Journals
2025 EN
Tan Zu Dienle · Ramdzan Khairun Nisha Mohamed · Denoun Leah Mary Lilly
+10 more
Societal Impact Statement Novel forest ecosystems consist of forest ecosystems dominated by non‐native tree species that are difficult to restore to their pre‐human disturbance states. Nevertheless, novel forests can provide numerous ecosystem services, such as carbon sequestration and storage. We quantified the aboveground living tree and soil carbon stocks in four novel forest sites in Singapore using forest inventory and airborne LiDAR data, and soil core data, respectively. We found that the carbon stored in the four sites is comparable to tropical secondary forests elsewhere. Our results show that novel forests can be protected as carbon stores. Summary Forest succession after the cessation of intense human land use may result in ecosystems with biotic or abiotic properties that differ from their historical states before anthropogenic activities. These ‘novel ecosystems’ often consist of communities dominated by non‐native species that are costly to restore to their original state. As novel ecosystems become more ubiquitous, there is a need to understand the opportunities and challenges in managing these ecosystems and the implications for the ecosystem services they provide. Here, we evaluated the role of novel forest ecosystems in Singapore, a tropical city‐state in Southeast Asia, in regulating carbon stocks and flows. Specifically, we mapped the distribution of aboveground carbon density (ACD) in living trees of four post‐agricultural, non‐native‐dominated forest sites across two time periods using a combination of field measurements (2013, 2023) and airborne LiDAR scans (2014, 2019). Soil carbon stock was estimated from soil cores collected at each site. We find that field‐estimated ACD in our plots can reach 129.8 Mg C ha −1 , with a mean sequestration rate for each site ranging between 0.3 and 2.6 Mg C ha −1 yr −1 . Soil carbon can be as high as 127.9 Mg C ha −1 down to 200 cm, comparable to the soil carbon found in other non‐wetland forest ecosystems in the region. Our study highlights the role of novel forests as carbon stores. Therefore, there is a need to consider management options for these ecosystems in highly urbanized landscapes.
Journals
2025 EN
Ibraheem Ahmed A. A. · Saleh Sarah A. · Emam Ahmed A.
+43 more
ABSTRACT Objective Recently, angiotensin‐converting enzyme 2 ( ACE2 ) gene has emerged as a potential candidate gene for susceptibility to SARS‐CoV‐2 infection. We investigated whether ACE2 G8790A (rs2285666) polymorphism could be a genetic marker for susceptibility to COVID‐19 and disease severity in Egyptian children and adolescents. Methods This was a prospective case‐control study included 580 cases diagnosed with COVID‐19, and 580 matched control children and adolescents. The ACE2 G8790A (rs2285666) polymorphism was genotyped using polymerase chain reaction ( PCR ) and ACE2 serum level was measured by ELISA . Results The ACE2 A/A genotype and A ‐allele were significantly more represented in cases with COVID‐19 as compared to control group (44% vs. 30%; OR = 2.83; [95% CI: 1.27–2.63]; p = 0.006; for the A/A genotype) and (65% vs. 51%; OR = 1.9; [95% CI: 1.06–1.72]; p = 0.01; for the A ‐allele). The presence of ACE2 G/G genotype was an independent risk factor for severe disease (adjusted OR: 2.08; [95% CI: 1.57–6.78]; p = 0.003). Conclusion The ACE2 G8790A (rs2285666) polymorphism may confer susceptibility to COVID‐19 in Egyptian children and adolescents. The ACE2 G/G genotype and G‐ allele was associated with lower ACE2 serum levels and may constitute independent risk factors for disease severity.
