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Objectives: Although metabolically healthy obesity (MHO) has begun to be seen as a being benign phenomenon, this conclusion is still not completely certain. Obesity is also associated with low-grade systemic inflammation and endothelial dysfunction. Thus, we aimed to assess Pulse Wave Velocity (PWV) as a marker of arterial stiffness and CV risk among individuals with MHO, metabolically unhealthy obesity (MUO), and metabolically healthy normal-weight (MHN)., Methods: 150 participants (n = 50 MHO, n = 50 MUO, n = 50 MHN) who had been admitted to our outpatient clinics were enrolled in this cross-sectional study. Demographic, anthropometric, clinical, and laboratory data, including hs-CRP and PWV, were recorded for all subjects., Results: hs-CRP and PWV were higher in MUO and MHO than MHN individuals (P < .05). hs-CRP showed a strong positive correlation with PWV (r = 0.85, P < .001). After adjusting for other risk factors, multivariate linear regression analysis showed that the PWV was independently associated with BMI (β = 0.08, P = .03), WC (β = 0.04, P = .04) and hs-CRP (β = 6.08, P < .001)., Conclusions: PWV, which is an important non-invasive marker of cardiovascular risk, is higher in MHO than in MHN as in MUO individuals. Moreover, PWV was positively correlated with the serum hs-CRP level as a conventional marker for systemic inflammation. Thus, MHO can be seen as a cardiometabolic risk marker., (© 2021 John Wiley & Sons Ltd.)

Purpose: This study aimed to test the hypothesis model showing the relationship between nurses' individual and working characteristics, nursing work environment, subjective career success, job satisfaction, intent to leave, and professional commitment., Design and Methods: A cross-sectional and correlational design was utilized for the study. The study sample consisted of 604 nurses working in four hospitals in Istanbul, Turkey. Data were collected using the Nurse Information Form, Subjective Career Success Inventory, Practice Work Environment Scale of the Nursing Work Index, Job Satisfaction Global Item, Intent to Leave Subscale, and Professional Commitment Scale. Data were analyzed using descriptive and correlation analysis, and the hypothesis model was tested using structural equation modeling., Findings: The hypothesis model that was established to test the antecedents and outcomes of subjective career success in nurses was acceptable and had a good fit. Having a master's degree, work schedule with rotating shifts (negative), good individual income, participation in hospital affairs, staffing and resource adequacy, and nurse-physician relations were significantly associated with the subjective career success of nurses. Subjective career success had a positive effect on job satisfaction and professional commitment and a negative significant effect on intent to leave in nurses., Conclusions: This study revealed that human capital, objective career success, and some characteristics of the nursing work environment were significantly associated with nurses' subjective career success, and that increased subjective career success produced positive professional and organizational outcomes., Clinical Relevance: The results of this study, which revealed the antecedents and outcomes of nurses' career success, should be taken into consideration by managers who wish to retain a qualified nursing workforce., (© 2021 Sigma Theta Tau International.)

Introduction: Solid Pulmonary Nodule (SPN) is defined as parenchymal radiopacity smaller than 3 cm in diameter. Evaluating the metastatic nature of the SPNs detected in the thorax computed tomography (TCT) examination for staging purposes in cancer patients becomes a fundamental problem for the physician. Invasive procedures, additional imaging or follow-up imaging, are often used to differentiate metastatic and non-metastatic nodules. In this study, we aimed to distinguish SPNs detected in patients diagnosed with bladder cancer (BC) as metastatic and non-metastatic nodules by texture analysis., Materials and Methods: TCT images of patients diagnosed with BC in our hospital from January 2007 until December 2017 were retrospectively evaluated. A total of 46 patients with SPN, including metastatic (n= 19) and non-metastatic (n= 27), were included in the study. Short axis diameter, long-axis diameter, nodule volume and volume histogram values of the nodules were obtained. Chisquare test was used to evaluate dependent variables, and the Mann-Whitney U test was used to evaluate independent variables. ROC curves of the obtained data were plotted. Statistically, the significant p-value was determined as less than 0.05., Result: A significant difference was found between SPN long axis, short axis and volume values. In the volumetric histogram analysis, the maximum density value and the mean density value were found to be statistically significant. When the average of the highest densities in the volume histogram data was evaluated, the area under the curve value was 0.702 (95% CI, 519-854). The metastatic nodule could be distinguished with a sensitivity of 88% and a specificity of 70% when the volume histogram has the maximum density threshold of 50 HU., Conclusions: In this study, we concluded that SPN detected on CT images can be distinguished as metastatic and non-metastatic nodules using texture analysis method without invasive procedures.

Background: Riedel thyroiditis (RT) is a rare form of thyroiditis; thus, data about the disease course and treatment options are limited. Therefore, we aimed to assess the clinical, serological, radiological, and histopathological features, as well as short- and long-term follow-up of RT patients under glucocorticoid (GC) and tamoxifen citrate (TMX). Parameters related to IgG4-related diseases (IgG4-RD) were also investigated., Methods: Eight patients with RT diagnosed between 2000 and 2019 were enrolled. Data were collected in a retrospective and prospective manner. The diagnosis was confirmed with histopathological features in all patients. Results of the treatment with GCs on short- to mid-term, followed by TMX in the long term, were evaluated., Results: The mean age at diagnosis was 40.5 ± 6.8 years; female predominance was observed (F/M:7/1). Parameters related to IgG4-RD, like increase in IgG4 serum levels, total plasmablast counts, and IgG4+ plasmablasts, were negative in most of our patients in both active and inactive states of the disease. Likewise, an increased ratio of IgG4/IgG-positive plasma cells >40% could only be observed in 2 cases. GCs followed by TMX were given to the patients with an over-all median follow-up time of 67 (8-216) months. All the patients considerably improved clinically and had a reduction in the size of the mass lesion on GCs, followed by TMX therapy. None of the patients had a recurrence under TMX therapy for a median period of 18.5 (7-96) months., Conclusion: Even though RT is suggested to be a member of IgG4-RD, serologic or histological evidence of IgG4 elevation or positivity is only useful for diagnosis and follow-up of RT. The diagnosis should be based on clinical and radiological evidence and confirmed by histopathology. GCs are effective for initial treatment, and TMX is a successful and safe therapeutic option for long-term maintenance therapy., Competing Interests: None of the authors have any potential conflicts of interest associated with this research., (Copyright © 2020 by S. Karger AG, Basel.)

The influence of chronic lymphocytic thyroiditis (CLT) on clinicopathological features and behavior of differentiated thyroid carcinoma (DTC) is still debated. In the present study, we aimed to evaluate the prognosis of DTC on the presence of CLT. A total of 649 total thyroidectomized patients (379 female, 270 male) with DTC, who had follow-up data for at least 36 months were included. Clinical, histopathological data, preoperative thyroid peroxidase antibody (TPO-ab), thyroglobulin antibody (Tg-ab), thyroid-stimulating hormone (TSH) levels, and presence of recurrent/persistent disease (R/PD) were evaluated retrospectively. Presence of CLT was defined by histopathology. Frequency of CLT was 32% (n = 208) among DTC patients. Mean tumor size (maximal diameter) was smaller in CLT group when compared to non-CLTs (p = 0.006). Capsular invasion, vascular invasion, tumor stage, risk groups, and R/PD were negatively associated with CLT (p < 0.01, p = 0.04, p = 0.03, p = 0.02, p < 0.01, respectively). Extrathyroidal extension was more frequent in non-CLT group when compared CLT (p = 0.052). Preoperative TSH level was positively associated with lymph node metastasis (LNM) and higher in patients with lateral LNM when compared to central LNM (p < 0.01). Central LNM, lateral LNM, stage 4 tumor, and intermediate- and high-risk tumor groups increased the risk of R/PH, 2.5-, 2.9-, 12.7-, 2.3-, and 4.2-fold, respectively. Presence of CLT was independently related with favorable outcomes, as the risk of R/PD was decreased by 0.49-fold. In conclusion, coexistence of CLT was negatively associated with tumor size, capsular invasion, vascular invasion, and tumor stage in DTC. Risk of R/PD was decreased by approximately half in patients with CLT.

