HPV status and immunohistochemical analysis of p16, p53 and PD­L1 expression as prognostic biomarkers in patients with squamous cell anal cancer receiving definitive radiotherapy/chemoradiotherapy.

Anal squamous cell carcinoma (SCC) treated with definitive radiotherapy (RT)/chemoradiotherapy (CRT) has shown high success rates, yet challenges such as treatment resistance and recurrence persist. The present study aimed to investigate the associations between immunohistochemical (IHC) evaluation, treatment response and prognosis in anal SCC. A retrospective cohort analysis included 42 patients with anal SCC treated at a single institution between 2006 and 2022. Human papillomavirus (HPV) status was determined, and the IHC analysis of p16, p53 and PD-L1 expression was conducted using formalin-fixed, paraffin-embedded biopsies. A complete response to RT/CRT was observed in 71.4% of patients. Recurrence occurred in 38.1% of cases, of which 7.1% had local-regional recurrence (LRR), 14.3% had distant recurrence (DR), and 16.7% had both LRR and DR. HPV positivity (71.4%) was significantly associated with p16 positivity. Lack of complete response was associated with HPV-negative status, p16-negative status, increased recurrence and DR. In addition, recurrence was significantly associated with p53-positive status, and p53 positivity was significantly associated with increased LRR. PD-L1 positivity, defined as a combined positive score (CPS) ≥1% was found in 73.8% of the patients, and exhibited significant associations with HPV positivity and p16 positivity. PD-L1 CPS ≥ 1% was also associated with an increased LRR. Univariate analysis revealed that age <65 years, a complete response and HPV positivity were associated with increased 5-year overall survival (OS), while a complete response, HPV positivity and p53-negative status were associated with increased 5-year disease-free survival (DFS). Multivariate analysis identified that age <65 years and HPV positivity are independent prognostic factors for 5-year OS, and a complete response and p53-negative status are independent prognostic factors for 5-year DFS. In conclusion, these findings suggust that the identification of HPV status and poor prognostic biomarkers at diagnosis may be used to guide personalized treatment strategies, with the combination of immunotherapy with standard CRT potentially providing improved outcomes.

Retrospective evaluation of "Rods and Rings" pattern detected in the anti-nuclear antibody (ANA) indirect immunofluorescence (IIF) test.

Introduction: Anti-rods and rings (anti-RR) antibodies have recently been described as a cytoplasmic pattern in IIF-based screening of autoantibodies on HEp-2 cells and ICAP has named it as AC-23. It is most frequently related to drug-induced antibody generation. This study aimed to investigate the clinical significance of AC-23 positivity and its relevance to the diagnosis and/or follow-up of the associated diseases and/or drug use. Methods: A multicenter retrospective study was conducted among 10 hospitals from six different provinces in Türkiye from January 2017 to December 2021. The laboratory data and clinical information of 600 patients with positive anti-RR antibodies out of 547.558 HEp-2 IIF ANA samples were analyzed. Results: The distribution of AC-23 positive patients by year indicated a steady increase between 2017-2021. Anti-RR prevalence in post-COVID-19 period was significantly higher than that of pre-COVID-19 period (p=0.00). Concomitant ANA positivity was detected in 56.5% of patients, the most common patterns being AC-4 and AC-5 (41.1%). The most frequent pathology among the anti-RR positive patients was an autoimmune disease (19.83%); 28.57% of which had rheumatoid arthritis and 17.65% autoimmune liver disease. Among the 600 patients, 65 (10.83%) were diagnosed as hepatitis C virus (HCV) infection. Available data for 38 of the HCV patients revealed that 71.05% of them had a history of interferon alfa+ribavirin and 28.95% of them had a history of NS3/4/5A/5B polymerase inhibitor or protease inhibitor drug use. Significant increase in the rate of anti-RR positivity was observed in the post-COVID-19 period when compared to pre-COVID-19 period (p:0.00). Discussion: This is the first multicenter study in Türkiye about the clinical association of anti-RR antibodies which may be ignored during routine HEp-2 IIF testing. Pathologies other than HCV should be taken into consideration in terms of the possible role of anti-RR in autoimmune diseases and other pathologies. The preliminary data obtained in this study suggest that anti-RR antibody development might also be associated to COVID-19, supporting the several previous data related to the potential of viruses triggering the formation of autoantibodies. Large-scale prospective studies should elucidate the clinical significance of RR pattern and determine its role in patient diagnosis and follow-up.

