Peptide-conjugated Nanoparticle Platforms for Targeted Delivery, Imaging, and Biosensing Applications

Peptides have become an indispensable tool in engineering of multifunctional nanostructure platforms for biomedical applications such as targeted drug and gene delivery, imaging and biosensing. They can be covalently incorporated into a variety of nanoparticles (NPs) including polymers, metallic nanoparticles, and others. Using different bioconjugation techniques, multifunctional peptide-modified NPs can be formulated to produce therapeutical and diagnostic platforms offering high specificity, lower toxicity, biocompatibility, and stimuli responsive behavior. Targeting peptides can direct the nanoparticles into specific tissues for targeted drug and gene delivery and imaging applications due to their specificity towards certain receptors. Furthermore, due to their stimuli-responsive features, they can offer controlled release of therapeutics into desired sites of disease. In addition, peptide-based biosensors and imaging agents can provide non-invasive detection and monitoring of diseases including cancer, infectious diseases, and neurological disorders. In this review, we covered the design and formulation of recent peptide-based NP platforms, as well as their utilization in in vitro and in vivo applications such as targeted drug and gene delivery, targeting, sensing, and imaging applications. In the end, we provided the future outlook to design new peptide conjugated nanomaterials for biomedical applications.

Computational insights on the hydride and proton transfer mechanisms of L-proline dehydrogenase

L-Proline dehydrogenase (ProDH) is a flavin-dependent oxidoreductase, which catalyzes the oxidation of L-proline to (S)-1-pyrroline-5-carboxylate. Based on the experimental studies, a stepwise proton and hydride transfer mechanism is supported. According to this mechanism, the amino group of L-proline is deprotonated by a nearby Lys residue, which is followed by the hydride transfer process from C5 position of L-proline to N5 position of isoalloxazine ring of FAD. It was concluded that the hydride transfer step is rate limiting in the reductive half-reaction, however, in the overall reaction, the oxidation of FAD is the rate limiting step. In this study, we performed a computational mechanistic investigation based on ONIOM method to elucidate the mechanism of the reductive half-reaction corresponding to the oxidation of L-proline into iminoproline. Our calculations support the stepwise mechanism in which the deprotonation occurs initially as a fast step as result of a proton transfer from L-proline to the Lys residue. Subsequently, a hydride ion transfers from L-proline to FAD with a higher activation barrier. The enzyme-product complex showed a strong interaction between reduced FAD and iminoproline, which might help to explain why a step in the oxidative half-reaction is rate-limiting.

The safety and efficacy of first-line atezolizumab plus bevacizumab in patients with unresectable hepatocellular carcinoma: A multicenter real-world study from Turkey

The aim of the study was to evaluate the real-world clinical outcomes of atezolizumab and bevacizumab (Atez/Bev) as the initial therapy for advanced hepatocellular carcinoma (HCC). We retrospectively analyzed 65 patients treated with Atez/Bev for advanced HCC from 22 institutions in Turkey between September 2020 and March 2023. Responses were evaluated by RECIST v1.1 criteria. The median progression-free survival (PFS) and overall survival (OS) were calculated using the Kaplan-Meier method. Cox regression model was employed to conduct multivariate analyses. The median age was 65 (range, 22-89) years, and 83.1% of the patients were male. A total of 1.5% achieved a complete response, 35.4% had a partial response, 36.9% had stable disease, and 26.2% had progressive disease. The disease control rate was 73.8% and associated with alpha-fetoprotein levels at diagnosis and concomitant antibiotic use. The incidence rates of any grade and grade ≥ 3 adverse events were 29.2% and 10.7%, respectively. At a median follow-up of 11.3 (3.4-33.3) months, the median PFS and OS were 5.1 (95% CI: 3-7.3) and 18.1 (95% CI: 6.2-29.9) months, respectively. In univariate analyses, ECOG-PS ≥ 1 (relative to 0), Child-Pugh class B (relative to A), neutrophil-to-lymphocyte ratio (NLR) > 2.9 (relative to ≤ 2.9), and concomitant antibiotic use significantly increased the overall risk of mortality. Multivariate analysis revealed that ECOG-PS ≥ 1 (HR: 2.69, P = .02), NLR > 2.9 (HR: 2.94, P = .017), and concomitant antibiotic use (HR: 4.18, P = .003) were independent predictors of OS. Atez/Bev is an effective and safe first-line therapy for advanced-stage HCC in a real-world setting. The survival benefit was especially promising in patients with a ECOG-PS score of 0, Child-Pugh class A, lower NLR, and patients who were not exposed to antibiotics during the treatment.

Computational Insights on the Hydride and Proton Transfer Mechanisms of D-Arginine Dehydrogenase

D-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is an amine oxidase which catalyzes the conversion of D-arginine into iminoarginine. It contains a non-covalent FAD cofactor that is involved in the oxidation mechanism. Based on substrate, solvent, and multiple kinetic isotope effects studies, a stepwise hydride transfer mechanism is proposed. It was shown that D-arginine binds to the active site of enzyme as α-amino group protonated, and it is deprotonated before a hydride ion is transferred from its α-C to FAD. Based on a mutagenesis study, it was concluded that a water molecule is the most likely catalytic base responsible from the deprotonation of α-amino group. In this study, we formulated computational models based on ONIOM method to elucidate the oxidation mechanism of D-arginine into iminoarginine using the crystal structure of enzyme complexed with iminoarginine. The calculations showed that Arg222, Arg305, Tyr249, Glu87, His 48, and two active site water molecules play key roles in binding and catalysis. Model systems showed that the deprotonation step occurs prior to hydride transfer step, and active site water molecule(s) may have participated in the deprotonation process.

