. As a result, the presumptive diagnoses were concordant with the original diagnoses in 118 cases (93.7%). The major reason of discordant cases was that the similarity of the IHC profile between two or three different neoplasms. The expert supporting system algorithm presented in this study is in its elementary stage and need more optimization using more advanced technology such as deep-learning with data of real cases, especially in differentiating T-cell lymphomas. Although it needs more refinement, it may be used to aid pathological decision making in future. A further application to determine IHC antibodies for a certain subset of differential diagnoses might be possible in near future.

Keywords: database, expert supporting system, immunohistochemistry, probabilistic decision tree

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Authors: I. Ramalho, S. Campos, M. Dias

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Introduction: Endometriosis may play a role in the pathogenesis of ovarian cancer (OC), however, the risk and prognosis have not been well established. The association between these two pathologies could have an important impact on prevention and early diagnosis of OC. Objective: To analyze the prevalence of endometriosis associated ovarian cancer and related clinical, epidemiological and histopathological issues. Design: We conducted a retrospective case series analysis of patients diagnosed with endometriosis and ovarian cancer in the Gynecology Department of Coimbra University Hospital Center since 2006 to 2015. Methods: We collected data from women diagnosed with ovarian cancer, with anatomopathology records reporting findings of endometriosis in ovarian cancer patients. Patients were retrieved from the pathological records and appropriate medical records were retrospectively reviewed. Statistical analysis was performed using SPSS 22.0. Results: Histological evidence of endometriosis was found in 17 out of 261 patients diagnosed with ovarian cancer (OC) (6.51%). The most usual symptoms were pelvic pain, abdominal distension, asthenia, ascites, weight loss and nausea. Mean age at diagnosis was 61.2 ± 15.1, 41-86 years old, 33.3% were pre-menopausal patients and cancer stage distribution was predominantly stage I (31.3%) and stage III (56.3%). OC occurred unilaterally in 14 patients and 2 patients were diagnosed with a synchronous ovarian and endometrial cancer. Regarding histological type, 10 OC were classified as clear cell carcinoma (CCC), 4 endometrioid carcinomas (EC) and 3 mixed type (clear cell and endometrioid). Four ovarian carcinomas presumably arose from endometriomas: 3 CCC and 1 EC. Conclusions: In accordance with previous studies, clear cell was the most common pathological type in endometriotic patients, followed by endometrioid carcinomas, and two rare synchronous ovarian and endometrial carcinomas were registered. Although endometriosis association to OC is uncommon, endometriosis should be managed with special care in order to early diagnosis.

Keywords: endometriosis, histology, observational study, ovarian cancer

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Authors: Akarsh Verma, Avinash Parashar

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The aim of this article is to study the effects of hydroxyl functional group on the mechanical strength and fracture toughness of graphene. This functional group forms the backbone of intrinsic atomic structure of graphene oxide (GO). Molecular dynamics-based simulations were performed in conjunction with reactive force field (ReaxFF) parameters to capture the mode-I fracture toughness of hydroxyl functionalised graphene. Moreover, these simulations helped in concluding that spatial distribution and concentration of hydroxyl functional group significantly affects the fracture morphology of graphene nanosheet. In contrast to literature investigations, atomistic simulations predicted a transition in the failure morphology of hydroxyl functionalised graphene from brittle to ductile as a function of its spatial distribution on graphene sheet.