APOBEC3B (A3B) is one of seven human APOBEC3 DNA cytosine deaminases that restrict viral infections as part of the overall innate immune response, but it also plays a major role in tumor evolution by mutating genomic DNA. Given the importance of A3B as a restriction factor of viral infections and as a driver of multiple human cancers, selective antibodies against A3B are highly desirable for its specific detection in various research and possibly diagnostic applications. Here, we describe a high-affinity minimal antibody, designated 5G7, obtained via a phage display screening against the C-terminal catalytic domain (ctd) of A3B. 5G7 also binds APOBEC3A that is highly homologous to A3Bctd but does not bind the catalytic domain of APOBEC3G, another Z1-type deaminase domain. The crystal structure of 5G7 shows a canonical arrangement of the heavy and light chain variable domains, with their complementarity-determining region (CDR) loops lining an antigen-binding cleft that accommodates a pair of α-helices. To understand the mechanism of A3Bctd recognition by 5G7, we used the crystal structures of A3Bctd and 5G7 as templates and computationally predicted the A3B-5G7 complex structure. Stable binding poses obtained by the simulation were further tested by site-directed mutagenesis and in vitro binding analyses. These studies mapped the epitope for 5G7 to a portion of C-terminal α6 helix of A3Bctd, with Arg374 playing an essential role. The same region of A3Bctd was used previously as a peptide antigen for generating a rabbit monoclonal antibody (mAb 5210-87-13), suggesting that this region is particularly immunogenic and that these antibodies from very different origins may share similar binding modes. Our studies provide a platform for the development of selective antibodies against A3B and other APOBEC3 family enzymes.

The tumor suppressor p53 plays a vital role in responding to cell stressors such as DNA damage, hypoxia, and tumor formation by inducing cell-cycle arrest, senescence, or apoptosis. Expression level alterations and mutational frequency implicates p53 in most human cancers. In this review, we show how both computational and experimental methods have been used to provide an integrated view of p53 dynamics, function, and reactivation potential. We argue that p53 serves as an exceptional case study for developing methods in modeling intrinsically disordered proteins. We describe how these methods can be leveraged to improve p53 reactivation molecule design and other novel therapeutic modalities, such as PROteolysis TARgeting Chimeras (PROTACs)., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Aim: To evaluate whether there is a statistically significant difference between the cord blood gas parameters of pregnancies complicated with preeclampsia and uncomplicated pregnancies and to show whether the amount of proteinuria affects fetal cord blood gas parameters in pregnancies complicated with preeclampsia., Methods: The study was designed retrospectively. Between 2016 and 2019, the neonatal results and cord blood gas results of 109 pregnant women who were diagnosed with preeclampsia and 75 nonpreeclamptic randomly selected pregnant women were compared. The preeclampsia group was divided into groups according to amount of proteinuria. SPSS 21.0 statistics program was used, and comparative analysis was carried out., Results: The data of the 109 preeclampsia cases and 75 control groups included in the study were compared, and there was no statistical difference between the fetal cord blood gas parameters between the groups (p > 0.05). The median first and fifth minute Apgar scores were found significantly lower in the preeclampsia group compared to the control group (6, 8 and 8, 9, respectively; p < 0.001). Also, the amount of proteinuria does not alter cord blood gas parameters (p > 0.05)., Conclusion: Preeclampsia poses a risk for the neonatal period as it reduces the neonatal Apgar scores due to the chronic hypoxic process it creates. However, it was observed that the amount of proteinuria, which is one of the diagnostic criteria, did not affect neonatal results on Apgar scores or fetal cord blood gas parameters., (© 2021 Japan Society of Obstetrics and Gynecology.)

Background: Iodine uptake is a main factor affecting thyroid disease. In Turkey, mandatory salt iodization began in 1999-2000., Aims: This study in 2009 determined the prevalence of thyroid diseases in older people in Mamak district, Ankara after iodization to ascertain if salt iodization alone is sufficient to reach adequate iodine levels in the older population., Methods: All Mamak residents ≥ 65 years were eligible for inclusion in the study. Demographic data and medical history were recorded. All participants had a thyroid ultrasound. Blood samples were taken to assess thyroid function and autoantibodies, and urine samples to assess iodine concentration. Participants with low levels of thyroid stimulating hormone underwent scintigraphy to assess thyroid uptake. Fine-needle aspiration biopsy was done of nodules ≥ 1.5 cm where thyroid stimulating hormone was not suppressed., Results: Of 1200 eligible residents, 979 were included. Their mean age was 70.9 (standard deviation (SD) 5.7) years; 49.7% were women. Mean urinary iodine concentration was 98 (SD 81.29) μg/L. Goitre was found in 18.2% (89/487) of women and 6.7% (33/492) of men (P < 0.001) and 43.8% (428/979) had nodules. Subclinical hypothyroidism was found in 5.8% (57/979) of the participants, overt hyperthyroidism in 0.8% (8/979), subclinical hyperthyroidism in 2.2% (22/979) and T3 thyrotoxicosis in 0.3% (3/979). Toxic multinodular goitre and toxic adenoma caused 80% of hyperthyroidism cases. Biopsy detected no malignant pathology., Conclusion: After salt iodization, iodine levels have not yet reached favourable levels in older people. Iodization of salt seems insufficient to achieve these levels in older people; alternative iodine supplementation should be considered., (Copyright © World Health Organization (WHO) 2021. Open Access. Some rights reserved. This work is available under the CC BY-NC-SA 3.0 IGO license (https://creativecommons.org/licenses/by-nc-sa/3.0/igo).)

RNA modifications are essential for proper RNA processing, quality control, and maturation steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveillance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essential for the correct assembly of small nucleolar ribonucleoproteins (snRNPs) and ribosomal RNA (rRNA) processing. Here, we review rRNA modifications and RNA quality control mechanisms in general and discuss the specific function of SMUG1 in rRNA metabolism. Cells lacking SMUG1 have elevated levels of immature rRNA molecules and accumulation of 5-hydroxymethyluridine (5hmU) in mature rRNA. SMUG1 may be required for post-transcriptional regulation and quality control of rRNAs, partly by regulating rRNA and stability.

The tumor suppressor p53 is the most frequently mutated gene in human cancer, and thus reactivation of mutated p53 is a promising avenue for cancer therapy. Analysis of wildtype p53 and the Y220C cancer mutant long-timescale molecular dynamics simulations with Markov state models and validation by NMR relaxation studies has uncovered the involvement of loop L6 in the slowest motions of the protein. Due to its distant location from the DNA-binding surface, the conformational dynamics of this loop has so far remained largely unexplored. We observe mutation-induced stabilization of alternate L6 conformations, distinct from all experimentally-determined structures, in which the loop is both extended and located further away from the DNA-interacting surface. Additionally, the effect of the L6-adjacent Y220C mutation on the conformational landscape of the functionally-important loop L1 suggests an allosteric role to this dynamic loop and the inactivation mechanism of the mutation. Finally, the simulations reveal a novel Y220C cryptic pocket that can be targeted for p53 rescue efforts. Our approach exemplifies the power of the MSM methodology for uncovering intrinsic dynamic and kinetic differences among distinct protein ensembles, such as for the investigation of mutation effects on protein function., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Human immunodeficiency virus type 1 (HIV-1) Vif recruits a cellular ubiquitin ligase complex to degrade antiviral APOBEC3 enzymes (APOBEC3C-H) and PP2A phosphatase regulators (PPP2R5A to PPP2R5E). While APOBEC3 antagonism is the canonical function of HIV-1 Vif, this viral accessory protein is also known to trigger G 2 /M cell cycle arrest. Vif initiates G 2 /M arrest by degrading multiple PPP2R5 family members, an activity prevalent among diverse HIV-1 and simian immunodeficiency virus (SIV) isolates. Here, computational protein-protein docking was used to delineate a Vif/CBF-β/PPP2R5 complex in which Vif is predicted to bind the same PPP2R5 surface as physiologic phosphatase targets. This model was tested using targeted mutagenesis of amino acid residues within or adjacent to the putative interface to show loss or retention, respectively, of Vif-induced PPP2R5 degradation activity. Additionally, expression of a peptide that mimics cellular targets of PPP2R5s robustly inhibited Vif-mediated degradation of PPP2R5A but not APOBEC3G. Moreover, live-cell imaging studies examining Vif-mediated degradation of PPP2R5A and APOBEC3G within the same cell revealed that PPP2R5A degradation kinetics are comparable to those of APOBEC3G with a half-life of roughly 6 h postinfection, demonstrating that Vif can concurrently mediate the degradation of distinct cellular substrates. Finally, experiments with a panel of patient-derived Vif isolates indicated that PPP2R5A degradation activity is common in patient-derived isolates. Taken together, these results support a model in which PPP2R5 degradation and global changes in the cellular phosphoproteome are likely to be advantageous for viral pathogenesis. IMPORTANCE A critical function of HIV-1 Vif is to counteract the family of APOBEC3 innate immune proteins. It is also widely accepted that Vif induces G 2 /M cell cycle arrest in several different cell types. Recently, it has been shown that Vif degrades multiple PPP2R5 phosphoregulators to induce the G 2 /M arrest phenotype. Here, computational approaches are used to test a structural model of the Vif/PPP2R5 complex. In addition, imaging studies are used to show that Vif degrades these PPP2R5 substrates in roughly the same time frame as APOBEC3 degradation and that this activity is prevalent in patient-derived Vif isolates. These studies are important by further defining PPP2R5 proteins as a bona fide substrate of HIV-1 Vif., (Copyright © 2020 American Society for Microbiology.)