Computational Mechanistic Study of l-Aspartate Oxidase by ONIOM Method

l-Aspartate oxidase (Laspo) is responsible for the oxidation of l-aspartate into iminoaspartate using flavin as a cofactor. During this process flavin is reduced, and it can be reoxidized by either molecular oxygen or fumarate. The overall fold and the catalytic residues of Laspo are similar to succinate dehydrogenase and fumarate reductase. On the basis of deuterium kinetic isotope effects as well as other kinetic and structural data, it is proposed that the enzyme can catalyze the oxidation of l-aspartate through a mechanism similar to amino acid oxidases. It is suggested that a proton is removed from the α-amino group, while a hydride is transferred from C2 to flavin. It is also suggested that the hydride transfer is a rate-limiting step. However, there is still an ambiguity about the stepwise or concerted mechanism of hydride- and proton-transfer steps. In this study, we formulated some computational models to study the hydride-transfer mechanism using the crystal structure of Escherichia colil-aspartate oxidase in complexes with succinate. The calculations involved our own N-layered integrated molecular orbital and molecular mechanics method, and we evaluated the geometry and energetics of the hydride/proton-transfer processes while probing the roles of active site residues. Based on the calculations, it is concluded that proton- and hydride-transfer steps are decoupled, and a stepwise mechanism might be operative as opposed to the concerted one.

Effects of age and comorbidities on prognosis and mortality in geriatric patient groups in ıntensive Care

Backround

Treatment of geriatric intensive care patients is tiring and difficult for intensive care physicians due to comorbidities, accompanying acute illnesses and vulnerabilities.

Aim

The aim of our study was to determine other factors affecting mortality and morbidity with age in geriatric intensive care patients.

Patients and Methods

A total of 937 geriatric intensive care patients were divided into three groups as young-old (65-74 years), middle-old (75-84 years), and oldest-old (85 years and more). Demographic characteristics such as age, gender, and comorbid diseases (oncological malignancy, chronic renal failure, sepsis, chronic anemia, hypertension, diabetes mellitus, chronic obstructive pulmonary disease, pulmonary embolism) were recorded. The number of patients who needed a mechanical ventilator, developed decubit ulcers, underwent percutaneous tracheostomy, and renal replacement therapy were recorded. In addition, the number of central venous catheter insertions for patients, Acute Physiology and Chronic Health Evaluation II scores (APACHE II), hospitalization days, and mortality rates were recorded and compared.

Results

In the comparison between the groups in terms of gender, in the 65-74 years' age group, male gender was higher, while in the age group of 85 years and more, the female gender was found to be statistically higher. Among comorbid diseases, the rate of oncological malignancy was found to be statistically significantly lower in patients aged 85 years and more. Comparing the APACHE II scores of the patients as per the groups, scores were found to be statistically significantly higher in the oldest-old group. APACHE II Score, central venous catheter application, chronic obstructive pulmonary disease, chronic renal failure, sepsis, oncological malignancy, and renal replacement therapy were shown to be statistically significant as factors affecting death. The factors affecting the survival or hospitalization time of the patients of decubit ulcer, mechanical ventilator, percutaneous tracheostomy, chronic obstructive pulmonary disease, Sepsis, APACHE II Score, and age were shown to be statistically significant.

Conclusion

Our study showed that not only age has an effect on mortality and morbidity in geriatric intensive care patients but also comorbidities and intensive care treatments of the patients are also effective in this process.

Prevalence and predictors of psychological assistance services for older individuals in Turkish society

Background/aim

Due to the high contribution of psychological problems to the decline in the comfortable lifestyle of the older individuals, determining the factors that affect individuals' receiving psychological services and searching for solutions based on these factors is one of the primary concerns of national and international decision-makers. This study aimed to identify the factors that affect older individuals' access to psychological assistance services in Turkey.

Methods

In this study, the Turkish Health Research micro dataset, which was conducted by the Turkish Statistical Institute (TURKSTAT) in 2016 and 2019, was employed. In this dataset, the data of 7,252 older individuals were analyzed. Using binary logistic analysis, the factors that are effective for obtaining psychological assistance for the older individuals were identified.

Results

According to the results of the analysis, factors such as gender, education, general health status, disease status, payment of health expenditures, and body mass index affected older individuals who received psychological assistance.

Conclusion

In recent years, there has been a rise in the availability of psychological assistance services for the older individuals. By identifying factors that increase the likelihood of receiving psychological assistance services, this study is expected to contribute to the creation and regulation of psychological assistance services to prevent possible psychological problems that may occur in old age, minimize the problems experienced by individuals, and promote a more comfortable lifestyle.

Predictors of left ventricular ejection function decline in young patients with ST-segment elevation myocardial infarction

OBJECTIVE:

A decrease in the left ventricular ejection fraction (≤40%) in the setting of ST-segment elevation myocardial infarction is a significant predictor of mortality in the young ST-segment elevation myocardial infarction population. In this study, we aimed to investigate the predictors of left ventricular ejection fraction reduction and evaluate the long-term mortality rates in young ST-segment elevation myocardial infarction patients with or without decreased left ventricular ejection fraction.

METHODS:

We enrolled retrospectively 411 consecutive ST-segment elevation myocardial infarction patients aged 45 years or below who underwent primary percutaneous coronary intervention. Young ST-segment elevation myocardial infarction patients were divided into two groups according to their left ventricular ejection fraction (≤40%, n=72 and >40%, n=339), which were compared with each other.

RESULTS:

Statin use, white blood cell count, C-reactive protein, peak creatine kinase-MB, prolonged ischemia time, left anterior descending artery-related infarction, proximally/ostial located lesion, and no-reflow were independently associated with low left ventricular ejection fraction. Additionally, long-term mortality was considerably higher in the left ventricular ejection fraction ≤40% group than those in the left ventricular ejection fraction>40% group (18.1% versus 2.4%; p<0.001).

CONCLUSIONS:

In young ST-segment elevation myocardial infarction patients, lesion properties (left anterior descending lesion, proximally located lesion), no-reflow, and prolonged ischemia time appeared to be important determinants for the left ventricular ejection fraction decline, rather than coronary disease severity or demographic and hematological parameters. Statin use may be preventive in the development of left ventricular ejection fraction decline in young ST-segment elevation myocardial infarction patients.