Keywords: graphene, graphene oxide, ReaxFF, molecular dynamics

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Authors: Titus A. Beu

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Many modern gene-delivery protocols rely on condensed complexes of DNA with polycations to introduce the genetic payload into cells by endocytosis. In particular, polyethyleneimine (PEI) stands out by a high buffering capacity (enabling the efficient condensation of DNA) and relatively simple fabrication. Realistic computational studies can offer essential insights into the formation process of DNA-PEI polyplexes, providing hints on efficient designs and engineering routes. We present comprehensive computational investigations of solvated PEI and DNA-PEI polyplexes involving calculations at three levels: ab initio, all-atom (AA), and coarse-grained (CG) molecular mechanics. In the first stage, we developed a rigorous AA CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field (FF) for PEI on the basis of accurate ab initio calculations on protonated model pentamers. We validated this atomistic FF by matching the results of extensive molecular dynamics (MD) simulations of structural and dynamical properties of PEI with experimental data. In a second stage, we developed a CG MARTINI FF for PEI by Boltzmann inversion techniques from bead-based probability distributions obtained from AA simulations and ensuring an optimal match between the AA and CG structural and dynamical properties. In a third stage, we combined the developed CG FF for PEI with the standard MARTINI FF for DNA and performed comprehensive CG simulations of DNA-PEI complex formation and condensation. Various technical aspects which are crucial for the realistic modeling of DNA-PEI polyplexes, such as options of treating electrostatics and the relevance of polarizable water models, are discussed in detail. Massive CG simulations (with up to 500 000 beads) shed light on the mechanism and provide time scales for DNA polyplex formation independence of PEI chain size and protonation pattern. The DNA-PEI condensation mechanism is shown to primarily rely on the formation of DNA bundles, rather than by changes of the DNA-strand curvature. The gained insights are expected to be of significant help for designing effective gene-delivery applications.

Keywords: DNA condensation, gene-delivery, polyethylene-imine, molecular dynamics.

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Authors: Ebraheem Al-Jouri, Youssef Abu-Ahmad, Ramasamy Srinivasan

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The parasitoid, Diadegma semiclausum (Hymenoptera: Ichneumonidae) is one of the most effective exotic parasitoids of diamondback moth (DBM), Plutella xylostella in the lowland areas of Homs, Syria. Molecular evolution studies are useful tools to shed light on the molecular bases of insect geographical spread and adaptation to new hosts and environment and for designing better control strategies. In this study, molecular evolution analysis was performed based on the 42 nuclear internal transcribed spacer-2 (ITS2) sequences representing the D. semiclausum and eight other Diadegma spp. from Syria and worldwide. Possible recombination events were identified by RDP4 program. Four potential recombinants of the American D. insulare and D. fenestrale (Jeju) were detected. After detecting and removing recombinant sequences, the ratio of non-synonymous (dN) to synonymous (dS) substitutions per site (dN/dS=ɷ) has been used to identify codon positions involved in adaptive processes. Bayesian techniques were applied to detect selective pressures at a codon level by using five different approaches including: fixed effects likelihood (FEL), internal fixed effects likelihood (IFEL), random effects method (REL), mixed effects model of evolution (MEME) and Program analysis of maximum liklehood (PAML). Among the 40 positively selected amino acids (aa) that differed significantly between clades of Diadegma species, three aa under positive selection were only identified in D. semiclausum. Additionally, all D. semiclausum branches tree were highly found under episodic diversifying selection (EDS) at p≤0.05. Our study provide evidence that both recombination and positive selection have contributed to the molecular diversity of Diadegma spp. and highlights the significant contribution of D. semiclausum in adaptive evolution and influence the fitness in the DBM parasitoid.

Keywords: diadegma sp, DBM, ITS2, phylogeny, recombination, dN/dS, evolution, positive selection

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Authors: Zain Ul Abdin, Mirza Aizaz Asim, Rao Sohail Ahmad Khan, Luqman Amrao, Fiaz Hussain, Hasooba Hira, Saqi Kosar Abbas

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The success of Integrated vector management programmes mainly depends on the correct identification of insect vector species involved in vector borne diseases. Based on molecular data the most important insect species involved as vectors for Zoonotic diseases in Pakistan were identified. The precise and accurate identification of such type of organism is only possible through molecular based techniques like “DNA barcoding”. Morphological species identification in insects at any life stage, is very challenging, therefore, DNA barcoding was used as a tool for rapid and accurate species identification in a wide variety of taxa across the globe and parallel studies revealed that DNA barcoding data can be effectively used in resolving taxonomic ambiguities, detection of cryptic diversity, invasion biology, description of new species etc. A comprehensive survey was carried out for the collection of insects (both adult and immature stages) in district Faisalabad, Pakistan and their DNA was extracted and mitochondrial cytochrome oxidase subunit I (COI-59) barcode sequences was used for molecular identification of immature and adult life stage.This preliminary research work opens new frontiers for developing sustainable insect vectors management programmes for saving lives of mankind from fatal diseases.