Objectives: To describe biochemical and clinical features, and therapeutic outcomes of acromegaly patients in Turkey., Methods: Retrospective multicenter epidemiological study of 547 patients followed in 10 centers of the Turkish Acromegaly registry., Results: A total of 547 acromegaly patients (55% female) with a median age of 41 was included in this study. Majority of patients had a macroadenoma (78%). Transsphenoidal surgery was performed as primary treatment in 92% of the patients (n = 503). Surgical remission rate was 39% (197/503) in all operated patients. Overall disease control was achieved in 70% of patients. Remission group were significantly older than non-remission group (p = .002). Patients with microadenomas had significantly higher remission rates than patients with macroadenomas (p < .001). Patients with microadenomas were significantly older at the time of diagnosis when compared to patients with macroadenomas (p < .001). Preoperative growth hormone (GH) and insulin-like growth factor 1 (IGF-1) levels were significantly lower in the remission group (p < .001). Initial IGF-1 and GH levels were significantly higher in macroadenomas compared to microadenomas (p < .001). Medical treatment was administered as a second-line treatment (97%) in almost all patients without remission. Radiotherapy was preferred in 21% of the patients mostly as a third line treatment., Conclusions: This is one of the largest real life studies evaluating the epidemiological characteristics and treatment outcomes of patients with acromegaly who were followed in different centers in Turkey. Transsphenoidal surgery in the treatment of acromegaly still remains the most valid method. Medical treatment options may improve long-term disease outcomes in patients who cannot be controlled with surgical treatment (up to 70%)., Competing Interests: Declaration of Competing Interest The authors have no competing interests to declare., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Objective: This study aimed to evaluate the effects of different surface conditoning methods on surface texture and shear bond strength (SBS) of brackets bonded to resin nanoceramic material., Methods: Ceramic specimens were divided into two groups as metal brackets and ceramic brackets. In each group, the following five subgroups were conditoned with orthophosphoric acid (OPA), hydrofluoric acid (HFA), silica coating with Cojet, Nd: Yag laser, and Femtosecond (Fs) laser. Extra samples were used for scanning electron microscopy and 3D profilometer evaluation., Results: All surface conditioning methods caused optimum or higher SBS. Metal brackets had higher SBS than porcelain brackets, but this difference reached statistical significance only in Fs laser group. OPA caused surface modification comparable to HFA because of polymer content of resin nanoceramic. Although Fs laser and Cojet conditioning caused optimum or higher SBS, surface damage of these methods to the resin nanoceramic specimens clearly seen on 3D profilometer., Conclusion: HFA and Nd: Yag laser are effective surface conditioning methods for resin nanoceramics. OPA combined with silane application caused optimum SBS and can be used as an alternative to HFA. Surface texture changes should be considered to determine surface damage while deciding the optimum surface conditioning method for ceramics other than SBS., Competing Interests: Conflict of Interest: The author has no conflict of interest to declare., (© Copyright 2020 by Turkish Orthodontic Society.)

The single-stranded DNA cytosine deaminase APOBEC3B (A3B) functions in innate immunity against viruses, but it is also strongly implicated in eliciting mutations in cancer genomes. Because of the critical role of A3B in promoting virus and tumor evolution, small molecule inhibitors are desirable. However, there is no reported structure for any of the APOBEC3-family enzymes in complex with a small molecule bound in the active site, which hampers the development of small molecules targeting A3B. Here we report high-resolution structures of an active A3B catalytic domain chimera with loop 7 residues exchanged with those from the corresponding region of APOBEC3G (A3G). The structures reveal novel open conformations lacking the catalytically essential zinc ion, with the highly conserved active site residues extensively rearranged. These inactive conformations are stabilized by 2-pyrimidone or an iodide ion bound in the active site. Molecular dynamics simulations corroborate the remarkable plasticity of the engineered active site and identify key interactions that stabilize the native A3B active site. These data provide insights into A3B active site dynamics and suggest possible modes of its inhibition by small molecules, which would aid in rational design of selective A3B inhibitors for constraining virus and tumor evolution., Competing Interests: RSH and DAH are co‐founders, shareholders, and consultants of ApoGen Biotechnologies Inc HA and REA are consultants for ApoGen Biotechnologies Inc REA is a co‐founder of Actavalon Inc The other authors have no competing financial interests to declare., (© 2019 The Authors.)

Background: This study was designed to detect the potential association of a nonfunctional adrenal incidentaloma (NFAI) with insulin resistance and associated metabolic disturbances, with a subsequent increase in cardiovascular risk factors., Methods: Eighty-three NFAI patients and 56 volunteers (controls) without any adrenal abnormalities on computed tomography (CT) were included. Fasting blood glucose (FBG), fasting insulin, lipid profiles, uric acid, homocysteine, fibrinogen, high sensitivity C-reactive protein (hs-CRP), and adiponectin levels were measured in both groups. Blood pressure (BP), waist circumference, body mass index (BMI), and carotid intima media thickness (CIMT) were evaluated in both the patients and volunteers., Results: There were no significant difference between the NFAI and control groups with respect to age, sex, BMI, waist circumference, systolic and diastolic BP, smoking, concomitant disease, and medications. Fasting insulin and glucose levels and homeostasis model of assessment-insulin resistance (HOMA-IR) scores were significantly higher in the NFAI group as compared with those in the control group (p<0.01). The frequency of metabolic syndrome in the NFAI group was higher than that in the control group (p<0.01). All the lipid fractions, except triglyceride (TG), (p<0.05), homocysteine (p=0.01), and fibrinogen levels (p<0.001), were significantly higher in the NFAI group as compared with the levels in the control group. There were no significant differences between the NFAI and control groups in terms of uric acid, hs-CRP, and adiponectin levels. The CIMT values in the NFAI group were significantly higher than those in the control group (0.74±0.14 vs. 0.53±0.09, p<0.001). The mean CIMT value showed a statistically positive correlation with age (r=0.245, p=0.004); the HOMA-IR score (r=0.490, p<0.001); and FBG (r=0.521, p<0.001), fasting insulin (r=0.432, p<0.001), total cholesterol (TC) (r=0.267, p=0.002), and fibrinogen (r=0.398, p<0.001) levels in the NFAI group., Conclusions: The results indicated that the NFAI patients had an elevated risk of insulin resistance, with metabolic syndrome and increased CIMT values. Long-term follow-up studies should be designed to evaluate postsurgical alterations in metabolic parameters and cardiovascular risk factors in NFAI patients., (Copyright © 2019 SEEN y SED. Publicado por Elsevier España, S.L.U. All rights reserved.)