Antiprotozoal activity of different Xenorhabdus and Photorhabdus bacterial secondary metabolites and identification of bioactive compounds using the easyPACId approach

Natural products have been proven to be important starting points for the development of new drugs. Bacteria in the genera Photorhabdus and Xenorhabdus produce antimicrobial compounds as secondary metabolites to compete with other organisms. Our study is the first comprehensive study screening the anti-protozoal activity of supernatants containing secondary metabolites produced by 5 Photorhabdus and 22 Xenorhabdus species against human parasitic protozoa, Acanthamoeba castellanii, Entamoeba histolytica, Trichomonas vaginalis, Leishmania tropica and Trypanosoma cruzi, and the identification of novel bioactive antiprotozoal compounds using the easyPACId approach (easy Promoter Activated Compound Identification) method. Though not in all species, both bacterial genera produce antiprotozoal compounds effective on human pathogenic protozoa. The promoter exchange mutants revealed that antiprotozoal bioactive compounds produced by Xenorhabdus bacteria were fabclavines, xenocoumacins, xenorhabdins and PAX peptides. Among the bacteria assessed, only P. namnaoensis appears to have acquired amoebicidal property which is effective on E. histolytica trophozoites. These discovered antiprotozoal compounds might serve as starting points for the development of alternative and novel pharmaceutical agents against human parasitic protozoa in the future.

The professional seniority affects the clinical application of total neoadjuvant therapy for locally advanced rectal cancer

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Background: Total neoadjuvant therapy (TNT) integrates whole planned systemic chemotherapy within standard neoadjuvant protocols either before or after radiotherapy for locally advanced rectal cancer (LARC). Preference of neoadjuvant treatment type may vary among the medical oncologists. This study aimed to evaluate impact of professional seniority on TNT approach for LARC. Methods: A 20-item questionnaire was presented to medical oncologists as a cross-sectional survey during a national oncology congress via tablets. The evaluation was stratified by position; early-career oncologists (ECOs) and seniors. 2 questions were about experience regarding rectal cancer treatment. 5 questions were about physicians’ choice of screening and treatment in LARC and the factors affecting their treatment choices. 13 questions were about TNT approach (the sequencing of treatment, denominators of sequencing, chemotherapy choice, treatment response evaluation, operation preferences, adjuvant treatment and its denominators). Results: 189 medical oncologists were included (62.4% (n = 118) ECOs). An endorectal ultrasound was significantly preferred by the seniors (p = 0.039) in addition to conventional staging tools. 65.6% (n = 124) of the participants preferred long-course chemoradiation as their favorite neoadjuvant treatment approach. External sphincter invasion, threatened circumferential resection margin (CRM) and clinical stage were the most common denominators of TNT regardless of experience. ECOs favored short-course RT (p = 0.009) while the seniors chose long-course chemoradiotherapy (p = 0.041) as the index step of TNT. 57% (n = 108) of the physicians preferred to monitor treatment response for TNT at 8-weeks periods. Almost half of the participants (47.1%) reported pathological complete response (pCR) rates between 25-50% with TNT in their clinical practice. The physicians who prefer to give adjuvant treatment after completion of TNT make individualized decisions when surgical pathology reveals non-pCR, CRM and lymph node involvement. There was a significant difference between the ECOs and seniors (63.6 vs 45.1%, p = 0.013) in terms of choosing the adjuvant chemotherapy based on CRM positivity. Majority of the senior medical oncologists (88%) and ECOs (76.3%) agree that TNT should be the standardized neoadjuvant treatment approach for LARC. The preferred adjuvant chemotherapy after TNT was capecitabine-oxaliplatin (51.1%) or capecitabine alone (46%). Conclusions: TNT for LARC is well accepted among the medical oncologists and the professional seniority seems to affect its clinical application.

The prognostic impact of intramural invasion in patients undergoing surgery for non-metastatic colon cancer

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Background: The invasion of extramural veins is an independent predictor of poor outcome in colorectal cancer whereas the significance of intramural component of venous as well as lymphatic and perineural invasion is less clear. We aimed to search the prognostic impact of these invasion patterns and their association with various clinicopathological variables. Methods: All patients undergone surgery for colon cancer between December 2014 and December 2020 were analyzed retrospectively and patients with stage II and III disease were enrolled. The patients were divided into four categories as no invasion, intramural invasion only, extramural invasion only or both (intramural and extramural) for vascular invasion (VI), lymphatic invasion (LI) and perineural invasion (PNI). 5-year disease-free (DFS) and overall-survival (OS) were the primary outcomes. Results: 626 patients were included (47.1% stage II patients). There was no significant difference between the presence of ‘intramural only’ venous (DFS, 87.2 vs 88.4% p = 0.84; OS, 88.3 vs 90.7% p = 0.90), lymphatic (DFS, 89.5 vs 85.1%, p = 0.13; OS, 89.5 vs 89.4%, p = 0.9) and perineural invasion (DFS, 89.1 vs 80.9%, p = 0.26; OS, 90.6 vs 84.8%, p = 0.12) compared to ‘no invasion’ in terms of DFS and OS. Invasion of both intramural and extramural compartments for each of these parameters demonstrated poor survival. Presence of exclusively extramural venous and perineural invasion without intramural invasion had adverse effect on DFS (87.2 vs 78.7%, p = 0.036, 89.1 vs 80.9%, p = 0.044, respectively) but not OS (88.3 vs 89.3%, p = 0.78, 90.6 vs 83.8%, p = 0.215, respectively). Tumor sidedness did not have impact on the depth and rate of lymphatic invasion however right-sided and dMMR tumors exhibited less venous and perineural invasion (24.7 vs 33.9% p = 0.007; 34.5 vs 41.5% p = 0.034 and 13.5 vs 33.5% p < 0.001; 25 vs 41.4% p = 0.004, respectively). The ratio of stage III patients with venous, lymphatic and perineural invasion was consistently higher when compared with stage II patients (for LI 69.8 vs 39.7% vs p < 0.001; for VI 36.9 vs 22.7% p < 0.001; for PNI 51.4 vs 24.4% p < 0.001). Low grade tumors exhibited less LI and PNI when compared with high grade tumors (for LI 53.2 vs. 71.3% p = 0.004, for PNI 37.1 vs. 48.3% p = 0.031) however there was no significant difference for venous invasion rates among two groups. Conclusions: Presence of merely intramural component of invasion may not be considered a synonym for lymphovascular invasion which is supposed to be a high-risk factor for systemic recurrence.