Keywords: zoonotic diseases, cytochrome oxidase, and insect vectors, CO1

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Authors: Hanaa M. Abu El Einin, Ahmed T. Sharaf El- Din

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Biomphalaria snails play an integral role in the transmission of Schistosoma mansoni, the causative agent for human schistosomiasis. Two species of Biomphalaria were reported from Egypt, Biomphalaria alexandrina and Biomphalaria glabrata, and later on a hybrid of B. alexandrina and B. glabrata was reported in streams at Nile Delta. All were known to be excellent hosts of S. mansoni. Host-parasite relationship can be viewed in terms of snail susceptibility and parasite infectivity. The objective of this study will highlight the progress that has been made in using molecular approaches to describe the correct identification of snail species that participating in transmission of schistosomiasis, rapid diagnose of infection in addition to susceptibility and resistance type. Snails were identified using of molecular methods involving Randomly Amplified Polymorphic DNA (RAPD), Polymerase Chain Reaction, Restriction Fragment Length Polymorphisms (PCR-RFLP) and Species - specific- PCR. Molecular approaches to diagnose parasite in snails from Egypt: Nested PCR assay and small subunit (SSU) rRNA gene. Also RAPD PCR for study susceptible and resistance phenotype. The results showed that RAPD- PCR, PCR-RFLP and species-specific-PCR techniques were confirmed that: no evidence for the presence of B. glabrata in Egypt, All Biomphalaria snails collected identified as B. alexandrina snail i-e B alexandrinia is a common and no evidence for hybridization with B. glabrata. The adopted specific nested PCR assay revealed much higher sensitivity which enables the detection of S. mansoni infected snails down to 3 days post infection. Nested PCR method for detection of infected snails using S. mansoni fructose -1,6- bisphosphate aldolase (SMALDO) primer, these primers are specific only for S. mansoni and not cross reactive with other schistosomes or molluscan aldolases Nested PCR for such gene is sensitive enough to detect one cercariae. Genetic variations between B. alexandrina strains that are susceptible and resistant to Schistosoma infec¬tion using a RAPD-PCR showed that 39.8% of the examined snails collected from the field were resistant, while 60.2% of these snails showed high infection rates. In conclusion the genetics of the intermediate host plays a more important role in the epidemiological control of schistosomiasis.

Keywords: biomphalaria, molecular differentiation, parasite detection, schistosomiasis

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Authors: Ronit Chakraborty, Sugata Banerji

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There has been a marked increase in the reported prevalence of Autism Spectrum Disorder (ASD) among children in the US over the past two decades. This research has analyzed the growth in state-level ASD prevalence against 45 different potentially explanatory factors, including socio-economic, demographic, healthcare, public policy, and political factors. The goal was to understand if these factors have adequate predictive power in modeling the differential growth in ASD prevalence across various states and if they do, which factors are the most influential. The key findings of this study include (1) the confirmation that the chosen feature set has considerable power in predicting the growth in ASD prevalence, (2) the identification of the most influential predictive factors, (3) given the nature of the most influential predictive variables, an indication that a considerable portion of the reported ASD prevalence differentials across states could be attributable to over and under diagnosis, and (4) identification of Florida as a key outlier state pointing to a potential under-diagnosis of ASD there.

Keywords: autism spectrum disorder, clustering, machine learning, predictive modeling

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Authors: Somayeh Akrami, Habib Onsori, Elham Tahmassebian

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Species of Anemone narcissiflora is belonged to Anemone genus of Ranunculaceae family. This species has two subspecies named narcissiflora and willdenowii which the latest is recorded in Iran in 2010. Some samples of A. narcissiflora is gathered from kuhkamar-zonouz region of East -Azerbaijan province, Iran to study the genetic diversity of the species by using RAPD molecular markers, and estimation of genetic diversity were evaluated with the using 10mer RAPD primers by PCR-RAPD method. 39 polymorphic bands were produced from the six primers used in this technique that the maximum band is related to the RP1 primer, the lowest band is related to the RP7 and the average band for all primers were 6.5 polymorphic bands. Cluster analysis of samples in done by UPGMA method in NTSYSpc 2.02 software. Dendrogram resulting from migrating bands showed that the studied samples can be divided into two groups. The first group includes samples with 1-2 flowers and the second group consists of two sub-groups which the first subgroup consists of samples with 3-5 flowers, and the second subgroup consists of samples with 6-7 flowers. The results of the comparison and analysis of the data obtained from RAPD technique and similarity matrix represents the genetic variation between collected samples. This study shows that RAPD markers can determine the polymorphisms between different genotypes of A. narcissiflora and their hybrids. So RAPD technique can serve as a suitable molecular method to determine the genetic diversity of samples.