COVID-19 Antibody Levels among Various Vaccination Groups, One-Year Antibody Follow-Up in Two University Hospitals from Western and Central Turkey.

Various clinical outcomes, reinfections, vaccination programs, and antibody responses resulted from the COVID-19 pandemic. This study investigated the time-dependent changes in SARS-CoV-2 antibody responses in infected and/or vaccinated and unvaccinated individuals and to provide insights into spike and nucleocapsid antibodies, which fluctuate during infectious and non-infectious states. This cohort study was carried out at the Ege University Faculty of Medicine hospital in Izmir (western Turkey) and the Erciyes University Faculty of Medicine hospital in Kayseri (central Turkey) between December 2021 and January 2023, which coincided with the second half of COVID-19 pandemic. The study included 100 COVID-19 PCR-positive patients and 190 healthcare workers (HCWs). Antibody levels were followed up via quantitative anti-SARS-CoV-2 spike and qualitative anti-nucleocapsid immunoassays (Elecsys™). Antibody levels declined after infection but persisted for at least 6-8 months. Individuals who had received only CoronaVac had higher anti-nucleocapsid antibody levels in the early months than those who received mixed vaccination. However, anti-spike antibodies persisted longer and at higher levels in individuals who had received mixed vaccinations. This suggests that combining two different vaccine platforms may provide a synergistic effect, resulting in more durable and broad-spectrum immunity against SARS-CoV-2. The study provides information about the vaccination and antibody status of healthcare workers in the second half of the pandemic and provides valuable insights into the dynamics of antibody responses to COVID-19 infection and vaccination.

Efficacy of coronavirus disease 2019 vaccines in patients with rheumatic diseases.

Objectives: In this study, we report the immune response to the BNT162b2 vaccine and CoronaVac vaccine after a two-dose vaccination and the effects of conventional drugs, immunosuppressive drugs, and new-generation therapies on vaccine responses in patients with rheumatic and musculoskeletal diseases (RMDs). Patients and methods: This is a prospective observational study conducted with 94 patients (65 males, 29 females; mean age: 42.7±12.1 years; range, 19 to 69 years) between May 2021 and January 2022. The immunogenicity of the two-dose regimens of the BNT162b2 and CoronaVac vaccines in adult patients with RMD was analyzed according to disease and treatments. Serum immunoglobulin G antibody levels against SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) spike proteins were measured four weeks after the second dose of vaccines. Results: Patients on regimens including mycophenolate, rituximab, and steroids were less likely to develop an antibody response (p=0.001, p=0.06, and p=0.001, respectively). Impairment of vaccine response by other conventional disease-modifying antirheumatic drugs and by anti-tumor necrosis factor treatments was not shown. Younger participants appeared more likely to develop an antibody response. The CoronaVac vaccine was less likely to develop an antibody response compared to the BNT162b2 vaccine (p=0.002). Systemic lupus erythematosus and vasculitis had the lowest antibody titers compared to other RMDs. Conclusion: Patients receiving mycophenolate mofetil, rituximab, and steroids should be warned about the risk of a suboptimal vaccine response. If possible, vaccination strategies should be changed, and the dose modification of drugs should be made during the vaccination. Further studies are required to determine the responses to SARS-CoV-2 vaccination and optimization of vaccine response in patients with RMDs.

Regulatory B Cells Profile in Kidney Transplant Recipients With Chronic-Active Antibody-Mediated Rejection.