Background: Diagnostic accuracy of fine-needle aspiration cytology (FNAC) in large and subcentimeter nodules is still debated. We aimed to evaluate the impact of nodule size on efficacy of the ultrasound-guided FNAC., Methods: B-mode grayscale ultrasound (US), US-guided FNAC according to Bethesda system and histopathological data of 514 nodules from 371 patients, who underwent thyroidectomy were examined retrospectively. Nodules were grouped by maximal diameter; group A nodules were smaller than 10 mm (n = 59), group B nodules were between 10 and 29 mm (n = 218), and group C nodules were 30 mm or greater (n = 130)., Results: Sensitivity, specificity, and accuracy of FNAC was 92.0%, 100%, and 95.1% in group A, 80.7%, 99.1%, and %92.9 in group B, 70.0%, 98.9%, and 95.8% in group C nodules, respectively. The prevalence of papillary thyroid cancer (PTC) and incidental PTC were 44.2% (n = 164) and 6.4% (n = 24), respectively. Malignancy rate was more frequent in group A when compared to groups B and C (P < 0.01). Nodule size was positively associated with follicular cancer risk (P = 0.009). The thyroid stimulating hormone level was positively associated with malignancy (P = 0.02) and optimal cut-off value was 0.96 mIU/L. False-negative rate was 8.0%, 19.3%, and 30.0% in groups A, B, and C nodules, respectively., Conclusions: Although the malignancy rate was low in nodules ≥30 mm, diagnostic surgery for large nodules should be considered because of decreased reliability of FNAC, ineffectiveness of clinical and sonographic criteria. False-negative rate was relatively low and malignancy rate was high in subcentimeter nodules, supporting the accuracy of FNAC., (© 2019 Wiley Periodicals, Inc.)

APOBEC3B (A3B) is a prominent source of mutation in many cancers. To date, it has been difficult to capture the native protein-DNA interactions that confer A3B's substrate specificity by crystallography due to the highly dynamic nature of wild-type A3B active site. We use computational tools to restore a recent crystal structure of a DNA-bound A3B C-terminal domain mutant construct to its wild type sequence, and run molecular dynamics simulations to study its substrate recognition mechanisms. Analysis of these simulations reveal dynamics of the native A3Bctd-oligonucleotide interactions, including the experimentally inaccessible loop 1-oligonucleotide interactions. A second series of simulations in which the target cytosine nucleotide was computationally mutated from a deoxyribose to a ribose show a change in sugar ring pucker, leading to a rearrangement of the binding site and revealing a potential intermediate in the binding pathway. Finally, apo simulations of A3B, starting from the DNA-bound open state, experience a rapid and consistent closure of the binding site, reaching conformations incompatible with substrate binding. This study reveals a more realistic and dynamic view of the wild type A3B binding site and provides novel insights for structure-guided design efforts for A3B.

Using a novel chemistry-based assay for identifying electrophilic natural products in unprocessed extracts, we identified the PI3-kinase/mTOR dual inhibitor neolymphostin A from Salinispora arenicola CNY-486. The method further showed that the vinylogous ester substituent on the neolymphostin core was the exact site for enzyme conjugation. Tandem MS/MS experiments on PI3Kα treated with the inhibitor revealed that neolymphostin covalently modified Lys802 with a shift in mass of +306 amu, corresponding to addition of the inhibitor and elimination of methanol. The binding pose of the inhibitor bound to PI3Kα was modeled, and hydrogen-deuterium exchange mass spectrometry experiments supported this model. Against a panel of kinases, neolymphostin showed good selectivity for PI3-kinase and mTOR. In addition, the natural product blocked AKT phosphorylation in live cells with an IC 50 of ∼3 nM. Taken together, neolymphostin is the first reported example of a covalent kinase inhibitor from the bacterial domain of life.

The "guardian of the genome", p53, functions as a tumor suppressor that responds to cell stressors such as DNA damage, hypoxia, and tumor formation by inducing cell-cycle arrest, senescence, or apoptosis. Mutation of p53 disrupts its tumor suppressor function, leading to various types of human cancers. One particular mutant, R175H, is a structural mutant that inactivates the DNA damage response pathway and acquires oncogenic functions that promotes both cancer and drug resistance. Our current work aims to understand how p53 wild-type function is disrupted due to the R175H mutation. We use a series of atomistic integrative models built previously from crystal structures of the full-length p53 tetramer bound to DNA and model the R175H mutant using in silico site-directed mutagenesis. Explicitly solvated all-atom molecular dynamics (MD) simulations on wild-type and the R175H mutant p53 reveal insights into how wild-type p53 searches and recognizes DNA, and how this mechanism is disrupted as a result of the R175H mutation. Specifically, our work reveals the optimal quaternary DNA binding mode of the DNA binding domain and shows how this binding mode is altered via symmetry loss as a result of the R175H mutation, indicating a recognition mechanism that is reminiscent of the asymmetry seen in wild type p53 binding to nonspecific genomic elements. Altogether our work sheds new light into the hitherto unseen molecular mechanisms governing transcription factor, DNA recognition.

APOBEC enzymes are DNA cytosine deaminases that normally serve as virus restriction factors, but several members, including APOBEC3H, also contribute to cancer mutagenesis. Despite their importance in multiple fields, little is known about cellular processes that regulate these DNA mutating enzymes. We show that APOBEC3H exists in two distinct subcellular compartments, cytoplasm and nucleolus, and that the structural determinants for each mechanism are genetically separable. First, native and fluorescently tagged APOBEC3Hs localize to these two compartments in multiple cell types. Second, a series of genetic, pharmacologic, and cell biological studies demonstrate active cytoplasmic and nucleolar retention mechanisms, whereas nuclear import and export occur through passive diffusion. Third, APOBEC3H cytoplasmic retention determinants relocalize APOBEC3A from a passive cell-wide state to the cytosol and, additionally, endow potent HIV-1 restriction activity. These results indicate that APOBEC3H has a structural zipcode for subcellular localization and selecting viral substrates for restriction., (Copyright © 2018 American Society for Microbiology.)

Objective: To determine the presence of lower urinary tract symptoms (LUTS), nocturia, sexual dysfunction (SD), and the status of quality of life (QOL) in men with obstructive sleep apnea syndrome (OSAS) and after continuous positive airway pressure (CPAP) treatment, the changes in the presence of these conditions and the improvements of QOL., Materials and Methods: In this study, 126 patients with suspicious diagnosis of OSAS were enrolled prospectively. International Prostate Symptom Score (IPSS), International Consultation on Incontinence Questionnaire-Male LUTS (ICIQ-MLUTS), Overactive Bladder Symptoms Score (OABS-V8), Nocturia Quality of Life (Nqol), voiding diary, International Index of Erectile Function (IIEF-15) questionnaire, and Short form 36 (SF-36) to assess the presence of SD, LUTS, nocturia, and the status of QOL were filled by patients before polysomnography. The same forms were filled in the third month of treatment by the patients directed to CPAP treatment due to moderate and severe OSAS., Results: There were significant differences in IPSS, IIEF, OABSS, ICIQ-MLUTS, Nqol and SF-36 scores, frequency of nocturia, and night-time urine volume according to OSAS severity. Among the factors affecting the QOL, there was strong correlation between ED and SF-36 sub-domains compared with the other factors. After CPAP treatment significant changes and improvements on these symptoms and QOL were observed., Conclusion: In patient with OSAS, the severity of SD and LUTS and their effect on QOL differ according to the severity of OSAS and CPAP treatment improves the negative impact of these conditions on QOL., (Copyright © 2018. Published by Elsevier Inc.)