Keywords: Anemone narcissiflora, genetic diversity, RAPD-PCR

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Authors: Surabhi Agrawal Kohli, Sunita Gupta, Esha Khanuja, Parul Garg, P. Gupta

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Background: Adenomyosis is a common gynaecological condition that affects the menstruating women. Uterine enlargement, dysmenorrhoea, and menorrhagia are regarded as the cardinal clinical symptoms of adenomyosis. Classically it was thought, compared with ultrasonography, when adenomyosis is suspected, MRI enables more accurate diagnosis of the disease. Materials and Methods: 172 subjects were enrolled after an informed consent that had complaints of HMB, dyspareunia, dysmenorrhea, and chronic pelvic pain. Detailed history of the enrolled subjects was taken, followed by a clinical examination. These patients were then subjected to TVS where myometrial echo texture, presence of myometrial cysts, blurring of endomyometrial junction was noted. MRI was followed which noted the presence of junctional zone thickness and myometrial cysts. After hysterectomy, histopathological diagnosis was obtained. Results: 78 participants were analysed. The mean age was 44.2 years. 43.5% had parity of 4 or more. heavy menstrual bleeding (HMB) was present in 97.8% and dysmenorrhea in 93.48 % of HPE positive patient. Transvaginal sonography (TVS) and MRI had a sensitivity of 89.13% and 80.43%, specificity of 90.62% and 84.37%, positive likelihood ratio of 9.51 and 5.15, negative likelihood ratio of 0.12 and 0.23, positive predictive value of 93.18% and 88.1%, negative predictive value of 85.29% and 75% and a diagnostic accuracy of 89.74% and 82.5%. Comparison of sensitivity (p=0.289) and specificity (p=0.625) showed no statistically significant difference between TVS and MRI. Conclusion: Prevalence of 30.23%. HMB with dysmenorrhoea and chronic pelvic pain helps in diagnosis. TVS (Endomyometrial junction blurring) is both sensitive and specific in diagnosing adenomyosis without need for additional diagnostic tool. Both TVS and MRI are equally efficient, however because of certain additional advantages of TVS over MRI, it may be used as the first choice of imaging. MRI may be used additionally in difficult cases as well as in patients with existing co-pathologies.

Keywords: adenomyosis, heavy menstrual bleeding, MRI, TVS

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Authors: Richa Mardianingrum, Srie R. N. Endah

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In this research, we have designed four isoniazid derivatives i.e., isonicotinohydrazide (1-isonicotinoyl semicarbazide, 1-thiosemi isonicotinoyl carbazide, N '-(1,3-dimethyl-1 h-pyrazole-5-carbonyl) isonicotino hydrazide, and N '-(1,2,3- 4-thiadiazole-carbonyl) isonicotinohydrazide. The docking and molecular dynamic have performed to them in order to study its interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (InhA). Based on this research, all of the compounds were predicted to have a stable interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (INHA) receptor, so they could be used as an anti-tuberculosis drug candidate.

Keywords: anti-tuberculosis, docking, Inhibin alpha subunit, InhA, inhibition, synthesis, isonicotinohydrazide

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Authors: Khabat Barkhordari

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

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Authors: Tahani H. Alluhaybi, Leila Mejrissi

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In the present theoretical study, we investigated adiabatically the electronic structure of the (BaNa)+ by the use of the ab initio calculation. We optimized a large atomic GTO basis set for Na and Ba atoms. The (BaNa)+ molecular ion is considered a two-electron thank to a non-empirical pseudo-potentials approach applied to Ba and Na cores with the Core Polarization Potentials operator (CPP). Then, we performed the Full Configuration Interaction (FCI) method. Accordingly, we calculated the adiabatic Potential Energy Curves (PECs) and their spectroscopic constants (well depth De, transition energies Te, the equilibrium distances Re, vibrational constant ⍵e, and anharmonic constant ⍵exe) for 10 electronic states in Σ+ symmetry. Then we determined the vibrational level energies and their spacing, and the electric Permanent Dipole Moments (PDM).