Computational Analysis of the Inhibition Mechanism of NOTUM by the ONIOM Method

Notum is a member of serine hydrolyses that cleaves the palmitoleate moiety from Wingless-related integration site (Wnt) ligands. This enzyme plays crucial functions through modulating the Wnt signaling pathway. Inhibition of Notum carries therapeutic effects against a number of maladies including osteoporosis, cancer, and Alzheimer's disease. Recently, a class of irreversible inhibitors based on esters of 4-(indolin-1-yl)-4-oxobutanoic acid have been reported. Using the crystal structures of enzyme-4-(indolin-1-yl)-4-oxobutanoate adduct and 4-(indolin-1-yl)-4-oxobutanoic acid-enzyme complex, we studied computationally the proposed inhibition mechanism using model systems based on the own n-layered integrated molecular orbital and molecular mechanics (ONIOM) method. In the first place, model systems were formulated to investigate the transesterification between the catalytic serine residue, Ser-232, and the methyl ester of 4-(indolin-1-yl)-4-oxobutanoate. In the second place, the hydrolysis mechanism of the resultant enzyme-inhibitor adduct was studied. The energetics of these steps were analyzed using a density functional theory functional in the ONIOM method. In addition, the roles of active-site residues during these steps were highlighted. It was found that the hydrolysis of the covalent adduct is highly endergonic corroborating the irreversible inhibition mechanism. These results will shed light not only on the inhibition mechanism but also on the catalytic mechanism.

Computational Analysis of Histone Deacetylase 10 Mechanism by the ONIOM Method: A Complementary Approach to X-ray and Kinetics Studies

Histone deacetylase 10 (HDAC 10) catalyzes deacetylation of N⁸-acetylspermidine into spermidine in the cytosolic region of eukaryotic cells. Inhibition of HDAC 10 has clinical importance in certain types of cancers. Recently, X-ray crystal structures corresponding to the substrate-bound, tetrahedral intermediate-bound, and product-bound enzymes have been resolved using variant forms of humanized HDAC 10. Based on these structures, it was proposed that Y307 residue polarizes the carbonyl of the acetyl group in N⁸-acetylspermidine together with a zinc atom, which is coordinated by D174, H176, D267, and an H₂O molecule. The H₂O molecule undergoes nucleophilic addition to the carbonyl carbon of N⁸-acetylspermidine to form the tetrahedral intermediate. During this process, it is suggested that H136 acts as a general base to deprotonate the H₂O molecule. It is further proposed that the protonation of the amide N atom of the tetrahedral intermediate by H137 causes the deacetylation forming the final products, spermidine and acetate ion. In this study, computational models based on the ONIOM method were employed to study the proposed mechanism for the two steps of the deacetylation process based on the crystal structure of the substrate-bound enzyme. The energy profiles of each step as well as the roles of the active site residues were investigated for the catalysis. The calculated activation barrier is in good agreement with the reported k_cat value.

Association between RS Time in Electrocardiogram and Right Ventricular Functions in Patients with Chronic Obstructive Pulmonary Disease

OBJECTIVE

The occurrence of right ventricular (RV) dysfunction in chronic obstructive pulmonary disease (COPD) results in an increased risk of mortality. We aimed to study the diagnostic value of RS time in the recognition of COPD patients with RV dysfunction.

METHODS

120 consecutive COPD patients were divided into two groups, patients with and without RV dysfunction, and compared them in terms of parameters including RS time. RS time was defined as the longest interval from the beginning of the QRS complex to the nadir of the S- or S'-wave in the inferolateral leads on an electrocardiogram.

RESULTS

RV dysfunction was observed in 36% of consecutive COPD patients with a mean age of 63.4 ± 9.8 years (83.3% male) and a mean forced expiratory volume in 1 s of 1.51 ± 0.62 lt. The heart rate, right QRS axis deviation frequency, S1S2S3 pattern frequency, and RS time (p < 0.01) were significantly higher in the patients with RV dysfunction than in those without. Body surface area, heart rate, and RS time (p < 0.001) were independent predictors of an RV dysfunction. An ROC analysis showed that the best RS time cutoff value for the prediction of RV dysfunction was 60 ms with a sensitivity of 81.4% and a specificity of 74.0%.

CONCLUSION

In patients with COPD, RS time prolongation, which can be easily and quickly determined from the electrocardiogram, may be a marker for RV dysfunction.

Pristine biochar performance investigation to remove metals in primary and secondary treated municipal wastewater for groundwater recharge application

In this study, pristine biochar derived from date palm at 500°C was used in batch reactors (simulating blending adsorbent in aeration tank) and fixed-bed columns (simulating holding adsorbent in fixed-bed reactors). The removal performance of the biochar was assessed toward single and mixed-metal solutions as well as synthetic primary and secondary treated wastewater for copper (Cu2+), iron (Fe2+), nickel (Ni2+) and zinc (Zn2+). The order of maximum adsorption capacities of the metal ions at pH 7 followed: Fe2+ (2.92/2.94 mg/g)>Cu2+(2.69/2.78 mg/g) >Zn2+(2.03/2.19 mg/g)>Ni2+(1.69/1.02 mg/g) in single/mixed-metal solutions and Zn2+(2.91/11.26 mg/g)>Fe2+(0.60/5.29 mg/g)>Cu2+(0.56/5.05 mg/g)>Ni2+(0.13/2.02 mg/g) in synthetic primary/secondary treated wastewater. Blending biochar in aeration tank reduced metal concentrations. The metal ion concentrations in the final effluent were below the World Health Organization drinking water limits (2, 0.3, 0.1 and 3 mg/L for Cu2+, Fe2+, Ni2+ and Zn2+, respectively) suggesting that treated secondary wastewater can be spread into potable aquifers following disinfection. The Freundlich and the Pseudo-second order models fit best the batch experimental data. Experimental data from column analysis fit well to the Thomas model. The adsorption of metal ions on the surface of biochar was confirmed by Scanning electron microscopy, Energy dispersive X-ray studies, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy and X-ray diffraction. Desorption studies using different eluents demonstrated the reusability potential of the studied biochar.