Introduction: Minimally invasive surgery is an alternative surgical approach for primary hyperparathyroidism with less surgical trauma and anaesthesia complications. When combined with intraoperative measurement of parathyroid hormone (PTH), cure rates are exceeding 97%. Preoperative intact PTH determination in washout samples is really very useful when parathyroid lesions cannot be easily distinguished from thyroid lesions or sometimes lymph nodes. Herein, we aimed to report our institutional experience about parathyroid fine-needle aspiration (FNA) method and suggest a cut-off ratio for this purpose., Methods: In our clinic, we performed ultrasonography (USG)-guided parathyroid FNA procedure for 131 patients diagnosed with primary hyperparathyroidism between January 2005 and January 2016. Both cytologic evaluation and intact PTH determination were performed in washout samples. Eighty-seven of the study group also had a parathyroid scintigraphy. Both demographic features and laboratory results were all recorded., Results: Median serum PTH level was 142 (113-197), while mean PTH washout level was 1824 (0-3953). When three of the localization techniques are compared with each other, FNA-PTH washout group had a better diagnostic accuracy (90.8%) when compared to cytology (7.92%) and MIBI (67.8%) groups. Both MIBI and FNA-PTH washout group had 100% positive predictive value (PPV) and 100% specificity. We found values greater than 436.5 pg/mL for FNA-PTH washout with a sensitivity of 90.3% and specificity of 88.9% (P < 0.01 and AUC 94.3 (87.8-100)) and a cut-off for FNA/serum PTH greater than 3.05 with a sensitivity of 91.2% and specificity of 89% (P = 0.02 and AUC 94.5 (88.8-100)) which implicate parathyroid lesions., Conclusion: According to the literature, PTH determination in washout samples has a specificity of 75%-100% and sensitivity of 70%-100%. This approach has better results than both cytology and scintigraphy in case of concomitant multinodular thyroid disease in experienced hands. Although there is not a definite cut-off for PTH levels in washout samples, we agree with the need of ratios rather than cut-offs in this issue., (© 2018 John Wiley & Sons Ltd.)

The APOBEC3 family of cytosine deaminases catalyzes the conversion of cytosines-to-uracils in single-stranded DNA. Traditionally, these enzymes are associated with antiviral immunity and restriction of DNA-based pathogens. However, a role for these enzymes in tumor evolution and metastatic disease has also become evident. The primary APOBEC3 candidate in cancer mutagenesis is APOBEC3B (A3B) for three reasons: (1) A3B mRNA is upregulated in several different cancers, (2) A3B expression and mutational loads correlate with poor clinical outcomes, and (3) A3B is the only family member known to be constitutively nuclear. Previous studies have mapped non-canonical A3B nuclear localization determinants to a single surface-exposed patch within the N-terminal domain (NTD). Here, we show that A3B has an additional, distinct, surface-exposed NTD region that contributes to nuclear localization. Disruption of residues within the first 30 amino acids of A3B (import surface 1) or loop 5/α-helix 3 (import surface 2) completely abolish nuclear localization. These import determinants also graft into NTDs of related family members and mediate re-localization from cell-wide-to-nucleus or cytoplasm-to-nucleus. These findings demonstrate that both sets of residues are required for non-canonical A3B nuclear localization and describe unique surfaces that may serve as novel therapeutic targets., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Gram-negative bacteria are surrounded by a secondary membrane of which the outer leaflet is composed of the glycolipid lipopolysaccharide (LPS), which guards against hydrophobic toxins, including many antibiotics. Therefore, LPS synthesis in bacteria is an attractive target for antibiotic development. LpxH is a pyrophosphatase involved in LPS synthesis, and previous structures revealed that LpxH has a helical cap that binds its lipid substrates. Here, crystallography and hydrogen-deuterium exchange MS provided evidence for a highly flexible substrate-binding cap in LpxH. Furthermore, molecular dynamics simulations disclosed how the helices of the cap may open to allow substrate entry. The predicted opening mechanism was supported by activity assays of LpxH variants. Finally, we confirmed biochemically that LpxH is inhibited by a previously identified antibacterial compound, determined the potency of this inhibitor, and modeled its binding mode in the LpxH active site. In summary, our work provides evidence that the substrate-binding cap of LpxH is highly dynamic, thus allowing for facile substrate binding and product release between the capping helices. Our results also pave the way for the rational design of more potent LpxH inhibitors., (© 2018 Bohl et al.)

Ensemble docking corresponds to the generation of an "ensemble" of drug target conformations in computational structure-based drug discovery, often obtained by using molecular dynamics simulation, that is used in docking candidate ligands. This approach is now well established in the field of early-stage drug discovery. This review gives a historical account of the development of ensemble docking and discusses some pertinent methodological advances in conformational sampling., (Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

A sensitive analytical methodology was investigated to concentrate and determine of sildenafil citrate (SLC) present at trace level in herbal supplementary products. The proposed method is based on simple and sensitive pre-concentration of SLC by using magnetic solid phase extraction with new developed magnetic nanodiamond/graphene oxide hybrid (Fe 3 O 4 @ND@GO) material as a sorbent. Experimental variables affecting the extraction efficiency of SLC like; pH, sample volume, eluent type and volume, extraction time and amount of adsorbent were studied and optimized in detail. Determination of sildenafil citrate after magnetic solid phase extraction (MSPE) was carried out by HPLC-DAD system. The morphology, composition, and properties of the synthesized hybrid material was characterized by Fourier transform infrared spectrometry (FT-IR), Raman spectrometry (Raman), X-ray diffraction spectrometry (XRD), scanning electron microscopy (SEM), mapping photographs, zeta potential analyzer, and BET surface area analysis. Under optimized conditions, linear range was ranged from 5.00 to 250.00 ng mL -1 with R 2 of 0.9952. The limit of detection (LOD) was 1.49 ng mL -1 and the recoveries at two spiked levels were ranged from 94.0 to 104.1% with the relative standard deviation (RSD) < 7.1% (n = 5). The enhancement factor (EF) was 86.9. The results show that the combination MSPE with HPLC-DAD is a suitable and sensitive method for the determination of SLC in real samples., (Copyright © 2018 Elsevier B.V. All rights reserved.)

The APOBEC3B (A3B) single-stranded DNA (ssDNA) cytosine deaminase has important roles in innate immunity but is also a major endogenous source of mutations in cancer. Previous structural studies showed that the C-terminal catalytic domain of human A3B has a tightly closed active site, and rearrangement of the surrounding loops is required for binding to substrate ssDNA. Here we report structures of the A3B catalytic domain in a new crystal form that show alternative, yet still closed, conformations of active site loops. All-atom molecular dynamics simulations support the dynamic behavior of active site loops and recapitulate the distinct modes of interactions that maintain a closed active site. Replacing segments of A3B loop 1 to mimic the more potent cytoplasmic deaminase APOBEC3A leads to elevated ssDNA deaminase activity, likely by facilitating opening of the active site. These data collectively suggest that conformational equilibrium of the A3B active site loops, skewed toward being closed, controls enzymatic activity by regulating binding to ssDNA substrates.

Background: Computed tomography (CT) with Hounsfield unit (HU) is being used with increasing frequency for determining bone density. Established correlations between HU and bone density have been shown in the literature. The aim of this retrospective study was to determine the bone density changes of the stabilized and adjacent segment vertebral bodies by comparing HU values before and after lumbar posterior stabilization., Methods: Sixteen patients who had similar diagnosis of lumbar spondylosis and stenosis were evaluated in this study. Same surgical procedures were performed to all of the patients with L2-3-4-5 transpedicular screw fixation, fusion and L3-4 total laminectomy. Bone mineral density measurements were obtained with clinical CT. Measurements were obtained from stabilized and adjacent segment vertebral bodies. Densities of vertebral bodies were evaluated with HU before the surgeries and approximately one year after the surgeries. The preoperative HU value of each vertebra was compared with postoperative HU value of the same vertebrae by using statistical analysis., Results: The HU values of vertebra in the stabilized and adjacent segments consistently decreased after the operations. There were significant differences between the preoperative HU values and the postoperative HU values of the all evaluated vertebral bodies in the stabilized and adjacent segments. Additionally first sacral vertebra HU values were found to be significantly higher than lumbar vertebra HU values in the preoperative group and postoperative group., Conclusions: Decrease in the bone density of the adjacent segment vertebral bodies may be one of the major predisposing factors for adjacent segment disease (ASD)., Competing Interests: Conflicts of Interest: The authors have no conflicts of interest to declare.