Journals
2025 EN
Durrani Naveed Ur Rehman · Mohammed Maria Bashir Ibrahim · Cyprian Farhan Sachal
+1 more
ABSTRACT Introduction There is a need for a better understanding of the use of antenatal steroids (ANS) in late preterm infants due to their efficacy and safety profile from existing evidence. Aims To identify the real‐world impact of ANS on short‐term outcomes in late preterm infants at a quaternary care setting in Qatar. Methods Retrospective chart review of 654 late preterm infants delivered at Sidra Medicine between 1st January 2018 and 29th February 2024. After excluding criteria, infants were categorized based on their exposure to ANS. We utilized regression models to analyze the relationship between ANS exposure and primary and secondary outcomes, including respiratory distress, Noninvasive respiratory support, hypoglycemia, and length of NICU stay, respectively, while adjusting for relevant maternal and infant characteristics. Results Our findings reveal no significant protective effect of any ANS dosage against respiratory distress (adjusted odd ratio (aOR) 0.78; 95% CI: 0.46–1.32; p = 0.357). Conversely, ANS exposure was associated with an increased risk of hypoglycemia (aOR 1.22; 95% CI: 0.81–1.84; p = 0.350) and prolonged stay in NICU (incidence rate ratio [IRR] 1.90; 95% CI: 1.74–2.08; p < 0.001). Conclusion Our study findings suggest a lack of protection against respiratory distress in late preterm infants with any ANS, highlighting the need for better understanding and adopting an individualized approach.
Journals
2025 EN
Adaikalam Stephanie A. · Rose Rebecca S. · Sammour Ibrahim A.
+3 more
ABSTRACT Objectives: Tracheobronchomalacia (TBM) is common in Grade 3 Bronchopulmonary Dysplasia (BPD), but there is wide variation in frequency and method of evaluation. Objective quantitative methods are needed for translational studies and future drug trials. This study aimed to determine whether positive end‐expiratory pressure (PEEP) and oxygen saturation index (OSI) can predict TBM in Grade 3 BPD. Methods: We retrospectively reviewed flexible bronchoscopy videos from a cohort of infants with Grade 3 BPD to determine the presence of TBM. PEEP and mean OSI in the week before the first bronchoscopy were assessed as predictors of TBM using multiple logistic regression. Subject Demographics: The study included 56 infants with Grade 3 BPD with a median gestational age (GA) of 25.3 weeks (IQR 2.8) and median post‐menstrual age (PMA) at first bronchoscopy of 40.7 weeks (IQR 6.1). Results: Thirty‐seven subjects (66%) were found to have TBM, although 13 subjects lacked evidence of TBM on the first evaluation (false negative rate 35%). PEEP and OSI had 86% sensitivity for predicting TBM, but only 30% specificity ( p = 0.02). In a post‐hoc analysis of the 13 initial bronchoscopies that “missed” TBM, 10 had a higher level of sedation in the first evaluation compared to the later assessment that revealed TBM. Conclusions: We found that PEEP and OSI are sensitive but not specific for predicting TBM in Grade 3 BPD. In addition, there are frequent false negative evaluations when bronchoscopy is performed under higher levels of sedation. We propose a more precise bronchoscopy method for quantifying TBM.
Journals
2025 EN
Toma Haneen · Alnaimi Amal · AbuHasan Mutasim
+2 more
ABSTRACT Introduction Obstructive sleep apnea (OSA) occurs predominantly during REM sleep (REM‐OSA) compared to NREM sleep (NREM‐OSA) in both children and adults. However, it is not clear whether REM‐OSA and NREM‐OSA are separate clinical phenotypes of OSA or represent 2 ends of OSA severity spectrum. Objective We aimed to compare clinical and polysomnography (PSG) characteristics of REM‐OSA versus NREM‐OSA in children, and to evaluate the effect of these characteristics on REM‐related over NREM‐related obstructive AHI ratio (REM‐OAHI/NREM‐OAHI). Methods Clinical and PSG data of all children diagnosed with moderate to severe OSA by PSG between 2019 and 2024 were collected and analyzed. REM‐OSA was defined as REM‐OAHI/NREM‐OAHI ratio of ≥2. NREM‐OSA was defined as REM‐OAHI/NREM‐OAHI of < 2. Results A total of 253 patients (169 male and 84 female) met the inclusion criteria. REM‐OSA was identified in 174 (68.7%) patients, and NREM‐OSA in 79 (31.2%) patients. There was no significant difference between REM‐OSA and NREM OSA groups in gender, BMI, clinical diagnosis, symptoms or oxygenation indices. However, REM‐OSA group had lower OAHI and less severe OSA than NREM‐OSA group ( p = 0.004, p = 0.003, respectively). Regression analysis showed that low OAHI was the only significant predictor of REM‐OSA and the only predictor of high REM‐AHI/NREM‐AHI ratio, respectively ( p = 0.001, p = 0.001). Conclusion REM‐OSA and NREM‐OSA are not likely to be separate clinical phenotypes of OSA but only markers of the disease severity, with NREM‐OSA indicating more severe disease.