Synthesis of a 2D copper(II)-carboxylate framework having ultrafast adsorption of organic dyes

Two-dimensional (2D) coordination polymers are very interesting materials for their attractive applications. A novel 2D metal-organic framework (MOF) was derived from copper(II) and amino benzoic acid under both room temperature and solvothermal reaction conditions using different solvents. From both of the synthesis methods, an identical MOF was crystalized with monoclinic crystal system having P2₁/c space group. Hirshfeld surface analysis is carried out to explore the non-covalent interactions obtained from single crystal XRD investigation in terms of percentage contribution of each interatomic contact involved in packing of molecules into MOF structure. The microstructure analysis and surface morphology studies revealed the 2D layered regular pattern of rhombus disks of ~5 μm thickness throng together via clustering of these rhombic shaped flakes as flowers (ranging 50-100 μm in size) having uniform elemental composition. This 2D MOF efficiently adsorbed organic dyes (methylene blue, methyl orange, and methyl red) from their aqueous solutions. The 2D copper-carboxylate framework (1.2 g/L) exhibited high adsorption rates for organic dyes (0.15-0.19 mM), and >90% of these dyes could be captured as soon as they are exposed to MOF suspension (1 min) in each case. The dye removal efficiency is credited to synergy among structure, ionic strength, shapes and dimensions of dyes with respect to MOF structure. The microstructure of MOF along with electronic interactions like electrostatic, hydrogen bonding, π-π interactions and coordination to open metal sites, might contribute to the ultrafast dye adsorption process by MOF. The adsorption phenomenon is spontaneous and followed the pseudo-second order kinetic mechanism. DFT calculations revealed important electronic parameters of the dyes and model MOF systems, and novel insights with respect to possible dye-MOF interactions. The MOF remained quite stable during the dye adsorption and was regenerated easily for the successful subsequent use.

A Review of Carbon Footprint Reduction in Construction Industry, from Design to Operation

Construction is among the leading industries/activities contributing the largest carbon footprint. This review paper aims to promote awareness of the sources of carbon footprint in the construction industry, from design to operation and management during manufacturing, transportation, construction, operations, maintenance and management, and end-of-life deconstruction phases. In addition, it summarizes the latest studies on carbon footprint reduction strategies in different phases of construction by the use of alternative additives in building materials, improvements in design, recycling construction waste, promoting the utility of alternative water resources, and increasing efficiencies of water technologies and other building systems. It was reported that the application of alternative additives/materials or techniques/systems can reduce up to 90% of CO₂ emissions at different stages in the construction and building operations. Therefore, this review can be beneficial at the stage of conceptualization, design, and construction to assist clients and stakeholders in selecting materials and systems; consequently, it promotes consciousness of the environmental impacts of fabrication, transportation, and operation.

Investigation of the relationship between obesity and Blastocystis infection in an adult population in Aydin, Turkey

Blastocystis is one of the most frequent protozoa in human faecal samples, however, little is known about its relation with obesity. The present study aimed to analyse Blastocystis infection and subtypes in three adult populations classified according to body mass index (BMI). Faecal samples from 346 individuals were classified according to BMI: control (124 cases), overweight (110 cases), and obese (112 cases). Nucleic acid extraction from the samples was followed by amplification of partial 18S ribosomal RNA (18S rRNA) gene of Blastocystis. The neighbourjoining method was used to construct a phylogenetic tree from evolutionary distance data. Clinical findings were compared between Blastocystis infected and non-infected cases. Blastocystis was detected in 52 (15%) of 346 individuals with PCR assay. Blastocystis was less frequent in obese group (8%) than both control group (18.2%) and overweight group (18.5%). Subtype distribution was as follows: ST3 (n=21; 43.8%), ST2 (n=15; 31.3%), ST1 (n=10; 20.8%) and ST7 (n=2; 4.2%). The overall nucleotide diversity of 18S ribosomal RNA gene was 0.049. None of the gastrointestinal symptoms and gender was not significantly related with the infection. Despite the cross sectional nature of the study including a specific population, it suggests a negative association between Blastocystis infection and obesity. In addition, the lack of significant relation further supports asymptomatic colonization of Blastocystis.

Effects of cordierite particulate filters on diesel engine exhaust emissions in terms of pollution prevention approaches for better environmental management

In this study, a specific diesel fuel is experimentally tested in a 4-cylindered diesel engine with and without a cordierite-based diesel particulate filter (CPF) to show the prevention of emissions by using an after treatment system (ATS). In this context, engine exhaust emissions, total particle concentration (TPC) and soot concentration are investigated. The diesel engine is firstly evaluated with the data directly measured from the engine output (DEO) (without after treatment option), and then the changes in the exhaust emission are examined by using an ATS which is a cordierite-based diesel particulate filter to prevent pollution. In this regard, total particle concentration of DEO option is found to be 6134041.20 1/cm³ and total particle concentration by using CPF is obtained to be 707.84 1/cm³. 99.99% reduction in TPC is achieved thanks to the use of CPF. The soot concentration of DEO option is calculated to be 2.158 mg/m³. However, the soot concentration is found to be 0.014 mg/m³ by using the CPF. The particulate matters are burned at high temperatures after being filtered at the exhaust output thanks to the regeneration process within the CPF after treatment. CO emissions decreased from 0.7489 g/kWh to 0.7273 g/kWh with the CPF utilization, while HC emissions decreased from 0.0965 g/kWh to 0.0900 g/kWh via CPF. However, an increase in CO₂ and NO_x emissions are observed due to oxidation in the CPF.