The protein arginine methyltransferase (PRMT) family of enzymes comprises nine family members in mammals. They catalyze arginine methylation, either monomethylation or symmetric/asymmetric dimethylation of histone and non-histone proteins. PRMT methylation of its substrate proteins modulates cellular processes such as signal transduction, transcription, and mRNA splicing. Recent studies have linked overexpression of PRMT5, a member of the PRMT superfamily, to oncogenesis, making it a potential target for cancer therapy. In this study, we developed a highly sensitive (Z' score = 0.7) robotic high throughput screening (HTS) platform to discover small molecule inhibitors of PRMT5 by adapting the AlphaLISA™ technology. Using biotinylated histone H4 as a substrate, and S-adenosyl-l-methionine as a methyl donor, PRMT5 symmetrically dimethylated H4 at arginine (R) 3. Highly specific acceptor beads for symmetrically dimethylated H4R3 and streptavidin-coated donor beads bound the substrate, emitting a signal that is proportional to the methyltransferase activity. Using this powerful approach, we identified specific PRMT5 inhibitors P1608K04 and P1618J22, and further validated their efficacy and specificity for inhibiting PRMT5. Importantly, these two compounds exhibited much more potent efficacy than the commercial PRMT5 inhibitor EPZ015666 in both pancreatic and colorectal cancer cells. Overall, our work highlights a novel, powerful, and sensitive approach to identify specific PRMT5 inhibitors. The general principle of this HTS screening method can not only be applied to PRMT5 and the PRMT superfamily, but may also be extended to other epigenetic targets. This approach allows us to identify compounds that inhibit the activity of their respective targets, and screening hits like P1608K04 and P1618J22 may serve as the basis for novel drug development to treat cancer and/or other diseases.

Background Previous studies from western countries demonstrated the effectiveness of Teratology Information Service (TIS) counselling in reducing the teratogenic risk perception of pregnant women. Objective To assess whether TIS counselling would be effective in reducing the teratogenic risk perception of the Turkish pregnant women. Setting A TIS (Terafar) operating in a university hospital in Turkey. Methods A cross-sectional survey study. Pregnant women with non-teratogenic medication exposures were asked to assign scores on visual analogue scales (VAS) in response to the questions aiming to measure their teratogenic risk perception. The mean score before and after counselling were compared and the associations with maternal socio-demographic characteristics were analysed using SPSS (Version 20.0). Main outcome measures The differences in the mean scores of the perception regarding the baseline risk of pregnancy, own teratogenic risk and the likelihood of termination of pregnancy before and after counselling and their possible associations with maternal socio-demographic characteristics. Results 102 pregnant women participated in the study. The counselling significantly reduced the mean own teratogenic risk perception score and the mean score for the likelihood of termination of pregnancy whereas the mean baseline risk perception score was not significantly changed. Pregnancy week <8 and the exposed number of active ingredients <3 were significantly associated with the difference in the mean score for the likelihood of termination of pregnancy. Conclusions TIS counselling lowers the teratogenic risk perception of Turkish pregnant women and increases their likelihood to continue the pregnancy as it does in the western countries.

Aim of this study is to compare the effects of partial nephrectomy (PN) and radical nephrectomy (RN) for stage I renal cell carcinoma (RCC) on renal functions in patients with diabetes mellitus (DM) and/or hypertension (HT). Charts of patients who underwent surgery for stage I RCC in our department were retrospectively reviewed and patients with DM and/or HT were enrolled. Preoperative and postoperative estimated glomerular filtration rates (eGFR) were calculated according to the Modification of Diet in Renal Disease (MDRD) formulation for both RN and PN groups. Groups were compared for patient demographics, preoperative eGFR, postoperative eGFR and ΔeGFR [(preoperative eGFR) - (postoperative eGFR)] which reflects the renal functional loss. There were 85 patients in the RN and 33 patients in the PN groups. Demographic data were similar but the patients in the PN group had smaller tumor size compared to RN group (32.2 ± 11.8 mm vs 47.1 ± 15.2 mm, p < 0.001). Preoperative eGFR did not differ between groups (75 ± 28.4 mL/min/1.73 m 2 vs 75.5 ± 23.8 mL/min/1.73 m 2 in RN and PN groups, p = 0.929). However, there were significant differences between groups in terms of postoperative eGFR (57.5 ± 21.7 mL/min/1.73 m 2 vs 74 ± 27.5 mL/min/1.73 m 2 in RN and PN groups, p < 0.001) and ΔeGFR (17.5 ± 4.2 mL/min/1.73 m 2 vs 1.5 ± 0.4 mL/min/1.73 m 2 in RN and PN groups, p < 0.001). Our findings favor the use of PN over RN for stage I RCC whenever feasible in patients with predisposing systemic diseases for chronic kidney disease for better preservation of renal functions., (Copyright © 2017 Kaohsiung Medical University. Published by Elsevier Taiwan. All rights reserved.)

African trypanosomiasis occurs in 36 countries in sub-Saharan Africa with 10,000 reported cases annually. No definitive remedy is currently available and if left untreated, the disease becomes fatal. Structural and biochemical studies of trypanosomal terminal uridylyl transferases (TUTases) demonstrated their functional role in extensive uridylate insertion/deletion of RNA. Trypanosoma brucei RNA Editing TUTase 1 (TbRET1) is involved in guide RNA 3' end uridylation and maturation, while TbRET2 is responsible for U-insertion at RNA editing sites. Two additional TUTases called TbMEAT1 and TbTUT4 have also been reported to share similar function. TbRET1 and TbRET2 are essential enzymes for the parasite viability making them potential drug targets. For this study, we clustered molecular dynamics (MD) trajectories of four TUTases based on active site shape measured by Pocket Volume Measurer (POVME) program. Among the four TUTases, TbRET1 exhibited the largest average pocket volume, while TbMEAT1's and TbTUT4's active sites displayed the most flexibility. A side pocket was also identified within the active site in all TUTases with TbRET1 having the most pronounced. Our results indicate that TbRET1's larger side pocket can be exploited to achieve selective inhibitor design as FTMap identifies it as a druggable pocket., Competing Interests: Rommie E. Amaro is a co-founder of, on the scientific advisory board of, and has equity interest in Actavalon, Inc.

Pancreatic ductal adenocarcinoma (PDAC) and colorectal cancer (CRC) are notoriously challenging for treatment. Hyperactive nuclear factor κB (NF-κB) is a common culprit in both cancers. Previously, we discovered that protein arginine methyltransferase 5 (PRMT5) methylated and activated NF-κB. Here, we show that PRMT5 is highly expressed in PDAC and CRC. Overexpression of PRMT5 promoted cancer progression, while shRNA knockdown showed an opposite effect. Using an innovative AlphaLISA high throughput screen, we discovered a lead compound, PR5-LL-CM01, which exhibited robust tumor inhibition effects in both cancers. An in silico structure prediction suggested that PR5-LL-CM01 inhibits PRMT5 by binding with its active pocket. Importantly, PR5-LL-CM01 showed higher anti-tumor efficacy than the commercial PRMT5 inhibitor, EPZ015666, in both PDAC and CRC. This study clearly highlights the significant potential of PRMT5 as a therapeutic target in PDAC and CRC, and establishes PR5-LL-CM01 as a promising basis for new drug development in the future.

APOBEC-catalyzed cytosine-to-uracil deamination of single-stranded DNA (ssDNA) has beneficial functions in immunity and detrimental effects in cancer. APOBEC enzymes have intrinsic dinucleotide specificities that impart hallmark mutation signatures. Although numerous structures have been solved, mechanisms for global ssDNA recognition and local target-sequence selection remain unclear. Here we report crystal structures of human APOBEC3A and a chimera of human APOBEC3B and APOBEC3A bound to ssDNA at 3.1-Å and 1.7-Å resolution, respectively. These structures reveal a U-shaped DNA conformation, with the specificity-conferring -1 thymine flipped out and the target cytosine inserted deep into the zinc-coordinating active site pocket. The -1 thymine base fits into a groove between flexible loops and makes direct hydrogen bonds with the protein, accounting for the strong 5'-TC preference. These findings explain both conserved and unique properties among APOBEC family members, and they provide a basis for the rational design of inhibitors to impede the evolvability of viruses and tumors., Competing Interests: RSH and DAH are co-founders, shareholders, and consultants of ApoGen Biotechnologies Inc. HA and REA are consultants for ApoGen Biotechnologies Inc. REA is a co-founder of Actavalon Inc. The other authors have no competing financial interests to declare.