This study aims to reveal the relationship between regulatory B cell (Breg) subsets and chronic-active antibody-mediated rejection (c-aABMR) in renal transplant recipients. Our study involved 3 groups of participants: renal transplant recipients with biopsy-proven c-aABMR as the chronic rejection group (c-aABMR, n = 23), recipients with stable graft functions as the patient control group (PC; n = 11), and healthy volunteers (HV; n = 11). Breg subsets, immature/transitional B cells, plasmablastic cells, B10 cells, and BR1 cells were isolated from venous blood samples by flow cytometry. The median values of Breg frequencies in the total lymphocyte population were analyzed. There were no significant differences between the study groups for immature and/or transitional B cell frequencies. Plasmablastic cell frequencies of the c-aABMR group (7.80 [2.10-27.40]) and the PC group (6.00 [1.80-55.50]) were similar, but both of these values were significantly higher than the HVs' (3.40 [1.20-8.50]), (respectively, P = .005 and P = .039). B10 cell frequencies were also similar, comparing the c-aABMR (4.20 [0.10-7.40]) and the PC groups (4.10 [0.10-5.90]), whereas the HVs (5.90 [2.90-8.50]) had the highest B10 cell frequency with an only statistical significance against the PC group (respectively, P = .09 and P = .028). The c-aABMR and the PC groups were similar regarding BR1 cell frequencies. However, the HV group significantly had the highest frequency of BR1 cells (5.50 [2.80-10.80]) than the other groups (P < .001 for both). We demonstrated that frequencies of B10 and BR1 cells were higher in HVs than in transplant recipients, regardless of rejection state. However, there was no significant relation between Breg frequencies and the c-aABMR state.

Dataset on the global distribution of shallow groundwater.

Shallow groundwater (GW), defined as the water table of unconfined or perched aquifers that is near enough to the land surface to influence the vadose zone and the surface soil moisture, impacts land surface water, energy, and carbon cycles by providing additional moisture to the root zone via capillary fluxes. Although the interactions of shallow GW and the terrestrial land surface are widely recognized, incorporating shallow GW into the land surface, climate, and agroecosystem models is not yet possible due to the lack of groundwater data. Groundwater systems are affected by various factors, including climate, land use/land cover, ecosystems, GW extractions, and lithology. Although GW wells are the most direct and accurate way of monitoring water table depths at point scales, upscaling GW levels from point scale to areal or regional scale poses significant challenges. Here, we provide high spatiotemporal resolution global maps of the terrestrial land surface areas influenced by shallow GW from mid-2015 to 2021 (a separate NetCDF file for each year) in a 9 km spatial and daily temporal resolution. We derived this data from NASA's Soil Moisture Active Passive (SMAP) mission spaceborne soil moisture observations with a temporal resolution of 3 days and approximately 9 km grid resolution. This spatial scale corresponds to SMAP's "Equal Area Scalable Earth" (EASE) grids. The central assumption is that the monthly moving average of soil moisture observations and their coefficient of variation are sensitive to shallow GW regardless of the prevailing climate. We process the Level-2 enhanced passive soil moisture SMAP (SPL2SMP_E) product to detect shallow GW signals. The presence of shallow GW data is calculated by an ensemble machine learning model, which is trained using simulations from a variably saturated soil moisture flow model (Hydrus-1D). The simulations span various climates, soil textures, and lower boundary conditions. The spatiotemporal distribution of shallow GW data based on SMAP soil moisture observations is provided for the first time with this dataset. The data are of value in a wide variety of applications. The most direct use is in climate and land surface models as lower boundary conditions or as a diagnostic tool to verify model results. Some other applications may include flood risk analyses and regulation, identifying geotechnical issues such as shallow GW-triggered liquefaction, global food security, ecosystem services, watershed management, crop yield, vegetation health, water storage trends, and tracking mosquito-borne diseases by identifying wetlands, among other applications.

Interfacial characteristics of BIOfactor MTA and Biodentine with dentin.