Computational Analysis of the Nicotine Oxidoreductase Mechanism by the ONIOM Method

Nicotine oxidoreductase (NicA2) is a monoamine oxidase (MAO)-based flavoenzyme that catalyzes the oxidation of S-nicotine into N-methylmyosmine. Due to its nanomolar binding affinity toward nicotine, it is seen as an ideal candidate for the treatment of nicotine addiction. Based on the crystal structure of the substrate-bound enzyme, hydrophobic interactions mainly govern the binding of the substrate in the active site through Trp108, Trp364, Trp427, and Leu217 residues. In addition, Tyr308 forms H-bonding with the pyridyl nitrogen of the substrate. Experimental and computational studies support the hydride transfer mechanism for MAO-based enzymes. In this mechanism, a hydride ion transfers from the substrate to the flavin cofactor. In this study, computational models involving the ONIOM method were formulated to study the hydride transfer mechanism based on the crystal structure of the enzyme-substrate complex. The geometry and energetics of the hydride transfer mechanism were analyzed, and the roles of active site residues were highlighted.

Tailored total neoadjuvant therapy for locally advanced rectal cancer: One size may not fit for all!

While current neoadjuvant protocols have proven benefits on local control for majority of patients with locally advanced rectal cancer, there are certain clinical conditions that require future advances for improving the outcomes. Total neoadjuvant therapy incorporates systemic chemotherapy planned within standard neoadjuvant protocols either before or after radiotherapy for locally advanced rectal cancer as a whole. Enhanced compliance with planned oncological therapy, tumour downstaging, administration of chemotherapy at the earliest time in the disease course to help assessing chemosensitivity are the proposed benefits of total neoadjuvant therapy in patients with locally advanced rectal cancer. Patient selection criteria for administration of total neoadjuvant therapy in the recent guidelines are unclear. Since current literature is inconclusive for the optimal sequence and type of radiotherapy and chemotherapy, premature incorporation of total neoadjuvant therapy for all locally advanced rectal cancers may result in overtreatment and subsequently toxicity. This article aims to discuss the current literature and to propose a future perspective by considering real-life scenarios reflecting patients' needs for treatment of locally advanced rectal cancer.

Liver and Pancreatic Injury in Response to ALK Inhibitors in a Patient with Primary Signet Ring Cell Carcinoma of the Lung: A Case Report

We report a patient with stage IV anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancer (primary lung signet ring cell adenocarcinoma) who received serial crizotinib, chemotherapy, and lorlatinib over more than 4 years. The patient discontinued crizotinib after approximately 4 months due to crizotinib-associated hepatotoxicity. Twenty-five days later, when transaminases had normalized, crizotinib was resumed. However, the patient's liver enzymes rapidly increased again, and crizotinib was discontinued. After 6 cycles of platinum-based chemotherapy, lorlatinib was initiated. Hepatotoxicity did not recur with lorlatinib, a next-generation ALK inhibitor, but grade 4 hypertriglyceridemia and acute pancreatitis were induced by lorlatinib after 4 months. To our knowledge, this is the first case report of acute pancreatitis with lorlatinib. Additionally, stereotactic body radiation therapy (SBRT) was performed for residual small primary lesions in the lung without stopping lorlatinib. Given the rarity of radiation pneumonitis, especially with the relatively small fields treated by SBRT, we suspect that lorlatinib enhanced the pulmonary toxicity. Physicians should be aware that ALK inhibitors, such as lorlatinib and crizotinib, have potentially lethal side effects.

Mechanistic study of L-6-hydroxynicotine oxidase by DFT and ONIOM methods

L-6-Hydroxynicotine oxidase (LHNO) is a member of monoamine oxidase (MAO) family and catalyzes conversion of (S)-6-hydroxynicotine to 6-hydroxypseudooxynicotine during bacterial degradation of nicotine. Recent studies indicated that the enzyme catalyzes oxidation of carbon-nitrogen bond instead of previously proposed carbon-carbon bond. Based on kinetics and mutagenesis studies, Asn166, Tyr311, and Lys287 as well as an active site water molecule have roles in the catalysis of the enzyme. A number of studies including experimental and computational methods support hydride transfer mechanism in MAO family as a common mechanism in which a hydride ion transfer from amine substrate to flavin cofactor is the rate-limiting step. In this study, we formulated computational models to study the hydride transfer mechanism using crystal structure of enzyme-substrate complex. The calculations involved ONIOM and DFT methods, and we evaluated the geometry and energetics of the hydride transfer process while probing the roles of active site residues. Based on the calculations involving hydride, radical, and polar mechanisms, it was concluded that hydride transfer mechanism is the only viable mechanism for LHNO.

Molecular characterisation of Trichomonas vaginalis isolates in Southwest Turkey with multilocus sequence typing and genetic structure analysis in relation to different countries

Trichomonas vaginalis, a flagellated protozoan parasite, is among the most common sexually transmitted pathogens in the world. The present study aimed to identify the genetic profiles of T. vaginalis in the southwest of Turkey with multilocus sequence typing (MLST) and to analyse the genetic structure of the parasite in a collection of isolates from different countries. The study included 27 T. vaginalis isolates from symptomatic females in Aydin, Turkey. Seven housekeeping genes of T. vaginalis were partially amplified and sequenced after genomic DNA extraction from in vitro cultures. The allele profiles and sequence types (STs) of the isolates were determined by using the MLST database (https://pubmlst.org/tvaginalis). The genetic structure and differentiation of the parasite were analysed in relation to findings from other countries by assembling the available MLST sequences. When referred to the database, a total of 22 STs, including 18 new STs were found; besides, there were two new allele types. The genetic analysis of MLST data demonstrated the presence of two main genetic structures: Type I and Type II. In addition, the neighbor-joining method also revealed that the isolates were clustered into two groups. The genetic types distributed almost equally in the Netherlands and the USA, however, the predominance of Type I was noted in Turkey and the UK. The genetic differentiation among four countries was significant (p < .05), the gene flow was relatively high between the Netherlands and the USA, in contrast to Turkey. Finally, genetic variations were originated within populations (93.8%) rather than among populations (6.2%). In conclusion, we studied the genetic diversity of T. vaginalis isolates with MLST in the southwest of Turkey and showed the origin of genetic differentiation of the parasite among different countries. The presentation of MLST profiles and genetic variance of T. vaginalis isolates will contribute to the development of new diagnostic and treatment options for the parasite.