Terminal uridyltransferases (TUTases) execute 3' RNA uridylation across protists, fungi, metazoan and plant species. Uridylation plays a particularly prominent role in RNA processing pathways of kinetoplastid protists typified by the causative agent of African sleeping sickness, Trypanosoma brucei In mitochondria of this pathogen, most mRNAs are internally modified by U-insertion/deletion editing while guide RNAs and rRNAs are U-tailed. The founding member of TUTase family, RNA editing TUTase 1 (RET1), functions as a subunit of the 3' processome in uridylation of gRNA precursors and mature guide RNAs. Along with KPAP1 poly(A) polymerase, RET1 also participates in mRNA translational activation. RET1 is divergent from human TUTases and is essential for parasite viability in the mammalian host and the insect vector. Given its robust in vitro activity, RET1 represents an attractive target for trypanocide development. Here, we report high-resolution crystal structures of the RET1 catalytic core alone and in complex with UTP analogs. These structures reveal a tight docking of the conserved nucleotidyl transferase bi-domain module with a RET1-specific C2H2 zinc finger and RNA recognition (RRM) domains. Furthermore, we define RET1 region required for incorporation into the 3' processome, determinants for RNA binding, subunit oligomerization and processive UTP incorporation, and predict druggable pockets., (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Objective: Discordance between insulin-like growth factor-1 (IGF-1) and growth hormone (GH) levels is an important problem in the follow-up of patients diagnosed with acromegaly. Our aims were to evaluate the discordance between IGF-1 and GH levels and compare the performance of different cut-off levels for the nadir in GH (GHn) in acromegalic patients., Methods: The study included 63 acromegalic patients in a follow-up at a tertiary care university hospital facility. Levels of IGF-1, IGF binding protein-3 (IGFBP-3), and GH were investigated. The baseline GH and GHn levels were evaluated after an oral glucose tolerance test (cut-offs of 0.4 and 1 ng/mL, respectively). The discordance rates between GHn and IGF-1 levels, and IGF-1/IGFBP-3 ratios were determined., Results: We first adopted a GHn cut-off value of 1 ng/mL and found that 27 patients (42.9%) exhibited biochemical remission (BR) (IGF-1 <95 th percentile, GH <1), and 25 patients (39.7%) had no BR (NBR) (IGF-1 ≥95 th percentile, GH >1). Discordance in the presence of normal IGF-1 and nonsuppressed GH (DC1) occurred in 2 of 63 (3.2%) patients; discordance in the presence of high IGF-1 and suppressed GH (DC2) occurred in 9 of 63 (14.3%) patients. If the GHn cut-off value adopted was 0.4 ng/mL, the distributions were 17 of 63 (27.0%) patients in BR, 29 of 63 (46.0%) patients in NBR, 12 of 63 (19.0%) in DC1, and 5 of 63 (7.9%) patients in DC2. If only the baseline GH values were considered, the distributions were very similar to those with a GHn cut-off value of 0.4 ng/mL. The IGF-1/IGFBP-3 ratio was lowest in the BR group., Conclusion: Adopting a GHn cut-off value of 0.4 ng/mL did not increase the test performance compared with baseline GH only. In contrast, in the follow-up of acromegalic patients, the IGF-1/IGFBP-3 ratio might be a useful measurement when discordance between IGF-1 and GH levels occurs. We propose that these values be considered in clinical practice., Abbreviations: BR = biochemical remission DC1 = discordance group 1 DC2 = discordance group 2 DM = diabetes mellitus GH = growth hormone GHn = nadir in GH IGF-1 = insulin-like growth factor-1 IGFBP-3 = IGF binding protein-3 LAR = long-acting release NBR = not in biochemical remission OGTT = oral glucose tolerance test.

Aim: The aim of this study was to investigate the clinical importance of incidental focal or diffuse fluorine-18 fluorodeoxyglucose (F-FDG) uptake in the thyroid gland on positron emission tomography (PET)/computed tomography (CT) and to evaluate the additive value of thyroid ultrasonography (US) in defining the malignancy potential of thyroid incidentalomas., Patients and Methods: A total of 1450 patients, who had undergone a PET/CT scan for staging or restaging of various malignancies, were screened retrospectively and 52 (3.6%) patients with focal or diffuse F-FDG uptake in the thyroid gland on PET/CT were enrolled in the study. None of the patients had any history of thyroid diseases. Thyroid US with elastography for a thyroid nodule was performed for all the patients cross-sectionally. Thyroid fine-needle aspiration biopsy (FNAB) was also applied at the same time as the thyroid US to 34 patients with a nodule(s) 10 mm or more in diameter or less than 10 mm, but with malignancy potential ultrasonographically. The cytology results were compared with the thyroid US and F-FDG PET/CT findings., Results: Although 39 patients had focal (group 1) F-FDG uptake in the thyroid gland, the remaining 13 patients had diffuse (group 2) uptake. In group 1, FNAB was performed in 32 patients. In 10 of 32 (31%) patients, FNAB results were concordant with malignant cytology (seven primary thyroid malignancy and three metastasis to thyroid). In group 2, in one of two patients who had undergone FNAB, malignant cytology (metastasis to thyroid) was detected. Although the difference between the maximum standardized uptake value (SUVmax) of malignant and benign nodules was statistically significant (10.2±8.9 vs. 5.6±3.0, P=0.013), the difference between the nodule sizes was not statistically significant (20.0±7.3 vs. 16.7±7.4, P=0.923). The presence of suspicious US findings and a high elastography score (≥4) were also statistically significant (P<0.001 and P=0.035, respectively). In the receiver-operator characteristic analysis, a 5.3 cut-off SUVmax was calculated with 82% sensitivity and 65% specificity for predicting malignant cytology., Conclusion: Focal F-FDG uptake was associated with a higher prevalence of malignant thyroid nodule compared with diffuse F-FDG uptake. In particular, if a focal thyroid incidentaloma with high SUVmax (>5.5), suspicious US findings, and a high elastography score (≥4) is detected, a pathological diagnosis, either by histology or by cytology examination, should be made, especially when the patient has a long life expectancy.

Background: The optimal therapeutic choice for Graves' hyperthyroidism in the presence of moderate-severe Graves' orbitopathy (GO) remains controversial., Objectives: We aimed to compare GO course in patients with moderate-severe GO treated with early total thyroidectomy (TTx) versus antithyroid drug (ATD) regimens, in a prospective, randomized manner., Methods: Forty-two patients with moderate-severe GO were enrolled. A total of 4.5 g of pulse corticosteroids were given intravenously to all patients before randomization. Patients in the first group were given TTx, whereas patients in the second group were treated with ATDs. TSH was kept between 0.4 and 1 mIU/l. The clinical course of GO was evaluated with proptosis, lid aperture, clinical activity score (CAS), and diplopia., Results: Eighteen and 24 patients were randomized to the TTx and ATD groups, respectively. Thyroid autoantibodies decreased significantly, and there were significant improvements in proptosis, lid aperture, and CAS in the TTx group. While in the ATD group the decrement in thyroid autoantibodies was not significant, there were significant improvements in proptosis and CAS. When the TTx group was compared with the ATD group, anti-TPO, anti-Tg, and TSH-receptor antibodies were significantly decreased in the TTx group (p < 0.01), but there was no significant difference with respect to proptosis, lid aperture, CAS, and diplopia between the two groups during a median (min.-max.) follow-up period of 60 months (36-72)., Conclusion: Although no definitive conclusions could be drawn from the study, mainly due to limited power, early TTx and the ATD treatment regimens, followed by intravenous pulse corticosteroid therapy, seemed to be equally effective on the course of GO in this relatively small group of patients with moderate-severe GO during a median (min.-max.) follow-up period of 60 months (36-72).