Journals
2025 EN
Fatehi Vahid · Salahzadeh Zahra · Farhoudi Mehdi
+2 more
ABSTRACT Background and Purpose Stroke is among the most prevalent medical conditions and often leads to persistent complications within the central nervous system. It results in both physical and cognitive impairments that can substantially affect individuals' ability to perform activities of daily living (ADL). Conventional rehabilitation exercises are frequently lengthy, repetitive, and unengaging, which may reduce adherence and limit therapeutic outcomes. Therefore, there is a pressing need to explore innovative approaches that enhance motivation, increase the frequency and duration of exercises, and improve patient satisfaction. Methods This protocol describes a randomized, two‐blind controlled trial with blinded outcome assessment. The study will be conducted at a physiotherapy clinic in Tabriz and will compare standard rehabilitation with an intervention combining standard rehabilitation and a virtual reality (VR)‐based serious game. Results A VR‐based serious game is an innovative technology incorporating advanced user‐computer interaction to deliver simulation and engagement through visual and auditory feedback. Due to the ongoing debate about the effectiveness of VR‐based serious gaming interventions and the limited availability of high‐quality clinical trials, further research is warranted. To date, no studies have examined the integration of VR with conventional treatments or compared it with standard physiotherapy practices. Discussion The aim of this study is to investigate the effect of a VR‐based serious game on promoting cognitive‐motor rehabilitation in stroke patients, with a focus on improving performance in daily life activities. This protocol outlines the methodology for a prospective randomized controlled trial designed to generate evidence supporting the use of VR technologies in stroke rehabilitation.
Journals
2025 EN
Choudhary Preeti · Kunnakkattu Ibrahim Roshan · Nair Sreenath
+5 more
Abstract The Protein Data Bank (PDB) is the primary global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands, proteins, and nucleic acids. PDB contains over 47,000 unique small molecules bound to the macromolecules. Despite the extensive data available, the complexity of small‐molecule data in the PDB necessitates specialized tools for effective analysis and visualization. PDBe has developed a number of tools, including PDBe CCDUtils ( https://github.com/PDBeurope/ccdutils ) for accessing and enriching ligand data, PDBe Arpeggio ( https://github.com/PDBeurope/arpeggio ) for analyzing interactions between ligands and macromolecules, and PDBe RelLig ( https://github.com/PDBeurope/rellig ) for identifying the functional roles of ligands (such as reactants, cofactors, or drug‐like molecules) within protein–ligand complexes. The enhanced ligand annotations and data generated by these tools are presented on the novel PDBe‐KB ligand pages, offering a comprehensive overview of small molecules and providing valuable insights into their biological contexts (example page for Imatinib: https://pdbe.org/chem/sti ). By improving the standardization of ligand identification, adding various annotations, and offering advanced visualization capabilities, these tools help researchers navigate the complexities of small molecules and their roles in biological systems, facilitating mechanistic understanding of biological functions. The ongoing enhancements to these resources are designed to support the scientific community in gaining valuable insights into ligands and their applications across various fields, including drug discovery, molecular biology, systems biology, structural biology, and pharmacology.
Journals
2025 EN
Saleh Ibrahim G. · Shimogawa Marie · Ramirez Jennifer
+15 more
Abstract Alpha‐synuclein (αS) and tau play important roles in the pathology of Parkinson's disease and Alzheimer's disease, respectively, as well as numerous other neurodegenerative diseases. Both proteins are classified as intrinsically disordered proteins (IDPs), as they have no stable structure that underlies their function in healthy tissue, and both proteins are prone to aggregation in disease states. There is substantial interest in understanding the roles that post‐translational modifications (PTMs) play in regulating the structural dynamics and function of αS and tau monomers, as well as their propensity to aggregate. While there have been many valuable insights into site‐specific effects of PTMs garnered through chemical synthesis and semi‐synthesis, these techniques are often outside of the expertise of biochemistry and biophysics laboratories wishing to study αS and tau. Therefore, we have assembled a primer on genetic code expansion and enzymatic modification approaches to installing PTMs into αS and tau site‐specifically, including isotopic labeling for NMR and fluorescent labeling for biophysics and microscopy experiments. These methods should be enabling for those wishing to study authentic PTMs in αS or tau as well as the broader field of IDPs and aggregating proteins.