Keywords: Ab initio, dipole moment, non-empirical pseudo-potential, potential energy curves, spectroscopic constants, vibrational energy

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Authors: Manas Kotepui, Chatree Ratcha, Kwuntida Uthaisar

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Malaria infection is still to be considered a major public health problem in Thailand. This study, a retrospective data of patients in Surat Thani Province, Southern Thailand during 2012-2015 was retrieved and analyzed. These data include demographic data, clinical characteristics and laboratory diagnosis. Statistical analyses were performed to demonstrate the frequency, proportion, data tendency, and group comparisons. Total of 395 malaria patients were found. Most of patients were male (253 cases, 64.1%). Most of patients (262 cases, 66.3%) were admitted at 6 am-11.59 am of the day. Three hundred and fifty-five patients (97.5%) were positive with P. falciparum. Hemoglobin, hematocrit, and MCHC between P. falciparum and P. vivax were significant different (P value<0.05).During 2012-2015, prevalence of malaria was highest in 2013. Neutrophils, lymphocytes, and monocytes were significantly changed among patients with fever ≤ 3 days compared with patients with fever >3 days. This information will guide to understanding pathogenesis and characteristic of malaria infection in Sothern Thailand.

Keywords: prevalence, malaria, Surat Thani, Thailand

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Authors: M. Nazim, S. Ameen, H. K. Seo, H. S. Shin

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Energy is the basis of life and strong attention has been growing for the cost-effective energy production. Recently, solution-processed small molecule organic solar cells (SMOSCs) have grown much attention due to the wages such as well-defined molecular structures, definite molecular weight, easy synthesis and easy purification techniques. In particular, the size of donor (D) and acceptor (A) unit is a crucial factor for the exciton-diffusion towards D-A interface and then charge-separation for the effective charge-transport to the electrodes. Furan-bridged materials are more electron-rich, high fluorescence, with better molecular-packing, and greater rigidity and greater solubility than their thiophene-counterparts In this work, a furan-bridged thiazolo[5,4-d]thiazole based organic small molecule (RFTzR) was formulated and applied for BHJ organic solar cells (OSCs). The introduction of furan spacer with two terminal alkyl units improved its absorption and solubility in the common organic solvents, significantly. RFTzR exhibited a HOMO and LUMO energy levels of -5.36 eV and -3.14 eV, respectively. The fabricated solar cell devices of RFTzR (donor) with PC60BM (acceptor) as photoactive materials showed high performance of 2.72% (RFTzR:PC60BM, 2:1, w/w) ratio with open-circuit voltage of 0.756 V and high photocurrent density of 10.13 mA/cm².

Keywords: chromophore, organic solar cells, photoactive materials, small molecule

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Authors: Sarah Jacqueline Saram, Diya Baker, Jaishree Gandhewar

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Named after the Slovakian microbiologist, Miroslav Kocur, the Kocuria spp. are an emerging cause of significant human infections. Their predilection for immunocompromised states, such as malignancy and metabolic disorders, is highlighted in the literature. The coagulase-negative, gram-positive cocci are commensals found in the skin and oropharynx of humans, and their growing presence as responsible organisms in ocular infections cannot be ignored. The severe, rapid, and unrelenting disease course associated with Kocuria keratitis is underlined in the literature. However, the clinical features are variable, which may impede making a diagnosis. Here, we describe a first account of an initial misdiagnosis due to reliance on subjective analysis features on a confocal microscope, which ultimately led to a delay in commencing the correct treatment. In documenting this, we hope to underline to clinicians the difficulties in recognising a Kocuria Rhizophilia keratitis due to its similar clinical presentation to an Acanthamoeba Keratitis, thus emphasizing the need for early investigations such as corneal scrapes to secure the correct diagnosis and prevent further harm and vision loss for the patient.