Background/aim: The aim of this study was to determine the effects of resveratrol on the alterations of cavernosal eNOS and LOX-1 mRNA expression in the hypercholesterolemic condition., Materials and Methods: Twenty-one New Zealand white male rabbits were separated into three groups. Rabbits were fed with a normal dietary intake for the control group and a 2% cholesterol diet for the hypercholesterolemia and resveratrol groups for 6 weeks. Resveratrol 4 mg/kg daily was administered for the resveratrol group. Cavernosal LOX-1 and eNOS mRNA expressions were determined with real-time RT-PCR in all groups. The statistical analysis was performed with the Kruskal-Wallis and Mann-Whitney U tests., Results: We found no difference between mean LOX-1 mRNA expression levels in the three groups. Lower mean eNOS mRNA expression level was determined in the hypercholesterolemia group when compared with the control group (P = 0.011). Mean eNOS mRNA expression level in the resveratrol group was similar to that in the control group but significantly higher than that in the hypercholesterolemia group (P < 0.001)., Conclusion: This preliminary study demonstrates the beneficial effects of resveratrol on cavernosal eNOS expression. The presence of cavernosal LOX-1 expression was also shown for the first time. Resveratrol may be an alternative option in hypercholesterolemic erectile dysfunction with further studies supporting its beneficial effects on the corpus cavernosum.

Purpose: Patients receiving treatment for benign prostate hyperplasia may have persistent storage symptoms. There has been increasing debate on the precision and accuracy of the International Prostate Symptom Score questionnaires over other questionnaires in evaluating all the complaints of lower urinary tract symptoms (LUTS). The aim of this study was to perform the validity and reliability analysis of the Turkish version of the Internatinal Consultation on Incontinence Questionnaire-Male LUTS (ICIQ-MLUTS)., Methods: Linguistic validation was studied (i.e., translation and back translation). Intelligibility was completed between October 2013 and November 2013. Data was collected between November 2013 and March 2014. The stability and reliability of the form were measured with the Cronbach test., Results: In total, 117 male patients were included in the study. At the first visit, the mean age of the patients was 59 years (range, 18-84 years). For reliability, the Cronbach alpha value was 0.798, demonstrating the internal consistency of the form (r>0.7). The internal consistency of each question was examined separately and found to be over 0.7. For the evaluation of test-retest reliability, the test was administered to 116 patients for a second time with an interval of 2-4 weeks. The first and second test scores for each question were found to be correlated (r=0.741)., Conclusions: ICIQ-MLUTS is a new questionnaire, which can be used for evaluating male LUTS in Turkey. We believe that the Turkish version of the ICIQ-MLUTS is an important breakthrough in our country.

Purpose: To determine the proportion of patients with undetected symptoms of overactive bladder by using the overactive bladder-validated 8 (OAB-V8) screening questionnaire and investigate these symptoms were undetected in female patients who were hospitalized., Methods: We invited 2,250 female patients hospitalized in the Aegean region of Turkey to answer a self-administered questionnaire. The questionnaire included questions on evidence of lower urinary tract symptoms (OAB-V8), relevant medical history, and demographic data. Patients with a total OAB-V8 score≥8 were defined as having OAB symptoms., Results: The proportion of patients with OAB symptoms in this study was 40.6%. Nearly 57% of the patients with OAB symptoms had not been previously admitted to any hospital for lower urinary tract symptoms (LUTS). The two most common reasons why women with OAB symptoms did not admit themselves to a hospital because of LUTS were as follows: "I did not think I had a disease" and "The symptoms did not bother me," with a response rate of 74.7%. The mean OAB-V8 scores of the patients with these two responses were significantly lower than those of the other patients (P<0.001)., Conclusions: This is the first study to demonstrate a significant proportion of women with undetected OAB symptoms. The main reasons the women did not admit themselves to a hospital were their unawareness of the disease and because the LUTS were not bothersome. Public awareness programs on this disease may resolve this problem.

This paper aims to provide a full understanding of the sludge reduction mechanisms in the oxic-settling-anaerobic (OSA) process and presents an evaluation of the sludge reduction efficiencies and sludge characteristics in this process compared to the conventional activated sludge process. Fifty-eight percent reduction in observed yield in the OSA process was achieved compared to the control system at the end of the operational period with no deterioration of effluent quality. The settleability of sludge in the OSA process was also found to be better than that of the control system in terms of sludge volume index. In long-term operation, capillary suction time and specific resistance to filtration values confirmed that the OSA process showed good filterability characteristics. The results of batch experiments showed that higher endogenous respiration in the systems might lead to lower sludge production and that energy uncoupling had only a limited impact on sludge reduction.

Introduction: Oxidative stress dependent-decrease in nitric oxide (NO) bioavailability plays an integral role in hypercholesterolemia-induced erectile dysfunction (ED). Resveratrol has been demonstrated to exert beneficial effects against oxidative stress and improve NO bioavailability., Aim: The protective and restorative potentials of resveratrol on endothelium-dependent relaxations were evaluated in hypercholesterolemic rabbit corpus cavernosum (CC)., Methods: Hypercholesterolemia was induced by administering 2% cholesterol diet (CD) (w/w) to the rabbits for 6 weeks. Two different protocols were applied to test the effects of resveratrol on hypercholesterolemia-induced ED. In Protocol-1 (P1), resveratrol was administrated to the rabbits simultaneously with CD in order to evaluate the protective effect, and for Protocol-2 (P2), resveratrol was administrated for 6 weeks after termination of CD in order to evaluate the restorative effect., Main Outcome Measures: Endothelium-dependent relaxations of CC were evaluated by using organ bath studies. In order to elucidate the possible molecular mechanisms, we measured endothelial NO synthase (eNOS) and phosphovasodilator-stimulated phosphoprotein (VASP) expressions and activations, NADPH oxidase, superoxide dismutase (SOD), and catalase (CAT) and glutathione peroxidase (GPx) activity in cavernosal tissues obtained at the end of the study., Results: Resveratrol showed an improvement in the endothelium-dependent relaxation responses in vitro. We demonstrated significantly increased activatory-phosphorylation (p[S1177]-eNOS) and activated phosphovasodilator-stimulated phosphoprotein (phospho-VASP) levels, but reduced phosphorylation (p[T495]-eNOS) of eNOS and NADPH oxidase activity in the resveratrol-administered HC animals compared with hypercholesterolemic control rabbits in the P1. In the P2, resveratrol exhibited an improvement in endothelium-dependent relaxation responses and more pronounced effects on eNOS activation., Conclusion: Resveratrol administration, either simultaneously with HC diet or after HC, caused an improvement in the endothelium-dependent relaxation responses in the CC, suggesting its potential in both protective and restorative purposes in hypercholesterolemic rabbit CC., (Copyright © 2016 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.)

APOBEC3 family DNA cytosine deaminases provide overlapping defenses against pathogen infections. However, most viruses have elaborate evasion mechanisms such as the HIV-1 Vif protein, which subverts cellular CBF-β and a polyubiquitin ligase complex to neutralize these enzymes. Despite advances in APOBEC3 and Vif biology, a full understanding of this direct host-pathogen conflict has been elusive. We combine virus adaptation and computational studies to interrogate the APOBEC3F-Vif interface and build a robust structural model. A recurring compensatory amino acid substitution from adaptation experiments provided an initial docking constraint, and microsecond molecular dynamic simulations optimized interface contacts. Virus infectivity experiments validated a long-lasting electrostatic interaction between APOBEC3F E289 and HIV-1 Vif R15. Taken together with mutagenesis results, we propose a wobble model to explain how HIV-1 Vif has evolved to bind different APOBEC3 enzymes and, more generally, how pathogens may evolve to escape innate host defenses., (Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.)

Epithelioid hemangioendothelioma is a rare vascular tumor mostly seen in liver, lung, and bone. Involvement of the adrenal gland has not been reported previously. Here, we report the first case of adrenal malignant epithelioid hemangioendothelioma in an 81-year-old man who was successfully treated by laparoscopic excision., (Copyright © 2015 Elsevier Inc. All rights reserved.)

It is widely accepted that protein receptors exist as an ensemble of conformations in solution. How best to incorporate receptor flexibility into virtual screening protocols used for drug discovery remains a significant challenge. Here, stepwise methodologies are described to generate and select relevant protein conformations for virtual screening in the context of the relaxed complex scheme (RCS), to design small molecule libraries for docking, and to perform statistical analyses on the virtual screening results. Methods include equidistant spacing, RMSD-based clustering, and QR factorization protocols for ensemble generation and ROC analysis for ensemble selection.