Relationship between the Severity of Coronary Artery Disease and Catheter-Associated Urethral Stricture in Patients with Acute Coronary Syndrome

Background: Different arterial segments throughout the vascular system develop similar grades of atherosclerosis concomitantly. Urethral ischemia has been proposed as a cause of urethral stricture. Therefore, we aimed to investigate the relationship between coronary artery disease severity using a SYNTAX score and urethral stricture occurrence after urethral catheterization in patients with non-ST-segment-elevation acute coronary syndrome (ACS). Methods: This retrospective study consisted of 306 men with urethral catheters that were diagnosed with ACS and underwent coronary angiography between January 2016 and January 2018 in Kars Kafkas University and Osmaniye Government Hospital, Turkey. Hospital records were reviewed to collect the follow-up data of the patients regarding the occurrence of urethral stricture after urethral catheterization. The study population was divided into 2 groups according to urethral stricture development, and both groups were compared statistically. Results: SYNTAX scores were significantly higher in patients with urethral stricture than in those without urethral stricture (14.86±7.11 vs. 29.25±9.79; P<0.001). The SYNTAX score (OR=1.27; 95% CI: 1.16-1.39; P<0.001), diabetes, and serum albumin were found to be the independent predictors of urethral stricture. The receiver operating characteristic curve analysis showed that the cutoff value of the SYNTAX score for urethral stricture prediction was greater than 22.5, with 76.7% sensitivity and 85.1% specificity (AUC=0.88, 95% CI: 0.84-0.91; P<0.001). Conclusion: Coronary artery disease severity graded according to the SYNTAX score is an independent predictor of urethral stricture occurrence in ACS patients with a urethral catheter inserted.

Ligand photodissociation in Ru(ii)–1,4,7-triazacyclononane complexes enhances water oxidation and enables electrochemical generation of surface active species

Ligand transformations involved in metal complexes during water oxidation (WO), such as ligand decomposition, partial oxidation, or complete dissociation have been reported, however, ligand photodissociation has not been reported yet.

Environmental pollution cost analyses of biodiesel and diesel fuels for a diesel engine

In this study, Japanese Industrial Standard diesel no 2 and waste cooking oil biodiesel fuels are compared in terms of environmental pollution cost analysis. The experiments of the diesel and biodiesel fueled diesel engine are done at 100 Nm, 200 Nm and full load (294 Nm), while engine speed is constant at 1800 rpm. The method used in this study consists of a combination of economic and environmental parameters. According to the analyses, the total environmental pollution cost of the biodiesel is higher than the diesel fuel. On the other hand, the total cost of the CO₂ emissions of the diesel fuel is generally found to be higher than biodiesel fuel in terms of the life cycle based environmental pollution cost. The specific environmental pollution cost is found as minimum at full load to be 2.217 US cent/kWh for the diesel fuel and 2.449 US cent/kWh for the biodiesel fuel at full load. On the other hand, the life cycle based specific environmental pollution cost is determined as minimum at full load to be 5.050 US cent/kWh for the diesel fuel and 5.309 US cent/kWh for the biodiesel fuel. The biodiesel fuel has higher values than diesel fuel in terms of the specific environmental pollution cost rates. The maximum total carbon dioxide emission rate is found as 0.2405 × 10^-3 kg/kJ for the biodiesel fuel at 100 Nm engine torque and the minimum one is obtained as 0.1884 × 10^-3 kg/kJ for the diesel fuel at full load. When the payback periods of the fuels are examined, biodiesel has longer period than diesel. The environmental payback period and life cycle based environmental payback period are also compared for fuels. In this context, the biodiesel has longer environmental payback periods rates than diesel. Consequently, the biodiesel fueled engine has higher environmental pollution cost rates than the diesel fueled engine, while the total carbon dioxide parameter of the diesel fuel is close to the biodiesel fuel's rate. Also, all of the other environmental parameters of diesel fuel is generally better than biodiesel. Consequently, the diesel fuel is generally better option than the biodiesel considering environmental aspects. For better environmental management, the diesel fuel utilization in the diesel engine is slightly better option than biodiesel fuel in terms of environmental pollution cost analysis.

Clinicopathological and prognostic significance of microsatellit instability (MSI) status and PDl-1 expression in Turkish patients with gastric cancer

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Background: The aim of this study was to evaluate the prognostic role of microsatellite instability (MSI) status and PD-L1 expression in surgically resected gastric cancer and the relationship of these parameters with clinicopathological features. Methods: Eighty six gastric cancer patients which had curative surgical resection at Acibadem Atakent and Maslak Hospitals between 2010 and 2017 were analysed. Tumor samples were evaluated with MSI and PD-L1 antibodies by immunohistochemical (IHC) methods. PD-L1 IHC scoring was performed using the combined positive score (CPS). Survival analysis was accomplished using the Kaplan-Meier method. Cox proportional hazard regression model was used to identify independent risk factors that affect patients' overall survival. Results: The rate of PD-L1 expression in tumor cells was 34.9% (n = 30) and the frequency of PD-L1 expression in immune cells with CPS (≥1%) was 57% (n = 49). MSI-H was detected in 11.6%(n = 10), and more observed in PD-L1 positive cases (p = 0.021). MSI-H status was significantly correlated with older age, increased tumor size, presence of PD-L1 expression, and adenocarcinoma subtype. PD-L1 expression was associated with lymph node metastasis, adenocarcinoma subtype, microsatellite instability, presence of preoperative treatment and improved response to preoperative chemotherapy. In our study, the impact of MSI status on survival was not demonstrated, but PD-L1 expression positivity(≥1%) in both tumor cells (15.7 vs 53.4 months, p = 0.008)and in immune cells (20.4 vs NR; p = 0.027) was associated with short overall survival. PD -L1 expression in tumor cells was an independent prognostic factor for overall survival in multivariate analysis (HR: 2.28, p = 0.047). Conclusions: PD-L1 expression was related to a poor prognosis in patients with gastric cancer and can represent a rational approach for PD-1/PD-L pathway-targeted immunotherapy.