Journals
2025 EN
Esen Baris · Seymen Hulya · Armutlu Ayşe
+10 more
ABSTRACT Background PSMA PET/CT has previously shown superior performance in nodal staging of prostate cancer (PCa) and may be used to reduce the number of unnecessary PLND procedures. This study aims to assess the performance of PSMA PET/CT in nodal staging of intermediate‐risk prostate cancer and to evaluate the effect of PLND on oncological outcomes of intermediate‐risk prostate cancer patients with a negative PSMA PET/CT. Methods A total of 308 patients with intermediate‐risk PCa who underwent PSMA PET/CT for nodal staging between January 2014 and July 2024 were included in the study. Patients who underwent PLND had higher PSA and higher rates of PIRADS‐5 and biopsy grade‐group 3 disease. A 1:1 propensity score matching was performed to eliminate patient characteristics differences between groups and 140 patients were included in the final analysis. PSA persistence rates ( ≥ 0.1 ng/dL) and biochemical recurrence (BCR; ≥ 0.2 ng/dL) rates after RP were recorded. Kaplan‐Meier curves were constructed to evaluate oncological outcomes. Log‐rank test was utilized to compare oncological outcomes in patients with and without PLND. Results The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of PSMA PET/CT on nodal staging were 53.3%, 95%, 47.1%, and 96.1%, respectively. The NPV of PSMA PET/CT in patients with biopsy GG3 disease (96.3%) was similar to those with biopsy GG2 disease (95.6%). The median follow‐up after propensity score matching was 20.7 months. The 24‐month BCR‐free survival rates were 83.7% and 86.9% in the PLND‐RP group and RP‐only groups, respectively ( p = 0.078). Conclusions NPV of PSMA PET/CT in determining LNI was remarkable in patients with intermediate‐risk PCa and PLND was found to have no impact on oncological outcomes. Therefore PLND may be omitted to decrease surgery‐related complications in patients with intermediate‐risk PCa a negative PSMA PET/CT for nodal staging.
Journals
2025 EN
Asiri Ibrahim M. · Chen Ronald C. · Master Viraj
+8 more
ABSTRACT Background This study investigates the association between thromboembolic events (TE) and castration‐resistant prostate cancer (CRPC) patients receiving oral androgen receptor pathway inhibitors (ARPi) compared to those undergoing chemotherapy, both with and without a pre‐existing history of cardiovascular disease (CVD). Methods A total of 2779 men diagnosed with CRPC were identified using the Surveillance, Epidemiology, and End Results (SEER) Medicare Linked Database from 2012 to 2016. Patients were stratified based on their CVD history. Within each CVD stratum (pre‐existing CVD vs. no pre‐existing CVD), patients were further categorized into two treatment groups: those receiving oral ARPi and those undergoing chemotherapy. Unadjusted and inverse probability treatment weight (IPTW)‐adjusted proportional hazards models, using Fine and Gray's method, were applied to evaluate the potential association between ARPi treatment and TE. Results Patients with pre‐existing CVD treated with ARPi exhibited a significantly lower crude hazard ratio (HR) for TE compared to chemotherapy (HR 0.39, 95% CI 0.27–0.58, p < 0.001). However, after adjustment using IPTW, this association was no longer significant (adjusted hazard ratio [AHR] 1.00, 95% CI 0.75–1.32, p = 0.99). For patients without CVD, ARPi use was also associated with a reduced risk of TE in the crude analysis (HR 0.53, 95% CI 0.32–0.87, p = 0.01), but this effect was not statistically significant after IPTW adjustment (HR 0.99, 95% CI 0.69–1.41, p = 0.94). Conclusion ARPi demonstrated no significant effect on TE risk compared to chemotherapy, regardless of pre‐existing CVD status. Similarly, when excluding patients with a prior history of TE, ARPi use remained non‐significantly associated with new TE in the IPTW‐adjusted competing risk analysis, highlighting the need for further investigation.