The objective of this study was to characterize the interface between dentin and MTA-Angelus (Angelus, Londrina, Brasil), Biodentine (Septodont, France) and BIOfactor MTA (Imicryl, Konya, Turkey) using scanning electron microscopy (SEM), energy disperse X-ray spectroscopy (SEM-EDS) and confocal laser scanning microscopy (CLSM). Fifteen dentin segments were obtained from previously extracted single-rooted human teeth. Canal lumens were instrumented with diamond burs and then randomly filled with MTA-Angelus, Biodentine or BIOfactor MTA and placed in distilled water or Hanks' Balanced Salt Solution (HBSS) for 28-days. The samples were examined with SEM and the thickness of the interfacial layer measured. SEM-EDS analysis was performed to determine principal elemental composition of the material, dentin, and interfacial area. The marginal adaptation of cements to dentin was assessed by confocal microscopy and the percentage of material penetration was calculated. An interfacial layer was evident in approximately 70% of SEM images in both MTA-Angelus and BIOfactor samples. The thickness of interfacial layer was significantly higher in HBSS than in distilled water for all groups. MTA Angelus resulted in the thickest interfacial layer in distilled water while Biodentine had the thickest interfacial layer in HBSS. Calcium levels within the BIOfactor MTA-dentin interface were higher than both dentin and cement. Dentin penetration was higher in BIOfactor MTA and silicon was evident in all material-dentin interfaces. All calcium silicate-based materials promoted the formation of an interfacial layer. BIOfactor MTA exhibited promising characteristics with its good marginal adaptation even though it presented a moderately thick interfacial layer. RESEARCH HIGHLIGHTS: A distinguishable interfacial layer was observed in most of the samples within the BIOfactor MTA, MTA-Angelus and Biodentine groups. The elemental constitution of the interfacial layer was different from that of the calcium silicate based materials.

Detection of Phenylarsine Oxide in Drinking Water Using an Impedimetric Electrochemical Sensor with Gelatin-Based Solid Electrolyte Enriched with Mercaptoethanol: A Novel Prospective Green Biosensor Methodology.

A simple, inexpensive, rapid, and label-free detection of phenylarsine oxide (PAO) in the field is a significant and unmet need because of its fatally acute and chronic effects on human health. A simple, fast, sensitive, and relatively low-cost arsenic detection system with an eco-friendly sensor could fill this gap. To monitor arsenic in situ, a reliable, portable impedimetric electrochemical sensor is the most suitable platform, which is real-time, fast, low-cost, and easy to design and use and has high sensitivity at low detection limits in the nanogram per mL range. The detection system in this study has a patent-applied green sensor with minimum harm to nature and the potential to dissolve in nature. The electrode containing 15 mL of distilled water (DIW) + 2 g gelatin + 1.75 g glycerol was determined to be the most suitable for determining the amount of inorganic arsenic in the range of 1-100 ng/mL using a gelatin-based solid electrochemical sensor enriched with 2-mercaptoethanol. Impedance measurements were performed to analyze the stability of the sensor in both deionized water and drinking water, as well as for arsenic detection. Among the procedures examined, the procedure prepared with 15 mL DIW + 2 g glycerol + 1.75 g gelatin resulted in the best stability in aqueous medium and in sensitivity with resistance changes (-ΔR ct (%)) of 12% (±0.62%), 26% (±2.3%), and 40% (±3.8%) for the concentrations of 1, 10, and 100 ng/mL PAO in drinking water, respectively. With this detection methodology, there is the potential to detect not only arsenic but also other heavy metals in waters and different biomarkers in human fluids.

Quantitative Antibody Levels Against SARS-CoV-2 Spike Protein in COVID-19 and Multisystem Inflammatory Syndrome in Children.