Association of Serum Osmolarity With Contrast-Induced Nephropathy in Patients With ST-Segment Elevation Myocardial Infarction

Contrast-induced nephropathy (CIN) is a prevalent and serious complication after primary percutaneous coronary intervention (pPCI). Although the association between serum osmolarity and chronic kidney disease is well established, its relation to CIN in patients with ST-segment elevation myocardial infarction (STEMI) undergoing pPCI needs to be elucidated. We evaluated the predictive value of serum osmolarity for CIN development in patients with STEMI (n = 768) undergoing pPCI. Serum osmolarity on admission was calculated. The study population was divided into 2 groups according to CIN development, and both groups were compared according to clinical, laboratory, and demographic features, including the serum osmolarity. Serum osmolarity was significantly higher in patients with CIN than in those without CIN (278 [8] vs 284 [9]; P = .024). Serum osmolarity (odds ratio: 1.052; 95% confidence interval: 1.018-1.086; P = .002), hemoglobin, contrast media volume, creatinine on admission, basal SYNergy between PCI with TAXus and cardiac surgery II score, and left ventricular ejection fraction were found to be independent predictors of CIN. Serum osmolarity (given the simple calculation of this parameter on admission) can be useful to define patients with STEMI undergoing pPCI who are more likely to develop CIN.

Comparative Computational Approach To Study Enzyme Reactions Using QM and QM-MM Methods

Choline oxidase catalyzes oxidation of choline into glycine betaine through a two-step reaction pathway employing flavin as the cofactor. On the light of kinetic studies, it is proposed that a hydride ion is transferred from α-carbon of choline/hydrated-betaine aldehyde to the N5 position of flavin in the rate-determining step, which is preceded by deprotonation of hydroxyl group of choline/hydrated-betaine aldehyde to one of the possible basic side chains. Using the crystal structure of glycine betaine-choline oxidase complex, we formulated two computational systems to study the hydride-transfer mechanism including main active-site amino acid side chains, flavin cofactor, and choline as a model system. The first system used pure density functional theory calculations, whereas the second approach used a hybrid ONIOM approach consisting of density functional and molecular mechanics calculations. We were able to formulate in silico model active sites to study the hydride-transfer steps by utilizing noncovalent chemical interactions between choline/betaine aldehyde and active-site amino acid chains using an atomistic approach. We evaluated and compared the geometries and energetics of hydride-transfer process using two different systems. We highlighted chemical interactions and studied the effect of protonation state of an active-site histidine base on the energetics of transfer. Furthermore, we evaluated energetics of the second hydride-transfer process as well as hydration of betaine aldehyde.

A rare cause of acute renal failure: Aortic occlusion

Aortic occlusion usually occurs in the infrarenal abdominal aorta while occlusion of the suprarenal aorta is much less common. The clinical presentation may vary from limb ischemia, neurologic symptoms of the lower extremities, abdominal symptoms, renal failure, and resistant hypertension (HTN). We present a case of suprarenal aortic occlusion presenting with renal failure and resistant HTN but without lower limb ischemia.

Adsorptive removal capacity of gravel for metal cations in the absence/presence of competitive adsorption

Locally available and low cost granular gravel as an adsorbent material was employed to determine its capacity to remove metal cations Cu(II), Fe(II), Ni(II), and Zn(II) from single metal solution and landfill leachate samples. Adsorption kinetics and mechanism under different parameters including dosage, time, and pH were studied. It was found that the experimental results fitted to the Freundlich model suggesting an adsorption process on a multilayer heterogeneous surface for both single metal solution and landfill leachate samples. The adsorption of metal cations followed second-order kinetics occurring in a single step on the surface of gravel. The order of removal efficiency of metals was found to be Cu(II)(98%) > Fe(II)(87.5%) > Zn(II)(76.05%) > Ni(II)(36.38%) in single metal solution and Cu(II)(98.3%) > Fe(II)(83%) > Zn(II)(48%) > Ni(II)(27.32%) in landfill leachate sample at pH 7. The regeneration efficiency of the metals adsorbed on the gravel resulted in the order of Fe(II)(99.54%) > Cu(II)(99%) > Ni(II)(49.46%) > Zn (II)(2.25%).

Prognostic value of preoperative neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio in patients with epithelial ovarian cancer

PURPOSE

The neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) have recently been evaluated in many cancers in prediction of survival outcomes. The purpose of this study was to investigate the impact of NLR and PLR on the prognosis of patients with epithelial ovarian cancer (EOC).

MATERIALS AND METHODS

A total of 208 patients with EOC were included in the study. Hematological parameters and clinicopathological data during diagnosis were retrospectively evaluated. The cut-off values were determined by calculating receiver operating characteristic (ROC) curve analysis of the patients.

RESULTS

The median over-all survival (OS) of patients with low NLR was 69 months (95% CI, 43.0-94.9) whereas high NLR was 36 months (95% CI, 29.1-42.8). The median OS with low PLR patients was 76 months (95% CI, 46.4-105.5) and high PLR was 35 months (95% CI, 28.5-41.4). In serous tumors (70.7%), the median OS with low NLR and high NLR was 54 months (95% CI, 27.9-80.0) and 34 months (95% CI, 28.2-39.7), and for the median OS with low PLR and high PLR it was 51 months (95% CI, 2 1.2-80.7) and 35 months (95% CI, 27.8-42.1), respectively.

CONCLUSION

The present findings showed that the high NLR and high PLR were associated with poor prognosis and these values are significantly remarkable in EOC patients.