Keywords: keratitis, cornea, infection, rare, Kocuria

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Authors: Amjad Al Shammari, Ashraf Ibrahim, Laila Seada

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Background and Objectives: Incidence of thyroid carcinoma has been increasing world-wide. In the present study, we evaluated diagnostic accuracy of Fine needle aspiration (FNA) and its efficiency in early detecting neoplastic lesions of thyroid gland over a 3-year period. Methods: Data have been retrieved from pathology files in King Khalid Hospital. For each patient, age, gender, FNA, site & size of nodule and final histopathologic diagnosis were recorded. Results: Study included 490 cases where 419 of them were female and 71 male. Male to female ratio was 1:6. Mean age was 43 years for males and 38 for females. Cases with confirmed histopathology were 131. In 101/131 (77.1%), concordance was found between FNA and histology. In 30/131 (22.9%), there was discrepancy in diagnosis. Total malignant cases were 43, out of which 14 (32.5%) were true positive and 29 (67.44%) were false negative. No false positive cases could be found in our series. Conclusion: FNA could diagnose benign nodules in all cases, however, in malignant cases, ultrasound findings have to be taken into consideration to avoid missing of a microcarcinoma in the contralateral lobe.

Keywords: FNA, hail, histopathology, thyroid

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Authors: Christina Eleftheria Tzeliou, Demeter Tzeli

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Introduction: Molecular Logic Gates (MLGs) are molecular machines that can perform complex work, such as solving logic operations. Molecular switches, which are molecules that can experience chemical changes are examples of successful types of MLGs. Recently, Quintana-Romero and Ariza-Castolo studied experimentally six stable pseudo-hemi-indigo-derived MLGs capable of solving complex logic operations. The MLG design relies on a molecular switch that experiences Z and E isomerism, thus the molecular switch's axis has to be a double bond. The hemi-indigo structure was preferred for the assembly of molecular switches due to its interaction with visible light. Z and E pseudo-hemi-indigo isomers can also be utilized for selective isomerization as they have distinct absorption spectra. Methodology: Here, the photophysical properties of pseudo-hemi-indigo derivatives are examined, i.e., derivatives of molecule 1 with anthracene, naphthalene, phenanthrene, pyrene, and pyrrole. In conjunction with some trials that were conducted, the level of theory mentioned subsequently was determined. The structures under study were optimized in both cis and trans conformations at the PBE0/6-31G(d,p) level of theory. The absorption spectra of the structures were calculated at PBE0/DEF2TZVP. In all cases, the absorption spectra of the studied systems were calculated including up to 50 singlet- and triplet-spin excited electronic states. Transition states (cis → cis, cis → trans, and trans → trans) were obtained in cases where it was possible, with PBE0/6-31G(d,p) for the optimization of the transition states and PBE0/DEF2TZVP for the respective absorption spectra. Emission spectra were obtained for the first singlet state of each molecule in cis both and trans conformations in PBE0/DEF2TZVP as well. All studies were performed in chloroform solvent that was added as a dielectric constant and the polarizable continuum model was also employed. Findings: Shifts of up to 25 nm are observed in the absorption spectra due to cis-trans isomerization, while the transition state is shifted up to about 150 nm. The electron density distribution is also examined, where charge transfer and electron transfer phenomena are observed regarding the three excitations of interest, i.e., H-1 → L, H → L and H → L+1. Emission spectra calculations were also carried out at PBE0/DEF2TZVP for the complete investigation of these molecules. Using protonation as input, selected molecules act as MLGs. Conclusion: Theoretical data so far indicate that both cis-trans isomerization, and cis-cis and trans-trans conformer isomerization affect the UV-visible absorption and emission spectra. Specifically, shifts of up to 30 nm are observed, while the transition state is shifted up to about 150 nm in cis-cis isomerization. The computational data obtained are in agreement with available experimental data, which have predicted that the pyrrole derivative is a MLG at 445 nm and 400 nm using protonation as input, while the anthracene derivative is a MLG that operates at 445 nm using protonation as input. Finally, it was found that selected molecules are candidates as MLG using protonation and light as inputs. These MLGs could be used as chemical sensors or as particular intracellular indicators, among several other applications. Acknowledgements: The author acknowledges the Hellenic Foundation for Research and Innovation for the financial support of this project (Fellowship Number: 21006).

Keywords: absorption spectra, DFT calculations, isomerization, molecular logic gates

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