The majority of children with coronavirus diseases 2019 (COVID-19) are asymptomatic or develop mild symptoms, and a small number of patients require hospitalization. Multisystem inflammatory syndrome in children (MIS-C) is one of the most severe clinical courses of COVID-19 and is suggested to be a hyperinflammatory condition. This study aimed to compare quantitative antibody levels against SARS-CoV-2 spike protein in children with COVID-19 and MIS-C. Blood samples from 75 patients [n = 36 (48%) with mild/asymptomatic (group 1), n = 22 (29.3%) with moderate-to-severe SARS-CoV-2 infection (group 2) and n = 17 (22.6%) patients with MIS-C (group 3)] were analyzed 3 months after COVID-19. The majority of the children with asymptomatic/mild COVID-19 symptoms (80.6%), moderate/severe disease (90.9%), and MIS-C (82.4%) had detectable IgG antibodies to SARS-CoV-2 spike protein (p = 0.567). The mean antibody value against SARS-CoV-2 spike protein was 321.9 ± 411.6 in group 1, 274 ± 261 in group 2, and 220 ± 299 in group 3, respectively (p > 0.05). Patients diagnosed with COVID-19 (asymptomatic/mild+moderate/severe) and those with MIS-C were also compared; the antibody positivity rates [COVID-19 group: 85.5%, MIS-C group: 82.4%, (p = 0.833)] and mean antibody values [COVID-19 group: 303.9 ± 360.3, MIS-C group: 220 ± 299, (p > 0.05)] were similar in both groups. In conclusion, the majority of children with COVID-19 and MIS-C developed a detectable antibody level against SARS-CoV-2 spike protein 3 months after COVID-19. Quantitative antibody levels were similar in both asymptomatic/mild disease, moderate/severe disease, and MIS-C group. Long-term studies evaluating antibody responses in children with COVID-19 and MIS-C are needed for more accurate vaccine schedules.

Rapid, label-free genetic detection of enteropathogens in stool without genetic isolation or amplification.

Current genetic detection methods require gene isolation, gene amplification and detection with a fluorescent-tagged probe. They typically require sophisticated equipment and expensive fluorescent probes, rendering them not widely available for rapid acute infection diagnoses at the point of care to ensure timely treatment of the diseases. Here we report a rapid genetic detection method that can detect the bacterial gene directly from patient stools using a piezoelectric plate sensor (PEPS) in conjunction with a continuous flow system with two temperature zones. With stools spiked with sodium dodecyl sulfate (SDS) in situ bacteria lysing and DNA denaturation occurred in the high-temperature zone whereas in situ specific detection of the denatured DNA by the PEPS occurred in the lower-temperature zone. The outcome was a rapid genetic detection method that directly detected bacterial genes from stool in < 40 min without the need of gene isolation, gene amplification, or expensive fluorescent tag but with polymerase chain reaction (PCR) sensitivity. In 40 blinded patient stools, it detected the toxin B gene of Clostridium difficile with 95% sensitivity and 95% specificity. The all-electrical, label-free nature of the detection further supports its potential as a low-cost genetic test that can be used at the point of care.

The prospective evaluation of risk factors and clinical influence of carbapenem resistance in children with gram-negative bacteria infection.

BACKGROUND: Carbapenem-resistant gram-negative (CRGN) infections have been increasing in recent years and associated with significant morbidity, mortality, and health care costs. The aim of this study was to evaluate the epidemiologic and clinical risk characteristics, risk factors, and outcome of CRGN infections and to compare with carbapenem-sensitive gram-negative (CSGN) infections in children. METHODS: Newly diagnosed CRGN infections in hospitalized children younger than age 18 years were prospectively recorded and all patients infected with a CSGN pathogen in the same unit within 48 hours of diagnosis were included in a control group between April 1, 2014, and December 31, 2014. RESULTS: Twenty-seven patients with CRGN infections and 28 patients with CSGN infections were enrolled in this study. Ventilator-associated pneumonia was the most common type of infection in both groups. Prior exposure to carbapenems (relative risk [RR], 11.368; 95% confidence interval [CI], 1.311-98.589), prolonged hospitalization (RR, 5.100; 95% CI, 1.601-16.242) were found to be independent risk factors for acquiring CRGN infections. Septic shock was significantly more frequent in the CRGN group (RR, 9.450; 95% CI, 1.075-83.065). The in-hospital mortality was higher in the CRGN group (RR, 7.647; 95% CI, 1.488-39.290). CONCLUSIONS: Prior carbapenem exposure and prolonged hospitalization are the most important risk factors for acquiring CRGN infections in our hospital. This study demonstrated, similar to previous reports, that carbapenem resistance increases morbidity, mortality, and health care costs.